WO2022129210A2 - Inhibition of virus protease - Google Patents

Inhibition of virus protease Download PDF

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Publication number
WO2022129210A2
WO2022129210A2 PCT/EP2021/085966 EP2021085966W WO2022129210A2 WO 2022129210 A2 WO2022129210 A2 WO 2022129210A2 EP 2021085966 W EP2021085966 W EP 2021085966W WO 2022129210 A2 WO2022129210 A2 WO 2022129210A2
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alkyl
group
pentyl
butyl
formula
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PCT/EP2021/085966
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French (fr)
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WO2022129210A3 (en
Inventor
Grzegorz Maria POPOWICZ
Michael Sattler
Kamyar HADIAN
Oliver Plettenburg
Andre MOURAO
Karl Kenji SCHORPP
Valeria NAPOLITANO
Krzysztof Pyrc
Katarzyna Owczarek
Agnieszka DABROWSKA
Pawel BOTWINA
Aleksandra MILEWSKA
Tony FROEHLICH
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Helmholtz Zentrum Muenchen - Deutsches Forschungszentrum Für Gesundheit Und Umwelt (Gmbh)
Jagiellonian University
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Priority claimed from LU102310A external-priority patent/LU102310B1/en
Application filed by Helmholtz Zentrum Muenchen - Deutsches Forschungszentrum Für Gesundheit Und Umwelt (Gmbh), Jagiellonian University filed Critical Helmholtz Zentrum Muenchen - Deutsches Forschungszentrum Für Gesundheit Und Umwelt (Gmbh)
Publication of WO2022129210A2 publication Critical patent/WO2022129210A2/en
Publication of WO2022129210A3 publication Critical patent/WO2022129210A3/en

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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
    • A61K31/47—Quinolines; Isoquinolines
    • A61K31/473—Quinolines; Isoquinolines ortho- or peri-condensed with carbocyclic ring systems, e.g. acridines, phenanthridines
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A61P31/14—Antivirals for RNA viruses
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D219/00—Heterocyclic compounds containing acridine or hydrogenated acridine ring systems
    • C07D219/04—Heterocyclic compounds containing acridine or hydrogenated acridine ring systems with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals, directly attached to carbon atoms of the ring system
    • C07D219/08—Nitrogen atoms
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D401/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom
    • C07D401/02—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing two hetero rings
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D401/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom
    • C07D401/02—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing two hetero rings
    • C07D401/04—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing two hetero rings directly linked by a ring-member-to-ring-member bond
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D403/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00
    • C07D403/02—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing two hetero rings
    • C07D403/04—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing two hetero rings directly linked by a ring-member-to-ring-member bond
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D403/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00
    • C07D403/02—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing two hetero rings
    • C07D403/12—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing two hetero rings linked by a chain containing hetero atoms as chain links
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D405/00—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom
    • C07D405/02—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom containing two hetero rings
    • C07D405/12—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom containing two hetero rings linked by a chain containing hetero atoms as chain links
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
    • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Definitions

  • the present invention relates to a composition, comprising at least one compound according to formula (I) as well as to a composition comprising at least one compound according to formula (I) and/or dimers of compounds according to formula (I), in particular for use in the treatment of diseases caused by betacoronaviruses, leishmaniasis, and trypanosomiasis.
  • Coronaviruses have been considered a potential threat since 2002, when the SARS- CoV virus emerged in southern China to spread through continents and disappear shortly thereafter 1 ,2 rapidly. Ten years later, the second coronavirus - MERS-CoV - gave a final warning to be prepared 3 . Still, the emergence of the SARS-CoV-2 and subsequent pandemic met the public unprepared and paralyzed the modern world in an unprecedented way. At present, 1.4 million fatalities, have already been crossed and the northern hemisphere is facing the long the winter season, which due to the appearance of other comorbidities (low/dry air, coinfections, pollution, dysregulated immune responses) may still increase these numbers drastically 4 ' 6 .
  • the coronaviral genome encodes for several structural and non-structural proteins.
  • the most promising targets are the Spike (S) protein, as the target for neutralizing antibodies and entry inhibitors, the nsp12 polymerase, targeted by several compounds including the remdesivir, nsp14 and nsp16 methyltransferases essential for the capping of viral RNA, and two cysteine proteases M pro and PL pro , responsible for the viral proteome maturation and indispensable for the infection.
  • PLpro is also responsible for type I interferon response attenuation.
  • a potential target is SARS-CoV-2 PL pro .
  • the present invention is related to a composition comprising at least one compound according to formula (I)
  • RT is selected from the group consisting of H, (Ci-C 6 )alkyl, (CH 2 ) 0 (Ci-C 6 )alkyl ,(Ci-C 6 )cycloalkyl, (Ci-C 6 )heterocyclyl, or absent, preferably methyl;; o is 1 to 3, preferably 1 ;
  • R 2 is selected from the group consisting of H, (Ci-C 6 )alkyl,-(CH 2 ) r CONH(CH 2 ) s R6, -(CH- (CH 2 ) p COvinyl, -(CH 2 ) q R 6 , -CO(Ci-C 6 )alkyl preferably H;
  • R 3 is selected from the group consisting of H, (Ci-C 6 )alkyl, -(CH 2 ) r CONH(CH 2 ) s R6, - (CH 2 ) p COvinyl, -(CH 2 ) q R 6 , -CO(Ci-C 6 )alkyl, preferably H; p is 1-3, preferably 1 ; q is 1-3, preferably 1 ; r is 1-3, preferably 1 ; s is 1-3, preferably 1 ;
  • R 4 is selected from the group consisting of H, (Ci-C 6 )alkyl
  • R 5 is selected from the group consisting of H, (Ci-C 6 )alkyl; if R 2 and R 5 are both (Ci-C 6 )alkyl, R 2 and R 5 may be connected to form a 4 to 6 membered ring; if R 3 and R 4 are both (Ci-C 6 )alkyl, R 3 and R 4 may be connected to form a 4 to 6 membered ring; R 6 is selected from the group consisting of
  • X' is an anion or absent ; if X' is absent then RT is absent; for use in the treatment of diseases caused by betacoronaviruses, leishmaniasis, and trypanosomiasis.
  • the invention is further directed to a composition in which at least one compound according to formula (I) and at least one compound according to formula (III) are bonded together via one or two linker systems wherein optionally a) the linker system is (C 2 -Ci 0 )alkyl, preferably (C 2 -Ci 0 )alkenyl, preferably (C 3 -C 8 )alkyl, or (C 3 - 8 )alkenyl; wherein optionally at least one or at least two CH 2 -groups in these alkyl or alkenyl groups are substituted by O, S, S(O)i.
  • the linker system is (C 2 -Ci 0 )alkyl, preferably (C 2 -Ci 0 )alkenyl, preferably (C 3 -C 8 )alkyl, or (C 3 - 8 )alkenyl; wherein optionally at least one or at least two CH 2 -groups in these alkyl or alkeny
  • the invention is further directed to a composition comprising at least one compound according to formula (I)
  • RT is selected from the group consisting of H, (Ci-C 6 )alkyl, (CH 2 ) 0 (Ci-C 6 )alkyl ,(Ci-C 6 )cycloalkyl, (Ci-C 6 )heterocyclalkyl, or absent, preferably methyl; o is 1 to 3, preferably 1 ;
  • R 2 is selected from the group consisting of H, (Ci-C 6 )alkyl,-(CH 2 ) r CONH(CH 2 ) s R6, -(CH- (CH 2 ) p COvinyl, -(CH 2 ) q R 6 , -CO(Ci-C 6 )alkyl preferably H;
  • R 3 is selected from the group consisting of H, (Ci-C 6 )alkyl, -(CH 2 ) r CONH(CH 2 )sR 8 , - (CH 2 ) p COvinyl, -(CH 2 ) q R 6 , -CO(Ci-C 6 )alkyl, preferably H; p is an integer between 1 to 3, preferably 1 ; q is an integer between 1 to 3, preferably 1 ; r is an integer between 1 to 3, preferably 1 ; s is an integer between 1 to 3, preferably 1;
  • R 4 is selected from the group consisting of H, (Ci-C 6 )alkyl
  • R 5 is selected from the group consisting of H, (Ci-C 6 )alkyl; if R 2 and R 5 are both (Ci-C 6 )alkyl, R 2 and R 5 may be connected to form a 4 to 6 membered ring; if R 3 and R 4 are both (Ci-C 6 )alkyl, R 3 and R 4 may be connected to form a 4 to 6 membered ring; ) °>
  • R 6 is selected from the group consisting of ;
  • X' is an anion or absent; if X' is absent then RT is absent; with the provisio that the compound according to formula (I) is not selected from the group
  • the inventive compounds block the replication of the selected betacoronaviruses, including with nanomolar IC 50 , showing high selectivity and good effectiveness (see Figures 8 to 14). Further, it has been shown that the inventive compounds are effective against Trypanosoma and Leishmania parasites.
  • Fig. 1 Inhibiton of PL pro in the presence of ACF.
  • AMC assay using RLRGG-AMC as substrate and PL pro performed in technical triplicates. Vertical Y-axis shows fluorescent signal (rising, as the substrate is proteolytically cleaved). Horizontal X-axis indicate time. An inhibition profile is observable.
  • B As in (A), only with ISG15-AMC instead of RLRGG-AMC
  • C Time course analysis of tri-ubiquitin K48-linked (2 pM) hydrolysis using 100 nM PL pro in the presence of different ACF concentrations.
  • FIG. 2 The inhibition of virus replication by selected compounds.
  • Fig. 3 The crystal structure of SARS-Cov2-PL pro in complex with proflavine.
  • SCoV2- PL pro is represented as a solid surface, whereas proflavine is represented as a stick model.
  • A a zoom-in of the two proflavine molecules in the S3-S5 pockets of the enzyme active site.
  • B a zoom-in on a proflavine molecule between two crystal neighbors of PL pro .
  • Fig. 4 Details of the molecular interactions between the SARS-CoV2-PL pro and proflavines.
  • A, B Both proflavine molecules bind cooperatively in the substrate pocket of the enzyme forming a non-covalent inhibitor. Both polar (gray) and hydrophobic (red) interactions as well as TT-TT stacking (green) are involved. Main residues involved in the interactions are shown as a stick-model.
  • C, D 2D plots of molecular interactions between proflavine-l, proflavine-ll and PL pro .
  • Each proflavine molecule uses different properties for form interaction. The aromatic nitrogen of proflavine-l must be desolvated for binding. This explains the higher affinity of acriflavine than proflavine as it contains N-methylated components.
  • Fig. 5 Both proflavine molecules mimic native substrate interactions.
  • A Comparison of SARS-CoV2-PL pro complexed with proflavine (in gray) and ISG15 host-cell substrate (in cyan; PDB ID:6YVA). The active site is marked by a dashed oval.
  • B Substrate recognition cleft interaction of proflavines and the C-terminal tail of ISG15. Proflavine molecules overlap with the RLRGG motif of the substrate.
  • the two arginines in P3 and P5 turn their lipophilic carbons in the same directions as the aromatic carbons of the proflavine-ll molecule in the S3-S5 pockets.
  • the amide nitrogen H-bond donors of the peptide backbone correspond well with the proflavine-ll donors and the interactions are well preserved.
  • the side chain of the leucin in position P4 points exactly of the proflavine ring in the S4 pocket.
  • Fig. 6 Overlay of 1 H, 15 N TROSY NMR spectra of PL pro with different amount of ACF added. The entire spectrum is shown in the middle, magnification of a few regions above and below. A number of peaks shift with the addition of ACF. The bulk of the spectra remains similar to the reference apo-PL pro . This indicated that the overall fold of the protein is intact and the compound binds in a distinct binding pocket.
  • Fig. 7 The cytotoxicity of ACF in vitro.
  • FIG. 8 The inhibition of virus replication by ACF in A549 ACE2+ (A) and Vero (B) cells.
  • Figure 10 The inhibition of virus replication by ACF in A549 ACE2+ cells.
  • Cells were infected with the SARS-CoV-2 in presence of 500 nM Acriflavine, 10 pM Remdesivir or vessel control for 24 h and 48 h.
  • Cell nuclei are denoted in blue, actin is denoted in red and SARS- CoV-2 N-protein is denoted in green.
  • FIG 11 Antiviral activity of ACF against SARS-CoV-2 in human airway epithelium.
  • A In-house HAE
  • B MucilAirTM.
  • Figure 12 The inhibition of virus replication by ACF in well differentiated HAE cultures.
  • Figure 13 Time of addition study. The inhibition of virus replication in Vero cells by ACF added after post-infection (time denoted on the x-axis).
  • FIG. 14 ACF inhibits betacoronaviruses. Replication of (A) MERS-CoV, (B) HCoV- OC43, HCoV-NL63 (C) and (D) FIPV in vitro in the presence or absence of inhibitors, as assessed with RT-qPCR on cell culture supernatants. Single round of infection was recorded (24 h). All experiments were performed at least in 2 biological repetitions, each in triplicate. The results are presented as average values with standard deviations (error bars). An asterisk (p ⁇ 0.05) indicates values that are significantly different from the non-treated control. ACF: acriflavin, rem: remdesivir.
  • Figure 15 Proflavine molecule at the interface between SARS-CoV2-PL pro asymmetric units.
  • A Most probably due to a crystal packing molecule of proflavine was found on top of the catalytic triad (C111, H272, D286). Important residues are highlighted as stick model. Two water molecules (red spheres) mediate a hydrogen bond with D286. Hydrogen bonds are represented as yellow dashed lines.
  • B 2D plot of the molecular interactions between proflavine and the residues of SARS-CoV2-PL pro .
  • Figure 16 Comparison of SARS-CoV2-PL pro in the proflavine-bound and apo-state. Bound PL pro is colored in gray; whereas the unbound PL pro (PDB ID: 7D47) is colored in yellow.
  • the BL2 loop is involved in an induced fit rearrangement upon the binding mostly due to the movement of the Tyr268.
  • the side-chain of Tyr268 participates in a TT-TT stacking with proflavine molecules.
  • Figure 17 Electron density map showing the fractional presence of additional aromatic proflavine-like molecules TT-TT stacked one on top of the other between two copies of SARS- CoV2-PL pro present in the crystal lattice.
  • 2F O -F C electron density map is contoured at 2CE.
  • the electron density of the identified proflavine molecules is colored in blue; whereas additional electron density is colored in green.
  • the densities are most likely caused by weak and transiently-bound proflavines. We did not model them in the crystal structure as their electron density was much weaker than active site-bound molecules.
  • FIG. 18 SARS-CoV-2 M pro activity is not significantly inhibited by ACF.
  • the digestion of fluorogenic substrate was recorded in the absence and presence of ACF (A). Only small decrease of M pro activity is observed at physiologically irrelevant ACF concentration of 100 pM (B). The vertical shift in signal levels is caused by ACF absorbance.
  • Figure 21 Composition of commercial acriflavine (cACF) sold by Sigma Aldrich (A8251): 56% proflavine (PF), 17% acriflavine (ACF) and about 26% of their side methylated derivatives.
  • cACF commercial acriflavine
  • PF proflavine
  • ACF acriflavine
  • Figure 22 Map of pETM-5a.
  • alkyl refers to a monoradical of a saturated straight or branched hydrocarbon.
  • the alkyl group comprises from 1 to 10 carbon atoms, i.e., 1, 2, 3, 4, 5, 6, 7, 8, 9, 9 carbon atoms, more preferably 1 to 5 carbon atoms, such as 1 to 4 or 1 to 2 carbon atoms.
  • Exemplary alkyl groups include methyl, ethyl, propyl, iso-propyl, butyl, iso-butyl, tert-butyl, n- pentyl, iso-pentyl, sec-pentyl, neo-pentyl, 1,2-dimethyl-propyl, iso-amyl, n-hexyl, iso-hexyl, sechexyl, 2-ethyl-hexyl, n-heptyl, iso-heptyl, n-octyl, 2-ethyl-hexyl, n-nonyl, n-decyl, and the like.
  • alkylene refers to a diradical of a saturated straight or branched hydrocarbon.
  • the alkylene comprises from 1 to 10 carbon atoms, i.e., 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 carbon atoms, more preferably 1 to 8 carbon atoms, such as 1 to 6 or 1 to 4 carbon atoms.
  • Exemplary alkylene groups include methylene, ethylene (i.e., 1 ,1-ethylene, 1,2-ethylene), propylene (i.e., 1,1-propylene, 1,2-propylene (-CH(CH 3 )CH 2 -), 2,2-propylene (-C(CH 3 ) 2 -), and
  • the butylene isomers e.g., 1,1-butylene, 1 ,2-butylene, 2,2-butylene, 1 ,3- butylene, 2,3-butylene (cis or trans or a mixture thereof), 1 ,4-butylene, 1 ,1-iso-butylene, 1 ,2-iso- butylene, and 1,3-iso-butylene
  • the pentylene isomers e.g., 1,1-pentylene, 1 ,2-pentylene, 1,3- pentylene, 1,4-pentylene, 1,5-pentylene, 1,1-iso-pentylene, 1,1 -sec-pentyl, 1,1-neo-pentyl
  • the hexylenisomers e.g., 1,1-hexylene, 1 ,2-hexylene, 1,3-hexylene, 1,4-hexylene, 1,5-hexylene, 1 ,
  • alkenylene refers to a diradical of an unsaturated straight or branched hydrocarbon having at least one carbon-carbon double bond.
  • the maximal number of carbon-carbon double bonds in the alkenylene group can be equal to the integer which is calculated by dividing the number of carbon atoms in the alkenylene group by 2 and, if the number of carbon atoms in the alkenylene group is uneven, rounding the result of the division down to the next integer.
  • the maximum number of carbon-carbon double bonds is 4.
  • the alkenylene group has 1 to 4, i.e., 1, 2, 3, or 4, carbon-carbon double bonds.
  • the alkenylene group comprises from 2 to 10 carbon atoms, i.e., 2, 3, 4, 5, 6, 7, 8, 9, or 10 carbon atoms, more preferably 2 to 8 carbon atoms, such as 2 to 6 carbon atoms or 2 to 4 carbon atoms.
  • the alkenylene group comprises from 2 to 10 carbon atoms and 1 , 2, 3, 4, or 5 carbon-carbon double bonds, more preferably it comprises 2 to 8 carbon atoms and 1 , 2, 3, or 4 carbon-carbon double bonds, such as 2 to 6 carbon atoms and 1 , 2, or 3 carbon-carbon double bonds or 2 to 4 carbon atoms and 1 or 2 carbon-carbon double bonds.
  • the carbon-carbon double bond(s) may be in cis (Z) or trans (E) configuration.
  • exemplary alkenylene groups include ethen-1 ,2-diyl, vinyliden, 1-propen-1 ,2-diyl, 1-propen-1 ,3-diyl, 1-propen-2,3-diyl, allyliden, 1-buten-1 ,2-diyl, 1-buten-1 ,3-diyl, 1-buten-1 ,4-diyl, 1-buten-2,3-diyl, 1-buten-2,4-diyl, 1-buten-3,4-diyl, 2-buten-1 ,2-diyl, 2-buten-1 ,3-diyl, 2-buten-1 ,4-diyl, 2-buten-2,3-diyl, 2-buten-diyl, 2-buten-
  • cycloalkyl represents cyclic non-aromatic versions of “alkyl” with preferably 3 to 6 carbon atoms, such as 3 to 6 carbon atoms, i.e., 3, 4, 5, or 6, carbon atoms, more preferably 5 to 6 carbon atoms, even more preferably 6 carbon atoms.
  • exemplary cycloalkyl groups include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl.
  • alkenyl refers to a monoradical of an unsaturated straight or branched hydrocarbon having at least one carbon-carbon double bond.
  • the maximal number of carbon-carbon double bonds in the alkenyl group can be equal to the integer which is calculated by dividing the number of carbon atoms in the alkenyl group by 2 and, if the number of carbon atoms in the alkenyl group is uneven, rounding the result of the division down to the next integer.
  • the maximum number of carbon-carbon double bonds is 4.
  • the alkenyl group has 1 to 4, i.e., 1, 2, 3, or 4, carbon-carbon double bonds.
  • the alkenyl group comprises from 2 to 10 carbon atoms, i.e., 2, 3, 4, 5, 6, 7, 8, 9, or 10 carbon atoms, more preferably 2 to 8 carbon atoms, such as 2 to 6 carbon atoms or 2 to 4 carbon atoms.
  • the alkenyl group comprises from 2 to 10 carbon atoms and 1 , 2, 3, 4, or 5 carbon-carbon double bonds, more preferably it comprises 2 to 8 carbon atoms and 1 , 2, 3, or 4 carbon-carbon double bonds, such as 2 to 6 carbon atoms and 1 , 2, or 3 carbon-carbon double bonds or 2 to 4 carbon atoms and 1 or 2 carbon-carbon double bonds.
  • the carbon-carbon double bond(s) may be in cis (Z) or trans (E) configuration.
  • Exemplary alkenyl groups include vinyl, 1-propenyl, 2-propenyl (i.e., allyl), 1-butenyl, 2-butenyl, 3-butenyl, 1-pentenyl, 2-pentenyl, 3-pentenyl, 4-pentenyl, 1-hexenyl, 2-hexenyl, 3-hexenyl, 4-hexenyl, 5-hexenyl, 1-heptenyl, 2-heptenyl, 3-heptenyl, 4-heptenyl, 5- heptenyl, 6-heptenyl, 1 -octenyl, 2-octenyl, 3-octenyl, 4-octenyl, 5-octenyl, 6-octenyl, 7-octenyl, 1-nonenyl, 2-nonenyl, 3-nonenyl, 4-non
  • alkenylene refers to a diradical of an unsaturated straight or branched hydrocarbon having at least one carbon-carbon double bond.
  • the maximal number of carbon-carbon double bonds in the alkenylene group can be equal to the integer which is calculated by dividing the number of carbon atoms in the alkenylene group by 2 and, if the number of carbon atoms in the alkenylene group is uneven, rounding the result of the division down to the next integer.
  • the maximum number of carbon-carbon double bonds is 4.
  • the alkenylene group has 1 to 4, i.e., 1, 2, 3, or 4, carbon-carbon double bonds.
  • the alkenylene group comprises from 2 to 10 carbon atoms, i.e., 2, 3, 4, 5, 6, 7, 8, 9, or 10 carbon atoms, more preferably 2 to 8 carbon atoms, such as 2 to 6 carbon atoms or 2 to 4 carbon atoms.
  • the alkenylene group comprises from 2 to 10 carbon atoms and 1 , 2, 3, 4, or 5 carbon-carbon double bonds, more preferably it comprises 2 to 8 carbon atoms and 1 , 2, 3, or 4 carbon-carbon double bonds, such as 2 to 6 carbon atoms and 1 , 2, or 3 carbon-carbon double bonds or 2 to 4 carbon atoms and 1 or 2 carbon-carbon double bonds.
  • the carbon-carbon double bond(s) may be in cis (Z) or trans (E) configuration.
  • exemplary alkenylene groups include ethen-1 ,2-diyl, vinyliden, 1-propen-1 ,2-diyl, 1-propen-1 ,3-diyl, 1-propen-2,3-diyl, allyliden, 1-buten-1 ,2-diyl, 1-buten-1 ,3-diyl, 1-buten-1 ,4-diyl, 1-buten-2,3-diyl, 1-buten-2,4-diyl, 1-buten-3,4-diyl, 2-buten-1 ,2-diyl, 2-buten-1 ,3-diyl, 2-buten-1 ,4-diyl, 2-buten-2,3-diyl, 2-buten- 2,4-diyl, 2-buten-3,4-diyl, and the like. If an alkenylene group is
  • aryl refers to a monoradical of an aromatic cyclic hydrocarbon.
  • the aryl group contains 6 to 10 (e.g., 6 to 10, such as 5, 6, or 10) carbon atoms which can be arranged in one ring (e.g., phenyl) or two or more condensed rings (e.g., naphthyl).
  • exemplary aryl groups include, phenyl, indenyl, naphthyl, azulenyl, fluorenyl, anthryl, and phenanthryl.
  • aryl refers to a monocyclic ring containing 6 carbon atoms or an aromatic bicyclic ring system containing 10 carbon atoms. Preferred examples are phenyl and naphthyl.
  • -(Ci-C 6 )alkyl(C6-Ci 0 )aryl means that an aryl group comprising an alkyl substituent is attached to the overall molecule via that alkyl substituent.
  • heteroaryl means an aryl group as defined above in which one or more carbon atoms in the aryl group are replaced by heteroatoms of O, S, or N.
  • heteroaryl refers to a five or six-membered aromatic monocyclic ring wherein 1, 2, or 3 carbon atoms are replaced by the same or different heteroatoms of O, N, or S.
  • it means an aromatic bicyclic or tricyclic ring system wherein 1, 2, 3, 4, or 5 carbon atoms are replaced with the same or different heteroatoms of O, N, or S.
  • heteroaryl groups include furanyl, thienyl, oxazolyl, isoxazolyl, oxadiazolyl (1,2,5- and 1 ,2,3-), pyrrolyl, imidazolyl, pyrazolyl, triazolyl (1 ,2,3- and 1,2,4-), tetrazolyl, thiazolyl, isothiazolyl, thiadiazolyl (1,2,3- and 1 ,2,5-), pyridyl, pyrimidinyl, pyrazinyl, triazinyl (1,2,3-, 1,2,4-, and 1,3,5-), benzofuranyl (1- and 2-), indolyl, isoindolyl, benzothienyl (1- and 2-), 1 H
  • Exemplary 5- or 6-memered heteroaryl groups include furanyl, thienyl, oxazolyl, isoxazolyl, oxadiazolyl (1 ,2,5- and 1 ,2,3-), pyrrolyl, imidazolyl, pyrazolyl, triazolyl (1 ,2,3- and 1,2,4-), thiazolyl, isothiazolyl, thiadiazolyl (1,2,3- and 1,2,5-), pyridyl, pyrimidinyl, pyrazinyl, triazinyl (1 ,2,3-, 1,2,4-, and 1 ,3,5-), and pyridazinyl.
  • -(Ci-C 6 )alkyl(C5-Ci 0 )heteroaryl means that a heteroaryl group comprising an alkylsubstituent group is attached to the overall molecule via that alkyl substituent.
  • heterocyclyl means a cycloalkyl group as defined above in which from 1 , 2, 3, or 4 carbon atoms in the cycloalkyl group are replaced by heteroatoms of O, S, or N.
  • the maximum number of O atoms is 1
  • the maximum number of S atoms is 1
  • the maximum total number of O and S atoms is 2.
  • heterocyclyl is also meant to encompass partially or completely hydrogenated forms (such as dihydro, tetrahydro or perhydro forms) of the above-mentioned heteroaryl groups.
