Faculty of Chemistry and Chemical Engineering, Malek Ashtar University of Technology, Tehran, Iran.
Department of Biology, Faculty of Science, Bu-Ali Sina, University, Hamedan, Iran.
PLoS One. 2022 Jul 28;17(7):e0268156. doi: 10.1371/journal.pone.0268156. eCollection 2022.
Despite using effective drugs and vaccines for Covid 19, due to some limitations of current strategies and the high rate of coronavirus mutation, the development of medicines with effective inhibitory activity against this infection is essential. The SARS-CoV-2 enters the cell by attaching its receptor-binding domain (RBD) of Spike to angiotensin-converting enzyme-2 (ACE2). According to previous studies, the natural peptide Urtica dioica agglutinin (UDA) exhibited an antiviral effect on SARS-CoV, but its mechanism has not precisely been elucidated. Here, we studied the interaction between UDA and RBD of Spike protein of SARS-CoV-2. So, protein-protein docking of RBD-UDA was performed using Cluspro 2.0. To further confirm the stability of the complex, the RBD-UDA docked complex with higher binding affinity was studied using Molecular Dynamic simulation (via Gromacs 2020.2), and MM-PBSA calculated the binding free energy of the system. In addition, ELISA assay was used to examine the binding of UDA with RBD protein. Results were compared to ELISA of RBD-bound samples of convalescent serum IgG (from donors who recovered from Covid 19). Finally, the toxicity of UDA is assessed by using MTT assay. The docking results show UDA binds to the RBD binding site. MD simulation illustrates the UDA-RBD complex is stable during 100 ns of simulation, and the average binding energy was calculated to be -47.505 kJ/mol. ELISA and, MTT results show that UDA binds to RBD like IgG-RBD binding and may be safe in human cells. Data presented here indicate UDA interaction with S-protein inhibits the binding sites of RBD, it can prevent the virus from attaching to ACE2 and entering the host cell.
尽管针对新冠病毒使用了有效的药物和疫苗，但由于当前策略存在一些局限性，以及冠状病毒突变率较高，因此开发对这种感染具有有效抑制活性的药物至关重要。SARS-CoV-2 通过其 Spike 上的受体结合域（RBD）与血管紧张素转换酶 2（ACE2）结合进入细胞。根据先前的研究，天然肽荨麻凝集素（UDA）对 SARS-CoV 表现出抗病毒作用，但尚未精确阐明其机制。在这里，我们研究了 UDA 与 SARS-CoV-2 的 Spike 蛋白 RBD 之间的相互作用。因此，使用 Cluspro 2.0 进行了 RBD-UDA 的蛋白质-蛋白质对接。为了进一步确认复合物的稳定性，使用分子动力学模拟（通过 Gromacs 2020.2）研究了与更高结合亲和力的 RBD-UDA 对接复合物，并通过 MM-PBSA 计算了系统的结合自由能。此外，使用 ELISA 测定法检查 UDA 与 RBD 蛋白的结合。将结果与来自从新冠病毒中康复的供体的恢复期血清 IgG（RBD 结合样品）的 ELISA 进行比较。最后，通过 MTT 测定法评估 UDA 的毒性。对接结果表明 UDA 结合到 RBD 结合位点。MD 模拟表明，在 100 ns 的模拟过程中，UDA-RBD 复合物是稳定的，平均结合能计算为-47.505 kJ/mol。ELISA 和 MTT 结果表明，UDA 像 IgG-RBD 结合一样与 RBD 结合，并且在人细胞中可能是安全的。这里提供的数据表明，UDA 与 S 蛋白的相互作用抑制了 RBD 的结合位点，它可以防止病毒与 ACE2 结合并进入宿主细胞。
