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WO 2011/043817 Al 14 April 2011 (14.04.2011) PCT (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2011/043817 Al 14 April 2011 (14.04.2011) PCT (51) International Patent Classification: 10010 (US). ARNOLD, Lee, D. [US/US]; 55 Chestnut A61F 2/00 (2006.01) Street, Mt. Sinai, NY 11766 (US). (21) International Application Number: (74) Agents: GOLDMAN, Michael, L. et al; Nixon Peabody PCT/US20 10/002708 LLP, Patent Group, 1100 Clinton Square, Rochester, NY 14604-1792 (US). (22) International Filing Date: 7 October 2010 (07.10.2010) (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, (25) Filing Language: English AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, (26) Publication Langi English CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (30) Priority Data: HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, 61/278,523 7 October 2009 (07.10.2009) US KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, (71) Applicants (for all designated States except US): COR¬ ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NELL UNIVERSITY [US/US]; Cornell Center For NO, NZ, OM, PE, PG, PH, PL, PT, RO, RS, RU, SC, SD, Technology Enterprise, & Commercialization, 395 Pine SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, Tree Road, Suite 310, Ithaca, NY 14850 (US). PURDUE TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. RESEARCH FOUNDATION [US/US]; 3000 Kent Av (84) Designated States (unless otherwise indicated, for every enue, West Lafayette, IN 47906 (US). COFERON, INC. kind of regional protection available): ARIPO (BW, GH, [US/US]; 55 1 Fifth Avenue, 34th Floor, New York, NY GM, KE, LR, LS, MW, MZ, NA, SD, SL, SZ, TZ, UG, 10176 (US). ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, MD, RU, TJ, (72) Inventors; and TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, (75) Inventors/Applicants (for US only): BARANY, Francis EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, [US/US]; 450 East 63rd Street, Apt. 12c, New York, NY LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, 10065 (US). PINGLE, Maneesh [IN/US]; 5 15 East 75th Street, Apt. 2F, New York, NY 10021 (US). GW, ML, MR, NE, SN, TD, TG). BERGSTROM, Donald [US/US]; 3416 Hamilton Street, Published: West Lafayette, IN 47906 (US). GIARDINA, Sarah, F. — with international search report (Art. 21(3)) [AU/US]; 240 East 25th Street, Apt.4, New York, NY (54) Title: COFERONS AND METHODS OF MAKING AND USING THEM Linker Element (Dynamic combinatorial chemistry element, Barcode MW usually under 450) - (Optional: bead, or position; used to guide Connector synthesis and/or identify (Optional) diversity element. Removed from final drug molecule) † Ligand / Pharmacophore (Diversity Element, binds to target. MW Aprox. 400-800) 00 o Figure 1 (57) Abstract: The present invention is directed to a monomer useful in preparing therapeutic compounds. The monomer includes one or more pharmacophores which potentially binds to a target molecule with a dissociation constant of less than 300 µΜ and a linker element connected to the pharmacophore. The linker element has a molecular weight less than 500 daltons, is connected, di- Q rectly or indirectly through a connector, to the pharmacophore. COFERONS AND METHODS OF MAKING AND USING THEM [0001] This application claims the benefit of U.S. Provisional Patent Application Serial No. 61/278,523, filed October 7, 2009, which is hereby incorporated by reference in its entirety. [0002] This invention was made with government support under Public Health Service grant AI062579-03 from the National Institute of Allergy and Infectious Diseases and Grant No. CA65930-08 from the National Cancer Institute. The government has certain rights in this invention. FIELD OF THE INVENTION [0003] The present invention is directed to coferons and methods of making and using them. BACKGROUND OF THE INVENTION [0004] Cancers arise due to mutations or dysregulation of genes involved in DNA replication and repair, cell cycle control, anchorage independent growth, angiogenesis, apoptosis, tissue invasion, and metastasis (Hanahan, D. et al., Cell 100(1): 57-70 (2000)). These processes are controlled by networks of genes in the p53, cell cycle, apoptosis, Wnt signaling, RPTK signaling, and TGF-beta signaling pathways. Such genes and their protein products are the targets of many current and developing therapies. [0005] Signaling pathways are used by cells to generate biological responses to external or internal stimuli. A few thousand gene products control both ontogeny/development of higher organisms and sophisticated behavior by their many different cell types. These gene products work in different combinations to achieve their goals, and do so through protein-protein interactions. The evolutionary architecture of such proteins is through modular protein domains that recognize and/or modify certain motifs. For example, different tyrosine kinases (such as Abl) will add phosphate