Bhagat Ankita, Kelam Lakshmi Mounika, Samanta Nilanjan, Sobhia M Elizabeth
Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S Nagar, Mohali, Punjab 160062 India.
In Silico Pharmacol. 2025 Sep 4;13(3):125. doi: 10.1007/s40203-025-00409-2. eCollection 2025.
The global health crisis caused by SARS-CoV-2 underscores the urgent need for effective antiviral therapeutics. The SARS-CoV-2 main protease (Mpro) is a crucial enzyme in viral replication, making it a prime target for drug development. In this study, we designed and evaluated peptide inhibitors targeting Mpro by introducing systematic mutations in the Nsp10/11 cleavage site peptide (QLMPER). A library of 214 mutant peptides was generated, from which 25 single-mutant and 70 multi-mutant peptides exhibited strong interactions with Mpro. The top four multi-mutant peptides were selected based on docking scores, molecular dynamics (MD) simulations, and MM-GBSA (Molecular Mechanics-Generalized Born Surface Area) binding free energy calculations. Triplicate 100 ns molecular dynamics simulations assessed the stability of these complexes, revealing that M3 exhibited the highest structural stability and lowest binding free energy (- 34 kcal/mol), outperforming the wild-type peptide (- 4.28 kcal/mol). Computational infrared (IR) spectral analysis confirmed structural modifications induced by mutations, while HOMO-LUMO analysis indicated enhanced reactivity for M3 (FLFPFR). These findings suggest that M3 (FLFPFR) is a promising candidate for SARS-CoV-2 inhibition, highlighting the potential of rationally designed peptide inhibitors in antiviral drug discovery.
Computational workflow for design and evaluation of mutant peptides against SARS-CoV-2 Mpro, highlighting the workflow, key interactions, and improved binding of mutants at S2 and S3/S4 subsites.
The online version contains supplementary material available at 10.1007/s40203-025-00409-2.
由严重急性呼吸综合征冠状病毒2（SARS-CoV-2）引发的全球健康危机凸显了对有效抗病毒疗法的迫切需求。SARS-CoV-2主要蛋白酶（Mpro）是病毒复制中的关键酶，使其成为药物开发的主要靶点。在本研究中，我们通过在Nsp10/11切割位点肽（QLMPER）中引入系统性突变，设计并评估了靶向Mpro的肽抑制剂。生成了一个包含214个突变肽的文库，其中25个单突变肽和70个多突变肽与Mpro表现出强烈相互作用。基于对接分数、分子动力学（MD）模拟和MM-GBSA（分子力学-广义玻恩表面积）结合自由能计算，选择了前四个多突变肽。一式三份的100纳秒分子动力学模拟评估了这些复合物的稳定性，结果显示M3表现出最高的结构稳定性和最低的结合自由能（-34千卡/摩尔），优于野生型肽（-4.28千卡/摩尔）。计算红外（IR）光谱分析证实了突变引起的结构修饰，而HOMO-LUMO分析表明M3（FLFPFR）的反应性增强。这些发现表明M3（FLFPFR）是一种有前景的SARS-CoV-2抑制候选物，突出了合理设计的肽抑制剂在抗病毒药物发现中的潜力。
针对SARS-CoV-2 Mpro的突变肽设计和评估的计算工作流程，突出了工作流程、关键相互作用以及突变体在S2和S3/S4亚位点的改善结合。
在线版本包含可在10.1007/s40203-025-00409-2获取的补充材料。
