A Novel Urease Inhibitor of Ruminal Microbiota Screened through Molecular Docking.

Zhenyu Zhang,Jiaqi Wang,Xiaoyin Zhang,Nan Zheng,Ming Li,Shengguo Zhao

doi:10.3390/ijms21176006

Abstract

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, IC50 = 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.

Highlights

Urease is a metalloenzyme, which carries two nickel ions in its active site [1]
A urease inhibitor could efficiently decrease the ureolytic activity of urease and so it was considered to be a viable method for increasing the utilization of both dietary urea and endogenous urea for ruminal microbiota and ruminant animals, which holds great significance for animal production and environment N conservation [5]
The results demonstrated that the pharmacophore possessed six chemical characteristics including two hydrogen bond acceptors (HBA), one hydrophobic group (HY), two hydrogen bond donors (HBD), and one aromatic ring (RA)

Summary

Introduction

Urease (urea amidohydrolases, EC 3.5.1.5) is a metalloenzyme, which carries two nickel ions in its active site [1]. Urease catalyzes the hydrolysis of urea into ammonia and carbohydrate [2]. Excessive urease activity of urease producing bacteria makes them of great concern both in medicine and agriculture fields. The excessive rate of urea hydrolysis in rumen makes it difficult for the efficient assimilation of ammonia with carbon skeletons to form microbial protein, leading to a waste of N nutrition for the animal and environmental N contamination. A urease inhibitor could efficiently decrease the ureolytic activity of urease and so it was considered to be a viable method for increasing the utilization of both dietary urea and endogenous urea for ruminal microbiota and ruminant animals, which holds great significance for animal production and environment N conservation [5]

Methods

Results

Discussion

Conclusion