US20140329889A1 - Cyclic di-nucleotide induction of type i interferon - Google Patents

Cyclic di-nucleotide induction of type i interferon Download PDF

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US20140329889A1
US20140329889A1 US14/268,967 US201414268967A US2014329889A1 US 20140329889 A1 US20140329889 A1 US 20140329889A1 US 201414268967 A US201414268967 A US 201414268967A US 2014329889 A1 US2014329889 A1 US 2014329889A1
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cyclic
nucleotide
cells
sting
cell
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Russell E. Vance
Ming C. Hammond
Dara Burdette
Ellie J. Diner
Stephen C. Wilson
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University of California
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University of California
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Publication of US20140329889A1 publication Critical patent/US20140329889A1/en
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Priority to US16/279,950 priority patent/US20190292216A1/en
Priority to US17/464,494 priority patent/US11873319B2/en
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
    • C07H21/02—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with ribosyl as saccharide radical
    • 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
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7084—Compounds having two nucleosides or nucleotides, e.g. nicotinamide-adenine dinucleotide, flavine-adenine dinucleotide
    • 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
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A61P35/04—Antineoplastic agents specific for metastasis
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A61P37/04—Immunostimulants

Definitions

  • Interferons are proteins having a variety of biological activities, some of which are antiviral, immunomodulating and antiproliferative. They are relatively small, species-specific, single chain polypeptides, produced by mammalian cells in response to exposure to a variety of inducers such as viruses, polypeptides, mitogens and the like. Interferons protect animal tissues and cells against viral attack and are an important host defense mechanism. In most cases, interferons provide better protection to tissues and cells of the kind from which they have been produced than to other types of tissues and cells, indicating that human-derived interferon could be more efficacious in treating human diseases than interferons from other species.
  • Interferons may be classified as Type-I, Type-II and Type-Ill interferons.
  • Mammalian Type-I interferons include IFN- ⁇ (alpha), IFN- ⁇ (beta), IFN- ⁇ (kappa), IFN- ⁇ (delta), IFN- ⁇ (epsilon), IFN- ⁇ (tau), IFN- ⁇ (omega), and IFN- ⁇ (zeta, also known as limitin).
  • Agents that induce interferon production find use as vaccine adjuvants and in formulations that initiate effector and memory T-cell responses.
  • Effective adjuvants enhance specific immune responses to antigens while minimizing toxic side effects, reducing the dose and dosage of vaccinations, and broadening the immune response.
  • effective adjuvants may be coformulated with antigens derived from intracellular pathogens and cancer cells to activate an effective cellular and humoral immune response to treat intracellular pathogens and reduce tumor burden.
  • the immunomodulatory activity of interferon proteins, and the signaling pathways that regulate interferon production are drawing interest as a target for designing new adjuvants.
  • Interferons have potential in the treatment of a large number of human cancers since these molecules have anti-cancer activity that acts at multiple levels.
  • interferon proteins can directly inhibit the proliferation of human tumor cells.
  • the anti-proliferative activity is also synergistic with a variety of approved chemotherapeutic agents such as cisplatin, 5FU and paclitaxel.
  • the immunomodulatory activity of interferon proteins can lead to the induction of an anti-tumor immune response. This response includes activation of NK cells, stimulation of macrophage activity and induction of MHC class I surface expression, leading to the induction of anti-tumor cytotoxic T lymphocyte activity.
  • interferons play a role in cross-presentation of antigens in the immune system.
  • IFN- ⁇ protein may have anti-angiogenic activity.
  • Angiogenesis new blood vessel formation, is critical for the growth of solid tumors.
  • IFN- ⁇ may inhibit angiogenesis by inhibiting the expression of pro-angiogenic factors such as bFGF and VEGF.
  • interferon proteins may inhibit tumor invasiveness by modulating the expression of enzymes, such as collagenase and elastase, which are important in tissue remodeling.
  • Interferons also appear to have antiviral activities that are based on two different mechanisms. For instance, type I interferon proteins ( ⁇ and ⁇ ) can directly inhibit the replication of human hepatitis B virus (“HBV”) and hepatitis C virus (“HCV”), but can also stimulate an immune response that attacks cells infected with these viruses.
  • HBV human hepatitis B virus
  • HCV hepatitis C virus
  • compositions are provided for increasing the production of a type I interferon (IFN) in a cell. Aspects of the methods include increasing the level of a 2′-5′ phosphodiester linkage comprising cyclic-di-nucleotide in a cell in a manner sufficient to increase production of the type I interferon (IFN) by the cell. Also provided are compositions and kits for practicing the subject methods.
  • a method for increasing the production of a type I interferon (IFN) in a cell by increasing the level of a 2′-5′ phosphodiester linkage containing cyclic-di-nucleotide in the cell in a manner sufficient to increase production of the type I interferon (IFN) by the cell.
  • IFN type I interferon
  • the method includes the step of contacting the cell with the cyclic-di-nucleotide.
  • the cyclic-di-nucleotide has two 2′-5′ phosphodiester linkages. In other embodiments, the cyclic-di-nucleotide has a 2′-5′ phosphodiester linkage and a 3′-5′ phosphodiester linkage.
  • the cyclic-di-nucleotide comprises a guanosine nucleoside. In some embodiments, the cyclic-di-nucleotide contains two guanosine nucleosides. In certain embodiments, the cyclic-di-nucleotide comprises an adenosine nucleoside. In some embodiments, the cyclic-di-nucleotide contains two adenosine nucleosides. In other embodiments, the cyclic-di-nucleotide comprises an adenosine nucleoside and a guanosine nucleoside.
  • the cyclic-di-nucleotide has the following formula:
  • the cyclic-di-nucleotide has the following formula:
  • the level of the cyclic-di-nucleotide is increased by increasing the activity of a cGAMP synthase (cGAS) in the cell.
  • cGAS cGAMP synthase
  • the activity of the cGAS is increased by enhancing expression of a nucleic acid encoding cGAS.
  • the activity of the cGAS is increased by introducing a nucleic acid encoding the cGAS into the cell.
  • the method is for increasing the production of interferon (IFN) alpha.
  • IFN interferon alpha.
  • the IFN is interferon beta.
  • the method is for increasing the production of a type I interferon (IFN) in a mammalian cell.
  • mammalian cell is a human cell.
  • the cell is in vitro. In other embodiments, the cell is in vivo.
  • a method for increasing the production of a type I interferon (IFN) in a subject includes the step of administering to the subject an amount of a 2′-5′ phosphodiester linkage comprising cyclic-di-nucleotide active agent effective to increase the production of the type I interferon in the subject.
  • the active agent can include, but is not limited to, any of the 2′-5′ phosphodiester linkage containing cyclic-di-nucleotides described herein.
  • the cyclic-di-nucleotide has two 2′-5′ phosphodiester linkages.
  • the cyclic-di-nucleotide has a 2′-5′ phosphodiester linkage and a 3′-5′ phosphodiester linkage.
  • the cyclic-di-nucleotide contains a guanosine nucleoside. In certain embodiments, the cyclic-di-nucleotide contains two guanosine nucleosides. In some embodiments, the cyclic-di-nucleotide contains an adenosine nucleoside. In specific embodiments, the cyclic-di-nucleotide contains two adenosine nucleosides. In other embodiments, the cyclic-di-nucleotide contains an adenosine and a guanosine nucleoside. In some embodiments, the cyclic-di-nucleotide has the following formula:
  • the cyclic-di-nucleotide has the following formula:
  • the 2′-5′ phosphodiester linkage comprising cyclic-di-nucleotide active agent includes an agent that increases cellular activity of a cGAMP synthase (cGAS).
  • the agent comprises a nucleic acid encoding the cGAS.
  • the method is for increasing the production of interferon (IFN) alpha in a subject. In other embodiments, the method is for increasing the production of interferon beta in a subject.
  • IFN interferon
  • the subject has a viral infection. In certain embodiments, the subject has a bacterial infection. In other embodiments, the subject has a neoplastic disease. In certain embodiments, the subject is mammal. In some embodiments, the mammal is a human.
  • a method for increasing a stimulator of interferon genes (STING) mediated response in a subject includes the step of administering to the subject an amount of a STING active agent effective to increase a STING mediated response in the subject.
  • the STING mediated response is non-responsive to a cyclic-di-nucleotide having two 3′-5′ phosphodiester bonds.
  • the STING active agent can include, but is not limited to, any of the 2′-5′ phosphodiester linkage containing cyclic-di-nucleotides described herein.
  • the cyclic-di-nucleotide has two 2′-5′ phosphodiester linkages.
  • the cyclic-di-nucleotide has a 2′-5′ phosphodiester linkage and a 3′-5′ phosphodiester linkage.
  • the cyclic-di-nucleotide contains a guanosine nucleoside. In certain embodiments, the cyclic-di-nucleotide contains two guanosine nucleosides. In some embodiments, the cyclic-di-nucleotide contains an adenosine nucleoside. In specific embodiments, the cyclic-di-nucleotide contains two adenosine nucleosides. In other embodiments, the cyclic-di-nucleotide contains an adenosine and a guanosine nucleoside. In some embodiments, the cyclic-di-nucleotide has the following formula:
  • the cyclic-di-nucleotide has the following formula:
  • the STING active agent includes an agent that increases cellular activity of a cGAMP synthase (cGAS).
  • the agent comprises a nucleic acid encoding the cGAS.
  • the STING active agent includes an agent that increases cellular activity of STING.
  • the agent comprises a nucleic acid encoding the STING.
  • the subject has a viral infection. In certain embodiments, the subject has a bacterial infection. In other embodiments, the subject has a neoplastic disease. In certain embodiments, the subject is mammal. In some embodiments, the mammal is a human.
  • a cyclic-di-nucleotide comprising a 2′-5′ phosphodiester linkage.
  • Such cyclic-di-nucleotides are useful, for example, in practicing the subject methods, including, but not limited to, methods for increasing the production of a type I interferon in a cell or a subject.
  • the cyclic-di-nucleotide has two 2′-5′ phosphodiester linkages. In other embodiments, the cyclic-di-nucleotide has a 2′-5′ phosphodiester linkage and a 3′-5′ phosphodiester linkage.
  • the cyclic-di-nucleotide contains a guanosine nucleoside. In some embodiments, the cyclic-di-nucleotide contains two guanosine nucleosides. In certain embodiments, the cyclic-di-nucleotide contains an adenosine nucleoside. In some embodiments, the cyclic-di-nucleotide contains two adenosine nucleosides. In other embodiments, the cyclic-di-nucleotide contains an adenosine and a guanosine nucleoside.
  • the cyclic-di-nucleotide has the following formula:
  • the cyclic-di-nucleotide has the following formula:
  • composition containing a 2′-5′ phosphodiester linkage containing cyclic-di-nucleotiden and a pharmaceutically acceptable carrier.
  • the cyclic-di-nucleotide has two 2′-5′ phosphodiester linkages. In other embodiments, the cyclic-di-nucleotide has a 2′-5′ phosphodiester linkage and a 3′-5′ phosphodiester linkage. In certain embodiments of the composition, the cyclic-di-nucleotide contains a guanosine nucleoside. In some embodiments, the cyclic-di-nucleotide contains two guanosine nucleosides. In certain embodiments, the cyclic-di-nucleotide contains an adenosine nucleoside.
  • the cyclic-di-nucleotide contains two adenosine nucleosides. In other embodiments, the cyclic-di-nucleotide contains an adenosine and a guanosine nucleoside.
  • the cyclic-di-nucleotide has the following formula:
  • the cyclic-di-nucleotide has the following formula:
  • FIGS. 1A-1F show the variable responsiveness of human STING variants to cyclic-di-nucleotides maps to arginine 232.
  • THP-1 cells were transduced with vectors encoding an shRNA targeting STING or a control shRNA. Cells were then stimulated with cyclic-di-GMP (cdG), dsDNA, cyclic-di-AMP (cdA), poly-inosine:cytosine (pI:C), or Sendai Virus, and induction of human interferon- ⁇ mRNA was assessed by quantitative reverse transcriptase PCR.
  • B Western blotting confirmed that knockdown of STING was effective.
  • HEK293T cells were transfected with the indicated amounts of various mouse (m) or human (h) STING expression plasmid and then stimulated 6 h later by transfection with synthetic cdG (5 ⁇ M). GT denotes the null 1199N allele of Sting from Goldenticket (Gt) mice. STING activation was assessed by use of a co-transfected IFN-luciferase reporter construct.
