Design of Mutation-resistant HIV Protease Inhibitors with the Substrate Envelope Hypothesis
Chemical Biology and Drug Design
These authors contributed equally to this study. There is a clinical need for HIV protease inhibitors that can evade resistance mutations. One possible approach to designing such inhibitors relies upon the crystallographic observation that the substrates of HIV protease occupy a rather constant region within the binding site. In particular, it has been hypothesized that inhibitors which lie within this region will tend to resist clinically relevant mutations. The present study offers the first
... rospective evaluation of this hypothesis, via computational design of inhibitors predicted to conform to the substrate envelope, followed by synthesis and evaluation against wild-type and mutant proteases, as well as structural studies of complexes of the designed inhibitors with HIV protease. The results support the utility of the substrate envelope hypothesis as a guide to the design of robust protease inhibitors. The value of HIV protease (HIVP) as a drug-target is powerfully validated by the fall in morbidity and mortality of HIV-positive individuals when the protease inhibitors were introduced to clinical practice (1). However, the utility of the first-generation protease inhibitors is challenged by the emergence of resistance and cross-resistance, which is associated primarily with mutations of protease that lead to decreased affinity of the inhibitors. There is thus a need for inhibitors that will retain affinity in the face of mutations. One approach to this problem is to seek inhibitors that bind wild-type protease so tightly that the losses in affinity produced by mutations can be tolerated. Another approach is to devise inhibitors with asymmetric, flexible chemical groups that can adapt conformationally to form stabilizing interactions with both wild-type and mutant proteases (2). The present study explores a third approach which is based upon the availability of crystal structures of inactivated HIVP with substrate peptides whose sequences reflect the various sites in the Gag-Pol gene product that are cleaved by protease (3). These structures reveal that the substrates all occupy essentially the same region of the binding site despite their differing amino acid sequences. The border of this region has been termed the substrate envelope (4). It has furthermore been remarked that key resistance mutations of HIVP lie where inhibitors project outside the substrate envelope (5). These observations lead to the hypothesis that an inhibitor which fits within the substrate envelope will resist clinically relevant mutations. The rationale is that any mutation of HIVP that reduces the affinity of such an inhibitor should also reduce the affinity of substrate, and hence diminish the viability of the virus. This substrate envelope hypothesis is supported by a retrospective data analysis (6), but has not heretofore been tested prospectively. This paper presents the first prospective evaluation of the substrate envelope hypothesis. Computational methods were used to design a focused combinatorial library of compounds that would fit within the substrate envelope and also bind with high affinity. The two nanomolar inhibitors that resulted were assayed against a panel of clinically relevant mutants of HIVP, and the resulting resistance profiles were compared with those of a panel of well-known HIVP inhibitors. The complexes of the two designed inhibitors were furthermore solved crystallographically and used to evaluate the accuracy of the computational designs.