Singh Khushboo, Patten J J, Dimet-Wiley Andrea, Davey Robert A, Watowich Stanley J, Chandra Amit, Leverett Jesse
Nutrilite, Amway Corporation, Buena Park, CA, 90621, USA.
Department of Virology, Immunology, Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA.
Sci Rep. 2025 Jul 2;15(1):22840. doi: 10.1038/s41598-025-05907-z.
The main protease (M) of SARS-CoV-2 plays a crucial role in viral replication and is a prime target for therapeutic interventions. Phytochemicals, known for their antiviral properties, have been previously identified as potential M inhibitors in several in silico studies. However, the efficacy of these remains in question owing to the inherent flexibility of the M binding site, posing challenges in selecting suitable protein structures for virtual screening. In this study, we conducted an extensive analysis of the M binding pocket, utilizing molecular dynamics (MD) simulations, principal component analysis (PCA) and free energy landscape (FEL) to explore its conformational diversity. Based on pocket volume and shape-based clustering, five representative protein conformations were selected for virtual screening. Virtual screening of a library of ~ 48,000 phytochemicals suggested 39 phytochemicals as potential M inhibitors. Based on subsequent MM-GBSA binding energy calculations and ADMET property predictions, five compounds were advanced to cell-based viral replication inhibition assays, with three compounds (demethoxycurcumin, shikonin, and withaferin A) exhibiting significant (EC50 < 10 μm) inhibition of SARS-CoV-2 replication. Our study provides an understanding of the binding interactions between these phytochemicals and M, contributing significantly to the identification of promising M inhibitors. Furthermore, beyond its impact on therapeutic development against SARS-CoV-2, this research highlights a crucial role of proper nutrition in the fight against viral infections.
严重急性呼吸综合征冠状病毒2（SARS-CoV-2）的主要蛋白酶（M）在病毒复制中起关键作用，是治疗干预的主要靶点。植物化学物质因其抗病毒特性而闻名，此前在多项计算机模拟研究中已被确定为潜在的M抑制剂。然而，由于M结合位点固有的灵活性，这些植物化学物质的功效仍存在疑问，这给虚拟筛选中合适蛋白质结构的选择带来了挑战。在本研究中，我们对M结合口袋进行了广泛分析，利用分子动力学（MD）模拟、主成分分析（PCA）和自由能景观（FEL）来探索其构象多样性。基于口袋体积和形状聚类，选择了五个代表性蛋白质构象进行虚拟筛选。对约48000种植物化学物质库的虚拟筛选表明，有39种植物化学物质为潜在的M抑制剂。基于随后的MM-GBSA结合能计算和ADMET性质预测，将五种化合物推进到基于细胞的病毒复制抑制试验，其中三种化合物（去甲氧基姜黄素、紫草素和吴茱萸次碱）对SARS-CoV-2复制表现出显著（EC50＜10μm）抑制作用。我们的研究提供了对这些植物化学物质与M之间结合相互作用的理解，对有前景的M抑制剂的鉴定有重大贡献。此外，除了对SARS-CoV-2治疗开发的影响外，本研究还突出了合理营养在抗击病毒感染中的关键作用。
