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Computational and preclinical prediction of the antimicrobial properties of an agent isolated from Monodora myristica: a novel DNA gyrase inhibitor

The African nutmeg (Monodora myristica) is a medically useful plant. We, herein, aimed to critically examine whether bioactive compounds identified in the extracted oil of Monodora myristica could act as antimicrobial agents. To this end, we employed the Schrödinger platform as the com- putational t...

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Main Authors: Onikanni, Sunday Amos, Lawal, Bashir, Fadaka, Adewale Oluwaseun, Bakare, Oluwafemi, Ezekiel, Adewole, Bakhtiar, Muhammad Taher, Khotib, Junaidi, Darnis, Deny Susanti, Oyinloye, Babatunji Emmanuel, Ajiboye, Basiru Olaitan, Ojo, Oluwafemi Adeleke, Sibuyi, Nicole Remaliah Samantha
Format: Article
Language:English
English
Published: Multidisciplinary Digital Publishing Institute (MDPI) 2023
Subjects:
QD Chemistry
Online Access:http://irep.iium.edu.my/103628/2/103628_Computational%20and%20preclinical%20prediction%20of%20the%20antimicrobial.pdf
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https://www.mdpi.com/1420-3049/28/4/1593/pdf?version=1675770149
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spelling my.iium.irep.1036282023-04-17T01:44:43Z http://irep.iium.edu.my/103628/ Computational and preclinical prediction of the antimicrobial properties of an agent isolated from Monodora myristica: a novel DNA gyrase inhibitor Onikanni, Sunday Amos Lawal, Bashir Fadaka, Adewale Oluwaseun Bakare, Oluwafemi Ezekiel, Adewole Bakhtiar, Muhammad Taher Khotib, Junaidi Darnis, Deny Susanti Oyinloye, Babatunji Emmanuel Ajiboye, Basiru Olaitan Ojo, Oluwafemi Adeleke Sibuyi, Nicole Remaliah Samantha QD Chemistry The African nutmeg (Monodora myristica) is a medically useful plant. We, herein, aimed to critically examine whether bioactive compounds identified in the extracted oil of Monodora myristica could act as antimicrobial agents. To this end, we employed the Schrödinger platform as the com- putational tool to screen bioactive compounds identified in the oil of Monodora myristica. Our lead compound displayed the highest potency when compared with levofloxacin based on its binding affinity. The hit molecule was further subjected to an Absorption, Distribution, Metabolism, Excre- tion (ADME) prediction, and a Molecular Dynamics (MD) simulation was carried out on molecules with PubChem IDs 529885 and 175002 and on three standards (levofloxacin, cephalexin, and novo- biocin). The MD analysis results demonstrated that two molecules are highly compact when com- pared to the native protein; thereby, this suggests that they could affect the protein on a structural and a functional level. The employed computational approach demonstrates that conformational changes occur in DNA gyrase after the binding of inhibitors; thereby, this resulted in structural and functional changes. These findings expand our knowledge on the inhibition of bacterial DNA gy- rase and could pave the way for the discovery of new drugs for the treatment of multi-resistant bacterial infections. Multidisciplinary Digital Publishing Institute (MDPI) 2023-02-07 Article PeerReviewed application/pdf en http://irep.iium.edu.my/103628/2/103628_Computational%20and%20preclinical%20prediction%20of%20the%20antimicrobial.pdf application/pdf en http://irep.iium.edu.my/103628/3/103628_%20Computational%20and%20preclinical%20prediction%20of%20the%20antimicrobial_Scopus.pdf Onikanni, Sunday Amos and Lawal, Bashir and Fadaka, Adewale Oluwaseun and Bakare, Oluwafemi and Ezekiel, Adewole and Bakhtiar, Muhammad Taher and Khotib, Junaidi and Darnis, Deny Susanti and Oyinloye, Babatunji Emmanuel and Ajiboye, Basiru Olaitan and Ojo, Oluwafemi Adeleke and Sibuyi, Nicole Remaliah Samantha (2023) Computational and preclinical prediction of the antimicrobial properties of an agent isolated from Monodora myristica: a novel DNA gyrase inhibitor. Molecules, 28 (1953). pp. 1-16. ISSN 1420-3049 https://www.mdpi.com/1420-3049/28/4/1593/pdf?version=1675770149
institution Universiti Islam Antarabangsa Malaysia
