Inhibition of ruminal bacterial urease activity could slow down the decomposition of urea to ammonia, which would lead to a decrease in urea synthesis in the liver and urea-N emission in the urine. In order to find a rumen bacterial urease specific inhibitor that is environmentally friendly, we used the homology model of rumen bacterial urease as the target to screen natural compounds from plants by molecular docking. The screening results showed that coptisine had the most potential to inhibit the activity of rumen bacterial urease with an IC(50) of 2.45 muM, which was superior to the traditional inhibitor acetohydroxamic acid. The enzyme kinetics results indicated coptisine was mixed type inhibitor of rumen bacterial urease with a K(i) value of 0.68 muM. Coptisine significantly decreased the release of NH(3) and decomposition of urea and improved microbial fermentation in a rumen fermentation system in vitro. Thiol-containing compounds or boric acid significantly decreased the inhibitory capacity of coptisine toward rumen bacterial urease, which indicated that coptisine could interact with both the urease active center Ni and amino acid residues possessing sulfhydryl groups in the flap area. The molecular docking results showed that coptisine acted as the metal acceptor for one nickel ion in the active site, and formed hydrogen bonds with the amino acid residues His320 and His362, which were located in the active site and flap region, respectively. These findings emphasized the potential role of coptisine in reducing nitrogen emissions that originate from ruminants by regulating rumen bacterial urease activity. CI - Copyright (c) 2021 Elsevier B.V. All rights reserved.