  • (D) Gt (STING-null) macrophages were transduced with retroviral vectors encoding the indicated STING alleles and were then stimulated 48 h later by transfection with cdG (5 ⁇ M) or dsDNA 70-mer oligonucleotide (0.5 ⁇ g/mL). IFN induction was measured by qRT-PCR. ND, not detected.
  • FIG. 2 shows the sequence alignment of hSTING variants.
  • hSTING was cloned from THP-1 cells compared to the reference STING allele (NCBI NP — 938023.1).
  • FIG. 3 shows that R232 of human STING is required for responsiveness to c-di-GMP, but not for binding of c-di-GMP.
  • A 293T cells were transfected with the indicated alleles of mouse (m)STING or human (h)STING and were then stimulated with c-di-GMP (cdG). STING activity was detected by the induction of a co-transfected IFN-luciferase reporter construct and expressed as fold-induction over luciferase activity of unstimulated cells.
  • Lysates of transfected 293T cells were UV crosslinked in the presence of ⁇ 32P-c-di-GMP, resolved by SDS-PAGE, and then analyzed by autoradiography. Lysates were also western blotted for STING and ACTIN as expression controls in parallel.
  • FIG. 4 shows that G230A and H232R are both required for optimal responsiveness to c-di-nucleotides but are not required for binding to c-di-nucleotides.
  • A, B 293T cells were transfected with the indicated alleles of mouse (m)STING or human (h)STING and were then stimulated with c-di-GMP (cdG). STING activity was detected by the induction of a cotransfected IFN-luciferase reporter construct.
  • FIG. 5 shows that STING variants are responsive to cGAS.
  • A HEK293T cells were transfected with the indicated STING alleles and with human and mouse cGAS (wt and GS>AA mutants) as indicated. STING activation was assessed by a co-transfected IFN-luciferase reporter construct.
  • B HEK293T cells were transfected with the indicated STING alleles and with a mammalian expression vector encoding a cGAMP synthase (DncV) from V. cholerae . STING activation was assessed as in A.
  • DncV mammalian expression vector encoding a cGAMP synthase
  • FIG. 6 shows that cGAS produces a non-canonical cyclic dinucleotide containing a 2′-5′ phosphodiester linkage.
  • WspR, DncV and cGAS were mixed with ⁇ 32 P-GTP or ⁇ 32 P-ATP and the indicated unlabeled nucleotides. Reactions were mixed with TLC running buffer and nucleic acid species were resolved on a PEI-Cellulose TLC plate.
  • FIGS. 7A-7D provide additional NMR analysis of the cGAS product. All data acquisition was performed in D2O and at 50° C.
  • A, B Multiplicity-edited 1H-13C HSQC experiment in a 900 MHz field. Positive phased signals corresponding to methine and methyl protons are shown in green, negative phased signals corresponding to methylene protons are shown in blue.
  • C 1 H- 1 H COSY experiment in a 600 MHz field.
  • D 1 H- 1 H NOESY experiment in a 900 MHz field.
  • compositions are provided for increasing the production of a type I interferon (IFN) in a cell. Aspects of the methods include increasing the level of a 2′-5′ phosphodiester linkage comprising cyclic-di-nucleotide in a cell in a manner sufficient to increase production of the type I interferon (IFN) by the cell. Also provided are compositions and kits for practicing embodiments of the subject methods.
  • methods of increasing the production of a type I interferon (IFN) in a cell e.g., in vitro or in vivo are provided.
  • IFN type I interferon
  • the subject methods increase type-I interferon production in a cell, as compared to a control.
  • the magnitude of the increase may vary, and in some instances is 2-fold or greater, such as 5-fold or greater, including 10-fold or greater, as compared to a suitable control.
  • the methods are methods of increasing type-I interferon production in a cell, e.g., by a magnitude of 2-fold or greater, such as 5-fold or greater, including 10-fold or greater, as compared to a suitable control.
  • Interferon production can be measured using any suitable method, including, but not limited to, vesicular stomatitis virus (VSV) challenge bioassay, enzyme-linked immunosorbent assay (ELISA) replicon based bioassays or by using a reporter gene (e.g., luciferase) cloned under regulation of a Type I interferon signaling pathway.
  • VSV vesicular stomatitis virus
  • ELISA enzyme-linked immunosorbent assay
  • the methods may be used to increase the production of any type I interferon including, but not limited to: IFN- ⁇ (alpha), IFN- ⁇ (beta), IFN- ⁇ (kappa), IFN- ⁇ (delta), IFN- ⁇ (epsilon), IFN- ⁇ (tau), IFN- ⁇ (omega), and IFN- ⁇ (zeta, also known as limitin).
  • IFN- ⁇ alpha
  • IFN- ⁇ beta
  • IFN- ⁇ kappa
  • IFN- ⁇ delta
  • IFN- ⁇ epsilon
  • IFN- ⁇ tau
  • IFN- ⁇ miga
  • IFN- ⁇ zeta, also known as limitin
  • the method is for increasing the production of IFN- ⁇ .
  • aspects of the methods include increasing the level of a 2′-5′ phosphodiester linkage comprising cyclic-di-nucleotide in a cell in a manner sufficient to increase production of the type I interferon by the cell.
  • increasing the level of a 2′-5′ phosphodiester linkage comprising cyclic-di-nucleotide is meant that the subject methods increase the amount of a 2′-5′ phosphodiester linkage comprising cyclic-di-nucleotide as compared to a control.
  • 2′-5′ phosphodiester linkage comprising cyclic-di-nucleotides can increase the levels of type I interferon production.
  • the magnitude of the increase may vary, and in some instances is 2-fold or greater, such as 5-fold or greater, including 10-fold or greater, 15-fold greater, 20-fold greater, 25-fold greater, 30-fold greater, 35-fold greater, 40-fold greater, 45-fold greater, 50-fold greater, or 100 fold greater, as compared to a suitable control.
  • the method includes providing a target cell with a cyclic-di-nucleotide active agent that increases 2′-5′ phosphodiester linkage comprising cyclic-di-nucleotide levels in the target cell.
  • Cyclic-di-nucleotide active agents may vary, and include, but are not limited to: small molecules, nucleic acid, protein, and peptide agents.
  • the cyclic-di-nucleotide active agent increases IFN- ⁇ (alpha), IFN- ⁇ (beta), IFN- ⁇ (kappa), IFN- ⁇ (delta), IFN- ⁇ (epsilon), IFN- ⁇ (tau), IFN- ⁇ (omega), and/or IFN- ⁇ (zeta, also known as limitin) in a cell or subject as compared to a control that has not been contacted with the cyclic-di-nucleotide active agent.
  • the increase is from 1.5-fold increase to 50-fold increase or more, including 2-fold increase to 45-fold increase, 5-fold increase to 40-fold increase, 10-fold increase to 35-fold increase, 15-fold increase to 30-fold increase, 20-fold increase to 30-fold increase, and the like.
  • the cyclic-di-nucleotide active agent is a 2′-5′ phosphodiester linkage containing cyclic-di-nucleotide or a functional analogue thereof.
  • 2′-5′ phosphodiester linkage containing cyclic-di-nucleotide include, but are not limited to, those 2′-5′ phosphodiester linkage containing cyclic-di-nucleotides described herein.
  • cyclic-di-nucleotide refers to a compound containing two nucleosides (i.e., a first and second nucleoside), wherein the 2′ or 3′ carbon of each nucleoside is linked to the 5′ carbon of the other nucleoside by a phosphodiester bond. Therefore, a 2′-5′ phosphodiester linkage containing cyclic-di-nucleotide refers to a cyclic-di-nucleotide, wherein the 2′ carbon of at least the first or second nucleosides is linked to the 5′ carbon of the other nucleoside. 2′-5′ phosphodiester linkage containing cyclic-di-nucleotide are discussed in greater detail below.
  • Functional analogues of 2′-5′ phosphodiester linkage containing cyclic-di-nucleotides are those compounds that exhibit similar functional activity (e.g., increasing the production of a type I IFN) and may have a similar structure to a 2′-5′ phosphodiester linkage containing cyclic-di-nucleotide.
  • the functional analogue is a small molecule agent.
  • Naturally occurring or synthetic small molecule compounds of interest include numerous chemical classes, such organic molecules, including small organic compounds having a molecular weight of more than 50 and less than about 2,500 daltons.
  • Candidate agents comprise functional groups necessary for structural interaction with proteins, particularly hydrogen bonding, and typically include at least an amine, carbonyl, hydroxyl or carboxyl group, preferably at least two of the functional chemical groups.
  • the candidate agents may comprise cyclical carbon or heterocyclic structures and/or aromatic or polyaromatic structures substituted with one or more of the above functional groups.
  • Candidate agents are also found among biomolecules including peptides, saccharides, fatty acids, steroids, purines, pyrimidines, derivatives, structural analogs or combinations thereof. Such molecules may be identified, among other ways, by employing suitable screening protocols.
  • the cyclic-di-nucleotide active agent is an agent that increases the cellular activity of a cyclic GMP-AMP synthase (cGAS).
  • cGAS cyclic GMP-AMP synthase
  • increasing the levels cGMP synthase (cGAS) can increase the production and/or activity of cyclic-di-nucleotide in a cell.
  • a target cell may be contacted with an agent that increases cGMP synthase production and/or cellular activity in a manner sufficient to increase the production of Type I interferon in the cell.
  • the cyclic-di-nucleotide active agent is a nucleic acid encoding a cGAS.
  • Nucleic acids encoding various cGAS enzymes include, but are not limited to, those described in: Sun et al. Science 339(6121):786-91 and those deposited in GENBANK and assigned deposit numbers: NM — 138441.2 and NP — 612450.2 (human); NM — 173386.4 and NP — 775562.2 ( mus musculus ).
  • nucleic acid encoding cGAS has the following sequence:
  • the nucleic acid encoding cGAS is a nucleic acid with 40% to 99%, 45% to 99%, 50% to 99%, 55% to 99%, 60% to 99%, 65% to 99%, 70% to 99%, 75% to 99%, 80% to 99%, 85% to 99%, 90% to 99% or, 95% to 99% sequence identity with a wild type cGAS nucleic acid sequence.
  • the nucleic acid encoding cGAS is a nucleic acid with 40% to 50%, 50% to 60%, 60% to 70%, 70% to 80%, 80% to 90%, or 90 to 99% sequence identity with a wild type cGAS nucleic acid sequence.
  • the nucleic acid encoding cGAS is a nucleic acid with 40% or more, 45% or more, 50% or more, 55% or more, 60% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more or 99% or more sequence identity with a wild type cGAS nucleic acid sequence.
  • the cyclic-di-nucleotide active agent is a vector containing a nucleic acid encoding cGAS.
  • Vectors may be provided directly to the subject cells.
  • the cells are contacted with vectors having the nucleic acid encoding the cyclic-di-nucleotide active agent(s) (e.g., a nucleic acid encoding cGAS) such that the vectors are taken up by the cells.
  • Methods for contacting cells with nucleic acid vectors that are plasmids such as electroporation, calcium chloride transfection, and lipofection, are well known in the art.
  • the cells are contacted with viral particles comprising the nucleic acid encoding the cyclic-di-nucleotide agent(s).
  • Retroviruses for example, lentiviruses, are particularly suitable to the method of the invention. Commonly used retroviral vectors are “defective”, i.e., unable to produce viral proteins required for productive infection. Rather, replication of the vector requires growth in a packaging cell line. To generate viral particles comprising nucleic acids of interest, the retroviral nucleic acids comprising the nucleic acid are packaged into viral capsids by a packaging cell line.
  • Different packaging cell lines provide a different envelope protein (ecotropic, amphotropic or xenotropic) to be incorporated into the capsid, this envelope protein determining the specificity of the viral particle for the cells (ecotropic for murine and rat; amphotropic for most mammalian cell types including human, dog and mouse; and xenotropic for most mammalian cell types except murine cells).
  • the appropriate packaging cell line may be used to ensure that the cells are targeted by the packaged viral particles.
  • Vectors used for providing the nucleic acids encoding the cyclic-di-nucleotide activity active agent(s) to the subject cells may include suitable promoters for driving the expression, that is, transcriptional activation, of the nucleic acid of interest.
  • the nucleic acid of interest will be operably linked to a promoter.
  • This may include ubiquitously acting promoters, for example, the CMV- ⁇ -actin promoter, or inducible promoters, such as promoters that are active in particular cell populations or that respond to the presence of drugs such as tetracycline.
