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  • C07D277/02—Heterocyclic compounds containing 1,3-thiazole or hydrogenated 1,3-thiazole rings not condensed with other rings
  • C07D277/20—Heterocyclic compounds containing 1,3-thiazole or hydrogenated 1,3-thiazole rings not condensed with other rings having two or three double bonds between ring members or between ring members and non-ring members
  • C07D277/32—Heterocyclic compounds containing 1,3-thiazole or hydrogenated 1,3-thiazole rings not condensed with other rings having two or three double bonds between ring members or between ring members and non-ring members with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals, directly attached to ring carbon atoms
  • C07D277/36—Sulfur atoms
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  • A61K31/16—Amides, e.g. hydroxamic acids
  • A61K31/17—Amides, e.g. hydroxamic acids having the group >N—C(O)—N< or >N—C(S)—N<, e.g. urea, thiourea, carmustine
• • A—HUMAN NECESSITIES
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  • A61K31/33—Heterocyclic compounds
  • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
  • A61K31/41—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with two or more ring hetero atoms, at least one of which being nitrogen, e.g. tetrazole
  • A61K31/425—Thiazoles
  • A61K31/426—1,3-Thiazoles
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  • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
  • A61K31/41—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with two or more ring hetero atoms, at least one of which being nitrogen, e.g. tetrazole
  • A61K31/425—Thiazoles
  • A61K31/427—Thiazoles not condensed and containing further heterocyclic rings
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  • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
  • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
  • A61K31/47—Quinolines; Isoquinolines
  • A61K31/472—Non-condensed isoquinolines, e.g. papaverine
  • A61K31/4725—Non-condensed isoquinolines, e.g. papaverine containing further heterocyclic rings
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  • A61K31/00—Medicinal preparations containing organic active ingredients
  • A61K31/33—Heterocyclic compounds
  • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
  • A61K31/53—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with three nitrogens as the only ring hetero atoms, e.g. chlorazanil, melamine
• • 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
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  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P35/00—Antineoplastic agents
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  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D207/00—Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom
  • C07D207/02—Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom with only hydrogen or carbon atoms directly attached to the ring nitrogen atom
  • C07D207/44—Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom with only hydrogen or carbon atoms directly attached to the ring nitrogen atom having three double bonds between ring members or between ring members and non-ring members
  • C07D207/444—Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom with only hydrogen or carbon atoms directly attached to the ring nitrogen atom having three double bonds between ring members or between ring members and non-ring members having two doubly-bound oxygen atoms directly attached in positions 2 and 5
  • C07D207/448—Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom with only hydrogen or carbon atoms directly attached to the ring nitrogen atom having three double bonds between ring members or between ring members and non-ring members having two doubly-bound oxygen atoms directly attached in positions 2 and 5 with only hydrogen atoms or radicals containing only hydrogen and carbon atoms directly attached to other ring carbon atoms, e.g. maleimide
  • C07D207/452—Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom with only hydrogen or carbon atoms directly attached to the ring nitrogen atom having three double bonds between ring members or between ring members and non-ring members having two doubly-bound oxygen atoms directly attached in positions 2 and 5 with only hydrogen atoms or radicals containing only hydrogen and carbon atoms directly attached to other ring carbon atoms, e.g. maleimide with hydrocarbon radicals, substituted by hetero atoms, directly attached to the ring nitrogen atom
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  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D239/00—Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings
  • C07D239/02—Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings not condensed with other rings
  • C07D239/24—Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings not condensed with other rings having three or more double bonds between ring members or between ring members and non-ring members
  • C07D239/28—Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings not condensed with other rings having three or more double bonds between ring members or between ring members and non-ring members with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, directly attached to ring carbon atoms
  • C07D239/46—Two or more oxygen, sulphur or nitrogen atoms
  • C07D239/48—Two nitrogen atoms
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  • C07—ORGANIC CHEMISTRY
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  • C07D251/00—Heterocyclic compounds containing 1,3,5-triazine rings
  • C07D251/02—Heterocyclic compounds containing 1,3,5-triazine rings not condensed with other rings
  • C07D251/12—Heterocyclic compounds containing 1,3,5-triazine rings not condensed with other rings having three double bonds between ring members or between ring members and non-ring members
  • C07D251/26—Heterocyclic compounds containing 1,3,5-triazine rings not condensed with other rings having three double bonds between ring members or between ring members and non-ring members with only hetero atoms directly attached to ring carbon atoms
  • C07D251/40—Nitrogen atoms
  • C07D251/54—Three nitrogen atoms
  • C07D251/66—Derivatives of melamine in which a hetero atom is directly attached to a nitrogen atom of melamine
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  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D403/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00
  • C07D403/02—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing two hetero rings
  • C07D403/12—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing two hetero rings linked by a chain containing hetero atoms as chain links
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  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D405/00—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom
  • C07D405/02—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom containing two hetero rings
  • C07D405/12—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom containing two hetero rings linked by a chain containing hetero atoms as chain links
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  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D417/00—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00
  • C07D417/02—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00 containing two hetero rings
  • C07D417/12—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00 containing two hetero rings linked by a chain containing hetero atoms as chain links

Definitions

• the present invention refers to compounds with cellular RNA helicase and /or ATPase DDX3 inhibitory activity and their therapeutic use, in particular for the treatment of viral and neoplastic diseases.