building IIUM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider International Islamic University Malaysia
content_source IIUM Repository (IREP)
url_provider http://irep.iium.edu.my/
language English
English
topic QD Chemistry
spellingShingle QD Chemistry
Onikanni, Sunday Amos
Lawal, Bashir
Fadaka, Adewale Oluwaseun
Bakare, Oluwafemi
Ezekiel, Adewole
Bakhtiar, Muhammad Taher
Khotib, Junaidi
Darnis, Deny Susanti
Oyinloye, Babatunji Emmanuel
Ajiboye, Basiru Olaitan
Ojo, Oluwafemi Adeleke
Sibuyi, Nicole Remaliah Samantha
Computational and preclinical prediction of the antimicrobial properties of an agent isolated from Monodora myristica: a novel DNA gyrase inhibitor
description The African nutmeg (Monodora myristica) is a medically useful plant. We, herein, aimed to critically examine whether bioactive compounds identified in the extracted oil of Monodora myristica could act as antimicrobial agents. To this end, we employed the Schrödinger platform as the com- putational tool to screen bioactive compounds identified in the oil of Monodora myristica. Our lead compound displayed the highest potency when compared with levofloxacin based on its binding affinity. The hit molecule was further subjected to an Absorption, Distribution, Metabolism, Excre- tion (ADME) prediction, and a Molecular Dynamics (MD) simulation was carried out on molecules with PubChem IDs 529885 and 175002 and on three standards (levofloxacin, cephalexin, and novo- biocin). The MD analysis results demonstrated that two molecules are highly compact when com- pared to the native protein; thereby, this suggests that they could affect the protein on a structural and a functional level. The employed computational approach demonstrates that conformational changes occur in DNA gyrase after the binding of inhibitors; thereby, this resulted in structural and functional changes. These findings expand our knowledge on the inhibition of bacterial DNA gy- rase and could pave the way for the discovery of new drugs for the treatment of multi-resistant bacterial infections.
format Article
author Onikanni, Sunday Amos
Lawal, Bashir
Fadaka, Adewale Oluwaseun
Bakare, Oluwafemi
Ezekiel, Adewole
Bakhtiar, Muhammad Taher
Khotib, Junaidi
Darnis, Deny Susanti
Oyinloye, Babatunji Emmanuel
Ajiboye, Basiru Olaitan
Ojo, Oluwafemi Adeleke
Sibuyi, Nicole Remaliah Samantha
author_facet Onikanni, Sunday Amos
Lawal, Bashir
Fadaka, Adewale Oluwaseun
Bakare, Oluwafemi
Ezekiel, Adewole
Bakhtiar, Muhammad Taher
Khotib, Junaidi
Darnis, Deny Susanti
Oyinloye, Babatunji Emmanuel
Ajiboye, Basiru Olaitan
Ojo, Oluwafemi Adeleke
Sibuyi, Nicole Remaliah Samantha
author_sort Onikanni, Sunday Amos
title Computational and preclinical prediction of the antimicrobial properties of an agent isolated from Monodora myristica: a novel DNA gyrase inhibitor
title_short Computational and preclinical prediction of the antimicrobial properties of an agent isolated from Monodora myristica: a novel DNA gyrase inhibitor
title_full Computational and preclinical prediction of the antimicrobial properties of an agent isolated from Monodora myristica: a novel DNA gyrase inhibitor
title_fullStr Computational and preclinical prediction of the antimicrobial properties of an agent isolated from Monodora myristica: a novel DNA gyrase inhibitor
title_full_unstemmed Computational and preclinical prediction of the antimicrobial properties of an agent isolated from Monodora myristica: a novel DNA gyrase inhibitor
title_sort computational and preclinical prediction of the antimicrobial properties of an agent isolated from monodora myristica: a novel dna gyrase inhibitor
publisher Multidisciplinary Digital Publishing Institute (MDPI)
publishDate 2023
url http://irep.iium.edu.my/103628/2/103628_Computational%20and%20preclinical%20prediction%20of%20the%20antimicrobial.pdf
http://irep.iium.edu.my/103628/3/103628_%20Computational%20and%20preclinical%20prediction%20of%20the%20antimicrobial_Scopus.pdf
http://irep.iium.edu.my/103628/
https://www.mdpi.com/1420-3049/28/4/1593/pdf?version=1675770149
_version_ 1765296472415272960
score 13.211869

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