Discovery of novel inhibitors of HIV-1 reverse transcriptase through virtual screening of experimental and theoretical ensembles.
Non-nucleoside reverse transcriptase inhibitors (NNRTIs) are potent anti-HIV chemotherapeutics. Although there are FDA-approved NNRTIs, challenges such as the development of resistance have limited their utility. Here, we describe the identification of novel NNRTIs through a combination of computational and experimental approaches. Based on the known plasticity of the NNRTI binding pocket (NNIBP), we adopted an ensemble-based virtual screening strategy: coupling receptor conformations from 10 X-ray crystal structures with 120 snapshots from a total of 480 ns of molecular dynamics (MD) trajectories. A screening library of 2864 National Cancer Institute (NCI) compounds was built and docked against the ensembles in a hierarchical fashion. Sixteen diverse compounds were tested for their ability to block HIV infection in human tissue cultures using a luciferase-based reporter assay. Three promising compounds were further characterized, using a HIV-1 RT-based polymerase assay, to determine the specific mechanism of inhibition. We found that 2 of the three compounds inhibited the polymerase activity of RT (with potency similar to the positive control, the FDA-approved drug nevirapine). Through a computational approach, we were able to discover two compounds which inhibit HIV replication and block the activity of RT, thus offering the potential for optimization into mature inhibitors.
['Ivetac|Anthony|A|', 'Swift|Sara E|SE|', 'Boyer|Paul L|PL|', 'Diaz|Arturo|A|', 'Naughton|John|J|', 'Young|John A T|JA|', 'Hughes|Stephen H|SH|', 'McCammon|J Andrew|JA|']
D001665:Binding Sites D004353:Drug Evaluation, Preclinical D057809:HEK293 Cells D054303:HIV Reverse Transcriptase D015497:HIV-1 D006801:Humans D056004:Molecular Dynamics Simulation D017434:Protein Structure, Tertiary D018894:Reverse Transcriptase Inhibitors D054852:Small Molecule Libraries D014779:Virus Replication
reverse transcriptase virtual screening NNRTI molecular dynamics HIV