Small molecule antagonists of proteins

Biochemical Pharmacology

Volumn 65, Issue 1, 2003, Pages 1-8

  Gadek, Thomas R ^a   Nicholas, John B ^a  

^a GENENTECH INC   (United States)

Author keywords

Antagonist; Drug design; Inhibitor; Lead identification; Protein protein interactions

Indexed keywords

ABCIXIMAB; ACETYLSALICYLIC ACID; AGGRESSTAT; CELL RECEPTOR; DACLIZUMAB; EFALIZUMAB; ENZYME INHIBITOR; EPTIFIBATIDE; G PROTEIN COUPLED RECEPTOR; IBUPROFEN; INDOMETACIN; NAPROXEN; NONSTEROID ANTIINFLAMMATORY AGENT; PROTEIN INHIBITOR; PROTEINASE INHIBITOR; RECEPTOR BLOCKING AGENT; UNCLASSIFIED DRUG; VASCULOTROPIN RECEPTOR; VINBLASTINE;

AMINO ACID COMPOSITION; BINDING KINETICS; CALCULATION; DRUG DESIGN; DRUG INDUSTRY; DRUG MECHANISM; DRUG PROTEIN BINDING; DRUG RESEARCH; DRUG SCREENING; ELECTRICITY; HUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN TARGETING; REVIEW; STRUCTURE ACTIVITY RELATION;

EID: 0037212039     PISSN: 00062952     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-2952(02)01479-X     Document Type: Note

References (49)

