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  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
  • C12Q1/25—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving enzymes not classifiable in groups C12Q1/26 - C12Q1/66
• • 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
  • A61K31/41—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with two or more ring hetero atoms, at least one of which being nitrogen, e.g. tetrazole
  • A61K31/415—1,2-Diazoles
  • A61K31/4155—1,2-Diazoles non condensed and containing further heterocyclic rings
• • 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
  • A61K31/41—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with two or more ring hetero atoms, at least one of which being nitrogen, e.g. tetrazole
  • A61K31/42—Oxazoles
  • A61K31/421—1,3-Oxazoles, e.g. pemoline, trimethadione
• • 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
  • A61K31/41—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with two or more ring hetero atoms, at least one of which being nitrogen, e.g. tetrazole
  • A61K31/42—Oxazoles
  • A61K31/422—Oxazoles not condensed and containing further heterocyclic rings
• • 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
  • A61K31/41—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with two or more ring hetero atoms, at least one of which being nitrogen, e.g. tetrazole
  • A61K31/425—Thiazoles
  • A61K31/427—Thiazoles not condensed and containing further heterocyclic rings
• • 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
  • A61P31/04—Antibacterial agents
• • G—PHYSICS
  • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
  • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
  • G16B15/00—ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
• • G—PHYSICS
  • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
  • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
  • G16B15/00—ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
  • G16B15/20—Protein or domain folding
• • G—PHYSICS
  • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
  • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
  • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• • 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

• This invention is in the field of medicinal chemistry and relates to novel compounds, and pharmaceutical compositions thereof, that inhibit DNA gyrases .
• the invention also relates to methods of using the compounds and pharmaceutical compositions of this invention to treat bacterial infections, including nosocomial infections, that are susceptible to gyrase inhibition.
• Gyrase is one of the topoisomerases, a group of enzymes which catalyze the interconversion of topological isomers of DNA (see generally, Kornberg and Baker, DNA Replication, 2d Ed., Chapter 12, 1992, W.H. Freeman and Co.; Drlica, Molecular Microbiology, 1992, 6, 425; Drlica and Zhao, Microbiology and Molecular Biology Reviews, 1997, 61, 377). Gyrase itself controls DNA supercoiling and relieves topological stress that occurs when the DNA strands of a parental duplex are untwisted during the replication process. Gyrase also catalyzes the conversion of relaxed, closed circular duplex DNA to a negatively superhelical form which is more favorable for recombination.
• the mechanism of the supercoiling reaction involves the wrapping of gyrase around a region of the DNA, double strand breaking in that region, passing a second region of the DNA through the break, and rejoining the broken strands.
• a cleavage mechanism is characteristic of a type II topoisomerase .
• the supercoiling reaction is driven by the binding of ATP to gyrase.
• the ATP is then hydrolyzed during the reaction. This ATP binding and subsequent hydrolysis cause conformational changes in the DNA-bound gyrase that are necessary for its activity. It has also been found that the level of DNA supercoiling (or relaxation) is dependent on the ATP/ADP ratio. In the absence of ATP, gyrase is only capable of relaxing supercoiled DNA.
• Bacterial DNA gyrase is a 400 kilodalton protein tetramer consisting of two A (gyrA) and two B subunits (gyrB) . Binding and cleavage of the DNA is associated with gyrA, whereas ATP is bound and hydrolyzed by the gyrB protein. GyrB consists of an amino-terminal domain which has the ATPase activity, and a carboxy- terminal domain which interacts with gyrA and DNA.
• eukaryotic type II topoisomerases are homodimers that can relax negative and positive supercoils, but cannot introduce negative supercoils.
• an antibiotic based on the inhibition of bacterial DNA gyrase would be selective for this - enzyme and be relatively inactive against the eukaryotic type II topoisomerases .
• the widely-used quinolone antibiotics inhibit bacterial DNA gyrase.
• the quinolones include the early compounds such as nalidixic acid and oxolinic acid, as well as the later, more potent fluoroquinolones such as norfloxacin, ciprofloxacin, and gatifloxacin. These compounds bind to gyrA and stabilize the cleaved complex, thus inhibiting overall gyrase function, leading to cell death.
• drug resistance has also been recognized as a problem for this class of compounds (WHO Report, "Use of Quinolones in Food Animals and Potential Impact on Human Health", 1998) .
• bacteria exposed to earlier compounds often quickly develop cross-resistance to more potent compounds in the same class.
• inhibitors that bind to gyrB There are fewer known inhibitors that bind to gyrB. Examples include the coumarins, novobiocin and coumermycin Al, cyclothialidine, cinodine, and clerocidin. The coumarins have been shown to bind to gyrB very tightly. For example, novobiocin makes a network of hydrogen bonds with the protein and several hydrophobic contacts. While novobiocin and ATP do appear to bind within the ATP binding site, there is minimal overlap in the bound orientation of the twq compounds. The overlapping portions are the sugar unit of novobiocin and the ATP adenine (Maxwell, Trends in Microbiology, 1997, 5, 102) .
• the most prevalent point mutation is at a surface arginine residue that binds to the carbonyl of the coumarin ring (Argl36 in E. coli gyrB) . While enzymes with this mutation show lower supercoiling and ATPase activity, they are also less sensitive to inhibition by coumarin drugs (Maxwell, Mol . Microbiol . , 1993, 9, 681).
• the coumarins Despite being potent inhibitors of gyrase supercoiling, the coumarins have not been widely used as antibiotics. They are generally not suitable due to their low permeability in bacteria, eukaryotic toxicity, and poor water solubility (Maxwell, Trends in
• antibiotics that represent a new class of compounds not previously used to treat bacterial infection. Such compounds would be particularly useful in treating nosocomial infections in hospitals where the formation and transmission of resistant bacteria are becoming increasingly prevalent.
• These compounds when complexed with bacterial DNA gyrase, are comprised of the following features: (a) HBA, (b) HBD, (c) Grpl and/or Grpla, and (d) at least two features selected from Grp2, Grp3 or Grp4 :
• HBA is a hydrogen bond acceptor
• HBD is a hydrogen bond donor
• Grpl is a chemical moiety having a buried non-polar surface area in the range of about 30-250 (A) 2 and a buried polar surface area in the range of about 40-160 (A) 2 ;
• Grpla is a chemical moiety having a buried non-polar surface area in the range of about 35-260 (A) 2 and a buried polar surface area in the range of about 0-110 (A) 2 ;
• Grp2 is a chemical moiety having a buried non-polar surface area in the range of about 50-300 (A) 2 and a buried polar surface area in the range of about 0-150 (A) 2 ;
• Grp3 is a chemical moiety having a buried non-polar surface area in the range of about 215-500 (A) 2 and a buried polar surface area in the range of about 25-140 (A) 2 ;
• Grp4 is a chemical moiety having a buried non-polar surface area in the range of about 150-350 (A) 2 and a buried polar surface area in the range of about 0-100 (A) 2 , provided that Grp4 is other than a coumarin ring; and the distances in angstroms between the features are in the following ranges:
• buried surface area is the surface area of the inhibitor compound that is lost upon binding to the gyrase B subunit.
