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.