• the invention relates also to a method for identifying compounds endowed with binding capacities to the target sites on DDX3.
• HIV-1 integrase such as integrase interactor 1 (Inil) which has amino acid similarity to the yeast transcriptional activator SNF5, a component of the multiprotein SWI/SNF complex (Kalpana et al., 1994), and HMGA1, a non-histone chromosomal protein important for transcriptional control and chromosomal architecture (Farnet and Bushman, 1997).
• the Debyser group has recently identified Lens Epithelium Derived Growth Factor (LEDGF) as a novel binding partner of HIV-1 integrase (Cherepanov et al, 2003), using Fluorescence Cross Correlation Spectroscopy as an innovative technology to study protein- protein interactions in the living cell (Maertens et al., 2005).
• LEDGF Lens Epithelium Derived Growth Factor
• Other steps of the replicative cycle of HIV-1 require the essential contribution of specific cellular proteins, including viral transcription (cellular Cyclin Tl (Wei et al., 1998)) and viral assembly and egress (e.g. TSG101, a member of the cellular ESCRT machinery (von Schwedler et al., 2003)).
• Keppler group previously demonstrated that immuno- competent rats, that transgenically express the human CD4/CCR5 receptor complex, support a robust cellular infection and transient, low- level viremia (Keppler et al, 2005; Keppler et al., 2002; Keppler et al, 2001).
• primary macrophages from transgenic rats supported the full HIV-1 replication cycle and secreted infectious virions.
• nucleo-cytoplasmic transport processes take place through the nuclear pore complex (NPC), a large dynamic multi-protein assembly that acts as the passageway for transport (Pante, 2004). This active transport can also occur against a concentration gradient, and is mediated by soluble transport factors, that in turn shuttle between the nucleus and the cytoplasm.
• NPC nuclear pore complex
• soluble transport factors that in turn shuttle between the nucleus and the cytoplasm.
• HIV-1 Rev molecules that are theoretically small enough for passive diffusion
• HIV-1 Rev are actively and selectively transported, since regulated transport appears to be more efficient and more amendable for specific regulation (Pemberton and Paschal, 2005). HIV-1 has a total of nine genes that are expressed by alternative splicing of a single, initial pro viral transcript that also forms the RNA genome.
• HIV-1 replication requires the nuclear export and translation of unspliced, singly-spliced and multiply- spliced derivatives of this initial transcript.
• Fully spliced mRNAs encode the viral regulatory proteins Tat, Rev and Nef
• incompletely spliced HIV-1 mRNAs primarily encode viral auxiliary (Vif, Vpr, Vpu) and structural proteins.
• the HIV-1 Rev is a sequence-specific nuclear mRNA-export factor. In the absence of Rev function, the incompletely spliced HIV-1 mRNAs that encode the viral structural proteins are retained in the cell nucleus, whereas nuclear export of fully-spliced HIV-1 mRNAs, including the mRNA encoding Rev itself, is independent of Rev function.
• Rev response element nuclear export of unspliced HIV-1 mRNAs also requires a structured cz ' s-acting RNA sequence, called the Rev response element (RRE), which is specifically bound by Rev.
• RRE Rev response element
• the nuclear retention of the incompletely spliced viral mRNAs in the absence of Rev results from the fact that splice sites present in the retained introns are recognized by cellular mRNA processing factors, termed splicing commitment factors, that normally prevent cellular pre-mRNAs (i.e. incompletely spliced cellular mRNAs) from exiting the nucleus. (Cullen, 2003).
• the HIV- 1 Rev protein has two distinct functional domains, an N-terminal sequence required for RRE binding and Rev multimerization and a 10-amino-acid leucine-rich domain near the C-terminus that serves as the Rev nuclear export signal (NES).