  • transcriptional activation it is intended that transcription will be increased above basal levels in the target cell by 10 fold or more, by 100 fold or more, by 1000 fold or more.
  • vectors used for providing cyclic-di-nucleotide active agent(s) to the subject cells may include nucleic acid sequences that encode for selectable markers in the target cells, so as to identify cells that have taken up the cyclic-di-nucleotide activity active agent(s).
  • Cyclic-di-nucleotide active agent(s) may also be provided to cells as polypeptides.
  • the cyclic-di-nucleotide active agent is a cGAS polypeptide.
  • Amino acid sequences of various cGAS enzymes include, but are not limited to, those described in: Sun et al. Science 339(6121):786-91 and those deposited in GENBANK and assigned deposit numbers: NM — 138441.2 and NP — 612450.2 (human); NM — 173386.4 and NP — 775562.2 ( mus musculus ).
  • the cGAS polypeptide has the following sequence:
  • the cGAS polypeptide is a polypeptide that has 40% to 99%, 45% to 99%, 50% to 99%, 55% to 99%, 60% to 99%, 65% to 99%, 70% to 99%, 75% to 99%, 80% to 99%, 85% to 99%, 90% to 99% or, 95% to 99% sequence identity with a wild type cGAS amino acid sequence.
  • the cGAS polypeptide is a polypeptide that has 40% to 50%, 50% to 60%, 60% to 70%, 70% to 80%, 80% to 90%, or 90 to 99% sequence identity with a wild type cGAS amino acid sequence.
  • the cGAS polypeptide is a polypeptide that has 40% or more, 45% or more, 50% or more, 55% or more, 60% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more or 99% or more sequence identity with a wild type cGAS amino acid sequence.
  • Such polypeptides may optionally be fused to a polypeptide domain that increases solubility of the product.
  • the domain may be linked to the polypeptide through a defined protease cleavage site, e.g., a TEV sequence, which is cleaved by TEV protease.
  • the linker may also include one or more flexible sequences, e.g., from 1 to 10 glycine residues.
  • the cleavage of the fusion protein is performed in a buffer that maintains solubility of the product, e.g., in the presence of from 0.5 to 2 M urea, in the presence of polypeptides and/or polynucleotides that increase solubility, and the like.
  • Domains of interest include endosomolytic domains, e.g., influenza HA domain; and other polypeptides that aid in production, e.g., IF2 domain, GST domain, GRPE domain, and the like.
  • the polypeptide may be formulated for improved stability.
  • the peptides may be PEGylated, where the polyethyleneoxy group provides for enhanced lifetime in the blood stream.
  • the cyclic-di-nucleotide active agent(s) may be fused to a polypeptide permeant domain to promote uptake by the cell.
  • a permeant domains are known in the art and may be used in the non-integrating polypeptides of the present invention, including peptides, peptidomimetics, and non-peptide carriers.
  • a permeant peptide may be derived from the third alpha helix of Drosophila melanogaster transcription factor Antennapaedia, referred to as penetratin, which comprises the amino acid sequence RQIKIWFQNRRMKWKK (SEQ ID NO:03).
  • the permeant peptide comprises the HIV-1 tat basic region amino acid sequence, which may include, for example, amino acids 49-57 of naturally-occurring tat protein.
  • Other permeant domains include poly-arginine motifs, for example, the region of amino acids 34-56 of HIV-1 rev protein, nona-arginine, octa-arginine, and the like.
  • the nona-arginine (R9) sequence is one of the more efficient PTDs that have been characterized (Wender et al. 2000; Uemura et al. 2002).
  • the site at which the fusion is made may be selected in order to optimize the biological activity, secretion or binding characteristics of the polypeptide. The optimal site will be determined by routine experimentation.
  • an effective amount of the active agent i.e., a cyclic-di-nucleotide active agent (such as described above) is provided in the target cell or cells.
  • effective amount or “efficacious amount” means the amount of the active agent that, when contacted with the cell, e.g., by being introduced into the cell in vitro, by being administered to a subject, etc., is sufficient to result in increased levels of a cyclic-di-nucleotide in the cell.
  • the “effective amount” will vary depending on cell and/or the organism and/or compound and or the nature of the desired outcome and/or the disease and its severity and the age, weight, etc., of the subject to be treated.
  • the effective amount of the active agent is provided in the cell by contacting the cell with the active agent.
  • Contact of the cell with the active agent may occur using any convenient protocol.
  • the protocol may provide for in vitro or in vivo contact of the active agent with the target cell, depending on the location of the target cell.
  • the target cell is an isolated cell, e.g., a cell in vitro (i.e., in culture), or a cell ex vivo (“ex vivo” being cells or organs are modified outside of the body, where such cells or organs are typically returned to a living body)
  • the active agent may be introduced directly into the cell under cell culture conditions permissive of viability of the target cell.
  • Such techniques include, but are not necessarily limited to: viral infection, transfection, conjugation, protoplast fusion, electroporation, particle gun technology, calcium phosphate precipitation, direct microinjection, viral vector delivery, and the like.
  • the choice of method is generally dependent on the type of cell being contacted and the nature of the active agent, and the circumstances under which the transformation is taking place (e.g., in vitro, ex vivo, or in vivo).
  • a general discussion of these methods can be found in Ausubel, et al, Short Protocols in Molecular Biology, 3rd ed., Wiley & Sons, 1995.
  • the active agent may be administered to the organism or subject in a manner such that the agent is able to contact the target cell(s), e.g., via an in vivo protocol.
  • in vivo it is meant in the target construct is administered to a living body of an animal.
  • the cyclic-di-nucleotide active agent is employed to modulate c-di-AMP activity in mitotic or post-mitotic cells in vitro or ex vivo, i.e., to produce modified cells that can be reintroduced into an individual.
  • Mitotic and post-mitotic cells of interest in these embodiments include any eukaryotic cell, e.g., pluripotent stem cells, for example, ES cells, iPS cells, and embryonic germ cells; somatic cells, for example, hematopoietic cells, fibroblasts, neurons, muscle cells, bone cells, vascular endothelial cells, gut cells, and the like, and their lineage-restricted progenitors and precursors; and neoplastic, or cancer, cells, i.e., cells demonstrating one or more properties associated with cancer cells, e.g., hyperproliferation, contact inhibition, the ability to invade other tissue, etc.
  • the eukaryotic cells are cancer cells.
  • the eukaryotic cells are hematopoietic cells, e.g., macrophages, NK cells, etc.
  • Cells may be from any mammalian species, e.g., murine, rodent, canine, feline, equine, bovine, ovine, primate, human, etc.
  • Cells may be from established cell lines or they may be primary cells, where “primary cells”, “primary cell lines”, and “primary cultures” are used interchangeably herein to refer to cells and cells cultures that have been derived from a subject and allowed to grow in vitro for a limited number of passages, i.e., splittings, of the culture.
  • primary cultures are cultures that may have been passaged 0 times, 1 time, 2 times, 4 times, 5 times, 10 times, or 15 times, but not enough times go through the crisis stage.
  • the primary cell lines of the present invention are maintained for fewer than 10 passages in vitro.
  • the cells may be harvested from an individual by any convenient method.
  • blood cells e.g., leukocytes, e.g., macrophages
  • leukocytes e.g., macrophages
  • cells from tissues such as skin, muscle, bone marrow, spleen, liver, pancreas, lung, intestine, stomach, etc.
  • An appropriate solution may be used for dispersion or suspension of the harvested cells.
  • Such solution will generally be a balanced salt solution, e.g., normal saline, PBS, Hank's balanced salt solution, etc., conveniently supplemented with fetal calf serum or other naturally occurring factors, in conjunction with an acceptable buffer at low concentration, generally from 5-25 mM.
  • Convenient buffers include HEPES, phosphate buffers, lactate buffers, etc.
  • the cells may be used immediately, or they may be stored, frozen, for long periods of time, being thawed and capable of being reused.
  • the cells may be frozen in 10% DMSO, 50% serum, 40% buffered medium, or some other such solution as is commonly used in the art to preserve cells at such freezing temperatures, and thawed in a manner as commonly known in the art for thawing frozen cultured cells.
  • the cyclic-di-nucleotide active agent(s) may be produced by eukaryotic cells or by prokaryotic cells, it may be further processed by unfolding, e.g., heat denaturation, DTT reduction, etc. and may be further refolded, using methods known in the art.
  • Modifications of interest that do not alter primary sequence include chemical derivatization of polypeptides, e.g., acylation, acetylation, carboxylation, amidation, etc. Also included are modifications of glycosylation, e.g., those made by modifying the glycosylation patterns of a polypeptide during its synthesis and processing or in further processing steps; e.g., by exposing the polypeptide to enzymes which affect glycosylation, such as mammalian glycosylating or deglycosylating enzymes. Also embraced are sequences that have phosphorylated amino acid residues, e.g., phosphotyrosine, phosphoserine, or phosphothreonine.
  • cyclic-di-nucleotide active agent polypeptides e.g., cGAS polypeptides
  • cGAS polypeptides cyclic-di-nucleotide active agent polypeptides
  • Analogs of such polypeptides include those containing residues other than naturally occurring L-amino acids, e.g., D-amino acids or non-naturally occurring synthetic amino acids. D-amino acids may be substituted for some or all of the amino acid residues.
  • the cyclic-di-nucleotide active agent (s) may be prepared by in vitro synthesis, using any suitable method.
  • Various commercial synthetic apparatuses are available, for example, automated synthesizers by Applied Biosystems, Inc., Beckman, etc. By using synthesizers, naturally occurring amino acids may be substituted with unnatural amino acids. The particular sequence and the manner of preparation will be determined by convenience, economics, purity required, and the like.
  • cysteines can be used to make thioethers, histidines for linking to a metal ion complex, carboxyl groups for forming amides or esters, amino groups for forming amides, and the like.
  • the cyclic-di-nucleotide active agent(s) may also be isolated and purified in accordance with conventional methods of recombinant synthesis.
  • a lysate may be prepared of the expression host and the lysate purified using HPLC, exclusion chromatography, gel electrophoresis, affinity chromatography, or other purification technique.
  • the compositions which are used will include 20% or more by weight of the desired product, such as 75% or more by weight of the desired product, including 95% or more by weight of the desired product, and for therapeutic purposes, may be 99.5% or more by weight, in relation to contaminants related to the method of preparation of the product and its purification (where the percentages may be based upon total protein).
  • the cyclic-di-nucleotide active agent(s) be they small molecules (e.g., 2′-5′ phosphodiester linkage containing cyclic-di-nucleotides) polypeptides or nucleic acids that encode cyclic-di-nucleotide active agent polypeptides (e.g., cGAS)—may be provided to the cells for a sufficient period of time, e.g., from 30 minutes to 24 hours, e.g., 1 hour, 1.5 hours, 2 hours, 2.5 hours, 3 hours, 3.5 hours 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 12 hours, 16 hours, 18 hours, 20 hours, or any other period from 30 minutes to 24 hours, which may be repeated with a frequency of every day to every 4 days, e.g., every 1.5 days, every 2 days, every 3 days, or any other frequency from about every day to about every four
  • the agent(s) may be provided to the subject cells one or more times, e.g., one time, twice, three times, or more than three times, and the cells allowed to incubate with the agent(s) for some amount of time following each contacting event e.g., 16-24 hours, after which time the media is replaced with fresh media and the cells are cultured further.
  • two or more, three or more, four or more, five or more, six or more, seven or more, eight or more, nine or more, or ten or more different cyclic-di-nucleotide active agents are provided to a cell in a manner sufficient to increase production of a type I interferon by the cell.
  • the active agents include two or more different 2′-5′ phosphodiester linkage comprising cyclic-di-nucleotides.
  • the active agents include a 2′-5′ phosphodiester linkage containing cyclic-di-nucleotide and a nucleic acid encoding cGAS or a cGAS polypeptide.
  • the cyclic-di-nucleotide active agent(s) may be provided simultaneously, e.g., as two cyclic-di-nucleotides delivered simultaneously or a cyclic-di-nucleotide and a vector containing a nucleic acid encoding cGAS delivered simultaneously. Alternatively, they may be provided consecutively, e.g., the first cyclic-di-nucleotide active agent being provided first, followed by the cyclic-di-nucleotide active agent, etc. or vice versa.
  • An effective amount of cyclic-di-nucleotide active agent(s) are provided to the cells to result in a change in cyclic-di-nucleotide levels.
  • An effective amount of cyclic-di-nucleotide active agent is the amount to result in a 2-fold increase or more in the amount of cyclic-di-nucleotide production observed relative to a negative control, e.g., a cell contacted with an empty vector or irrelevant polypeptide.
