Anti-methanogenic effect of pyrogallol in Spirulina platensis – molecular docking and dynamics simulation on methyl-coenzyme M reductase

SADID, Muhammad Maulana and ANAM, Moh Sofi’ul (2024) Anti-methanogenic effect of pyrogallol in Spirulina platensis – molecular docking and dynamics simulation on methyl-coenzyme M reductase. Journal of Life Science and Biomedicine. pp. 45-53. ISSN 2251-9939

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Abstract

Methane, along with carbon dioxide and nitrogen oxides, is a key greenhouse gas contributing significantly to the global concern over climate change. This study investigated the anti-methanogenic properties of pyrogallol in Spirulina platensis using molecular docking and dynamics simulation on methyl-coenzyme M reductase (MCR). The Swiss ADME web server was used to identify pyrogallol's absorption, distribution, metabolism, and excretion (ADME) properties. Molecular docking studies were conducted using UCSF Chimera with the Vina script as the executor. The docking results were further analyzed through molecular dynamics simulation using Gromacs-2024. ADME analysis indicated that pyrogallol meets Lipinski’s Rule of Five. Docking studies revealed that pyrogallol has a binding affinity of 4.6 kJ/mol with 2 hydrogen bonds and 1 hydrophobic interaction. Additionally, the MCR-pyrogallol simulation results showed fluctuating root mean square deviation (RMSD) values that stabilized at t = 26,200 until the end of the simulation with an average value of 2.50 nm. Moreover, the hydrogen bonds formed during the simulation fluctuated, with no bonds observed for more than 75% of the simulation time. The energy released during the simulation reached –300.24 kJ/mol with an average of –5.19 kJ/mol. In conclusion, the pyrogallol compound in Spirulina plantensis can potentially inhibit the MCR enzyme, thereby reducing methane production and mitigating the impact of climate change.

Item Type:	Article
Keywords:	Anti-methanogenic, methyl-coenzyme M reductase, molecular docking, pyrogallol, Spirulina platensis
Subjects:	R Medicine > RA Public aspects of medicine > RA0421 Public health. Hygiene. Preventive Medicine R Medicine > RJ Pediatrics > RJ101 Child Health. Child health services S Agriculture > SF Animal culture
Divisions:	Journal of Life Sciences and Biomedicine (JLSB)
Page Range:	pp. 45-53
Journal or Publication Title:	Journal of Life Science and Biomedicine
Journal Index:	Not Index
Volume:	14
Number:	3
Publisher:	Scienceline Publication
Identification Number:	https://doi.org/10.54203/jlsb.2024.5
ISSN:	2251-9939
Depositing User:	Dr. Zohreh Yousefi
URI:	https://eprints.science-line.com/id/eprint/1292

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