• polar surface area is that portion of the buried surface area corresponding to all of the present nitrogen and oxygen atoms .
• non-polar surface area is that portion of the buried surface area corresponding to all other atoms. The calculation of these surface areas is known in the computational chemistry literature. See F. Eisenhaber, P. Lijnzaad, P. Argos, and M. Scharf, "The Double Cubic Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies", J.
• substitute refers to the replacement of a hydrogen atom in a compound with a substituent group.
• substitute does not include those hydrogen atoms which form a part of a hydrogen bonding moiety which is capable of. forming a hydrogen bond with a suitable hydrogen bond acceptor, such as a carbonyl oxygen, of an amino acid residue in the gyrase binding site.
• strain energy is used in this application to refer to the difference between the conformational energy of the unbound (or free) compound and that of the compound when bound to gyrase . The strain energy can be determined by the following steps: Evaluate the energy of the molecule when it has the conformation necessary for binding to gyrase .
• strain energy is the strain energy.
• the strain energy for binding of a potential inhibitor to gyrase is the difference between the free conformation energy and the bound conformation energy.
• the strain energy of an inhibitor of the present invention is less than about 10 kcal/mol.
• hydrophobic refers to a moiety which tends not to dissolve in water and is fat-soluble.
• Hydrophobic moieties include, but are not limited to, hydrocarbons, such as alkanes, alkenes, alkynes, cycloalkanes, cycloalkenes, cycloalkynes and aromatic compounds, such as aryls, certain saturated and unsaturated heterocycles and moieties that are substantially similar to the side chains of hydrophobic natural and unnatural -amino acids, including valine, leucine, isoleucine, methionine, phenylanine, ⁇ -amino isobutyric acid, alloisoleucine, tyrosine, and tryptophan.
• hydrogen bond refers to a favorable interaction that occurs whenever a suitable donor atom, X, bearing a proton, H, and a suitable acceptor atom, Y, have a separation of between 2.5A and 3.5A and where the angle X-H - - - Y is greater than 90 degrees.
• Suitable donor and acceptor atoms are well understood in medicinal chemistry (G.C. Pimentel and A.L. McClellan, The Hydrogen Bond, Freeman, San Francisco, I960; R. Taylor and 0. Kennard, "Hydrogen Bond Geometry in Organic Crystals", Accounts of Chemical Research, 17, pp. 320-326 (1984)).
• the compounds of this invention were designed to bind to bacterial DNA gyrase subunit B at the ATP binding site of the enzyme.
• the structure of this binding site has been described, and is known to be fairly well conserved across different strains of bacteria (Lewis, R.J. et al . , EMBO J. , 15, 1412 (1996); Holdgate, G.A. et al . , Biochemistry, 36, 9663 (1997); Brino, L. et al . , J. Biol . Chem. , 275, 9468 (2000); Tsai, F.T. et al., Proteins, 28(1), 41. (1997); Wigley, D.B.
• GRID (Goodford, P. J. A Computational Procedure for Determining Energetically Favorable Binding Sites on Biologically Important Macromolecules. J. Med. Chem. 1985, 28, 849-857) . GRID is available from Oxford University, Oxford, UK.
• MCSS (Miranker, A.; Karplus, M. Functionality Maps of Binding Sites: A Multiple Copy Simultaneous Search Method. Proteins: Structure, Function and Genetics 1991, 11, 29-34) .
• MCSS is available from Molecular Simulations, Inc., San Diego, CA.
• DOCK (Kuntz, I. D.; Blaney, J. M. ; Oatley, S. J. ; Langridge, R. ; Ferrin, T. E. A Geometric Approach to Macromolecule-Ligand Interactions. J. Mol. Biol. 1982, 161, 269-288) . DOCK is available from the University of California, San Francisco, CA.
• CAVEAT Bartlett, P. A.; Shea, G. T.; Telfer, S. J. ; Waterman, S. CAVEAT: A Program to Facilitate the Structure-Derived Design of Biologically Active Molecules. In "Molecular Recognition in Chemical and Biological Problems," Special Pub., Royal Chem. Soc. 1989, 78, 182-196) .
• CAVEAT is available from the University of California, Berkeley, CA and Molecular Simulations, Inc., San Diego, CA.
• 3D Database systems such as MACCS-3D (MDL Information Systems, San Leandro, Calif.). This area has been recently reviewed by Martin (Martin, Y.C. 3D Database Searching in Drug Design. J. Med. Chem. 1992, 35, 2145).
• the inhibitors of this invention may be constructed "de novo" using either an empty active site or optionally including some portions of a known inhibitor.
• Such methods are well known in the art. They include, for example: 1. LUDI (Bohm, H. J. The Computer Program LUDI :
• a variety of conventional techniques may be used to carry out each of the above evaluations as well as the evaluations necessary in screening a candidate compound for gyrase inhibiting activity. Generally, these techniques involve determining the location and binding proximity of a given moiety, the occupied space of a bound inhibitor, the amount of complementary contact surface between the inhibitor and protein, the deformation energy of binding of a given compound and some estimate of hydrogen bonding strength and/or electrostatic interaction energies. Examples of conventional techniques useful in the above evaluations include: quantum mechanics, molecular mechanics, molecular dynamics, Monte Carlo sampling, systematic searches and distance geometry methods [G. R. Marshall, Ann. Rev. Pharmacol . Toxicol . , 1987, 27, 193]. Specific computer software has been developed for use in carrying out these methods. Examples of programs designed for such uses include: Gaussian 92, revision E.2 [M. J. Frisch, Gaussian, Inc., Pittsburgh, PA. ⁇ 1993]; AMBER, version 4.0 [P. A. Kollman, University of California at San
• Different classes of active gyrase inhibitors may interact in similar ways with the various binding regions of the gyrase active site.
• the spatial arrangement of these important groups is often referred to as a pharmacophore.
• the concept of the pharmacophore has been well described in the literature [D. Mayer, C. B. Naylor, I. Motoc, and G. R. Marshall, J " . Comp . Aided Molec. Design, 1987, 1, 3; A. Hopfinger and B. J. Burke, in Concepts and Applications of Molecular Similarity, 1990, M. A. Johnson and G. M. Maggiora, Ed. , Wiley] .
• gyrase inhibitors of this invention may also use different scaffolds or core structures, but all of these cores will allow the necessary moieties to be placed in the active site such that the specific interactions necessary for binding may be obtained.
• These compounds are best defined in terms of their ability to match the pharmacophore, i.e., their structural identity relative to the shape and properties of the active site of bacterial DNA gyrase.
• Distances to or from any given group are calculated from the center of mass of that group.
• the term "center of mass” refers to a point in three- dimensional space which represents a weighted average position of the masses that make up an object. Distances between groups may be readily determined using any modeling software and other suitable chemical structure software.
• pharmacophore modeling software enables one to determine pharmacophore models from a variety of structural information and data.
• the software may also be used to search a database of three-dimensional structures in order to identify compounds that meet specific pharmacophore requirements. Examples of this software include:
• DISCO (Martin, Y.C., Bures, M.G., Danaher, E.A., DeLazzer, J. , Lico, A., Pavlik, P.A. , J " . Comput . Aided Mol . Design, 1993, 7, 83).