  • heterocyclyl groups include morpholino, isochromanyl, chromanyl, pyrrolidinyl, imidazolidinyl, pyrazolidinyl, piperidinyl, piperazinyl, indolinyl, isoindolinyl, di- and tetrahydrofuranyl, di- and tetrahydrothienyl, di- and tetrahydrooxazolyl, di- and tetrahydroisoxazolyl, di- and tetrahydrooxadiazolyl (1 ,2,5- and 1 ,2,3-), dihydropyrrolyl, dihydroimidazolyl, dihydropyrazolyl, di- and tetrahydrotriazolyl (1 ,2,3- and 1 ,2,4-), di- and tetrahydrothiazolyl, di- and tetrahydrothiazolyl, di- and tetrahydrothiadiazol
  • Exemplary 5- or 6-memered heterocyclyl groups include morpholino, pyrrolidinyl, imidazolidinyl, pyrazolidinyl, piperidinyl, piperazinyl, di- and tetrahydrofuranyl, di- and tetrahydrothienyl, di- and tetrahydrooxazolyl, di- and tetrahydroisoxazolyl, di- and tetrahydrooxadiazolyl (1 ,2,5- and 1 ,2,3-), dihydropyrrolyl, dihydroimidazolyl, dihydropyrazolyl, di- and tetrahydrotriazolyl (1 ,2,3- and 1 ,2,4-), di- and tetrahydrothiazolyl, di- and tetrahydroisothiazolyl, di- and tetrahydrothiadiazolyl (1 ,2,3- and 1 ,2,5-), di-
  • halogen means fluoro, chloro, bromo, or iodo; preferably chloro, or fluoro, more preferably fluoro.
  • complex of a compound refers to a compound of higher order which is generated by association of the compound with other one or more other molecules.
  • exemplary complexes of a compound include, but are not limited to, solvates, clusters, and chelates of said compound.
  • solvate refers to an addition complex of a dissolved material in a solvent (such as an organic solvent (e.g., an aliphatic alcohol (such as methanol, ethanol, n-propanol, isopropanol), acetone, acetonitrile, ether, and the like), water or a mixture of two or more of these liquids), wherein the addition complex exists in the form of a crystal or mixed crystal.
  • a solvent such as an organic solvent (e.g., an aliphatic alcohol (such as methanol, ethanol, n-propanol, isopropanol), acetone, acetonitrile, ether, and the like), water or a mixture of two or more of these liquids)
  • a solvent such as an organic solvent (e.g., an aliphatic alcohol (such as methanol, ethanol, n-propanol, isopropanol), acetone, acetonitrile, ether, and the like
  • isotopically labeled compounds one or more atoms are replaced by a corresponding atom having the same number of protons but differing in the number of neutrons.
  • a hydrogen atom may be replaced by a deuterium atom.
  • Exemplary isotopes which can be used in the compounds of the present invention include deuterium, 11 C, 13 C, 14 C, 15 N, 18 F, 32 S, 36 CI, and 125 l.
  • RT is selected from the group consisting of H, (Ci-C 6 )alkyl, (CH 2 ) 0 (Ci-C 6 )alkyl ,(C C 6 )cycloalkyl, (Ci-C 6 )heterocyclyl, or absent, preferably selected from the group consisting of methyl, ethyl, propyl, cyclopropyl, butyl, cyclobutyl, pentyl, cyclopentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl, 3-pentyl, 2-methylbutyl, 3-methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut-2-yl, 2-methylbut-2-yl, 2,2-dimethylpropyl
  • R 2 is selected from the group consisting of H, (Ci-C 6 )alkyl,-(CH 2 ) r CONH(CH 2 ) s R6, -(CH- (CH 2 ) p COvinyl, -(CH 2 ) q R 6 , -CO(Ci-C 6 )alkyl; preferably selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl, 3-pentyl, 2-methylbutyl, 3-methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut-2-yl, 2-methylbut-
  • R 3 is selected from the group consisting of H, (Ci-C 6 )alkyl, -(CH 2 ) r CONH(CH 2 ) s R6, - (CH 2 ) p COvinyl, -(CH 2 ) q R 6 , -CO(Ci-C 6 )alkyl, preferably selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl,
  • p is an integer between 1 to 3, preferably 1 ;
  • q is an integer between 1 to 3, preferably 1 ;
  • r is an integer between 1 to 3, preferably 1 ;
  • s is an integer between 1 to 3, preferably 1 ;
  • R 4 is selected from the group consisting of H, (Ci-C 6 )alkyl
  • R 5 is selected from the group consisting of H, (Ci-C 6 )alkyl; [0059] if R 2 and R 5 are both (Ci-C 6 )alkyl, R 2 and R 5 may be connected to form a 4 to 6 membered ring;
  • R 3 and R 4 are both (Ci-C 6 )alkyl, R 3 and R 4 may be connected to form a 4 to 6 membered ring;
  • R 6 is selected from the group consisting of
  • X' is an anion or absent
  • the compound according to formula (I) is not selected from the
  • X' is preferably selected from the group consisting of napsylate, tetrafluoroborate, formate , trifluoroacetate, glycollylarsanilate, nitrate, benzoate, hexylresorcinate, oleate, bitartrate, hydroxynaphthoate, pantothenate, bicarbonate, hydrabamine, pamoate, camsylate, isethionate, polygalacturonate, propionate, salicylate, lactobionate, stearate, decanoate, edetate, maleate, succinate, estolate, mandelate, teoclate, gluceptate, acetate, glutamate, muscate, aspartate, glycolate, benzenesulfonate, hexanoate, octanoate, sulfonate, chloride, iodide, bromide, phosphate, phosphonate
  • composition in another embodiment, there are at least two compounds according to formula (I) present.
  • Ri is (Ci-C 6 )alkyl, preferably selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl, 3-pentyl, 2-methylbutyl, 3- methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut-2-yl, 2-methylbut-2-yl, 2,2-dimethylpropyl, hexyl, 2-hexyl, 3-hexyl, 2-methylpentyl, 3-methylpentyl, 2,2-dimethylbutyl, and 2,3-dimethylbutyl, more preferably methyl; R 2 and R 3 are H; and in
  • the second compound (lb) RT is (Ci-C 6 )alkyl, preferably selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tertbutyl, 2-pentyl, 3-pentyl, 2-methylbutyl, 3-methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut-2- yl, 2-methylbut-2-yl, 2,2-dimethylpropyl, hexyl, 2-hexyl, 3-hexyl, 2-methylpentyl, 3-methylpentyl,
  • R 2 or R 3 in the second compound is (Ci-C 6 )alkyl, preferably selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl, 3-pentyl, 2- methylbutyl, 3-methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut-2-yl, 2-methylbut-2-yl, 2,2- dimethylpropyl, hexyl, 2-hexyl, 3-hexyl, 2-methylpentyl, 3-methylpentyl, 2,2-dimethylbutyl, and
  • composition may comprise at least one dimer of the compound according to the formula (I) of claim 1, according to formula (II):
  • R 3 in formula (II) is a linker selected from the group consisting of -(CH 2 ) t -, -(CH 2 ) t Q(CH 2 ) u -, - CO(CH 2 ) t -, -CO(CH 2 ) t CO-; t is an integer between 1 to 4; u is an integer between 1 to 4;
  • (I) and (I)’ are based on formula (I) in claim 1 and may be identical or different, preferably identical.
  • composition may further comprise at least one compound according to formula (III)
  • R 4 is H, halogen, (Ci-C 6 )alkyl, (C 3 -C 6 )cycloalkyl, or -O(Ci-C 6 )alkyl; preferably H.
  • R 5 is H, halogen, (Ci-C 6 )alkyl, (C 3 -C 6 )cycloalkyl, or -O(Ci-C 6 )alkyl; preferably H.
  • R 6 is H, halogen, (Ci-C 6 )alkyl, (C3-C 6 )cycloalkyl, or -O(Ci-C 6 )alkyl; preferably H
  • R 7 is H, (Ci-C 6 ) alkyl, preferably methyl
  • Z is H, halogen, (Ci-C 6 )alkyl, (C3-C 6 )cycloalkyl, -O(Ci-C 6 )alkyl, -(Ci-C 6 )alkyl(C6-Cio)aryl, - (Ci-C 6 )alkyl(C5-Cio)heteroaryl; preferably H.
  • Y is -NH 2 , -NHR 8 , halogen, (Ci-C 6 )alkyl, (C3-C 6 )cycloalkyl; preferably -NH 2
  • R 8 is H, (Ci-C 6 ) alkyl, preferably methyl
  • R 4 is (Ci-C 6 )alkyl, preferably selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl, 3-pentyl, 2-methylbutyl, 3-methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut-2-yl, 2-methylbut-
  • R 5 is (Ci-C 6 )alkyl, preferably selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl,
  • R 6 is (Ci-C 6 )alkyl, preferably selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl,
  • R 7 is (Ci-C 6 )alkyl, preferably selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl,
  • R 8 is (Ci-C 6 )alkyl, preferably selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl, 3-pentyl, 2-methylbutyl, 3-methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut-2-yl, 2-methylbut-
  • Y is (Ci-C 6 )alkyl, preferably selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl,
  • Z is (Ci-C 6 )alkyl, preferably selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl,
  • the molar ratio of the at least one compound according to formula (I) may be 5 to 100, preferably 10 to 40, more preferably 15 to 30 mol-% based on the overall molar ratio of parent compounds (I) and (III) of the composition and compound (III) may be 0 to 95, preferably 60 to 90, more preferably 70 to 85 mol%.-% based on the overall molar ratio of parent compounds (I) and (III) in the composition.
  • At least two compounds according to formula (III) are present; preferably in the first compound (Illa) R 4 , R 5 , R 6 , R 7 , and Z are H; Y is -NH 2 ; in the second compound (lllb) R 4 , R 5 , R 6 , and Z are H; Y is -NH 2 , and R 7 is (Ci-C 6 )alkyl, preferably selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl, 3-pentyl, 2-methylbutyl, 3-methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut-2-yl, 2-methylbut-2-yl, 2,2-dimethylpropyl, hexyl, 2-
  • At least two compounds according to formula (I) and at least two compounds according to formula (III) are present, preferably (la), (lb), (Ila) and (lllb) as defined above present.
  • the molar ratio based on the overall molar ratio of compounds (la), (lb), (Illa) and (lllb) in the composition is for
  • Compound (I) and/or (III) may be a solvate, hydrate, salt, complex, or isotopically enriched form, preferably a salt.
  • Compound (I) may be a salt, wherein the salt comprises an anion selected preferably from the group consisting of tetrafluoroborate, formate , trifluoroacetate napsylate, glycollylarsanilate, nitrate, benzoate, hexylresorcinate, oleate, bitartrate, hydroxynaphthoate, pantothenate, bicarbonate, hydrabamine, pamoate, camsylate, isethionate, polygalacturonate, propionate, salicylate, lactobionate, stearate, decanoate, edetate, maleate, succinate, estolate, mandelate, teoclate, gluceptate, acetate, glutamate, muscate, aspartate, glycolate, benzenesulfonate, hexanoate, octanoate, sulfonate, chloride, iod
  • Compound (III) may be a salt, preferably the salt comprises an anion selected preferably from the group consisting of tetrafluoroborate, formate , trifluoroacetate, napsylate, glycollylarsanilate, nitrate, benzoate, hexylresorcinate, oleate, bitartrate, hydroxynaphthoate, pantothenate, bicarbonate, hydrabamine, pamoate, camsylate, isethionate, polygalacturonate, propionate, salicylate, lactobionate, stearate, decanoate, edetate, maleate, succinate, estolate, mandelate, teoclate, gluceptate, acetate, glutamate, muscate, aspartate, glycolate, benzenesulfonate, hexanoate, octanoate, sulfonate, chloride, io
  • a sulfonate used in the present invention may be a sulfonate according to formula (IV) wherein R g is selected from the group consisting of phenyl, 4-nitrophenyl, 4-methylphenyl, 4- trifluoromethyphenyl, trifluoromethyl, and (Ci-C 5 )alkyl.
  • R g is (Ci-C 5 )alkyl and/or
  • (Ci-C 5 )alkyl is selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, isopropyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl, 3-pentyl, 2-methylbutyl, 3- methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut-2-yl, 2-methylbut-2-yl, 2,2-dimethylpropyl, preferably methyl.
  • the invention is further directed to a composition in which at least one compound according to formula (I) and at least one compound according to formula (III) are bonded together via one or two linker systems.
  • the linker system may be -(C 2 -Ci 0 )alkylene or (C 2 -Ci 0 )alkenylene, preferably (C 3 - C 8 )alkylene, or (C 3-8 )alkenylene; wherein optionally at least one or at least two CH 2 -groups in these alkyl or alkenyl groups are substituted by O, S, S(O)i.
  • the acridine compounds (III) of the invention can be produced by applying suitable known method of synthesizing acridine derivatives, e.g. as described in Prager, R. H., Williams, C. M., Science of Synthesis (2005) 15, 987; Gensicka-Kowalewska M., Cholewinski G, Dzierzbicka, K. RSC Adv. (2017), 7, 15776 Matejova, M.; Janovec, L; Imrich, J. ARKIVOC 2015 (v), 134 and references cited therein.
  • anilineacetophenones coupled to aryl bromides e.g. via Ullman coupling and subsequently performing a cyclization under appropriate conditions e.g. acid catalysis (Ullmann, F; Torre, A. L., Ber. Dtsch. Chem. Ges., (1904) 37, 2922, Mayer, F; Freund, W., Ber. Dtsch. Chem. Ges., (1922) 55, 2049) or via 2-anilinobenzaldehyde derivatives, e.g. obtained by the McFadyen-Stevens reaction, followed by conversion to acridine derivatives (Graboyes, H.; Anderson, E. L.; Levinson, S.
  • acid catalysis Ullmann, F; Torre, A. L., Ber. Dtsch. Chem. Ges., (1904) 37, 2922, Mayer, F; Freund, W., Ber. Dtsch. Chem. Ges., (1922) 55, 2049
  • acridin- 9(10H)-ones are useful precursors of acridine derivatives, which can be obtained by various methods (e.g. described in Prager, R.H.; Williams, C.M. Science of Synthesis (2005), 1029).
  • Acridine derivatives modified in position 9 can for example be obtained by reacting the corresponding acridine-9(10H)-one derivatives, e.g. with phosphorous oxychloride or thionyl chloride to give 9-CI derivatives (Anuradha, S., Poonam, PChem. Biol. Drug Des. (2017), 90, 926; Nakajima, M., Nagasawa, S., Matsumoto, K., Kuribara, T., Muranaka, A., Uchiyama, M., Nemoto, T, Angew. Chem. Int. Ed.
  • Fused derivatives containing two acridine rings can be synthesized by adaption of methods described in the literature, e.g. starting from diphenyl anilines and reacting these with dicarboxylic acids, using the Bernthsen condensation (Eldho, N. V.; Saminathan, M.; Ramaiah, D., Synth. Commun., (1999) 29, 4007).
  • linker systems with two activated functionalities e.g. malonyl chloride, succinic anhydride, glutaric acid, succinyl chloride, 1,3-dibromopropane, 1,4-dibromobutane, glutaroyl dischloride, 1,3-diiodopropane, 1 ,4-diiodobutane, glutaraldehyde, 4-chlorobutanolyl chloride or 5-chloropentanoyl chloride, e.g. Frohlich, T.; Reiter, C.; Saeed, M. E.
  • two activated functionalities e.g. malonyl chloride, succinic anhydride, glutaric acid, succinyl chloride, 1,3-dibromopropane, 1,4-dibromobutane, glutaroyl dischloride, 1,3-diiodopropane, 1 ,4-dii
  • the compounds of the present invention may be for use in the treatment of diseases caused by betacoronaviruses, leishmaniasis, trypanosomiasis.
  • the treatment is caused by human and veterinary coronaviruses that belong to subgenera hibecovirus, nobecovirus, embecovirus, merbecovirus and sarbecovirus, preferably coronaviruses.
  • the treatment is caused by human coronavirus HKLI1 (HCoV- HKLI1), human coronavirus OC43 (HCoV-OC43), Middle East respiratory syndrome-related coronavirus (MERS-CoV).
  • HCV-HKLI1 human coronavirus HKLI1
  • HoV-OC43 human coronavirus OC43
  • MERS-CoV Middle East respiratory syndrome-related coronavirus
  • the treatment is caused by severe acute respiratory syndrome-related coronaviruses, preferably SARS-CoV, more preferably SARS-CoV-2.
  • the treatment is caused by a virus that evolve or mutate from the species described in the three paragraphs above.
  • the disease to be treated is the severe acute respiratory syndrome, preferably SARS-CoV or SARS-CoV-2, more preferably SARS-CoV-2.
  • the disease to be treated is the Middle East respiratory syndrome (MERS-CoV).
  • MERS-CoV Middle East respiratory syndrome
  • the disease to be treated is pneumonia.
  • the invention is directed to a composition comprising at least the composition as descibed above and at least one pharmaceutically acceptable carrier, thus to a pharmaceutical composition.
  • “Pharmaceutical composition” refers to one or more active ingredients, and one or more inert ingredients that make up the carrier, as well as any product which results, directly or indirectly, from combination, complexation or aggregation of any two or more of the ingredients, or from dissociation of one or more of the ingredients, or from other types of reactions or interactions of one or more of the ingredients. Accordingly, the pharmaceutical compositions of the present invention encompass any composition made by admixing a compound or composition of the present invention and a pharmaceutically acceptable carrier.
  • Carrier refers to a diluent, adjuvant, excipient, or vehicle with which the therapeutic is administered.
  • Such pharmaceutical carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, including but not limited to peanut oil, soybean oil, mineral oil, sesame oil and the like. Water is a preferred carrier when the pharmaceutical composition is administered orally.
  • Saline and aqueous dextrose are preferred carriers when the pharmaceutical composition is administered intravenously. Saline solutions and aqueous dextrose and glycerol solutions are preferably employed as liquid carriers for injectable solutions.
  • Suitable pharmaceutical excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like.
  • the composition if desired, can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents. These compositions can take the form of solutions, suspensions, emulsions, tablets, pills, capsules, powders, sustained-release formulations and the like.
  • the composition can be formulated as a suppository, with traditional binders and carriers such as triglycerides.
  • Oral formulation can include standard carriers such as pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate, etc. Examples of suitable pharmaceutical carriers are described in "Remington's Pharmaceutical Sciences” by E.W. Martin. Such compositions will contain a therapeutically effective amount of the therapeutic, preferably in purified form, together with a suitable amount of carrier so as to provide the form for proper administration to the patient. The formulation should suit the mode of administration.
  • the amount of active ingredient in particular, the amount of the compound of the present invention, optionally together with other therapeutically active agents, if present in the pharmaceutical formulations/compositions
  • the amount of active ingredient may range from about 0.01% to about 99%, preferably from about 0.1% to about 70%, most preferably from about 1% to about 30%, wherein the reminder is preferably composed of the one or more pharmaceutically acceptable excipients.
  • a physician or veterinarian having ordinary skill in the art can readily determine and prescribe the effective amount of the pharmaceutical composition required.
  • the physician or veterinarian could start with doses of the compounds of the invention employed in the pharmaceutical composition at levels lower than that required in order to achieve the desired therapeutic effect and gradually increase the dosage until the desired effect is achieved.
  • a suitable daily dose of a composition of the invention will be that amount of the compound which is the lowest dose effective to produce a therapeutic effect.
  • Such an effective dose will generally depend upon the factors described above.
  • Administration may carried out oral, by inhalation, intravenous, intramuscular, intraperitoneal, or subcutaneous, preferably administered proximal to the site of the target.
  • the effective daily dose of a pharmaceutical composition may be administered as two, three, four, five, six or more subdoses administered separately at appropriate intervals throughout the day, optionally, in unit dosage forms. While it is possible for a compound of the present invention to be administered alone, it is preferable to administer the compound as a pharmaceutical formulation/composition.
  • the amount of active ingredient, e.g., a compound of the invention, in a unit dosage form and/or when administered to an indiviual or used in therapy, may range from about 0.1 mg to about 1000mg (for example, from about 1mg to about 500mg, such as from about 10mg to about 200mg) per unit, administration or therapy.
  • a suitable amount of such active ingredient may be calculated using the mass or body surface area of the individual, including amounts of between about 1mg/Kg and 10mg/Kg (such as between about 2mg/Kg and 5mg/Kg), or between about 1mg/m 2 and about 400mg/m 2 (such as between about 3mg/m 2 and about 350mg/m 2 or between about 10mg/m 2 and about 200mg/m 2 ).
  • the invention is directed to a composition for use as described above, formulated as an inhalative drug.
  • composition for use as described above is formulated as an oral drug.
  • Scheme 1 Synthetic route for the preparation of different 3,6-diaminoacridin-10-ium derivatives alkylated at the N10 position.
  • Scheme 2 Synthetic routes for the preparation of 3,6-diaminoacridin-10-ium derivatives that are dual alkylated at the N6 position.
  • Air and water sensitive reactions were performed in flame-dried glassware under an argon atmosphere.
  • Solvents used for column chromatography, extractions and recrystallization were purchased in technical grade and were distilled prior to use.
  • Solvents used for reversed phase chromatography and HPLC-MS analyses were purchased from Thermofisher Scientific in HPLC-quality. Reagents and dry solvents were purchased from Sigma Aldrich, ABCR, Alfa Aesar, Thermofisher Scientific, TCI, Carl Roth and Merck and were used without further purification.
  • Analytical thin layer chromatography was performed on silica coated plates (silica gel 60 F254) purchased from VWR. Compounds were detected by ultraviolet (UV) irradiation at 254 or 366 nm. Manual flash column chromatography was performed using silica gel 60 (particle size: 0.040-0.063 mm) available from VWR. Automated preparative chromatography was performed on a Grace Reveleris Prep purification system using linear gradient elution and Buchi Reveleris Silica 40 pm cartridges for normal-phase and Buchi Reveleris C1840 pm cartridges for reverse-phase separations.
  • AVHD400 or AVHD500 spectrometer operating at either 400 MHz or 500 MHz.
  • HPLC-UV/MS analyses were performed on a Dionex UltiMate 3000 HPLC system coupled with a Thermo ScientificTM ISQTM EC Single Quadrupole Mass Spectrometer, using the following methods: Thermo ScientificTM AccucoreTM RP-MS LC-column (2.1 x 50 mm, 2.6 pm); gradient method A): 5 to 95% of acetonitrile + 0.1% formic acid v/v in water + 0.1% formic acid v/v over 5 min period; flow rate: 0.6 mL/min; gradient method B): 5 to 10% of acetonitrile + 0.1% formic acid v/v in water + 0.1% formic acid v/v over 9.5 min period; 10 to 20% of acetonitrile + 0.1% formic acid v/v in water + 0.1% formic acid v/v over 4.0 min period; 20 to 95% of acetonitrile + 0.1% formic acid v/v in water + 0.1% for
  • Neutral proflavine (nPF) was obtained from commercially available proflavine hemisulfate monohydrate, which was purchased from Sigma Aldrich. The procedure is as follows: Proflavine hemisulfate monohydrate (2.00 g, 7.24 mmol) was dissolved in water (100 mL) and then aqueous ammonia (10%) was added until the pH reached a value of 8. The formed orange precipitate was filtered off, washed with water (3 x 20 mL) and dried in vacuo to yield neutral proflavine (nPF) (1.26 g, 6.02 mmol, 83%).
  • the resulting reaction mixture was allowed to reach room temperature and stirred for 15 h. After this time period, the reaction was quenched by pouring the mixture into an aqueous solution of NaHCO 3 (40%, 300 mL), which was then stored at 5 °C overnight. The following day, the obtained precipitate was filtered, washed with water (3 x 50 mL) and dried. The crude product was recrystallized from ethanol in order to yield pure pivalate amide protected proflavine TF 139 as a beige solid (1.52 g, 4.03 mmol, 48%).
  • TF 156 3,6-Diamino-10-ethylacridin-10-ium chloride (TF 156).
  • Pivalate protected diaminoacridine derivative TF 153 400 mg, 0.811 mmol, 1.0 eq
  • ethanol 10.0 mL
  • hydrochloric acid 6.0 M in H 2 O, 3.38 mL, 20.28 mmol, 25.0 eq
  • the resulting reaction mixture was heated until reflux and stirred overnight. The following day, the solvent was removed under reduced pressure and the crude material was taken up in a mixture of EtOH and dichloromethane and stored for 1 day at 8 °C.
  • the obtained deep red precipitate was filtered off, washed with Et 2 O (2 x 10.0 mL) and dried in vacuum.
  • the desired target compound TF 163 (106 mg, 0.338 mmol, 74%) exhibited a purity greater than 95% and therefore no further purification was necessary.
  • the vector map can be found at HMGU-PEPF website.
  • the plasmids were transformed into E. coli BL21 (DE3), and the transformed cells were cultured at 37 °C in terrific broth (TB) media containing 100 mg/L kanamycin. After the GD600 reached 2, the culture was cooled to 18 °C and supplemented with 0.25 mM IPTG.
  • the vector petM5a yielded more soluble protein and it was used for all protein expression.
  • preculture was gown in M9 minimal media followed by inoculation (OD 6 oo 0.05) into 1 L of D2O M9 minimal media supplemented with 15N-Ammoniun chloride.
  • GD600 reached 0.8
  • the culture was cooled to 18°C and supplemented with 0.25mM IPTG.
  • the cells were harvested through centrifugation, and the pellets were resuspended in lysis buffer (20 mM Tris-HCI, pH 8.5, 350 mM NaCI, 10% glycerol, 10mM imidazole, 5mM betamercaptoethanol) and sonicated at 4 °C.
  • the insoluble material was removed through centrifugation at 24,000 rpm.
  • the fusion protein was first purified by Ni-NTA affinity chromatography, the supernatant was applied to nickel resin and washed with 10 times the column volume with lysis buffer followed by a wash step of lysis buffer supplemented with 20mM imidazol.
  • the protein was eluted with 3 times column volume by a buffer containing high imidazole concentration, 20 mM Tris-HCI, pH 8.5, 350 mM NaCI, 5% glycerol, 350mM imidazole, 5mM beta-mercaptoethanol.
  • TEV protease 1mg was added and the solution was dialyzed overnight at 4°C against a buffer containing low imidazole concentration, 20 mM Tris- HCI, pH 8.5, 150 mM NaCI, 5% glycerol, 10mM imidazole, 1mM Beta mercaptoethanol. The next day, the protein was applied to a nickel column and the flow though was collected followed by concentration using a top centrifuge concentrator with a 30kDa cut off up to a volume of 2mL.
  • the protein was applied to a size exclusion chromatography column, High load S75 (GE- Helathcare, chigaco, USA), pre-equilibrated with the final buffer, 20mM Tris pH 8.0, 40mM NaCI and 2mM DTT. The purity of the protein was accessed by SDS page gel.
  • TEV and uncut M pro were removed by a second NiNTA purification step.
  • the protein was further purified by size exclusion chromatography (Superdex s75, GE Healthcare) in 50mM Tris pH 7.4, 150mM NaCI, 2mM P-mercaptoethanol.
  • the assay was designed to measure p
  • the assay buffer contained 50 mM Tris (pH 8.0), 0.01 % (w/v) BSA and 10 mM DTT.