  • an effective amount or dose of a cyclic-di-nucleotide active agent will result in a 2-fold increase, a 3-fold increase, a 4-fold increase or more in the amount of cyclic-di-nucleotide observed, in some instances a 5-fold increase, a 6-fold increase or more, sometimes a 7-fold or 8-fold increase or more in the amount of activity observed, e.g., an increase of 10-fold, 50-fold, or 100-fold or more, in some instances, an increase of 200-fold, 500-fold, 700-fold, or 1000-fold or more, in the amount of activity observed.
  • the amount of activity may be measured by any suitable method.
  • the amount of interferon produced by the cell may be assessed after contact with the cyclic-di-nucleotide active agent(s), e.g., 2 hours, 4 hours, 8 hours, 12 hours, 24 hours, 36 hours, 48 hours, 72 hours or more after contact with the cyclic-di-nucleotide active agent(s).
  • cyclic-di-nucleotide active agent(s) may occur in any culture media and under any culture conditions that promote the survival of the cells.
  • cells may be suspended in any appropriate nutrient medium that is convenient, such as Iscove's modified DMEM or RPMI 1640, supplemented with fetal calf serum or heat inactivated goat serum (about 5-10%), L-glutamine, a thiol, particularly 2-mercaptoethanol, and antibiotics, e.g., penicillin and streptomycin.
  • the culture may contain growth factors to which the cells are responsive. Growth factors, as defined herein, are molecules capable of promoting survival, growth and/or differentiation of cells, either in culture or in the intact tissue, through specific effects on a transmembrane receptor. Growth factors include polypeptides and non-polypeptide factors.
  • a cell may be modified ex vivo to have an increase in cyclic-di-nucleotide levels.
  • it may be desirous to select for the modified cell, e.g., to create an enriched population of modified cells.
  • Any convenient modification to the cells that marks the cells as modified with a cyclic-di-nucleotide active agent may be used.
  • a selectable marker may be inserted into the genome of the cell, so that the population of cells may be enriched for those comprising the genetic modification by separating the genetically marked cells from the remaining population. Separation may be by any convenient separation technique appropriate for the selectable marker used.
  • cells may be separated by fluorescence activated cell sorting
  • fluorescence activated cell sorting if a fluorescent marker has been inserted, cells may be separated from the heterogeneous population by affinity separation techniques, e.g., magnetic separation, affinity chromatography, “panning” with an affinity reagent attached to a solid matrix, or other convenient technique.
  • Techniques providing accurate separation include fluorescence activated cell sorters, which can have varying degrees of sophistication, such as multiple color channels, low angle and obtuse light scattering detecting channels, impedance channels, etc.
  • the cells may be selected against dead cells by employing dyes associated with dead cells (e.g., propidium iodide). Any technique may be employed which is not unduly detrimental to the viability of the genetically modified cells.
  • Cell compositions that are highly enriched for cells comprising cyclic-di-nucleotide active agent(s) are achieved in this manner.
  • “highly enriched” it is meant that the genetically modified cells will be 70% or more, 75% or more, 80% or more, 85% or more, 90% or more of the cell composition, for example, about 95% or more, or 98% or more of the cell composition.
  • the composition may be a substantially pure composition of cells comprising cyclic-di-nucleotide active agent(s).
  • Cells comprising cyclic-di-nucleotide active agent(s) produced by the methods described herein may be used immediately.
  • the cells may be frozen at liquid nitrogen temperatures and stored for long periods of time, being thawed and capable of being reused.
  • the cells may be frozen in 10% DMSO, 50% serum, 40% buffered medium, or some other such solution as is commonly used in the art to preserve cells at such freezing temperatures, and thawed in a manner as commonly known in the art for thawing frozen cultured cells.
  • the cells comprising cyclic-di-nucleotide active agent(s) may be cultured in vitro under various culture conditions.
  • the cells may be expanded in culture, i.e., grown under conditions that promote their proliferation.
  • Culture medium may be liquid or semi-solid, e.g., containing agar, methylcellulose, etc.
  • the cell population may be suspended in an appropriate nutrient medium, such as Iscove's modified DMEM or RPMI 1640, normally supplemented with fetal calf serum (about 5-10%), L-glutamine, a thiol, particularly 2-mercaptoethanol, and antibiotics, e.g., penicillin and streptomycin.
  • the culture may contain growth factors to which the regulatory T cells are responsive. Growth factors, as defined herein, are molecules capable of promoting survival, growth and/or differentiation of cells, either in culture or in the intact tissue, through specific effects on a transmembrane receptor. Growth factors include polypeptides and non-polypeptid
  • Cells that have been modified with cyclic-di-nucleotide active agent(s) may be transplanted to a subject to treat a disease or as an antiviral, antipathogenic, or anticancer therapeutic or for biological research.
  • the subject may be a neonate, a juvenile, or an adult.
  • Mammalian species that may be treated with the present methods include canines and felines; equines; bovines; ovines; etc. and primates, particularly humans. Animal models, particularly small mammals, e.g., murine, lagomorpha, etc., may be used for experimental investigations.
  • Cells may be provided to the subject alone or with a suitable substrate or matrix, e.g., to support their growth and/or organization in the tissue to which they are being transplanted.
  • at least 1 ⁇ 10 3 cells will be administered, for example 5 ⁇ 10 3 cells, 1 ⁇ 10 4 cells, 5 ⁇ 10 4 cells, 1 ⁇ 10 5 cells, 1 ⁇ 10 6 cells or more.
  • the cells may be introduced to the subject via any of the following routes: parenteral, subcutaneous, intravenous, intracranial, intraspinal, intraocular, or into spinal fluid.
  • the cells may be introduced by injection, catheter, or the like.
  • Examples of methods for local delivery include, e.g., through an Ommaya reservoir, e.g., for intrathecal delivery (see, e.g., U.S. Pat. Nos. 5,222,982 and 5,385,582, incorporated herein by reference); by bolus injection, e.g., by a syringe, e.g., into a joint; by continuous infusion, e.g., by cannulation, e.g., with convection (see e.g., US Application No. 20070254842, incorporated here by reference); or by implanting a device upon which the cells have been reversibly affixed (see e.g., US Application Nos. 20080081064 and 20090196903, incorporated herein by reference).
  • the cyclic-di-nucleotide active agent(s) are employed to increase the production of type I interferon in vivo.
  • the cyclic-di-nucleotide active agent(s) are administered directly to the individual.
  • the cyclic-di-nucleotide active agent administered to the subject contains a 2′-5′ phosphodiester linkage containing cyclic-di-nucleotide.
  • Cyclic-di-nucleotide active agent(s) may be administered by any suitable methods for the administration of peptides, small molecules and nucleic acids to a subject.
  • the cyclic-di-nucleotide active agent(s) can be incorporated into a variety of formulations. More particularly, the cyclic-di-nucleotide active agent(s) of the present invention can be formulated into pharmaceutical compositions by combination with appropriate pharmaceutically acceptable carriers or diluents. Pharmaceutical compositions that can be used in practicing the subject methods are described below.
  • an effective amount of the cyclic-di-nucleotide active agent is administered to the subject.
  • an “effective amount” or a “therapeutically effective amount” of the cyclic-di-nucleotide active agent it is meant an amount that is required to reduce the severity, the duration and/or the symptoms of the disease.
  • the effective amount of a pharmaceutical composition containing a cyclic-di-nucleotide active agent, as provided herein is between 0.025 mg/kg and 1000 mg/kg body weight of a human subject.
  • the pharmaceutical composition is administered to a human subject at an amount of 1000 mg/kg body weight or less, 950 mg/kg body weight or less, 900 mg/kg body weight or less, 850 mg/kg body weight or less, 800 mg/kg body weight or less, 750 mg/kg body weight or less, 700 mg/kg body weight or less, 650 mg/kg body weight or less, 600 mg/kg body weight or less, 550 mg/kg body weight or less, 500 mg/kg body weight or less, 450 mg/kg body weight or less, 400 mg/kg body weight or less, 350 mg/kg body weight or less, 300 mg/kg body weight or less, 250 mg/kg body weight or less, 200 mg/kg body weight or less, 150 mg/kg body weight or less, 100 mg/kg body weight or less, 95 mg/kg body weight or less, 90 mg/kg body weight or less, 85 mg/kg body weight or less, 80 mg/kg body weight or less, 75 mg/kg body weight or less, 70 mg/kg body weight or less, or 65 mg/
  • a method for increasing a stimulator of interferon genes (STING) mediated response in a subject e.g., a STING mediated immune response.
  • the method includes the step of administering to the subject an amount of a STING active agent effective to increase a STING mediated response in the subject.
  • STING mediated response refers to any response that is mediated by STING, including, but not limited to, immune responses to bacterial pathogens, viral pathogens, and eukaryotic pathogens. See, e.g., Ishikawa et al. Immunity 29: 538-550 (2008); Ishikawa et al.
  • STING also functions in certain autoimmune diseases initiated by inappropriate recognition of self DNA (see, e.g., Gall et al. Immunity 36: 120-131 (2012), as well as for the induction of adaptive immunity in response to DNA vaccines (see, e.g., Ishikawa et al. Nature 461: 788-792 (2009).
  • increasing a STING mediated response in a subject is meant an increase in a STING mediated response in a subject as compared to a control subject (e.g., a subject who is not administered a STING active agent).
  • the method is for increasing a stimulator of interferon genes (STING) mediated response in a subject, wherein the STING mediated response is non-responsive to a cyclic-di-nucleotide having two 3′-5′ phosphodiester bonds (i.e., a canonical cyclic dinucleotide).
  • STING stimulator of interferon genes
  • the STING active agent is a cyclic-di-nucleotide active agent described herein (e.g., cyclic-di-nucleotide, nucleic acid encoding cGAS).
  • the STING active agent is a nucleic acid encoding STING or a STING polypeptide.
  • Nucleic acids encoding various STINGs include, but are not limited to, those described in: Nitta et al. Hepatology 57(1): 46-58 (2013) and Jin et al. J. Immunol. 190(6): 2835-2843 (2013) and those deposited in GENBANK and assigned deposit numbers: NM — 198282.2 and NP — 938023.1 (human); NM — 028261.1 and NP — 082537.1 ( mus musculus ); and NM — 057386.4 and NP — 476734.1 ( Drosophila melanogaster ).
  • the nucleic acid encoding STING has the following sequence:
  • the nucleic acid encoding STING is a nucleic acid with 40% to 99%, 45% to 99%, 50% to 99%, 55% to 99%, 60% to 99%, 65% to 99%, 70% to 99%, 75% to 99%, 80% to 99%, 85% to 99%, 90% to 99% or, 95% to 99% sequence identity with a wild type STING nucleic acid sequence.
  • the nucleic acid encoding STING is a nucleic acid with 40% to 50%, 50% to 60%, 60% to 70%, 70% to 80%, 80% to 90%, or 90 to 99% sequence identity with a wild type STING nucleic acid sequence.
  • the nucleic acid encoding STING is a nucleic acid with 40% or more, 45% or more, 50% or more, 55% or more, 60% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more or 99% or more sequence identity with a wild type STING nucleic acid sequence.
  • Amino acid sequences of STING include, but are not limited to, those described in: Nitta et al. Hepatology 57(1): 46-58 (2013) and Jin et al. J. Immunol. 190(6): 2835-2843 (2013) and those deposited in GENBANK and assigned deposit numbers: NM — 198282.2 and NP — 938023.1 (human); NM — 028261.1 and NP — 082537.1 ( mus musculus ); and NM — 057386.4 and NP — 476734.1 ( Drosophila melanogaster ).
  • the STING polypeptide has the following sequence:
  • the STING polypeptide has the following sequence:
  • the STING polypeptide is a polypeptide that has 40% to 99%, 45% to 99%, 50% to 99%, 55% to 99%, 60% to 99%, 65% to 99%, 70% to 99%, 75% to 99%, 80% to 99%, 85% to 99%, 90% to 99% or, 95% to 99% sequence identity with a wild type STING amino acid sequence.
  • the cGAS polypeptide is a polypeptide that has 40% to 50%, 50% to 60%, 60% to 70%, 70% to 80%, 80% to 90%, or 90 to 99% sequence identity with a wild type STING amino acid sequence.
  • the STING polypeptide is a polypeptide that has 40% or more, 45% or more, 50% or more, 55% or more, 60% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more or 99% or more sequence identity with a wild type STING amino acid sequence.
