Chemical and structural lessons from recent successes in protein-protein interaction inhibition (2P2I)

Current Opinion in Chemical Biology

Volumn 15, Issue 4, 2011, Pages 475-481

  Morelli, Xavier ^a   Bourgeas, Raphaël ^a   Roche, Philippe ^a  

^a CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

4 [4 (4' CHLORO 2 BIPHENYLYLMETHYL) 1 PIPERAZINYL] N [4 [3 DIMETHYLAMINO 1 (PHENYLTHIOMETHYL)PROPYLAMINO] 3 NITROBENZENESULFONYL]BENZAMIDE; CASPASE 9; FTSZ PROTEIN; INTEGRASE; INTERLEUKIN 2; INTERLEUKIN 2 RECEPTOR; LIGAND; LYMPHOTOXIN; NANOPARTICLE; NAVITOCLAX; NUTLIN 3; PROTEIN BAD; PROTEIN BAK; PROTEIN BCL 2; PROTEIN BCL XL; PROTEIN INHIBITOR; PROTEIN MDM2; PROTEIN P53; SECOND MITOCHONDRIAL ACTIVATOR OF CASPASE; SILICON; TUMOR NECROSIS FACTOR ALPHA; TUMOR NECROSIS FACTOR RECEPTOR; TUMOR NECROSIS FACTOR RECEPTOR 1A; UNCLASSIFIED DRUG; X LINKED INHIBITOR OF APOPTOSIS;

BINDING AFFINITY; CHEMICAL ANALYSIS; CLINICAL TRIAL (TOPIC); COMPLEX FORMATION; DIARRHEA; DRUG ABSORPTION; DRUG BINDING; DRUG BIOAVAILABILITY; DRUG DELIVERY SYSTEM; DRUG DETERMINATION; DRUG MECHANISM; DRUG POTENCY; DRUG SAFETY; DRUG STABILITY; HUMAN; HYDROPHOBICITY; IC 50; KNOWLEDGE; MICROEMULSION; MOLECULAR WEIGHT; NANOEMULSION; NANOENCAPSULATION; NANOPARTICLE DRUG DELIVERY SYSTEM; PARTICLE SIZE; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN TARGETING; REVIEW; THROMBOCYTOPENIA;

COMPUTER SIMULATION; DRUG DESIGN; HUMANS; LIGANDS; MODELS, CHEMICAL; MOLECULAR STRUCTURE; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 79960990847     PISSN: 13675931     EISSN: 18790402     Source Type: Journal    
DOI: 10.1016/j.cbpa.2011.05.024     Document Type: Review

References (55)