  • RLRGG-AMC was used as fluorogenic substrate for PLPro 40 pl of PLPro protein (end concentration 60 nM) was incubated with 10 pl RLRGG-AMC substrate (end concentration 400 nM).
  • the assay final volume 50 pl was incubated for 30 min.
  • the release of AMC (Ex. 360 nm I Em. 487 nm) was measured on an Envision plate reader (Perkin Elmer, Waltham, MA).
  • the assay was designed to measure PL PRO protease activity under screening conditions in white 384-well Optiplates.
  • the assay buffer contained 50 mM Tris (pH 8.0), 0.01 % (w/v) BSA and 10 mM DTT.
  • RLRGG-AMC was used as fluorogenic substrate for PLPro 40 pl of PLPro protein (end concentration 60 nM) was incubated with 10 pl RLRGG-AMC substrate (end concentration 400 nM).
  • the assay final volume 50 pl was incubated for 30 min.
  • the release of AMC (Ex. 360 nm I Em. 487 nm) was measured on an Envision plate reader (Perkin Elmer, Waltham, MA).
  • RLRGG-AMC or ISG15-AMC was used as substrate for PL PRO and the release of AMC fluorescence was measured (Ex. /Em. 360/487 nm) on an Envision plate reader.
  • 40 pl of a 75 nM PLpro solution in assay buffer 50 mM Tris (pH 8,0), 0.01% (w/v) BSA and 10 mM DTT was pipeted into 384 well plates and different concentration of ACF (50 pM - 0 pM, final concentration) was added. The mixture was incubated for 1 hour at RT.
  • reaction was initiated by adding 10 pl of 2 pM RLRGG-AMC (400 nM final) or 10 pl of 0.5 pM ISG15-AMC (100 nM, final), respectively.
  • Initial velocities of AMC release were normalized to the DMSO control.
  • IC 5 o value was calculated using GraphPad Prism. The experiment was repeated three times.
  • RLRGG-AMC or ISG15-AMC was used as substrate for PL PRO and the release of AMC fluorescence was measured (Ex./Em. 360/487 nm) on an Envision plate reader.
  • 40 pl of a 75 nM PLpro solution in assay buffer 50 mM Tris (pH 8,0), 0.01% (w/v) BSA and 10 mM DTT was pipetted into 384 well plates and different concentration of ACF (50 pM - 0 pM, final concentration) was added. The mixture was incubated for 1 hour at RT.
  • reaction was initiated by adding 10 pl of 2 pM RLRGG-AMC (400 nM final) or 10 pl of 0.5 pM ISG15-AMC (100 nM, final), respectively.
  • Initial velocities of AMC release were normalized to the DMSO control.
  • IC 50 value was calculated using GraphPad Prism. The experiment was repeated three times.
  • Vero (Cercopithecus aethiops’ kidney epithelial; ATCC CCL-81), HRT-18 (ATCC CRL-11663) cells, derivative of HRT-18 (ileocecal colorectal adenocarcinoma; ATCC CCL-244), CRFK (Felis catus, kidney cortex; ATCC® CCL-94) were cultured in Dulbecco’s MEM (Thermo Fisher Scientific, Tru) supplemented with 5% fetal bovine serum (heat-inactivated; Thermo Fisher Scientific, Poland) and antibiotics: penicillin (100 U/ml), streptomycin (100 pg/ml), and ciprofloxacin (5 pg/ml).
  • A549 cells with ACE2 overexpression (A549 ACE2+ ) 31 were cultured in the same manner with supplementation with G418 (5 mg/ml; BioShop, Canada).
  • LLC-MK2 cells (ATCC CCL-7; Macaca mulatta kidney epithelial cells) were maintained in minimal essential medium (MEM; two parts Hanks' MEM and one part Earle's MEM [Life Technologies, Tru]) 5% fetal bovine serum (heat-inactivated; Thermo Fisher Scientific, Tru), penicillin (100 ll/rnl), streptomycin (100 ll/rnl ), and ciprofloxacin (5 pg/ml).
  • MEM minimal essential medium
  • fetal bovine serum heat-inactivated
  • penicillin 100 ll/rnl
  • streptomycin 100 ll/rnl
  • ciprofloxacin 5 pg/ml
  • HSF Primary human skin fibroblasts
  • MEM Thermo Fisher Scientific, Tru
  • fetal bovine serum heat-inactivated; Thermo Fisher Scientific, Poland
  • 1% nonessential amino acids Life Technologies
  • antibiotics penicillin (100 ll/rnl), streptomycin (100 pg/ml), and ciprofloxacin (5 pg/ml).
  • HAE Human airway epithelial
  • MucilAirTM- Bronchial (Epithelix Sari, Switzerland) HAE cultures were also used for the ex vivo analysis. MucilAirTM cultures were maintained as suggested by the provider in MucilAirTM culture medium.
  • SARS-CoV-2 strain used in the study was isolated in house and is designated PL_P07 [GISAID Clade G, Pangolin lineage B.1] (accession numbers for the GISAID database: hCoV-19/Poland/PL_P07/2020).
  • Reference SARS-CoV-2 strain 026V-03883 was kindly granted by Christian Drosten, Charite - Universitatstechnik Berlin, Germany by the European Virus Archive - Global (EVAg); https://www.european-virus-archive.com/).
  • All SARS-CoV-2 stocks were generated by infecting monolayers of Vero cells. The cells were incubated at 37 °C under 5% CO 2 . The virus-containing liquid was collected at day 2 post-infection (p.i.), aliquoted and stored at -80°C. Control samples from mock-infected cells was prepared in the same manner.
  • MERS-CoV stock (isolate England 1 , 1409231v, National Collection of Pathogenic Viruses, Public Health England, United Kingdom) was generated by infecting monolayers of Vero cells. The cells were incubated at 37°C under 5% CO 2 . The virus-containing liquid was collected at day 3 p.i., aliquoted and stored at -80°C. Control samples from mock- infected cells were prepared in the same manner.
  • FIPV stock strain 79-1146 was generated by infecting CRFK cells in 90% confluency. The cells were incubated at 37 °C under 5% CO 2 . The virus-containing liquid was collected at day 3 p.i., aliquoted and stored at -80°C. Control samples from mock-infected cells were prepared in the same manner.
  • the HCoV-NL63 stock (isolate Amsterdam 1) was generated by infecting monolayers of LLC-MK2 cells. The cells were incubated at 32 °C under 5% CO 2 and then lysed by two freeze-thaw cycles at 6 days p.i. The virus-containing liquid was aliquoted and stored at -80°C. A control LLC-MK2 cell lysate from mock-infected cells was prepared in the same manner.
  • the HCoV-OC43 stock (ATCC: VR-1558) was generated by infecting monolayers of HRT-18 cells. The cells were incubated at 32 °C under 5% CO 2 and then lysed by two freezethaw cycles at 5 days post-infection (p.i.). The virus-containing liquid was aliquoted and stored at -80°C. A control HRT-18G cell lysate from mock-infected cells was prepared in the same manner.
  • Virus yields were assessed by titration on fully confluent cells in 96-well plates, according to the method of Reed and Muench. Plates were incubated at 32°C or 37°C for times indicated above, and the cytopathic effect (CPE) was scored by observation under an inverted microscope.
  • CPE cytopathic effect
  • Cell viability was evaluated using the XTT Cell Viability Assay kit (Biological Industries, Cromwell, CT, USA) according to the manufacturer’s protocol. Vero, A549 ACE2+ , CRFK, HRT-18, LLC-MK2 and HSF cells were cultured on 96-well plates. Cells were incubated with ACF for 24 h at 37°C in an atmosphere containing 5% CO 2 . After incubation, the medium was discarded and 100 pL of fresh medium was added to each well.
  • Vero, A549 ACE2+ , CRFK, HRT-18, LLC-MK2 and HSF cells were cultured on 96-well plates. Cells were incubated with ACF for 24 h at 37°C in an atmosphere containing 5% CO 2 . After incubation, the medium was discarded and 100 pL of fresh medium was added to each well.
  • Vero cells were seeded in culture medium on 96-well plates (TPP, Trasadingen, Switzerland) at 2 days before infection. Subconfluent cells were infected with SARS-CoV-2 viruses at 1600 50% tissue culture infectious dose (TCID 50 )/mL. Infection was performed in the presence of 100 nM, 1 pM and 10 pM concentration of compounds listed in Table 2. After 2 h of incubation at 37°C, cells were rinsed twice with PBS and fresh medium without compounds was added. The infection was carried out for 48 h and the cytopathic effect (CPE) was assessed. Culture supernatants were collected from wells where CPE reduction was observed.
  • CPE cytopathic effect
  • SARS-CoV-2 virus at 5000 TCID 50 /ml in the presence of ACF, remdesivir or PBS.
  • Two concentrations of ACF (400 nM and 500 nM) and the controls were added to the apical side of the inserts followed by the addition of the virus diluted in PBS. Infection time was of 2 hours at 37°C. After the infection, the apical side of the HAE were washed three times with PBS and each compound was re-applied and incubated again for 30 minutes at 37°C. After the last incubation with the ACF, the samples (50pL) were collected and the HAE were left in air-liquid interphase. Every 24 hours the HAE were incubated for 30 minutes with the ACF dilutions or controls, and the samples were collected. After collecting last samples cells were fixed with 3.7% paraformaldehyde and stained as described below.
  • Virus yield was measured using the RT-qPCR method described below.
  • RNA was isolated according to the manufacturer’s instructions.
  • Viral RNA was quantified using quantitative PCR coupled with reverse transcription (RT-qPCR) (GoTaq Probe 1-Step RT-qPCR System, Promega, Poland) using CFX96 Touch real-time PCR detection system (Bio-Rad, Poland). The reaction was carried out in the presence of the probes and primers indicated in the Table 1. The heating scheme was as follows: 15 min at 45°C and 2 min at 95°C, followed by 40 cycles of 15 s at 95°C and 1 min at 58°C or 60°C (specified in Table 1). In order to assess the copy number for the N gene, standards were prepared and serially diluted.
  • Vero cells were seeded on coverslips in 12-well plate (TPP, Trasadingen, Switzerland) at 2 days before experiment. ACF at 1 pM or DMSO at 0,01% concentration were applied on cells. After 1h cells were fixed with 3.7% paraformaldehyde (PFA) for 15 min. Fluorescent images were acquired under EVOS XL Core Imaging System.
  • A549 ACE2+ cells were seeded on coverslips in 12 well plate (TPP, Trasadingen,
  • Subconfluent cells were infected with SARS-CoV— 2 in the presence of ACF or remdesivir. After 2h infection unbound virions were washed off twice with PBS and fresh medium supplemented with compounds was added. The infection was carried out for 24 h whereupon cells were fixed with 3.7% paraformaldehyde (PFA) for 1 h. Fixed cells were permeabilized using 0,5% Tween-20 (10 min, room temperature [RT]) and unspecific binding sites were blocked with 5% bovine serum albumin (BSA) in PBS (4°C, overnight) prior to staining.
  • PFA paraformaldehyde
  • Fluorescent images were acquired under Zeiss LSM 880 confocal microscope.
  • Drug-resistant SARS-CoV-2 was obtained by serial passages of the virus in the presence of increasing concentrations of ACF or remdesivir, starting at a concentration equivalent to their IC 50 .
  • Vero cells were seeded in 12 well plate and infected with SARS-CoV-2 in the presence of the drug or PBS. When CPE was observed, samples were collected, aliquoted, frozen and used to infect cells for the next passage. Infection was repeated with increasing concentrations of the compound (IC 50 dose was doubled every 2 passages). After 5 passages, culture supernatants were collected, RNA was isolated and viral RNA was sequenced (NGS, Illumina). All experiments were carried out in triplicate.
  • Crystals of PL pro -proflavine complex grew at room temperature in 0.05 M Hepes sodium salt pH 7, 0.05M magnesium sulfate and 1.6 M lithium sulfate. Crystals suitable for testing were moved in cryo-protectant solution containing the harvesting solution supplemented with 25% (v/v) glycerol and snap frozen in liquid nitrogen.
  • PL pro -proflavine crystals were measured at Swiss Light Source (SLS, Villigen, Switzerland), beamline PXIII. The best dataset was collected at 2.7 A resolution and it was indexed and integrated using XDS software 34 ; scaled and merged using STARANISO webserver 35 . Crystal belongs to space group P6 5 22. Matthews coefficient analysis suggested the presence of two PL pro -proflavine molecules in the asymmetric unit. Molecular replacement solution was found using Phaser 36,37 and the apo PL pro structure (PDB code: 6W9C) as searching model. Model and restraints for proflavine was prepared using Lidia, the ligand builder in Coot 38 .
  • the initial model was subjected to several iterations of manual and automated refinement cycles using COOT and REFMAC5, respectively 39,40 . Throughout the refinement, 5% of the reflections were used for cross-validation analysis 41 , and the behavior of Rfree was employed to monitor the refinement strategy.
  • the commercial ACF is a mixture of 3,6-diaminoadridin-10-ium (proflavine) and
  • the NMR analysis is based on the fact that the protons of the methyl group at position 10 of acriflavine (ACF) have a very distinct chemical shift of 3.94 ppm (4.04 ppm for side methylated ACF), whereas the protons of the methyl group connected to the amino group at position 3, like it is the case in side methylated PF and ACF, have a much lower chemical shift of 2.87 and 2.98 ppm, respectively.
  • ACF acriflavine
  • the IC 50 of ACF with ISG15-AMC (1.46 pM) was comparable to the IC 50 that was determined with the RLRGG-AMC substrate.
  • AMC assays are fluorescence-based assays that are susceptible to autofluorescence or quenching effects of the compounds, further conducted gelbased de-ubiquiniting assays have been conducted to confirm the results.
  • the protease activity of PL pro and the inhibitory potential of ACF on tri-ubiquitin K48 chains have been tested. First, K48 tri-ubiqiutin has ben incubated with PL pro and samples of different time points were taken to analyze the cleavage of these chains in Western Blot assays.
  • the hit compounds were tested in cell culture and cytotoxicity was verified on Vero cells at three concentrations (100 nM, 1 pM, 10 pM) using the XTT assay. At the same time, the cytopathic effect (CPE) reduction assay was carried out. Amongst 13 compounds, three hampered the development of the cytopathic effect, but the initial RT-qPCR analysis revealed that only ACF inhibited virus replication ( Figure 2).
  • Table 3 CPE reduction assay. Initial screen of 13 proposed compounds in given concentrations. Table shows results of cytopathic effect (CPE) reduction assay obtained by microscopic observations. CPE - cytopathic effect; RED - CPE reduction; TOX - toxicity.
  • CPE cytopathic effect
  • NMR ligand-based binding analysis was carried out to validate PL pro -ligand interaction.
  • the direct interaction of ACF with PL pro was also observed by NMR ligand based assay (peaks of the ACF partially disappear in the presence of the protein) and the results are presented in Figure 3.
  • ACF is not a SARS-CoV-2 M pro inhibitor
  • the second molecule, Kir proflavine- II is TT-TT stacked at 3.5A on top of the other and occupies the S3 and S5 pockets ( Figure 4 C, D).
  • Gly163 and Asp164 form a hydrogen bond with the primary amine group at position 3 (2.9 A) and the imine group of the acridine moiety (2.9 A), respectively.
  • Tyr268 forms a T-shape TT-TT staked interaction (5.1 A) with this proflavine-ll.
  • this provides unique binding model where two proflavines, tightly TT-TT stacked, cooperate in blocking the substrate pocket. It is clear that, both molecules are requested for the inhibition.
  • the electron density analysis shows weaker trace of at least two more proflavines that can be allocated on top of the other two at optimal distance for TT-TT staking forming a continuous, DNA-like stacking from one to another PLpro molecule in the same asymmetric unit. Their electron density is much weaker and does not allow to build these molecules unambiguously ( Figure 17). However, they are not involved in any interaction with PL pro .
  • Shin et al. solved the crystal structure of SARS-CoV2-PL pro in complex with ISG15 (interferon-induced gene 15) bearing the RLRGG recognition motif at the C-terminus (1).
  • the amino group at position 3 of proflavine-l I is located in similar position as amide nitrogen of the glycine P2.
  • Side-methylated proflavine also present in commercial acriflavine preparations (see Figure 21), would, therefore, mimic the P2 amino acid.
  • Vero cells which are broadly used simian model and human A549 ACE2+ cells overexpressing the ACE2 receptor 43 . All experiments were carried out in parallel.
  • the IC 50 value calculated based on the presented data was 64 nM for the Vero cells and 86 nM for A549 ACE2+ cells.
  • Selectivity index (SI) values for Vero and A549 ACE2+ models are 53 and 36, respectively.
  • ACF hampers SARS-CoV-2 replication in the HAE ex vivo model.
  • a lower viral yield was detected in the cultures treated with ACF in comparison with the PBS control.
  • ACF treated HAE showed an even higher inhibition of virus replication than the positive control with 10 pM remdesivir after 144 h of infection.
  • the virus was under the detection limits in the ACF 500 nM treatment.
  • ACF may be used as a generic anticoronaviral drug
  • its activity against other betacoronaviruses (MERS-CoV, HCoV-OC43) and alphacoronaviruses (HCoV- NL63 and feline infectious peritonitis virus (FIPV) was tested.
  • IC 50 21 nM
  • SI 162
  • No effect on any of tested alphacoronaviruses replication in tested concentrations (Figure 14) was observed.
  • rhodesiense STIB 900 in 50 pL was added to each well and the plate incubated at 37 °C under a 5% CO 2 atmosphere for 70 h.
  • 10 pL resazurin solution (resazurin, 12.5 mg in 100 mL double-distilled water) was then added to each well and incubation continued for a further 2-4 h. 45 Then the plates were read with a Spectramax Gemini XS microplate fluorometer (Molecular Devices Cooperation, Sunnyvale, CA, USA) using an excitation wave length of 536 nm and an emission wave length of 588 nm.
  • Rat skeletal myoblasts (L-6 cells) were seeded in 96-well microtitre plates at 2000 cells/well in 100 pL RPMI 1640 medium with 10% FBS and 2 mM L-glutamine. After 24 h the medium was removed and replaced by 100 pL per well containing 5000 trypomastigote forms of T. cruzi Tulahuen strain C2C4 containing the p-galactosidase (Lac Z) gene. 47 After 48 h the medium was removed from the wells and replaced by 100 pL fresh medium with or without a serial drug dilution of eleven 3-fold dilution steps covering a range from 100 to 0.002 pg/mL.
  • Amastigotes of L. donovani strain MHOM/ET/67/L82 are grown in axenic culture at 37 °C in SM medium 48 at pH 5.4 supplemented with 10% heat-inactivated fetal bovine serum under an atmosphere of 5% CO 2 in air.
  • One hundred microlitres of culture medium with 105 amastigotes from axenic culture with or without a serial drug dilution are seeded in 96-well microtitre plates.
  • Serial drug dilutions of eleven 3-fold dilution steps covering a range from 100 to 0.002 pg/mL are prepared. After 70 h of incubation the plates are inspected under an inverted microscope to assure growth of the controls and sterile conditions.
  • Assays were performed in 96-well microtiter plates, each well containing 100 pl of RPMI 1640 medium supplemented with 1 % L-glutamine (200 mM) and 10% fetal bovine serum, and 4000 L-6 cells (a primary cell line derived from rat skeletal myoblasts). 49 Serial drug dilutions of eleven 3-fold dilution steps covering a range from 100 to 0.002 pg/mL were prepared. After 70 h of incubation the plates were inspected under an inverted microscope to assure growth of the controls and sterile conditions. 10 pL of resazurin was then added to each well and the plates incubated for another 2 h.

Abstract

The present invention relates to a composition, comprising at least one compound according to formula (I) as well as to a composition comprising at least one compound according to formula (I) and/or dimers of compounds according to formula (I) in particular for use in the treatment of diseases caused by betacoronaviruses, leishmaniasis, and trypanosomiasis.

Description

Inhibition of virus protease
TECHNICAL FIELD OF THE INVENTION
The present invention relates to a composition, comprising at least one compound according to formula (I) as well as to a composition comprising at least one compound according to formula (I) and/or dimers of compounds according to formula (I), in particular for use in the treatment of diseases caused by betacoronaviruses, leishmaniasis, and trypanosomiasis.
BACKGROUND ART
[001] Coronaviruses have been considered a potential threat since 2002, when the SARS- CoV virus emerged in southern China to spread through continents and disappear shortly thereafter1 ,2 rapidly. Ten years later, the second coronavirus - MERS-CoV - gave a final warning to be prepared3. Still, the emergence of the SARS-CoV-2 and subsequent pandemic met the public unprepared and paralyzed the modern world in an unprecedented way. At present, 1.4 million fatalities, have already been crossed and the northern hemisphere is facing the long the winter season, which due to the appearance of other comorbidities (low/dry air, coinfections, pollution, dysregulated immune responses) may still increase these numbers drastically4'6.
[002] While the worldwide hunt for a vaccine is bringing optimistic news, a timeline to an effective one remains to be unkown, and the dark horses face issues with the safety7. At the same time, worldwide efforts are undertaken to design and develop new antivirals8. While the development of novel antivirals is essential, realistically, the drug development timeline is too long to hope for the completely new compounds to find their way to the clinic during this season or even this pandemic. The new compounds are developed to become the future drugs for pandemics that are yet to come. Pragmatically, the focus should be and has been given to the repurposing of existing drugs with known safety profiles. The initial hits did not fulfill the hopes, and several inhibitors were already abandoned, e.g., the HIV-1 protease inhibitors lopinavir and ritonavir. Some others are still in clinic, but no evident proof of effectiveness has been provided. While there are high hopes given to the remdesivir, results of the clinical trials show that its efficacy in monotherapy is low. On the other hand, it is already speculated that identification of other antivirals effective against SARS-CoV-2 may give a chance to use the strategy developed for the HIV-1 , employing several compounds targeting different molecular targets. In such a way emergence of resistant mutants is limited and the synergy of action allows for effective limitation of virus replication.
[003] The coronaviral genome encodes for several structural and non-structural proteins. The most promising targets are the Spike (S) protein, as the target for neutralizing antibodies and entry inhibitors, the nsp12 polymerase, targeted by several compounds including the remdesivir, nsp14 and nsp16 methyltransferases essential for the capping of viral RNA, and two cysteine proteases Mpro and PLpro, responsible for the viral proteome maturation and indispensable for the infection. PLpro is also responsible for type I interferon response attenuation.
[004] There is a need for further therapeutics for treatment of a SARS-CoV-2 infection. A potential target is SARS-CoV-2 PLpro.
SUMMARY OF THE INVENTION
[005] The present invention is related to a composition comprising at least one compound according to formula (I)
Figure imgf000003_0001
RT is selected from the group consisting of H, (Ci-C6)alkyl, (CH2)0(Ci-C6)alkyl ,(Ci-C6)cycloalkyl, (Ci-C6)heterocyclyl, or absent, preferably methyl;; o is 1 to 3, preferably 1 ;
R2 is selected from the group consisting of H, (Ci-C6)alkyl,-(CH2)rCONH(CH2)sR6, -(CH- (CH2)pCOvinyl, -(CH2)qR6, -CO(Ci-C6)alkyl preferably H;
R3 is selected from the group consisting of H, (Ci-C6)alkyl, -(CH2)rCONH(CH2)sR6, - (CH2)pCOvinyl, -(CH2)qR6, -CO(Ci-C6)alkyl, preferably H; p is 1-3, preferably 1 ; q is 1-3, preferably 1 ; r is 1-3, preferably 1 ; s is 1-3, preferably 1 ;
R4 is selected from the group consisting of H, (Ci-C6)alkyl;
R5 is selected from the group consisting of H, (Ci-C6)alkyl; if R2 and R5 are both (Ci-C6)alkyl, R2 and R5 may be connected to form a 4 to 6 membered ring; if R3 and R4 are both (Ci-C6)alkyl, R3 and R4 may be connected to form a 4 to 6 membered ring; R6 is selected from the group consisting of
Figure imgf000004_0001
X' is an anion or absent ; if X' is absent then RT is absent; for use in the treatment of diseases caused by betacoronaviruses, leishmaniasis, and trypanosomiasis.
[006] The invention is further directed to a composition in which at least one compound according to formula (I) and at least one compound according to formula (III) are bonded together via one or two linker systems wherein optionally a) the linker system is (C2-Ci0)alkyl, preferably (C2-Ci0)alkenyl, preferably (C3-C8)alkyl, or (C3- 8)alkenyl; wherein optionally at least one or at least two CH2-groups in these alkyl or alkenyl groups are substituted by O, S, S(O)i.2, NH or N(Ci-C4)alkyl and/or b) connecting is performed preferably via position 5, 7, 8 or by substitution of the nitrogen in position 6 in formula (I) and position 5, 7, 8 or by substitution of the nitrogen in position 6 or 10 in formula (IV) wherein the underlying aromatic system in formula (I) and (III) is numbered according to formula
Figure imgf000004_0002
(IV).
[007] The invention is further directed to a composition comprising at least one compound according to formula (I)
Figure imgf000004_0003
RT is selected from the group consisting of H, (Ci-C6)alkyl, (CH2)0(Ci-C6)alkyl ,(Ci-C6)cycloalkyl, (Ci-C6)heterocyclalkyl, or absent, preferably methyl; o is 1 to 3, preferably 1 ;
R2 is selected from the group consisting of H, (Ci-C6)alkyl,-(CH2)rCONH(CH2)sR6, -(CH- (CH2)pCOvinyl, -(CH2)qR6, -CO(Ci-C6)alkyl preferably H;
R3 is selected from the group consisting of H, (Ci-C6)alkyl, -(CH2)rCONH(CH2)sR8, - (CH2)pCOvinyl, -(CH2)qR6, -CO(Ci-C6)alkyl, preferably H; p is an integer between 1 to 3, preferably 1 ; q is an integer between 1 to 3, preferably 1 ; r is an integer between 1 to 3, preferably 1 ; s is an integer between 1 to 3, preferably 1;
R4 is selected from the group consisting of H, (Ci-C6)alkyl;
R5 is selected from the group consisting of H, (Ci-C6)alkyl; if R2 and R5 are both (Ci-C6)alkyl, R2 and R5 may be connected to form a 4 to 6 membered ring; if R3 and R4 are both (Ci-C6)alkyl, R3 and R4 may be connected to form a 4 to 6 membered ring; ) °>
R6 is selected from the group consisting of
Figure imgf000005_0001
;
X' is an anion or absent; if X' is absent then RT is absent; with the provisio that the compound according to formula (I) is not selected from the group
Figure imgf000005_0002
As shown in the examples, the inventive compounds block the replication of the selected betacoronaviruses, including with nanomolar IC50, showing high selectivity and good effectiveness (see Figures 8 to 14). Further, it has been shown that the inventive compounds are effective against Trypanosoma and Leishmania parasites.
