Quantitative structure-activity relationships between hydroxamic acids and their urease inhibitory potency

In Silico study of the active site of Helicobacter pylori urease and its inhibition by hydroxamic acids

Hydroxamic acids have emerged as the most promising candidates from among the different classes of inhibitors of urease. In order to understand the mechanism of their action, we have studied in detail using quantum mechanics the active site of Helicobacter pylori urease complexed with acetohydroxamic acid. A diverse library of ligands having the hydroxamate moiety has been prepared and docked into the active site of urease using the QM/MM methodology. It is found that hydroxamic acids with hydrophobic groups attached to them are more potent inhibitors of urease because they can easily penetrate the hydrophobic environment surrounding the active site. The -CONHO^- moiety of the hydroxamic acid is also found to be absolutely necessary for chelation and inhibition of urease. In order to determine the roles of residues His 221 and Ala 365, which are not part of the active site, but are nevertheless involved in hydrogen bonding with the ligand, we have performed Molecular Dynamics simulations, both on the wild urease and also on its mutated counterpart, with the two residues substituted, respectively, by alanine and glycine.

Three-dimensional quantitative structure-activity relationship and comparative molecular field analysis of dipeptide hydroxamic acid Helicobacter pylori urease inhibitors

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.

Molecular modeling studies on the urease active site and the enzyme-catalyzed urea hydrolysis

These studies are an attempt to gain better insight into the pharmacophore requirements of urease. On the basis of published information on this enzyme (EXAFS, amino acid sequence, essential groups at the active site) a hypothetical nickel-tripeptide complex, as preliminary substitute for the urease active site was modeled using computer-aided molecular modeling techniques. The results suggest two alternative docking modes of urea and reaction intermediates, corresponding to two different reaction mechanisms. Both binding modes are compatible with the docking of known potent inhibitors such as selected hydroxamic acids and phosphorodiamides. The results can be used to help in the design of new potential inhibitors of urease.

S.E.M. study of urease-induced crystalluria in the presence of hydroxamic derivatives

The effect of 3 hydroxamic acid derivatives on urease-induced crystalluria was studied in vitro. Acetohydroxamic acid is more effective than salicylhydroxamic and gentisohydroxamic acids in inhibiting the kinetic of urease enzymatic reaction and in retarding the formation of struvite and apatite. Crystal deposits studied by scanning electron microscope (S.E.M.) and X-ray microanalysis indicated that acetohydroxamic acid favours the formation of large crystals of struvite, and less aggregation is observed. Salicyl and gentiso derivatives favour the formation of brushite together with struvite and apatite.

Urinary calculi: microbiological and crystallographic studies

Although referred to as "urinary calculus disease", the formation of stone in the urinary tract is not caused by a single etiological agent. As such, diverse clinical investigations to diagnose the cause of stone formation must be carried out and the course of management after diagnosis must inevitably be different in each case. This review will cover all aspects of calculus formation, but will give particular attention to calculi caused by infection of the urinary tract with urease-producing bacteria. This is a recurrent, potentially life-threatening disease which has led clinicians to refer to the condition as "stone cancer". Because the etiology of infection stones is so different from stones caused by metabolic disorders, the two disease patterns should be considered separately, a fact often overlooked in epidemiological studies of stone formation. The importance of analysis of calculi as an aid to management is thus emphasized; identification of stone type will help to indicate appropriate therapy. A review of methods of analysis will be covered, particularly crystallographic analysis. Inhibition of bacterial urease as a means of management of infection stones will be discussed together with problems encountered and brighter hopes for the future.