1. Overington J.P., Al-Lazikani B., Hopkins A.L. How many drug targets are there?. Nat Rev Drug Discov 2006, 5:993-996.
2. Fosslien E. Cardiovascular complications of non-steroidal anti-inflammatory drugs. Ann Clin Lab Sci 2005, 35:347-385.
3. Lievens S., Eyckerman S., Lemmens I., Tavernier J. Large-scale protein interactome mapping: strategies and opportunities. Expert Rev Proteomics 2010, 7:679-690.
4. Venkatesan K., Rual J., Vazquez A., Stelzl U., Lemmens I., Hirozane-Kishikawa T., Hao T., Zenkner M., Xin X., Goh K., et al. An empirical framework for binary interactome mapping. Nat Methods 2009, 6:83-90.
5. Stumpf M., Thorne T., de Silva E., Stewart R., An H., Lappe M., Wiuf C. Estimating the size of the human interactome. Proc Natl Acad Sci USA 2008, 105:6959-6964.
6. Wells J., McClendon C. Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 2007, 450:1001-1009.
7. Fry D.C. Drug-like inhibitors of protein-protein interactions: a structural examination of effective protein mimicry. Curr Protein Peptide Sci 2008, 9:240-247.
8. Lessene G., Czabotar P.E., Colman P.M. BCL-2 family antagonists for cancer therapy. Nat Rev Drug Discov 2008, 7:989-1000.
9. Azmi A.S., Mohammad R.M. Non-peptidic small molecule inhibitors against Bcl-2 for cancer therapy. J Cell Physiol 2009, 218:13-21.
10. Cossu F., Mastrangelo E., Milani M., Sorrentino G., Lecis D., Delia D., Manzoni L., Seneci P., Scolastico C., Bolognesi M. Designing Smac-mimetics as antagonists of XIAP, cIAP1, and cIAP2. Biochem Biophys Res Commun 2009, 378:162-167.
11. Crisostomo F.R., Feng Y., Zhu X., Welsh K., An J., Reed J.C., Huang Z. Design and synthesis of a simplified inhibitor for XIAP-BIR3 domain. Bioorg Med Chem Lett 2009, 19:6413-6418.
12. Christ F., Voet A., Marchand A., Nicolet S., Desimmie B.A., Marchand D., Bardiot D., Van der Veken N.J., Van Remoortel B., Strelkov S.V., et al. Rational design of small-molecule inhibitors of the LEDGF/p75-integrase interaction and HIV replication. Nat Chem Biol 2010, 6:442-448.
13. De Luca L., Ferro S., Gitto R., Barreca M.L., Agnello S., Christ F., Debyser Z., Chimirri A. Small molecules targeting the interaction between HIV-1 integrase and LEDGF/p75 cofactor. Bioorg Med Chem 2010, 18:7515-7521.
14. Porter J.R., Helmers M.R., Wang P., Furman J.L., Joy S.T., Arora P.S., Ghosh I. Profiling small molecule inhibitors against helix-receptor interactions: the Bcl-2 family inhibitor BH3I-1 potently inhibits p53/hDM2. Chem Commun (Camb) 2010, 46:8020-8022.
15. Azmi A.S., Wang Z., Philip P.A., Mohammad R.M., Sarkar F.H. Emerging Bcl-2 inhibitors for the treatment of cancer. Expert Opin Emerg Drugs 2011, 16:59-70.
16. De Luca L., De Grazia S., Ferro S., Gitto R., Christ F., Debyser Z., Chimirri A. HIV-1 integrase strand-transfer inhibitors: design, synthesis and molecular modeling investigation. Eur J Med Chem 2011, 46:756-764.
17. Popowicz G.M., Dömling A., Holak T.A. The structure-based design of Mdm2/Mdmx-p53 inhibitors gets serious. Angew Chem Int Ed Engl 2011, 50:2680-2688.
18. Rinaldi M., Tintori C., Franchi L., Vignaroli G., Innitzer A., Massa S., Esté J.A., Gonzalo E., Christ F., Debyser Z., et al. A versatile and practical synthesis toward the development of novel HIV-1 integrase inhibitors. ChemMedChem 2011, 6:343-352.
19. Voet A., Callewaert L., Ulens T., Vanderkelen L., Vanherreweghe J.M., Michiels C.W., De Maeyer M. Structure based discovery of small molecule suppressors targeting bacterial lysozyme inhibitors. Biochem Biophys Res Commun 2011, 19:19.