BRIEF DESCRIPTION OF THE FIGURES
[008] Fig. 1 : Inhibiton of PLpro in the presence of ACF. (A) AMC assay using RLRGG-AMC as substrate and PLpro performed in technical triplicates. Vertical Y-axis shows fluorescent signal (rising, as the substrate is proteolytically cleaved). Horizontal X-axis indicate time. An inhibition profile is observable. (B) As in (A), only with ISG15-AMC instead of RLRGG-AMC (C) Time course analysis of tri-ubiquitin K48-linked (2 pM) hydrolysis using 100 nM PLpro in the presence of different ACF concentrations.
[009] Fig. 2: The inhibition of virus replication by selected compounds. Figure shows RT- qPCR analysis of cell culture supernatants infected with SARS-CoV-2; tissue culture infectious dose (TCID50) = 1600 /mL) with presence of compounds after 48 h of infection. Experiment was performed in duplicate. The results are presented as average values with standard deviations (error bars).
[0010] Fig. 3: The crystal structure of SARS-Cov2-PLpro in complex with proflavine. SCoV2- PLpro is represented as a solid surface, whereas proflavine is represented as a stick model. (A) a zoom-in of the two proflavine molecules in the S3-S5 pockets of the enzyme active site. (B) a zoom-in on a proflavine molecule between two crystal neighbors of PLpro.
[0011] Fig. 4: Details of the molecular interactions between the SARS-CoV2-PLpro and proflavines. (A, B) Both proflavine molecules bind cooperatively in the substrate pocket of the enzyme forming a non-covalent inhibitor. Both polar (gray) and hydrophobic (red) interactions as well as TT-TT stacking (green) are involved. Main residues involved in the interactions are shown as a stick-model. (C, D) 2D plots of molecular interactions between proflavine-l, proflavine-ll and PLpro. Each proflavine molecule uses different properties for form interaction. The aromatic nitrogen of proflavine-l must be desolvated for binding. This explains the higher affinity of acriflavine than proflavine as it contains N-methylated components.
[0012] Fig. 5: Both proflavine molecules mimic native substrate interactions. (A) Comparison of SARS-CoV2-PLpro complexed with proflavine (in gray) and ISG15 host-cell substrate (in cyan; PDB ID:6YVA). The active site is marked by a dashed oval. (B) Substrate recognition cleft interaction of proflavines and the C-terminal tail of ISG15. Proflavine molecules overlap with the RLRGG motif of the substrate. The two arginines in P3 and P5 turn their lipophilic carbons in the same directions as the aromatic carbons of the proflavine-ll molecule in the S3-S5 pockets. The amide nitrogen H-bond donors of the peptide backbone correspond well with the proflavine-ll donors and the interactions are well preserved. The side chain of the leucin in position P4 points exactly of the proflavine ring in the S4 pocket.
[0013] Fig. 6: Overlay of 1H,15N TROSY NMR spectra of PLpro with different amount of ACF added. The entire spectrum is shown in the middle, magnification of a few regions above and below. A number of peaks shift with the addition of ACF. The bulk of the spectra remains similar to the reference apo-PLpro. This indicated that the overall fold of the protein is intact and the compound binds in a distinct binding pocket.
[0014] Fig. 7: The cytotoxicity of ACF in vitro.
[0015] Fig. 8: The inhibition of virus replication by ACF in A549ACE2+ (A) and Vero (B) cells. Figure shows RT-qPCR analysis of cell culture supernatants infected with SARS-CoV-2; tissue culture infectious dose (TCID50) = 1600 /mL) with presence of ACF after 24 h of infection. All experiments were performed at least in 3 biological repetitions, each in triplicate. The results are presented as average values with standard deviations (error bars). An asterisk (p < 0.05) indicates values that are significantly different from the control.
[0016] Figure 9: The inhibition of virus replication by ACF in Vero cells. Cells were infected with the SARS-CoV-2 in presence of Acriflavine for 48 h. Images show the reduction of cytopathic effect. Scale bar = 100 pm.
[0017] Figure 10: The inhibition of virus replication by ACF in A549ACE2+ cells. Cells were infected with the SARS-CoV-2 in presence of 500 nM Acriflavine, 10 pM Remdesivir or vessel control for 24 h and 48 h. Cell nuclei are denoted in blue, actin is denoted in red and SARS- CoV-2 N-protein is denoted in green. Each image represents maximum projection of 5 pm section. Scale bar = 20 pm.
[0018] Figure 11 : Antiviral activity of ACF against SARS-CoV-2 in human airway epithelium. (A) In-house HAE (B) MucilAir™. The figures show RT-qPCR analysis of HAE culture supernatants infected with SARS-CoV-2; tissue culture infectious dose (TCID50) = 5000 /mL). Remdesivir and PBS were used as controls. The assay was performed at least in duplicate and median values with range are presented.
[0019] Figure 12: The inhibition of virus replication by ACF in well differentiated HAE cultures. Cells were infected with the SARS-CoV-2 in presence of 500 nM Acriflavine, 10 pM Remdesivir or vessel control. At day 6 p.i. cells were fixed and immunostained. Cell nuclei are denoted in blue, actin in red and SARS-CoV-2 N-protein in green. Each image represents maximum projection of 3 pm section. Scale bar = 10 pm.
[0020] Figure 13: Time of addition study. The inhibition of virus replication in Vero cells by ACF added after post-infection (time denoted on the x-axis). Figure shows RT-qPCR analysis of cell culture supernatants infected with SARS-CoV-2; tissue culture infectious dose (TCID50) = 1600 /ml). All experiments were performed at least in 3 biological repetitions, each in triplicate. The results are presented as average values with standard deviations (error bars). An asterisk (p < 0.05) indicates values that are significantly different from the control.
[0021] Figure 14: ACF inhibits betacoronaviruses. Replication of (A) MERS-CoV, (B) HCoV- OC43, HCoV-NL63 (C) and (D) FIPV in vitro in the presence or absence of inhibitors, as assessed with RT-qPCR on cell culture supernatants. Single round of infection was recorded (24 h). All experiments were performed at least in 2 biological repetitions, each in triplicate. The results are presented as average values with standard deviations (error bars). An asterisk (p < 0.05) indicates values that are significantly different from the non-treated control. ACF: acriflavin, rem: remdesivir.
[0022] Figure 15: Proflavine molecule at the interface between SARS-CoV2-PLpro asymmetric units. (A) Most probably due to a crystal packing molecule of proflavine was found on top of the catalytic triad (C111, H272, D286). Important residues are highlighted as stick model. Two water molecules (red spheres) mediate a hydrogen bond with D286. Hydrogen bonds are represented as yellow dashed lines. (B) 2D plot of the molecular interactions between proflavine and the residues of SARS-CoV2-PLpro.
[0023] Figure 16: Comparison of SARS-CoV2-PLpro in the proflavine-bound and apo-state. Bound PLpro is colored in gray; whereas the unbound PLpro (PDB ID: 7D47) is colored in yellow. The BL2 loop is involved in an induced fit rearrangement upon the binding mostly due to the movement of the Tyr268. The side-chain of Tyr268 participates in a TT-TT stacking with proflavine molecules.
[0024] Figure 17: Electron density map showing the fractional presence of additional aromatic proflavine-like molecules TT-TT stacked one on top of the other between two copies of SARS- CoV2-PLpro present in the crystal lattice. 2FO-FC electron density map is contoured at 2CE. The electron density of the identified proflavine molecules is colored in blue; whereas additional electron density is colored in green. The densities are most likely caused by weak and transiently-bound proflavines. We did not model them in the crystal structure as their electron density was much weaker than active site-bound molecules.
[0025] Figure 18: SARS-CoV-2 Mpro activity is not significantly inhibited by ACF. The digestion of fluorogenic substrate was recorded in the absence and presence of ACF (A). Only small decrease of Mpro activity is observed at physiologically irrelevant ACF concentration of 100 pM (B). The vertical shift in signal levels is caused by ACF absorbance.
[0026] Figure 19: (A) Summary of the high-throughput screening campaign (16 x 384-well plates). RLRGG-AMC peptide was used as a substrate for His-PLPro. Each dot represents the data of one compound in one well (n = 1). Controls without protease are located in column 24 and ACF as representative hit is depicted in blue. (B) Two representative screening plates with ACF and Proflavine Hemisulfate as hits (blue) are depicted side by side. (C) Dose response curves of eleven hits. These hits were re-ordered and re-tested in ten-point titrations on the primary screening assay (mean ± SD, n = 2). Shown are inhibition curves and IC50 values. (D) as in (C). Analogs of ACF were tested in ten-point titrations on the primary assay (mean ± SD, n = 3). (E) Inhibition curve of the known PLPro inhibitor GLR-0617 (mean ± SD, n = 3). [0027] Figure 20: Kinetic assays of His-PLpro DUB activity in the presence of different concentrations of ACF. RLRGG-AMC in (A) and ISG15-AMC in (B) were used as subtrates. Reactions were performed in triplicates. (C) Time course analysis of tri-ubiquitin K48-linked (2 pM) hydrolysis using 100 nM His-PLpro.
[0028] Figure 21 : Composition of commercial acriflavine (cACF) sold by Sigma Aldrich (A8251): 56% proflavine (PF), 17% acriflavine (ACF) and about 26% of their side methylated derivatives.
[0029] Figure 22: Map of pETM-5a.
DETAILED DESCRIPTION OF THE INVENTION
[0030] The solution of the present invention is described in the following, exemplified in the appended examples, illustrated in the Figures and reflected in the claims. >
[0031] Definitions
[0032] It is noted that as used herein, the singular forms “a”, “an”, and “the”, include plural references unless the context clearly indicates otherwise. Thus, for example, reference to “a reagent” includes one or more of such different reagents and reference to “the method” includes reference to equivalent steps and methods known to those of ordinary skill in the art that could be modified or substituted for the methods described herein.
[0033] Unless otherwise indicated, the term "at least" preceding a series of elements is to be understood to refer to every element in the series. Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the present invention.
[0034] The term "and/or" wherever used herein includes the meaning of "and", "or" and "all or any other combination of the elements connected by said term".
[0035] Throughout this specification and the claims which follow, unless the context requires otherwise, the word “comprise”, and variations such as “comprises” and “comprising”, will be understood to imply the inclusion of a stated integer or step or group of integers or steps but not the exclusion of any other integer or step or group of integer or step. When used herein the term “comprising” can be substituted with the term “containing” or “including” or sometimes when used herein with the term “having”. When used herein “consisting of" excludes any element, step, or ingredient not specified.
[0036] The term "alkyl" refers to a monoradical of a saturated straight or branched hydrocarbon. Preferably, the alkyl group comprises from 1 to 10 carbon atoms, i.e., 1, 2, 3, 4, 5, 6, 7, 8, 9, 9 carbon atoms, more preferably 1 to 5 carbon atoms, such as 1 to 4 or 1 to 2 carbon atoms. Exemplary alkyl groups include methyl, ethyl, propyl, iso-propyl, butyl, iso-butyl, tert-butyl, n- pentyl, iso-pentyl, sec-pentyl, neo-pentyl, 1,2-dimethyl-propyl, iso-amyl, n-hexyl, iso-hexyl, sechexyl, 2-ethyl-hexyl, n-heptyl, iso-heptyl, n-octyl, 2-ethyl-hexyl, n-nonyl, n-decyl, and the like. [0037] The term "alkylene" refers to a diradical of a saturated straight or branched hydrocarbon. Preferably, the alkylene comprises from 1 to 10 carbon atoms, i.e., 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 carbon atoms, more preferably 1 to 8 carbon atoms, such as 1 to 6 or 1 to 4 carbon atoms. Exemplary alkylene groups include methylene, ethylene (i.e., 1 ,1-ethylene, 1,2-ethylene), propylene (i.e., 1,1-propylene, 1,2-propylene (-CH(CH3)CH2-), 2,2-propylene (-C(CH3)2-), and
1.3-propylene), the butylene isomers (e.g., 1,1-butylene, 1 ,2-butylene, 2,2-butylene, 1 ,3- butylene, 2,3-butylene (cis or trans or a mixture thereof), 1 ,4-butylene, 1 ,1-iso-butylene, 1 ,2-iso- butylene, and 1,3-iso-butylene), the pentylene isomers (e.g., 1,1-pentylene, 1 ,2-pentylene, 1,3- pentylene, 1,4-pentylene, 1,5-pentylene, 1,1-iso-pentylene, 1,1 -sec-pentyl, 1,1-neo-pentyl), the hexylenisomers (e.g., 1,1-hexylene, 1 ,2-hexylene, 1,3-hexylene, 1,4-hexylene, 1,5-hexylene, 1 ,6-hexylene, and 1,1-isohexylene), and the like.
[0038] The term "alkenylene" refers to a diradical of an unsaturated straight or branched hydrocarbon having at least one carbon-carbon double bond. Generally, the maximal number of carbon-carbon double bonds in the alkenylene group can be equal to the integer which is calculated by dividing the number of carbon atoms in the alkenylene group by 2 and, if the number of carbon atoms in the alkenylene group is uneven, rounding the result of the division down to the next integer. For example, for an alkenylene group having 9 carbon atoms, the maximum number of carbon-carbon double bonds is 4. Preferably, the alkenylene group has 1 to 4, i.e., 1, 2, 3, or 4, carbon-carbon double bonds. Preferably, the alkenylene group comprises from 2 to 10 carbon atoms, i.e., 2, 3, 4, 5, 6, 7, 8, 9, or 10 carbon atoms, more preferably 2 to 8 carbon atoms, such as 2 to 6 carbon atoms or 2 to 4 carbon atoms. Thus, in a preferred embodiment, the alkenylene group comprises from 2 to 10 carbon atoms and 1 , 2, 3, 4, or 5 carbon-carbon double bonds, more preferably it comprises 2 to 8 carbon atoms and 1 , 2, 3, or 4 carbon-carbon double bonds, such as 2 to 6 carbon atoms and 1 , 2, or 3 carbon-carbon double bonds or 2 to 4 carbon atoms and 1 or 2 carbon-carbon double bonds. The carbon-carbon double bond(s) may be in cis (Z) or trans (E) configuration. Exemplary alkenylene groups include ethen-1 ,2-diyl, vinyliden, 1-propen-1 ,2-diyl, 1-propen-1 ,3-diyl, 1-propen-2,3-diyl, allyliden, 1-buten-1 ,2-diyl, 1-buten-1 ,3-diyl, 1-buten-1 ,4-diyl, 1-buten-2,3-diyl, 1-buten-2,4-diyl, 1-buten-3,4-diyl, 2-buten-1 ,2-diyl, 2-buten-1 ,3-diyl, 2-buten-1 ,4-diyl, 2-buten-2,3-diyl, 2-buten-
2.4-diyl, 2-buten-3,4-diyl, and the like. If an alkenylene group is attached to a nitrogen atom, the double bond cannot be alpha to the nitrogen atom.
[0039] The term "cycloalkyl" represents cyclic non-aromatic versions of "alkyl" with preferably 3 to 6 carbon atoms, such as 3 to 6 carbon atoms, i.e., 3, 4, 5, or 6, carbon atoms, more preferably 5 to 6 carbon atoms, even more preferably 6 carbon atoms. Exemplary cycloalkyl groups include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl. [0040] The term "alkenyl" refers to a monoradical of an unsaturated straight or branched hydrocarbon having at least one carbon-carbon double bond. Generally, the maximal number of carbon-carbon double bonds in the alkenyl group can be equal to the integer which is calculated by dividing the number of carbon atoms in the alkenyl group by 2 and, if the number of carbon atoms in the alkenyl group is uneven, rounding the result of the division down to the next integer. For example, for an alkenyl group having 9 carbon atoms, the maximum number of carbon-carbon double bonds is 4. Preferably, the alkenyl group has 1 to 4, i.e., 1, 2, 3, or 4, carbon-carbon double bonds. Preferably, the alkenyl group comprises from 2 to 10 carbon atoms, i.e., 2, 3, 4, 5, 6, 7, 8, 9, or 10 carbon atoms, more preferably 2 to 8 carbon atoms, such as 2 to 6 carbon atoms or 2 to 4 carbon atoms. Thus, in a preferred embodiment, the alkenyl group comprises from 2 to 10 carbon atoms and 1 , 2, 3, 4, or 5 carbon-carbon double bonds, more preferably it comprises 2 to 8 carbon atoms and 1 , 2, 3, or 4 carbon-carbon double bonds, such as 2 to 6 carbon atoms and 1 , 2, or 3 carbon-carbon double bonds or 2 to 4 carbon atoms and 1 or 2 carbon-carbon double bonds. The carbon-carbon double bond(s) may be in cis (Z) or trans (E) configuration. Exemplary alkenyl groups include vinyl, 1-propenyl, 2-propenyl (i.e., allyl), 1-butenyl, 2-butenyl, 3-butenyl, 1-pentenyl, 2-pentenyl, 3-pentenyl, 4-pentenyl, 1-hexenyl, 2-hexenyl, 3-hexenyl, 4-hexenyl, 5-hexenyl, 1-heptenyl, 2-heptenyl, 3-heptenyl, 4-heptenyl, 5- heptenyl, 6-heptenyl, 1 -octenyl, 2-octenyl, 3-octenyl, 4-octenyl, 5-octenyl, 6-octenyl, 7-octenyl, 1-nonenyl, 2-nonenyl, 3-nonenyl, 4-nonenyl, 5-nonenyl, 6-nonenyl, 7-nonenyl, 8-nonenyl, 1- decenyl, 2-decenyl, 3-decenyl, 4-decenyl, 5-decenyl, 6-decenyl, 7-decenyl, 8-decenyl, 9- decenyl, and the like. If an alkenyl group is attached to a nitrogen atom, the double bond cannot be alpha to the nitrogen atom.
[0041] The term "alkenylene" refers to a diradical of an unsaturated straight or branched hydrocarbon having at least one carbon-carbon double bond. Generally, the maximal number of carbon-carbon double bonds in the alkenylene group can be equal to the integer which is calculated by dividing the number of carbon atoms in the alkenylene group by 2 and, if the number of carbon atoms in the alkenylene group is uneven, rounding the result of the division down to the next integer. For example, for an alkenylene group having 9 carbon atoms, the maximum number of carbon-carbon double bonds is 4. Preferably, the alkenylene group has 1 to 4, i.e., 1, 2, 3, or 4, carbon-carbon double bonds. Preferably, the alkenylene group comprises from 2 to 10 carbon atoms, i.e., 2, 3, 4, 5, 6, 7, 8, 9, or 10 carbon atoms, more preferably 2 to 8 carbon atoms, such as 2 to 6 carbon atoms or 2 to 4 carbon atoms. Thus, in a preferred embodiment, the alkenylene group comprises from 2 to 10 carbon atoms and 1 , 2, 3, 4, or 5 carbon-carbon double bonds, more preferably it comprises 2 to 8 carbon atoms and 1 , 2, 3, or 4 carbon-carbon double bonds, such as 2 to 6 carbon atoms and 1 , 2, or 3 carbon-carbon double bonds or 2 to 4 carbon atoms and 1 or 2 carbon-carbon double bonds. The carbon-carbon double bond(s) may be in cis (Z) or trans (E) configuration. Exemplary alkenylene groups include ethen-1 ,2-diyl, vinyliden, 1-propen-1 ,2-diyl, 1-propen-1 ,3-diyl, 1-propen-2,3-diyl, allyliden, 1-buten-1 ,2-diyl, 1-buten-1 ,3-diyl, 1-buten-1 ,4-diyl, 1-buten-2,3-diyl, 1-buten-2,4-diyl, 1-buten-3,4-diyl, 2-buten-1 ,2-diyl, 2-buten-1 ,3-diyl, 2-buten-1 ,4-diyl, 2-buten-2,3-diyl, 2-buten- 2,4-diyl, 2-buten-3,4-diyl, and the like. If an alkenylene group is attached to a nitrogen atom, the double bond cannot be alpha to the nitrogen atom.
[0042] The term "aryl" or "aromatic ring" refers to a monoradical of an aromatic cyclic hydrocarbon. Preferably, the aryl group contains 6 to 10 (e.g., 6 to 10, such as 5, 6, or 10) carbon atoms which can be arranged in one ring (e.g., phenyl) or two or more condensed rings (e.g., naphthyl). Exemplary aryl groups include, phenyl, indenyl, naphthyl, azulenyl, fluorenyl, anthryl, and phenanthryl. Preferably, "aryl" refers to a monocyclic ring containing 6 carbon atoms or an aromatic bicyclic ring system containing 10 carbon atoms. Preferred examples are phenyl and naphthyl. Wherein “-(Ci-C6)alkyl(C6-Ci0)aryl” means that an aryl group comprising an alkyl substituent is attached to the overall molecule via that alkyl substituent.
[0043] The term "heteroaryl" means an aryl group as defined above in which one or more carbon atoms in the aryl group are replaced by heteroatoms of O, S, or N. Preferably, heteroaryl refers to a five or six-membered aromatic monocyclic ring wherein 1, 2, or 3 carbon atoms are replaced by the same or different heteroatoms of O, N, or S. Alternatively, it means an aromatic bicyclic or tricyclic ring system wherein 1, 2, 3, 4, or 5 carbon atoms are replaced with the same or different heteroatoms of O, N, or S. Preferably, in each ring of the heteroaryl group the maximum number of O atoms is 1 , the maximum number of S atoms is 1, and the maximum total number of O and S atoms is 2. Exemplary heteroaryl groups include furanyl, thienyl, oxazolyl, isoxazolyl, oxadiazolyl (1,2,5- and 1 ,2,3-), pyrrolyl, imidazolyl, pyrazolyl, triazolyl (1 ,2,3- and 1,2,4-), tetrazolyl, thiazolyl, isothiazolyl, thiadiazolyl (1,2,3- and 1 ,2,5-), pyridyl, pyrimidinyl, pyrazinyl, triazinyl (1,2,3-, 1,2,4-, and 1,3,5-), benzofuranyl (1- and 2-), indolyl, isoindolyl, benzothienyl (1- and 2-), 1 H-indazolyl, benzimidazolyl, benzoxazolyl, indoxazinyl, benzisoxazolyl, benzothiazolyl, benzisothiazolyl, benzotriazolyl, quinolinyl, isoquinolinyl, benzodiazinyl, quinoxalinyl, quinazolinyl, benzotriazinyl (1,2,3- and 1,2,4-benzotriazinyl), pyridazinyl, phenoxazinyl, thiazolopyridinyl, pyrrolothiazolyl, phenothiazinyl, isobenzofuranyl, chromenyl, xanthenyl, phenoxathiinyl, pyrrolizinyl, indolizinyl, indazolyl, purinyl, quinolizinyl, phthalazinyl, naphthyridinyl (1,5-, 1,6-, 1 ,7-, 1,8-, and 2,6-), cinnolinyl, pteridinyl, carbazolyl, phenanthridinyl, acridinyl, perimidinyl, phenanthrolinyl (1,7-, 1,8-, 1 ,10-, 3,8-, and 4,7-), phenazinyl, oxazolopyridinyl, isoxazolopyridinyl, pyrrolooxazolyl, and pyrrolopyrrolyl. Exemplary 5- or 6-memered heteroaryl groups include furanyl, thienyl, oxazolyl, isoxazolyl, oxadiazolyl (1 ,2,5- and 1 ,2,3-), pyrrolyl, imidazolyl, pyrazolyl, triazolyl (1 ,2,3- and 1,2,4-), thiazolyl, isothiazolyl, thiadiazolyl (1,2,3- and 1,2,5-), pyridyl, pyrimidinyl, pyrazinyl, triazinyl (1 ,2,3-, 1,2,4-, and 1 ,3,5-), and pyridazinyl. Wherein for example “-(Ci-C6)alkyl(C5-Ci0)heteroaryl” means that a heteroaryl group comprising an alkylsubstituent group is attached to the overall molecule via that alkyl substituent.
[0044] The term "heterocyclyl" means a cycloalkyl group as defined above in which from 1 , 2, 3, or 4 carbon atoms in the cycloalkyl group are replaced by heteroatoms of O, S, or N. Preferably, in each ring of the heterocyclyl group the maximum number of O atoms is 1 , the maximum number of S atoms is 1, and the maximum total number of O and S atoms is 2. The term "heterocyclyl" is also meant to encompass partially or completely hydrogenated forms (such as dihydro, tetrahydro or perhydro forms) of the above-mentioned heteroaryl groups. Exemplary heterocyclyl groups include morpholino, isochromanyl, chromanyl, pyrrolidinyl, imidazolidinyl, pyrazolidinyl, piperidinyl, piperazinyl, indolinyl, isoindolinyl, di- and tetrahydrofuranyl, di- and tetrahydrothienyl, di- and tetrahydrooxazolyl, di- and tetrahydroisoxazolyl, di- and tetrahydrooxadiazolyl (1 ,2,5- and 1 ,2,3-), dihydropyrrolyl, dihydroimidazolyl, dihydropyrazolyl, di- and tetrahydrotriazolyl (1 ,2,3- and 1 ,2,4-), di- and tetrahydrothiazolyl, di- and tetrahydrothiazolyl, di- and tetrahydrothiadiazolyl (1,2,3- and 1,2,5-), di- and tetrahydropyridyl, di- and tetrahydropyrimidinyl, di- and tetrahydropyrazinyl, di- and tetrahydrotriazinyl (1 ,2,3-, 1 ,2,4-, and 1 ,3,5-), di- and tetrahydrobenzofuranyl (1- and 2-), di- and tetrahydroindolyl, di- and tetrahydroisoindolyl, di- and tetrahydrobenzothienyl (1- and 2), di- and tetrahydro-1 H-indazolyl, di- and tetrahydrobenzimidazolyl, di- and tetrahydrobenzoxazolyl, di- and tetrahydroindoxazinyl, di- and tetrahydrobenzisoxazolyl, di- and tetrahydrobenzothiazolyl, di- and tetrahydrobenzisothiazolyl, di- and tetrahydrobenzotriazolyl, di- and tetrahydroquinolinyl, di- and tetrahydroisoquinolinyl, di- and tetrahydrobenzodiazinyl, di- and tetrahydroquinoxalinyl, di- and tetrahydroquinazolinyl, di- and tetrahydrobenzotriazinyl (1,2,3- and 1 ,2,4-), di- and tetrahydropyridazinyl, di- and tetrahydrophenoxazinyl, di- and tetrahydrothiazolopyridinyl (such as 4,5,6-7-tetrahydro[1,3]thiazolo[5,4-c]pyridinyl or 4,5,6-7-tetrahydro[1,3]thiazolo[4,5- c]pyridinyl, e.g., 4,5,6-7-tetrahydro[1,3]thiazolo[5,4-c]pyridin-2-yl or 4, 5,6-7- tetrahydro[1 ,3]thiazolo[4,5-c]pyridin-2-yl), di- and tetrahydropyrrolothiazolyl (such as 5,6- dihydro-4H-pyrrolo[3,4-d][1,3]thiazolyl), di- and tetrahydrophenothiazinyl, di- and tetrahydroisobenzofuranyl, di- and tetrahydrochromenyl, di- and tetrahydroxanthenyl, di- and tetrahydrophenoxathiinyl, di- and tetrahydropyrrolizinyl, di- and tetrahydroindolizinyl, di- and tetrahydroindazolyl, di- and tetrahydropurinyl, di- and tetrahydroquinolizinyl, di- and tetrahydrophthalazinyl, di- and tetrahydronaphthyridinyl (1 ,5-, 1 ,6-, 1,7-, 1,8-, and 2,6-), di- and tetrahydrocinnolinyl, di- and tetrahydropteridinyl, di- and tetrahydrocarbazolyl, di- and tetrahydrophenanthridinyl, di- and tetrahydroacridinyl, di- and tetrahydroperimidinyl, di- and tetrahydrophenanthrolinyl (1,7-, 1,8-, 1 ,10-, 3,8-, and 4,7-), di- and tetrahydrophenazinyl, di- and tetrahydrooxazolopyridinyl, di- and tetrahydroisoxazolopyridinyl, di- and tetrahydropyrrolooxazolyl, and di- and tetrahydropyrrolopyrrolyl. Exemplary 5- or 6-memered heterocyclyl groups include morpholino, pyrrolidinyl, imidazolidinyl, pyrazolidinyl, piperidinyl, piperazinyl, di- and tetrahydrofuranyl, di- and tetrahydrothienyl, di- and tetrahydrooxazolyl, di- and tetrahydroisoxazolyl, di- and tetrahydrooxadiazolyl (1 ,2,5- and 1 ,2,3-), dihydropyrrolyl, dihydroimidazolyl, dihydropyrazolyl, di- and tetrahydrotriazolyl (1 ,2,3- and 1 ,2,4-), di- and tetrahydrothiazolyl, di- and tetrahydroisothiazolyl, di- and tetrahydrothiadiazolyl (1 ,2,3- and 1 ,2,5-), di- and tetrahydropyridyl, di- and tetrahydropyrimidinyl, di- and tetrahydropyrazinyl, di- and tetrahydrotriazinyl (1 ,2,3-, 1 ,2,4-, and 1 ,3,5-), and di- and tetrahydropyridazinyl.
