Exploring the New Potential Antiviral Constituents of Moringa Oliefera for SARS-COV-2 Pathogenesis: An Molecular Docking and Dynamic Studies

Overview

Journal Chem Phys Lett

Date 2021 Feb 1

PMID 33518774

Citations 21

Authors

Shabbir Muhammad

Sayyeda Hira Hassan

Abdullah G Al-Sehemi

Hafiz Abdullah Shakir

Muhammad Khan

Muhammad Irfan

Javed Iqbal

Affiliations

Soon will be listed here.

Abstract

The interactions of two crucial proteins of COVID-19 have been investigated with potential antiviral compounds from using quantum chemical, molecular docking and dynamic methods. The results of the present investigation show that ellagic acid and apigenin possess the highest binding affinities of -7.1 and -6.5 Kcal.molagainst nsp9 and -6.9 and -7.1 Kcal.mol against nsp10, respectively. The dynamic behavior of individual proteins and their respective best docked ligand-protein complexes are also studied at 30 ns timescale. Both of these compounds also show the highest intestinal absorption and total clearance rate as compared to the other compounds under present investigation without any toxicity.

Citing Articles

Remedying SARS-CoV-2 through nature: a review highlighting the potentiality of herbs, trees, mushrooms, and endophytic microorganisms in controlling Coronavirus.

Patni B, Bhattacharyya M, Pokhriyal A, Pandey D Planta. 2025; 261(4):89.

PMID: 40089556 DOI: 10.1007/s00425-025-04647-8.

Biological properties of : A systematic review of the last decade.

Soto J, Gomez A, Vasquez M, Barreto A, Molina K, Zuniga-Gonzalez C F1000Res. 2025; 13:1390.

PMID: 39895949 PMC: 11782934. DOI: 10.12688/f1000research.157194.2.

COVID-19-Associated Sepsis: Potential Role of Phytochemicals as Functional Foods and Nutraceuticals.

De Souza Goncalves B, Sangani D, Nayyar A, Puri R, Irtiza M, Nayyar A Int J Mol Sci. 2024; 25(15).

PMID: 39126050 PMC: 11312872. DOI: 10.3390/ijms25158481.

Moringa oleifera and Its Biochemical Compounds: Potential Multi-targeted Therapeutic Agents Against COVID-19 and Associated Cancer Progression.

Yousefi Rad A, Rastegari A, Shahanipour K, Monajemi R Biochem Genet. 2024; .

PMID: 38583096 DOI: 10.1007/s10528-024-10758-w.

A comprehensive review of the phytochemicals, health benefits, pharmacological safety and medicinal prospects of .

Camilleri E, Blundell R Heliyon. 2024; 10(6):e27807.

PMID: 38496871 PMC: 10944276. DOI: 10.1016/j.heliyon.2024.e27807.

References

Dong L, Hu S, Gao J . Discovering drugs to treat coronavirus disease 2019 (COVID-19). Drug Discov Ther. 2020; 14(1):58-60. DOI: 10.5582/ddt.2020.01012. View

Gahtori J, Pant S, Srivastava H . Modeling antimalarial and antihuman African trypanosomiasis compounds: a ligand- and structure-based approaches. Mol Divers. 2019; 24(4):1107-1124. DOI: 10.1007/s11030-019-10015-y. View

Khan M, Ather A, Thompson K, Gambari R . Extracts and molecules from medicinal plants against herpes simplex viruses. Antiviral Res. 2005; 67(2):107-19. DOI: 10.1016/j.antiviral.2005.05.002. View

Smith D, Beaumont K, Maurer T, Di L . Clearance in Drug Design. J Med Chem. 2018; 62(5):2245-2255. DOI: 10.1021/acs.jmedchem.8b01263. View

Phillips J, Hardy D, Maia J, Stone J, Ribeiro J, Bernardi R . Scalable molecular dynamics on CPU and GPU architectures with NAMD. J Chem Phys. 2020; 153(4):044130. PMC: 7395834. DOI: 10.1063/5.0014475. View

Kampf G, Todt D, Pfaender S, Steinmann E . Persistence of coronaviruses on inanimate surfaces and their inactivation with biocidal agents. J Hosp Infect. 2020; 104(3):246-251. PMC: 7132493. DOI: 10.1016/j.jhin.2020.01.022. View

