Molecular Docking studies of Apigenin, Kaempferol, and Quercetin as potential target against spike receptor protein of SARS COV

Hardeep Tuli; Shivani Sood; Abhishek Pundir; Deepika Choudhary; Kuldeep  Dhama; Gurpreet Kaur; Prachi Seth; Amit Vashishth; Pawan Kumar

doi:10.18006/2022.10(1).144.149

Authors

Hardeep Tuli Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana, India
Shivani Sood GIOSTAR-USA, Global Institute of Stem Cell Therapy and Research, Mohali, 140308
Abhishek Pundir Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana, India
Deepika Choudhary Quality Assurance Consultant, Kangra, H.P., India
Kuldeep Dhama Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh- 243122, India https://orcid.org/0000-0001-7469-4752
Gurpreet Kaur Department of Physics, Maharishi Markandeshwar (Deemed to be University), Mullana, India
Prachi Seth Department of Applied Science and Humanities, JMIT, Radaur, India
Amit Vashishth School of Agriculture, RNB Global University, Bikaner 334601, Rajasthan, India
Pawan Kumar Institute of Plant Sciences, Agricultural Research Organisations, Rishon LeZion, Israel

DOI:

https://doi.org/10.18006/2022.10(1).144.149

Keywords:

Binding Affinity, Covid, Molecular Docking, Phytochemicals, PYRX, Flavonoids

Abstract

COVID-19 has been categorized as a pandemic in early 2020 and is known to cause by Severe Acute Respiratory Syndrome Coronavirus (SARS–CoV2). Numerous investigators and people in the scientific community are trying to find a superlative way to avert and cure the ailment by using phytochemicals. Abundant studies have revealed that flavonoids can be very operative in averting virus-mediated infection. The purpose of this study was to accomplish molecular docking studies among plant-derived flavonoids (Apigenin, Kaempferol, and Quercetin) and spike receptor (PDB ID: 2AJF) protein of coronavirus. Pyrx virtual screening tool and biovia discovery studio visualizer were utilized in the current molecular docking investigations. Outcomes of docking studies exposed that selected phytochemicals have interacted with targeted spike receptor protein with binding energies in the range of -6.3 to -7.3 kcal. In conclusion among the various selected ligands, quercetin may be a better inhibitor for the deactivation of SARS-Coronavirus.

References

Hagar, M., Ahmed, H.A., Aljohani, G., & Alhaddad, O.A. (2020). Investigation of some antiviral N-heterocycles as COVID 19 drug: Molecular docking and DFT calculations. International Journal of Molecular Sciences, 21(11), 1-13. DOI: https://doi.org/10.3390/ijms21113922

Hall, J.D.C., & Ji, H.F. (2020). A search for medications to treat COVID-19 via in silico molecular docking models of the SARS-CoV-2 spike glycoprotein and 3CL protease. Travel Medicine and Infectious Disease, 35, 101646. DOI: https://doi.org/10.1016/j.tmaid.2020.101646

Khaerunnisa, S., Kurniawan, H., Awaluddin, R., Suhartati, S., Soetjipto, S. (2020). Potential inhibitor of COVID-19 main protease (Mpro) from several medicinal plant compounds by molecular docking study. Preprints, 2020, 2020030226. DOI: 10.20944/preprints202003.0226.v1). DOI: https://doi.org/10.20944/preprints202003.0226.v1

Lipinski, C.A., Lombardo, F., Dominy, B.W., & Feeney, P.J. (2001). Experimental and computational approaches to a estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 46, 3-26. DOI: https://doi.org/10.1016/S0169-409X(00)00129-0

Rivas, F. (2019). Identification of substituted 5-membered heterocyclic compounds as potential antileukemic agents. European Journal of Medicinal Chemistry, 164, 391-398. DOI: https://doi.org/10.1016/j.ejmech.2018.12.059

Silveira, D., Prieto-Garcia, J.M., Boylan, F., Estrada, O., et al. (2020). COVID-19: is there evidence for the use of herbal medicines as adjuvant symptomatic therapy? Frontiers in Pharmacology, 11, 1-44. DOI: https://doi.org/10.3389/fphar.2020.581840

Sood, S., Aggarwal, V., Aggarwal, D., Upadhyay, S.K., et al. (2020). COVID-19 pandemic: from molecular biology, pathogenesis, detection, and treatment to global societal impact. Current Pharmacology Reports, 6(5), 212-227. DOI: https://doi.org/10.1007/s40495-020-00229-2

Sood, S., Bhatia, G.K., Seth, P., Kumar, P., et al. (2021). Efficacy and safety of new and emerging drugs for COVID-19: Favipiravir and Dexamethasone. Current Pharmacology Reports, 7(2), 49-54. DOI: https://doi.org/10.1007/s40495-021-00253-w

Talwar, S., Sood, S., Kumar, J., Chauhan, R., Sharma, M., & Tuli, H.S. (2020). Ayurveda and Allopathic Therapeutic Strategies in Coronavirus Pandemic Treatment 2020. Current Pharmacology Reports, 22, 1-10. DOI: https://doi.org/10.1007/s40495-020-00245-2

Trott, O., & Olson, A.J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31, 455–461. DOI: https://doi.org/10.1002/jcc.21334

Tuli, H.S., Bhatia, G.K., Sood, S., Debnath, P., Aggarwal, D., & Upadhyay, S.K. (2021c). In Silico Analysis and Molecular Docking Studies of Plumbagin and Piperine Ligands as Potential Inhibitors of Alpha-Glucosidase Receptor. Biointerface Research in Applied Chemistry, 11, 9629 – 9637. DOI: https://doi.org/10.33263/BRIAC112.96299637

Tuli, H.S., Bhatia, G.K., Sood, S., Debnath, P., et al. (2020). In Silico evaluation of harmane & palmarin as α Glucosidase inhibitors: Hope for the discovery of antihyperglycemic compounds. International Journal of Pharmaceutical Research, 12, 1331-1336. DOI: https://doi.org/10.31838/ijpr/2020.SP1.176

Tuli, H.S., Sak, K., Aggarwal, P., Iqubal, A., et al. (2021b). Molecular evolution of severe acute respiratory syndrome coronavirus 2: Hazardous and more hazardous strains behind the coronavirus disease 2019 pandemic and their targeting by drugs and vaccines. Frontiers in Cellular and Infection Microbiology, 11, 763687. DOI: https://doi.org/10.3389/fcimb.2021.763687

Tuli, H.S., Sood, S., Kaur, J., Kumar, P., et al. (2021a). Mechanistic insight into anti-COVID-19 drugs: recent trends and advancements. 3 Biotech, 11(2), 1-18. DOI: https://doi.org/10.1007/s13205-021-02644-8

Vardhan, S., & Sahoo, S.K. (2020). Searching inhibitors for three important proteins of COVID-19 through molecular docking studies. Preprint from arXiv, 1-15. Available at https://arxiv.org/abs/2004.08095.

Vashishth, A., & Tehri, N. (2020). Novel coronavirus covid-19: characteristics, transmission, pathogenesis and pandemic report. Journal of Biology and Nature, 11(3), 15-21.

World Health Organization (2020). Coronavirus disease (covid-2019) situation reports.