[0045] The term "halogen" means fluoro, chloro, bromo, or iodo; preferably chloro, or fluoro, more preferably fluoro.
[0046] The term "complex of a compound" as used herein refers to a compound of higher order which is generated by association of the compound with other one or more other molecules. Exemplary complexes of a compound include, but are not limited to, solvates, clusters, and chelates of said compound.
[0047] The term "solvate" as used herein refers to an addition complex of a dissolved material in a solvent (such as an organic solvent (e.g., an aliphatic alcohol (such as methanol, ethanol, n-propanol, isopropanol), acetone, acetonitrile, ether, and the like), water or a mixture of two or more of these liquids), wherein the addition complex exists in the form of a crystal or mixed crystal. The amount of solvent contained in the addition complex may be stoichiometric or non- stoichiometric. A "hydrate" is a solvate wherein the solvent is water.
[0048] In isotopically labeled compounds one or more atoms are replaced by a corresponding atom having the same number of protons but differing in the number of neutrons. For example, a hydrogen atom may be replaced by a deuterium atom. Exemplary isotopes which can be used in the compounds of the present invention include deuterium, 11C, 13C, 14C, 15N, 18F, 32S, 36CI, and 125l.
Compounds
[0049] The present invention relates to a composition comprising at least one compound according to formula (I)
Figure imgf000015_0001
[0050] RT is selected from the group consisting of H, (Ci-C6)alkyl, (CH2)0(Ci-C6)alkyl ,(C C6)cycloalkyl, (Ci-C6)heterocyclyl, or absent, preferably selected from the group consisting of methyl, ethyl, propyl, cyclopropyl, butyl, cyclobutyl, pentyl, cyclopentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl, 3-pentyl, 2-methylbutyl, 3-methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut-2-yl, 2-methylbut-2-yl, 2,2-dimethylpropyl, hexyl, 2-hexyl, 3-hexyl, 2- methylpentyl, 3-methylpentyl, 2,2-dimethylbutyl, and 2,3-dimethylbutyl,
Figure imgf000016_0001
, preferably methyl;.
[0051] R2 is selected from the group consisting of H, (Ci-C6)alkyl,-(CH2)rCONH(CH2)sR6, -(CH- (CH2)pCOvinyl, -(CH2)qR6, -CO(Ci-C6)alkyl; preferably selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl, 3-pentyl, 2-methylbutyl, 3-methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut-2-yl, 2-methylbut-
2-yl, 2,2-dimethylpropyl, hexyl, 2-hexyl, 3-hexyl, 2-methylpentyl, 3-methylpentyl, 2,2- dimethylbutyl, and 2,3-dimethylbutyl, more preferably methyl.
[0052] R3 is selected from the group consisting of H, (Ci-C6)alkyl, -(CH2)rCONH(CH2)sR6, - (CH2)pCOvinyl, -(CH2)qR6, -CO(Ci-C6)alkyl, preferably selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl,
3-pentyl, 2-methylbutyl, 3-methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut-2-yl, 2-methylbut- 2-yl, 2,2-dimethylpropyl, hexyl, 2-hexyl, 3-hexyl, 2-methylpentyl, 3-methylpentyl, 2,2- dimethylbutyl, and 2,3-dimethylbutyl, more preferably methyl.
[0053] p is an integer between 1 to 3, preferably 1 ;
[0054] q is an integer between 1 to 3, preferably 1 ;
[0055] r is an integer between 1 to 3, preferably 1 ;
[0056] s is an integer between 1 to 3, preferably 1 ;
[0057] R4 is selected from the group consisting of H, (Ci-C6)alkyl;
[0058] R5 is selected from the group consisting of H, (Ci-C6)alkyl; [0059] if R2 and R5 are both (Ci-C6)alkyl, R2 and R5 may be connected to form a 4 to 6 membered ring;
[0060] if R3 and R4 are both (Ci-C6)alkyl, R3 and R4 may be connected to form a 4 to 6 membered ring;
[0061] R6 is selected from the group consisting of
Figure imgf000017_0001
[0062] X' is an anion or absent;
[0063] if X' is absent then RT is absent.
[0064] In one embodiment, the compound according to formula (I) is not selected from the
Figure imgf000017_0002
[0065] X' is preferably selected from the group consisting of napsylate, tetrafluoroborate, formate , trifluoroacetate, glycollylarsanilate, nitrate, benzoate, hexylresorcinate, oleate, bitartrate, hydroxynaphthoate, pantothenate, bicarbonate, hydrabamine, pamoate, camsylate, isethionate, polygalacturonate, propionate, salicylate, lactobionate, stearate, decanoate, edetate, maleate, succinate, estolate, mandelate, teoclate, gluceptate, acetate, glutamate, muscate, aspartate, glycolate, benzenesulfonate, hexanoate, octanoate, sulfonate, chloride, iodide, bromide, phosphate, phosphonate, lactate, malate, citrate, tartrate, fumarate, gluconate, sulfate or hemisulfate, more preferably tetrafluoroborate, chloride, iodide, bromide and sulfonate, most preferably chloride.
[0066] In another embodiment, in the composition there are at least two compounds according to formula (I) present.
[0067] Preferably in the first compound (la)
Ri is (Ci-C6)alkyl, preferably selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl, 3-pentyl, 2-methylbutyl, 3- methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut-2-yl, 2-methylbut-2-yl, 2,2-dimethylpropyl, hexyl, 2-hexyl, 3-hexyl, 2-methylpentyl, 3-methylpentyl, 2,2-dimethylbutyl, and 2,3-dimethylbutyl, more preferably methyl; R2 and R3 are H; and in
[0068] the second compound (lb) RT is (Ci-C6)alkyl, preferably selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tertbutyl, 2-pentyl, 3-pentyl, 2-methylbutyl, 3-methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut-2- yl, 2-methylbut-2-yl, 2,2-dimethylpropyl, hexyl, 2-hexyl, 3-hexyl, 2-methylpentyl, 3-methylpentyl,
2.2-dimethylbutyl, and 2,3-dimethylbutyl, more preferably methyl; and one of R2 or R3 in the second compound is (Ci-C6)alkyl, preferably selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl, 3-pentyl, 2- methylbutyl, 3-methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut-2-yl, 2-methylbut-2-yl, 2,2- dimethylpropyl, hexyl, 2-hexyl, 3-hexyl, 2-methylpentyl, 3-methylpentyl, 2,2-dimethylbutyl, and
2.3-dimethylbutyl, more preferably methyl and the other one of R2 or R3 is H.
[0069] The composition may comprise at least one dimer of the compound according to the formula (I) of claim 1, according to formula (II):
(|)-R3-(|)’
(II)
General formula (II) expresses that two compounds according to formula (I) as defined above may be connected via the rest R3 in formula (I).
R3 in formula (II) is a linker selected from the group consisting of -(CH2)t-, -(CH2)tQ(CH2)u-, - CO(CH2)t-, -CO(CH2)tCO-; t is an integer between 1 to 4; u is an integer between 1 to 4;
(I) and (I)’ are based on formula (I) in claim 1 and may be identical or different, preferably identical.
[0070] The composition may further comprise at least one compound according to formula (III)
Figure imgf000018_0001
[0071] R4 is H, halogen, (Ci-C6)alkyl, (C3-C6)cycloalkyl, or -O(Ci-C6)alkyl; preferably H. [0072] R5 is H, halogen, (Ci-C6)alkyl, (C3-C6)cycloalkyl, or -O(Ci-C6)alkyl; preferably H.
[0073] R6 is H, halogen, (Ci-C6)alkyl, (C3-C6)cycloalkyl, or -O(Ci-C6)alkyl; preferably H
[0074] R7 is H, (Ci-C6) alkyl, preferably methyl;
[0075] Z is H, halogen, (Ci-C6)alkyl, (C3-C6)cycloalkyl, -O(Ci-C6)alkyl, -(Ci-C6)alkyl(C6-Cio)aryl, - (Ci-C6)alkyl(C5-Cio)heteroaryl; preferably H.
[0076] Y is -NH2, -NHR8, halogen, (Ci-C6)alkyl, (C3-C6)cycloalkyl; preferably -NH2
[0077] R8 is H, (Ci-C6) alkyl, preferably methyl;
[0078] In one embodiment, R4 is (Ci-C6)alkyl, preferably selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl, 3-pentyl, 2-methylbutyl, 3-methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut-2-yl, 2-methylbut-
2-yl, 2,2-dimethylpropyl, hexyl, 2-hexyl, 3-hexyl, 2-methylpentyl, 3-methylpentyl, 2,2- dimethylbutyl, and 2,3-dimethylbutyl, more preferably methyl.
[0079] In one embodiment, R5 is (Ci-C6)alkyl, preferably selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl,
3-pentyl, 2-methylbutyl, 3-methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut-2-yl, 2-methylbut-
2-yl, 2,2-dimethylpropyl, hexyl, 2-hexyl, 3-hexyl, 2-methylpentyl, 3-methylpentyl, 2,2- dimethylbutyl, and 2,3-dimethylbutyl, more preferably methyl.
[0080] In one embodiment, R6 is (Ci-C6)alkyl, preferably selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl,
3-pentyl, 2-methylbutyl, 3-methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut-2-yl, 2-methylbut-
2-yl, 2,2-dimethylpropyl, hexyl, 2-hexyl, 3-hexyl, 2-methylpentyl, 3-methylpentyl, 2,2- dimethylbutyl, and 2,3-dimethylbutyl, more preferably methyl.
[0081] In one embodiment, R7 is (Ci-C6)alkyl, preferably selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl,
3-pentyl, 2-methylbutyl, 3-methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut-2-yl, 2-methylbut- 2-yl, 2,2-dimethylpropyl, hexyl, 2-hexyl, 3-hexyl, 2-methylpentyl, 3-methylpentyl, 2,2- dimethylbutyl, and 2,3-dimethylbutyl, more preferably methyl. [0082] In one embodiment, R8 is (Ci-C6)alkyl, preferably selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl, 3-pentyl, 2-methylbutyl, 3-methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut-2-yl, 2-methylbut-
2-yl, 2,2-dimethylpropyl, hexyl, 2-hexyl, 3-hexyl, 2-methylpentyl, 3-methylpentyl, 2,2- dimethylbutyl, and 2,3-dimethylbutyl, more preferably methyl.
[0083] In one embodiment, Y is (Ci-C6)alkyl, preferably selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl,
3-pentyl, 2-methylbutyl, 3-methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut-2-yl, 2-methylbut-
2-yl, 2,2-dimethylpropyl, hexyl, 2-hexyl, 3-hexyl, 2-methylpentyl, 3-methylpentyl, 2,2- dimethylbutyl, and 2,3-dimethylbutyl, more preferably methyl.
[0084] In one embodiment, Z is (Ci-C6)alkyl, preferably selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl,
3-pentyl, 2-methylbutyl, 3-methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut-2-yl, 2-methylbut- 2-yl, 2,2-dimethylpropyl, hexyl, 2-hexyl, 3-hexyl, 2-methylpentyl, 3-methylpentyl, 2,2- dimethylbutyl, and 2,3-dimethylbutyl, more preferably methyl.
[0085] The molar ratio of the at least one compound according to formula (I) may be 5 to 100, preferably 10 to 40, more preferably 15 to 30 mol-% based on the overall molar ratio of parent compounds (I) and (III) of the composition and compound (III) may be 0 to 95, preferably 60 to 90, more preferably 70 to 85 mol%.-% based on the overall molar ratio of parent compounds (I) and (III) in the composition.
[0086] In one embodiment, in the composition at least two compounds according to formula (III) are present; preferably in the first compound (Illa) R4, R5, R6, R7, and Z are H; Y is -NH2; in the second compound (lllb) R4, R5, R6, and Z are H; Y is -NH2, and R7 is (Ci-C6)alkyl, preferably selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl, 3-pentyl, 2-methylbutyl, 3-methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut-2-yl, 2-methylbut-2-yl, 2,2-dimethylpropyl, hexyl, 2-hexyl, 3-hexyl, 2- methylpentyl, 3-methylpentyl, 2,2-dimethylbutyl, and 2,3-dimethylbutyl, more preferably methyl.
[0087] In one embodiment, in the composition at least two compounds according to formula (I) and at least two compounds according to formula (III) are present, preferably (la), (lb), (Ila) and (lllb) as defined above present. [0088] Preferably, in the embodiment wherein (la), (lb), (Illa) and (lllb) are present in the composition, the molar ratio based on the overall molar ratio of compounds (la), (lb), (Illa) and (lllb) in the composition is for
(la) 5 to 30, preferably 10 to 25, more preferably 12 to 20 mol-%;
(lb) 1 to 10, preferably 2 to 8, more preferably 2 to 5 mol-%;
(Illa) 5 to 60, preferably 30 to 60, more preferably 50 to 60 mol-%; and
(lllb) 5 to 30, preferably 15 to 30, more preferably 20 to 25 mol-%
[0089] Compound (I) and/or (III) may be a solvate, hydrate, salt, complex, or isotopically enriched form, preferably a salt.
[0090] Compound (I) may be a salt, wherein the salt comprises an anion selected preferably from the group consisting of tetrafluoroborate, formate , trifluoroacetate napsylate, glycollylarsanilate, nitrate, benzoate, hexylresorcinate, oleate, bitartrate, hydroxynaphthoate, pantothenate, bicarbonate, hydrabamine, pamoate, camsylate, isethionate, polygalacturonate, propionate, salicylate, lactobionate, stearate, decanoate, edetate, maleate, succinate, estolate, mandelate, teoclate, gluceptate, acetate, glutamate, muscate, aspartate, glycolate, benzenesulfonate, hexanoate, octanoate, sulfonate, chloride, iodide, bromide, phosphate, phosphonate, lactate, malate, citrate, tartrate, fumarate, gluconate, sulfate or hemisulfate, more preferably a sulfate, hemisulfate, or chloride, most preferably chloride.
[0091] Compound (III) may be a salt, preferably the salt comprises an anion selected preferably from the group consisting of tetrafluoroborate, formate , trifluoroacetate, napsylate, glycollylarsanilate, nitrate, benzoate, hexylresorcinate, oleate, bitartrate, hydroxynaphthoate, pantothenate, bicarbonate, hydrabamine, pamoate, camsylate, isethionate, polygalacturonate, propionate, salicylate, lactobionate, stearate, decanoate, edetate, maleate, succinate, estolate, mandelate, teoclate, gluceptate, acetate, glutamate, muscate, aspartate, glycolate, benzenesulfonate, hexanoate, octanoate, sulfonate, chloride, iodide, bromide, phosphate, phosphonate, lactate, malate, citrate, tartrate, fumarate, gluconate, sulfate or hemisulfate, more preferably a tetrafluoroborate, sulfate, hemisulfate, chloride, most preferably chloride.
[0092] A sulfonate used in the present invention may be a sulfonate according to formula (IV)
Figure imgf000021_0001
wherein Rg is selected from the group consisting of phenyl, 4-nitrophenyl, 4-methylphenyl, 4- trifluoromethyphenyl, trifluoromethyl, and (Ci-C5)alkyl. [0093] In one embodiment, Rg is (Ci-C5)alkyl and/or
(Ci-C5)alkyl is selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, isopropyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl, 3-pentyl, 2-methylbutyl, 3- methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut-2-yl, 2-methylbut-2-yl, 2,2-dimethylpropyl, preferably methyl.
[0094] The invention is further directed to a composition in which at least one compound according to formula (I) and at least one compound according to formula (III) are bonded together via one or two linker systems.
[0095] The linker system may be -(C2-Ci0)alkylene or (C2-Ci0)alkenylene, preferably (C3- C8)alkylene, or (C3-8)alkenylene; wherein optionally at least one or at least two CH2-groups in these alkyl or alkenyl groups are substituted by O, S, S(O)i.2, NH or N(Ci-C4)alkyl and/or connecting is performed preferably via position 5, 7, 8 or by substitution of the nitrogen in position 6 in formula (I) and position 5, 7, 8 or by substitution of the nitrogen in position 6 or 10 in formula (III) wherein the underlying aromatic system in formula (I) and (III) is numbered according to formula (
Figure imgf000022_0001
[0096] The acridine compounds (III) of the invention can be produced by applying suitable known method of synthesizing acridine derivatives, e.g. as described in Prager, R. H., Williams, C. M., Science of Synthesis (2005) 15, 987; Gensicka-Kowalewska M., Cholewinski G, Dzierzbicka, K. RSC Adv. (2017), 7, 15776 Matejova, M.; Janovec, L; Imrich, J. ARKIVOC 2015 (v), 134 and references cited therein.
[0097] Frequently applied methods involve ring closures, aromatization of intermittently obtained di- and tetrahydroacridines, as well as ring rearrangement reactions. Furthermore, synthetic routes to access quinolines may be adapted. For example, this may involve conversion of diphenylamines and carboxylic acids, using the Bernthsen reaction (Bernthsen, A., Justus Liebigs Ann. Chem., (1884) 224, 1), arylation of phenylacetonitriles (Jawdosiuk, M.; Czyzewski, J.; Makosza, M., J. Chem. Soc., Chem. Commun. (1973), 794), anilineacetophenones, coupled to aryl bromides e.g. via Ullman coupling and subsequently performing a cyclization under appropriate conditions e.g. acid catalysis (Ullmann, F; Torre, A. L., Ber. Dtsch. Chem. Ges., (1904) 37, 2922, Mayer, F; Freund, W., Ber. Dtsch. Chem. Ges., (1922) 55, 2049) or via 2-anilinobenzaldehyde derivatives, e.g. obtained by the McFadyen-Stevens reaction, followed by conversion to acridine derivatives (Graboyes, H.; Anderson, E. L.; Levinson, S. H.; Resnick, T. M., J. Heterocycl. Chem., (1975) 12, 1225). Furthermore, acridin- 9(10H)-ones are useful precursors of acridine derivatives, which can be obtained by various methods (e.g. described in Prager, R.H.; Williams, C.M. Science of Synthesis (2005), 1029).
[0098] Acridine derivatives modified in position 9 can for example be obtained by reacting the corresponding acridine-9(10H)-one derivatives, e.g. with phosphorous oxychloride or thionyl chloride to give 9-CI derivatives (Anuradha, S., Poonam, PChem. Biol. Drug Des. (2017), 90, 926; Nakajima, M., Nagasawa, S., Matsumoto, K., Kuribara, T., Muranaka, A., Uchiyama, M., Nemoto, T, Angew. Chem. Int. Ed. (2020), 59, 6847), with phosphorous tribromide to give 9-Br- derivatives (Kishimoto, M., Kondo, K., Akita, M., Yoshizawa, M. Chem. Commun. 2017, 53,1425) or with P4S10 to give 9-thiol-acridines (Poulallion, P, Galy, J.-P, Vincent, E.-J., Galy, A.-M., Barbe, J., Atassi, G. J. Heterocyclic Chem. (1986), 23, 1141). These derivatives can then be processed further e.g. by substituting the introduced chlorine or by transition metal catalyzed couplings of bromine.
[0099] Fused derivatives containing two acridine rings can be synthesized by adaption of methods described in the literature, e.g. starting from diphenyl anilines and reacting these with dicarboxylic acids, using the the Bernthsen condensation (Eldho, N. V.; Saminathan, M.; Ramaiah, D., Synth. Commun., (1999) 29, 4007).
[00100] Alternatively, other linking methods to connect two heterocycles can be applied, e.g. using linker systems with two activated functionalities (e.g. malonyl chloride, succinic anhydride, glutaric acid, succinyl chloride, 1,3-dibromopropane, 1,4-dibromobutane, glutaroyl dischloride, 1,3-diiodopropane, 1 ,4-diiodobutane, glutaraldehyde, 4-chlorobutanolyl chloride or 5-chloropentanoyl chloride, e.g. Frohlich, T.; Reiter, C.; Saeed, M. E. M.; Hutterer, C.; Hahn, F.; Leidenberger, M.; Friedrich, O.; Kappes, B.; Marschall, M.; Efferth, T.; Tsogoeva, S. B., ACS Med. Chem. Lett. (2017), 9, 534-539; Frohlich, T.; Hahn, F.; Belmudes, L.; Leidenberger, M.; Friedrich, O.; Kappes, B.; Coute, Y; Marschall, M.; Tsogoeva, S. B., Chem. Eur. J. (2018) 24, 8103-8113).
[00101] Specific compounds as described above are listed in the following tablel . Table 1: Specific compounds
Figure imgf000024_0001
Figure imgf000025_0001
Medical applications
[00102] The compounds of the present invention may be for use in the treatment of diseases caused by betacoronaviruses, leishmaniasis, trypanosomiasis.
[00103] In one embodiment, the treatment is caused by human and veterinary coronaviruses that belong to subgenera hibecovirus, nobecovirus, embecovirus, merbecovirus and sarbecovirus, preferably coronaviruses.
[00104] In another embodiment, the treatment is caused by human coronavirus HKLI1 (HCoV- HKLI1), human coronavirus OC43 (HCoV-OC43), Middle East respiratory syndrome-related coronavirus (MERS-CoV).
[00105] In a further embodiment, the treatment is caused by severe acute respiratory syndrome-related coronaviruses, preferably SARS-CoV, more preferably SARS-CoV-2. [00106] In another embodiment, the treatment is caused by a virus that evolve or mutate from the species described in the three paragraphs above.
[00107] In one embodiment, the disease to be treated is the severe acute respiratory syndrome, preferably SARS-CoV or SARS-CoV-2, more preferably SARS-CoV-2.
[00108] In a further embodiment, the disease to be treated is the Middle East respiratory syndrome (MERS-CoV).
[00109] In a further embodiment, the disease to be treated is pneumonia.
Pharmaceutical compositions
[00110] Further, the invention is directed to a composition comprising at least the composition as descibed above and at least one pharmaceutically acceptable carrier, thus to a pharmaceutical composition.
[00111] “Pharmaceutical composition" refers to one or more active ingredients, and one or more inert ingredients that make up the carrier, as well as any product which results, directly or indirectly, from combination, complexation or aggregation of any two or more of the ingredients, or from dissociation of one or more of the ingredients, or from other types of reactions or interactions of one or more of the ingredients. Accordingly, the pharmaceutical compositions of the present invention encompass any composition made by admixing a compound or composition of the present invention and a pharmaceutically acceptable carrier.
[00112] "Carrier" refers to a diluent, adjuvant, excipient, or vehicle with which the therapeutic is administered. Such pharmaceutical carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, including but not limited to peanut oil, soybean oil, mineral oil, sesame oil and the like. Water is a preferred carrier when the pharmaceutical composition is administered orally. Saline and aqueous dextrose are preferred carriers when the pharmaceutical composition is administered intravenously. Saline solutions and aqueous dextrose and glycerol solutions are preferably employed as liquid carriers for injectable solutions. Suitable pharmaceutical excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like. The composition, if desired, can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents. These compositions can take the form of solutions, suspensions, emulsions, tablets, pills, capsules, powders, sustained-release formulations and the like. The composition can be formulated as a suppository, with traditional binders and carriers such as triglycerides. Oral formulation can include standard carriers such as pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate, etc. Examples of suitable pharmaceutical carriers are described in "Remington's Pharmaceutical Sciences" by E.W. Martin. Such compositions will contain a therapeutically effective amount of the therapeutic, preferably in purified form, together with a suitable amount of carrier so as to provide the form for proper administration to the patient. The formulation should suit the mode of administration.
[00113] Generally, out of 100% (for the pharmaceutical formulations/compositions), the amount of active ingredient (in particular, the amount of the compound of the present invention, optionally together with other therapeutically active agents, if present in the pharmaceutical formulations/compositions) may range from about 0.01% to about 99%, preferably from about 0.1% to about 70%, most preferably from about 1% to about 30%, wherein the reminder is preferably composed of the one or more pharmaceutically acceptable excipients.
[00114] A physician or veterinarian having ordinary skill in the art can readily determine and prescribe the effective amount of the pharmaceutical composition required. For example, the physician or veterinarian could start with doses of the compounds of the invention employed in the pharmaceutical composition at levels lower than that required in order to achieve the desired therapeutic effect and gradually increase the dosage until the desired effect is achieved. In general, a suitable daily dose of a composition of the invention will be that amount of the compound which is the lowest dose effective to produce a therapeutic effect. Such an effective dose will generally depend upon the factors described above. Administration may carried out oral, by inhalation, intravenous, intramuscular, intraperitoneal, or subcutaneous, preferably administered proximal to the site of the target. If desired, the effective daily dose of a pharmaceutical composition may be administered as two, three, four, five, six or more subdoses administered separately at appropriate intervals throughout the day, optionally, in unit dosage forms. While it is possible for a compound of the present invention to be administered alone, it is preferable to administer the compound as a pharmaceutical formulation/composition.
[00115] The amount of active ingredient, e.g., a compound of the invention, in a unit dosage form and/or when administered to an indiviual or used in therapy, may range from about 0.1 mg to about 1000mg (for example, from about 1mg to about 500mg, such as from about 10mg to about 200mg) per unit, administration or therapy. In certain embodiments, a suitable amount of such active ingredient may be calculated using the mass or body surface area of the individual, including amounts of between about 1mg/Kg and 10mg/Kg (such as between about 2mg/Kg and 5mg/Kg), or between about 1mg/m2 and about 400mg/m2 (such as between about 3mg/m2 and about 350mg/m2 or between about 10mg/m2 and about 200mg/m2).