• NES Rev nuclear export signal
• the Crml -dependent cellular RNA export pathway The Crml -dependent cellular RNA export pathway.
• Crml is a member of the karyopherin-beta family of nucleocytoplasmic-transport factors.
• Karyopherin-beta members associate with karyopherin- alpha in the cytoplasm, forming a heterodimeric complex with proteins containing a nuclear localisation signal (NLS).
• NPC nuclear pore complex
• karyopherin -beta interacts with the nuclear pore complex (NPC), facilitating the import of the karyopherin -alpha/NLS -protein complex.
• NPC nuclear pore complex
• members of the karyopherin -beta family have been identified which regulate nuclear export, rather than import, pathways.
• One of such proteins is Crml, which shares homology with karyopherin betal, beta2, beta3 and beta4.
• Crml Human Crml is localized both at the NPC and in the nucleoplasm and seems to shuttle between the nucleus and cytoplasm. It is now clear that Crml is the crucial nuclear export factor for two classes of cellular RNAs, that is, U-rich small nuclear RNAs and ribosomal R As. Crml binds its cargo in the nucleus in the presence of the GTP -bound form of the Ran GTPase. After nuclear export, hydrolysis of the bound GTP to GDP causes a conformational shift that induces cytoplasmic cargo release, thus providing the directionality of this export pathway. Crml also interacts with components of the NPC, the portal used for all nucleocytoplasmic transport, and this interaction is essential for Crml -mediated nuclear RNA export.
• the DDX3 family of cellular RNA helicases The DDX3 family of cellular RNA helicases.
• RNA helicase DDX3 was identified as an essential co factor for Rev/RRE-mediated HIV RNA-export (Yedavalli et al, 2004).
• RNA helicases from the DEAD-box family are found in almost all organisms and have important roles in RNA metabolism. They are associated with many processes ranging from RNA synthesis to RNA degradation.
• DEAD-box proteins use the energy from ATP hydrolysis to rearrange inter- or intra-molecular RNA structures or dissociate RNA-protein complexes.
• Human DEAD-box family includes 36 members. The majority of DEAD-box family members have demonstrated functions in ribosome biogenesis and translation initiation.
• the first feature is dysregulation in cancer, which occurs in the form of involvement in recurrent chromosomal translocations (DDX6, DDX10) or overexpression (DDX1, DDX6, DDX4).
• the second feature is the involvement of DDX members in tissue- organ differentiation (DDX4 in germ cell development, DDX5 in organ differentiation, DDX25 in spermatogenesis, and DDX41 in visual system development). Therefore, putative RNA helicases may have a function in differentiation, possibly by their effect on the expression of critical differentiation genes.
• DDX3 expression was found to be induced in HIV-1 infected cells by the viral transcriptional activator Tat, but it apparently plays no role in HIV-1 transcription. Instead, DDX3 was shown to be an RNA-dependent ATPase/helicase which functions in the Rev- RRE/CRMl pathway for the export of unspliced/partially spliced HIV-1 transcripts.
• DDX3 is a nucleo-cytoplasmic shuttling protein that binds Crml and associates to the cytoplasmic side of nuclear pores. Its enzymatic activity, as well as its physical interaction with Crml is necessary for Rev/RRE mediated nuclear export of viral RNAs. However, the molecular details of its role(s) in this pathway are yet to be elucidated.
• DDX3 hepatocellular carcinoma
• HCCs hepatocellular carcinoma
• HCV hepatitis B virus
• DDX3 expression in HCCs is differentially regulated by the gender and, moreover, there is a tendency that the downregulation of DDX3 expression in HCCs is more frequent in males than in females.
• siRNA small interfering RNAs
• HCV hepatitis C virus
• DDX3 expression correlates with an aggressive tumoral phenotype.
• the human breast cell line, MCF 10A was characterized for the gene expression pattern. Of the differential genes expressed, it was found consistent activation of DDX3, a member of the DEAD box RNA helicase family. Overexpression of DDX3 in MCF 10A cells induced an epithelial-mesenchymal-like transformation, exhibited increased motility and invasive properties, and formed colonies in soft-agar assays.
• MCF 10A-DDX3 cells repressed E-cadherin expression as demonstrated by both immunoblots and by E-cadherin promoter-reporter assays.
• E-cadherin promoter-reporter assays an in vivo association of DDX3 and the E-cadherin promoter was demonstrated by chromatin immunoprecipitation assays.
