分子对接和分子动力学模拟发现姜黄素类似物可作为 SARS-CoV-2 的合理双抑制剂。
Molecular Docking and Molecular Dynamics Simulations Discover Curcumin Analogue as a Plausible Dual Inhibitor for SARS-CoV-2.
机构信息
Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea.
Division of Life Science and Applied Life Science (BK21 FOUR), College of Natural Sciences, Gyeongsang National University, Jinju 52828, Korea.
出版信息
Int J Mol Sci. 2022 Feb 4;23(3):1771. doi: 10.3390/ijms23031771.
Recently, the world has been witnessing a global pandemic with no effective therapeutics yet, while cancer continues to be a major disease claiming many lives. The natural compound curcumin is bestowed with multiple medicinal applications in addition to demonstrating antiviral and anticancer activities. In order to elucidate the impact of curcumin on COVID-19 and cancer, the current investigation has adapted several computational techniques to unfold its possible inhibitory activity. Accordingly, curcumin and similar compounds and analogues were retrieved and assessed for their binding affinities at the binding pocket of SARS-CoV-2 main protease and DDX3. The best binding pose was escalated to molecular dynamics simulation (MDS) studies to assess the time dependent stability. Our findings have rendered one compound that has demonstrated good molecular dock score complemented by key residue interactions and have shown stable MDS results inferred by root mean square deviation (RMSD), radius of gyration (Rg), binding mode, hydrogen bond interactions, and interaction energy. Essential dynamics results have shown that the systemadapts minimum energy conformation to attain a stable state. The discovered compound (curA) could act as plausible inhibitor against SARS-CoV-2 and DDX3. Furthermore, curA could serve as a chemical scaffold for designing and developing new compounds.
最近,全球正面临着一种尚无有效疗法的大流行疾病,而癌症仍然是导致许多人死亡的主要疾病。天然化合物姜黄素除了具有抗病毒和抗癌活性外,还具有多种药用用途。为了阐明姜黄素对 COVID-19 和癌症的影响,本研究采用了几种计算技术来揭示其可能的抑制活性。因此,检索并评估了姜黄素和类似化合物及其类似物在 SARS-CoV-2 主蛋白酶和 DDX3 的结合口袋中的结合亲和力。最佳结合构象被提升到分子动力学模拟(MDS)研究中,以评估时间依赖性稳定性。我们的研究结果提供了一种化合物,该化合物表现出良好的分子对接评分,并具有关键残基相互作用,并且通过均方根偏差(RMSD)、回转半径(Rg)、结合模式、氢键相互作用和相互作用能量推断出稳定的 MDS 结果。基本动力学结果表明,该系统采用最小能量构象以达到稳定状态。发现的化合物(curA)可能是针对 SARS-CoV-2 和 DDX3 的有前途的抑制剂。此外,curA 可以作为设计和开发新化合物的化学支架。