Molecular docking and molecular dynamics simulation studies reveal repurposing I-Motif ligand as a promising protease inhibitor against SARS-CoV-2 variants

The COVID-19 caused by the SARS-CoV-2 virus has escalated into a global pandemic, urgently necessitating effective treatments. Tremendous research of the SARS-CoV-2 main protease have enabled insight understanding of its mechanism and potential inhibitors. Due to its crucial role in viral replication, the protease is considered an attractive target for antiviral therapy. This study aimed to identify novel potent inhibitors of main protease protein by repurposing i-Motif (iM) binding compounds from the G4LDB database. iM ligands are known for their ability to stabilise iM structures in DNA, and their repurposing as protein inhibitors is an alternative therapeutic approach. To achieve this, we performed <i>in silico</i> studies with six iM binding compounds. Molecular docking, molecular dynamics (MD) simulations and MM/GBSA binding free energy analysis revealed favourable conformational stability and superior binding affinity of the three proposed iM ligands, including iML0042 (−59.91 ± 3.82 kcal/mol), iML0043 (−56.37 ± 3.87 kcal/mol), and iML0094 (−84.68 ± 3.40 kcal/mol), to SARS-CoV-2 Mpro variants compared to the reference inhibitor nirmatrelvir (−34.35 ± 3.74 kcal/mol). The results suggested that repurposing iM ligands as protease inhibitors is a promising strategy. Our findings revealed significant candidate inhibitors and are recommended for further development as potential protease inhibitors against SARS-CoV-2.

由严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）引发的新型冠状病毒肺炎（COVID-19）已升级为全球大流行，亟需有效的治疗手段。针对SARS-CoV-2主蛋白酶的大量研究已使学界对其作用机制与潜在抑制剂形成了深入认知。鉴于该蛋白酶在病毒复制过程中发挥关键作用，其被视为抗病毒治疗的极具吸引力的靶点。本研究旨在通过重新利用G4配体数据库（G4LDB）中的i-基序（i-Motif, iM）结合化合物，筛选新型强效的主蛋白酶抑制剂。已知iM配体能够稳定DNA中的iM结构，将其重新开发为蛋白酶抑制剂是一种颇具潜力的治疗策略。为达成研究目标，我们对6种iM结合化合物开展了计算机（in silico）研究。通过分子对接、分子动力学（MD）模拟以及MM/GBSA结合自由能分析，结果显示，相较于参比抑制剂奈玛特韦（nirmatrelvir，结合自由能为−34.35 ± 3.74 kcal/mol），3种候选iM配体——包括iML0042（−59.91 ± 3.82 kcal/mol）、iML0043（−56.37 ± 3.87 kcal/mol）及iML0094（−84.68 ± 3.40 kcal/mol）——对SARS-CoV-2主蛋白酶（Mpro）变体展现出更优的构象稳定性与结合亲和力。研究结果表明，将iM配体重新用作蛋白酶抑制剂是一条颇具前景的途径。本研究发现了极具潜力的候选抑制剂，推荐进一步开发为针对SARS-CoV-2的潜在蛋白酶治疗药物。