1. DeWitt D.L., Smith W.L. Primary structure of prostaglandin G/H synthase from sheep vesicular gland determined from the complementary DNA sequence. Proc. Natl. Acad. Sci. U.S.A. 85:1988;1412-1416.
2. Hardman JG, Limbird LE, editors. Goodman and Gilman's the pharmacological basis of therapeutics. New York: McGraw-Hill; 2001.
3. Schramm V.L. Enzymatic transition-state analysis and transition-state analogs. Methods Enzymol. 308:1999;301-355.
4. Wolfenden R., Snider M.J. The depth of chemical time and the power of enzymes as catalysts. Acc. Chem. Res. 34:2001;938-945.
5. Rich DH, Salituro FG, Holladay MW, Schmidt PG. Design and Discovery of Aspartyl Protease Inhibitors. Mechanistic and Clinical Implications. ACS Symp Ser 251. Conformationally directed drug design; 1984, p. 211-37.
6. Lunney EA, Humblet C. Structure-based design: from renin to HIV-1 protease. In: Mannhold R, Kubinyi H, Timmerman H, editors. Methods and Principles in Medicinal Chemistry, vol. 6. Weinheim: Wiley-VCH; 1998, p. 37-71.
7. Wlodawer A., Vondrasek J. Inhibitors of HIV-1 protease: a major success of structure-assisted drug design. Annu. Rev. Biophys. Biomol. Struct. 27:1998;249-284.
8. Thompson L.A., Tebben A.J. Pharmacokinetics and design of aspartyl protease inhibitors. Annu. Rep. Med. Chem. 36:2001;247-256.
9. Lu Z.-L., Saldanha J.W., Hulme E.C. Seven-transmembrane receptors: crystals clarify. Trends Pharmacol. Sci. 23:2002;140-146.
10. Martin J.L. Protein crystallography and examples of its applications in medicinal chemistry. Curr. Med. Chem. 3:1996;419-436.
11. Visiers I., Ballesteros J.A., Weinstein H. Three-dimensional representations of G protein-coupled receptor structures and mechanisms. Methods Enzymol. 343:2001;329-371.
12. Ballesteros J., Palczewski K. G protein-coupled receptor drug discovery: implications from the crystal structure of rhodopsin. Curr. Opin. Drug Discov. Dev. 4:2001;561-574.
13. * interactions in the C-terminal aromatic residue for agonist activity and its structure resemblance with AT1 non-peptide antagonists. Bioorg. Med. Chem. 9:2001;1639-1647.
14. Matsoukas J.M., Polevaya L., Ancans J., Mavromoustakos T., Kolocouris A., Roumelioti P., Vlahakos D.V., Yamdagni R., Wu Q., Moore G.J. The design and synthesis of a potent angiotensin II cyclic analogue confirms the ring cluster receptor conformation of the hormone angiotensin II. Bioorg. Med. Chem. 8:2000;1-10.
15. Wolin R., Connolly M., Afonso A., Hey J.A., She H., Rivelli M.A., Willams S.M., West R.E. Jr. Novel H3 receptor antagonists. Sulfonamide homologs of histamine. Bioorg. Med. Chem. Lett. 8:1998;2157-2162.
16. Timmermans P.B.M.W.M., Wong P.C., Chiu A.T., Herblin W.F., Benfield P., Carini D.J., Lee R.J., Wexler R.R., Saye J.A.M., Smith R.D. Angiotensin II receptors and angiotensin II receptor antagonists. Pharmacol. Rev. 45:1993;205-251.
17. Toogood P.L. Inhibition of protein-protein association by small molecules: approaches and progress. J. Med. Chem. 45:2002;1543-1558.
18. Ockey D.A., Gadek T.R. Inhibitors of protein-protein interactions. Expert Opin. Ther. Pat. 12:2002;393-400.
19. Von Angerer E. New inhibitors of tubulin polymerization. Expert Opin. Ther. Pat. 9:1999;1069-1081.
20. Jordan A., Hadfield J.A., Lawrence N.J., Mcgown A.T. Tubulin as a target for anticancer drugs: agents which interact with the mitotic spindle. Med. Res. Rev. 18:1998;259-296.
21. Rai S.S., Wolff J. Localization of the vinblastine-binding site on β-tubulin. J. Biol. Chem. 271:1996;14707-14711.
22. Hamel E. Natural products which interact with tubulin in the vinca domain: maytansine, rhizoxin, phomopsin A, dolastatins 10 and 15 and halichondrin B. Pharmacol. Ther. 55:1992;31-51.
23. Uckun F.M., Sudbeck E.A., Mao C., Ghosh S., Liu X.-P., Vassilev A.O., Navara C.S., Narla R.K. Structure-based design of novel anticancer agents. Curr. Cancer Drug Targets. 1:2001;59-71.
24. Reilly T.M., Mousa S.A., Racanelli A.L. New antiplatelet drugs. Expert Opin. Emerg. Drugs. 4:1999;197-208.
25. Liu G. Small molecule antagonists of the LFA-1/ICAM-1 interaction as potential therapeutic agents. Expert Opin. Ther. Pat. 11:2001;1383-1393.
26. Weitz-Schmidt G., Welzenbach K., Brinkmann V., Kamata T., Kallen J., Bruns C., Cottens S., Takada Y., Hommel U. Statins selectively inhibit leukocyte function antigen-1 by binding to a novel regulatory integrin site. Nat. Med. 7:2001;687-692.
27. Liu G., Huth J.R., Olejniczak E.T., Mendoza R., DeVries P., Leitza S., Reilly E.B., Okasinski G.F., Fesik S.W., von Geldern T.W. Novel p-arylthio cinnamides as antagonists of leukocyte function-associated antigen-1/intracellular adhesion molecule-1 interaction. 2. Mechanism of inhibition and structure-based improvement of pharmaceutical properties. J. Med. Chem. 44:2001;1202-1210.
28. Gadek T.R., Burdick D.J., McDowell R.S., Stanley M.S., Marsters J.C. Jr., Paris K.J., Oare D.A., Reynolds M.E., Ladner C., Zioncheck K.A., Lee W.P., Gribling P., Dennis M.S., Skelton N.J., Tumas D.B., Clark K.R., Keating S.M., Beresini M.H., Tilley J.W., Presta L.G., Bodary S.C. Generation of an LFA-1 antagonist by the transfer of the ICAM-1 immunoregulatory epitope to a small molecule. Science. 295:2002;1086-1089.
29. Itokawa T., Nokihara H., Nishioka Y., Sone S., Iwamoto Y., Yamada Y., Cherrington J., McMahon G., Shibuya M., Kuwano M., Ono M. Antiangiogenic effect by SU5416 is partly attributable to inhibition of Flt-1 receptor signaling. Mol. Cancer Ther. 1:2002;295-302.
30. Larrivee B., Karsan A. Signaling pathways induced by vascular endothelial growth factor. Int. J. Mol. Med. 5:2000;447-456.
31. Traver D., Zon L.I. Walking the walk: migration and other common themes in blood and vascular development. Cell. 108:2002;731-734.
32. Xiong J.-P., Stehle T., Zhang R., Joachimiak A., Frech M., Goodman S.L., Arnaout M.A. Crystal structure of the extracelluar segment of intergrin αVβ3 in complex with an Arg-Gly-Asp ligand. Science. 296:2002;151-155.
33. Jones S., Thorton J.M. Principles of protein-protein interactions. Proc. Natl. Acad. Sci. U.S.A. 93:1996;13-20.
34. Janin J. Principles of protein-protein recognition from structure to thermodynamics. Biochemie. 7:1995;497-505.
35. Lo Conte L., Chothia C., Janin J. The atomic structure of protein-protein recognition sites. J. Mol. Biol. 285:1999;2177-2198.
36. Miller S., Lesk A.M., Chothia C. Interior and surface of monomeric proteins. J. Mol. Biol. 328:1987;834-836.
37. Bogan A.A., Thorn K.S. Anatomy of hot spots in protein interfaces. J. Mol. Biol. 280:1998;1-9.
38. Clackson T., Wells J.A. A hot spot of binding energy in a hormone-receptor interface. Science. 267:1995;383-386.
39. Jackson R.M. Comparison of protein-protein interactions in serine protease-inhibitor and antibody-antigen complexes: implications for the protein docking problem. Protein Sci. 8:1999;603-613.
40. Janin J. The kinetics of protein-protein recognition. Proteins. 28:1997;153-161.
41. Wells J.A. Binding in the growth hormone receptor complex. Proc. Natl. Acad. Sci. U.S.A. 93:1996;7-12.
42. Schreiber G., Fersht A.R. Rapid, electrostatically assisted association of proteins. Nat. Struct. Biol. 3:1996;427-431.
43. Schreiber G., Fersht A.R. Interaction of barnase with its polypeptide inhibitor barstar studied by protein engineering. Biochemistry. 32:1993;5145-5150.
44. Schreiber G., Fersht A.R. Energetics of protein-protein interactions: analysis of the barnase-barstar interface by single mutations and double mutant cycles. J. Mol. Biol. 248:1995;478-486.
45. Vijayakumar M., Wong K.-Y., Schreiber G., Fersht A.R., Szabo A., Zhou H.-X. Electrostatic enhancement of diffusion-controlled protein-protein association: comparison of theory and experiment on barnase and barstar. J. Mol. Biol. 278:1998;1015-1024.
46. Selzer T., Albeck S., Schreiber G. Rational design of faster associating and tighter binding protein complexes. Nature. 7:2000;537-541.
47. Northrup S.H., Erickson H.P. Kinetics of protein-protein association explained by Brownian dynamics computer simulation. Proc. Natl. Acad. Sci. U.S.A. 89:1992;3338-3342.
48. Goodford P.J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem. 28:1985;849-857.
49. Smith G.R., Sternberg M.J.E. Prediction of protein-protein interactions by docking methods. Curr. Opin. Struct. Biol. 12:2002;28-35.