title: Testing the substrate-envelope hypothesis with designed pairs of compounds.
abstract: Acquired resistance to therapeutic agents is a significant barrier to the development of clinically effective treatments for diseases in which evolution occurs on clinical time scales, frequently arising from target mutations. We previously reported a general strategy to design effective inhibitors for rapidly mutating enzyme targets, which we demonstrated for HIV-1 protease inhibition [Altman et al. J. Am. Chem. Soc. 2008, 130, 6099-6113]. Specifically, we developed a computational inverse design procedure with the added constraint that designed inhibitors bind entirely inside the substrate envelope, a consensus volume occupied by natural substrates. The rationale for the substrate-envelope constraint is that it prevents designed inhibitors from making interactions beyond those required by substrates and thus limits the availability of mutations tolerated by substrates but not by designed inhibitors. The strategy resulted in subnanomolar inhibitors that bind robustly across a clinically derived panel of drug-resistant variants. To further test the substrate-envelope hypothesis, here we have designed, synthesized, and assayed derivatives of our original compounds that are larger and extend outside the substrate envelope. Our designs resulted in pairs of compounds that are very similar to one another, but one respects and one violates the substrate envelope. The envelope-respecting inhibitor demonstrates robust binding across a panel of drug-resistant protease variants, whereas the envelope-violating one binds tightly to wild type but loses affinity to at least one variant. This study provides strong support for the substrate-envelope hypothesis as a design strategy for inhibitors that reduce susceptibility to resistance mutations.
authors: Department of Biological Engineering, ‡Department of Chemistry, and ○Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States.
authors: Yang
authors: Y
authors: Shen
authors: Michael D
authors: MD
authors: Altman
authors: Akbar
authors: A
authors: Ali
authors: Madhavi N L
authors: MN
authors: Nalam
authors: Hong
authors: H
authors: Cao
authors: Tariq M
authors: TM
authors: Rana
authors: Celia A
authors: CA
authors: Schiffer
authors: Bruce
authors: B
authors: Tidor
mesh_terms: D003198:Computer Simulation; D018360:Crystallography, X-Ray; D024882:Drug Resistance, Viral / Q000187:drug effects; D017320:HIV Protease Inhibitors / Q000737:chemistry* / Q000494:pharmacology; D015497:HIV-1 / Q000187:drug effects*; D006801:Humans; D020128:Inhibitory Concentration 50; D008958:Models, Molecular; D009154:Mutation; D013379:Substrate Specificity; D015678:Viral Structural Proteins / Q000737:chemistry* / Q000378:metabolism
chemical_list: D017320:HIV Protease Inhibitors; D015678:Viral Structural Proteins
references: Eur J Pharm Sci. 2000 Oct;11(4):265-83
references: 11033070
references: Nature. 2000 Aug 17;406(6797):775-81
references: 10963607
references: Chem Biol Drug Des. 2009 Sep;74(3):234-45
references: 19703025
references: Annu Rev Biochem. 1993;62:543-85
references: 8352596
references: J Med Chem. 2006 Dec 14;49(25):7342-56
references: 17149864
references: J Virol. 2011 Jul;85(13):6106-16
references: 21507982
references: Science. 1990 Feb 23;247(4945):954-8
references: 2106161
references: J Med Chem. 1998 Aug 27;41(18):3467-76
references: 9719600
references: Proc Natl Acad Sci U S A. 2010 Dec 7;107(49):20986-91
references: 21084633
references: Proteins. 2007 Aug 1;68(2):561-7
references: 17474129
references: Antimicrob Agents Chemother. 2000 Aug;44(8):2093-9
references: 10898681
references: Biochem J. 1990 Dec 1;272(2):281-95
references: 1980062
references: Structure. 2002 Mar;10(3):369-81
references: 12005435
references: J Med Chem. 2012 Jul 26;55(14):6328-41
references: 22708897
references: Proc Natl Acad Sci U S A. 1994 Apr 26;91(9):4096-100
references: 8171040
references: J Am Chem Soc. 2008 May 14;130(19):6099-113
references: 18412349
references: J Virol. 2010 May;84(10):5368-78
references: 20237088
references: J Med Chem. 2010 Nov 11;53(21):7699-708
references: 20958050
references: J Chem Inf Model. 2005 Jan-Feb;45(1):177-82
references: 15667143
references: Chem Biol. 2004 Oct;11(10):1333-8
references: 15489160
references: Proc Natl Acad Sci U S A. 1995 Mar 28;92(7):2484-8
references: 7708670
references: J Med Chem. 2012 Feb 23;55(4):1424-44
references: 22239221
references: J Med Chem. 1997 Nov 21;40(24):3979-85
references: 9397180
references: Am J Med. 2006 Jun;119(6 Suppl 1):S3-10; discussion S62-70
references: 16735149
references: Antimicrob Agents Chemother. 1998 Dec;42(12):3218-24
references: 9835517
references: Proteins. 2007 Apr 1;67(1):232-42
references: 17243183
references: Protein Sci. 2002 Feb;11(2):418-29
references: 11790852
references: Am J Health Syst Pharm. 1997 Jun 15;54(12):1420-33; quiz 1444-6
references: 9194989
references: Annu Rev Med. 2002;53:615-27
references: 11818492
references: Science. 1990 Apr 20;248(4953):358-61
references: 2183354
references: J Med Chem. 2005 Mar 24;48(6):1813-22
references: 15771427