20. Vu B.T., Vassilev L. Small-molecule inhibitors of the p53-MDM2 interaction. Curr Top Microbiol Immunol 2011, 348:151-172.
21. Wang S. Design of small-molecule Smac mimetics as IAP antagonists. Curr Top Microbiol Immunol 2011, 348:89-113.
22. White P.W., Faucher A.M., Goudreau N. Small molecule inhibitors of the human papillomavirus e1-e2 interaction. Curr Top Microbiol Immunol 2011, 348:61-88.
23. Wilson C.G., Arkin M.R. Small-molecule inhibitors of IL-2/IL-2R: lessons learned and applied. Curr Top Microbiol Immunol 2011, 348:25-59.
24. Pagliaro L., Felding J., Audouze K., Nielsen S.J., Terry R.B., Krog-Jensen C., Butcher S. Emerging classes of protein-protein interaction inhibitors and new tools for their development. Curr Opin Chem Biol 2004, 8:442-449.
25. Neugebauer A., Hartmann R.W., Klein C.D. Prediction of protein-protein interaction inhibitors by chemoinformatics and machine learning methods. J Med Chem 2007, 50:4665-4668.
26. Higueruelo A.P., Schreyer A., Bickerton G.R.J., Pitt W.R., Groom C.R., Blundell T.L. Atomic interactions and profile of small molecules disrupting protein-protein interfaces: the TIMBAL database. Chem Biol Drug Des 2009, 74:457-467.
27. Bourgeas R., Basse M.-J., Morelli X., Roche P. Atomic analysis of protein-protein interfaces with known inhibitors: the 2P2I database. PLoS ONE 2010, 5:e9598.
28. Reynes C., Host H., Camproux A.C., Laconde G., Leroux F., Mazars A., Deprez B., Fahraeus R., Villoutreix B.O., Sperandio O. Designing focused chemical libraries enriched in protein-protein interaction inhibitors using machine-learning methods. PLoS Comput Biol 2010, 6:e1000695.
29. Sperandio O., Reynès C., Camproux A., Villoutreix B. Rationalizing the chemical space of protein-protein interaction inhibitors. Drug Discov Today 2010, 15:220-229.
30. Abad-Zapatero C., Metz J.T. Ligand efficiency indices as guideposts for drug discovery. Drug Discov Today 2005, 10:464-469.
31. Tse C., Shoemaker A.R., Adickes J., Anderson M.G., Chen J., Jin S., Johnson E.F., Marsh K.C., Mitten M.J., Nimmer P., et al. ABT-263: a potent and orally bioavailable Bcl-2 family inhibitor. Cancer Res 2008, 68:3421-3428.
32. Ackler S., Mitten M.J., Foster K., Oleksijew A., Refici M., Tahir S.K., Xiao Y., Tse C., Frost D.J., Fesik S.W., et al. The Bcl-2 inhibitor ABT-263 enhances the response of multiple chemotherapeutic regimens in hematologic tumors in vivo. Cancer Chemother Pharmacol 2010, 66:869-880.
33. Tahir S.K., Wass J., Joseph M.K., Devanarayan V., Hessler P., Zhang H., Elmore S.W., Kroeger P.E., Tse C., Rosenberg S.H., et al. Identification of expression signatures predictive of sensitivity to the Bcl-2 family member inhibitor ABT-263 in small cell lung carcinoma and leukemia/lymphoma cell lines. Mol Cancer Ther 2010, 9:545-557.
34. Vogler M., Furdas S.D., Jung M., Kuwana T., Dyer M.J., Cohen G.M. Diminished sensitivity of chronic lymphocytic leukemia cells to ABT-737 and ABT-263 due to albumin binding in blood. Clin Cancer Res 2010, 16:4217-4225.
35. Gandhi L., Camidge D.R., Ribeiro de Oliveira M., Bonomi P., Gandara D., Khaira D., Hann C.L., McKeegan E.M., Litvinovich E., Hemken P.M., et al. Phase I study of Navitoclax (ABT-263), a novel Bcl-2 family inhibitor, in patients with small-cell lung cancer and other solid tumors. J Clin Oncol 2011, 29:909-916.
