Retroviral proteases: correlating substrate recognition with both selected and native inhibitor resistance

A diverse group of retroviral proteases were analyzed to correlate mechanisms of substrate recognition with resistance to HIV-1 protease active-site inhibitors. Here it was shown that HIV-1 protease utilized a pathway common to many retroviral proteases, for recognition of mutated Gag/Pol cleavage sites, in order to become resistant to active-site inhibitors. While HIV-1 and HIV-2 resulted from independent cross-species transmissions of simian immunodeficiency virus into humans, HIV-2 has native primary resistance to many HIV-1 protease inhibitors as do many other retroviral proteases. The native multi-drug resistance of those proteases contributed to the lack of treatments for the respective life-long infections. Analysis of interactions between retroviral proteases and Gag/Pol substrates revealed that protease interactions weighted towards cleavage site residues P4-P4' resulted in inhibitor sensitivity, while interactions weighted towards residues P12-P5/P5'-P12' gave inhibitor resistance. In addition, a mechanism was identified for human T-cell leukemia virus type-1 protease that allowed re-weighting of the protease interactions with substrate residues P4-P4' and P12-P5/P5'-P12' using anti-parallel beta-sheets that connected the protease flaps to the substrate-grooves. Those anti-parallel beta-sheets are common to all studied retroviral proteases. The critical role of the retroviral protease substrate-grooves in substrate recognition and inhibitor resistance makes them a potential target.