• RT reverse transcriptase
• PR protease
• I integrase
• one class of drugs inhibits HIV entry in cells by competing for the recepetor/coreceptor usage. While drugs directed against RT and PR are widely used, their efficacy is hampered by mutations in the target enzymes, leading invariably to drug resistance and chemotherapy failure.
• the protein DDX3 has been shown to 1) be an essential cofactor for the replication of the HIV-1 and HCV viruses; 2) be involved in the proliferation of cancer cells.
• the DDX3- inhibitors are therefore considered as potential agents not only in the treatment of HIV-1 infections, but also for other viruses such as HCV, as well as in the treatment of various kinds of cancer, such as hepatocellular carcinoma.
• DDX3 -inhibitors to the existing antiviral and anticancer therapy would also improve the outcome of the treatment.
• Maga et al. J. Med. Chem. 2008, 51, 6635-6638 disclose a receptor-based Pharmacophore Models of the ATP -binding site to be used for the identification of DDX3 inhibitors.
• the three dimensional arrangements of the functional groups of an inhibitor described by the Pharmacophoric Models (essential for the effective binding to DDX3) has been used for a three-dimensional (3D) database search.
• the present invention describes compounds with cellular DDX3 inhibitory activity and their use in the treatment of viral and neoplastic diseases.
• a method for the identification of such inhibitors, based on an homology model of the closed conformation of DDX3 to locate the RNA-binding site and Virtual Docking protocol is disclosed. The synthesis of the compounds is also provided.
• the invention illustrate a novel approach to treat HIV/AIDS, namely targeting a cellular enzyme (the DEAD-box RNA helicases DDX3) which has been recognized as a co-factor for HIV replication, thus rendering the infected cell an unfavorable environment for viral replication.
• a cellular enzyme the DEAD-box RNA helicases DDX3
• the advantage of such approach is ideally represented by the possibility to overcome the drug resistance problem connected to common anti-HIV drugs, since cellular enzymes do not have the high mutation rates typical of viral enzymes.
• the present invention describes compounds able to suppress the enzymatic functions of the cellular protein DDX3 (Dead-box polypeptide 3; Ref. Seq. NP 001347), namely: ATP hydrolysis (ATPase) and/or DNA/RNA unwinding (helicase).
• Z represents CH 2 or S
• X and Y represent independently O or S
• n is comprised between 0 and 4
• Ri, R 2 , R 3 are each independently selected from the group of: H, a linear or branched alkyl group comprising 1 to 6 carbon atoms, unsubstituted or substituted phenyl radical, an unsubstituted or substituted phenylalkenyl radical, an unsubstituted or substituted phenyalkynyl radical, an unsubstituted or substituted biphenylalkyl radical, an unsubstituted or substituted heterocyclic radical, an unsubstituted or substituted polycyclic radical, an unsubstituted or substituted alicyclic radical or a radical of the formula (Ria- ) m (L-) p Rib-, wherein Ria and Rib may be the same or different and represent an unsubstituted or substituted heterocyclic radical or an unsubstituted or substituted phenyl radical, Ria also represents an unsubstitutetd or substituted polycyclic radical and L represents
• R 2 and R 3 together optionally form a cycloalkyl, cycloalkenyl, non-aromatic heterocyclic, or fused or polycyclic ring, 2-oxindole wherein said cycloalkyl, cycloalkenyl, non- aromatic heterocyclic and fused or polycyclic ring are optionally substituted with one or more substituents selected from the groups above described.
• fused or polycyclic ring examples include substituted or unsubstituted 2-oxindoles; substituted or unsubstituted lH-indene-l,3-diones wherein the heterocyclic radical is selected from the group consisting of morpholine, thiomorpholine, piperidine, piperazine, pyrrolidine, furan, thiophene, oxazole, oxadiazole, isoxazole, pyridine, 1,3-oxathiolane, thiazole, isothiazole, thiadiazole, imidazole, pyrrole, tetrazole or triazine;
• poly cyclic radical is selected from the group consisting benzo furan, isobenzofuran, benzothiophene, isobenzothiophene, benzoxazole, indole, 2-isoindole, 2- oxindole, 2-methylindole, benzopyrazole, quinoline, isoquinoline, tetrahydroquinoline, 1,3-benzodioxole, 1 ,2-benzodiazine, 1,3-benzodiazine, 1,2,3-benzotriazole, benzothiazole, benzimidazole, 1,2,3-benzotriazine, 1,2,4-benzotriazine, naphtalene, antracene or fluorene; wherein the alicyclic radical preferably comprises 5 to 8 carbon atoms.