• DISCO is available from Tripos Associates, St. Louis, MO. 2.
• CHEM-X which is developed and distributed by Chemical Design Ltd, Oxon, UK and Mahwah, NJ.
• a typical hydrogen bond acceptor is an oxygen or nitrogen, especially an oxygen or nitrogen that is sp 2 -hybridized or an ether oxygen.
• a typical hydrogen bond donor is an oxygen or nitrogen that bears a hydrogen. Examples of substructures or moieties containing a hydrogen bond acceptor and hydrogen bond donor that are separated by up to 4.0 A include, but are not limited to, those substructures listed in Table 1. The dotted lines indicate that either a single or double bond may be present .
• compounds of this invention When bound to a bacterial DNA gyrase subunit B, compounds of this invention bind to the ATP binding site of the enzyme. During such binding, the pharmacophore features of the compounds will occupy certain regions or pockets of the ATP binding site. In the gyrB subunit of Staphylococcus aureus , Grpl will occupy a region of the ATP binding site bounded by the following amino acids (with the corresponding E.
• Groupl is typically a small, relatively hydrophobic group containing up to about six carbons.
• the binding interaction may be enhanced using a Grpl moiety that is able to form a direct hydrogen bond with one or more of the following: the backbone carbonyl oxygen of Ile51, the sidechain oxygen or nitrogen of Asn54, the backbone carbonyl oxygen of Val79, a sidechain carboxyl oxygen of Asp81, the backbone carbonyl oxygen of Thrl73, or the backbone amide nitrogen of Ilel75.
• Grpl is separated from HBA by a distance between about 2.9 to about 6.4 A and is separated from HBD by a distance between about 1.8 to about 5.0 A; however, Grpl is closer in distance to HBD than it is to HBA.- •
• Grpl moieties include -CH(R 4 ) 2 , -C0 2 (C ⁇ -6 aliphatic) , -C0N(R) 2 , -CONH-OR, -S0 2 R, and -S0 2 N(R) 2/ where each R is independently selected from hydrogen or a C ⁇ -6 aliphatic group, and each R 4 is independently selected from hydrogen, an optionally substituted C ⁇ -6 aliphatic group, or two R 4 taken together with the carbon to which they are attached form a three to six membered aliphatic ring.
• Grpla when present, will occupy a region of the ATP binding site bounded by the following S . aureus amino acids (corresponding E. coli amino acids) : Ile51 (Val43) , Asn54 (Asn46) , Leul03 (Met95) , Serl29 (Vall20) , Vall31 (Vall23), Leul38 (Leul30) , Vall40 (Leul32) , Ilel75 (Vall67) , and Phel77 (Phel69) .
• the binding interaction may be enhanced using a Grpla moiety that is able to form a direct hydrogen bond with the side chain oxygen or nitrogen of Asn54 (Asn46) .
• pharmacophore features of the present compounds are not limited to distinct chemical moieties within the same compound.
• a chemical moiety may serve as parts of two pharmacophore features.
• the two groups may share the first carbon as a common branch point.
• ATP binding site bounded by the following amino acids in S. aureus gyrase (E. coli gyrase) : Asp57 (Asp49) , Glyl09 (GlylOl) , GlyllO (Glyl02) Asn54 (Asn46) , Ilel02 (Ile94) , Leul03 (Met95) and Serl29 (Vall20) .
• S. aureus gyrase E. coli gyrase
• Grp2 moieties include hydrogen, -C 1-4 aliphatic, -CONHR, -CN, -halo, -C0 2 R, -S0 2 R, -COR, -CON(R) 2 , -S0 2 N(R) 2 , -NRS0 2 R, -NRS0 2 N(R) 2 , -Q, -COQ, -S0 2 Q, -CONHQ, -S0 2 NRQ, -NRS0 2 Q, and -NRS0 2 NRQ, where .R is a C 1-3 aliphatic group and Q is a three to five-membered heterocyclyl or a five- or six-membered heteroaryl ring.
• Grp3 when present, ' will occupy a region of the
• ATP binding site bounded by the following S. aureus gyrase amino acids (E. coli amino acids) : Asn54 (Asn46) , Glu58 (Glu50) , Arg84 (Arg76) , Gly85 (Gly77) , Ile86 (Ile78), Ilel02 (Ile94) , Alal08 (AlalOO) , Glyl09 (GlylOl) , GlyllO (Glyl02), Lyslll (Lysl03) , Phell2
• Grp3 The interaction of Grp3 with this surrounding environment will be primarily hydrophobic in nature; however, the interaction may be enhanced using a Grp3 moiety that is able to form a direct hydrogen bond with one or more of the following: the sidechain oxygen or nitrogen of Asn54, a sidechain carboxyl oxygen of Glu58, a sidechain nitrogen of Arg84, the backbone carbonyl oxygen of Gly85.
• a preferred Grp3 is Ring A :
• Z is C-R 3 or N-R 3 ;
• R 3 is - (CH 2 ) P N(R 5 ) 2 or an optionally substituted group selected from C ⁇ - 8 aliphatic, heterocyclyl, heterocyclylalkyl, aryl, aralkyl, heteroaryl, or heteroaralkyl ;
• p is an integer from zero to four when Z is C-R 3 or an integer from one to four when Z is N-R 3 ; and each R 5 is independently selected from hydrogen, an optionally subtituted C ⁇ - 4 aliphatic group, or two R 5 taken al ⁇
• Ring A moieties include a thiazole, oxazole, i idazole and pyrazole.
• Grp4 when present, will occupy a region of the ATP binding site bounded by the following gyrase amino acids of S . aureus (E. coli) : Arg84 (Arg76) , Gly85 (Gly77) , Pro87 (Pro79) , Lyslll (Lysl03), Phell2 (Phel04) , Glyll3 (Aspl05) , Glyll4 (Aspl06) , and Argl44 (Argl36) .
• Grp4 The interaction of Grp4 with this surrounding environment can be either hydrophobic or polar in nature.
• Grp4 may optionally contain or be an acidic group such as a carboxylic acid, sulfate, sulfonic acid, phosphate or phosphonic acid.
• Grp4 may also optionally form ⁇ - ⁇ stacking interactions with Arg84 or Argl44 or may form hydrogen bonds to these same amino acids.
• Interaction of Grp4 with Pro87 would be primarily of a hydrophobic nature.
• Interaction of Grp4 with its surrounding environment may be further enhanced by using a Grp4 moiety that is able to form a hydrogen bond with the backbone carbonyl oxygen of Gly85.
• Preferred Ar groups include phenyl, pyridyl and pyri idinyl rings.
• Groups 1-4 may be attached to such a moiety by a suitable attachment means such as a valence bond, a suitable linker group or by a ring fusion.
• suitable linker groups include an alkylidene chain, an aliphatic or aryl ring, -S-, -0-, -C0NH-, -S0 2 NH-, -NHC0-, -CO-, -NH-, or -NHS0 2 -, or a combination thereof.
• the compounds of this invention will usually have a molecular weight of less than about 1000 Daltons, preferably less than about 700 Daltons, and more preferably between about 300 and 600 Daltons.