36. Sakuma Y., Tsunezumi J., Nakamura Y., Yoshihara M., Matsukuma S., Koizume S., Miyagi Y. ABT-263, a Bcl-2 inhibitor, enhances the susceptibility of lung adenocarcinoma cells treated with Src inhibitors to anoikis. Oncol Rep 2011, 25:661-667.
37. Buchwald P. Small-molecule protein-protein interaction inhibitors: therapeutic potential in light of molecular size, chemical space, and ligand binding efficiency considerations. IUBMB Life 2010, 62:724-731.
38. Fry D. Small-Molecule Inhibitors of Protein-Protein Interactions 2011, Springer, Nutley, New Jersey. L. Vassilev, D. Fry (Eds.).
39. Hopkins A.L., Groom C.R., Alex A. Ligand efficiency: a useful metric for lead selection. Drug Discov Today 2004, 9:430-431.
40. Bembenek S.D., Tounge B.A., Reynolds C.H. Ligand efficiency and fragment-based drug discovery. Drug Discov Today 2009, 14:278-283.
41. Nissink J.W. Simple size-independent measure of ligand efficiency. J Chem Inf Model 2009, 49:1617-1622.
42. Abad-Zapatero C., Perišić O., Wass J., Bento A.P., Overington J., Al-Lazikani B., Johnson M.E. Ligand efficiency indices for an effective mapping of chemico-biological space: the concept of an atlas-like representation. Drug Discov Today 2010, 15:804-811.
43. Vassilev L.T., Vu B.T., Graves B., Carvajal D., Podlaski F., Filipovic Z., Kong N., Kammlott U., Lukacs C., Klein C., et al. In vivo activation of the p53 pathway by small-molecule antagonists of MDM2. Science (New York, NY) 2004, 303:844-848.
44. Beretta G.L., Gatti L., Benedetti V., Perego P., Zunino F. Small molecules targeting p53 to improve antitumor therapy. Mini Rev Med Chem 2008, 8:856-868.
45. Endo S., Yamato K., Hirai S., Moriwaki T., Fukuda K., Suzuki H., Abei M., Nakagawa I., Hyodo I. Potent in vitro and in vivo antitumor effects of MDM2 inhibitor nutlin-3 in gastric cancer cells. Cancer Sci 2011, 102:605-613.
46. Sonnemann J., Palani C.D., Wittig S., Becker S., Eichhorn F., Voigt A., Beck J.F. Anticancer effects of the p53 activator nutlin-3 in Ewing's sarcoma cells. Eur J Cancer 2011, 47:1432-1441.
47. Rudin C.M., Oliveira M.R., Garon E.B., Bonomi P., Camidge D.R., Nolan C., Busman T., Krivoshik A., Humerickhouse R., Gandhi L. A phase IIa study of ABT-263 in patients with relapsed small-cell lung cancer (SCLC). J Clin Oncol 2010, 28. (suppl; abstr 7046).
48. Prokop A., Davidson J.M. Nanovehicular intracellular delivery systems. J Pharm Sci 2008, 97:3518-3590.
49. Drummond D.C., Noble C.O., Hayes M.E., Park J.W., Kirpotin D.B. Pharmacokinetics and in vivo drug release rates in liposomal nanocarrier development. J Pharm Sci 2008, 97:4696-4740.
50. Gupta S., Moulik S.P. Biocompatible microemulsions and their prospective uses in drug delivery. J Pharm Sci 2008, 97:22-45.
51. Salonen J., Kaukonen A.M., Hirvonen J., Lehto V.P. Mesoporous silicon in drug delivery applications. J Pharm Sci 2008, 97:632-653.
52. Santos H.A., Bimbo L.M., Lehto V.P., Airaksinen A.J., Salonen J., Hirvonen J. Multifunctional porous silicon for therapeutic drug delivery and imaging. Curr Drug Discov Technol 2011, [in press].
53. Cheng Y., Xu Z., Ma M., Xu T. Dendrimers as drug carriers: applications in different routes of drug administration. J Pharm Sci 2008, 97:123-143.
54. Cheng Y., Zhao L., Li Y., Xu T. Design of biocompatible dendrimers for cancer diagnosis and therapy: current status and future perspectives. Chem Soc Rev 2011, 40:2673-2703.
55. Koudelka K.J., Manchester M. Chemically modified viruses: principles and applications. Curr Opin Chem Biol 2010, 14:810-817.