Journal of Computer-Aided Molecular Design

, Volume 26, Issue 2, pp 215–232 | Cite as

Energetic basis for drug resistance of HIV-1 protease mutants against amprenavir

  • Parimal Kar
  • Volker KnechtEmail author


Amprenavir (APV) is a high affinity (0.15 nM) HIV-1 protease (PR) inhibitor. However, the affinities of the drug resistant protease variants V32I, I50V, I54V, I54M, I84V and L90M to amprenavir are decreased 3 to 30-fold compared to the wild-type. In this work, the popular molecular mechanics Poisson-Boltzmann surface area method has been used to investigate the effectiveness of amprenavir against the wild-type and these mutated protease variants. Our results reveal that the protonation state of Asp25/Asp25′ strongly affects the dynamics, the overall affinity and the interactions of the inhibitor with individual residues. We emphasize that, in contrast to what is often assumed, the protonation state may not be inferred from the affinities but requires pKa calculations. At neutral pH, Asp25 and Asp25′ are ionized or protonated, respectively, as suggested from pKa calculations. This protonation state was thus mainly considered in our study. Mutation induced changes in binding affinities are in agreement with the experimental findings. The decomposition of the binding free energy reveals the mechanisms underlying binding and drug resistance. Drug resistance arises from an increase in the energetic contribution from the van der Waals interactions between APV and PR (V32I, I50V, and I84V mutant) or a rise in the energetic contribution from the electrostatic interactions between the inhibitor and its target (I54M and I54V mutant). For the V32I mutant, also an increased free energy for the polar solvation contributes to the drug resistance. For the L90M mutant, a rise in the van der Waals energy for APV-PR interactions is compensated by a decrease in the polar solvation free energy such that the net binding affinity remains unchanged. Detailed understanding of the molecular forces governing binding and drug resistance might assist in the design of new inhibitors against HIV-1 PR variants that are resistant against current drugs.


HIV-1 PR Drug resistance Amprenavir MM-PBSA Normal mode analysis 



The work was supported by the Federal Ministry of Education and Research (BMBF), Germany. The authors thank Reinhard Lipowsky for support. P. K. is thankful to Dr. Siegfried Höfinger, University of Bologna, Italy for discussion.

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© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  1. 1.Department of Theory and Bio-SystemsMax Planck Institute of Colloids and InterfacesPotsdamGermany

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