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Virtual screening for the discovery of novel urease inhibitors of rumen bacterial urease

Inhibition of urea hydrolysis by rumen bacterial urease can improve the efficiency of dietary nitrogen utilization in animal production and decrease nitrogen pollution into the environment. The three dimensional structure of urease from the ruminal bacterium Ruminococcus albus 8 (RaUrease) was resolved by comparison with the crystal structure of urease from Helicobacter pylori (HpUrease, PDB ID 1E9Z) using Modeller. A reliable structure of RaUrease was generated using molecular dynamics simulation for 20 ns with the AMBER force field using the Gromacs system, and the stereochemical quality of the protein model was evaluated. On the basis of binding energies (<-9.8 kcal mol-1), 12 commercially available agents were selected as potential urease inhibitors. Characterization of the RaUrease-binding site for the compound with the highest predicted inhibitory activity indicated that van der Waals forces were more important than hydrogen bonds for rumen bacterial urease binding. The results of the present study may help design novel urease inhibitors for ruminants and alleviate nitrogen pollution derived from livestock production.