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5-(戊-3-基氧基)-7-氧杂双环[4.1.0]庚-3-烯-3-羧酸甲酯酰肼衍生物作为新型冠状病毒主要蛋白酶潜在抑制剂的研究:密度泛函理论和分子对接研究

Investigation of Methyl-5-(pentan-3-yloxy)-7-oxabicyclo[4.1.0]hept-3-ene-3-carboxyhydrazide Derivatives as Potential Inhibitors of COVID-19 Main Protease: DFT and Molecular Docking Study.

作者信息

Akinyele Olawale Folorunso, Fakola Emmanuel Gabriel, Adeboye Omolara Olubunmi, Chinuomah Sunday Chimela

机构信息

Department of Chemistry, Obafemi Awolowo University, Ile-Ife, Nigeria.

Department of Chemistry, Emmanuel Alayande College of Education, Oyo, Nigeria.

出版信息

Bioinform Biol Insights. 2023 Jun 23;17:11779322231182050. doi: 10.1177/11779322231182050. eCollection 2023.

Abstract

The search for effective therapeutics to combat COVID-19 has led to the exploration of the biological activity of numerous compounds. In this study, hydrazones derived from oseltamivir intermediate, methyl 5-(pentan-3-yloxy)-7-oxabicyclo[4.1.0]hept-3-ene-3-carboxylate have been investigated for their potential as drug candidates against the COVID-19 virus using computational methods, including density functional theory (DFT) studies, molecular docking, and absorption, distribution, metabolism, excretion and toxicity (ADMET) analysis. The DFT studies provide information on the electronic properties of the compounds while the molecular docking results using AutoDock reported the binding energies between the main protease of COVID-19 and the compounds. The DFT results revealed that the energy gap of the compounds ranged from 4.32 to 5.82 eV while compound HC had the highest energy gap (5.82 eV) and chemical potential (2.90 eV). The electrophilicity index values of the 11 compounds ranged from 2.49 to 3.86, thus they were classified as strong electrophiles. The molecular electrostatic potential (MESP) revealed electron-rich and electron-deficient regions of the compounds. The docking results reveal that all the compounds had better docking scores than remdesivir and chloroquine, frontline drugs employed in combating COVID-19, with HC having the best docking score of -6.5. The results were visualized using Discovery studio, which revealed hydrogen bonding, pi-alkyl interaction, alkyl interaction, salt bridge interaction, halogen interaction as being responsible for the docking scores. The drug-likeness results showed that the compounds qualify as oral drug candidates as none of them violated Vebers and Lipinski's rule. Thus, they could serve as potential inhibitors of COVID-19.

摘要

寻找对抗新冠病毒的有效疗法促使人们探索众多化合物的生物活性。在本研究中,利用包括密度泛函理论(DFT)研究、分子对接以及吸收、分布、代谢、排泄和毒性(ADMET)分析在内的计算方法,对源自奥司他韦中间体5-(戊-3-基氧基)-7-氧杂双环[4.1.0]庚-3-烯-3-羧酸甲酯的腙类化合物作为抗新冠病毒候选药物的潜力进行了研究。DFT研究提供了化合物电子性质的信息,而使用AutoDock进行的分子对接结果报告了新冠病毒主要蛋白酶与这些化合物之间的结合能。DFT结果表明,这些化合物的能隙范围为4.32至5.82 eV,其中化合物HC具有最高的能隙(5.82 eV)和化学势(2.90 eV)。11种化合物的亲电指数值范围为2.49至3.86,因此它们被归类为强亲电试剂。分子静电势(MESP)揭示了化合物的富电子和缺电子区域。对接结果显示,所有化合物的对接分数均优于抗击新冠病毒的一线药物瑞德西韦和氯喹,其中HC的对接分数最佳,为-6.5。使用Discovery studio对结果进行了可视化处理,结果显示氢键、π-烷基相互作用、烷基相互作用、盐桥相互作用、卤素相互作用是对接分数的成因。类药性质结果表明,这些化合物均符合口服药物候选物的标准,因为它们均未违反韦伯和利平斯基规则。因此,它们可作为新冠病毒的潜在抑制剂。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6401/10291538/ef1a434d056b/10.1177_11779322231182050-fig1.jpg

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