Targeting Natural Plant Metabolites for Hunting SARS-CoV-2 Omicron BA.1 Variant Inhibitors: Extraction, Molecular Docking, Molecular Dynamics, and Physicochemical Properties Study
| Title: | Targeting Natural Plant Metabolites for Hunting SARS-CoV-2 Omicron BA.1 Variant Inhibitors: Extraction, Molecular Docking, Molecular Dynamics, and Physicochemical Properties Study |
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| Authors: | Heba Ali Hassan, Ahmed R. Hassan, Eslam A. R. Mohamed, Ahmad Al-Khdhairawi, Hala E. Taha, Hanan M. El-Tantawy, Iman A. M. Abdel-Rahman, Ali E. Raslan, Khaled S. Allemailem, Ahmad Almatroudi, Faris Alrumaihi, Maha A. Alshiekheid, Hafiz Muzzammel Rehman, Mahmoud M. Abdelhamid, Islam M. Abdel-Rahman, Ahmed E. Allam |
| Source: | Current Issues in Molecular Biology, Vol 44, Iss 10, Pp 5028-5047 (2022) |
| Publisher Information: | MDPI AG, 2022. |
| Publication Year: | 2022 |
| Collection: | LCC:Biology (General) |
| Subject Terms: | Echium angustifolium, peach fruits, SARS-COV-2 Omicron, molecular docking, molecular dynamics, Biology (General), QH301-705.5 |
| More Details: | (1) Background: SARS-CoV-2 Omicron BA.1 is the most common variation found in most countries and is responsible for 99% of cases in the United States. To overcome this challenge, there is an urgent need to discover effective inhibitors to prevent the emerging BA.1 variant. Natural products, particularly flavonoids, have had widespread success in reducing COVID-19 prevalence. (2) Methods: In the ongoing study, fifteen compounds were annotated from Echium angustifolium and peach (Prunus persica), which were computationally analyzed using various in silico techniques. Molecular docking calculations were performed for the identified phytochemicals to investigate their efficacy. Molecular dynamics (MD) simulations over 200 ns followed by molecular mechanics Poisson–Boltzmann surface area calculations (MM/PBSA) were performed to estimate the binding energy. Bioactivity was also calculated for the best components in terms of drug likeness and drug score. (3) Results: The data obtained from the molecular docking study demonstrated that five compounds exhibited remarkable potency, with docking scores greater than −9.0 kcal/mol. Among them, compounds 1, 2 and 4 showed higher stability within the active site of Omicron BA.1, with ΔGbinding values of −49.02, −48.07, and −67.47 KJ/mol, respectively. These findings imply that the discovered phytoconstituents are promising in the search for anti-Omicron BA.1 drugs and should be investigated in future in vitro and in vivo research. |
| Document Type: | article |
| File Description: | electronic resource |
| Language: | English |
| ISSN: | 1467-3045 1467-3037 |
| Relation: | https://www.mdpi.com/1467-3045/44/10/342; https://doaj.org/toc/1467-3037; https://doaj.org/toc/1467-3045 |
| DOI: | 10.3390/cimb44100342 |
| Access URL: | https://doaj.org/article/aae6431fb38a40de9f579b64cb4f86a1 |
| Accession Number: | edsdoj.6431fb38a40de9f579b64cb4f86a1 |
| Database: | Directory of Open Access Journals |
| ISSN: | 14673045 14673037 |
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| DOI: | 10.3390/cimb44100342 |
| Published in: | Current Issues in Molecular Biology |
| Language: | English |