Title

Testing the substrate-envelope hypothesis with designed pairs of compounds

UMMS Affiliation

Department of Biochemistry and Molecular Pharmacology; Chemical Biology Program

Publication Date

2013-11-15

Document Type

Article

Disciplines

Biochemistry | Biochemistry, Biophysics, and Structural Biology | Chemistry | Medicinal Chemistry and Pharmaceutics | Molecular Biology | Pharmacology

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.

DOI of Published Version

10.1021/cb400468c

Source

ACS Chem Biol. 2013 Nov 15;8(11):2433-41. doi: 10.1021/cb400468c. Epub 2013 Sep 26. Link to article on publisher's site

Journal/Book/Conference Title

ACS chemical biology

Related Resources

Link to Article in PubMed

PubMed ID

23952265

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