Computational Prediction of Cymbopogon Citratus Compounds as Promising Inhibitors of Main Protease of SARS-CoV-2: Computational Prediction of Cymbopogon Citratus Compounds

Tuba Ahmad; Rashid Saif; Muhammad Hassan Raza; Muhammad Osama Zafar; Saeeda Zia; Mehwish Shafiq; Laraib Ali; Hooria Younas

doi:10.54393/fbt.v2i01.23

Authors

Tuba Ahmad Department of Biochemistry, Kinnaird College for Women, Lahore, Pakistan
Rashid Saif Decode Genomics, Punjab University Employees Housing Scheme, Lahore, Pakistan
Muhammad Hassan Raza Decode Genomics, Punjab University Employees Housing Scheme, Lahore, Pakistan
Muhammad Osama Zafar Decode Genomics, Punjab University Employees Housing Scheme, Lahore, Pakistan
Saeeda Zia Department of Sciences and Humanities, National University of Computer and Emerging Sciences, Lahore, Pakistan
Mehwish Shafiq Department of Biotechnology, Kinnaird College for Women, Lahore, Pakistan
Laraib Ali Department of Biotechnology, Kinnaird College for Women, Lahore, Pakistan
Hooria Younas Department of Biochemistry, Kinnaird College for Women, Lahore, Pakistan

DOI:

https://doi.org/10.54393/fbt.v2i01.23

Keywords:

SARS-CoV-2, Main Protease, COVID-19, MOE, Molecular Docking, MDS Analysis

Abstract

There is a dire need to develop any antiviral therapy for the treatment of SARS-CoV-2. Objective: To investigate the potential therapeutic drug agents from Cymbopogon citratus compounds against the main-protease (M^pro) of SARS-CoV-2. Methods: Initial screening was carried out using molecular docking, dynamic simulation followed by ADMET profiling and Lipinski’s physiochemical parameters for prediction of drug likeliness. MOE/PyRx was used for docking before determining the stability of the best complexes through NAMD/VMD softwares. Moreover, SwissADME and admetSAR web-based tools were used for drug likeliness of the best complexes. Results: Out of total 50 compounds, 11 presented the lowest binding energies which includes tannic acid, isoorientin, swertiajaponin, chlorogenic acid, cymbopogonol, warfarin, citral diethyl acetal, citral acetate, luteolin, kaempferol and cianidanol with binding energies of -8.12, -7.38, -7.33, -6.88, -6.48, -6.32, -6.31, -6.18, -6.18, -6.13 and -6.02, respectively. Current studies show isoorientin, chlorogenic acid and tannic acid as the promising drug agents using RMSD, Hbond, heatmap graphs. Conclusion: Further in-vivo experiments are suggested to ascertain the medicinal use of these potential inhibitors against COVID-19.

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