[00116] Further, the invention is directed to a composition for use as described above, formulated as an inhalative drug.
[00117] In a further embodiment, the composition for use as described above is formulated as an oral drug.
EXAMPLES OF THE INVENTION
Synthetic procedures
[00118] In general the compounds according to formula (I) may be synthesized according the schemes 1 to 3.
Figure imgf000028_0001
Scheme 1 : Synthetic route for the preparation of different 3,6-diaminoacridin-10-ium derivatives alkylated at the N10 position.
Figure imgf000029_0001
Scheme 2: Synthetic routes for the preparation of 3,6-diaminoacridin-10-ium derivatives that are dual alkylated at the N6 position.
Figure imgf000030_0001
Scheme 3. Synthetic routes for the preparation of 3,6-diaminoacridine derivatives containing a covalent warhead.
General methods:
[00119] Air and water sensitive reactions were performed in flame-dried glassware under an argon atmosphere. Solvents used for column chromatography, extractions and recrystallization were purchased in technical grade and were distilled prior to use. Solvents used for reversed phase chromatography and HPLC-MS analyses were purchased from Thermofisher Scientific in HPLC-quality. Reagents and dry solvents were purchased from Sigma Aldrich, ABCR, Alfa Aesar, Thermofisher Scientific, TCI, Carl Roth and Merck and were used without further purification.
[00120] Analytical thin layer chromatography (TLC) was performed on silica coated plates (silica gel 60 F254) purchased from VWR. Compounds were detected by ultraviolet (UV) irradiation at 254 or 366 nm. Manual flash column chromatography was performed using silica gel 60 (particle size: 0.040-0.063 mm) available from VWR. Automated preparative chromatography was performed on a Grace Reveleris Prep purification system using linear gradient elution and Buchi Reveleris Silica 40 pm cartridges for normal-phase and Buchi Reveleris C1840 pm cartridges for reverse-phase separations.
[00121] 1H, 19F and 13C NMR spectra were recorded at room temperature on a Bruker
AVHD400 or AVHD500 spectrometer operating at either 400 MHz or 500 MHz. NMR peaks are reported as follows: chemical shift (6) in parts per million (ppm) relative to residual nondeuterated solvent as internal standard (DMSO: <5 (1H) = 2.50 ppm, <5 (13C) = 39.5 ppm), multiplicity (s = singlet, d = doublet, t = triplet, q = quartet, m = multiplet and bs = broad signal), coupling constant (Hz) and integration.
[00122] HPLC-UV/MS analyses were performed on a Dionex UltiMate 3000 HPLC system coupled with a Thermo Scientific™ ISQ™ EC Single Quadrupole Mass Spectrometer, using the following methods: Thermo Scientific™ Accucore™ RP-MS LC-column (2.1 x 50 mm, 2.6 pm); gradient method A): 5 to 95% of acetonitrile + 0.1% formic acid v/v in water + 0.1% formic acid v/v over 5 min period; flow rate: 0.6 mL/min; gradient method B): 5 to 10% of acetonitrile + 0.1% formic acid v/v in water + 0.1% formic acid v/v over 9.5 min period; 10 to 20% of acetonitrile + 0.1% formic acid v/v in water + 0.1% formic acid v/v over 4.0 min period; 20 to 95% of acetonitrile + 0.1% formic acid v/v in water + 0.1% formic acid v/v over 1.0 min period; flow rate: 0.6 mL/min; gradient method C): 5 to 95% of acetonitrile + 0.1% formic acid v/v in water + 0.1% formic acid v/v over 10.0 min period; flow rate: 0.6 mL/min; UV detection at 254 nm. All target compounds exhibited a purity greater than 95%, which was determined by HPLC-UV/MS analyses.
[00123] Neutral proflavine (nPF) was obtained from commercially available proflavine hemisulfate monohydrate, which was purchased from Sigma Aldrich. The procedure is as follows: Proflavine hemisulfate monohydrate (2.00 g, 7.24 mmol) was dissolved in water (100 mL) and then aqueous ammonia (10%) was added until the pH reached a value of 8. The formed orange precipitate was filtered off, washed with water (3 x 20 mL) and dried in vacuo to yield neutral proflavine (nPF) (1.26 g, 6.02 mmol, 83%).
[00124] Synthetic procedures and spectroscopic data for 3,6-diaminoacridine derivatives TF 144, TF 145 and TF 156
Figure imgf000032_0001
TF 145: R = -CH3, 85% TF 144: R = -CH3, 82%
TF 156: R = -CH2CH3, 100% TF 153: R = -CH2CH3, 44%
Scheme 4. Synthetic route for the preparation of 3,6-diaminoacridine derivatives TF 144, TF 145 and TF 156.
[00125] Pivalate amide protected proflavine TF 139 was prepared in analogy to a literature known procedure (Scheme 4).1 , 53
[00126] /V,/V'-(acridine-3,6-diyl)bis(2,2-dimethylpropanamide) (TF 139). Neutral proflavine (nPF) (1.80 g, 8.60 mmol, 1.0 eq) and K2CO3 (11.89 g, 86.0 mmol, 10 eq) were dissolved in acetone (200 mL) under an argon atmosphere and cooled to 0 °C. Afterwards, pivaloyl chloride (3.18 mL, 3.11 g, 25.8 mmol, 3 eq) dissolved in acetone (50 mL) was slowly added at 0 °C. The resulting reaction mixture was allowed to reach room temperature and stirred for 15 h. After this time period, the reaction was quenched by pouring the mixture into an aqueous solution of NaHCO3 (40%, 300 mL), which was then stored at 5 °C overnight. The following day, the obtained precipitate was filtered, washed with water (3 x 50 mL) and dried. The crude product was recrystallized from ethanol in order to yield pure pivalate amide protected proflavine TF 139 as a beige solid (1.52 g, 4.03 mmol, 48%). 1H NMR (400 MHz, DMSO-d6): 5 = 9.56 (s, 2H), 8.82 (s, 1 H), 8.53 (s, 2H), 8.02 (d, J = 9.1 Hz, 2H), 7.79 (dd, J = 9.1 , 2.0 Hz, 2H), 1.30 (s, 18H) ppm. 13C NMR (101 MHz, DMSO-d6): 5 = 177.2, 149.7, 140.8, 134.8, 128.6, 122.5, 121.0, 115.1 , 27.1 ppm. HPLC-MS (ESI): m/z = 378 [M+H]+; retention time: 3.20 min (method A).
[00127] The spectroscopic data are in accordance with those reported in literature.1, 53
[00128] 10-Methyl-3,6-dipivalamidoacridin-10-ium tetrafluoroborate (TF 144). Pivalate amide protected proflavine TF 139 (750 mg, 1.99 mmol, 1.0 eq) was dissolved in a mixture of dry dichloromethane (10.0 mL) and dry acetonitrile (3.00 mL) under an argon atmosphere. Trimethyloxonium tetrafluoroborate (294 mg, 1.99 mmol, 1.0 eq) was added over a period of 1.5 h at room temperature. After stirring overnight, the crude reaction mixture was concentrated under reduced pressure. The formed precipitate was filtered off, washed with THF (2 x 15.0 mL) and dried under vacuum. The desired intermediate TF 144 was obtained as an orange solid (780 mg, 1.63 mmol, 82%). 1H NMR (400 MHz, DMSO-d6): 5 = 10.25 (s, 2H), 9.63 (s, 1 H), 9.04 (s, 2H), 8.43 (d, J = 9.1 Hz, 2H), 8.14 (dd, J = 9.1 , 1.7 Hz, 2H), 4.45 (s, 3H), 1.34 (s, 18H) ppm. 13C NMR (101 MHz, DMSO-d6): 5 = 178.5, 148.2, 146.8, 142.8, 132.8, 121.8, 120.9, 103.6, 37.4, 26.8 ppm. HPLC-MS (ESI): m/z = 392 [M]+; retention time: 9.22 min (method B).
[00129] 3,6-Diamino-10-methylacridin-10-ium chloride (TF 145). Pivalate protected diaminoacridine derivative TF 144 (750 mg, 1.57 mmol, 1.0 eq) was dissolved in ethanol (10.0 mL). After addition of hydrochloric acid (5.0 M in H2O, 7.85 mL, 39.25 mmol, 25.0 eq), the resulting reaction mixture was heated until reflux and stirred overnight. The following day, the solvent was removed under reduced pressure and the crude material was taken up in a mixture of EtOH and dichloromethane and stored for 1 day at 8 °C. The obtained red precipitate was filtered off, washed with cold EtOH (5.0 mL), THF (2 x 10.0 mL) as well as Et2O (2 x 10.0 mL) and dried in vacuum. The desired target compound TF 145 (345 mg, 1.33 mmol, 85%) exhibited a purity greater than 95% and therefore no further purification was necessary. 1H NMR (500 MHz, DMSO-d6): 5 = 8.72 (s, 1 H), 7.84 (d, J = 8.9 Hz, 2H), 7.58 (bs, 4H), 7.03 (dd, J = 8.9, 1.8 Hz, 2H), 6.93 (d, J = 2.2 Hz, 2H), 3.94 (s, 3H) ppm. 13C NMR (101 MHz, DMSO-d6): 5 = 157.3, 143.6, 142.8, 133.5, 116.7, 116.4, 93.9, 35.1 ppm. HPLC-MS (ESI): m/z = 224 [M]+; retention time: 9.68 min (method B).
[00130] 10-Ethyl-3,6-dipivalamidoacridin-10-ium tetrafluoroborate (TF 153). Pivalate amide protected proflavine TF 139 (750 mg, 1.99 mmol, 1.0 eq) was dissolved in a mixture of dry dichloromethane (20.0 mL) and dry acetonitrile (6.00 mL) under an argon atmosphere. Triethyloxonium tetrafluoroborate (378 mg, 1.99 mmol, 1.0 eq) was added over a period of 1.5 h at room temperature. After stirring overnight, the crude reaction mixture was concentrated under reduced pressure. The formed precipitate was filtered off, washed with THF (2 x 30.0 mL) and dried under vacuum. The desired intermediate TF 153 was obtained as a yellow solid (436 mg, 0.884 mmol, 44%). 1H NMR (400 MHz, DMSO-d6): 5 = 10.25 (s, 2H), 9.63 (s, 1 H), 9.01 (s, 2H), 8.44 (d, J = 9.1 Hz, 2H), 8.16 (dd, J = 9.1 , 1.6 Hz, 2H), 4.97 (q, J = 7.2 Hz, 2H), 1.70 (t, J = 7.2 Hz, 3H), 1.34 (s, 18H) ppm. 13C NMR (101 MHz, DMSO-d6): 5 = 178.5, 148.5, 147.1 , 141.7, 133.0, 122.0, 121.0, 103.0, 45.2, 26.8, 12.3 ppm. HPLC-MS (ESI): m/z = 406 [M]+; retention time: 5.13 min (method C).
[00131] 3,6-Diamino-10-ethylacridin-10-ium chloride (TF 156). Pivalate protected diaminoacridine derivative TF 153 (400 mg, 0.811 mmol, 1.0 eq) was dissolved in ethanol (10.0 mL). After addition of hydrochloric acid (6.0 M in H2O, 3.38 mL, 20.28 mmol, 25.0 eq), the resulting reaction mixture was heated until reflux and stirred overnight. The following day, the solvent was removed under reduced pressure and the crude material was taken up in a mixture of EtOH and dichloromethane and stored for 1 day at 8 °C. The obtained red precipitate was filtered off, washed with cold EtOH (5.0 mL), THF (2 x 10.0 mL) as well as Et2O (2 x 10.0 mL) and dried in vacuum. The desired target compound TF 156 (222 mg, 0.811 mmol, 100%) exhibited a purity greater than 95% and therefore no further purification was necessary. 1H NMR (400 MHz, DMSO-d6): 5 = 8.71 (s, 1 H), 7.84 (d, J = 8.9 Hz, 2H), 7.04 (d, J = 8.9 Hz, 2H), 6.97 (s, 2H), 4.47 (q, J = 7.0 Hz, 2H), 1.46 (t, J = 7.1 Hz, 3H). 13C NMR (101 MHz, DMSO-d6): 5 = 157.5, 143.0, 142.4, 133.6, 116.7, 116.5, 93.3, 42.7, 11.3 ppm. HPLC-MS (ESI): m/z = 238 [M]+; retention time: 10.53 min (method B).
[00132] Synthetic procedures and spectroscopic data for 3,6-diaminoacridine derivatives TF 155 and TF 163
Figure imgf000034_0001
Scheme 5. Synthetic route for the preparation of TF 152 and TF 155.
[00133] /V-(6-aminoacridin-3-yl)pivalamide (TF 152). Neutral proflavine (nPF) (1.00 g, 4.78 mmol, 1.0 eq) and K2CO3 (6.61 g, 47.80 mmol, 10 eq) were dissolved in acetone (100 mL) under an argon atmosphere. Afterwards, pivaloyl chloride (941 pL, 922 mg, 7.65 mmol, 1.6 eq) dissolved in acetone (20 mL) was slowly added via syringe pump (flow rate: 0.01 mL/min). The reaction mixture was stirred for a total of 3 days. After this time period, the solvent was removed under reduced pressure and the residue was purified by gradient flash column chromatography (CH2CI2/NH3 (7.0 M in MeOH): 1 , 2, 2.5, 3%) in order to yield mono pivalate amide protected proflavine TF 152 as an orange solid (897 mg, 3.06 mmol, 64%). Rf = 0.35 (CH2CI2/NH3 (7.0 M in MeOH) 9:1 , UV). 1H NMR (400 MHz, DMSO-d6): 5 = 9.42 (s, 1 H), 8.54 (s, 1 H), 8.34 (d, J = 2.0 Hz, 1 H), 7.85 (d, J = 9.0 Hz, 1 H), 7.76 (d, J = 9.0 Hz, 1 H), 7.60 (dd, J = 8.9, 2.1 Hz, 1 H), 7.02 (dd, J = 8.9, 2.2 Hz, 1 H), 6.88 (d, J = 2.1 Hz, 1H), 6.02 (s, 2H), 1.29 (s, 9H) ppm. 13C NMR (101 MHz, DMSO-d6): 5 = 176.9, 151.4, 150.8, 149.6, 140.4, 134.5, 129.3, 128.5, 120.8, 120.1, 120.0, 118.9, 114.9, 103.0, 27.2 ppm. HPLC-MS (ESI): m/z = 294 [M+H]+; retention time: 2.88 min (method A). [00134] /V-(6-(methylamino)acridin-3-yl)pivalamide (TF 154). Mono pivalate amide protected proflavine TF 152 (200 mg, 0.682 mmol, 1.0 eq) and pyridine (193 pL, 189 mg, 2.39 mmol, 3.5 eq) were dissolved in dry dioxane (10.0 mL) under an argon atmosphere. Afterwards, copper(ll) acetate (310 mg, 1.71 mmol, 2.5 eq) was added and the reaction mixture was stirred for 15 min. After addition of methyl boronic acid (102 mg, 1.71 mmol, 2.5 eq), the resulting reaction mixture was heated until reflux and stirred for 5 h. The crude mixture was then filtered through Celite, the solvent was removed under reduced pressure and the residue was purified by gradient flash column chromatography (CH2CI2/NH3 (7.0 M in MeOH): 1 , 2, 2.5, 3, 5%) in order to obtain side methylated diaminoacridine derivative TF 154 as a dark orange solid (107 mg, 0.348 mmol, 51%). F?f = 0.31 (CH2CI2/NH3 (7.0 M in MeOH) 9:1, UV). 1H NMR (400 MHz, DMSO-d6): 5 = 9.43 (s, 1 H), 8.54 (s, 1 H), 8.34 (s, 1 H), 7.86 (d, J = 9.1 Hz, 1 H), 7.74 (d, J = 9.0 Hz, 1H), 7.62 (dd, J = 9.0, 2.0 Hz, 1H), 7.01 (dd, J = 9.1 , 2.2 Hz, 1H), 6.69 - 6.57 (m, 2H), 2.85 (d, J = 4.8 Hz, 3H), 1.29 (s, 9H) ppm. HPLC-MS (ESI): m/z = 308 [M+H]+; retention time: 6.07 min (method C).
[00135] 3-Amino-6-(methylamino)acridin-10-ium trifluoroacetate (TF 155). Mono pivalate protected diaminoacridine derivative TF 154 (142 mg, 0.461 mmol, 1.0 eq) was dissolved in ethanol (5.0 mL). After addition of hydrochloric acid (6.0 M in H2O, 1.92 mL, 11.53 mmol, 25.0 eq), the resulting reaction mixture was heated until reflux and stirred overnight. The following day, the solvent was removed under reduced pressure and the crude material was purified via reversed-phase flash chromatography (C18, H2O/CH3CN + 0.1% TFA: 2, 4, 6, 8, 10, 15, 20, 50%). The desired target compound TF 155 (92.2 mg, 0.286 mmol, 62%) was obtained as darkbrown crystals. 1H NMR (400 MHz, DMSO-d6): 5 = 13.62 (s, 1H), 8.76 (s, 1 H), 7.89 - 7.74 (m, 3H), 7.05 - 6.90 (m, 2H), 6.76 - 6.66 (m, 1 H), 6.52 (s, 1 H), 2.89 (s, 3H) ppm. 13C NMR (101 MHz, DMSO-d6): 5 = 158.3, 158.0, 156.1 , 155.5, 142.6, 142.2, 131.8, 117.7, 116.4, 116.4, 93.5, 40.2, 39.9, 39.7, 39.5, 39.3, 39.1 , 38.9, 29.2 ppm. 19F NMR (376 MHz, DMSO-d6): 6 = -74.4 ppm. HPLC-MS (ESI): m/z = 224 [M+H]+; retention time: 4.95 min (method C).
Figure imgf000035_0001
TF 163 TF 161
74% 41 %
Scheme 6. Synthetic route for the preparation of TF 163. [00136] /V-(6-(piperidin-1-yl)acridin-3-yl)pivalamide (TF 161). Mono pivalate protected diaminoacridine derivative TF 152 (360 mg, 1.23 mmol, 1.0 eq) was dissolved in dry DCE (6.00 mL) under argon. Afterwards, glutaraldehyde (50%, 284 pL, 314 mg, 1.48 mmol, 1.2 eq), AcOH (7.02 pL, 7.38 mg, 0.123 mmol, 10mol%) as well as NaBH(OAc)3 (520 mg, 2.46 mmol, 2.0 eq) were added and the resulting reaction mixture was stirred overnight. The following day, the reaction was quenched with a saturated aqueous solution of NaHCO3 (25 mL) and the aqueous phase was extracted with EtOAc (3 x 35 mL). Afterwards, the combined organic layers were washed with brine (25 mL), dried over Na2SO4, filtered and concentrated under reduced pressure. The obtained residue was purified by gradient flash column chromatography (CH2CI2/NH3 (7.0 M in MeOH): 1 , 2, 2.5, 3%) and thereby the desired precursor TF 161 (182 mg, 0.503 mmol, 41%) was obtained as a red solid. 1H NMR (400 MHz, DMSO-d6): 5 = 9.36 (s, 1 H), 8.55 (s, 1 H), 8.41 (d, J = 2.0 Hz, 1H), 7.82 (t, J = 10.0 Hz, 2H), 7.66 (dd, J = 9.0, 2.0 Hz, 1H), 7.35 (dd, J = 9.3, 2.3 Hz, 1H), 7.12 (d, J = 2.4 Hz, 1 H), 3.49 - 3.34 (m, 4H), 1.80 - 1.59 (m, 6H), 1.29 (s, 9H) ppm. 13C NMR (101 MHz, DMSO-d6): 5 = 176.8, 152.3, 150.3, 140.7, 134.5, 128.7, 128.1, 121.4, 120.5, 119.7, 119.4, 114.5, 105.9, 93.5, 48.9, 27.0, 25.0, 23.9 ppm. HPLC-MS (ESI): m/z = 362 [M+H]+; retention time: 3.18 min (method A).
[00137] 3-Amino-6-(piperidin-1-yl)acridin-10-ium chloride (TF 163). Mono pivalate protected diaminoacridine derivative TF 161 (165 mg, 0.456 mmol, 1.0 eq) was dissolved in ethanol (7.0 mL). After addition of hydrochloric acid (6.0 M in H2O, 1.90 mL, 11.41 mmol, 25.0 eq), the resulting reaction mixture was heated until reflux and stirred overnight. The following day, the solvent was removed under reduced pressure and the crude material was taken up in a mixture of MeOH, Et2O and HCI (2.0 M in Et2O) and stored for 1 day at 8 °C. The obtained deep red precipitate was filtered off, washed with Et2O (2 x 10.0 mL) and dried in vacuum. The desired target compound TF 163 (106 mg, 0.338 mmol, 74%) exhibited a purity greater than 95% and therefore no further purification was necessary. 1H NMR (400 MHz, DMSO-d6): 5 = 8.80 (s, 1 H), 7.90 (d, J = 9.4 Hz, 1 H), 7.84 (d, J = 9.0 Hz, 1 H), 7.42 (dd, J = 9.3, 2.4 Hz, 1 H), 7.16 (d, J = 2.3 Hz, 1 H), 7.03 (dd, J = 9.0, 2.0 Hz, 1 H), 6.88 (d, J = 1.9 Hz, 1H), 5.26 (bs, 2H), 3.65 - 3.54 (m, 4H), 1.75 - 1.61 (m, 6H) ppm. 13C NMR (101 MHz, DMSO-d6): 5 = 156.3, 154.2, 142.6, 142.2, 142.0, 131.8, 131.3, 118.3, 117.2, 116.1, 115.9, 94.6, 93.4, 47.8, 25.1 , 23.9 ppm. HPLC-MS (ESI): m/z = 278 [M+H]+. [00138] The compounds according to formula (II) may be prepared as shown in scheme
7.
Figure imgf000037_0001
Scheme 7. Synthetic routes for the preparation of 3,6-diaminoacridine-derived dimers. Plasmids and proteins
[00139] Gene encoding the PLPro sequence (sars-cov2 nsp3 - 746-1060) was order from Integrated DNA Technologies (IDT-Coralville, USA) optimized for E.coli expression and cloned using the Slice method27 into several vectors, mainly, petM11 , petM 13 with a Cterminal 6-histag, pET22b-CPD and a new expression vector named petM5a, a modified petM11 vector. This petM5a vector contains an insertion of optimized codon sequence after the starting codon ATG, GTGAAGTATCAAAAG, based on Verma et a/.28, and followed by the N- terminal 6-Histidine tag, and by a TEV protease site. The vector map can be found at HMGU-PEPF website. The plasmids were transformed into E. coli BL21 (DE3), and the transformed cells were cultured at 37 °C in terrific broth (TB) media containing 100 mg/L kanamycin. After the GD600 reached 2, the culture was cooled to 18 °C and supplemented with 0.25 mM IPTG. The vector petM5a yielded more soluble protein and it was used for all protein expression. For label protein, preculture was gown in M9 minimal media followed by inoculation (OD6oo 0.05) into 1 L of D2O M9 minimal media supplemented with 15N-Ammoniun chloride. After GD600 reached 0.8, the culture was cooled to 18°C and supplemented with 0.25mM IPTG. After overnight induction, the cells were harvested through centrifugation, and the pellets were resuspended in lysis buffer (20 mM Tris-HCI, pH 8.5, 350 mM NaCI, 10% glycerol, 10mM imidazole, 5mM betamercaptoethanol) and sonicated at 4 °C. The insoluble material was removed through centrifugation at 24,000 rpm. The fusion protein was first purified by Ni-NTA affinity chromatography, the supernatant was applied to nickel resin and washed with 10 times the column volume with lysis buffer followed by a wash step of lysis buffer supplemented with 20mM imidazol. The protein was eluted with 3 times column volume by a buffer containing high imidazole concentration, 20 mM Tris-HCI, pH 8.5, 350 mM NaCI, 5% glycerol, 350mM imidazole, 5mM beta-mercaptoethanol. 1mg of TEV protease was added and the solution was dialyzed overnight at 4°C against a buffer containing low imidazole concentration, 20 mM Tris- HCI, pH 8.5, 150 mM NaCI, 5% glycerol, 10mM imidazole, 1mM Beta mercaptoethanol. The next day, the protein was applied to a nickel column and the flow though was collected followed by concentration using a top centrifuge concentrator with a 30kDa cut off up to a volume of 2mL. For the final step, the protein was applied to a size exclusion chromatography column, High load S75 (GE- Helathcare, chigaco, USA), pre-equilibrated with the final buffer, 20mM Tris pH 8.0, 40mM NaCI and 2mM DTT. The purity of the protein was accessed by SDS page gel.
[00140] Mpro construct comprising aminoacids 3264-3569 of SARS-CoV-2 polyprotein 1ab, N-terminal 6xHis and TEV protease cleavage site optimized for expression in E. coli was ordered from GeneArt and subcloned into expression plasmid pETDuet-1. Protein expression was carried out in E. coli strain BL21 in TB media. After reaching OD6oo=T2 the bacteria were induced by adding 0.5 mM IPTG, cultured for 3 h at 37°C and harvested by centrifugation. Cells were then resuspended in a lysis buffer containing 50 mM Tris pH 8.5, 300 mM NaCI, 5% glycerol, 1 % Triton X-100, 2 mM p-mercaptoethanol, and protease inhibitor coctail and disintegrated by sonication. The lysate was cleared by centrifugation, filtered through a 0.45 pm filter and the protein was purified by nickel affinity (Ni-NTA Agarose, Jena Bioscience). TEV cleavage was carried out overnight in 50mM Tris pH 8.5, 250 mM NaCI, 5% Glycerol and 4 mM P-mercaptoethanol. TEV and uncut Mpro were removed by a second NiNTA purification step. The protein was further purified by size exclusion chromatography (Superdex s75, GE Healthcare) in 50mM Tris pH 7.4, 150mM NaCI, 2mM P-mercaptoethanol.
PLPRO activity assay
[00141] The assay was designed to measure p|_PRO protease activity under screening conditions in white 384-well Optiplates. The assay buffer contained 50 mM Tris (pH 8.0), 0.01 % (w/v) BSA and 10 mM DTT. RLRGG-AMC was used as fluorogenic substrate for PLPro 40 pl of PLPro protein (end concentration 60 nM) was incubated with 10 pl RLRGG-AMC substrate (end concentration 400 nM). The assay (final volume 50 pl) was incubated for 30 min. The release of AMC (Ex. 360 nm I Em. 487 nm) was measured on an Envision plate reader (Perkin Elmer, Waltham, MA).
PLPRO activity assay
[00142] The assay was designed to measure PLPRO protease activity under screening conditions in white 384-well Optiplates. The assay buffer contained 50 mM Tris (pH 8.0), 0.01 % (w/v) BSA and 10 mM DTT. RLRGG-AMC was used as fluorogenic substrate for PLPro 40 pl of PLPro protein (end concentration 60 nM) was incubated with 10 pl RLRGG-AMC substrate (end concentration 400 nM). The assay (final volume 50 pl) was incubated for 30 min. The release of AMC (Ex. 360 nm I Em. 487 nm) was measured on an Envision plate reader (Perkin Elmer, Waltham, MA).
