Biological activity, molecular docking, and ADME predictions of amphibine analogues of Ziziphus spina-christi towards SARS-CoV-2 Mpro
Abstract
The main protease of the SARS-CoV-2 virus, SARS-CoV-2 Mpro, can be discovered as a promising target to treat the COVID-19 pandemic. The peptide-based inhibitors may present better options than small molecules to inhibit SARS-CoV-2 Mpro. Ziziphus spina-christi species reported have a peptide-based of alkaloids group, i.e., amphibine whose analogues can be identified the potential as an inhibitor of SARS-CoV-2 Mpro. The compound structure was drawn and optimized using semi-empirical AM-1 method using Quantum ESPRESSO v.6.6, while the biological activity using PASS. Prediction server and molecular docking simulation using MGLTools 1.5.6 with AutoDock 4.2 were performed. Afterward, the ADME profiles were predicted using the SWISS-ADME server. PASS server was predicting amphibine B-F and H showed potency both as antiviral and as a protease inhibitor. The molecular docking simulation of amphibine analogues showed lower binding energy than the native ligand. The binding energy of the native ligand was −7.69 Kcal/mol compared to the lowest binding energy of amphibine analogues was −10.10 Kcal/mol (amphibine-F). The ADME prediction showed that amphibine-F has the best bioavailability as an oral drug, amphibine-B, C, and D have good bioavailability, and amphibian-E and H have poor bioavailability. Concluded, amphibine B-F and H of amphibine analogues showed potency as COVID-19 treatment targeting SARS-CoV-2 Mpro.Copyright (c) 2021 Taufik Muhammad Fakih, Dwi Syah Fitra Ramadhan, Fitrianti Darusman
This work is licensed under a Creative Commons Attribution 4.0 International License.
COPYRIGHT AND LICENSE STATEMENT
COPYRIGHT
Biogenesis: Jurnal Ilmiah Biologi is published under the terms of the Creative Commons Attribution license. Authors hold the copyright and retain publishing rights without restriction to their work. Users may read, download, copy, distribute, and print the work in any medium, provided the original work is properly cited.
LICENSE TO PUBLISH
1. License
The use of the article will be governed by the Creative Commons Attribution license as currently displayed on http://creativecommons.org/licenses/by/4.0.
2. Author’s Warranties
The author warrants that the article is original, written by stated author/s, has not been published before, contains no unlawful statements, does not infringe the rights of others, is subject to copyright that is vested exclusively in the author and free of any third party rights, and that any necessary written permissions to quote from other sources have been obtained by the author(s).
3. User Rights
Under the Creative Commons Attribution license, the users are free to download, reuse, reprint, modify, distribute and/or copy the content for any purpose, even commercially, as long as the original authors and source are cited. No permission is required from the authors or the publishers.
4. Co-Authorship
If the article was prepared jointly with other authors, the corresponding author warrants that he/she has been authorized by all co-authors, and agrees to inform his/her co-authors of the terms of this statement.
5. Miscellaneous
Biogenesis: Jurnal Ilmiah Biologi may conform the article to a style of punctuation, spelling, capitalization, and usage that it deems appropriate. The author acknowledges that the article may be published so that it will be publicly accessible and such access will be free of charge for the readers.