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新型腙类似物作为SARS-CoV-2有效抑制剂的设计、合成、晶体结构:分子动力学模拟、MM-GBSA、对接及ADMET研究

Design, synthesis, crystal structure of novel hydrazone analogues as SARS-CoV-2 potent inhibitors: MD simulations, MM-GBSA, docking and ADMET studies.

作者信息

Santhosh C R, Chinnam Sampath, Ananthnag Guddekoppa S, Oduselu Gbolahan O, Chidambaram Kumarappan, Kerru Nagaraju, Kottam Nagaraju, Madhu G M

机构信息

Department of Chemistry, M.S. Ramaiah Institute of Technology (Affiliated to Visvesvaraya Technological University, Belgaum), Bengaluru, Karnataka 560054, India.

Department of Chemistry and BSN Center for Nanomaterials and Display, B.M.S. College of Engineering, Bull Temple Road, Bengaluru, Karnataka 560019, India.

出版信息

R Soc Open Sci. 2025 Jul 9;12(7). doi: 10.1098/rsos.250373. eCollection 2025 Jul.

Abstract

In this study, we have synthesized novel thiohydrazone and hydrazone analogues by one-pot methodology with good to excellent yields (85%-91%). molecular dynamics (MD) simulations, docking, and absorption, distribution, metabolism, excretion and toxicity (ADMET) were evaluated as inhibitor activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (PDB ID: 5N5O) main protease. The dynamics simulations studies and docking were conducted by GROMACS and AutoDock Vina. The ADMET studies of all the compounds were evaluated to understand drug-likeness and potential for therapeutic applications. All the synthesized compounds exhibited strong docking scores between -5.0 and -5.4 kcal mol to the targeted protein. MD simulations revealed that the protein-ligand complex demonstrated conformational stability throughout most of the 70 ns simulation period with root mean square deviation (RMSD) fluctuations below 3 Å. ADMET predictions indicated that all compounds possessed high gastrointestinal absorption, suggesting good oral bioavailability. By slow evaporation technique, crystals of compound were grown using ethanol and its single crystal X-ray diffraction analysis disclosed that it crystallized in the monoclinic (P2/c) crystal system. Crystal data outlined crystal packing, bond lengths, bond angles, intermolecular hydrogen bonding parameters, etc. This study offers further avenues in the discovery of novel and promising hydrazone analogues against SARS-CoV-2 main protease.

摘要

在本研究中,我们采用一锅法合成了新型硫腙和腙类似物,产率良好至优异(85%-91%)。通过分子动力学(MD)模拟、对接以及吸收、分布、代谢、排泄和毒性(ADMET)评估了它们对严重急性呼吸综合征冠状病毒2(SARS-CoV-2)(PDB ID:5N5O)主要蛋白酶的抑制活性。动力学模拟研究和对接分别由GROMACS和AutoDock Vina进行。对所有化合物进行ADMET研究以了解其类药性和治疗应用潜力。所有合成化合物与目标蛋白的对接分数在-5.0至-5.4 kcal/mol之间,显示出较强的结合能力。MD模拟表明,在70 ns的大部分模拟时间内,蛋白质-配体复合物表现出构象稳定性,均方根偏差(RMSD)波动低于3 Å。ADMET预测表明所有化合物具有高胃肠道吸收性,提示良好的口服生物利用度。通过缓慢蒸发技术,使用乙醇培养了化合物的晶体,其单晶X射线衍射分析表明它结晶于单斜晶系(P2/c)。晶体数据概述了晶体堆积、键长、键角、分子间氢键参数等。本研究为发现新型且有前景的针对SARS-CoV-2主要蛋白酶的腙类似物提供了进一步的途径。

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