Compound Screening
[00143] 40 pl of PLPRO protein (end concentration 60nM) in assay buffer (50 mM Tris (pH
8.0), 0.01 % (w/v) BSA and 10 mM DTT) was added to the screening plates using the MultiFlo dispensing system (BioTek). Compounds and DMSO (as control) were directly pipetted into the screening plates to achieve a final concentration of 10 pM using a Sciclone G3 liquid handling workstation (PerkinElmer, Waltham, USA). The drug repurposing collection30 was used to identify PLPRO inhibitors. The controls in the plates (first two and last two columns) included DMSO control (negative control with no compound) and control without protein (to obtain the assay window). After addition of 10 pl RLRGG-AMC substrate (end concentration 400 nM) with the MultiFlo, AMC fluorescence (Ex. 360 nm / Em. 487 nm) was measured using a Envision plate reader immediately after substrate addition (time point 0) and after 30 min (time point 1). Quality and robustness of the assay was calculated using Z' factor.
PLpro inhibitor IC50 determination
[00144] RLRGG-AMC or ISG15-AMC was used as substrate for PLPRO and the release of AMC fluorescence was measured (Ex. /Em. 360/487 nm) on an Envision plate reader. 40 pl of a 75 nM PLpro solution in assay buffer (50 mM Tris (pH 8,0), 0.01% (w/v) BSA and 10 mM DTT) was pipeted into 384 well plates and different concentration of ACF (50 pM - 0 pM, final concentration) was added. The mixture was incubated for 1 hour at RT. Then the reaction was initiated by adding 10 pl of 2 pM RLRGG-AMC (400 nM final) or 10 pl of 0.5 pM ISG15-AMC (100 nM, final), respectively. Initial velocities of AMC release were normalized to the DMSO control. IC5o value was calculated using GraphPad Prism. The experiment was repeated three times.
PLpro inhibitor IC50 determination
[00145] RLRGG-AMC or ISG15-AMC was used as substrate for PLPRO and the release of AMC fluorescence was measured (Ex./Em. 360/487 nm) on an Envision plate reader. 40 pl of a 75 nM PLpro solution in assay buffer (50 mM Tris (pH 8,0), 0.01% (w/v) BSA and 10 mM DTT) was pipetted into 384 well plates and different concentration of ACF (50 pM - 0 pM, final concentration) was added. The mixture was incubated for 1 hour at RT. Then the reaction was initiated by adding 10 pl of 2 pM RLRGG-AMC (400 nM final) or 10 pl of 0.5 pM ISG15-AMC (100 nM, final), respectively. Initial velocities of AMC release were normalized to the DMSO control. IC50 value was calculated using GraphPad Prism. The experiment was repeated three times.
Cells and viruses
[00146] Vero (Cercopithecus aethiops’ kidney epithelial; ATCC CCL-81), HRT-18 (ATCC CRL-11663) cells, derivative of HRT-18 (ileocecal colorectal adenocarcinoma; ATCC CCL-244), CRFK (Felis catus, kidney cortex; ATCC® CCL-94) were cultured in Dulbecco’s MEM (Thermo Fisher Scientific, Poland) supplemented with 5% fetal bovine serum (heat-inactivated; Thermo Fisher Scientific, Poland) and antibiotics: penicillin (100 U/ml), streptomycin (100 pg/ml), and ciprofloxacin (5 pg/ml). A549 cells with ACE2 overexpression (A549ACE2+)31 were cultured in the same manner with supplementation with G418 (5 mg/ml; BioShop, Canada).
[00147] LLC-MK2 cells (ATCC CCL-7; Macaca mulatta kidney epithelial cells) were maintained in minimal essential medium (MEM; two parts Hanks' MEM and one part Earle's MEM [Life Technologies, Poland]) 5% fetal bovine serum (heat-inactivated; Thermo Fisher Scientific, Poland), penicillin (100 ll/rnl), streptomycin (100 ll/rnl ), and ciprofloxacin (5 pg/ml). [00148] Primary human skin fibroblasts (HSF) were cultured in Dulbecco’s MEM (Thermo Fisher Scientific, Poland) supplemented with 10% fetal bovine serum (heat-inactivated; Thermo Fisher Scientific, Poland), 1% nonessential amino acids (Life Technologies) and antibiotics: penicillin (100 ll/rnl), streptomycin (100 pg/ml), and ciprofloxacin (5 pg/ml).
[00149] Human airway epithelial (HAE) cells were isolated from conductive airways resected from transplant patients. The study was approved by the Bioethical Committee of the Medical University of Silesia in Katowice, Poland (approval no: KNW/0022/KB1/17/10 dated 16.02.2010). Written consent was obtained from all patients. Cells were dislodged by protease treatment, and later mechanically detached from the connective tissue. Further, cells were trypsinized and transferred onto permeable Transwell insert supports (□ = 6.5 mm). Cell differentiation was stimulated by the media additives and removal of media from the apical side after the cells reached confluence. Finally, cells were cultured for 4-6 weeks to form well-differentiated, pseudostratified mucociliary epithelium. All experiments were performed in accordance with relevant guidelines and regulations. Commercially available MucilAir™- Bronchial (Epithelix Sari, Switzerland) HAE cultures were also used for the ex vivo analysis. MucilAir™ cultures were maintained as suggested by the provider in MucilAir™ culture medium.
[00150] All cells were maintained at 37°C under 5% CO2.
[00151] SARS-CoV-2 strain used in the study was isolated in house and is designated PL_P07 [GISAID Clade G, Pangolin lineage B.1] (accession numbers for the GISAID database: hCoV-19/Poland/PL_P07/2020). Reference SARS-CoV-2 strain 026V-03883 was kindly granted by Christian Drosten, Charite - Universitatsmedizin Berlin, Germany by the European Virus Archive - Global (EVAg); https://www.european-virus-archive.com/).
[00152] All SARS-CoV-2 stocks were generated by infecting monolayers of Vero cells. The cells were incubated at 37 °C under 5% CO2. The virus-containing liquid was collected at day 2 post-infection (p.i.), aliquoted and stored at -80°C. Control samples from mock-infected cells was prepared in the same manner.
[00153] MERS-CoV stock (isolate England 1 , 1409231v, National Collection of Pathogenic Viruses, Public Health England, United Kingdom) was generated by infecting monolayers of Vero cells. The cells were incubated at 37°C under 5% CO2. The virus-containing liquid was collected at day 3 p.i., aliquoted and stored at -80°C. Control samples from mock- infected cells were prepared in the same manner. [00154] FIPV stock (strain 79-1146) was generated by infecting CRFK cells in 90% confluency. The cells were incubated at 37 °C under 5% CO2. The virus-containing liquid was collected at day 3 p.i., aliquoted and stored at -80°C. Control samples from mock-infected cells were prepared in the same manner.
[00155] The HCoV-NL63 stock (isolate Amsterdam 1) was generated by infecting monolayers of LLC-MK2 cells. The cells were incubated at 32 °C under 5% CO2 and then lysed by two freeze-thaw cycles at 6 days p.i. The virus-containing liquid was aliquoted and stored at -80°C. A control LLC-MK2 cell lysate from mock-infected cells was prepared in the same manner.
[00156] The HCoV-OC43 stock (ATCC: VR-1558) was generated by infecting monolayers of HRT-18 cells. The cells were incubated at 32 °C under 5% CO2 and then lysed by two freezethaw cycles at 5 days post-infection (p.i.). The virus-containing liquid was aliquoted and stored at -80°C. A control HRT-18G cell lysate from mock-infected cells was prepared in the same manner.
[00157] Virus yields were assessed by titration on fully confluent cells in 96-well plates, according to the method of Reed and Muench. Plates were incubated at 32°C or 37°C for times indicated above, and the cytopathic effect (CPE) was scored by observation under an inverted microscope.
Cell viability assay
[00158] Cell viability was evaluated using the XTT Cell Viability Assay kit (Biological Industries, Cromwell, CT, USA) according to the manufacturer’s protocol. Vero, A549ACE2+, CRFK, HRT-18, LLC-MK2 and HSF cells were cultured on 96-well plates. Cells were incubated with ACF for 24 h at 37°C in an atmosphere containing 5% CO2. After incubation, the medium was discarded and 100 pL of fresh medium was added to each well. Then, 25 pL of the activated 2,3-bis-(2-methoxy-4-nitro-5-sulphenyl)-(2H)-tetrazolium-5-carboxanilide (XTT) solution was added and samples were incubated for 2 h at 37°C. The absorbance (A = 450 nm) was measured using a Spectra MAX 250 spectrophotometer (Molecular Devices, San Jose, CA, USA). The obtained results were normalized to the control samples, where cell viability was set to 100%.
Virus replication inhibition assay
[00159] Vero cells were seeded in culture medium on 96-well plates (TPP, Trasadingen, Switzerland) at 2 days before infection. Subconfluent cells were infected with SARS-CoV-2 viruses at 1600 50% tissue culture infectious dose (TCID50)/mL. Infection was performed in the presence of 100 nM, 1 pM and 10 pM concentration of compounds listed in Table 2. After 2 h of incubation at 37°C, cells were rinsed twice with PBS and fresh medium without compounds was added. The infection was carried out for 48 h and the cytopathic effect (CPE) was assessed. Culture supernatants were collected from wells where CPE reduction was observed.
[00160] For the detailed determination of the antiviral properties of ACF susceptible cells were seeded in culture medium on 96-well plates at 2 days before infection. Subconfluent cells were infected with SARS-CoV-2, MERS-CoV and FIPV viruses at TCID50 = 1600 and HCoV- NL63 at TCID50 = 4000 and HCoV-OC43 at TCID50 = 3000. Infection was performed in the presence of ACF. Control cells were inoculated with the same volume of mock as negative control and with 10 pM remdesivir as a positive control of coronavirus replication inhibition. After 2 h of incubation at 37°C, cells were rinsed twice with PBS and fresh medium without or with ACF or remdesivir was added. The infection was carried out for 24 h when the CPE in virus control was observed. Culture supernatants were collected.
[00161] Virus replication inhibition ex vivo was evaluated by infecting HAE cultures with
SARS-CoV-2 virus at 5000 TCID50/ml in the presence of ACF, remdesivir or PBS. Two concentrations of ACF (400 nM and 500 nM) and the controls were added to the apical side of the inserts followed by the addition of the virus diluted in PBS. Infection time was of 2 hours at 37°C. After the infection, the apical side of the HAE were washed three times with PBS and each compound was re-applied and incubated again for 30 minutes at 37°C. After the last incubation with the ACF, the samples (50pL) were collected and the HAE were left in air-liquid interphase. Every 24 hours the HAE were incubated for 30 minutes with the ACF dilutions or controls, and the samples were collected. After collecting last samples cells were fixed with 3.7% paraformaldehyde and stained as described below.
[00162] Virus yield was measured using the RT-qPCR method described below.
Isolation of nucleic acids, reverse transcription and quantitative PCR
[00163] A viral DNA/RNA kit (A&A Biotechnology, Poland) was used for nucleic acid isolation from cell culture supernatants. RNA was isolated according to the manufacturer’s instructions.
[00164] Viral RNA was quantified using quantitative PCR coupled with reverse transcription (RT-qPCR) (GoTaq Probe 1-Step RT-qPCR System, Promega, Poland) using CFX96 Touch real-time PCR detection system (Bio-Rad, Poland). The reaction was carried out in the presence of the probes and primers indicated in the Table 1. The heating scheme was as follows: 15 min at 45°C and 2 min at 95°C, followed by 40 cycles of 15 s at 95°C and 1 min at 58°C or 60°C (specified in Table 1). In order to assess the copy number for the N gene, standards were prepared and serially diluted.
ACF and virus visualization
[00165] Vero cells were seeded on coverslips in 12-well plate (TPP, Trasadingen, Switzerland) at 2 days before experiment. ACF at 1 pM or DMSO at 0,01% concentration were applied on cells. After 1h cells were fixed with 3.7% paraformaldehyde (PFA) for 15 min. Fluorescent images were acquired under EVOS XL Core Imaging System.
[00166] A549ACE2+ cells were seeded on coverslips in 12 well plate (TPP, Trasadingen,
Switzerland) at 2 days before infection. Subconfluent cells were infected with SARS-CoV— 2 in the presence of ACF or remdesivir. After 2h infection unbound virions were washed off twice with PBS and fresh medium supplemented with compounds was added. The infection was carried out for 24 h whereupon cells were fixed with 3.7% paraformaldehyde (PFA) for 1 h. Fixed cells were permeabilized using 0,5% Tween-20 (10 min, room temperature [RT]) and unspecific binding sites were blocked with 5% bovine serum albumin (BSA) in PBS (4°C, overnight) prior to staining. For visualization of viral particles anti-SARS-CoV-2 nucleocapsid protein antibody (Bioss, bsm-41412M) at 1 :200 dilution (2 h, RT) followed by Alexa Fluor 546 conjugated secondary antibody (Invitrogen, A-11003, 1:400 1 h, RT) was used. After incubations with antibodies cells were washed thrice with 0,5% Tween-20. After labeling virions actin cytoskeleton was visualized using Alexa-Fluor 647 conjugated Phalloidin (4 U/rnL, 1 h, RT, Thermo Scientific) and nuclear DNA was stained with 4’,6-diamidino-2-phenylindole (DAPI, 0.1 pg/mL, Sigma-Aldrich). Stained coverslips were mounted on glass slides with Prolong Diamond antifade mountant (Thermo Scientific, Poland). Fixed HAE cultures were permeabilized using 0,5% Triton X-100 (7 min RT) and unspecific binding sites were blocked with 5% BSA in PBS (1 h, 37°C) prior to staining. For visualization of virions anti-SARS-CoV-2 nucleocapsid protein antibody (Bioss bsm-41412M, 1 :200 2 h, RT) coupled with goat anti mouse Alexa Fluor 546 (Invitrogen, A-11003, 1 :400 1 h, RT) were used. Nuclear DNA was stained with DAPI (0.1 pg/mL, 20 min, RT, Sigma-Aldrich) and actin cytoskeleton with Alexa Fluor 647 conjugated phalloidin (4 U/rnL, 1 h, RT, Thermo Scientific). Stained HAE were cut from inserts and mounted on glass slides with cells facing coverslips.
[00167] Fluorescent images were acquired under Zeiss LSM 880 confocal microscope.
[00168] Table 2: Primers and probes used for a RT-qPCR.
Figure imgf000045_0001
Generation of resistance mutants
[00169] Drug-resistant SARS-CoV-2 was obtained by serial passages of the virus in the presence of increasing concentrations of ACF or remdesivir, starting at a concentration equivalent to their IC50. Vero cells were seeded in 12 well plate and infected with SARS-CoV-2 in the presence of the drug or PBS. When CPE was observed, samples were collected, aliquoted, frozen and used to infect cells for the next passage. Infection was repeated with increasing concentrations of the compound (IC50 dose was doubled every 2 passages). After 5 passages, culture supernatants were collected, RNA was isolated and viral RNA was sequenced (NGS, Illumina). All experiments were carried out in triplicate.
NMR hit validation
[00170] To prove the binding of ACF to PLpro in solution we have produced 13C-15N-2N labelled protein using by growing the bacteria cultured in minimal M9 medium. The remaining part of protein purification was identical to the one described above. NMR experiments were recorded at 298 K on a Bruker Avance III 900 MHz spectrometer (1H frequency 900 MHz) equipped with a 5 mm TCI cryoprobe. 1H,15N TROSY spectra32,33 were acquired with 40 scans and 1024 x 512 complex points on uniformly 2H,15N-labelled PLPro. Sample concentration was 0.17 mM in PBS buffer, pH 7.4 supplemented with 10% D2O. Spectra were processed and analysed using the AZARA suite of programs (v. 2.8, © 1993-2020; Wayne Boucher and Department of Biochemistry, University of Cambridge, unpublished).
Crystallization and structure solution
[00171] Plpro for crystallization was purified as described before. In the last step of purification, the protein was applied on a size exclusion chromatography S75 using as carrier buffer 20mM Tris pH 8, 40mM NaCI and 2mM Dithiothreitol (DTT). Purified protein was concentrated to 5-10 mg/ml using 30 kD cutoff Amicon Ultra Filter. PLpro-proflavine complex was prepared adding 5-molar excess compound to the concentrated protein. The final concentration of DMSO was never higher than 5%. Crystallization samples were prepared using commercial kits and an automated crystallization workstation (Mosquito, TTP LabTech). Both ACF and pure proflavine were used in the experiments. Crystals of PLpro-proflavine complex grew at room temperature in 0.05 M Hepes sodium salt pH 7, 0.05M magnesium sulfate and 1.6 M lithium sulfate. Crystals suitable for testing were moved in cryo-protectant solution containing the harvesting solution supplemented with 25% (v/v) glycerol and snap frozen in liquid nitrogen.
[00172] PLpro-proflavine crystals were measured at Swiss Light Source (SLS, Villigen, Switzerland), beamline PXIII. The best dataset was collected at 2.7 A resolution and it was indexed and integrated using XDS software34; scaled and merged using STARANISO webserver35. Crystal belongs to space group P6522. Matthews coefficient analysis suggested the presence of two PLpro-proflavine molecules in the asymmetric unit. Molecular replacement solution was found using Phaser36,37 and the apo PLpro structure (PDB code: 6W9C) as searching model. Model and restraints for proflavine was prepared using Lidia, the ligand builder in Coot38. The initial model was subjected to several iterations of manual and automated refinement cycles using COOT and REFMAC5, respectively39,40. Throughout the refinement, 5% of the reflections were used for cross-validation analysis41, and the behavior of Rfree was employed to monitor the refinement strategy.
Chemical characterization of the ACF components
[00173] The commercial ACF is a mixture of 3,6-diaminoadridin-10-ium (proflavine) and
3.6-diamino-10-methylacridin-10-ium (acriflavine). In order to perform the study using fully characterized material we have used NMR and HPLC techniques to analyze the commercial product.
[00174] HPLC-UV/MS and 1H-NMR analyses of commercial acriflavine hydrochloride (cACF) and proflavine hemisulfate (PF)
[00175] HPLC-UV/MS analyses of commercial acriflavine hydrochloride and proflavine hemisulfate were performed on a Dionex UltiMate 3000 HPLC system coupled with a Thermo Finnigan LCQ ultrafleet mass spectrometer, using the following method: Waters X-Bridge C18 (4.6 x 30 mm, 3.5 pm) column; gradient: 5 to 10% of acetonitrile + 0.1 % formic acid v/v in water + 0.1 % formic acid v/v over 9.5 min perd; 10 to 20% of acetonitrile + 0.1 % formic acid v/v in water + 0.1 % formic acid v/v over 4.0 min period; 20 to 95% of acetonitrile + 0.1 % formic acid v/v in water + 0.1 % formic acid v/v over 1.0 min period; flow rate: 0.6 mL/min; UV detection at 254 nm. 1H-NMR spectra were recorded at room temperature on a Bruker AV-HD400 operating at 400 MHz.
[00176] All biological experiments were conducted using the same batch of commercial acriflavine hydrochloride (cACF) purchased from Sigma Aldrich, which is sold as a mixture of
3.6-diaminoadridin-10-ium (proflavine; PF) and 3,6-diamino-10-methylacridin-10-ium (acriflavine, ACF). In order to determine the exact composition of the obtained commercial acriflavine (cACF) the mixture was analyzed by HPLC-MS and 1H-NMR spectroscopy. Both methods show that the used batch of commercial acriflavine contains three main components and that the composition is as follows: 56% proflavine (PF), 17% acriflavine (ACF) and 22-23% side methylated PF. The remaining 4-5% are other 3,6-diaminoacridine derivatives like for example side methylated ACF (4%). The NMR analysis is based on the fact that the protons of the methyl group at position 10 of acriflavine (ACF) have a very distinct chemical shift of 3.94 ppm (4.04 ppm for side methylated ACF), whereas the protons of the methyl group connected to the amino group at position 3, like it is the case in side methylated PF and ACF, have a much lower chemical shift of 2.87 and 2.98 ppm, respectively.1'3 The aromatic protons of the different 3,6-diaminoacridine derivatives almost exactly coincide with each other and consequently one of those peaks can be used for calibration of the integrals in the 1H-NMR spectrum. Integrating the overlapping doublets at 7.86-7.78 ppm as 2 protons and dividing the integrals of the separate signals for the methyl groups (4.04, 3.94 and 2.98 ppm) by 3 gives the percentages of side methylated PF (0.69:3 = 0.23; 23%) and side methylated ACF (0.13:3 = 0.04; 4%) as well as actual acriflavine (ACF) (0.52:3 = 0.17; 17%) present in the measured sample. As there are virtually no other 3,6-dimainoacridine derivatives other than PF, ACF and their side methylated derivatives, the remaining 56% can be attributed to proflavine (PF). This analysis fits perfectly the result obtained via the HPLC-MS technique. Commercial proflavine hemisulfate was also acquired from Sigma Aldrich and its purity was analyzed via HPLC-MS and 1H-NMR spectroscopy as well. The sample turned out to be 99% pure proflavine (PF) and was used as a reference for the analysis of commercial acriflavine (cACF). The signals found in the recorded 1H-NMR spectrum and the retention time obtained via the HPLC-UV-chromatogram (RT: 7.96 min) were in accordance with those of proflavine present in commercial acriflavine hydrochloride (RT: 7.89 min).
Statistical analysis
[00177] All experiments were performed in triplicate, and results are presented as mean ± SEM unless otherwise indicated. One-way ANOVA with Tukey HSD post-hoc test was used to assess statistical significance of acquired results. When the parametric test assumptions were violated, the nonparametric Kruskal-Wallis with Dunn’s post-hoc test was used. P values of 0.05 and less were considered significant.
RESULTS
HTS screen to identify PLpro inhibitors
[00178] In order to identify inhibitors for the PLpro, we established a fluorogenic protease assay using an AMC-labelled substrate and carried out a high-throughput screening with small molecule compounds at a final concentration of 10 pM (Figure 15 A, B). We used a repurposing drug library consisting of 5,632 small molecule compounds, which are either approved or are/have been under different stages of clinical testing30. Compounds that inhibited PLpro activity were selected upon calculation of the slope of activity (velocity) from time point 0 to 1. The average Z' factor for all plates was above 0.8, showing excellent screening quality. As a cut-off value for active compounds, we choose 4* standard deviation below median of all compound- treated wells (calculated per plate). After removing compounds that generated high fluorescence signal at time point 0 (suggesting unspecific compound interference), 11 compounds were selected for further conformation screens, which are listed in Table 2. Verification of primary screening hits
[00179] Eleven of these hits could be reordered and serial dilution experiments were carried out to determine IC50 values in the original screening assay (Figure 19C). Notably, not all of these hits were active in inhibiting PLpro. Some of the hits from the primary screening may have initially been identified as hits due to autofluorescence or quenching effects and thus displayed weaker dose-response effects in the follow-up analyses, since we determine the enzyme velocity and not just the endpoints of a reaction. Importantly, ACF showed a dosedependent PLpro inhibition with an IC50 of 1.66 pM and was the most active compound (Figure 19C). We then repeated this experiment with ACF and two derivatives of ACF, namely acridine orange base (Figure 19D) and acridine-3,6-diamine sulfate (Figure 19D) as well as the published positive control GRL-016713LQBJ (Figure 19E). All derivatives dose-dependently inhibited PLpro although to different degree. The effect of ACF on PLpro enzymatic activity using the ISG15-AMC as substrate has also ben tested. As previously shown, PLpro cleaves ISG15- AMC significantly faster than RLRGG-AMC. Nonetheless, the IC50 of ACF with ISG15-AMC (1.46 pM) (Figure 20B and Figure 19B) was comparable to the IC50 that was determined with the RLRGG-AMC substrate. Since AMC assays are fluorescence-based assays that are susceptible to autofluorescence or quenching effects of the compounds, further conducted gelbased de-ubiquiniting assays have been conducted to confirm the results. For this purpose, the protease activity of PLpro and the inhibitory potential of ACF on tri-ubiquitin K48 chains have been tested. First, K48 tri-ubiqiutin has ben incubated with PLpro and samples of different time points were taken to analyze the cleavage of these chains in Western Blot assays. It could be seen that PLpro efficiently cleaved K48 tri-ubiquitin to di-ubiquitin (Figure 1C). Next, PLpro was incubated with either DMSO or 5, 15, 25 pM of ACF, respectively, before adding K48 tri-ubiquitin chains to the reaction mixture. Also in this independent assay format, ACF reduced the protease activity in a dose-dependent manner (Figure 1C), thereby confirming that ACF is a specific PLpro inhibitor.
Cellular validation of the screening hits
[00180] The hit compounds were tested in cell culture and cytotoxicity was verified on Vero cells at three concentrations (100 nM, 1 pM, 10 pM) using the XTT assay. At the same time, the cytopathic effect (CPE) reduction assay was carried out. Amongst 13 compounds, three hampered the development of the cytopathic effect, but the initial RT-qPCR analysis revealed that only ACF inhibited virus replication (Figure 2).
[00181] Table 3: CPE reduction assay. Initial screen of 13 proposed compounds in given concentrations. Table shows results of cytopathic effect (CPE) reduction assay obtained by microscopic observations. CPE - cytopathic effect; RED - CPE reduction; TOX - toxicity.
Figure imgf000050_0001
[00173] Further, compounds have been tested in respect to viral replication and enzymatic activity of SARS-CoV-2 as listed in table4.
Table 4: Inhibition of enzymatic activity of SARS-CoV-2 and Inhibition of viral replication of SARS-CoV-2
Figure imgf000050_0002
Figure imgf000051_0001
Verification of the ACF as selective PLpro inhibitor
[00182] NMR ligand-based binding analysis was carried out to validate PLpro-ligand interaction. The direct interaction of ACF with PLpro was also observed by NMR ligand based assay (peaks of the ACF partially disappear in the presence of the protein) and the results are presented in Figure 3.
ACF is not a SARS-CoV-2 Mpro inhibitor
[00183] To check the specificity of ACF we have performed an enzymatic digestion assay using fluorescent Mpro substrate. The experiment shown that ACF is a very weak Mpro inhibitor with less than 50% inhibition at 100 pM of ACF concentration (Figure 17). We can, therefore, conclude that Mpro inhibition has no significant contribution in SARS-CoV-2 inhibition at submicromolar concentrations used in the other assays. Structural analysis of SARS-CoV-2 PLpro in complex with proflavine
[00184] To gain insight into the molecular basis of the SARS-CoV2-PLpro inhibition by acriflavine, we determined the X-ray crystal structure of the protein in complex with proflavine, one of its principal components. Crystallization of acriflavine complex did not yield diffracting crystals most likely doe to heterogenic nature of the mixture. The proflavine-complex structure was solved in P6522 space group. There are two molecules of complex in the asymmetric unit. I ntriguingly, it was found a disulfate bond which bridges two Cys270 of adjacent Plpro molecules from different asymmetric units. Analysis of the electron density map allowed to build unequivocally 3 molecules of proflavine for each protein molecule (Figure 3). One of these is located at the interface with the symmetric mate and it could be considered as a crystallographic artifact (Figure 3 inlet and Figure 15). More interestingly the other two molecules of proflavine are TT-TT stacked to each other and they accommodate the S3-S5 pockets of the PLpro substrate recognition cleft which is defined by the loop connecting the helices a3 and a4 and the so-called “blocking loop” BL242. Comparison with the apo structure of PLpro (PDB code: 7D47) reveals that although the overall structure is well preserved the BL2 loop undergoes an induced fit upon the binding. In particular, the side chain of Tyr268 rotates by about 57° inward the substrate recognition cleft and the loop moves by 2k in the same direction narrowing the substrate binding cleft (Figure 16).
