Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece.
J Chem Inf Model. 2013 Aug 26;53(8):2141-53. doi: 10.1021/ci4002102. Epub 2013 Jul 24.
The emergence of HIV-1 drug-resistant mutations is the major problem against AIDS treatment. We employed molecular dynamics (MD) calculations and free energy (MM-PBSA and thermodynamic integration) analyses on wild-type (WT) and mutated HIV-1 protease (HIV-1 PR) complexes with darunavir, amprenavir, indinavir, and saquinavir to clarify the mechanism of resistance due to the I50V flap mutation. Conformational analysis showed that the protease flaps are increasingly flexible in the I50V complexes. In the WT, stabilization of the HIV-1 PR structure is achieved via interflap and water-mediated hydrogen-bonding interactions between the flaps. Furthermore, hydrogen bonds between drugs and binding cavity residues (Asp29/29'/30/30') are crucial for effective inhibition. All these interactions were significantly diminished (or absent) in the mutated forms, thus denoting their importance toward binding. Thermodynamic integration calculations reproduced the experimental data to within ≈1 kcal mol⁻¹ and showed that the I50V mutation results in weaker binding free energies for all analyzed complexes with respect to the WT. It was observed that the loss in binding energy upon mutation was mostly enthalpically driven in all complexes, with the greatest effect coming from the reduction of van der Waals interactions. Our results motivated us to test two novel compounds that have been synthesized to maximize interactions with HIV-1 PR. MM-PBSA and TI calculations showed that compound 3c (Ghosh et al. Bioorg. Med. Chem. Lett. 2012, 22, 2308) is a promising protease inhibitor, which presents very effective binding to the WT PR (ΔG(MM-PBSA) = -17.2 kcal mol⁻¹, ΔG(exp) = -16.1 kcal mol⁻¹). Upon I50V mutation, the complex binding free energy was weakened by a ΔΔG(TI) of 1.8 kcal mol⁻¹, comparable to the marketed inhibitors. This predicts that I50V may confer low resistance to 3c. This computational comparative study contributes toward elucidation of the I50V drug-resistance mechanism in HIV-1 PR.
HIV-1 耐药突变的出现是艾滋病治疗的主要问题。我们采用分子动力学（MD）计算和自由能（MM-PBSA 和热力学积分）分析，研究了野生型（WT）和突变型 HIV-1 蛋白酶（HIV-1 PR）与达芦那韦、阿普那韦、茚地那韦和沙奎那韦复合物，以阐明 I50V 瓣突变引起耐药的机制。构象分析表明，蛋白酶瓣在 I50V 复合物中越来越灵活。在 WT 中，通过瓣之间的瓣间和水介导的氢键相互作用来稳定 HIV-1 PR 结构。此外，药物与结合腔残基（Asp29/29'/30/30'）之间的氢键对于有效抑制至关重要。所有这些相互作用在突变形式中都显著减弱（或不存在），因此表明它们对结合的重要性。热力学积分计算再现了实验数据，误差约为 1 kcal/mol，并表明 I50V 突变导致所有分析复合物相对于 WT 的结合自由能减弱。观察到所有复合物中突变引起的结合能损失主要是焓驱动的，最大的影响来自范德华相互作用的减少。我们的结果促使我们测试两种已合成的新型化合物，以最大限度地提高与 HIV-1 PR 的相互作用。MM-PBSA 和 TI 计算表明，化合物 3c（Ghosh 等人，Bioorg. Med. Chem. Lett. 2012, 22, 2308）是一种很有前途的蛋白酶抑制剂，对 WT PR 具有非常有效的结合（ΔG(MM-PBSA)=-17.2 kcal/mol，ΔG(exp)=-16.1 kcal/mol）。发生 I50V 突变后，复合物的结合自由能通过 1.8 kcal/mol 的 ΔΔG(TI)减弱，与市售抑制剂相当。这表明 I50V 可能对 3c 产生低耐药性。这项计算比较研究有助于阐明 HIV-1 PR 中 I50V 耐药机制。