  • the methods and compositions provided herein find use in a variety of applications, where such applications include increasing type I interferon (e.g., interferon- ⁇ ) in a subject is desired.
  • the methods and compositions provided herein find use in a variety of applications, where such applications include increasing STING mediated response in a subject is desired.
  • Specific applications of interest include those in which a subject is treated for a disease condition that would benefit from an increase in type I interferon by providing the subject with a therapeutically effective amount of a cyclic-di-nucleotide active agent.
  • the methods and compositions provided herein can be used to produce an ‘adjuvant’ effect in a vaccine to prevent an infection or other disease, wherein the active agent stimulates immunological memory to protect against future disease or infection.
  • subjects suitable for treatment with a method described herein include individuals having an immunological or inflammatory disease or disorder including, but not limited to a cancer, an autoimmune disease or disorder, an allergic reaction, a chronic infectious disease and an immunodeficiency disease or disorder.
  • subjects suitable for treatment with a method of the present invention include individuals having a cellular proliferative disease, such as a neoplastic disease (e.g., cancer).
  • a cellular proliferative disease such as a neoplastic disease (e.g., cancer).
  • Cellular proliferative disease is characterized by the undesired propagation of cells, including, but not limited to, neoplastic disease conditions, e.g., cancer.
  • Examples of cellular proliferative disease include, but not limited to, abnormal stimulation of endothelial cells (e.g., atherosclerosis), solid tumors and tumor metastasis, benign tumors, for example, hemangiomas, acoustic neuromas, neurofibromas, trachomas, and pyogenic granulomas, vascular malfunctions, abnormal wound healing, inflammatory and immune disorders, Bechet's disease, gout or gouty arthritis, abnormal angiogenesis accompanying, for example, rheumatoid arthritis, psoriasis, diabetic retinopathy, other ocular angiogenic diseases such as retinopathy of prematurity (retrolental fibroplastic), macular degeneration, corneal graft rejection, neurovascular glaucoma and Oster Webber syndrome, psoriasis, restenosis, fungal, parasitic and viral infections such cytomegaloviral infections.
  • Subjects to be treated according to the methods of the invention include any individual
  • subjects suitable for treatment with a subject method include individuals who have been clinically diagnosed as infected with a virus.
  • the virus is a hepatitis virus (e.g., HAV, HBV, HCV, delta, etc.), particularly HCV, are suitable for treatment with the methods of the instant invention.
  • Individuals who are infected with HCV are identified as having HCV RNA in their blood, and/or having anti-HCV antibody in their serum.
  • Such individuals include na ⁇ ve individuals (e.g., individuals not previously treated for HCV, particularly those who have not previously received IFN- ⁇ -based or ribavirin-based therapy) and individuals who have failed prior treatment for HCV.
  • subjects suitable for treatment with a method provided herein include an individual with a neurodegenerative disease or disorder, including, but not limited to, Parkinson's disease, Alzheimer's disease, Huntington's disease, and Amyotrophic lateral sclerosis (ALS).
  • a neurodegenerative disease or disorder including, but not limited to, Parkinson's disease, Alzheimer's disease, Huntington's disease, and Amyotrophic lateral sclerosis (ALS).
  • subjects suitable for treatment with a method of the present invention include individuals having multiple sclerosis.
  • Multiple sclerosis refers to an autoimmune neurodegenerative disease, which is marked by inflammation within the central nervous system with lymphocyte attack against myelin produced by oligodendrocytes, plaque formation and demyelization with destruction of the myelin sheath of axons in the brain and spinal cord, leading to significant neurological disability over time.
  • an otherwise healthy person presents with the acute or sub acute onset of neurological symptomatology (attack) manifested by unilateral loss of vision, vertigo, ataxia, dyscoordination, gait difficulties, sensory impairment characterized by paresthesia, dysesthesia, sensory loss, urinary disturbances until incontinence, diplopia, dysarthria or various degrees of motor weakness until paralysis.
  • the symptoms may be painless, remain for several days to a few weeks, and then partially or completely resolve.
  • a second attack will occur. During this period after the first attack, the patient is defined to suffer from probable MS. Probable MS patients may remain undiagnosed for years.
  • the second attack occurs the diagnosis of clinically definite MS (CDMS) is made (Poser criteria 1983; C. M. Poser et al., Ann. Neurol. 1983; 13, 227).
  • subject and patient mean a member or members of any mammalian or non-mammalian species that may have a need for the pharmaceutical methods, compositions and treatments described herein.
  • Subjects and patients thus include, without limitation, primate (including humans), canine, feline, ungulate (e.g., equine, bovine, swine (e.g., pig)), avian, and other subjects.
  • primate including humans
  • canine feline
  • ungulate e.g., equine, bovine, swine (e.g., pig)
  • avian avian
  • Humans and non-human animals having commercial importance are of particular interest.
  • “Mammal” means a member or members of any mammalian species, and includes, by way of example, canines; felines; equines; bovines; ovines; rodentia, etc. and primates, particularly humans.
  • Non-human animal models, particularly mammals, e.g., primate, murine, lagomorpha, etc. may be used for experimental investigations.
  • Treating” or “treatment” of a condition or disease includes: (1) preventing at least one symptom of the conditions, i.e., causing a clinical symptom to not significantly develop in a mammal that may be exposed to or predisposed to the disease but does not yet experience or display symptoms of the disease, (2) inhibiting the disease, i.e., arresting or reducing the development of the disease or its symptoms, or (3) relieving the disease, i.e., causing regression of the disease or its clinical symptoms.
  • the term “treating” is thus used to refer to both prevention of disease, and treatment of pre-existing conditions.
  • the prevention of cellular proliferation can be accomplished by administration of the subject compounds prior to development of overt disease, e.g., to prevent the regrowth of tumors, prevent metastatic growth, etc.
  • the compounds are used to treat ongoing disease, by stabilizing or improving the clinical symptoms of the patient.
  • the cyclic-di-nucleotide active agent described herein may be administered in combination with other pharmaceutically active agents, including other agents that treat the underlying condition or a symptom of the condition.
  • “In combination with” as used herein refers to uses where, for example, the first compound is administered during the entire course of administration of the second compound; where the first compound is administered for a period of time that is overlapping with the administration of the second compound, e.g., where administration of the first compound begins before the administration of the second compound and the administration of the first compound ends before the administration of the second compound ends; where the administration of the second compound begins before the administration of the first compound and the administration of the second compound ends before the administration of the first compound ends; where the administration of the first compound begins before administration of the second compound begins and the administration of the second compound ends before the administration of the first compound ends; where the administration of the second compound begins before administration of the first compound begins and the administration of the first compound ends before the administration of the second compound ends.
  • “in combination” can also refer to regimen involving administration of two or more compounds. “In combination with” as used herein also refers to administration of two or more compounds that may be administered in the same or different formulations, by the same of different routes, and in the same or different dosage form type.
  • agents for use in combination therapy of neoplastic disease include, but are not limited to, thalidomide, marimastat, COL-3, BMS-275291, squalamine, 2-ME, SU6668, neovastat, Medi-522, EMD121974, CAI, celecoxib, interleukin-12, IM862, TNP470, avastin, gleevec, herceptin, and mixtures thereof.
  • chemotherapeutic agents for use in combination therapy include, but are not limited to, daunorubicin, daunomycin, dactinomycin, doxorubicin, epirubicin, idarubicin, esorubicin, bleomycin, mafosfamide, ifosfamide, cytosine arabinoside, bis-chloroethylnitrosurea, busulfan, mitomycin C, actinomycin D, mithramycin, prednisone, hydroxyprogesterone, testosterone, tamoxifen, dacarbazine, procarbazine, hexamethylmelamine, pentamethylmelamine, mitoxantrone, amsacrine, chlorambucil, methylcyclohexylnitrosurea, nitrogen mustards, melphalan, cyclophosphamide, 6-mercaptopurine, 6-thioguanine, cytarabine, 5-azacytidine
  • antiviral agents can also be delivered in the treatment methods of the invention.
  • compounds that inhibit inosine monophosphate dehydrogenase may have the potential to exert direct anti viral activity, and such compounds can be administered in combination with the mutant Listeria , as described herein.
  • Drugs that are effective inhibitors of hepatitis C NS3 protease may be administered in combination with the mutant Listeria , as described herein.
  • Hepatitis C NS3 protease inhibitors inhibit viral replication.
  • Other agents such as inhibitors of HCV NS3 helicase are also attractive drugs for combinational therapy, and are contemplated for use in combination therapies described herein.
  • Ribozymes such as HeptazymeTM and phosphorothioate oligonucleotides which are complementary to HCV protein sequences and which inhibit the expression of viral core proteins are also suitable for use in combination therapies described herein.
  • agents for use in combination therapy of multiple sclerosis include, but are not limited to; glatiramer; corticosteroids; muscle relaxants, such as Tizanidine (Zanaflex) and baclofen (Lioresal); medications to reduce fatigue, such as amantadine (Symmetrel) or modafinil (Provigil); and other medications that may also be used for depression, pain and bladder or bowel control problems that can be associated with MS.
  • combination therapy compounds may be administered by the same route of administration (e.g., intrapulmonary, oral, enteral, etc.) that the cyclic-di-nucleotide active agents are administered.
  • the compounds for use in combination therapy with the cyclic-di-nucleotide active agent may be administered by a different route of administration.
  • the cyclic di-nucleotide active agent functions as an adjuvant when administered together with a drug or vaccine to treat or prevent a disease or condition, including, but not limited to, those diseases and conditions provided herein.
  • the cyclic di-nucleotide active agents are administered together with a vaccine.
  • Such active agents that are administered with a vaccine can function as an adjuvant to enhance the immune response elicited by the vaccine, including stimulating immunological memory to protect against future diseases and/or infections.
  • the cyclic di-nucleotide or STING active agents administered as an adjuvant for a vaccine can enhance the effectiveness of the vaccine by, e.g., increasing the immunogenicity of weaker antigens, reducing the amount of antigen required to elicit a immune response, reducing the frequency of immunization necessary to maintain protective immunity, enhance the efficacy of vaccines in immunocompromised or other individuals with reduced immune responses, and/or increase immunity at a target tissue, such as mucosal immunity.
  • the cyclic di-nucleotide active agents when co-administered with one or more antigens, can induce a particular cytokine profile to promote cellular and humoral immunity against the antigen and increase the effectiveness of vaccination.
  • Antigens used to prepare vaccines may be derived from a variety of microorganisms such as viruses, bacteria and parasites that contain substances that are not normally present in the body, as well as tumor cells. These substances can be used as antigens to produce an immune response to destroy both the antigen and cells containing the antigen, such as a bacterial cell or cancer cell.
  • isolated or crude antigens of microbial pathogens can be used in vaccines to treat infectious disease; isolated or crude tumor cell antigens can be used in vaccines to treat cancer; isolated or crude antigens known to be associated with a pathologically aberrant cell can be used to treat a variety of diseases in which it is beneficial to target particular cells for destruction.
  • Microorganisms that may be a source of antigen include clinically relevant microorganisms, such as bacteria, including pathogenic bacteria; viruses (e.g., Influenza, Measles, Coronavirus); parasites (e.g., Trypanosome, Plasmodium, Leishmania ); fungi (e.g., Aspergillus, Candida, Coccidioides, Cryptococcus ); and the like.
  • viruses e.g., Influenza, Measles, Coronavirus
  • parasites e.g., Trypanosome, Plasmodium, Leishmania
  • fungi e.g., Aspergillus, Candida, Coccidioides, Cryptococcus
  • fungi e.g., Aspergillus, Candida, Coccidioides, Cryptococcus
  • the antigen may be from bacteria, particularly pathogenic bacteria, such as the causative agent of anthrax ( Bacillus anthracis ), plague ( Yersinia pestis ), tuberculosis ( Mycobacterium tuberculosis ), salmonellosis ( Salmonella enterica ), stomach cancer ( Helicobacter pylori ), sexually transmitted diseases ( Chlamydia trachomatis or Neisseria gonorrhea ), and the like.
  • pathogenic bacteria such as the causative agent of anthrax ( Bacillus anthracis ), plague ( Yersinia pestis ), tuberculosis ( Mycobacterium tuberculosis ), salmonellosis ( Salmonella enterica ), stomach cancer ( Helicobacter pylori ), sexually transmitted diseases ( Chlamydia trachomatis or Neisseria gonorrhea ), and the like.
