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,
making it an attractive target for antiretroviral therapy. As such it is
one of the most well characterised 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; namely, the Exo site, flap-top
pocket, face site, and Eye site. However, some pockets on the surface of
proteins remain unformed in the apo structure and these “cryptic
sites” have also been known to accommodate small molecule ligands. To
date, no cryptic sites have been identified in the structure of the
HIV-1 protease. Here, we characterise a novel cryptic cantilever pocket
on the surface of the HIV-1 protease through mixed-solvent molecular
dynamics simulations using several probes: acetone, benzene, imidazole,
isopropanol, and phenol. Structure-based analysis of the cryptic
cantilever pocket suggest that the pocket may be amenable to ligand
binding. Interestingly, we note that several homologous retroviral
proteases exhibit evolutionarily conserved dynamics in the cantilever
region and possess a conserved pocket in the cantilever region.
Immobilisation of the cantilever region of the HIV-1 protease via
disulphide cross-linking resulted in curling-in of the flap tips and the
propensity for the protease to adopt a semi-open flap conformation.
Together these results suggest that the mobility of the cantilever
region plays a key role in the global dynamics of retroviral proteases.
Moreover, the cryptic cantilever pocket of the HIV protease may
represent an interesting target for future fragment-based ligand
screening campaigns.