Thermodynamics-based drug design: Strategies for inhibiting protein-protein interactions

Future Medicinal Chemistry

Volumn 3, Issue 9, 2011, Pages 1129-1137

  Schön, Arne ^a   Lam, Sonia Y ^a   Freire, Ernesto ^a  

^a JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

4 BENZOYL 1 [(4 METHOXY 1H PYRROLO[2,3 B]PYRIDIN 3 YL)OXOACETYL] 2 METHYLPIPERAZINE; CHEMOKINE RECEPTOR; GLYCOPROTEIN GP 120; GLYCOPROTEIN GP 41; HUMAN IMMUNODEFICIENCY VIRUS FUSION INHIBITOR; NBD 556; UNCLASSIFIED DRUG; VIRUS PROTEIN;

ALLOSTERISM; AMINO ACID SEQUENCE; BINDING AFFINITY; COMPETITIVE INHIBITION; DRUG BINDING SITE; DRUG DESIGN; DRUG MECHANISM; DRUG POTENCY; DRUG PROTEIN BINDING; DRUG TARGETING; ENZYME INHIBITION; GENETIC POLYMORPHISM; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; INHIBITION KINETICS; ISOTHERMAL TITRATION CALORIMETRY; MOLECULAR MODEL; MUTATIONAL ANALYSIS; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN INDUCTION; PROTEIN PROTEIN INTERACTION; PROTEIN VARIANT; RECEPTOR BLOCKING; REVIEW; SIGNAL TRANSDUCTION; SITE DIRECTED MUTAGENESIS; THERMODYNAMICS; VIRUS ENTRY;

ALLOSTERIC REGULATION; BINDING SITES; BINDING, COMPETITIVE; DRUG DESIGN; HIV ENVELOPE PROTEIN GP120; HUMANS; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPS; PROTEINS; THERMODYNAMICS;

EID: 79961045182     PISSN: 17568919     EISSN: 17568927     Source Type: Journal    
DOI: 10.4155/fmc.11.81     Document Type: Review

References (41)