• suitable cycloalkyls are cyclopentyl, cyclohexyl, methylcyclohexyl and norbornyl.
• heterocyclic radical substituents, the polycyclic radical substituents and the alicyclic radical substituents being at least one selected from the group consisting of straight or branched chain, saturated or unsaturated aliphatic group having 1-6 carbon atoms, halogen, perhaloalkyl, monohaloalkyl, dihaloalkyl, alkoxy, acyl, acyloxy, acyloxyalkyl, phenylalkoxy, hydroxy, hydroxyalkyl, thio, alkylthio, nitro, carboxy, carbalkoxy;
• phenyl radical substituents, the phenylalkenyl radical substituents, the phenylalkynyl radical substituents or the biphenylalkyl radical substituents are selected from the group consisting of a straight or branched chain, saturated or unsaturated aliphatic group having 1-6 carbon atoms, halogen, nitro, carboxy, carboxy alkyl, alkoxy, hydroxy, hydroxyalkyl, perhaloalkoxy, acyl, acyloxy, acyloxyalkyl, cyano, carbalkoxy, thio, alkythio, alkylsulfmyl, alkylsulfonyl, amino, alkylamino, dialkylamino, aminoalkyl, alkylaminoalkyl, dialkylaminoalkyl, sulfonamido, carboxamido, alkanoylamino;
• W is absent or represents independently O, S, NH, NHCH 2 or N-R 5 wherein R 5 is a linear or branched alkyl group comprising 1 to 6 carbon atoms;
• A is absent or represents CONH, NHCO, NHCONH;
• R4 represents H, unsubstituted or substituted alkyl from 1 to 6 carbon atoms, unsubstituted or substituted alkenyl, unsubstituted or substituted alkynyl, halogen, haloalkyl, COOH, OCH 3 , N0 2 , NH 2 , CN, OZ' or SZ' where Z' is H, or unsubstituted or substituted alkyl from 1 to 6 carbon atoms;
• the compound is the compound l id, 14f, 14g, 15h, 15k, 38, FE56, FE56M, FE56F, FE56N, FE56AN or 22.
• Ri is independently selected from the group of substituted phenyl radical or polycyclic radical
• the compound is the compound 35b, 35c, 35f, FE-70, FE-77, FE-69, FE- 74.
• the compound is the compound EI-01 , EI-01A, EI-01B, 25, 26, 27, 29, 30, 31.
• the compound is an inhibitor of the human DEAD-box RNA helicases DDX3. Still preferably the compound is an inhibitor of ATPase and/or helicase of the human DEAD-box RNA helicases DDX3.
• the pathology modulated by DDX3 activity and/or expression is an infection or a hyperproliferative disease.
• the infection is a viral infection.
• the viral infection is caused by HIV, HBV, HCV or poxviruses. More preferably it is caused by HIV-1.
• the hyperproliferative disease is a tumor.
• the tumour is selected from the group of: hepatocellular carcinoma, cervical cancer, breast cancer, lymphomas, leukemias.
• composition comprising the compound as defined above, or a pharmaceutically acceptable salt, solvate, or hydrate thereof and pharmaceutically acceptable excipients for use as a treatment of a pathology modulated by DDX3 activity and/or expression.
• a pathology modulated by DDX3 activity and/or expression is defined as a pathology that can be induced, trigerred or enhanced by DDX3 protein.
• the activity of DDX3 can be measured by techniques known in the art for instance by measuring the enzymatic activity of the protein (ATPase or helicase activity).
• the expression of DDX3 is also measured by commonly used methods in the art.
• the compounds of the present invention are particularly suitable for the treatment of patient that are resistant to at least one currently used treatment for HIV infection. For instance, patient resistant to RT inhibitors, PR inhibitors and/or IN inhibitors.
• the compounds as defined above and suitable excipients and/or diluents may be administered in combination with pharmaceutical compositions of approved drugs for the treatment of the HIV-1 infections as part of highly active antiretro viral therapy (HAART).
• HAART highly active antiretro viral therapy
• the pharmaceutical composition of the invention may comprise a combination of at least two of the compounds of the invention or a pharmaceutically acceptable salt thereof, and suitable excipients and/or diluents and may be also administered in combination with pharmaceutical compositions of approved drugs for the treatment of the HCV infections as part of combinatorial multidrug anti-HCV therapy.