• the present compounds form favorable binding interactions within the ATP binding site of the bacterial DNA gyrB subunit.
• one embodiment of the present invention relates to an enzyme-inhibitor complex comprising a bacterial DNA gyrase and a bacterial DNA gyrase inhibitor wherein the inhibitor is comprised of the following features: (a) HBA, (b) HBD, (c) Grpl and/or Grpla, and (d) at least two features selected from Grp2, Grp3 or Grp4 , and the distances between the features is as described above.
• a general process for designing a gyrase inhibitor that embodies the present invention comprises the following steps. First, one selects a moiety that contains HBA and HBD separated by up to 4.0 A. Ideally, the moiety is chosen such that HBD would be capable of forming a direct hydrogen bond with one or both of the side chain carboxyl oxygens of Asp81 and/or HBA would be in the vicinity of the sidechain oxygen of Thrl73 and is capable of forming a water-bridged hydrogen bond with one of the side chain carboxyl oxygens of Asp81. Examples of such moieties are listed in Table 1. Second, one selects a Grpl and/or Grpla moiety and a means of attachment to the HBA/HBD moiety.
• Grpl and/or Grpla so attached is within the requisite distance to HBA and HBD, and is capable of forming satisfactory interactions with its gyrase binding site environment as described above. Confirming that the satisfactory interactions would be achievable is within the knowledge of one skilled in the art using computational methods such as those described above.
• one may build the rest of the inhibitor by selecting from at least two groups of Grps 2-4 and corresponding means of attachment to provide the desired distances between groups and satisfactory interactions. The following process may be used to identify gyrase inhibitors of this invention.
• One or more molecular structures are..provided individually or as members of any suitable commercial or proprietary structure-searchable database of chemical compounds.
• a 2-D substructure searching program (such as Daylight®, CIS, Santa Fe, NM) is applied to select one or more structures containing HBA/HBD pairs wherein there is one to four bonds separating HBA and HBD (which will typically allow HBA and HBD to be separated by up to 4.0 A when converted below to a three-dimensional structure) .
• step (1) The molecular structures selected from step (1) are then converted to their respective three-dimensional ⁇ structures (for example, by using CORINA software available from Molecular Networks, GmbH, Germany) .
• the selected molecules may be placed into the active site of gyrB such that the HBA/HBD moiety is constrained to make the appropriate hydrogen bond interactions.
• HBD is capable of forming a direct hydrogen bond with one or both of the side chain carboxyl oxygens of Asp81 and/or HBA is capable of forming a water-bridged hydrogen bond with Asp81 and is in the vicinity of the sidechain oxygen of Thrl73.
• step (3) After selecting a molecular structure from step (3) (that is constrained with respect to the HBA/HBD,
• the remainder of the structure is then analyzed to determine whether at least two of the Grp2 , Grp3 and Grp4 features are present .
• the docking method allows one to confirm whether these group (s) fit appropriately into the respective regions of the ATP binding site defined above.
• the distances and the polar/non-polar surface areas are checked to determine whether they are within the specified ranges. It would be apparent to one skilled in the art that the above steps do not need to be performed in the above order.
• molecular fragments are selected that have the appropriate buried polar and non-polar surface areas described above. The following steps describe this process.
• HBA/HBD moieties are provided as molecular fragments.
• Table 1 lists a number of suitable fragments. Alternatively, these may be identified by searching a database of compounds as described in the first step of the previous process and selecting all molecules containing HBA/HBD pairs where there is one to four bonds separating HBA and HBD.
• This step is similar to the second step of the previous method, except that the HBA/HBD moiety is docked as a molecular fragment rather than as a whole compound.
• the HBA/HBD moiety is constrained to make the appropriate hydrogen bond interactions in the gyrB ATP site.
• Bacterial DNA gyrase inhibitors may also be obtained by modifying compound structures to include the pharmacophore features described above. Accordingly, one embodiment of this invention relates to a method of designing a bacterial DNA gyrase inhibitor comprising the steps of:
• gyrase inhibitor comprises the following features: (a) HBA, (b) HBD, (c) at least one feature selected from Grpl or Grpla, and (d) at least two features selected from Grp2, Grp3 or Grp4 ; wherein:
• HBA is a hydrogen bond acceptor and HBD is a hydrogen bond donor
• Grpl is a chemical moiety which, when bound to the ATP binding site of a bacterial DNA gyrase, has a buried non-polar surface area in the range of about 30-250 (A) 2 and a buried polar surface area in the range of about 40- 160 (A) 2 ;
• Grpla is a chemical moiety which, when bound to the ATP binding site of a bacterial DNA gyrase, has a buried non-polar surface area in the range of about 35-260 (A) 2 and a buried polar surface area in the range of about 0-
• Grp2 is a chemical moiety which, when bound to the ATP binding site of a bacterial DNA gyrase, has a buried non-polar surface area in the range of about 50-300 (A) 2 and a buried polar surface area in the range of about 0-150 (A) 2 ;
• Grp3 is a chemical moiety which, when bound to the ATP binding site of a bacterial DNA gyrase, has a buried non-polar surface area in the range of about 215-500 (A) 2 and a buried polar surface area in the range of about 25-140 (A) 2 ;
• Grp4 is a chemical moiety which, when bound to the ATP binding site of a bacterial DNA gyrase, has a buried non-polar surface area in the range of about 150-350 (A) 2 and a buried polar surface area in the range of about 0-100 (A) 2 , provided that Grp4 is other than a coumarin ring; and the distances in angstroms between the features are in the following ranges:
• R 2 is selected from hydrogen or, when R 1 is -C0 2 (C ⁇ _ 3 aliphatic) or -CONH(C ⁇ -3 aliphatic), R 2 is further selected from -halo, -CN, -C ⁇ _ 4 aliphatic, a three to five-membered heterocyclyl, or a five-membered heteroaryl ;
• Ring A is a heteroaryl ring selected from thiazole, oxazole, imidazole or pyrazole, wherein said imidazole is optionally attached by a C ⁇ _ 3 bridge from an imidazole ring nitrogen to Ar to form a five- to seven- membered fused ring;
• Z is C-R 3 or N-R 3 ;
• R 3 is - (CH 2 ) P N(R 5 ) _ or an optionally substituted group selected from C 1-8 aliphatic, heterocyclyl, heterocyclylalkyl, aryl, aralkyl, heteroaryl, or heteroaralkyl ; each R 4 is indepependently selected from hydrogen, an optionally subtituted C ⁇ _ 6 aliphatic group, or two R 4 taken together with the carbon to which they are attached form a three to six membered aliphatic ring; each R 5 is independently selected from hydrogen, an optionally subtituted C ⁇ _ 4 aliphatic group, or two R 5 taken together with the nitrogen to which they are attached form a five or six membered heterocyciic ring; p is an integer from zero to four when Z is C-R 3 or an integer from one to four when Z is N-R 3 ; and Ar is an optionally substituted aryl, heteroaryl, or heterocyclyl ring.
• the pyrazole ring of formula I is a moiety that contains both HBA and HBD.