  • Other representative examples include antigens from certain viruses, such as influenza virus(
  • Fungi of interest include, but are not limited to Candida albicans or Aspergillus spp., and parasites of interest include the causative agents of trypanosomiasis, leishmania , pneumonic plague, and lyme disease (Borrellia burgdorferi).
  • a pathologically aberrant cell to be used in a vaccine can be obtained from any source such as one or more individuals having a pathological condition or ex vivo or in vitro cultured cells obtained from one or more such individuals, including a specific individual to be treated with the resulting vaccine.
  • a vaccine formulation for use with an adjuvant containing cyclic di-nucleotide active agents may include, e.g., attenuated and inactivated viral and bacterial pathogens from infected patients or propagated cultures, purified macromolecules, polysaccharides, toxoids, recombinant antigens, organisms containing a foreign gene from a pathogen, synthetic peptides, polynucleic acids, antibodies and tumor cells.
  • Recombinant antigens may be obtained, for example, by isolating and cloning a gene encoding any immunogenic polypeptide, in, e.g., bacterial, yeast, insect, reptile or mammalian cells using recombinant methods well known in the art and described, for example in Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York (1992) and in Ansubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Md. (1998).
  • a number of genes encoding surface antigens from viral, bacterial and protozoan pathogens have been successfully cloned, expressed and used as antigens for vaccine development.
  • the major surface antigen of hepatitis B virus, HbsAg, the b subunit of choleratoxin, the enterotoxin of E. coli , the circumsporozoite protein of the malaria parasite, and a glycoprotein membrane antigen from Epstein-Barr virus, as well as tumor cell antigens have been expressed in various well known vector/host systems, purified and used in vaccines.
  • a vaccine formulation containing cyclic di-nucleotide or STING active agents may advantageously contain other vaccine adjuvants and carriers.
  • These carriers and adjuvants include, but are not limited to, ion exchange resins, 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, phosphate buffered saline solution, water, emulsions (e.g.
  • 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 and polyethylene glycol.
  • any convenient method for determining if a vaccine compound or formulation induces an innate, humoral, cell-mediated, or any combination of these types of immune response may be employed.
  • the ability of a vaccine compound or formulation to induce an innate immune response through STING can be determined using methods described herein as well as other methods. Such methods for detecting an innate immune response can be generally performed within hours of vaccine administration.
  • the ability of a vaccine compound or formulation to induce a humoral response can be determined by measuring the titer of antigen-specific antibodies in an animal primed with the vaccine and boosted with the antigen, or determining the presence of antibodies cross-reactive with an antigen by ELISA, Western blotting or other well-known methods.
  • Cellular immune responses can be determined, for example, by measuring cytotoxic T cell response to antigen using a variety of methods, such as, e.g., FACS sorting, and other methods well known in the art. Methods of detecting humoral and cellular immune responses can be generally performed days or weeks after vaccine administration.
  • cyclic-di-nucleotide refers to a compound containing two nucleosides (i.e., a first and second nucleoside), wherein the 2′ or 3′ carbon of each nucleoside is linked to the 5′ carbon of the other nucleoside by a phosphodiester bond.
  • a 2′-5′ phosphodiester linkage containing cyclic-di-nucleotide refers to a cyclic-di-nucleotide, wherein the 2′ carbon of at least one of the nucleosides is linked to the 5′ carbon of the other nucleoside.
  • 2′-5′ phosphodiester linkage containing cyclic-di-nucleotides can be used in practicing the methods described herein for increasing production of a type I interferon in a cell or subject.
  • a “cyclic-di-nucleotide” also includes all of the stereoisomeric forms of the cyclic-di-nucleotides described herein.
  • nucleoside refers to a composition containing a nitrogenous base covalently attached to a sugar (e.g., ribose or deoxyribose) or an analog thereof.
  • a sugar e.g., ribose or deoxyribose
  • nucleosides include, but are not limited to cytidine, uridine, adenosine, guanosine, thymidine and inosine.
  • the nucleoside contains a deoxyribose sugar.
  • Analogs of nucleosides include, but are not limited to dexoyadenosine analogues (e.g., Didanosine and Vidarabine); deoxycytidine analogues (e.g., Cytarabine, Ematricitabine, Lamivudine, and Zalcitabine); deoxyguanosine analogues (Abacavir and Entecavir); (deoxy-) thymidine analogues (e.g., Stavudine, Telbivudine, and Zidovudine); and deoxyuridine alaogues (e.g., Idoxuridine and Trifluridine).
  • dexoyadenosine analogues e.g., Didanosine and Vidarabine
  • deoxycytidine analogues e.g., Cytarabine, Ematricitabine, Lamivudine, and Zalcitabine
  • deoxyguanosine analogues
  • cyclic-di-nucleotides can increase type-I IFN production in a cell.
  • cyclic-di-nucleotides increase type-I IFN production through a mechanism that involves stimulator of interferon genes (STING).
  • Cyclic-di-nucleotides include those specifically described herein as well as isoforms (e.g., tautomers) of those specifically described herein that can be used in practicing the subject methods. Cyclic-di-nucleotides can be obtained using any suitable method. For example, cyclic-di-nucleotides may be made by chemical synthesis using nucleoside derivatives as starting material. Cyclic-di-nucleotides can also be produced by in vitro synthesis, using recombinant purified cGAMP synthase (cGAS), as described in the Experimental Section below. Moreover, the structures of such cyclic-di-nucleotides can be confirmed using NMR analysis.
  • cGAMP synthase recombinant purified cGAMP synthase
  • Cyclic-di-nucleotides provided herein can be described by the following nomenclature: cyclic[X 1 (A-5′)pX 2 (B-5′)p], wherein X 1 and X 2 are the first and second nucleoside, A is the carbon of the first nucleoside (e.g., 2′ or 3′ position) that is linked to the 5′ carbon of the second nucleoside via a phosphodiester bond and B is the carbon of the second nucleoside (e.g., 2′ or 3′ position) that is linked to the 5′ carbon of the first nucleoside by a phosphodiester bond.
  • cyclic[G(2′-5′)pA(3′-5′)p] has the following formula:
  • the cyclic-di-nucleotide contains a 2′-5′ phosphodiester bond.
  • the cyclic-di-nucleotide further contains a 3′-5′ phosphodiester bond (e.g., cyclic[X 1 (2′-5′)pX 2 (3′-5′)p] or cyclic[X 1 (3′-5′)pX 2 (2′-5′)p]).
  • the cyclic-di-nucleotide contains two 2′-5′ phosphodiester bonds (cyclic[X 1 (2′-5′)pX 2 (2′-5′)p]).
  • the cyclic-di-nucleotide is:
  • the cyclic-di-nucleotide is:
  • the cyclic-di-nucleotide has the following formula:
  • X and Y can be any organic molecule including a nitrogenous base.
  • a “nitrogenous base” refers to nitrogen-containing molecules having the chemical properties of a base including, but not limited to, pyrimidine derivatives (e.g., cytosine, thymine, and uracil) and purine derivatives (e.g., adenine and guanine), as well as substituted pyrimidine and purine derivatives, pyrimidine and purine analogs, and their tautomers.
  • X and Y are each one of the following:
  • the cyclic-di-nucleotide has the following formula (cyclic[G(2′5′)pA(3′5′)p]):
  • the cyclic-di-nucleotide has the following formula (cyclic[G(3′5′)pA(2′5′)p]):
  • the cyclic-di-nucleotide has the following formula cyclic[G(2′5′)pA(2′5′)p]:
  • the cyclic-di-nucleotide has the following formula cyclic[A(2′5′)pA(3′5′)p]:
  • the cyclic-di-nucleotide has the following formula cyclic[G(2′5′)pG(3′5′)p]:
  • the cyclic-di-nucleotide has the following formula cyclic[A(2′5′)pA(2′5′)p]:
  • the cyclic-di-nucleotide has the following formula cyclic[G(2′5′)pG(2′5′)p]:
  • the cyclic-di-nucleotide has one of the following formulas:
  • R is any amino acid side chain.
  • a pharmaceutical composition that contains any of the cyclic-di-nucleotide active agents provided herein and a pharmaceutically acceptable carrier.
  • the cyclic-di-nucleotide active agent is one or more cyclic-di-nucleotides.
  • carrier refers to a diluent, adjuvant, excipient, or vehicle with which the mitochondrial transport protein inhibitor is administered.
  • Such pharmaceutical carriers can be, for example, sterile liquids, such as saline solutions in water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like.
  • a saline solution is a preferred carrier when the pharmaceutical composition is administered intravenously.
  • Saline solutions and aqueous dextrose and glycerol solutions can also be employed as liquid carriers, particularly 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, emulsion, tablets, pills, capsules, powders, sustained-release formulations and the like.
  • composition can be formulated as a suppository, with traditional binders and carriers such as triglycerides.
  • the inhibitors can be formulated as neutral or salt forms.
  • Pharmaceutically acceptable salts include those formed with free amino groups such as those derived from hydrochloric, phosphoric, acetic, oxalic, tartaric acids, etc., and those formed with free carboxyl groups such as those derived from sodium, potassium, ammonium, calcium, ferric hydroxides, isopropylamine, triethylamine, 2-ethylamino ethanol, histidine, procaine, etc. Examples of suitable pharmaceutical carriers are described in “Remington's Pharmaceutical Sciences” by E. W. Martin, hereby incorporated by reference herein in its entirety.
  • compositions will contain a therapeutically effective amount of the mitochondrial transport protein (e.g., a Miro protein, a TRAK protein, or Khc) inhibitor, preferably in purified form, together with a suitable amount of carrier so as to provide the form for proper administration to the patient.
  • the mitochondrial transport protein e.g., a Miro protein, a TRAK protein, or Khc
  • the formulation should suit the mode of administration.
  • the pharmaceutical composition can also include any of a variety of stabilizing agents, such as an antioxidant for example.
  • the pharmaceutical composition includes a polypeptide
  • the polypeptide can be complexed with various well-known compounds that enhance the in vivo stability of the polypeptide, or otherwise enhance its pharmacological properties (e.g., increase the half-life of the polypeptide, reduce its toxicity, enhance solubility or uptake). Examples of such modifications or complexing agents include sulfate, gluconate, citrate and phosphate.
  • the polypeptides of a composition can also be complexed with molecules that enhance their in vivo attributes. Such molecules include, for example, carbohydrates, polyamines, amino acids, other peptides, ions (e.g., sodium, potassium, calcium, magnesium, manganese), and lipids.
  • compositions intended for in vivo use may be sterile. To the extent that a given compound must be synthesized prior to use, the resulting product is typically substantially free of any potentially toxic agents, particularly any endotoxins, which may be present during the synthesis or purification process.
  • compositions for parental administration are also sterile, substantially isotonic and made under GMP conditions.
  • the pharmaceutical composition can be formulated for intravenous, oral, via implant, transmucosal, transdermal, intramuscular, intrathecal, or subcutaneous administration. In some embodiments, the pharmaceutical composition is formulated for intravenous administration. In other embodiments, the pharmaceutical composition is formulated for subcutaneous administration.
  • the following delivery systems, which employ a number of routinely used pharmaceutical carriers, are only representative of the many embodiments envisioned for administering the instant compositions.
  • Injectable drug delivery systems include solutions, suspensions, gels, microspheres and polymeric injectables, and can comprise excipients such as solubility-altering agents (e.g., ethanol, propylene glycol and sucrose) and polymers (e.g., polycaprylactones and PLGAs).
  • Implantable systems include rods and discs, and can contain excipients such as PLGA and polycaprylactone. Osteopontin or nucleic acids of the invention can also be administered attached to particles using a gene gun.
  • Oral delivery systems include tablets and capsules. These can contain excipients such as binders (e.g., hydroxypropylmethylcellulose, polyvinyl pyrilodone, other cellulosic materials and starch), diluents (e.g., lactose and other sugars, starch, dicalcium phosphate and cellulosic materials), disintegrating agents (e.g., starch polymers and cellulosic materials) and lubricating agents (e.g., stearates and talc).
  • excipients such as binders (e.g., hydroxypropylmethylcellulose, polyvinyl pyrilodone, other cellulosic materials and starch), diluents (e.g., lactose and other sugars, starch, dicalcium phosphate and cellulosic materials), disintegrating agents (e.g., starch polymers and cellulosic materials) and lubricating agents (e.
  • Transmucosal delivery systems include patches, tablets, suppositories, pessaries, gels and creams, and can contain excipients such as solubilizers and enhancers (e.g., propylene glycol, bile salts and amino acids), and other vehicles (e.g., polyethylene glycol, fatty acid esters and derivatives, and hydrophilic polymers such as hydroxypropylmethylcellulose and hyaluronic acid).