groups to specific tyrosines embedded in particular peptide sequences, while other enzymes (such as PTEN) act as phosphatases to remove certain signals. Proteins and other macromolecules may also be modified through methylation, acetylation, sumolation, ubiquitination, and these signals in turn are recognized by specific domains that activate the next step in the pathway. Such pathways usually are initiated through signals to receptors on the surface, which move to intracellular protein interactions and often lead to signaling through transcription factor interactions that regulate gene transcription. For example, in the Wnt pathway, Wnt interacts with the Frizzled receptor, signaling through Disheveled, which inhibits the Axin-APC-GSK3 complex, which binds to beta-catenin to inhibit the combination of beta-catenin with TCF4, translocation of this complex into the nucleus, and activation of Myc, Cyclin D, and other oncogenic protein transcription (Polakis, P. et al., Genes Dev 14(1 5): 1837-1 85 1 (2000); Nelson, W. J. et al., Science 303(5663): 1483-1487 (2004)). Signaling may also proceed from the nucleus to secreted factors such as chemokines and cytokines (Charo, I. F. et al., N Engl J Med 354(6):610- 621 (2006)). Protein-protein and protein-nucleic acid recognition often work through protein interactions domains, such as the SH2, SH3, and PDZ domains. Currently, there are over 75 such motifs reported in the literature (Hunter, et. al., Cell 100:1 13-127 (2000); Pawson et. al., Genes & Development 14:1027-1047 (2000)). These protein-interaction domains comprise a rich opportunity for developing targeted therapies. [0006] Other macromolecular interactions that can serve as potential targets include protein-nucleic acid interactions, protein-carbohydrate interactions and protein - lipid interactions. Protein-nucleic acid interactions of interest are the interactions between ribosomal proteins and nucleic acids involved in protein synthesis, especially protein synthesis in bacterial pathogens (Franceschi F et al, Biochem Pharmacol , 7 1 (7): 1016- 1025 (2006)). Interactions between transcription factors and nucleic acids sequences, such as those in promoter regions may also be targets for therapies (Gniazdowski M, et al., CurrMed Chem., 10(ll):909-24 (2003)). [0007] Lectins and other carbohydrate binding proteins are involved in many cellular processes, including trafficking and clearing of glycoproteins, cell adhesion, glycosylation, immune response, apoptosis and tumor genesis. Sugars generally bind to proteins weakly in shallow grooves close to the surface of the protein, with binding affinities in the mM to µΜ range. The sugar binding sites on proteins that are essential for microorganism pathogenesis may serve as targets for therapy (Ziolkowska N et al, Structure 14:1 127-1 135 (2006)). [0008] Protein-lipid interactions are most common in membrane proteins where the protein function is directly shaped by interactions with membrane lipids. These interaction are key components in sensory and signaling pathways (Phillips R et a , Nature 459:379-385 (2009)) and may serve as therapeutic targets. [0009] Cancer therapies may be divided into two classical groups: (i) small molecule drugs such as Gleevec that bind into a compact pocket, and (ii) antibody therapeutics such as herceptin which binds and inhibits the HER-2/neu member of the epidermal growth factor receptor (EGFR) family. Antibody and protein therapeutics work by binding over an extended area of the target protein. Antibodies fight cancers by inducing apoptosis, interfering with ligand-receptor interactions, or preventing expression of proteins required for tumor growth (Mehren et al., Ann Rev. Med. 54:343-69 (2003)). Additional successful cancer antibody therapeutics include Rituximab, an anti CD20 antibody, Erbitux (cetuximab) targeted to EGFR, and Avastin (bevacizumab) which interferes with vascular endothelial growth factor (VEGF) binding to its receptor (Mehren et al., Ann Rev. Med. 54:343-69 (2003)). Except for the skin rash associated with EGFR receptor antibodies (which ironically correlates with efficacy), antibody therapies are generally well tolerated and do not have the side-effects associated with traditional chemotherapy. [0010] Antibodies achieve their extraordinary specificity through the diversity generated in their complementarity-determining regions ("CDR's"). An IgG antibody binding surface consists of three CDRs from the variable heavy chain paired with three CDRs from the variable light chain domain. Each CDR consists of a loop of around a dozen amino acid residues, whose structure binds to the target surface with nanomolar affinity (Laune, et. al., J. Biol. Chem 272:30937-30944 (1997); Monnet, et al., J. Biol. Chem 274:3789-3796 (1999)). Thus, antibodies achieve their specificity by combining multiple weak interactions across a generally flat surface of approximately 1200-3000A2.
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