Khan Suliman, Hussain Arif, Vahdani Yasaman, Kooshki Hamideh, Mahmud Hussen Bashdar, Haghighat Setareh, Fatih Rasul Mohammed, Jamal Hidayat Hazha, Hasan Anwarul, Edis Zehra, Haj Bloukh Samir, Kasravi Shahab, Mahdi Nejadi Babadaei Mohammad, Sharifi Majid, Bai Qian, Liu Jianbo, Hu Bowen, Akhtari Keivan, Falahati Mojtaba
Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
Department of Medical Lab Technology, The University of Haripur, Haripur, Khyber Pakhtunkhwa, Pakistan.
Arab J Chem. 2021 Oct;14(10):103353. doi: 10.1016/j.arabjc.2021.103353. Epub 2021 Jul 28.
The aim of this study was to investigate the mechanism of interaction between quercetin-3-O-sophoroside and different SARS-CoV-2's proteins which can bring some useful details about the control of different variants of coronavirus including the recent case, Delta. The chemical structure of the quercetin-3-O-sophoroside was first optimized. Docking studies were performed by CoV disease-2019 (COVID-19) Docking Server. Afterwards, the molecular dynamic study was done using High Throughput Molecular Dynamics (HTMD) tool. The results showed a remarkable stability of the quercetin-3-O-sophoroside based on the calculated parameters. Docking outcomes revealed that the highest affinity of quercetin-3-O-sophoroside was related to the RdRp with RNA. Molecular dynamic studies showed that the target E protein tends to be destabilized in the presence of quercetin-3-O-sophoroside. Based on these results, quercetin-3-O-sophoroside can show promising inhibitory effects on the binding site of the different receptors and may be considered as effective inhibitor of the entry and proliferation of the SARS-CoV-2 and its different variants. Finally, it should be noted, although this paper does not directly deal with the exploring the interaction of main proteins of SARS-CoV-2 Delta variant with quercetin-3-O-sophoroside, at the time of writing, no direct theoretical investigation was reported on the interaction of ligands with the main proteins of Delta variant. Therefore, the present data may provide useful information for designing some theoretical studies in the future for studying the control of SARS-CoV-2 variants due to possible structural similarity between proteins of different variants.
本研究的目的是探究槲皮素 - 3 - O - 槐糖苷与不同的严重急性呼吸综合征冠状病毒2（SARS-CoV-2）蛋白之间的相互作用机制，这可以为控制包括最新病例德尔塔毒株在内的冠状病毒不同变种提供一些有用的细节。首先对槲皮素 - 3 - O - 槐糖苷的化学结构进行了优化。通过2019冠状病毒病（COVID-19）对接服务器进行对接研究。之后，使用高通量分子动力学（HTMD）工具进行分子动力学研究。结果基于计算参数显示了槲皮素 - 3 - O - 槐糖苷具有显著的稳定性。对接结果表明，槲皮素 - 3 - O - 槐糖苷与RNA依赖性RNA聚合酶（RdRp）的亲和力最高。分子动力学研究表明，在槲皮素 - 3 - O - 槐糖苷存在的情况下，目标刺突（E）蛋白趋于不稳定。基于这些结果，槲皮素 - 3 - O - 槐糖苷可能对不同受体的结合位点显示出有前景的抑制作用，并可被视为严重急性呼吸综合征冠状病毒2及其不同变种进入和增殖的有效抑制剂。最后需要指出的是，尽管本文没有直接探讨SARS-CoV-2德尔塔变种的主要蛋白与槲皮素 - 3 - O - 槐糖苷的相互作用，但在撰写本文时，尚未有关于配体与德尔塔变种主要蛋白相互作用的直接理论研究报道。因此，由于不同变种的蛋白之间可能存在结构相似性，本数据可能为未来设计一些理论研究以研究SARS-CoV-2变种的控制提供有用信息。