• R 1 is attached to the HBA/HBD moiety by a valence bond and satisfies the Grpl and/or Grpla requirements;
• R 2 satisfies the Grp2 requirements;
• Ring A including R 3 satisfies the Grp3 requirements;
• Ar is a Grp4 moiety.
• Such compounds are useful in methods of treating bacterial infections.
• the following definitions shall apply unless otherwise indicated.
• aliphatic as used herein means straight chained, branched or cyclic C1-C12 hydrocarbons which are completely saturated or which contain one or more units of unsaturation.
• suitable aliphatic groups include substituted or unsubstituted linear, branched or cyclic alkyl, alkenyl, alkynyl groups and hybrids thereof such as (cycloalkyl) alkyl, (cycloalkenyl) alkyl or (cycloalkyl) alkenyl .
• alkyl and “alkoxy” used alone or as part of a larger moiety refers to both straight and branched chains containing one to twelve carbon atoms.
• alkenyl and alkynyl used alone or as part of a larger moiety shall include both straight and branched chains containing two to twelve carbon atoms.
• haloalkyl means alkyl, alkenyl or alkoxy, as the case may be, substituted with one or more halogen atoms.
• halogen means F, CI , Br, or I.
• heteroatom means N, O or S .
• the nitrogen-containing compounds of this invention also include the corresponding N-oxides of the compounds as well as those having a quarternized form of any basic nitrogen.
• Rings having one to four heteroatoms .selected from N, 0, or S include heterocyciic aromatic (or heteroaryl) rings and non-aromatic heterocyciic rings.
• aromatic heterocyciic rings include 2- furanyl, 3-furanyl, N-imidazolyl, 2-imidazolyl, 4- imidazolyl, 5-imidazolyl, 3-isoxazolyl, 4-isoxazolyl, 5- isoxazolyl, 2-oxadiazolyl, 5-oxadiazolyl, 2-oxazolyl, 4- oxazolyl, 5-oxazolyl, 2-pyrrolyl, 3-pyrrolyl, 2-pyridyl, 3-pyridyl, 4-pyridyl, 2-pyrimidyl, 4-pyrimidyl, 5- pyrimidyl, 3-pyridazinyl, 2-thiazolyl, 4-thiazolyl, 5-thiazolyl, 5-tetrazolyl, 2-triazoly
• non-aromatic heterocyciic rings examples include 2-tetrahydrofuranyl, 3- tetrahydrofuranyl , 2-tetrahydrothiophenyl, 3- tetrahydrothiophenyl , 2 -morpholino, 3 -morpholino, 4- morpholino, 2-thiomorpholino, 3-thiomorpholino, 4- thiomorpholino, 1-pyrrolidinyl, 2 -pyrrolidinyl, 3- pyrrolidinyl, 1-piperazinyl, 2 -piperazinyl, 1- piperidinyl, 2 -piperidinyl, 3 -piperidinyl, 4 -piperidinyl, 4-thiazolidinyl, diazolonyl, N-substituted diazolonyl, 1- phthalimidinyl, benzoxane, benzotriazol-1-yl , benzopyrrolidine, benzopiperidine, benzoxolane, be
• An aryl group (carbocyclic and heterocyciic) or an aralkyl group, such as benzyl or phenethyl, may contain one or more substituents.
• suitable substituents on an unsaturated carbon atom of an aryl group include halogen, -R, -OR, -OH, -SH, -SR, protected OH (such as acyloxy) , phenyl (Ph) , substituted Ph, -OPh, substituted -OPh, substituted or unsubstituted five to six membered ring having one to four heteroatoms, -N0 2 , -CN, -NH 2 , -NHR, -N(R) 2 , -NHCOR, -NHCONHR, -NHC0N(R) 2 , -NRCOR, -NHC0 2 R, -C0 2 R, -C0 2 H, -COR, -CONHR,
• An aliphatic group or a non-aromatic heterocyciic ring may contain one or more substituents.
• An alkylidene chain may be substituted in the same manner as an aliphatic group.
• a substitutable nitrogen on an aromatic or non- aromatic heterocyciic ring may be optionally substituted. Suitable substituents on the nitrogen include R, COR, S(0) 2 R, and C0 2 R, where R is an aliphatic group or a substituted aliphatic group.
• I-A, I-B, I-C, I-D and I-E shown below:
• R 1 , R 2 , R 3 , and Ar are as described above and R 7 is hydrogen or a C ⁇ -6 aliphatic group.
• R 7 is hydrogen or a C ⁇ -6 aliphatic group.
• R 1 groups include -C (R 4 ) 2 NHCOR, -C(R 4 ) 2 NHC0 2 R, -C0 2 R, and -CONHR where R is an optionally substituted C ⁇ _ 4 aliphatic group and each R 4 is independently selected from hydrogen, a C ⁇ _ 3 alkyl group, or two R 4 taken together with the carbon to which they are attached form a three or four membered aliphatic ring.
• R examples include -C ⁇ _ 4 alkyl, -C ⁇ _ 4 haloalkyl, -allyl, -CH 2 C ⁇ CR 6 , -CH (C 1-3 alkyl) C ⁇ CR 6 , and -C (Me) 2 C ⁇ CR 6 , where R 6 is hydrogen, -C ⁇ -4 aliphatic, -CH 2 N(Me) 2 , or -CH 2 0(C 1 . 3 alkyl) .
• a preferred R 2 group is hydrogen.
• R 1 is -CONH(C ⁇ - 3 alkyl) or -C0 2 (C ⁇ _ 3 alkyl)
• other preferred R 2 are halo, -CN and -C ⁇ _ 4 alkyl groups.
• R 3 groups include C ⁇ - 6 aliphatic optionally substituted by alkoxy, alkylamino or dialkylamino, optionally substituted morpholinyl, piperazinyl, piperidinyl, pyridyl, phenyl or benzyl.
• Preferred Ar groups are aryl and heteroaryl groups including optionally substituted phenyl, pyridyl, and pyrimidinyl rings.
• optional substituents attached to Ar include one or more of the following: alkyl, alkoxy, hydroxy, carboxy, . halo, S0 2 R, S0 2 NHR, amino, alkylamino, dialkylamino, and pyridyl. Selected compounds of formula I are shown in Table 3 (R 2 is hydrogen) .
• IA refers to ring A thiazoles (X is sulfur)
• IB to oxazoles (X is oxygen)
• IC to imidazoles
• X is NH
• ID to pyrazoles
• Z is nitrogen
• the compounds of this invention may be prepared in general by methods known to those skilled in the art for analogous compounds and by referring to the synthetic schemes shown below.
• a general reference is Katritzky and Rees, Comprehensive Heterocyciic Chemistry, vol. 5, 1984, Pergamon Press.
• the Ar group of formula I may be represented by a phenyl ring. It will be apparent to one skilled in the art that these routes are generally applicable to compounds having aryl groups other than phenyl .