• the pharmaceutical composition of the invention may comprise a combination of at least two of the compounds of the invention or a pharmaceutically acceptable salt thereof, and suitable excipients and/or diluents and may be also administered in combination with pharmaceutical compositions of approved drugs for the treatment of cancers as part of combinatorial multidrug cancer therpay.
• the pharmaceutical composition comprising at least one or two of the compounds of the invention together with at least one approved compound for the treatment of HIV-1 infections are in the same formulation or a pharmaceutically acceptable salt thereof, and suitable excipients and/or diluents to be administered as such.
• the compounds of the invention or their salts may be administered as pure or as pharmaceutical formulations, i.e. suitable for parenteral, oral, or rectal administrations.
• Each of said formulations may contain excipients and/or fillers and/or additives and/or binders, coatings and/or suspending agents and/or emulsifying agents, preserving and/or control release agents, suitable for the selected pharmaceutical form.
• It is a further object of the invention a method for inhibiting the human DEAD-box RNA helicases DDX3 comprising contacting the compound of the invention or the composition as defined above with human DDX3, thereby inhibiting the activity of DDX3.
• It is a further object of the invention a process for the preparation of the compound as defined above. It is a further object of the invention a method for identifying a compound endowed with helicase inhibitory activity against the human DEAD-box RNA helicases DDX3 comprising using at least a portion of the homology model (namely the RNA binding site) of the close conformation of DDX3 as defined in Appendix I and Fig. 3.
• the method comprises:
• the candidate compound is selected from a library of compounds, selected from a from a database, is provided computationally, is designed de novo or is designed from a known DDX3 inhibitor.
• the sufficient level of binding is indicated by a calculated binding energy defined by a Chemscore value of at least 25.
• the compound has the formula 4 as defined above.
• composition comprising the compound identified by the method as described above or a pharmaceutically acceptable salt, solvate, or hydrate thereof and pharmaceutically acceptable excipients for use as a treatment of a pathology modulated by DDX3 activity and/or expression.
• a computer-readable data storage medium comprising a data storage material encoded with computer-readable data, wherein said data comprises the structure co-ordinates of the close conformation of DDX3 of Appendix 1 ;
• a working memory for storing instructions for processing said computer- readable data
• a central-processing unit coupled to said working memory and to said computer- readable data storage medium for processing said computer-machine readable data into said three-dimensional representation
• a display coupled to said central-processing unit for displaying said three- dimensional representation.
• a machine-readable data storage medium comprising a data storage material encoded with machine readable data, wherein the data is defined by at least a portion of the structure co-ordinates of the close conformation of DDX3 of Appendix 1.
• Figure 1 A) Antiviral activity (expressed as % of viral load with respect to the control) of compounds FE56 and FE66 at 0.3 ⁇ and 3 ⁇ doses against single round HIV-1 replication in HeLaCD4+ cells infected with a wild type HIV-1 strain. Measurements were performed at 72 h post infection.
• PBMCs phytohemagglutinin-stimulated peripheral blood mononuclear cells
• FIG. 1 Antiviral activity of DDX3 inhibitors.
• Figure 3 Schematic representation of in silico DDX3-closed model preparation.
• Figure 4 Schematic representation of in silico screening protocol (virtual docking) for the discovery of DDX3 inhibitors targeting the ATP- and/or the RNA-binding site.
• Mass spectra (MS) data were obtained using an Agilent 1100 LC/MSD VL system (G1946C) with a 0.4 mL/min flow rate using a binary solvent system of 95:5 methyl alcohol/ water. UV detection was monitored at 254 nm. Mass spectra were acquired in positive and negative mode scanning over the mass range.
• Microwave Irradiation Experiments Microwave Irradiation Experiments. Microwave irradiation experiments were conducted using a CEM Discover Synthesis Unit (CEM Corp., Matthews, NC). The machine consists of a continuous focused microwave power delivery system with operator- selectable power output from 0 to 300 W. The temperature of the contents of the vessels was monitored using a calibrate infrared temperature control mounted under the reaction vessel. All the experiments were performed using a stirring option whereby the contents of the vessel are stirred by means of rotating magnetic plate located below the floor of the microwave cavity and a Teflon-coated magnetic stir bar in the vessel.
• CEM Discover Synthesis Unit CEM Corp., Matthews, NC
• the machine consists of a continuous focused microwave power delivery system with operator- selectable power output from 0 to 300 W.
