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Minerva Biotechnology and Biomolecular Research 2022 September;34(3):114-21

DOI: 10.23736/S2724-542X.22.02869-3

Copyright © 2022 EDIZIONI MINERVA MEDICA

lingua: Inglese

Systematic structure guided clustering of chemical lead compounds targeting RdRp of SARS-CoV-2

Ahmad ALSULIMANI 1, Tulika BHARDWAJ 2, Essam M. JANAHI 3, Atiah H. ALMALKI 4, 5, Brij N. TEWARI 6, Mohd WAHID 7, Mustfa F. ALKHANANI 8, Pallavi SOMVANSHI 2, 9 , Shafiul HAQUE 7, 10

1 Department of Medical Laboratory Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia; 2 School of Computational & Integrative Sciences (SC&IS), Jawaharlal Nehru University, New Delhi, India; 3 Private Practitioner, Al Janabiyah, Bahrain; 4 Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, Taif, Saudi Arabia; 5 Unit of Addiction and Neuroscience Research, College of Pharmacy, Taif University, Al-Hawiah, Saudi Arabia; 6 Department of Microbiology, King George’s Medical University, Lucknow, India; 7 Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia; 8 Emergency Service Department, College of Applied Sciences, AlMaarefa University, Riyadh, Saudi Arabia; 9 Special Centre of Systems Medicine (SCSM), Jawaharlal Nehru University, New Delhi, India; 10 Faculty of Medicine, Görükle Campus, Bursa Uludağ University, Nilüfer, Turkey



BACKGROUND: To combat the global health issue caused by SARS-CoV2, scientists are attempting various therapeutic approaches towards drug discovery including computational biology and drug-repurposing. Recent studies have highlighted the conserved nature of RNA-dependent RNA polymerase (RdRp) of coronaviruses affecting human, bat and animals. In this study attempts have been made to identify the potential inhibitors of RdRp by utilizing molecular docking and MD simulation studies.
METHODS: Systematic structure-based screening of chemical compounds from public libraries was performed to identify the potential lead molecules inhibiting RdRp. This structure driven clustering of compounds is based on decision tree model generated by combining two properties: 1) shape descriptors; and 2) critical number of multiple bonds. The enabled screening of potential chemical compounds was subjected to molecular docking followed by molecular dynamics simulation studies.
RESULTS: The results revealed that the stability of protein-drug complex structure was in the order of RdRp-Oxoglaucine >RdRp-Flutroline >RdRp-Brucine complex.
CONCLUSIONS: This study identifies Oxoglaucine, Brucine and Flutroline as prospective inhibiting agents of SARS-CoV-2 RdRp and further warrants for experimental validation.


KEY WORDS: SARS-CoV-2; RNA-dependent RNA polymerase; Molecular docking simulation

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