Microsecond-Scale Simulations to Determine NNRTI Function Upon Drug Resistant Mutations in HIV-RT

Inhibition of the HIV Reverse Transcriptase enzyme has become an essential component in current drug regimens for the treatment of HIV.  There are two main classes of HIV-RT inhibitor drugs: nucleoside and non-nucleoside Reverse Transcriptase inhibitors (NNRTI's).  The latter class is highly target-specific, with fewer unintended side effects, and has thus become the more commonly used inhibitor.  Older NNRTI’s, such as nevirapine, are structurally rigid, exhibiting decreased inhibitory function upon development of common mutations in the NNRTI binding pocket located around 10 A˚ from the primer grip.  While newer generations, like rilpivirine, are more flexible and resistant to binding pocket mutations, the mechanism by which they actually inhibit protein function and avoid mutations is not well understood.  A full understanding of this mechanism would allow for modification of identified drug-design parameters essential to the process of drug binding and HIV-RT inhibition.  To this end, we have performed microsecond time-scale simulations with explicit solvent in an NPT ensemble under six different experimental conditions: Apo Wild‐Type, Apo Mutant, nevirapine‐bound Wild‐Type, nevirapine‐bound Mutant, rilpivirine‐bound Wild‐Type, and rilpivirine‐bound Mutant.  Analysis of these simulations involved Principle Component Analysis, inspection of protein conformations, and the calculation of mutual information between residues to determine long-range protein motions and allosteric networks of related residues.  Our results point to an inhibitory mechanism disrupting the catalytic triad of aspartic acids necessary for polymerization of HIV-encoding DNA.