• Reagents and conditions (a) (Et0 2 C) 2 CHBr, pyridine , toluene , heat (b) trif lie anhydride , 2 , 6-lutidine , CH 2 C1 2 , 0°C (c) Me 2 AlCl , MeNHOMe - HCl , CH 2 C1 2 / 0°C (d) piperidine, toluene, heat (e) LiCsCCH 2 N (Li ) C0 2 t-Bu, THF, 0°C ⁇ RT (f ) H 2 NNH 2 , EtOH, RT (g) trifluoroacetic acid, CH 2 C1 2 (h) imidazole-1-carboxylic acid methyl ester, acetonitrile , heat .
• Scheme I above shows a route for the preparation of thiazole compounds of this invention where the 4-position (R 3 ) of the thiazole ring is substituted by an amino group, illustrated here where Ar is phenyl and R 3 is piperidine. It will be apparent to one skilled in the art that the piperidine reactant in step (d) may be replaced by other amines to provide other 4- (amino group-substituted) thiazoles .
• Scheme II above shows a general route to thiazole compounds of formula IA wherein R 3 is an alkyl or aryl group.
• Reagents and conditions (a) Et0 2 CCH(Cl) COCH 2 OCH 3 , EtOH, heat (b) Me 2 AlCl, MeNHOMe-HCl, CH 2 C1 2 , 0°C (c) MeMgBr, THF, 0°C (d) KOtBu, diethyl oxalate, THF, RT (e) H 2 NNH 2 , acetic acid, EtOH (f) BBr 3 , CH 2 C1 2 (g) (R 4 ) 2 NH, THF (h) LiAlH 4 , THF (i) S0C1 2 , CH 2 C1 2 , 0°C (j) NH 3 , dioxane (k) imidazole-1-carboxylic acid methyl ester, acetonitrile, heat (1) EtNH 2 , MeOH, heat.
• Scheme IV above shows a route for the preparation of oxazole compounds IB of this invention where the 4 -position (R 3 ) of the oxazole ring is substituted by an amino group, illustrated here where Ar is phenyl and R 3 is piperidine.
• the formation of the oxazolone ring according to steps (a) and (b) is based on the method reported in Tetrahedron, Vol.29, 1983-1990 (1973) .
• Scheme V above shows a route for the preparation of oxazoles IB where the 4-position of the oxazole ring (R 3 ) is substituted by various groups, for example, an aliphatic group.
• the formation of the oxazole ring according to step (a) is based on the method reported in J. Chem. Soc, Chem. Commun., 29-30 (1995).
• Scheme VI shows a route for the preparation of oxazoles IB where the 4-position of the oxazole ring (R 3 ) is substituted by various groups, for example, an aliphatic group.
• Scheme VI above shows a route for the preparation of IB compounds where the 4-position of the oxazole ring (R 3 ) is substituted by an aryl group, as illustrated here using a phenyl group.
• Reagents and conditions (a) PhNHNH 2 , Et 2 0, RT (b) aq. NaOH, MeOH (c) carbonyldiimidazole, THF (d) MeNHOMe-HCl, diisopropylethylamine, DMF, 80°C (e) LiC ⁇ CCH 2 N (Li) C0 2 tBu, THF, 0°C -> RT (f) H 2 NNH 2 , EtOH, RT (g) CH 2 C1 2 , TFA (h) 1- imidazolecarboxylic acid methyl ester, acetonitrile, heat
• Scheme VII above shows a general route to formula ID pyrazoles. This route is particularly suitable for compounds where the R 3 substituent is aliphatic or aryl.
• Reagents and conditions (a) KOtBu, diethyloxalate, THF, RT (b) (i) H 2 NNHR, -HOAc, EtOH (ii) separate (c) aq. NaOH, MeOH (d) carbonyldiimidazole, THF (e) MeNHOMe-HCl, diisopropylethylamine, DMF, 80°C (f) LiC ⁇ CCH 2 N(Li) C0 2 tBu, THF, 0°C ⁇ RT (g) H 2 NNH 2 , EtOH, RT (h) CH 2 C1 2 , TFA (i) 1- imidazolecarboxylic acid methyl ester, acetonitrile, heat
• Scheme VIII above shows a general route for the preparation of formula IE pyrazoles.
• compositions and methods of this invention will be useful generally for controlling bacterial infections in vivo .
• bacterial organisms that may be controlled by the compositions and methods of this invention include, but are not limited to the following organisms: Streptococcus pneumoniae, Streptococcus pyogenes, Enterococcus fecalis, Enterococcus faecium, Klebsiella pneumoniae , Enterobacter sps . , Proteus sps., Pseudomonas aeruginosa, E. coli , Serratia marcesens, S. aureus, Coag. Neg. Staph.
• compositions and methods will therefore be useful for controlling, treating or reducing the advancement, severity or effects of nosocomial or non- nosocomial infections.
• nosocomial infection uses include, but are not limited to, urinary tract infections, pneumonia, surgical wound infections, bone and joint infections, and bloodstream infections.
• non-nosocomial uses include but are not limited to urinary tract infections, pneumonia, prostatitis, skin and soft tissue infections, bone and joint infections, intra-abdominal infections, meningitis, brain abscess, infectious diarrhea and gastrointestinal infections, surgical prophylaxis, and therapy for febrile neutropenic patients.
• the term "non-nosocomial infections" is also referred to as community acquired infections.
• compositions of this invention comprise a compound of formula I or a pharmaceutically acceptable salt thereof and a pharmaceutically acceptable carrier.
• Such compositions may optionally comprise an additional therapeutic agent.
• agents include, but are not limited to, an antibiotic, an anti-inflammatory agent, a matrix metalloprotease inhibitor, a lipoxygenase inhibitor, a cytokine antagonist, an immunosuppressant, an anti-cancer agent, an anti-viral agent, a cytokine, a growth factor, an immunomodulator, a prostaglandin or an anti-vascular hyperproliferation compound.
• pharmaceutically acceptable carrier refers to a non-toxic carrier that may be administered to a patient, together with a compound of this invention, and which does not destroy the pharmacological activity thereof .
• Pharmaceutically acceptable carriers that may be used in the pharmaceutical compositions of this invention include, but are not limited to, ion exchangers, alumina, aluminum stearate, lecithin, serum proteins, such as human serum albumin, buffer substances such as phosphates, glycine, sorbic acid, potassium sorbate, partial glyceride mixtures of saturated vegetable fatty acids, water, salts or electrolytes, such as protamine sulfate, disodium hydrogen phosphate, potassium hydrogen phosphate, sodium chloride, zinc salts, colloidal silica, magnesium trisilicate, polyvinyl pyrrolidone, cellulose-based substances, polyethylene glycol, sodium carboxymethylcellulose, polyacrylates, ⁇ waxes, polyethylene-polyoxypropylene-block polymers, wool fat and self-emulsifying drug delivery systems (SEDDS) such as ⁇ -tocopherol, polyethyleneglycol 1000 succinate, or other similar polymeric delivery matrices.
• SEDDS self
• compositions comprising only a compound of formula I as the active component
• methods for administering these compositions may additionally comprise the step of administering to the subject an additional agent.
• agents include, but are not limited to, an antibiotic, an anti-inflammatory agent, a matrix metalloprotease inhibitor, a lipoxygenase inhibitor, a cytokine antagonist, an immunosuppressant , an anti-cancer agent, an anti-viral agent, a cytokine, a growth factor, an immunomodulator, a prostaglandin or an anti-vascular hyperproliferation compound.
