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VOLUME 13 , ISSUE 2 ( July-December, 2023 ) > List of Articles

Original Article

Identification of Leading Compounds from Euphorbia neriifolia (Dudsor) Extracts as a Potential Inhibitor of SARS-CoV-2 ACE2-RBDS1 Receptor Complex: An Insight from Molecular Docking ADMET Profiling and MD-simulation Studies

Md Nur Islam, Md Enayet Ali Pramanik, Md Arju Hossain, Md Hasanur Rahman, Md Sahadot Hossen, Md Ashraful Islam, M Morsed Zaman Miah, Istiak Ahmed, AZM Mostaque Hossain, Md Jawadul Haque, AKM Monoarul Islam, Md Nowshad Ali, Rukhshana Akhter Jahan, Md Enamul Haque, Md Munzur Rahman, Md Sharif Hasan, Mohammad Motiur Rahman, Md Mamun Kabir, Prabir Mohan Basak, Md Abdul Mumit Sarkar, Md Shafiqul Islam, Md Rashedur Rahman, AKM Azad-ud-doula Prodhan, Ashik Mosaddik, Humayra Haque, Fahmida Fahmin, Haimanti Shukla Das, Md Manzurul Islam, Chandrima Emtia, Md Royhan Gofur

Keywords : Absorption, distribution, metabolism, excretion, and toxicity (ADMET), Angiotensin converting enzyme 2, Coronavirus disease-19, Euphorbia neriifolia and phytochemicals, Molecular docking, Molecular dynamics simulation, Molecular mechanics of generalized born and surface

Citation Information : Islam MN, Pramanik ME, Hossain MA, Rahman MH, Hossen MS, Islam MA, Miah MM, Ahmed I, Hossain AM, Haque MJ, Islam AM, Ali MN, Jahan RA, Haque ME, Rahman MM, Hasan MS, Rahman MM, Kabir MM, Basak PM, Sarkar MA, Islam MS, Rahman MR, Prodhan AA, Mosaddik A, Haque H, Fahmin F, Das HS, Islam MM, Emtia C, Gofur MR. Identification of Leading Compounds from Euphorbia neriifolia (Dudsor) Extracts as a Potential Inhibitor of SARS-CoV-2 ACE2-RBDS1 Receptor Complex: An Insight from Molecular Docking ADMET Profiling and MD-simulation Studies. Euroasian J Hepatogastroenterol 2023; 13 (2):89-107.

DOI: 10.5005/jp-journals-10018-1414

License: CC BY-NC 4.0

Published Online: 26-12-2023

Copyright Statement:  Copyright © 2023; The Author(s).


Coronavirus disease-19 (COVID-19) are deadly and infectious disease that impacts individuals in a variety of ways. Scientists have stepped up their attempts to find an antiviral drug that targets the spike protein (S) of Angiotensin converting enzyme 2 (ACE2) (receptor protein) as a viable therapeutic target for coronavirus. The most recent study examines the potential antagonistic effects of 17 phytochemicals present in the plant extraction of Euphorbia neriifolia on the anti-SARS-CoV-2 ACE2 protein. Computational techniques like molecular docking, absorption, distribution, metabolism, excretion, and toxicity (ADMET) investigations, and molecular dynamics (MD) simulation analysis were used to investigate the actions of these phytochemicals. The results of molecular docking studies showed that the control ligand (2-acetamido-2-deoxy-β-D-glucopyranose) had a binding potential of –6.2 kcal/mol, but the binding potentials of delphin, β-amyrin, and tulipanin are greater at –10.4, 10.0, and –9.6 kcal/mol. To verify their drug-likeness, the discovered hits were put via Lipinski filters and ADMET analysis. According to MD simulations of the complex run for 100 numbers, delphin binds to the SARS-CoV-2 ACE2 receptor's active region with good stability. In root-mean-square deviation (RMSD) and root mean square fluctuation (RMSF) calculations, delphinan, β-amyrin, and tulipanin showed reduced variance with the receptor binding domain subunit 1(RBD S1) ACE2 protein complex. The solvent accessible surface area (SASA), radius of gyration (Rg), molecular surface area (MolSA), and polar surface area (PSA) validation results for these three compounds were likewise encouraging. The convenient binding energies across the 100 numbers binding period were discovered by using molecular mechanics of generalized born and surface (MM/GBSA) to estimate the ligand-binding free energies to the protein receptor. All things considered, the information points to a greater likelihood of chemicals found in Euphorbia neriifolia binding to the SARS-CoV-2 ACE2 active site. To determine these lead compounds’ anti-SARS-CoV-2 potential, in vitro and in vivo studies should be conducted.

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