1. Wells JA, Mcclendon CL. Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 450(7172), 1001-1009 (2007). (Pubitemid 350273630)
2. Zinzalla G, Thurston DE. Targeting protein- protein interactions for therapeutic intervention: a challenge for the future. Future Med. Chem. 1(1), 65-93 (2009).
3. Callen JP. Complications and adverse reactions in the use of newer biologic agents. Semin. Cutan. Med. Surg. 26(1), 6-14 (2007). (Pubitemid 46349778)
4. Thurber GM, Schmidt MM, Wittrup KD. Factors determining antibody distribution in tumors. Trends Pharmacol. Sci. 29(2), 57-61 (2008).
5. Banner DW, D'arcy A, Janes W et al. Crystal structure of the soluble human 55 kd TNF receptor-human TNF beta complex: implications for TNF receptor activation. Cell 73(3), 431-445 (1993). (Pubitemid 23143344)
6. Shibata H, Yoshioka Y, Ohkawa A et al. Creation and x-ray structure analysis of the tumor necrosis factor receptor-1-selective mutant of a tumor necrosis factor-alpha antagonist. J. Biol. Chem. 283(2), 998-1007 (2008).
7. Hage T, Sebald W, Reinemer P. Crystal structure of the interleukin-4/receptor alpha chain complex reveals a mosaic binding interface. Cell 97(2), 271-281 (1999). (Pubitemid 29194277)
8. Rickert M, Wang X, Boulanger MJ, Goriatcheva N, Garcia KC. The structure of interleukin-2 complexed with its alpha receptor. Science 308(5727), 1477-1480 (2005). (Pubitemid 40791303)
9. Philo JS, Aoki KH, Arakawa T, Narhi LO, Wen J. Dimerization of the extracellular domain of the erythropoietin (EPO) receptor by EPO: one high-affinity and one low-affinity interaction. Biochemistry 35(5), 1681-1691 (1996). (Pubitemid 26055303)
10. Syed RS, Reid SW, Li C et al. Efficiency of signalling through cytokine receptors depends critically on receptor orientation. Nature 395(6701), 511-516 (1998). (Pubitemid 28462447)
11. Kelekar A, Chang BS, Harlan JE, Fesik SW, Thompson CB. Bad is a BH3 domain-containing protein that forms an inactivating dimer with Bcl-XL. Mol. Cell Biol. 17(12), 7040-7046 (1997). (Pubitemid 27505933)
12. Kussie PH, Gorina S, Marechal V et al. Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain. Science 274(5289), 948-953 (1996). (Pubitemid 26398409)
13. Sundstrom M, Lundqvist T, Rodin J, Giebel LB, Milligan D, Norstedt G. Crystal structure of an antagonist mutant of human growth hormone, G120R, in complex with its receptor at 2.9 resolution. J. Biol. Chem. 271(50), 32197-32203 (1996). (Pubitemid 26422254)
14. Walsh ST, Jevitts LM, Sylvester JE, Kossiakoff AA. Site2 binding energetics of the regulatory step of growth hormone-induced receptor homodimerization. Protein Sci. 12(9), 1960-1970 (2003). (Pubitemid 37022818)
15. Abbate EA, Berger JM, Botchan MR. The x-ray structure of the papillomavirus helicase in complex with its molecular matchmaker E2. Genes Dev. 18(16), 1981-1996 (2004). (Pubitemid 39071580)
16. Jansson M, Hallen D, Koho H et al. Characterization of ligand binding of a soluble human insulin-like growth factor I receptor variant suggests a ligand-induced conformational change. J. Biol. Chem. 272(13), 8189-8197 (1997). (Pubitemid 27147771)
17. Chi MM, Schlein AL, Moley KH. High insulin-like growth factor 1 (IGF-1) and insulin concentrations trigger apoptosis in the mouse blastocyst via down-regulation of the IGF-1 receptor. Endocrinology 141(12), 4784-4792 (2000). (Pubitemid 32055160)
18. Kaplan D. Autocrine secretion and the physiological concentration of cytokines. Immunol.Today 17(7), 303-304 (1996). (Pubitemid 26201728)
19. Jones S, Thornton JM. Principles of protein- protein interactions. Proc. Natl Acad. Sci. USA 93(1), 13-20 (1996).
20. Lo Conte L, Chothia C, Janin J. The atomic structure of protein-protein recognition sites. J. Mol. Biol. 285(5), 2177-2198 (1999). (Pubitemid 29078179)
21. Clackson T, Wells JA. A hot spot of binding energy in a hormone-receptor interface. Science 267(5196), 383-386 (1995).
22. Schön A, Madani N, Smith AB, Lalonde JM, Freire E. Some binding-related drug properties are dependent on thermodynamic signature. Chem. Biol. Drug Des. 77(3), 161-165 (2011).
23. Dalgleish AG, Beverley PC, Clapham PR, Crawford DH, Greaves MF, Weiss RA. The CD4 (T4) antigen is an essential component of the receptor for the AIDS retrovirus. Nature 312(5996), 763-767 (1984). (Pubitemid 15195924)
24. Klatzmann D, Champagne E, Chamaret S et al. T-lymphocyte T4 molecule behaves as the receptor for human retrovirus LAV. Nature 312(5996), 767-768 (1984). (Pubitemid 15195925)
25. Kadow J, Wang H-G, Lin P-F. Small-molecule HIV-1 gp120 inhibitors to prevent HIV-1 entry: an emerging opportunity for drug development. Curr. Opin. Investig. Drugs 7(8), 721-726 (2006). (Pubitemid 44263176)
26. Repik A, Clapham PR. Plugging gp120s cavity. Structure 16(11), 1603-1604 (2008).
27. Guo Q, Ho HT, Dicker I et al. Biochemical and genetic characterizations of a novel human immunodeficiency virus type 1 inhibitor that blocks gp120-CD4 interactions. J. Virol. 77(19), 10528-10536 (2003). (Pubitemid 37129696)
28. Lalonde JM, Elban MA, Courter JR et al. Design, synthesis and biological evaluation of small molecule inhibitors of CD4-gp120 binding based on virtual screening. Bioorg. Med. Chem. 19(1), 91-101 (2011).
29. Lin PF, Blair W, Wang T et al. A small molecule HIV-1 inhibitor that targets the HIV-1 envelope and inhibits CD4 receptor binding. Proc. Natl Acad. Sci. USA 100(19), 11013-11018 (2003). (Pubitemid 37140144)
30. Madani N, Schon A, Princiotto AM et al. Small-molecule CD4 mimics interact with a highly conserved pocket on HIV-1 gp120. Structure 16(11), 1689-1701 (2008).
31. Meanwell NA, Wallace OB, Fang H et al. Inhibitors of HIV-1 attachment. Part 2: an initial survey of indole substitution patterns. Bioorg. Med. Chem. Lett. 19(7), 1977-1981 (2009).
32. Meanwell NA, Wallace OB, Wang H et al. Inhibitors of HIV-1 attachment. Part 3: a preliminary survey of the effect of structural variation of the benzamide moiety on antiviral activity. Bioorg. Med. Chem. Lett. 19(17), 5136-5139 (2009).
33. Wang T, Kadow JF, Zhang Z et al. Inhibitors of HIV-1 attachment. Part 4: a study of the effect of piperazine substitution patterns on antiviral potency in the context of indole-based derivatives. Bioorg. Med. Chem. Lett. 19(17), 5140-5145 (2009).
34. Zhao Q, Ma L, Jiang S et al. Identification of N-phenyl-Ń-(2,2,6, 6-tetramethyl-piperidin-4-yl)-oxalamides as a new class of HIV-1 entry inhibitors that prevent gp120 binding to CD4. Virology 339(2), 213-225 (2005). (Pubitemid 41169789)
35. Schon A, Madani N, Klein JC et al. Thermodynamics of binding of a low-molecular-weight CD4 mimetic to HIV-1 gp120. Biochemistry 45(36), 10973-10980 (2006). (Pubitemid 44360167)
36. Hanna GJ, Lalezari J, Hellinger JA et al. Antiviral activity, pharmacokinetics, and safety of BMS-488043, a novel oral small-molecule HIV-1 attachment inhibitor, in HIV-1-infected subjects. Antimicrob. Agents Chemother. 55(2), 722-728 (2011).
37. Lu RJ, Tucker JA, Pickens J et al. Heterobiaryl human immunodeficiency virus entry inhibitors. J. Med. Chem. 52(14), 4481-4487 (2009).
38. Si Z, Madani N, Cox JM et al. Small-molecule inhibitors of HIV-1 entry block receptor-induced conformational changes in the viral envelope glycoproteins. Proc. Natl Acad. Sci. USA 101(14), 5036-5041 (2004). (Pubitemid 38469198)
39. Madani N, Perdigoto AL, Srinivasan K et al. Localized changes in the gp120 envelope glycoprotein confer resistance to human immunodeficiency virus entry inhibitors BMS-806 and #155. J. Virol. 78(7), 3742-3752 (2004). (Pubitemid 38578378)
40. Brower ET, Schon A, Freire E. Naturally occurring variability in the envelope glycoprotein of HIV-1 and development of cell entry inhibitors. Biochemistry 49(11), 2359-2367 (2010).
41. Delano WL. Unraveling hot spots in binding interfaces: progress and challenges. Curr. Opin. Struct. Biol. 12(1), 14-20 (2002).