Insilico Assessment of Hesperidin on Sars-Cov-2 Main Protease and Rna Polymerase: Molecular Docking and Dynamics Simulation Approach

Insilico Assessment of Hesperidin on Sars-Cov-2 Main Protease and Rna Polymerase: Molecular Docking and Dynamics Simulation Approach Publisher

Molaakbari E¹ ; Aallae MR² ; Golestanifar F² ; Garakaninejad Z² ; Khosravi A¹ ; Rezapour M³ ; Eshaghi Malekshah R⁴ ; Ghomi M⁵ ; Ren G⁶

Show Affiliations

1. Leishmaniasis Research Center, Kerman University of Medical Science, Kerman, Iran
2. Department of Chemistry, Shahid Bahonar University of Kerman, Kerman, Iran
3. Department of Biostatics and Data Science, University of Texas, Health Science Center at Houston, TX, United States
4. Biomaterial Research Centre, Tehran University of Medical Sciences, Tehran, Iran
5. Students Research Committee, Faculty of Medicine, Zabol University of Medical Sciences, Zabol, Iran
6. School of Physics, Engineering and Computer Science, University of Hertfordshire, Hatfield, AL10 9AB, United Kingdom

Source: Biochemistry and Biophysics Reports Published:2024

Abstract

The present study uses molecular docking and dynamic simulations to evaluate the inhibitory effect of flavonoid glycosides-based compounds on coronavirus Main protease (Mpro) and RNA polymerase. The Molegro Virtual Docker (MVD) software is utilized to simulate and calculate the binding parameters of compounds with coronavirus. The docking results show that the selected herbal compounds are more effective than those of chemical compounds. It is also revealed that five herbal ligands and two chemical ligands have the best docking scores. Furthermore, a Molecular Dynamics (MD) simulation was conducted for Hesperidin, confirming docking results. Analysis based on different parameters such as Root-mean-square deviation (RMSD), Root mean square fluctuation (RMSF), Radius of gyration (Rg), Solvent accessibility surface area (SASA), and the total number of hydrogen bonds suggests that Hesperidin formed a stable complex with Mpro. Absorption, Distribution, Metabolism, Excretion, And Toxicity (ADMET) analysis was performed to compare Hesperidin and Grazoprevir as potential antiviral medicines, evaluating both herbal and chemical ligand results. According to the study, herbal compounds could be effective on coronavirus and are admissible candidates for developing potential operative anti-viral medicines. Hesperidin was found to be the most acceptable interaction. Grazoprevir is an encouraging candidate for drug development and clinical trials, with the potential to become a highly effective Mpro inhibitor. Compared to RNA polymerase, Mpro showed a greater affinity for bonding with Hesperidin. van der Waals and electrostatic energies dominated, creating a stable Hesperidin-Mpro and Hesperidin-RNA polymerase complex. © 2024

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Style	Citing Format
MLA	Molaakbari E, et al.. "Insilico Assessment of Hesperidin on Sars-Cov-2 Main Protease and Rna Polymerase: Molecular Docking and Dynamics Simulation Approach." Biochemistry and Biophysics Reports, vol. 39, no. , 2024, pp. -.
APA	Molaakbari E, Aallae MR, Golestanifar F, Garakaninejad Z, Khosravi A, Rezapour M, Eshaghi Malekshah R, Ghomi M, Ren G (2024). Insilico Assessment of Hesperidin on Sars-Cov-2 Main Protease and Rna Polymerase: Molecular Docking and Dynamics Simulation Approach. Biochemistry and Biophysics Reports, 39(), -.
Chicago	Molaakbari E, Aallae MR, Golestanifar F, Garakaninejad Z, Khosravi A, Rezapour M, Eshaghi Malekshah R, Ghomi M, Ren G. "Insilico Assessment of Hesperidin on Sars-Cov-2 Main Protease and Rna Polymerase: Molecular Docking and Dynamics Simulation Approach." Biochemistry and Biophysics Reports 39, no. (2024): -.
Harvard	Molaakbari E et al. (2024) 'Insilico Assessment of Hesperidin on Sars-Cov-2 Main Protease and Rna Polymerase: Molecular Docking and Dynamics Simulation Approach', Biochemistry and Biophysics Reports, 39(), pp. -.
Vancouver	Molaakbari E, Aallae MR, Golestanifar F, Garakaninejad Z, Khosravi A, Rezapour M, et al.. Insilico Assessment of Hesperidin on Sars-Cov-2 Main Protease and Rna Polymerase: Molecular Docking and Dynamics Simulation Approach. Biochemistry and Biophysics Reports. 2024;39():-.
BibTex	@article{ author = {Molaakbari E and Aallae MR and Golestanifar F and Garakaninejad Z and Khosravi A and Rezapour M and Eshaghi Malekshah R and Ghomi M and Ren G}, title = {Insilico Assessment of Hesperidin on Sars-Cov-2 Main Protease and Rna Polymerase: Molecular Docking and Dynamics Simulation Approach}, journal = {Biochemistry and Biophysics Reports}, volume = {39}, number = {}, pages = {-}, year = {2024} }
RIS	TY - JOUR AU - Molaakbari E AU - Aallae MR AU - Golestanifar F AU - Garakaninejad Z AU - Khosravi A AU - Rezapour M AU - Eshaghi Malekshah R AU - Ghomi M AU - Ren G TI - Insilico Assessment of Hesperidin on Sars-Cov-2 Main Protease and Rna Polymerase: Molecular Docking and Dynamics Simulation Approach JO - Biochemistry and Biophysics Reports VL - 39 IS - SP - EP - PY - 2024 ER -

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