• the temperature of the contents of the vessels was monitored using a calibrate infrared temperature control mounted under the reaction vessel. All the experiments were performed using a stirring option whereby the contents of the vessel are stirred by means of rotating magnetic
• ATPase activity was tested with a luciferase-based luminescence assay (Easylite-Kinase, Perkin Elmer) on 96 wells microtiter plates. Briefly, recombinant purified human DDX3 (50-100 ng) was incubated in a 15 total reaction volume with reaction buffer (25 mM TrisHCl pH 7.5, 5 mM MgCl 2 ), in the presence of increasing amounts of ATP and/or different combinations of ATP and the inhibitor to be tested. Reference curves in the absence of inhibitor (giving the 100% of enzymatic activity) and in the absence of enzyme (giving the baseline), were also included in each experiment. Reading was performed with a Microbeta Trilux (Perkin Elmer) luminometer, according to the manufacturer's protocol.
• DDX3 wt and mutant forms were monitored by measuring the conversion of a double stranded (ds) DNA or RNA (labelled at the 5 '-end of one strand with a 6-FAM fluorescent group or P 32 , respectively) into single stranded (ss) nucleic acid. Reactions were performed in 50 mM TrisHCl pH 7.5, 1 mM DTT, 0.2 mg/ml BSA, 5% glycerol and 100 ⁇ ATP, 10 mM MgCl 2 at 37°C degrees for 10' and stopped by adding EDTA 50 mM pH 8. Products were separated through non-denaturating 8%PAGE at 5 W for 2 hours in TBE buffer at 4°C. Substrates and products were quantified by laser scanning densitometry (Thyphoon-TRIO, GE Healthcare).
• ATPase reactions were performed as described, in the presence of increasing amounts of inhibitor and variable ATP concentrations. Variations of the initial velocities of the reaction as a function of ATP concentrations in the absence or presence of 4 were analyzed with the equation:
• DDX3 Human recombinant DDX3 was cloned, expressed and purified as described (Franca et al. Proteins 2007, 67, 1 128-37).
• each HIV-1 plasmid construct was transfected into CD4 + HeLa cells by using the lipofectin reagent, according to the recommendations of the manufacturer (Invitrogen, Groningen, The Netherlands). After 3 days of incubation at 37°C, the cell supernatants, which contained reconstituted viable recombinant viruses, were collected. Quantification of the newly produced recombinant strains was obtained by determination of the HIV R A copy number in the cell culture supernatants.
• PBMCs were incubated at 37°C in 10 ml of RPMI 1640 medium (Eurobio, Les Ulis Cedex B, France) supplemented with 20% fetal calf serum (Life Technologies, Ltd., Paisley, Scotland), 2 mM 1-glutamine, 100 U of penicillin per ml, 100 ⁇ g of streptomycin per ml, 10% interleukin-2 (ZeptoMetrix Co., Buffalo, N.Y.), 5 ⁇ g of hydrocortisone (Sigma Chemical Co.) per ml and with fourfold dilutions of antiretroviral drugs.
• RPMI 1640 medium Eurobio, Les Ulis Cedex B, France
• 20% fetal calf serum Life Technologies, Ltd., Paisley, Scotland
• 2 mM 1-glutamine 100 U of penicillin per ml
• 100 ⁇ g of streptomycin per ml 100 ⁇ g of streptomycin per ml
• 10% interleukin-2 Zepto
• No-drug controls for each drug dilution were included in each assay. After 3, 5 and 7 days of incubation the HIV-1 RNA in the cell culture supernatant was quantified. Recombinant HIV-1 strains from treatment-naive patients and multidrug resistance-associated changes were assayed in parallel. The degree of inhibition of viral replication was measured by determining the HIV-1 RNA level in the supernatants of cell cultures and was expressed as the fold increase in the 50% inhibitory concentrations (IC 50 s) for resistant recombinant HIV-1 variants compared with the IC50S for the wild-type recombinant variant. Each test was performed in triplicate.
• the DDX3X(V168-G582) domain 2 has to rotate approximately 180° relative to domain 1 to obtain the closed conformation of the protein required for RNA binding. This rearrangement would bring positively charged patches on the solvent-exposed surface of domain 2 into closer proximity with positively charged surfaces on domain 1 , thus forming the RNA-binding site of the protein.
• a comparison of the closed structure of the VASA protein in complex with poly(U) with a modeled closed structure of the DDX3X(V168-G582) protein show that all amino acid residues that are involved in interaction with the RNA in the VASA- structure are present in the DDX3X(V168-G582) structure at corresponding positions. This indicates, as expected, that these residues are involved in RNA binding in both proteins, and that the RNA binding mode in this area should be very similar.
