HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants

UMMS Affiliation

Department of Biochemistry and Molecular Pharmacology

Publication Date


Document Type



Algorithms; Carbamates; Crystallography, X-Ray; Drug Design; Drug Resistance, Viral; HIV Protease; HIV Protease Inhibitors; HIV-1; Kinetics; Models, Molecular; Structure-Activity Relationship; Sulfonamides


Biochemistry, Biophysics, and Structural Biology | Pharmacology, Toxicology and Environmental Health


The acquisition of drug-resistant mutations by infectious pathogens remains a pressing health concern, and the development of strategies to combat this threat is a priority. Here we have applied a general strategy, inverse design using the substrate envelope, to develop inhibitors of HIV-1 protease. Structure-based computation was used to design inhibitors predicted to stay within a consensus substrate volume in the binding site. Two rounds of design, synthesis, experimental testing, and structural analysis were carried out, resulting in a total of 51 compounds. Improvements in design methodology led to a roughly 1000-fold affinity enhancement to a wild-type protease for the best binders, from a Ki of 30-50 nM in round one to below 100 pM in round two. Crystal structures of a subset of complexes revealed a binding mode similar to each design that respected the substrate envelope in nearly all cases. All four best binders from round one exhibited broad specificity against a clinically relevant panel of drug-resistant HIV-1 protease variants, losing no more than 6-13-fold affinity relative to wild type. Testing a subset of second-round compounds against the panel of resistant variants revealed three classes of inhibitors: robust binders (maximum affinity loss of 14-16-fold), moderate binders (35-80-fold), and susceptible binders (greater than 100-fold). Although for especially high-affinity inhibitors additional factors may also be important, overall, these results suggest that designing inhibitors using the substrate envelope may be a useful strategy in the development of therapeutics with low susceptibility to resistance.

DOI of Published Version



J Am Chem Soc. 2008 May 14;130(19):6099-113. Epub 2008 Apr 16. Link to article on publisher's site

Journal/Book/Conference Title

Journal of the American Chemical Society

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PubMed ID