  • solubilizers and enhancers e.g., propylene glycol, bile salts and amino acids
  • other vehicles e.g., polyethylene glycol, fatty acid esters and derivatives, and hydrophilic polymers such as hydroxypropylmethylcellulose and hyaluronic acid.
  • Dermal delivery systems include, for example, aqueous and nonaqueous gels, creams, multiple emulsions, microemulsions, liposomes, ointments, aqueous and nonaqueous solutions, lotions, aerosols, hydrocarbon bases and powders, and can contain excipients such as solubilizers, permeation enhancers (e.g., fatty acids, fatty acid esters, fatty alcohols and amino acids), and hydrophilic polymers (e.g., polycarbophil and polyvinylpyrolidone).
  • the pharmaceutically acceptable carrier is a liposome or a transdermal enhancer.
  • the pharmaceutical composition containing the cyclic-di-nucleotide active agent is formulated to cross the blood brain barrier (BBB).
  • BBB blood brain barrier
  • One strategy for drug delivery through the blood brain barrier (BBB) entails disruption of the BBB, either by osmotic means such as mannitol or leukotrienes, or biochemically by the use of vasoactive substances such as bradykinin.
  • a BBB disrupting agent can be co-administered with the therapeutic compositions when the compositions are administered by intravascular injection.
  • ND pharmaceutical composition behind the BBB may be by local delivery, for example by intrathecal delivery, e.g., through an Ommaya reservoir (see, e.g., U.S. Pat. Nos.
  • the pharmaceutical composition containing the cyclic-di-nucleotide or STING active agents is formulated in a delivery vehicle, e.g., to enhance cytosolic transport. Any convenient protocol may be employed to facilitate delivery of the cyclic-di-nucleotide active agent across the plasma membrane of a cell and into the cytosol.
  • the cyclic-di-nucleotide or STING active agents and an antigen effective for use in a vaccine may be formulated together to be delivered by the same delivery vehicle in the pharmaceutical composition.
  • the cyclic-di-nucleotide or STING active agents may be encapsulated in a delivery vehicle comprising liposomes in the pharmaceutical composition.
  • a delivery vehicle comprising liposomes in the pharmaceutical composition.
  • Methods of using liposomes for drug delivery and other therapeutic uses are known in the art. See, e.g., U.S. Pat. No. 8,329,213, U.S. Pat. No. 6,465,008, U.S. Pat. No. 5,013,556, US Application No. 20070110798, and Andrews et al., Mol Pharm 2012 9:1118, which are incorporated herein by reference.
  • Liposomes may be modified to render their surface more hydrophilic by adding polyethylene glycol (“pegylated”) to the bilayer, which increases their circulation time in the bloodstream. These are known as “stealth” liposomes and are especially useful as carriers for hydrophilic (water soluble) molecules, such as the cyclic-di-nucleot
  • nano- or microparticles made from biodegradable materials such as poly(lactic acid), poly( ⁇ -glutamic acid), poly(glycolic acid), polylactic-co-glycolic acid.
  • Polyethylenimine, or alginate microparticles, and cationic microparticles, including dedrimers, such as cyclodextrins may be employed as delivery vehicles for cyclic-di-nucleotide or STING active agents to promote cellular uptake. See, e.g., U.S. Pat. No. 8,187,571, Krishnamachari et al., Adv Drug Deliv Rev 2009 61:205, Garzon et al., 2005 Vaccine 23:1384, incorporated herein by reference.
  • photochemical internalization may be employed to enhance cytosolic uptake of cyclic-di-nucleotide or STING active agents.
  • the cyclic-di-nucleotide or STING active agents may be co-adiminstered with a photosensitizing agent. Then, exposure of the target cells to light of a specific wavelength triggers internalization of the cyclic-di-nucleotide or STING active agents.
  • the delivery vehicle for delivering the cyclic-di-nucleotide or STING active agents can also be targeting delivery vehicles, e.g., a liposome containing one or more targeting moieties or biodistribution modifiers on the surface of the liposome.
  • a targeting moiety can be any agent that is capable of specifically binding or interacting with a desired target.
  • the specific binding agent can be any molecule that specifically binds to a protein, peptide, biomacromolecule, cell, tissue, etc. that is being targeted (e.g., a protein peptide, biomacromolecule, cell, tissue, etc. wherein the cyclic-di-nucleotide or STING active agent exerts its desired effect).
  • the specific binding agent can be, but is not limited to, an antibody against an epitope of a peptidic analyte, or any recognition molecule, such as a member of a specific binding pair.
  • suitable specific binding pairs include, but are not limited to: a member of a receptor/ligand pair; a ligand-binding portion of a receptor; a member of an antibody/antigen pair; an antigen-binding fragment of an antibody; a hapten; a member of a lectin/carbohydrate pair; a member of an enzyme/substrate pair; biotin/avidin; biotin/streptavidin; digoxin/antidigoxin; a member of a peptide aptamer binding pair; and the like.
  • the specific binding moiety includes an antibody.
  • An antibody as defined here may include fragments of antibodies which retain specific binding to antigen, including, but not limited to, Fab, Fv, scFv, and Fd fragments, chimeric antibodies, humanized antibodies, single-chain antibodies, and fusion proteins comprising an antigen-binding portion of an antibody and a non-antibody protein.
  • the antibodies may also include Fab′, Fv, F(ab′) 2 , and or other antibody fragments that retain specific binding to antigen.
  • the targeting moiety is a binding agent that specifically interacts with a molecule expressed on a tumor cell or an immune cell (e.g., CD4, CD8, CD69, CD62L, and the like), such that the targeting delivery vehicle containing the cyclic-di-nucleotide or STING active agents is delivered to the site of a tumor or to specific immune cells.
  • a molecule expressed on a tumor cell or an immune cell e.g., CD4, CD8, CD69, CD62L, and the like
  • any combinations of the above listed delivery vehicles may be used advantageously to enhance delivery of the cyclic-di-nucleotide or STING active agents to the target cells.
  • Components of the pharmaceutical composition can be supplied either separately or mixed together in unit dosage form, for example, as a dry lyophilized powder or water free concentrate. Where the composition is to be administered by infusion, it can be dispensed with an infusion bottle containing sterile pharmaceutical grade water or saline. Where the composition is administered by injection, an ample of sterile water for injection or saline can be provided so that the ingredients may be mixed prior to administration.
  • the pharmaceutical composition is supplied as a dry sterilized lyophilized powder that is capable of being reconstituted to the appropriate concentration for administration to a subject.
  • the pharmaceutical composition is supplied as a water free concentrate.
  • the pharmaceutical composition is supplied as a dry sterile lyophilized powder at a unit dosage of at least 0.5 mg, at least 1 mg, at least 2 mg, at least 3 mg, at least 5 mg, at least 10 mg, at least 15 mg, at least 25 mg, at least 30 mg, at least 35 mg, at least 45 mg, at least 50 mg, at least 60 mg, or at least 75 mg.
  • Solutions, suspensions and powders for reconstitutable delivery systems include vehicles such as suspending agents (e.g., gums, xanthans, cellulosics and sugars), humectants (e.g., sorbitol), solubilizers (e.g., ethanol, water, PEG and propylene glycol), surfactants (e.g., sodium lauryl sulfate, Spans, Tweens, and cetyl pyridine), preservatives and antioxidants (e.g., parabens, vitamins E and C, and ascorbic acid), anti-caking agents, coating agents, and chelating agents (e.g., EDTA).
  • suspending agents e.g., gums, xanthans, cellulosics and sugars
  • humectants e.g., sorbitol
  • solubilizers e.g., ethanol, water, PEG and propylene glycol
  • the pharmaceutical composition is formulated as a salt form.
  • Pharmaceutically acceptable salts include those formed with anions such as those derived from hydrochloric, phosphoric, acetic, oxalic, tartaric acids, etc., and those formed with cations such as those derived from sodium, potassium, ammonium, calcium, ferric hydroxides, isopropylamine, triethylamine, 2-ethylamino ethanol, histidine, procaine, etc.
  • the pharmaceutical composition contains a prodrug derivative of any of the cyclic-di-nucleotide or STING active agents provided herein.
  • Such prodrugs can be subsequently converted to an active form of the cyclic-di-nucleotide or STING active agent in the body of the subject administered the pharmaceutical composition.
  • Kits with unit doses of the subject cyclic-di-nucleotide active agents e.g., one or more cyclic-di-nucleotides, e.g., in oral or injectable doses, are provided.
  • the one or more components are present in the same or different containers, as may be convenient or desirable.
  • the instructions may be provided in a variety of different formats.
  • the instructions may include complete protocols for practicing the subject methods or means for obtaining the same (e.g., a website URL directing the user to a webpage which provides the instructions), where these instructions may be printed on a substrate, where substrate may be one or more of: a package insert, the packaging, reagent containers and the like.
  • TLRs Toll-like receptors
  • RLRs RIG-1-like receptors
  • ds DNA The cytosolic presence of foreign double-stranded (ds) DNA triggers a potent antiviral response dominated by the production of type I interferons (IFNs) (Ishii et al., Nat. Immunol. (2006) 7: 40; Stetson et al., Immunity (2006) 24: 93).
  • IFNs type I interferons
  • the molecular mechanism linking dsDNA to interferon production has not been well characterized (Burdette & Vance, Nat. Immunol. (2013) 14: 19).
  • STING A host protein, STING, was identified and shown to be required for the IFN response to cytosolic dsDNA (Ishikawa & Barber, Nature (2008) 455: 674; Ishikawa et al., Nature (2009) 461: 788; Sun et al., Proc Natl Acad Sci USA (2009) 106: 8653; and Zhong et al., Immunity (2008) 29: 538). STING was also shown to be required for the interferon response to bacterially-derived second messengers called cyclic-di-nucleotides (CDNs)(Jin et al., J Immunol (2011) 187: 2595; and Sauer et al., Infect Immun (2011) 79: 688).
  • CDNs cyclic-di-nucleotides
  • CDNs are secreted or released into the cytosol by certain bacterial pathogens (Woodward et al., Science (2010) 328: 1703) and bind directly to STING (Burdette et al., Nature (2011) 478: 515).
  • a mutant (R231A) allele of mouse STING was identified that abolished responsiveness to CDNs but did not appreciably affect the interferon response to cytosolic DNA (Id).
  • Id interferon response to cytosolic DNA
  • 293T cells expressing wild-type mouse STING are responsive to CDNs but not to dsDNA.
  • the IFN responses to cytosolic CDNs and dsDNA both require STING, the responses to these chemically distinct ligands can be genetically uncoupled.
  • hSTING REF and hSTING THP-1 differ at four amino acid positions.
  • hSTING REF encodes a histidine (H) at amino acid position 232
  • hSTING THP-1 encodes an arginine (R) at this position, which corresponds to R231 in mSTING that is critical for responsiveness to CDNs. Therefore, the functionality of individual hSTING alleles were tested by expressing these alleles in 293T cells that lack endogenous STING (Burdette et al.).
  • 293T cells are not responsive to stimulation by dsDNA, presumably due to lack of expression of cGAS (Sun et al.) or perhaps other DNA sensors. Therefore, to test whether the hSTING variants could respond to DNA stimulation, STING-null (‘goldenticket’)(Sauer et al.), but (cGAS + ) macrophages were transduced with hSTING expression vectors. Interestingly, even the hSTING REF variant that is non-responsive to CDNs conferred responsiveness to dsDNA ( FIG. 1D ).
  • hSTING REF therefore phenocopies the R231A mutant of mouse STING, previously described that uncouples responsiveness to CDNs and dsDNA (Burdette et al.). Like the mSTING R231A variant, hSTING REF still bound to CDNs ( FIG. 1E ) (Huang et al., Ouyang et al., and Yin et al.), indicating that this allele is compromised at a step downstream of CDN binding.
  • mSTING R231A was also non-responsive to chemically synthesized cGAMP ( FIG. 1F ) (Kellenberger, et al., J Am Chem. Soc. (2013). 135:4906). This raised the question of whether R231A/R232H variants of STING would be responsive to the cGAS enzyme that is believed to activate STING via production of cGAMP. It was found that human or mouse cGAS expression was sufficient to robustly activate hSTING REF and mSTING R231A variants, even at very low levels of cGAS expression ( FIG. 5A ). Several explanations were considered for this result.
