Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.
Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA.
Viruses. 2023 Sep 27;15(10):2009. doi: 10.3390/v15102009.
A significant body of experimental structures of SARS-CoV-2 spike trimers for the BA.1 and BA.2 variants revealed a considerable plasticity of the spike protein and the emergence of druggable binding pockets. Understanding the interplay of conformational dynamics changes induced by the Omicron variants and the identification of cryptic dynamic binding pockets in the S protein is of paramount importance as exploring broad-spectrum antiviral agents to combat the emerging variants is imperative. In the current study, we explore conformational landscapes and characterize the universe of binding pockets in multiple open and closed functional spike states of the BA.1 and BA.2 Omicron variants. By using a combination of atomistic simulations, a dynamics network analysis, and an allostery-guided network screening of binding pockets in the conformational ensembles of the BA.1 and BA.2 spike conformations, we identified all experimentally known allosteric sites and discovered significant variant-specific differences in the distribution of binding sites in the BA.1 and BA.2 trimers. This study provided a structural characterization of the predicted cryptic pockets and captured the experimentally known allosteric sites, revealing the critical role of conformational plasticity in modulating the distribution and cross-talk between functional binding sites. We found that mutational and dynamic changes in the BA.1 variant can induce the remodeling and stabilization of a known druggable pocket in the N-terminal domain, while this pocket is drastically altered and may no longer be available for ligand binding in the BA.2 variant. Our results predicted the experimentally known allosteric site in the receptor-binding domain that remains stable and ranks as the most favorable site in the conformational ensembles of the BA.2 variant but could become fragmented and less probable in BA.1 conformations. We also uncovered several cryptic pockets formed at the inter-domain and inter-protomer interface, including functional regions of the S2 subunit and stem helix region, which are consistent with the known role of pocket residues in modulating conformational transitions and antibody recognition. The results of this study are particularly significant for understanding the dynamic and network features of the universe of available binding pockets in spike proteins, as well as the effects of the Omicron-variant-specific modulation of preferential druggable pockets. The exploration of predicted druggable sites can present a new and previously underappreciated opportunity for therapeutic interventions for Omicron variants through the conformation-selective and variant-specific targeting of functional sites involved in allosteric changes.
大量针对 SARS-CoV-2 刺突三聚体的 BA.1 和 BA.2 变异体的实验结构表明，刺突蛋白具有相当大的柔韧性，并出现了可成药的结合口袋。了解奥密克戎变异体诱导的构象动力学变化的相互作用，并确定 S 蛋白中隐藏的动态结合口袋，对于探索广谱抗病毒药物来对抗新兴变异体至关重要。在本研究中，我们探索了 BA.1 和 BA.2 奥密克戎变异体的多个开放和闭合功能刺突状态的构象景观，并对其结合口袋的宇宙进行了特征描述。通过使用原子模拟、动力学网络分析以及构象组合中结合口袋的变构导向网络筛选的组合，我们鉴定了所有实验已知的变构位点，并发现了 BA.1 和 BA.2 三聚体中结合位点分布的显著变异特异性差异。这项研究提供了对预测隐藏口袋的结构特征，并捕获了实验已知的变构位点，揭示了构象灵活性在调节功能结合位点的分布和串扰方面的关键作用。我们发现，BA.1 变异体的突变和动力学变化可以诱导 N 端结构域中已知可成药口袋的重塑和稳定，而该口袋在 BA.2 变异体中则发生了剧烈改变，可能不再可用于配体结合。我们的结果预测了受体结合域中实验已知的变构位点，该位点在 BA.2 变异体的构象组合中保持稳定，且排名最靠前，但在 BA.1 构象中可能会碎片化且不太可能出现。我们还发现了几个在结构域间和亚基间界面形成的隐藏口袋，包括 S2 亚基和茎螺旋区域的功能区域，这与口袋残基在调节构象转变和抗体识别中的已知作用一致。这项研究的结果对于理解 Spike 蛋白中可用结合口袋的动态和网络特征以及奥密克戎变异体对优先成药口袋的特异性调节的影响具有重要意义。通过构象选择性和针对涉及变构变化的功能位点的变异体特异性靶向，预测的成药位点的探索为针对奥密克戎变异体的治疗干预提供了一个新的、以前未被充分认识的机会。
