Free Energy Calculations

The drug-resistant protease variants have lower binding affinity to inhibitors than wild-type enzyme, while maintaining enough enzymatic activity for the virus to propagate. X-ray crystallography has been useful to elucidate the structural basis for the reduced affinity of drug-resistant variants for protease inhibitors. However, investigating binding energetics complements structural studies to arrive at a complete understanding of the critical components of differential binding affinity of resistant protease variants. We use free-energy decomposition to provide information about affinity changes due to specific kinds of interactions on an atomic level, which cannot be determined by experimental methods.

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For example, difference in affinity for Darunavir (DRV) between wild-type (WT) protease and the V82T/I84V drug-resistant variant was calculated by free energy simulations and experimentally validated using isothermal titration calorimetry. The Gibbs free energy change for DRV binding is -15.2 kcal/mol for WT protease and -13.6 kcal/mol for V82T/I84V variant. Free energy computations revealed that the altered protease-inhibitor van der Waals interactions are the dominant component of the change in affinity due to V82T/I84V mutations. These comparative free energy computations for DRV binding to WT and drug-resistant proteases explain the energetic basis of resistance against this very high-affinity inhibitor, complementing structural findings. This combined methodology contributes to developing better strategies to design robust protease inhibitors. (Cai & Schiffer, 2010)


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Gordon Research Conference: Drug Resistance

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July 29 - August 3, 2012

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