• the present homology model has been built as follows: the "closed" structure was built by alignment of the individual domains on the respective domains of the protein eIF4A (eukaryotic translation initiation factor) which is in a closed conformation (pdb entry 2J0S, homology 37%) and final optimization of the resulting structure [RMS 1.2 A]. 2J0S is cocrystallized with PolyU and this allowed the authors to immediately identify the binding site of nucleic acid for the authors' protein.
• eIF4A eukaryotic translation initiation factor
• the alignment has been performend using Pymol alignement function.
• the structure obtained has been used as target for the authors' virtual docking studies.
• Protein Preparation Wizard procedure was used to obtain a satisfactory starting structure for docking studies. This facility is designed to ensure chemical correctness and to optimize the protein structure for further analysis.
• the process adds hydrogens, neutralizes appropriate amino acid chains, and relieves steric clashes. In particular, it performs a series of restrained, partial minimizations on the cocrystallized structure, each of which employs a limited number of minimization steps. It is not intended to minimize the system completely.
• the minimization OPLS 2001 force field
• the final homology model is reported in Appendix I.
• ATOM 83 CA ASN A 173 33.562 72.353 13.261 1.00 0.00 C ATOM 84 C ASN A 173 34.580 71.735 12.309 1.00 0.00 c ATOM 85 O ASN A 173 34.499 70.537 12.047 1.00 0.00 o ATOM 86 CB ASN A 173 33.737 71.708 14.638 1.00 0.00 c ATOM 87 CG ASN A 173 35.208 71.734 15.053 1.00 0.00 c ATOM 88 ND2 ASN A 173 35.749 70.638 15.562 1.00 0.00 N ATOM 89 OD1 ASN A 173 35.893 72.734 14.856 1.00 0.00 o ATOM 90 H ASN A 173 31.595 71.498 13.217 1.00 0.00 H ATOM 91 HA ASN A 173 33.726 73.429 13.314 1.00 0.00 H ATOM 92 1HB ASN A 173 33.150 72.257 15.375 1.00 0.00 H ATOM
• ATOM 161 IHB HIS A 178 36.231 69.229 -1.762 1.00 0.00 H
• ATOM 162 2HB HIS A 178 36.112 70.312 -0.356 1.00 0.00 H
• ATOM 505 1HB TYR A 200 32.526 59.451 -12.076 1.00 0.00 H
• ATOM 506 2HB TYR A 200 31.362 60.777 -12.308 1.00 0.00 H
• ATOM 540 2HB ARG A 202 33.036 66.409 -12.645 1.00 0.00 H
• ATOM 558 1HB PRO A 203 33.554 65.186 -6.325 1.00 0.00 H
• ATOM 673 3HB ALA A 210 30.399 63.349 -0.402 1.00 0.00 H ATOM 674 N ILE A 211 33.312 63.034 0.169 1.00 0.00 N
• ATOM 702 2HB PRO A 212 38.660 64.914 1.540 1.00 0.00 H
• ATOM 703 IHG PRO A 212 36.001 66.369 1.642 1.00 0.00 H
• ATOM 742 1HD1 ILE A 214 29.715 60.361 3.040 1.00 0.00 H
• ATOM 818 2HB ARG A 218 33.089 65.007 11.184 1.00 0.00 H
• ATOM 822 2HD ARG A 218 36.096 65.544 13.191 1.00 0.00 H
• ATOM 869 1HB MET A 221 23.594 65.492 9.303 1.00 0.00 H
• ATOM 870 2HB MET A 221 24.216 66.870 8.363 1.00 0.00 H
• ATOM 884 2HB ALA A 222 26.573 64.607 3.563 1.00 0.00 H
• ATOM 885 3HB ALA A 222 25.306 63.513 2.960 1.00 0.00 H
• ATOM 894 1HB CYS A 223 19.991 67.136 3.960 1.00 0.00 H
• ATOM 904 1HB ALA A 224 22.313 66.322 -3.146 1.00 0.00 H
• ATOM 906 3HB ALA A 224 22.361 64.982 -1.976 1.00 0.00 H
• ATOM 908 CA GLN A 225 18.011 66.070 -4.016 1.00 0.00 C
• ATOM 918 1HB GLN A 225 16.719 66.782 -5.592 1.00 0.00 H
• ATOM 1007 2HB ALA A 232 26.914 56.387 -7.071 1.00 0.00 H

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