Bio-Mechanism of Catechin as Pheromone Signal Inhibitor: Prediction of Antibacterial Agent Action Mode by In Vitro and In Silico Study

The utilization of medicinal plants has long been explored for the discovery of antibacterial agents and the most effective mechanisms or new targets that can prevent and control the spread of antibiotic resistance. One kind of bacterial cell wall inhibition is the inactivation of the MurA enzyme th...

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Autores principales:	Dikdik Kurnia, Zenika Febian Ramadhanty, Aprilina Mora Ardani, Achmad Zainuddin, Hendra Dian Adhita Dharsono, Mieke Hemiawati Satari
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	catechin QS GBAP gelatinase MurA serine protease Organic chemistry QD241-441
Acceso en línea:	https://doaj.org/article/3ceddf929fb94efda9f1d02b8c92a143
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spelling	oai:doaj.org-article:3ceddf929fb94efda9f1d02b8c92a1432021-11-11T18:24:32ZBio-Mechanism of Catechin as Pheromone Signal Inhibitor: Prediction of Antibacterial Agent Action Mode by In Vitro and In Silico Study10.3390/molecules262163811420-3049https://doaj.org/article/3ceddf929fb94efda9f1d02b8c92a1432021-10-01T00:00:00Zhttps://www.mdpi.com/1420-3049/26/21/6381https://doaj.org/toc/1420-3049The utilization of medicinal plants has long been explored for the discovery of antibacterial agents and the most effective mechanisms or new targets that can prevent and control the spread of antibiotic resistance. One kind of bacterial cell wall inhibition is the inactivation of the MurA enzyme that contributes to the formation of peptidoglycan. Another approach is to interfere with the cell–cell communication of bacteria called the Quorum sensing (QS) system. The blocking of auto-inducer such as gelatinase biosynthesis-activating pheromone (GBAP) can also suppress the virulence factors of gelatinase and serine protease. This research, in particular, aims to analyze lead compounds as antibacterial and anti-QS agents from Gambir (<i>Uncaria gambir</i> Roxburgh) through protein inhibition by in silico study. Antibacterial agents were isolated by bioactivity-guided isolation using a combination of chromatographic methods, and their chemical structures were determined by spectroscopic analysis methods. The in vitro antibacterial activity was evaluated by disc diffusion methods to determine inhibitory values. Meanwhile, in the in silico analysis, the compound of <i>Uncaria gambir</i> was used as ligand and compared with fosfomycin, ambuic acid, quercetin, and taxifolin as the standard ligand. These ligands were attached to MurA, GBAP, gelatinase, and serine proteases using Autodock Vina in PyRx 0.8 followed by PYMOL for combining the ligand conformation and proteins. plus programs to explore the complex, and visualized by Discovery Studio 2020 Client program. The antibacterial agent was identified as catechin that showed inhibitory activity against <i>Enterococcus faecalis</i> ATCC 29212 with inhibition zones of 11.70 mm at 10%, together with MIC and MBC values of 0.63 and 1.25 μg/mL, respectively. In the in silico study, the molecular interaction of catechin with MurA, GBAP, and gelatinase proteins showed good binding energy compared with two positive controls, namely fosfomycin and ambuic acid. It is better to use catechin–MurA (−8.5 Kcal/mol) and catechin–gelatinase (−7.8 Kcal/mol), as they have binding energies which are not marginally different from quercetin and taxifolin. On the other hand, the binding energy of serine protease is lower than quercetin, taxifolin, and ambuic acid. Based on the data, catechin has potency as an antibacterial through the inhibition of GBAP proteins, gelatinase, and serine protease that play a role in the QS system. This is the first discovery of the potential of catechin as an alternative antibacterial agent with an effective mechanism to prevent and control oral disease affected by antibiotic resistance.Dikdik KurniaZenika Febian RamadhantyAprilina Mora ArdaniAchmad ZainuddinHendra Dian Adhita DharsonoMieke Hemiawati SatariMDPI AGarticlecatechinQSGBAPgelatinaseMurAserine proteaseOrganic chemistryQD241-441ENMolecules, Vol 26, Iss 6381, p 6381 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	catechin QS GBAP gelatinase MurA serine protease Organic chemistry QD241-441
