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A Novel Urease Inhibitor of Ruminal Microbiota Screened through Molecular Docking
Inhibition of the urease activity of ruminal microbiota is not only beneficial for increasing dietary and endogenic urea-N utilization efficiency in ruminants but also might be applicable for the preservation of nitrogen fertilizer in soil and treatment of gastrointestinal and urinary tract infectio...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7503308/ https://www.ncbi.nlm.nih.gov/pubmed/32825454 http://dx.doi.org/10.3390/ijms21176006 |
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author | Zhang, Zhenyu Li, Ming Zhang, Xiaoyin Zheng, Nan Zhao, Shengguo Wang, Jiaqi |
author_facet | Zhang, Zhenyu Li, Ming Zhang, Xiaoyin Zheng, Nan Zhao, Shengguo Wang, Jiaqi |
author_sort | Zhang, Zhenyu |
collection | PubMed |
description | Inhibition of the urease activity of ruminal microbiota is not only beneficial for increasing dietary and endogenic urea-N utilization efficiency in ruminants but also might be applicable for the preservation of nitrogen fertilizer in soil and treatment of gastrointestinal and urinary tract infections caused by ureolytic bacteria. To discover urease inhibitors to efficiently target ruminal microbiota, the identified ruminal microbial metagenomic urease gene was used to construct a homology model to virtually screen urease inhibitors from the ChemDiv database by molecular docking. The GMQE and QMEAN values of the homology model were 0.85 and −0.37, respectively, indicating a good model quality. The inhibition effect of the screened urease inhibitor for ruminal urea degradation was assessed by ruminal microbial fermentation in vitro. The toxic effect of the candidate inhibitor was performed using gut Caco-2 cells in vitro. The results showed that compound 3-[1-[(aminocarbonyl)amino]-5-(4-methoxyphenyl)-1H-pyrrol-2-yl] propanoic acid (ChemDiv_ID: 6238-0047, IC(50) = 65.86 μM) was found to be the most effective urease inhibitor among the candidate compounds. Compound 6238-0047 significantly lowered the amount of urea degradation and ammonia production in ruminal microbial fermentation. The 24 h degradation rate of compound 6238-0047 in ruminal microbial fermentation was 3.32%–16.00%. In addition, compound 6238-0047 (10–100 μM) had no significant adverse effect on the cell viability of Caco-2 cells. Molecular docking showed that compound 6238-0047 could interact with Asp359 in the active site and Cys318 in the flap region by the hydrogen bond and Pi-Alkyl interaction, respectively. Compound 6238-0047 could be used as a novel inhibitor for decreasing the urease activity of ruminal microbiota. |
format | Online Article Text |
id | pubmed-7503308 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-75033082020-09-23 A Novel Urease Inhibitor of Ruminal Microbiota Screened through Molecular Docking Zhang, Zhenyu Li, Ming Zhang, Xiaoyin Zheng, Nan Zhao, Shengguo Wang, Jiaqi Int J Mol Sci Article Inhibition of the urease activity of ruminal microbiota is not only beneficial for increasing dietary and endogenic urea-N utilization efficiency in ruminants but also might be applicable for the preservation of nitrogen fertilizer in soil and treatment of gastrointestinal and urinary tract infections caused by ureolytic bacteria. To discover urease inhibitors to efficiently target ruminal microbiota, the identified ruminal microbial metagenomic urease gene was used to construct a homology model to virtually screen urease inhibitors from the ChemDiv database by molecular docking. The GMQE and QMEAN values of the homology model were 0.85 and −0.37, respectively, indicating a good model quality. The inhibition effect of the screened urease inhibitor for ruminal urea degradation was assessed by ruminal microbial fermentation in vitro. The toxic effect of the candidate inhibitor was performed using gut Caco-2 cells in vitro. The results showed that compound 3-[1-[(aminocarbonyl)amino]-5-(4-methoxyphenyl)-1H-pyrrol-2-yl] propanoic acid (ChemDiv_ID: 6238-0047, IC(50) = 65.86 μM) was found to be the most effective urease inhibitor among the candidate compounds. Compound 6238-0047 significantly lowered the amount of urea degradation and ammonia production in ruminal microbial fermentation. The 24 h degradation rate of compound 6238-0047 in ruminal microbial fermentation was 3.32%–16.00%. In addition, compound 6238-0047 (10–100 μM) had no significant adverse effect on the cell viability of Caco-2 cells. Molecular docking showed that compound 6238-0047 could interact with Asp359 in the active site and Cys318 in the flap region by the hydrogen bond and Pi-Alkyl interaction, respectively. Compound 6238-0047 could be used as a novel inhibitor for decreasing the urease activity of ruminal microbiota. MDPI 2020-08-20 /pmc/articles/PMC7503308/ /pubmed/32825454 http://dx.doi.org/10.3390/ijms21176006 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Zhang, Zhenyu Li, Ming Zhang, Xiaoyin Zheng, Nan Zhao, Shengguo Wang, Jiaqi A Novel Urease Inhibitor of Ruminal Microbiota Screened through Molecular Docking |
title | A Novel Urease Inhibitor of Ruminal Microbiota Screened through Molecular Docking |
title_full | A Novel Urease Inhibitor of Ruminal Microbiota Screened through Molecular Docking |
title_fullStr | A Novel Urease Inhibitor of Ruminal Microbiota Screened through Molecular Docking |
title_full_unstemmed | A Novel Urease Inhibitor of Ruminal Microbiota Screened through Molecular Docking |
title_short | A Novel Urease Inhibitor of Ruminal Microbiota Screened through Molecular Docking |
title_sort | novel urease inhibitor of ruminal microbiota screened through molecular docking |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7503308/ https://www.ncbi.nlm.nih.gov/pubmed/32825454 http://dx.doi.org/10.3390/ijms21176006 |
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