PDF(Pubmed)
Abstract：
The first- and second-generation clinically used HIV-1 integrase (IN) strand transfer inhibitors (INSTIs) are key components of antiretroviral therapy (ART), which work by blocking the integration step in the HIV-1 replication cycle that is catalyzed by a nucleoprotein assembly called an intasome. However, resistance to even the latest clinically used INSTIs is beginning to emerge. Developmental third-generation INSTIs, based on naphthyridine scaffolds, are promising candidates to combat drug-resistant viral variants. Among these novel INSTIs, compound 4f exhibits two distinct conformations when binding with intasomes from HIV-1 and the closely related prototype foamy virus (PFV) despite the high structural similarity of their INSTI binding pockets. The molecular mechanism and the key active site residues responsible for these differing binding modes in closely related intasomes remain elusive. To unravel the molecular determinants governing the two distinct binding modes, we applied a novel molecular dynamics-based free energy method that utilizes alchemical pathways to overcome the sampling challenges associated with transitioning between the two bound conformations of ligand 4f within the crowded environments of the INSTI binding pockets in these intasomes. The calculated conformational free energies successfully recapitulate the experimentally observed binding mode preferences in the two viral intasomes. Analysis of the simulated structures suggests that the observed binding mode preferences are caused by amino acid residue differences in both the front and the central catalytic sub-pocket of the INSTI binding site in HIV-1 and PFV. Additional free energy calculations on mutants of HIV-1 and PFV revealed that while both sub-pockets contribute to binding mode selection, the central sub-pocket plays a more important role. These results highlight the importance of both side chain and solvent reorganization, as well as the conformational entropy in determining the ligand binding mode, and will help inform the development of more effective INSTIs for combatting drug-resistant viral variants.
摘要：
第一代和第二代临床使用的HIV-1整合酶（IN）链转移抑制剂（INSTIs）是抗逆转录病毒疗法（ART）的关键组成部分，它通过阻断HIV-1复制循环中的整合步骤起作用，该步骤由称为整合体的核蛋白组装催化。然而,甚至对最新临床使用的INSTIs的抵抗也开始出现。发展中的第三代INSTIs，基于萘啶支架，是对抗耐药病毒变体的有希望的候选人。在这些小说中，化合物4f在与HIV-1和密切相关的原型泡沫病毒（PFV）的溶体结合时表现出两种不同的构象，尽管它们的INSTI结合袋具有高度的结构相似性。分子机制和负责这些不同结合模式的关键活性位点残基在密切相关的肠小体仍然难以捉摸。为了解开控制两种不同结合模式的分子决定因素，我们应用了一种新颖的基于分子动力学的自由能方法,该方法利用炼金术途径克服了与在这些囊体中的INSTI结合袋的拥挤环境中配体4f的两种结合构象之间转换相关的采样挑战.计算出的构象自由能成功地概括了两个病毒肠溶体中实验观察到的结合模式偏好。模拟结构的分析表明，观察到的结合模式偏好是由HIV-1和PFV中INSTI结合位点的前部和中央催化子袋中的氨基酸残基差异引起的。对HIV-1和PFV突变体的其他自由能计算表明，虽然两个子袋都有助于结合模式选择，中央子口袋起着更重要的作用。这些结果突出了侧链和溶剂重组的重要性，以及确定配体结合模式的构象熵，并将有助于为开发更有效的INSTIs来对抗耐药病毒变体。
