Cooperative effects of drug-resistance mutations in the flap region of HIV-1 protease

Abstract

Understanding the interdependence of multiple mutations in conferring drug resistance is crucial to the development of novel and robust inhibitors. As HIV-1 protease continues to adapt and evade inhibitors while still maintaining the ability to specifically recognize and efficiently cleave its substrates, the problem of drug resistance has become more complicated. Under the selective pressure of therapy, correlated mutations accumulate throughout the enzyme to compromise inhibitor binding, but characterizing their energetic interdependency is not straightforward. A particular drug resistant variant (L10I/G48V/I54V/V82A) displays extreme entropy-enthalpy compensation relative to wild-type enzyme but a similar variant (L10I/G48V/I54A/V82A) does not. Individual mutations of sites in the flaps (residues 48 and 54) of the enzyme reveal that the thermodynamic effects are not additive. Rather, the thermodynamic profile of the variants is interdependent on the cooperative effects exerted by a particular combination of mutations simultaneously present.

Figure 1

HIV-1 protease colored by sequence conservation (41). Residues colored red are invariant in both untreated and treated populations of patients. Residues colored yellow are invariant only in the untreated population. Invariant glycine residues are colored blue. (a) The protease structure in unliganded (PDB code: 1HHP) and (b) liganded (PDB code: 1HXB) state. The side chains of the catalytic aspartic acids Asp25 in both monomers, as well as mutation sites Leu10, Ile54, and Val82 are displayed.

Figure 2

Changes in the thermodynamic parameters of binding relative to wild-type (WT) protease. The dark blue, magenta and cyan bars are changes in the free energy (ΔΔG), enthalpy (ΔΔH), and entropy (Δ(-TΔS)) of binding, respectively.

Figure 3

Positions of mutated residues displayed on inhibitor-bound HIV-1 protease structure (WT protease bound to SQV, PDB code 1HXB). Ile10, Gly48, Ile54, and Val82 side chains are in cyan van der Waal spheres. The SQV molecule is in stick representation and colored according to atom type, with grey for carbon, blue for nitrogen, and red for oxygen. (a) Front view, showing that neither residue 10 nor residue 54 is in contact with the inhibitor. (b) Top view, showing that residue 54 is in close contact with Ile50 of the other monomer.