spellingShingle	catechin QS GBAP gelatinase MurA serine protease Organic chemistry QD241-441 Dikdik Kurnia Zenika Febian Ramadhanty Aprilina Mora Ardani Achmad Zainuddin Hendra Dian Adhita Dharsono Mieke Hemiawati Satari Bio-Mechanism of Catechin as Pheromone Signal Inhibitor: Prediction of Antibacterial Agent Action Mode by In Vitro and In Silico Study
description	The utilization of medicinal plants has long been explored for the discovery of antibacterial agents and the most effective mechanisms or new targets that can prevent and control the spread of antibiotic resistance. One kind of bacterial cell wall inhibition is the inactivation of the MurA enzyme that contributes to the formation of peptidoglycan. Another approach is to interfere with the cell–cell communication of bacteria called the Quorum sensing (QS) system. The blocking of auto-inducer such as gelatinase biosynthesis-activating pheromone (GBAP) can also suppress the virulence factors of gelatinase and serine protease. This research, in particular, aims to analyze lead compounds as antibacterial and anti-QS agents from Gambir (<i>Uncaria gambir</i> Roxburgh) through protein inhibition by in silico study. Antibacterial agents were isolated by bioactivity-guided isolation using a combination of chromatographic methods, and their chemical structures were determined by spectroscopic analysis methods. The in vitro antibacterial activity was evaluated by disc diffusion methods to determine inhibitory values. Meanwhile, in the in silico analysis, the compound of <i>Uncaria gambir</i> was used as ligand and compared with fosfomycin, ambuic acid, quercetin, and taxifolin as the standard ligand. These ligands were attached to MurA, GBAP, gelatinase, and serine proteases using Autodock Vina in PyRx 0.8 followed by PYMOL for combining the ligand conformation and proteins. plus programs to explore the complex, and visualized by Discovery Studio 2020 Client program. The antibacterial agent was identified as catechin that showed inhibitory activity against <i>Enterococcus faecalis</i> ATCC 29212 with inhibition zones of 11.70 mm at 10%, together with MIC and MBC values of 0.63 and 1.25 μg/mL, respectively. In the in silico study, the molecular interaction of catechin with MurA, GBAP, and gelatinase proteins showed good binding energy compared with two positive controls, namely fosfomycin and ambuic acid. It is better to use catechin–MurA (−8.5 Kcal/mol) and catechin–gelatinase (−7.8 Kcal/mol), as they have binding energies which are not marginally different from quercetin and taxifolin. On the other hand, the binding energy of serine protease is lower than quercetin, taxifolin, and ambuic acid. Based on the data, catechin has potency as an antibacterial through the inhibition of GBAP proteins, gelatinase, and serine protease that play a role in the QS system. This is the first discovery of the potential of catechin as an alternative antibacterial agent with an effective mechanism to prevent and control oral disease affected by antibiotic resistance.
format	article
author	Dikdik Kurnia Zenika Febian Ramadhanty Aprilina Mora Ardani Achmad Zainuddin Hendra Dian Adhita Dharsono Mieke Hemiawati Satari
author_facet	Dikdik Kurnia Zenika Febian Ramadhanty Aprilina Mora Ardani Achmad Zainuddin Hendra Dian Adhita Dharsono Mieke Hemiawati Satari
author_sort	Dikdik Kurnia
title	Bio-Mechanism of Catechin as Pheromone Signal Inhibitor: Prediction of Antibacterial Agent Action Mode by In Vitro and In Silico Study
title_short	Bio-Mechanism of Catechin as Pheromone Signal Inhibitor: Prediction of Antibacterial Agent Action Mode by In Vitro and In Silico Study
title_full	Bio-Mechanism of Catechin as Pheromone Signal Inhibitor: Prediction of Antibacterial Agent Action Mode by In Vitro and In Silico Study
title_fullStr	Bio-Mechanism of Catechin as Pheromone Signal Inhibitor: Prediction of Antibacterial Agent Action Mode by In Vitro and In Silico Study
title_full_unstemmed	Bio-Mechanism of Catechin as Pheromone Signal Inhibitor: Prediction of Antibacterial Agent Action Mode by In Vitro and In Silico Study
title_sort	bio-mechanism of catechin as pheromone signal inhibitor: prediction of antibacterial agent action mode by in vitro and in silico study
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/3ceddf929fb94efda9f1d02b8c92a143
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Bio-Mechanism of Catechin as Pheromone Signal Inhibitor: Prediction of Antibacterial Agent Action Mode by In Vitro and In Silico Study

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