Beyond the Active Site: Allosteric Tail of HIV-1 Protease Is a Potential Target for Inhibiting Dimerization

HIV protease (HIVPR) is one of the key targets in AIDS therapy. All ten FDA-approved drugs targeting this enzyme compete with the substrates in binding to its active site. However, the emergence of drug-resistant mutants in active and nonactive sites of HIVPR has compromised the efficacy of these drugs. Nonetheless, darunavir (DRV) and tipranavir (TPV) have exhibited greater success than the other eight drugs, presumably due to their dual mode of action: (i) inhibiting protease activity and (ii) blocking protease dimerization. Although crystal structures have explained the inhibitory mechanism of protease activity, the mechanism of inhibiting the dimerization process is poorly understood. In this study, we employ advanced molecular dynamics simulation methods to identify the precise binding motifs of DRV and TPV with monomeric HIVPR. Our results suggest that both inhibitors bind stably to an allosteric pocket located in the tail region of the enzyme. Results also elucidate reversible association–dissociation of the drugs between the conventional active site and the newly identified tail cavity through surface diffusion. Structural analysis revealed that drug binding to the tail pocket induces a conformational extension of the C-terminal α-helix, a change that sequesters the terminal residues required for stable dimer formation. Our finding aligns very well with the reported ESI-MS spectra showing the tail interface as a crucial domain in forming a stable HIV protease dimer. Our result paves the way for designing a new class of HIVPR drugs that could target the C-terminal to effectively lock it in the monomeric form, potentially bypassing the cross-resistance due to active-site mutations.