Altman, Michael D.Ali, AkbarKumar Reddy, G. S. KiranNalam, Madhavi N. L.Anjum, Saima GhafoorCao, HongChellappan, SripriyaKairys, VisvaldasFernandes, Miguel X.Gilson, Michael K.Schiffer, Celia A.Rana, Tariq M.Tidor, Bruce2023-02-072023-02-072008Altman, M. D., Ali, A., Kumar Reddy, G. K., Nalam, M. N., Anjum, S. G., Cao, H., ... & Tidor, B. (2008). HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants. Journal of the American Chemical Society, 130(19), 6099-6113.http://hdl.handle.net/10400.13/5008The 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.engHIV-1Chemical structureCrystal structureGeneticsInhibitorsPeptides and proteins.Faculdade de Ciências Exatas e da Engenhariajournal article10.1021/ja076558p