Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
George Washington University School of Medicine and Health Sciences.
AIDS. 2018 Sep 24;32(15):2103-2111. doi: 10.1097/QAD.0000000000001951.
HIV-associated atherosclerosis is a major comorbidity due, in part, to systemic effects of the virus on cholesterol metabolism. HIV protein Nef plays an important role in this pathology by impairing maturation of the main cellular cholesterol transporter ATP-Binding Cassette (ABCA) 1. ABCA1 maturation critically depends on calnexin, an integral endoplasmic reticulum membrane chaperone, and Nef binds to the cytoplasmic domain of calnexin and impairs interaction of calnexin with ABCA1. Overarching goal of the present study was to model Nef-calnexin interaction interface, and identify small molecule compounds potentially inhibiting this interaction.
Molecular dynamics was utilized to build structure model of calnexin cytoplasmic domain, followed by global docking combined with application of QASDOM software developed by us for efficient analysis of receptor-ligand complexes. Structure-based virtual screening was performed for all sites identified by docking. A soluble analogue of a compound from the screening results list was tested for ability to down-regulate ABCA1.
We identified major interaction sites in calnexin and reciprocal sites in Nef. Virtual screening yielded a number of small-molecule compounds potentially blocking a calnexin site. Interestingly, one of the compounds, NSC13987, was previously identified by us as an inhibitor targeting a Nef site. An analogue of NSC13987, AMS-55, potently reversed the negative effect of Nef on ABCA1 abundance.
We have modelled Nef-calnexin interaction, predicted small molecule compounds that can potentially inhibit this interaction, and experimentally tested one of these compounds, confirming its effectiveness. These findings provide a platform for searching for new therapeutic agents to treat HIV-associated comorbidities.
HIV 相关的动脉粥样硬化是一种主要的合并症，部分原因是病毒对胆固醇代谢的全身性影响。HIV 蛋白 Nef 在这一病理过程中起着重要作用，它通过损害主要细胞胆固醇转运体 ATP 结合盒（ABCA）1 的成熟来发挥作用。ABCA1 的成熟严重依赖于内质网膜伴侣 calnexin，而 Nef 与 calnexin 的细胞质结构域结合，并损害 calnexin 与 ABCA1 的相互作用。本研究的总体目标是构建 Nef-calnexin 相互作用界面的结构模型，并鉴定可能抑制这种相互作用的小分子化合物。
利用分子动力学构建 calnexin 细胞质结构域的结构模型，然后进行全局对接，结合我们开发的 QASDOM 软件进行高效的受体-配体复合物分析。对对接鉴定的所有位点进行基于结构的虚拟筛选。从筛选结果列表中选择一种可溶性化合物类似物进行测试，以评估其下调 ABCA1 的能力。
我们确定了 calnexin 中的主要相互作用位点和 Nef 中的对应位点。虚拟筛选得到了一些可能阻断 calnexin 位点的小分子化合物。有趣的是，其中一种化合物 NSC13987 是我们之前鉴定的一种靶向 Nef 位点的抑制剂。NSC13987 的类似物 AMS-55 可有效地逆转 Nef 对 ABCA1 丰度的负面影响。
我们构建了 Nef-calnexin 相互作用模型，预测了可能抑制这种相互作用的小分子化合物，并通过实验测试了其中一种化合物，证实了其有效性。这些发现为寻找治疗 HIV 相关合并症的新治疗剂提供了一个平台。