Mathialagan S, Piotrowski M, Tess D, Feng B, Litchfield J, Varma M . Quantitative Prediction of Human Renal Clearance and Drug-Drug Interactions of Organic Anion Transporter Substrates Using In Vitro Transport Data: A Relative Activity Factor Approach. Drug Metab Dispos. 2017; 45(4):409-417. DOI: 10.1124/dmd.116.074294. View

Zhang L, Lin D, Sun X, Curth U, Drosten C, Sauerhering L . Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Science. 2020; 368(6489):409-412. PMC: 7164518. DOI: 10.1126/science.abb3405. View

Curreli F, Kwon Y, Belov D, Ramesh R, Kurkin A, Altieri A . Synthesis, Antiviral Potency, in Vitro ADMET, and X-ray Structure of Potent CD4 Mimics as Entry Inhibitors That Target the Phe43 Cavity of HIV-1 gp120. J Med Chem. 2017; 60(7):3124-3153. DOI: 10.1021/acs.jmedchem.7b00179. View

10.

Best R, Zhu X, Shim J, Lopes P, Mittal J, Feig M . Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles. J Chem Theory Comput. 2013; 8(9):3257-3273. PMC: 3549273. DOI: 10.1021/ct300400x. View

11.

Chen N, Zhou M, Dong X, Qu J, Gong F, Han Y . Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet. 2020; 395(10223):507-513. PMC: 7135076. DOI: 10.1016/S0140-6736(20)30211-7. View

12.

Tracy T, Chaudhry A, Prasad B, Thummel K, Schuetz E, Zhong X . Interindividual Variability in Cytochrome P450-Mediated Drug Metabolism. Drug Metab Dispos. 2015; 44(3):343-51. PMC: 4767386. DOI: 10.1124/dmd.115.067900. View

13.

Du X, Li Y, Xia Y, Ai S, Liang J, Sang P . Insights into Protein-Ligand Interactions: Mechanisms, Models, and Methods. Int J Mol Sci. 2016; 17(2). PMC: 4783878. DOI: 10.3390/ijms17020144. View

14.

Llorach-Pares L, Nonell-Canals A, Sanchez-Martinez M, Avila C . Computer-Aided Drug Design Applied to Marine Drug Discovery: Meridianins as Alzheimer's Disease Therapeutic Agents. Mar Drugs. 2017; 15(12). PMC: 5742826. DOI: 10.3390/md15120366. View

15.

Wang K, Zuo P, Liu Y, Zhang M, Zhao X, Xie S . Clinical and Laboratory Predictors of In-hospital Mortality in Patients With Coronavirus Disease-2019: A Cohort Study in Wuhan, China. Clin Infect Dis. 2020; 71(16):2079-2088. PMC: 7197616. DOI: 10.1093/cid/ciaa538. View

16.

Humphrey W, Dalke A, Schulten K . VMD: visual molecular dynamics. J Mol Graph. 1996; 14(1):33-8, 27-8. DOI: 10.1016/0263-7855(96)00018-5. View

17.

Lipinski C . Lead- and drug-like compounds: the rule-of-five revolution. Drug Discov Today Technol. 2014; 1(4):337-41. DOI: 10.1016/j.ddtec.2004.11.007. View

18.

Pires D, Blundell T, Ascher D . pkCSM: Predicting Small-Molecule Pharmacokinetic and Toxicity Properties Using Graph-Based Signatures. J Med Chem. 2015; 58(9):4066-72. PMC: 4434528. DOI: 10.1021/acs.jmedchem.5b00104. View

19.

Kolaczkowska E, Kubes P . Neutrophil recruitment and function in health and inflammation. Nat Rev Immunol. 2013; 13(3):159-75. DOI: 10.1038/nri3399. View

20.

Sousa S, Ribeiro A, Coimbra J, Neves R, Martins S, Moorthy N . Protein-ligand docking in the new millennium--a retrospective of 10 years in the field. Curr Med Chem. 2013; 20(18):2296-314. DOI: 10.2174/0929867311320180002. View