  • DncV produced some c-di-AMP if provided only ATP, and some c-di-GMP if provided only GTP, but preferred to make cGAMP when provided both ATP and GTP (Davies, et al., Cell (2012)149: 358). ( FIG. 6A ).
  • cGAS required both ATP and GTP substrates and the resulting product migratessignificantly differently than any of the canonical CDNs produced by DncV,
  • cGAS and DncV products were analyzed by specific nuclease digestion.
  • the cGAS product was partially cleaved by nuclease P1, which selectively digests 3′-5′ phosphodiester linkages, suggesting that the cGAS product contains at least one 3′-5′ phosphodiester linkage ( FIG. 6B ).
  • nuclease P1 digestion was incomplete as it did not lead to generation of GMP, in contrast to treatment of the cGAS product with snake venom phosphodiesterase, which cleaved both 2′-5′ and 3′-5′ phosphodiester linkages ( FIG. 3B ). This suggests that the cGAS product contains a 2′-5′ phosphodiester linkage.
  • CDNs have been proposed to be useful as vaccine adjuvants or immunotherapeutics (Chen, et al., Vaccine (2010) 28:3080).
  • a synthetic STING activator, DMXAA has been tested in human clinical trials as a novel chemotherapeutic agent.
  • DMXAA was not found to be efficacious in humans, likely because it is unable to stimulate hSTING (Conlon et al.).
  • our results are significant as they indicate that non-canonical 2′-5′ linked CDNs function as potent pan-agonists of diverse STING variants, including those variants that are only poorly responsive to canonical CDNs or DMXAA.
  • THP-1 cells were grown in RPMI 1640 supplemented with 10% FBS, penicillin-streptomycin and L-glutamine.
  • HEK293T cells were grown in DMEM supplemented with 10% FBS, penicillin-streptomycin and L-glutamine.
  • Gp2 retroviral packaging cell lines were maintained in DMEM supplemented with 10% FBS, penicillin-streptomycin and L-glutamine. Animal protocols were approved by the University of California, Berkeley Animal Care and Use Committee.
  • Knockdown of human STING (clone ID NM — 198282.1-90151c1) was achieved using pLKO.1 (The RNAi Consortium).
  • the sequence for knockdown of human STING is 5′-GCA GAG CTA TTT CCT TCC ACA (SEQ ID NO:07) which correspond to 5′-CCG GGC AGA GCT ATT TCC TTC CAC ACT CGA GTG TGG AAG GAA ATA GCT CTG CTT TTT G (SEQ ID NO:08) forward oligo and 5′-AAT TCA AAA
  • AGC AGA GCT ATT TCC TTC CAC ACT CGA GTG TGG AAG GAA ATA GCT CTG C (SEQ ID NO:09) reverse oligo.
  • Oligos were annealed and cloned into Agel and EcoRI digested pLKO.1 (Addgene) and retrovirally transduced into THP-1 cells in parallel with scramble shRNA control constructs. Stable cell lines were selected with puromycin. THP-1 cells were differentiated with 1 ⁇ g/mL PMA for 24 hours. Cells were allowed to rest for 24 hours and then restimulated for 6 hours with the indicated ligands. IFN induction was measured by qRT-PCR as described below.
  • Bone marrow macrophages and HEK293T cells were stimulated using Lipofectamine 2000 (Invitrogen). Unless otherwise specified, cyclic-di-GMP, cyclic-di-AMP, polyl:C and Vaccinia Virus 70 mer DNA was prepared as described previously (Burdette et al.) and used at similar concentrations. Sendai virus was purchased from Charles River Laboratories. cGAMP was synthesized as previously described (Kellenberger et al).
  • the THP-1 STING allele was amplified from cDNA using 5′ hSTING HindIII(5′-ATCGAA GCT TCC ACC ATG CCC CAC TCC AGC CTG) (SEQ ID NO:10) and 3′ hSTING NotI (5′-ATC GGC GGC CGC TCA GGC ATA GTC AGG CAC GTC ATA AGG ATA AGA GAA ATC CGT GCG GAG AG) (SEQ ID NO:11). Resulting PCR product was cloned into pCDNA3 using HindIII/NotI digestion.
  • THP-1 STING was amplified and cloned into MSCV2.2 using the 3′ primer listed above and 5′ hSTING XhoI (5′-ATC GCT CGA GCC ACC ATG CCC CAC TCC AGC CTG) (SEQ ID NO:12) and XhoI/NotI digestion.
  • IFN-luciferase, TK-Renilla and mouse STING plasmids were used as previously described (Burdette et al.). Mutations in human STING were introduced using Quikchange Site Directed Mutagenesis Kit (Stratagene).
  • cDNA clones corresponding to mouse and human cGAS were obtained from Open Biosystems and correspond to those described previously (Sun et al., Wu et al.).
  • Mouse cGAS was amplified from cDNA clones with an N-terminal flag tag with forward oligo 5′-mcGAS-KpnI (5′-ATC GGG TAC CCC ACC ATG GAT TAC AAG GAT GAC GAT GAC AAG GAA GAT CCG CGT AGA AGG) (SEQ ID NO:13) and reverse oligo 3′-mcGAS-NotI (5′-ATC GGC GGC CGC TCA AAG CTT GTC AAA AAT TGG) (SEQ ID NO:14).
  • forward oligo 5′-mcGAS-KpnI 5′-ATC GGG TAC CCC ACC ATG GAT TAC AAG GAT GAC GAT GAC AAG GAA GAT CCG CGT AGA AGG
  • reverse oligo 3′-mcGAS-NotI 5′-ATC GGC GGC CGC TCA AAG CTT GTC AAA AAT TGG
  • hcGAS was amplified with forward oligo 5′-hcGAS-flag-KpnI (5′-ATC GGG TAC CCC ACC ATG GAT TAC AAG GAT GAC GAT GAC AAG CAG CCT TGG CAC GGA AAG G) (SEQ ID NO:15) and reverse 3′-hcGAS-NotI (5′ATC GGC GGC CGC TCA AAA TTC ATC AAA AAC TGG AAA C) (SEQ ID NO:16). Both PCR products were cloned into pCDNA3 at KpnI and NotI restriction enzyme sites.
  • DncV was amplified using DncV fwd BamHI (5′-GCA TGG ATC CGC CAC CAT GAC TTG GAA CTT TCA CCA G) (SEQ ID NO:17) and DncV rev NotI (5′-GCA TGC GGC CGC TCA GCC ACT TAC CAT TGT GCT GC) (SEQ ID NO:18) and cloned into pCDNA3 using BamHI and NotI.
  • DncV was amplified using DncV fwd XhoI (5′-GCA TCT CGA GCC ACC ATG ACT TGG AAC TTT CAC CAG) (SEQ ID NO:19) and DncV rev NotI. Resulting DNA was cloned into MSCV 2.2 digested with XhoI/NotI. Constructs for bacterial mcGAS overexpression were constructed as follows.
  • N terminal His6-SUMO tag amplified by PCR using His6 SUMO Nco (5′-TAA TAA GGA GAT ATA CCA TGG GCA GCA GCC) (SEQ ID NO:20) and His6 SUMO Sal (5′-GAA TTC GTC GAC ACC AAT CTG TTC TCT GTG AGC) (SEQ ID NO:21) off of pCDF-Duet2 template (gift from M. Rape lab, UC-Berkeley) and cloned into pET28a using NcoI and SalI to make pET28a-H6SUMO.
  • His6 SUMO Nco 5′-TAA TAA GGA GAT ATA CCA TGG GCA GCA GCC
  • His6 SUMO Sal 5′-GAA TTC GTC GAC ACC AAT CTG TTC TCT GTG AGC
  • mcGAS Full length mcGAS was PCR amplified from the mouse cDNA clone described above using mcGAS fwd Sal (5′-GAT GTC GAC ATG GAA GAT CCG CGT AGA AGG ACG) (SEQ ID NO:22) and mcGAS rev Xho (5′-ATC CTC GAG TCA AAG CTT GTC AAA AAT TGG AAA CC) (SEQ ID NO:23) and cloned into pET28a-H6SUMO using SalI and XhoI to make pET28a-H6SUMO-mcGAS that expresses full length mcGAS fused to an N-terminal His6 SUMO tag.
  • Sal 5′-GAT GTC GAC ATG GAA GAT CCG CGT AGA AGG ACG
  • mcGAS rev Xho 5′-ATC CTC GAG TCA AAG CTT GTC AAA AAT TGG AAA CC
  • WspR construct (pQE-WspR*) was a generous gift from Steve Lory (Harvard). WspR purification and c-di-GMP synthesis reactions were carried out as previously described (Merighi, et al., Mol Microbiol (2007)65: 876). Overexpression strains and plasmids for DncV and mutant DncV were provided by J. Mekalanos. DncV protein was overexpressed and purified as previously described (Davies et al.). Briefly, DncV protein production was induced in mid-log phase for 3 h at 37° C. with 1 mM IPTG. Cells were lysed and DncV protein was purified under denaturing conditions.
  • the cGAS product was purified using reverse-phase HPLC on an Agilent 1260 Infinity HPLC equipped with an Agilent Polaris C18-A column (5 ⁇ m, 250 mm ⁇ 10 mm, 180 ⁇ ). Purification conditions include a 100% to 0% gradient of solvent A over 20 min at 50° C. and a flow rate of 5 mL/min, where solvent A is 100 mM ammonium acetate in water and solvent B is acetonitrile. Purified elution fractions were evaporated multiple times in order to remove excess ammonia. Resonance assignments were made using COSY, 1 H- 13 C HSQC, NOESY, 1 H- 13 C HMBC, and 1H- 31 P HMBC.
  • HEK293T cells were plated in TC-treated 96-well plates at 0.5%°-%106% cells°/0 ml-1. The next day, the cells were transfected with indicated constructs, together with IFN- ⁇ -firefly luciferase and TKRenilla luciferase reporter constructs. Following stimulation for 6% h with the indicated ligands, the cells were lysed in passive lysis buffer (Promega) for 5% min at 25° C.
  • passive lysis buffer Promega
  • the cell lysates were incubated with firefly luciferase substrate (Biosynth) and the Renilla luciferase substrate coelenterazine (Biotium), and luminescence was measured on a SpectraMax L microplate reader (Molecular Devices). The relative lfnb expression was calculated as firefly luminescence relative to Renilla luminescence.
  • reactions were removed and mixed 1:5 with TLC running buffer (1:1.5 (v/v) saturated NH4SO4 and 1.5M KH2PO4, pH 3.6) and spotted on PEIcellulose TLC plate (Sigma). Following solvent migration, the TLC plate was exposed to a phosphorimager screen and imaged using Typhoon scanner. For in vitro product transfection into 293T cells, reactions were scaled up, radiolabeled nucleotide was omitted and the concentration of ATP and GTP was increased to 2 mM.
  • the phosphorous nucleus, P-11 is correlated to the 2′ ribose proton (H-12) of guanosine as well as to the 5′ ribose methylene protons (H-10) and the 4′ ribose proton (H-9) of adenosine.
  • the other phosphorous nucleus (P-22) is correlated to the 3′ ribose proton (H-8) of adenosine as well as to the 5′ ribose methylene protons (H-21) and 4′ ribose proton (H-20) of guanosine.
  • the regiochemistry of the phosphodiester linkages was determined to be cyclic[G(2′-5′)pA(3′-5′)p].
  • the protons corresponding to the adenine nucleobase (H-2, H-5) and guanine nucleobase (H-17) were assigned based upon reference spectra for the individual nucleobases, 1H-13C HMBC, and 1H-13C HSQC NMR ( FIG. 7A and 7B ).
  • the 1H-1H NOESY experiment showed through-space interactions_between the adenine proton H-5 and the 3′ ribose proton (H-8) as well as between the guanine proton H-17 and the 1′ ribose proton (H-18) ( FIG. 7D ).
  • the remaining protons in the corresponding ribose spin systems were identified by 1H-1H COSY ( FIG. 7C ), and multiplicity edited 1H-13C HSQC ( FIGS. 7A and 7B ), which distinguished the 5′ methylene protons in particular (H-10 and H-21).
  • RNA from mammalian cell lines was extracted using Trizol reagent (Invitrogen) or RNeasy Mini Kit (Qiagen). RNA was treated with RQ1 RNase-free DNase (Promega). RNA was reverse transcribed with Superscript III (Invitrogen). Mouse ifnB was quantified relative to mouse rps17 as described previously (Woodward et al). Human ifnB was quantified relative to human S9 as described previously (Wu et al).

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