Energetic basis for drug resistance of HIV-1 protease mutants against amprenavir
Energetic basis for drug resistance of HIV-1 protease mutants against amprenavir
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DOI：
10.1007/s10822-012-9550-5
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发表时间：
2012-02-01
影响因子：
3.5
通讯作者：
Knecht, Volker
中科院分区：
文献类型：
--
作者：
Kar, Parimal;Knecht, Volker
安普那韦（APV）是一种高亲和力（0.15 nM）HIV-1蛋白酶（PR）抑制剂。然而，与野生型相比，耐药蛋白酶变体V32 I、I50 V、I54 V、I54 M、I84 V和L90 M对安普那韦的亲和力降低3至30倍。在这项工作中，流行的分子力学Poisson-Boltzmann表面积方法已被用来研究安普那韦对野生型和这些突变的蛋白酶变体的有效性。我们的研究结果表明，Asp 25/Asp 25 '的质子化状态强烈影响的动力学，整体亲和力和与单个残基的抑制剂的相互作用。我们强调，与通常假设的相反，质子化状态可能无法从亲和力推断，但需要pK（a）计算。在中性pH下，Asp 25和Asp 25 '分别被电离或质子化，如pK（a）计算所示。因此，在我们的研究中主要考虑这种质子化状态。突变引起的结合亲和力的变化与实验结果一致。结合自由能的分解揭示了结合和耐药性的机制。耐药性是由于APV和PR之间的货车范德华相互作用（V32 I、I50 V和I84 V突变体）的能量贡献增加或抑制剂与其靶标之间的静电相互作用（I54 M和I54 V突变体）的能量贡献增加所致。对于V32 I突变体，极性溶剂化的自由能增加也有助于耐药性。对于L90 M突变体，APV-PR相互作用的货车范德华能的升高通过极性溶剂化自由能的降低来补偿，使得净结合亲和力保持不变。对控制结合和耐药性的分子力的详细了解可能有助于设计针对对当前药物具有耐药性的HIV-1 PR变体的新抑制剂。
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 pK(a) calculations. At neutral pH, Asp25 and Asp25' are ionized or protonated, respectively, as suggested from pK(a) 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.