Journal
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Volume 6, Issue 4, Pages 1358-1368Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ct9004678
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Funding
- National Institutes of Health (NIH) [P01-GM66524, 1S10440166892993]
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Darunavir (DRV) is a high affinity (4.5 x 10(-12) M, Delta G = -15.2 kcal/mol) HIV-1 protease inhibitor. Two drug-resistant protease variants FLAP+ (L10I, G48V, I54V, V82A) and ACT (V82T, I84V) decrease the binding affinity with DRV by 1.0 ano 1.6 kcal/mol, respectively. In this study, the absolute and relative binding free energies of DRV with wild-type protease, FLAP+, and ACT were calculated with MM-PB/GBSA and thermodynamic integration methods, respectively. Free energy decomposition elucidated that the mutations conferred resistance by distorting the active site of HIV-1 protease so that the residues that lost binding free energy were not limited to the sites of mutation. Specifically the bis-tetrahydrofuranylurethane moiety of DRV maintained interactions with the FLAP+ and ACT variants, whereas the 4-amino phenyl group lost more binding free energy with the protease in the FLAP+ and ACT complexes than in the wild-type protease, which could account for the majority of the loss in binding free energy. This suggested that replacement of the 4-amino phenyl group might generate new inhibitors less susceptible to the drug resistant mutations.
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