Investigation of Neolamarckia cadamba phytoconstituents against SARS-CoV-2 3CL Pro: An In-Silico Approach

IF 0.7 Q4 CHEMISTRY, MULTIDISCIPLINARY

Orbital: The Electronic Journal of Chemistry Pub Date : 2023-04-12 DOI:10.17807/orbital.v15i1.17592

S. Arora, Kalpana Tirpude, Pallavi Rushiya, Nidhi Sapkal, Subhash Yende, Abhay Ittadwar, Sapan Shah

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Abstract

In present study, the inhibitory potential of Neolamarckia cadamba phytoconstituents was investigated against SARS-CoV-2 3CL protease (3CL pro) (PDB ID: 6M2N). Molecular docking was analyzed using AutoDock Vina software by setting the grid parameter as X= -33.163, Y= -65.074 and Z= 41.434 with dimensions of the grid box 25 × 25 × 25 Å. Remdesivir was taken as the standard for comparative analysis along with inhibitor 5, 6, 7-trihydroxy-2-phenyl-4H-chromen-4-one. Furthermore, the exploration of 2 D Hydrogen-bond interactions was performed by Biovia Discovery Studio 4.5 program to identify the interactions between an amino acid of target and ligand followed by assessment of physicochemical properties using Lipinski’s rule and Swiss ADME database. The decent bonding scores of secondary metabolites owing to hydrogen bonding with catalytic residues suggest the effectiveness of these phytochemicals towards 3CLpro. The results are further consolidated positively by Lipinski’s rule and Swiss ADME prediction. Thus reasonably, observations with docking studies suggest possibility of phytochemicals from Neolamarckia cadamba to inhibit the 3CLpro and consequently would be explored further as agents for preventing COVID-19.

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新木耳植物成分抗sars - cov - 23cl Pro的实验研究

本研究研究了cadamba植物成分对SARS-CoV-2 3CL蛋白酶(3CL pro) (PDB ID: 6M2N)的抑制作用。采用AutoDock Vina软件进行分子对接分析，网格参数设置为X= -33.163, Y= -65.074, Z= 41.434，网格框尺寸为25 × 25 × 25 Å。以雷姆德西韦为标准，与抑制剂5,6,7 -三羟基-2-苯基- 4h - chromen4 -one进行比较分析。此外，通过Biovia Discovery Studio 4.5程序进行二维氢键相互作用的探索，以确定目标氨基酸与配体之间的相互作用，然后使用Lipinski规则和瑞士ADME数据库评估物理化学性质。次级代谢物由于与催化残基氢键而形成的良好键合分数表明这些植物化学物质对3CLpro的有效性。利平斯基规则和瑞士ADME预测进一步积极地巩固了这一结果。因此，对接研究的观察结果合理地表明，新马菌中的植物化学物质可能抑制3CLpro，因此将进一步探索作为预防COVID-19的药物。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Orbital: The Electronic Journal of Chemistry CHEMISTRY, MULTIDISCIPLINARY-

CiteScore

1.10

自引率

0.00%

发文量

审稿时长

10 weeks

期刊介绍： Orbital: The Electronic Journal of Chemistry is a quarterly scientific journal published by the Institute of Chemistry of the Universidade Federal de Mato Grosso do Sul, Brazil. Original contributions (in English) are welcome, which focus on all areas of Chemistry and their interfaces with Pharmacy, Biology, and Physics. Neither authors nor readers have to pay fees. The journal has an editorial team of scientists drawn from regions throughout Brazil and world, ensuring high standards for the texts published. The following categories are available for contributions: 1. Full papers 2. Reviews 3. Papers on Education 4. History of Chemistry 5. Short communications 6. Technical notes 7. Letters to the Editor The Orbital journal also publishes a number of special issues in addition to the regular ones. The central objectives of Orbital are threefold: (i) to provide the general scientific community (at regional, Brazilian, and worldwide levels) with a formal channel for the communication and dissemination of the Chemistry-related literature output by publishing original papers based on solid research and by reporting contributions which further knowledge in the field; (ii) to provide the community with open, free access to the full content of the journal, and (iii) to constitute a valuable channel for the dissemination of Chemistry-related investigations.