• pharmaceutically effective amount refers to an amount effective in treating or ameliorating a bacterial infection in a patient.
• prophylactically effective amount refers to an amount effective in preventing or substantially lessening a bacterial infection in a patient.
• the compounds of this invention may be employed in a conventional manner for controlling bacterial infections levels in vivo and for treating diseases or reducing the advancement or severity of effects which are mediated by bacteria. Such methods of treatment, their dosage levels and requirements may be selected by those of ordinary skill in the art from available methods and techniques .
• a compound of this invention may be combined with a pharmaceutically acceptable adjuvant for administration to a patient suffering from a bacterial infection or disease in a pharmaceutically acceptable manner and in an amount effective to lessen the severity of that infection or disease.
• the compounds of this invention may be used in compositions and methods for treating or protecting individuals against bacterial infections or diseases over extended periods of time.
• the compounds may be employed in such compositions either alone or together with other compounds of this invention in a manner consistent with the conventional utilization of enzyme inhibitors in pharmaceutical compositions.
• a compound of this invention may be combined with pharmaceutically acceptable adjuvants conventionally employed in vaccines and administered in prophylactically effective amounts to protect individuals over an extended period of time against bacterial infections or diseases.
• the compounds of formula I may also be co- administered with other antibiotics to increase the effect of therapy or prophylaxis against various bacterial infections.
• the compounds of this invention are administered in combination therapies with other agents, they may be administered sequentially or concurrently to the patient.
• pharmaceutical or prophylactic compositions according to this invention comprise a combination of a compound of formula I and another therapeutic or prophylactic agent .
• compositions of this invention may be administered orally, parenterally, by inhalation spray, topically, via ophthalmic solution or ointment, rectally, nasally, buccally, vaginally or via an implanted reservoir.
• the pharmaceutical compositions of this invention may contain any conventional non-toxic pharmaceutically-acceptable carriers, adjuvants or vehicles.
• the pH of the formulation may be adjusted with pharmaceutically acceptable acids, bases or buffers to enhance the stability of the formulated compound or its delivery form.
• parenteral as used herein includes subcutaneous, intracutaneous, intravenous, intramuscular, intra-articular, intrasynovial , intrasternal, intrathecal, intralesional and intracranial injection or infusion techniques.
• compositions may be in the form of a sterile injectable preparation, for example, as a sterile injectable aqueous or oleaginous suspension.
• This suspension may be formulated according to techniques known in the art using suitable dispersing or wetting agents (such as, for example, Tween 80) and suspending agents.
• the sterile injectable preparation may also be a sterile injectable solution or suspension in a non-toxic parenterally-acceptable diluent or solvent, for example, as a solution in 1, 3-butanediol .
• suitable vehicles and solvents that may be employed are mannitol, water, Ringer's solution- and isotonic sodium chloride solution.
• sterile, fixed oils are conventionally employed as a solvent or suspending medium.
• any bland fixed oil may be employed including synthetic mono- or diglycerides .
• Fatty acids such as oleic acid and its glyceride derivatives are useful in the preparation of injectables, as are natural pharmaceutically-acceptable oils, such as olive oil or castor oil, especially in their polyoxyethylated versions.
• oils such as olive oil or castor oil, especially in their polyoxyethylated versions.
• These oil solutions or suspensions may also contain a long-chain alcohol diluent or dispersant, such as those described in Pharmacopeia Helvetica, or a similar alcohol.
• compositions of this invention may be orally administered in any orally acceptable dosage form including, but not limited to, capsules, tablets, and aqueous suspensions and solutions.
• carriers which are commonly used include lactose and corn starch.
• Lubricating agents such as magnesium stearate, are also typically added.
• useful diluents include lactose and dried corn starch.
• compositions of this invention may also be administered in the form of suppositories for rectal administration.
• These compositions can be prepared by mixing a compound of this invention with a suitable non-irritating excipient which is solid at room temperature but liquid at the rectal temperature and therefore will melt in the rectum to release the active components.
• suitable non-irritating excipient include, but are not limited to, cocoa butter, beeswax and polyethylene glycols.
• Topical administration of the pharmaceutical compositions of this invention is especially useful when the desired treatment involves areas or organs readily accessible by topical application.
• the pharmaceutical composition should be formulated with a suitable ointment containing the active components suspended or dissolved in a carrier.
• Carriers for topical administration of the compounds of this invention include, but are not limited to-, mineral oil, liquid petroleum, white petroleum, propylene glycol, polyoxyethylene polyoxypropylene compound, emulsifying wax and water.
• the pharmaceutical composition can be formulated with a suitable lotion or cream containing the active compound suspended or dissolved in a carrier.
• Suitable carriers include, but are not limited to, mineral oil, sorbitan monostearate, polysorbate 60, cetyl esters wax, cetearyl alcohol, 2-octyldodecanol, benzyl alcohol and water.
• the pharmaceutical compositions of this invention may also be topically applied to the lower intestinal tract by rectal suppository formulation or in a suitable enema formulation. Topically-administered transdermal patches are also included in this invention.
• compositions of this invention may be administered by nasal aerosol or inhalation.
• Such compositions are prepared according to techniques well-known in the art of pharmaceutical formulation and may be prepared as solutions in saline, employing benzyl alcohol or other suitable preservatives, absorption promoters to enhance bioavailability, fluorocarbons, and/or other solubilizing or dispersing agents known in the art .
• Dosage levels of between about 0.01 and about " 100 mg/kg body weight per day, preferably between 0.5 and about 75 mg/kg body weight per day and most preferably between about 1 and 50 mg/kg body weight per day of the active ingredient compound are useful in a monotherapy for the prevention and treatment of bacterial infections caused by bacteria such as Streptococcus pneumoniae, Streptococcus pyogenes , Enterococcus fecalis, Enterococcus faecium, Klebsiella pneumoniae, Enterobacter sps. Proteus sps . Pseudomonas aeruginosa, E. coli ,
• the pharmaceutical compositions of this invention will be administered from about 1 to 5 times per day or alternatively, as a continuous infusion. Such administration can be used as a chronic or acute therapy.
• the amount of active ingredient that may be combined with the carrier materials to produce a single dosage form will vary depending upon the host treated and the particular mode of administration.
• a typical preparation will contain from about 5% to about 95% active compound (w/w) .
• such preparations contain from about 20% to about 80% active compound.
• compositions of this invention comprise a combination of a compound of formula I and one or more additional therapeutic or prophylactic agents
• both the compound and the additional agent should be present at dosage levels of between about 10% to 80% of the dosage normally administered in a monotherapy regime.
• a maintenance dose of a compound, composition or combination of this invention may be administered, if necessary. Subsequently, the dosage, dosage form, or frequency of administration, or both, may need to be modified. in some .cases, patients may, however, require intermittent treatment on a long-term basis upon any recurrence or disease symptoms.
• One embodiment of this invention provides a method for treating or preventing a bacterial infection or disease in a subject comprising the step of administering to the subject any compound, pharmaceutical composition, or combination described herein and a pharmaceutically acceptable carrier.
