Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Tabuk, Tabuk, 71491, Saudi Arabia.
Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig, 44519, Egypt.
Cell Biochem Biophys. 2023 Dec;81(4):697-706. doi: 10.1007/s12013-023-01163-y. Epub 2023 Sep 2.
In our previous report, the unique architecture of the catalytic chamber of the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp), which harbours two distinctive binding sites, was fully characterized at molecular level. The significant differences in the two binding sites BS1 and BS2 in terms of binding pockets motif, as well as the preferential affinities of eight anti-viral drugs to each of the two binding sites were described. Recent Cryogenic Electron Microscopy (Cryo-EM) studies on the RdRp revealed that two suramin molecules, a SARS-CoV-2 inhibitor, bind to RdRp in two different sites with distinctive interaction landscape. Here, we provide the first account of investigating the combined inhibitor binding to both binding sites, and whether the binding of two inhibitors molecules concurrently is "Cooperative binding" or not. It should be noted that the binding of inhibitors to different sites do not necessary constitute mutually independent events, therefore, we investigated two scenarios to better understand cooperativity: simultaneous binding and sequential binding. It has been demonstrated by binding free energy calculations (MM/PBSA) and piecewise linear potential (PLP) interaction energy analysis that the co-binding of two suramin molecules is not cooperative in nature; rather, when compared to individual binding, both molecules adversely affect one another's binding affinities. This observation appeared to be primarily due to RdRp's rigidity, which prevented both ligands from fitting comfortably within the catalytic chamber. Instead, the suramin molecules showed a tendency to change their orientation within the binding pockets in order to maintain their binding to the protein, but at the expense of the ligand internal energies. Although co-binding resulted in the loss of several important key interactions, a few interactions were conserved, and these appear to be crucial in preserving the binding of ligands in the active site. The structural and mechanistic details of this study will be useful for future research on creating and developing RdRp inhibitors against SARS-CoV-2.
在我们之前的报告中，我们从分子水平上充分描述了 SARS-CoV-2 RNA 依赖性 RNA 聚合酶 (RdRp) 的催化腔独特的结构，该催化腔包含两个独特的结合位点。这两个结合位点 BS1 和 BS2 在结合口袋基序方面存在显著差异，以及八种抗病毒药物对两个结合位点的优先亲和力也存在显著差异。最近关于 RdRp 的低温电子显微镜 (Cryo-EM) 研究表明，两种苏拉明分子，一种 SARS-CoV-2 抑制剂，以两种不同的结合模式结合到 RdRp 上，具有独特的相互作用景观。在这里，我们首次报道了研究两种抑制剂同时结合两个结合位点的情况，以及两种抑制剂分子同时结合是否是“协同结合”。需要注意的是，抑制剂与不同的结合位点的结合不一定构成相互独立的事件，因此，我们研究了两种情况以更好地理解协同作用：同时结合和顺序结合。通过结合自由能计算（MM/PBSA）和分段线性势能 (PLP) 相互作用能分析表明，两种苏拉明分子的共结合本质上不是协同的；相反，与单独结合相比，两个分子都会对彼此的结合亲和力产生不利影响。这种观察结果似乎主要是由于 RdRp 的刚性，这阻止了两个配体舒适地容纳在催化腔中。相反，苏拉明分子在结合口袋中表现出改变其取向的趋势，以保持与蛋白质的结合，但代价是配体的内部能量。尽管共结合导致失去了几个重要的关键相互作用，但仍保留了一些相互作用，这些相互作用对于在活性位点中保持配体的结合至关重要。这项研究的结构和机制细节将有助于未来研究开发针对 SARS-CoV-2 的 RdRp 抑制剂。
