Unveiling a Hidden Pocket in HIV‐1 Protease: New Insights Into Retroviral Protease Cantilever‐Tip Region Characteristics

Abstract

The HIV‐1 protease is critical for the process of viral maturation and as such, it is one of the most well characterized proteins in the Protein Data Bank. There is some evidence to suggest that the HIV‐1 protease is capable of accommodating small molecule fragments at several locations on its surface outside of the active site. However, some pockets on the surface of proteins remain unformed in the apo structure and are termed “cryptic sites.” To date, no cryptic sites have been identified in the structure of HIV‐1 protease. Here, we characterize a novel cryptic cantilever pocket on the surface of the HIV‐1 protease through mixed‐solvent molecular dynamics simulations using several probes. Interestingly, we noted that several homologous retroviral proteases exhibit evolutionarily conserved dynamics in the cantilever region and possess a conserved pocket in the cantilever region. Immobilization of the cantilever region of the HIV‐1 protease via disulfide cross‐linking resulted in curling‐in of the flap tips and the propensity for the protease to adopt a semi‐open flap conformation. Structure‐based analysis and fragment‐based screening of the cryptic cantilever pocket suggested that the pocket may be capable of accommodating ligand structures. Furthermore, molecular dynamics simulations of a top scoring fragment bound to the cryptic pocket illustrated altered flap dynamics of the fragment‐bound enzyme. Together, these results suggest that the mobility of the cantilever region plays a key role in the global dynamics of retroviral proteases. Therefore, the cryptic cantilever pocket of the HIV‐1 protease may represent an interesting target for future in vitro studies.