• the compounds of this invention are also useful as commercial reagents which effectively bind to the gyrase B enzyme.
• the compounds of this invention, and their derivatives may be used to block gyrase B activity in biochemical or cellular assays for bacterial gyrase B or its homologs or may be derivatized to bind to a stable resin as a tethered substrate for affinity chromatography applications.
• the starting material 4-hydroxy-2-phenyl- thiazole-5- ⁇ arboxylic acid ethyl ester was prepared according to the procedure described by Kedersky et al . , J. Med. Chem. , 34, 2158 (1991). To a solution of the starting material (2.3 mmol) in CH 2 C1 2 (10 mL) at 0°C was successively added 2,6-lutidine (2.53 mmol) and trifluoromethanesulfonic anhydride (2.53 mmol). The reaction was stirred from 0°C to room temperature over a two hours period.
• the reaction was recooled to -78°C and 0.25g (0.24 mmol) of ethyl glyoxalate in toluene (50%) was added. The solution was warmed to room temperature and allowed to stir for 0.5 hours. The reaction was quenched with aqueous potassium sodium tartrate tetrahydrate and partitioned with ethyl acetate. The organic phase was twice washed with aqueous potassium sodium tartrate tetrahydrate, once with water, once with brine and dried over sodium sulfate.
• the reaction was stirred at 0°C for 3 hours and quenched with sodium bisulfite in 50% aqueous sodium bicarbonate.
• the mixture was diluted with dichloromethane and allowed to stir for 20 minutes at room temperature.
• the organic phase was washed twice with aqueous sodium bicarbonate, once with water, once with brine, and dried over sodium sulfate.
• the solvent was evaporated under reduced pressure and dissolved in ethyl alcohol (5ml) . 41mg (0.68 mmol) of glacial acetic acid was added followed by the addition of 34mg (0.68 mmol) of hydrazine monohydrate.
• the starting ketoester PhCOCH(Cl) C0 2 Et was prepared according to De Kimpe, et al . , Synthesis, 188 (1986).
• the starting ketoester (-27 mmole, l.O ⁇ eq) and benzamide (3.0 g, 25.0 mmole, leq) were heated neat at 150 °C for 4 hours.
• the mixture was then partitioned between CH 2 C1 2 and saturated NaHC0 3 .
• the organic phase was washed with water and brine, dried over anhydrous sodium sulfate and concentrated in vacuo. Residual benzamide was precipitated out with ether.
• the crude benzylamine was used without further purification.
• a heterogeneous mixture of benzylamine 32 mg, 0.101 mmole, l.Oeq
• ethyl acetate 1.5 ml
• ON NaHC0 3 1.5 ml
• the mixture was partitioned between ethyl acetate and saturated NaHC0 3 .
• the organic phase was washed with water and brine, then dried over anhydrous sodium sulfate and concentrated in vacuo to give a yellow oil.
• the crude diketoester was diluted EtOH (10 mL) , then treated sequentially with acetic acid (2 mL) and hydrazine (1 mL) and stirred at room temperature for 1 hour.
• the crude reaction was concentrated in vacuo to a thick oil, diluted with ethyl acetate, washed sequentially with water and brine, dried over Na 2 S0 4 , filtered, concentrated in vacuo, and flash chromatographed (silica gel, hexanes/ethyl acetate gradient) to give the title compound (1.76 g, 95% yield) as a yellow solid.
• the crude acid was suspended in THF (2 mL) , and carbonyldiimidazole was added (140 mg, 860 ⁇ moles) , and the mixture was stirred overnight at room temperature.
• the resulting acylimidazolide was treated with a preformed mixture of MeON(H) Me -HCI (140 mg, 1.43 mmole) and isopr ⁇ pylethylamine (250 ⁇ L, 1.43 mmoles) in DMF (1 L) and the resulting mixture heated to 90 °C overnight. The reaction was then cooled to room temperature and diluted with ethyl acetate.
• Compounds of this invention may also be tested for antimicrobial activity by susceptibility testing in liquid media.
• Such assays may be performed within the guidelines of the latest NCCLS document governing such practices: "M7-A5 Methods for dilution Antimicrobial Susceptibility Tests for Bacteria that Grow Aerobically; Approved Standard - Fifth Edition (2000)”.
• Other publications such as “Antibiotics in Laboratory Medicine” (Edited by V. Lorian, Publishers Williams and Wilkins, 1996) provide essential practical techniques in laboratory antibiotic testing. Essentially, several discrete bacterial colonies (3 to 7) from a freshly streaked plate are transferred to an appropriate rich broth medium such as MHB, supplemented where appropriate for the more fastidious organisms.
• the freshly picked colonies can be incubated at 37C for about 4 to 8 hrs until the culture equals or exceeds a turbidity of a 0.5 McFarland standard (approximately 1.5 x 10 8 cells per mL) and diluted to give the same CFU per mL as above.
• the inoculum can be prepared using a commercially available mechanical device (the BBL PROMPT System) that involves touching five colonies directly with a wand, containing Crosshatch grooves at its bottom, followed by suspension of the bacteria in an appropriate volume of saline. Dilution to the appropriate inoculum cell density can be made from this cell suspension.
• the broth used for testing consists of MHB supplemented with 50 mg per L of Ca 2+ and 25 mg per L of Mg 2+ .
• Standard dilution panels of control antibiotics are made and stored as in the NCCLS standard M7-A5, the dilution range typically being in the 128 ⁇ g per mL to 0.015 ⁇ g per mL (by 2-fold serial dilution) .
• the test compounds are dissolved and diluted fresh for experimentation on the same day; the same or similar ranges of concentration as above being used.
• the test compounds and controls are dispensed into a multiwell plate and test bacteria added such that the final inoculation is approximately 5 x 10 4 CFU per well and the final volume is 100 ⁇ L.
• the plates are incubated at 35C overnight (16 to 20 hr) and checked by eye for turbidity using a test reading mirror or quantitated with a multiwell plate reader.
• the endpoint minimal inhibitory concentration (MIC) is the lowest concentration of drug at which the microorganism tested does not grow. Such determinations are also compared to the appropriate tables contained in the above two publications to ensure that the range of antibacterial activity is within the acceptable range for this standardized assay. Selected compounds of this invention were found to be active in the above Susceptibility Testing in Liquid Media.
• Method B ATPase Assay
• the ATP hydrolysis activity of DNA gyrase was measured by coupling the production of ADP through pyruvate kinase/lactate dehydrogenase to the oxidation of NADH. This method has been described previously. (Tamura and Gellert, 1990, J. Biol. Chem.265, 21342- 21349) .
• ATPase assays were carried out at 30°C in buffered solutions containing 100 mM TRIS pH 7.6, 1.5 mM MgCl 2 , and 150 mM KCl .
• the coupling system contained (final concentrations) 2.5 mM phosphoenol pyruvate, 200 ⁇ M nicotinamide adenine dinucleotide (NADH) , 1 mM DTT, 30 ug/ml pyruvate kinase, and 10 ug/ml lactate dehydrogenase.
• Table 4 shows the activities of representative compounds tested in an E. coli gyrase A 2 B 2 ATPase assay.

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