Unbinding Dynamics of Large HIV Non-Nucleoside Reverse Transcriptase Inhibitors Revealed by Atomistic Milestoning Simulations.

Non-nucleoside reverse transcriptase inhibitors (NNRTIs) are a key component of anti-HIV therapy. Large and flexible NNRTIs, such as JLJ636, offer potential advantages in retaining efficacy against drug-resistant mutations in HIV reverse transcriptase. However, the dissociation pathways of such inhibitors from the enzyme's hydrophobic binding pocket remain unclear. In this study, we use atomistic simulations to investigate the unbinding dynamics of JLJ636. A combination of random acceleration molecular dynamics and Milestoning simulations is adopted to identify dissociation pathways, estimate mean residence time, and compute free energy profiles. Among the three candidate exit routes (termed the "entrance", "tunnel", and "groove" channels), the "tunnel" channel is most favorable, followed by the "groove" channel, while the "entrance" channel is rarely visited. This unbinding behavior differs significantly from that of smaller NNRTIs, such as JLJ135 and its analogues, which predominantly dissociate through the "entrance" channel.