High-resolution structures of HIV-1 reverse transcriptase/TMC278 complexes: Strategic flexibility explains potency against resistance mutations

Abstract

TMC278 is a diarylpyrimidine (DAPY) nonnucleoside reverse transcriptase inhibitor (NNRTI) that is highly effective in treating wild-type and drug-resistant HIV-1 infections in clinical trials at relatively low doses (ϳ25-75 mg/day). We have determined the structure of wild-type HIV-1 RT complexed with TMC278 at 1.8 Å resolution, using an RT crystal form engineered by systematic RT mutagenesis. This highresolution structure reveals that the cyanovinyl group of TMC278 is positioned in a hydrophobic tunnel connecting the NNRTI-binding pocket to the nucleic acid-binding cleft. The crystal structures of TMC278 in complexes with the double mutant K103N/Y181C (2.1 Å) and L100I/K103N HIV-1 RTs (2.9 Å) demonstrated that TMC278 adapts to bind mutant RTs. In the K103N/Y181C RT/TMC278 structure, loss of the aromatic ring interaction caused by the Y181C mutation is counterbalanced by interactions between the cyanovinyl group of TMC278 and the aromatic side chain of Y183, which is facilitated by an ϳ1.5 Å shift of the conserved Y183MDD motif. In the L100I/K103N RT/ TMC278 structure, the binding mode of TMC278 is significantly altered so that the drug conforms to changes in the binding pocket primarily caused by the L100I mutation. The flexible binding pocket acts as a molecular ''shrink wrap'' that makes a shape complementary to the optimized TMC278 in wild-type and drug-resistant forms of HIV-1 RT. The crystal structures provide a better understanding of how the flexibility of an inhibitor can compensate for drug-resistance mutations.drug design ͉ drug resistance ͉ nonnucleoside reverse transcriptase inhibitor ͉ polymerase ͉ x-ray crystallography C ombinations of drugs have been used to successfully treat HIV-1 infections, permitting dramatic reduction in viral loads and restoration of the immune system. However, drug treatments do not eliminate the infection and treatment must be life-long. There are problems with drug toxicity, and prolonged drug exposure can lead to the emergence of drug-resistant mutant viruses. Because toxicity and drug resistance complicate treatment strategies, the development of new anti-AIDS drugs remains essential., also referred to as rilpivirine and R278474, is a diarylpyrimidine (DAPY) nonnucleoside reverse transcriptase inhibitor (NNRTI) that was developed in a multidisciplinary structure-based design effort (3, 4) intended to discover drugs that can inhibit a wide range of the known drug-resistant HIV-1 strains. In cell-based assays, TMC278 inhibits a broad spectrum of HIV-1 variants (Table 1), including strains that are partially or completely resistant to the existing NNRTI drugs (3). Phase I and II clinical trials have shown that TMC278 effectively reduces viral load and maintains low viral load levels with no virus rebound in patients even after 48 weeks of treatment (5, 6).Crystal structures of HIV-1 RT/NNRTI complexes were solved in the course of developing TMC278 (7, 8) along a path that originated with the first-generation TIBO compounds (9). Most of those structures were obtained at ϳ...

The paradoxical effects of using antiretroviral-based microbicides to control HIV epidemics

“…Susceptibility to other classes of ARVs will be unaffected, and hence therapeutic options for the individuals who acquire resistance will be reduced but not eliminated. In addition, recently approved secondgeneration NNRTI drugs retain efficacy against most HIV variants that are resistant to first-generation NNRTI drugs (33,34). Other ARV-based microbicides could use different classes of drugs such as entry inhibitors.…”

Potent Inhibitors Active against HIV Reverse Transcriptase with K101P, a Mutation Conferring Rilpivirine Resistance

“…21,23,25 As reported in several studies, 11,12,17 rilpivirine has an excellent resistance profile specifically for variants with K103N, Y181C, and L100I mutations. In the panel of variants tested in this study, rilpivirine retains potency for variants with K103N and Y181C mutations in the low to midnanomolar range; this is in agreement with previously determined antiviral data.…”

“…In the panel of variants tested in this study, rilpivirine retains potency for variants with K103N and Y181C mutations in the low to midnanomolar range; this is in agreement with previously determined antiviral data. 11,12,21 However, the K101P mutation drastically affects rilpivirine potency, causing an 88-fold increase in EC 50 compared to the wild-type (WT X4) strain. The K101P mutation also affects the potency of NNRTI efavirenz in which there is an observed 58-fold increase in EC 50 compared to WT X4.…”

Fast and automated functional classification with MED‐SuMo: An application on purine‐binding proteins

“…It also provided opportunities for understanding, with greater accuracy, inhibitor-protein interactions and to determine reliably the structural effects of resistance mutations. 19 The Protein Data Bank (PDB 20,21 ) gathers today more than 59,000 protein structures. About 3000 protein structures are not associated with a function.…”