[00185] Looking closer at the intramolecular interactions, several Plpro residues are involved in the binding. One of the molecules termed proflavine-l is allocated in the S4 pocket (Figure 4 A, B). The side chain Tyr273 is involved in a hydrogen bond (2.9A) with the primary amine group at position 3 of proflavine-l which sits at the bottom of the substrate binding cleft. This latter forms a stacked-like CH/TT interaction with Pro247 (3.9A) and a L-shaped CH/TT interaction with Pro248 (4.6A). Moreover, the side chain of Tyr264 is engaged in a T-shaped TT- TT stacking interaction (3.5 A) with the same molecule. The second molecule, termen proflavine- II is TT-TT stacked at 3.5A on top of the other and occupies the S3 and S5 pockets (Figure 4 C, D). Gly163 and Asp164 form a hydrogen bond with the primary amine group at position 3 (2.9 A) and the imine group of the acridine moiety (2.9 A), respectively. In addition, Tyr268 forms a T-shape TT-TT staked interaction (5.1 A) with this proflavine-ll. Overall, this provides unique binding model where two proflavines, tightly TT-TT stacked, cooperate in blocking the substrate pocket. It is clear that, both molecules are requested for the inhibition. The electron density analysis shows weaker trace of at least two more proflavines that can be allocated on top of the other two at optimal distance for TT-TT staking forming a continuous, DNA-like stacking from one to another PLpro molecule in the same asymmetric unit. Their electron density is much weaker and does not allow to build these molecules unambiguously (Figure 17). However, they are not involved in any interaction with PLpro. [00186] Recently, Shin et al. solved the crystal structure of SARS-CoV2-PLpro in complex with ISG15 (interferon-induced gene 15) bearing the RLRGG recognition motif at the C-terminus (1). Comparison with our structure shows that proflavine molecule occupying S3 and S5 pockets well overlaps with the backbone of Arg151 and Arg153 in position P3 and P5, respectively (Figure 5). Whereas, the side chain of Leu152 in position P4 points exactly towards the other molecule of proflavine in the S4 pocket. All the interactions with PLpro residues are well preserved. This finding suggests that proflavine inhibits SARS-CoV2-PLpro by limiting access to the substrate. Moreover, since the imine group of the proflavine-l molecule in S4 pocket is not involved in any polar interactions, it can, with without being bond by theory, be assumed that the methylated (acriflavine) form is preferred at this position due to lack of desolvation penalty. The amino group at position 3 of proflavine-l I is located in similar position as amide nitrogen of the glycine P2. Side-methylated proflavine, also present in commercial acriflavine preparations (see Figure 21), would, therefore, mimic the P2 amino acid. These two, expected interactions of commercial acriflavine, explain why it is a significantly more potent inhibitor than pure proflavine.
NMR validation of the direct PLpro-ACF interaction
[00187] In order to confirm that ACF binds directly to PLpro in solution we have recorded 2D 1H,15N TROSY spectra of the PLpro in the absence and presence of different concentrations of ACF. The spectra indicated a well-folded, monomeric protein in solution (Figure 6). The addition of ACF caused several resonances to shift. The remaining bulk of the resonances was not altered. This indicates that the ACF binds to a spatially limited, distinct pocket of PLpro. Upon binding the fold and monomeric state of the protein was not altered. This proves that the third proflavine moiety observed in crystal structure at the interface between neighboring PLpro molecules is a crystallization artifact and that ACF does not cause dimerization of the PLpro in solution. The multiple TT-TT stacked electron densities observed in X-ray data between adjacent active sites also do not seem to cause oligomerization of the PLpro as this would cause much more resonances to shift upon addition of high concentration of ACF.
ACF and SARS-CoV-2 in cell culture
[00188] For the studies on the SARS-CoV-2, two cell culture models were used: Vero cells, which are broadly used simian model and human A549ACE2+ cells overexpressing the ACE2 receptor43. All experiments were carried out in parallel.
First the cytotoxicity of the compounds was evaluated on three human cell lines (A549ACE2+, Vero, HRT-18) and primary human fibroblasts (Figure 7). The CC50 values were estimated in both systems to be 3.1 pM for A549ACE2+, 3.4 pM for Vero, 2.1 pM for HRT-18, and 12 pM for primary human fibroblasts. Interestingly, ACF shows lower cytotoxicity in primary cells, compared to cell lines, what may be linked with previously described antineoplastic activity. [00189] Second, the full range dose-response experiment was carried out and the results are presented in Figure 8. The IC50 value calculated based on the presented data was 64 nM for the Vero cells and 86 nM for A549ACE2+ cells. Selectivity index (SI) values for Vero and A549ACE2+ models are 53 and 36, respectively.
[00190] Inhibition was also confirmed using inverted light microscopy and confocal microscopy. The reduction of cytopathic effect on Vero cells was observed under light microscopy at 48 hours post infection at different concentrations of ACF (Figure 9). After 24 h and 48 h of infection in the presence of 500 nM ACF, confocal microscopy images show nearly complete inhibition of SARS-CoV-2 replication was observed after 24 and 48 h, as determined with the amount of viral proteins and number of infected cells. While inhibition was also noted for remdesivir, it was inferior compared to ACF (Figure 10).
Ex vivo inhibition of SARS-CoV-2 infection in HAE cultures.
[00191] The antiviral activity of ACF was analysed on the HAE ex vivo model. Two different concentrations were evaluated (400 nM and 500 nM), PBS and remdesivir were used as controls. Each analysis was performed in duplicate and samples were collected for 144 hours. Figure 11 shows the inhibition of SARS-CoV2 replication in the presence of ACF and remdesivir.
[00192] The results show that ACF hampers SARS-CoV-2 replication in the HAE ex vivo model. A lower viral yield was detected in the cultures treated with ACF in comparison with the PBS control. ACF treated HAE showed an even higher inhibition of virus replication than the positive control with 10 pM remdesivir after 144 h of infection. At time points of 48 and 72 hours of infection, the virus was under the detection limits in the ACF 500 nM treatment.
Mechanism of action
[00193] To fully delineate the mechanic of the drug activity we carried out the time-of- addition experiment, where the cells were first infected with the virus and the ACF was added after 0, 2, 4 or 6 h. The results clearly show that the virus inhibition was maintaind also when the compound was not present during early stages of the infection. Consequently, it is inhibited mainly during the replication phase (Figure 13).
Pan-coronavirus activity of ACF
[00194] To verify whether ACF may be used as a generic anticoronaviral drug, its activity against other betacoronaviruses (MERS-CoV, HCoV-OC43) and alphacoronaviruses (HCoV- NL63 and feline infectious peritonitis virus (FIPV) was tested. ACF inhibited MERS-CoV even stronger than SARS-CoV-2 (IC50= 21 nM, SI = 162). Surprisingly, ACF exhibited weaker action on HCoV-OC43, only minor, not statistically significant inhibition was observed (< 1 log at 1 pM, IC50 = 105 nM, SI = 27). No effect on any of tested alphacoronaviruses replication in tested concentrations (Figure 14) was observed.
Biological activity of synthetic 3,6-diaminoacridine derivatives against Trypanosoma and Leish mania parasites
[00195] The biological activity of synthetic 3,6-diaminoacridine derivatives against Trypanosoma and Leishmania parasites has been tested.
Biological assay for evaluating the activity against Trypanosoma brucei rhodesiense STIB900
[00196] This stock was isolated in 1982 from a human patient in Tanzania and after several mouse passages cloned and adapted to axenic culture conditions44 Minimum Essential Medium (50 pL) supplemented with 25 mM HEPES, 1 g/L additional glucose, 1% MEM non- essential amino acids (100x), 0.2 mM 2-mercaptoethanol, 1 mM Na-pyruvate and 15% heat inactivated horse serum was added to each well of a 96-well microtiter plate. Serial drug dilutions of eleven 3-fold dilution steps covering a range from 100 to 0.002 pg/ml were prepared. Then 4x103 bloodstream forms of T. b. rhodesiense STIB 900 in 50 pL was added to each well and the plate incubated at 37 °C under a 5% CO2 atmosphere for 70 h. 10 pL resazurin solution (resazurin, 12.5 mg in 100 mL double-distilled water) was then added to each well and incubation continued for a further 2-4 h.45 Then the plates were read with a Spectramax Gemini XS microplate fluorometer (Molecular Devices Cooperation, Sunnyvale, CA, USA) using an excitation wave length of 536 nm and an emission wave length of 588 nm. Data were analyzed with the graphic programme Softmax Pro (Molecular Devices Cooperation, Sunnyvale, CA, USA), which calculated IC50 values by linear regression46 and 4-parameter logistic regression from the sigmoidal dose inhibition curves. Melarsoprol (Arsobal Sanofi-Aventis, received from WHO) is used as control.
Biological assay for evaluating the activity against Trypanosoma cruzi
[00197] Rat skeletal myoblasts (L-6 cells) were seeded in 96-well microtitre plates at 2000 cells/well in 100 pL RPMI 1640 medium with 10% FBS and 2 mM L-glutamine. After 24 h the medium was removed and replaced by 100 pL per well containing 5000 trypomastigote forms of T. cruzi Tulahuen strain C2C4 containing the p-galactosidase (Lac Z) gene.47 After 48 h the medium was removed from the wells and replaced by 100 pL fresh medium with or without a serial drug dilution of eleven 3-fold dilution steps covering a range from 100 to 0.002 pg/mL. After 96 h of incubation the plates were inspected under an inverted microscope to assure growth of the controls and sterility. Then the substrate CPRG/Nonidet (50 pL) was added to all wells. A color reaction developed within 2-6 h and could be read photometrically at 540 nm. Data were analyzed with the graphic programme Softmax Pro (Molecular Devices), which calculated IC50 values by linear regression46 and 4-parameter logistic regression from the sigmoidal dose inhibition curves. Benznidazole is used as control (IC50 = 0.5±0.2 pg/mL).
Biological assay for evaluating the activity against Leishmania donovani axenic amastigotes
[00198] Amastigotes of L. donovani strain MHOM/ET/67/L82 are grown in axenic culture at 37 °C in SM medium48 at pH 5.4 supplemented with 10% heat-inactivated fetal bovine serum under an atmosphere of 5% CO2 in air. One hundred microlitres of culture medium with 105 amastigotes from axenic culture with or without a serial drug dilution are seeded in 96-well microtitre plates. Serial drug dilutions of eleven 3-fold dilution steps covering a range from 100 to 0.002 pg/mL are prepared. After 70 h of incubation the plates are inspected under an inverted microscope to assure growth of the controls and sterile conditions. 10 pL of resazurin (12.5 mg resazurin dissolved in 100 mL distilled water) are then added to each well and the plates incubated for another 2 h. Then the plates are read with a Spectramax Gemini XS microplate fluorometer (Molecular Devices Cooperation, Sunnyvale, CA, USA) using an excitation wave length of 536 nm and an emission wave length of 588 nm. From the sigmoidal inhibition curves the IC50 values are calculated by linear regression46 and 4-parameter logistic regression using SoftmaxPro software (Molecular Devices Cooperation, Sunnyvale, CA, USA).
Biological assay for evaluating the in vitro cytotoxicity towards L-6 cells
[00199] Assays were performed in 96-well microtiter plates, each well containing 100 pl of RPMI 1640 medium supplemented with 1 % L-glutamine (200 mM) and 10% fetal bovine serum, and 4000 L-6 cells (a primary cell line derived from rat skeletal myoblasts).49 Serial drug dilutions of eleven 3-fold dilution steps covering a range from 100 to 0.002 pg/mL were prepared. After 70 h of incubation the plates were inspected under an inverted microscope to assure growth of the controls and sterile conditions. 10 pL of resazurin was then added to each well and the plates incubated for another 2 h. Then the plates were read with a Spectramax Gemini XS microplate fluorometer (Molecular Devices Cooperation, Sunnyvale, CA, USA) using an excitation wave length of 536 nm and an emission wave length of 588 nm. The IC50 values were calculated by linear regression46 and 4-parameter logistic regression from the sigmoidal dose inhibition curves using SoftmaxPro software (Molecular Devices Cooperation, Sunnyvale, CA, USA). Podophyllotoxin (Sigma P4405) is used as control. The biological assays for evaluating the activity against Trypanosoma and Leishmania parasites have been previously published elsewhere.50, 51 52
[00200] Table 5: Biological activity of synthetic 3,6-diaminoacridine derivatives against
Trypanosoma and Leishmania parasites.
Figure imgf000057_0001
Figure imgf000058_0001
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Claims

1 . A composition comprising at least one compound according to formula (I)
Figure imgf000063_0001
RT is selected from the group consisting of H, (Ci-C6)alkyl, (CH2)0(Ci-C6)alkyl ,(Ci- C6)cycloalkyl, (Ci-C6)heterocyclalkyl, or absent, preferably methyl; o is 1 to 3, preferably 1 ;
R2 is selected from the group consisting of H, (Ci-C6)alkyl,-(CH2)rCONH(CH2)sR6, -(CH- (CH2)pCOvinyl, -(CH2)qR6, -CO(Ci-C6)alkyl preferably H;
R3 is selected from the group consisting of H, (Ci-C6)alkyl, -(CH2)rCONH(CH2)s 6, - (CH2)pCOvinyl, -(CH2)qR6, -CO(Ci-C6)alkyl, preferably H; p is an integer between 1 to 3, preferably 1 ; q is an integer between 1 to 3, preferably 1 ; r is an integer between 1 to 3, preferably 1 ; s is an integer between 1 to 3, preferably 1 ;
R4 is selected from the group consisting of H, (Ci-C6)alkyl;
R5 is selected from the group consisting of H, (Ci-C6)alkyl; if R2 and R5 are both (Ci-C6)alkyl, R2 and R5 may be connected to form a 4 to 6 membered ring; if R3 and R4 are both (Ci-C6)alkyl, R3 and R4 may be connected to form a 4 to 6 membered ring;
R6 is selected from the group consisting of
Figure imgf000063_0002
X' is an anion or absent; if X' is absent then RT is absent; for use in the treatment of diseases caused by betacoronaviruses, leishmaniasis, trypanosomiasis
2. A composition comprising at least one dimer of the compound according to the formula (I) of claim 1 , according to formula (II)
(|)-R3-(|)’
(II) wherein (I) and (I)’ are based on formula (I) in claim 1 and may be identical or different, preferably identical;
R3 is -(CH2)t-, -(CH2)tQ(CH2)u-, -CO(CH2)t-, -CO(CH2)tCO-; t is an integer between 1 to 4; u is an integer between 1 to 4, for use in the treatment of diseases caused by betacoronaviruses, leishmaniasis, and trypanosomiasis.
3. The composition of claim 1 or 2, wherein a) the treatment is caused by human and veterinary coronaviruses that belong to subgenera hibecovirus, nobecovirus, embecovirus, merbecovirus and sarbecovirus, preferably coronaviruses or b) the treatment is caused by human coronavirus HKLI1 (HCoV-HKU1), human coronavirus OC43 (HCoV-OC43), Middle East respiratory syndrome-related coronavirus (MERS-CoV) or c) the treatment is caused by severe acute respiratory syndrome-related coronaviruses (SARS-CoV, SARS-CoV-2) or d) the treatment is caused by a virus that evolve or mutate from the species described in a) to c) or e) the disease is the severe acute respiratory syndrome, preferably SARS-CoV or SARS- CoV-2, more preferably SARS-CoV-2 or f) the disease is the Middle East respiratory syndrome (MERS-CoV) or g) the disease is pneumonia.
4. A composition comprising at least one compound according to formula (I)
Figure imgf000064_0001
RT is selected from the group consisting of H, (Ci-C6)alkyl, (CH2)0(Ci-C6)alkyl ,(Ci- C6)cycloalkyl, (Ci-C6)heterocyclalkyl, or absent, preferably methyl; o is 1 to 3, preferably 1 ;
R2 is selected from the group consisting of H, (Ci-C6)alkyl,-(CH2)rCONH(CH2)sR6, -(CH- (CH2)pCOvinyl, -(CH2)qR6, -CO(Ci-C6)alkyl preferably H;
R3 is selected from the group consisting of H, (Ci-C6)alkyl, -(CH2)rCONH(CH2)sR6, - (CH2)pCOvinyl, -(CH2)qR6, -CO(Ci-C6)alkyl, preferably H; p is an integer between 1 to 3, preferably 1 ; q is an integer between 1 to 3, preferably 1 ; r is an integer between 1 to 3, preferably 1 ; s is an integer between 1 to 3, preferably 1 ;
R4 is selected from the group consisting of H, (Ci-C6)alkyl;
R5 is selected from the group consisting of H, (Ci-C6)alkyl; if R2 and R5 are both (Ci-C6)alkyl, R2 and R5 may be connected to form a 4 to 6 membered ring; if R3 and R4 are both (Ci-C6)alkyl, R3 and R4 may be connected to form a 4 to 6 membered ring;
R6 is selected from the group consisting of
Figure imgf000065_0001
;
X' is an anion or absent; if X' is absent then RT is absent; with the provisio that the compound according to formula (I) is not selected from the group
Figure imgf000065_0002
5. A composition comprising at least one dimer of the compound according to the formula (I) of claim 1 or 4, according to formula (II)
(|)-R3-(|)’
(II) wherein
(I) and (I)’ are based on formula (I) in claim 1 and may be identical or different, preferably identical;
R3 is -(CH2)t-, -(CH2)tQ(CH2)u-, -CO(CH2)t-, -CO(CH2)tCO-; t is an integer between 1 to 4; u is an integer between 1 to 4.
6. The composition of any one of claims 1 to 5, wherein X' is selected from the group consisting of tetrafluoroborate, formate , trifluoroacetate, napsylate, glycollylarsanilate, nitrate, benzoate, hexylresorcinate, oleate, bitartrate, hydroxynaphthoate, pantothenate, bicarbonate, hydrabamine, pamoate, camsylate, isethionate, polygalacturonate, propionate, salicylate, lactobionate, stearate, decanoate, edetate, maleate, succinate, estolate, mandelate, teoclate, gluceptate, acetate, glutamate, muscate, aspartate, glycolate, benzenesulfonate, hexanoate, octanoate, sulfonate, chloride, iodide, bromide, phosphate, phosphonate, lactate, malate, citrate, tartrate, fumarate, gluconate, sulfate or hemisulfate, preferably chloride, iodide, bromide, tetrafluoroborate and sulfonate, most preferably chloride.
7. The composition of any one of claims 1 to 6, wherein i) RT is selected from the group consisting of methyl, ethyl, propyl, cyclopropyl, butyl, cyclobutyl, pentyl, cyclopentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl, 3-pentyl, 2-methylbutyl, 3-methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut-2-yl, 2- methylbut-2-yl, 2,2-dimethylpropyl, hexyl, 2-hexyl, 3-hexyl, 2-methylpentyl, 3-methylpentyl,
2,2-dimethylbutyl, and 2,3-dimethylbutyl,
Figure imgf000066_0001
preferably methyl; ii) R2 and/or R3 are independently selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl, 3-pentyl, 2- methylbutyl, 3-methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut-2-yl, 2-methylbut-2-yl, 2,2- dimethylpropyl, hexyl, 2-hexyl, 3-hexyl, 2-methylpentyl, 3-methylpentyl, 2,2-dimethylbutyl, and 2,3-dimethylbutyl, preferably methyl.
8. The composition of any one of claims 1 to 7, further comprising at least one compound according to formula (III)
Figure imgf000066_0002
wherein
R4 is H, halogen, (Ci-C6)alkyl, (C3-C6)cycloalkyl, or -O(Ci-C6)alkyl; preferably H;
R5 is H, halogen, (Ci-C6)alkyl, (C3-C6)cycloalkyl, or -O(Ci-C6)alkyl; preferably H;
R6 is H, halogen, (Ci-C6)alkyl, (C3-C6)cycloalkyl, or -O(Ci-C6)alkyl; preferably H;
R7 is H, (Ci-C6) alkyl, preferably methyl or H;
Z is H, halogen, (Ci-C6)alkyl, (C3-C6)cycloalkyl, -O(Ci-C6)alkyl, -(Ci-C6)alkyl(C6-Cio)aryl, -(C C6)alkyl(C5-Cio)heteroaryl; preferably H;
Y is -NH2, -NHR8, halogen, (Ci-C6)alkyl, (C3-C6)cycloalkyl; preferably -NH2
R8 is H, (Ci-C6)alkyl, preferably methyl;
9. The composition of claim 8 for use, wherein a) the molar ratio of the at least one compound according to formula (I) is 5 to 100, preferably 10 to 40, preferably 15 to 30 mol-% based on the overall molar ratio of parent compounds (I) and (III) of the composition and compound (III) is 0 to 95, preferably 60 to 90, more preferably 70 to 85 mol%.-% based on the overall molar ratio of parent compounds (I) and (II) of the composition and/or b) R4, R5, R6, R?, and/or R8 are (Ci-C6)alkyl, preferably independently selected from the group of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tertbutyl, 2-pentyl, 3-pentyl, 2-methylbutyl, 3-methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut- 2-yl, 2-methylbut-2-yl, 2,2-dimethylpropyl, hexyl, 2-hexyl, 3-hexyl, 2-methylpentyl, 3- methylpentyl, 2,2-dimethylbutyl, and 2,3-dimethylbutyl, more preferably methyl and/or c) Y is (Ci-C6)alkyl, preferably independently selected from the group of methyl, ethyl, propyl, butyl, pentyl, iso-propyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl, 3-pentyl, 2- methylbutyl, 3-methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut-2-yl, 2-methylbut-2-yl, 2,2- dimethylpropyl, hexyl, 2-hexyl, 3-hexyl, 2-methylpentyl, 3-methylpentyl, 2,2-dimethylbutyl, and 2,3-dimethylbutyl, more preferably methyl.
10. The composition of any one of claims 1 to 3 and 6 to 9 wherein a) the compound according to formula (I) and/or (I)’ is selected from the group consisting of
Figure imgf000067_0001
Figure imgf000068_0001
Figure imgf000069_0001
11. The compound according to claim 4 or 5, wherein a) the compound according to formula (I) and/or (I)’ is selected from the group consisting of
Figure imgf000069_0002
b) the compound of formula (II) is selected from the group consisting of
Figure imgf000070_0002
12. The composition of any one of claims 1 to 11 for use, wherein compound (I), (II) and/or (III) is a solvate, hydrate, salt, complex, or isotopically enriched form, preferably a salt.
13. The composition of claim 12, wherein compound (I), (II), or (III) is a salt, wherein the salt comprises an anion selected preferably from the group consisting of tetrafluoroborate, trifluoroacetate, formate, napsylate, glycollylarsanilate, nitrate, benzoate, hexylresorcinate, oleate, bitartrate, hydroxynaphthoate, pantothenate, bicarbonate, hydrabamie, pamoate, camsylate, isethionate, polygalacturonate, propionate, salicylate, lactobionate, stearate, decanoate, edetate, maleate, succinate, estolate, mandelate, teoclate, gluceptate, acetate, glutamate, muscate, aspartate, glycolate, benzenesulfonate, hexanoate, octanoate, sulfonate, chloride, iodide, bromide, phosphate, phosphonate, lactate, malate, citrate, tartrate, fumarate, gluconate, sulfate or hemisulfate, more preferably a tetrafluoroborate, sulfonate, sulfate, hemisulfate, or chloride, most preferably chloride.
14. The composition of claims 6, and 13 wherein the sulfonate is a sulfonate according to formula (IV)
Figure imgf000070_0001
wherein Rg is selected from the group consisting of phenyl, 4-nitrophenyl, 4-methylphenyl, 4- trifluoromethyphenyl, trifluoromethyl, and (Ci-C5)alkyl.
15. The composition of claim 14 wherein a) Rg is (Ci-C5)alkyl and/or b) (Ci-C5)alkyl is selected from the group consisting of methyl, ethyl, propyl, butyl, pentyl, isopropyl, sec-propyl, iso-butyl, sec-butyl, tert-butyl, 2-pentyl, 3-pentyl, 2-methylbutyl, 3- methylbutyl (/so-pentyl Oder /so-amyl), 3-methylbut-2-yl, 2-methylbut-2-yl, 2,2-dimethylpropyl, preferably methyl.
16. A composition in which at least one compound according to formula (I) and at least one compound according to formula (III) are bonded together via one or two linker systems wherein optionally a) the linker system is (C2-Ci0)alkylene, or (C2-Ci0)alkenyl, preferably (C3-C8)alkyl, or (C3- 8)alkenyl; wherein optionally at least one or at least two CH2-groups in these alkyl or alkenyl groups are substituted by O, S, S(O)i.2, NH or N(Ci-C4)alkyl and/or b) connecting is performed preferably via position 5, 7, 8 or by substitution of the nitrogen in position 6 in formula (I) and position 5, 7, 8 or by substitution of the nitrogen in position 6 or
10 in formula (III) wherein the underlying aromatic system in formula (I) and (III) is numbered according to formula (
Figure imgf000071_0001
and/or c) the composition is for use in the treatment of betacoronaviruses, leishmaniasis, trypanosomiasis optionally i) the treatment is caused by human and veterinary coronaviruses that belong to subgenera hibecovirus, nobecovirus, embecovirus, merbecovirus and sarbecovirus, preferably coronaviruses or ii) the treatment is caused by human coronavirus HKLI1 (HCoV-HKU1), human coronavirus OC43 (HCoV-OC43), Middle East respiratory syndrome-related coronavirus (MERS-CoV) or iii) the treatment is caused by severe acute respiratory syndrome-related coronaviruses (SARS-CoV, SARS-CoV-2) or iv)the treatment is caused by a virus that evolve or mutate from the species described in i) to iii) or d) the disease caused by the betacoronavirus is the severe acute respiratory syndrome, preferably SARS-CoV or SARS-CoV-2, more preferably SARS-CoV-2 or e) the disease caused by the betacoronavirus is the Middle East respiratory syndrome (MERS-CoV) or f) the disease caused by the betacoronavirus is pneumonia.
17. The composition of any one of claims 1 to 16 further comprising at least one pharmaceutically acceptable carrier.
18. The composition for use of any one of claims 1 to 17 formulated as an inhalative drug.
19. The composition for use of any one of claims 1 to 17 formulated as an oral drug.
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