A homology model of Helicobacter pylori urease was developed by using the crystal structure of urease from Klebsiella aerogenes (EC 3.5.1.5) as a template. The acetohydroxamic acid moiety was docked into the active pocket of the enzyme model, followed by relaxation of the complex by use of molecular dynamics. The resulting conformation was used as a template to construct 24 potential dipeptide hydroxamic acid inhibitors with which comparative molecular field analysis (CoMFA) was performed. The resulting model provided a cross-validation correlation coefficient (q 2 L00 ) of 0.610, a conventional r 2 value of 0.988, and an F (Fisher indication of statistical significance) value of 294.88. We were able to validate the CoMFA model by using the 50% inhibitory concentrations of six compounds that were not included in the construction of the model. A very good structural correlation was observed between the amino acids in the model urease's active pocket and the contour maps derived from the CoMFA model. This correlation, accompanied by the validation supplied by use of the CoMFA data, illustrates that the model can aid in the prediction and design of novel H. pylori urease inhibitors.Helicobacter pylori is a gram-negative, spiral bacterium thought to affect about 90% of the world's population (11). It is well accepted that H. pylori infection is etiologically associated with chronic active gastritis, peptic ulcer diseases, mucosa-associated lymphoid tissue-type gastric carcinoma, and other gastric cancers (16). Although H. pylori infection has been implicated as an etiological factor in chronic gastric reflux disease, new studies show that H. pylori infection may provide a protective mechanism against such disease; however, the results of those studies remain controversial (8, 18). Eradication therapy heals gastritis and results in cure of peptic ulcer and the remission of mucosa-associated lymphoid tissue-type gastric carcinomas (22). Although most infections can be controlled by antibiotic therapy (17, 27), H. pylori antibiotic resistance is becoming somewhat commonplace (1). Antibiotic resistance in a microorganism as widespread as H. pylori is a cause for immediate concern and warrants a dedicated search for the discovery of new drug therapies.H. pylori, characterized by its strong urease activity (5), has received a great deal of attention from the scientific community over the past two decades. It is now clear that for survival the organism requires the production of a urease enzyme to help produce ammonia to counteract the strong acidic environment of the stomach (19). It has been estimated that over 5% of the total protein in the cell is represented by this enzyme (12). The urease reaction not only provides an environment with a pH suitable for H. pylori colonization of the stomach mucosal lining but also provides the mechanism for eventual gastric wall damage that increases the overall likelihood and the severity of gastric ulcers (20). Ureases are ubiquitous in nature and are inhibited, in general, by a var...