Therapy for urolithiasis by hydroxamic acids. II. Urease inhibitory potency and urinary excretion rate of hippurohydroxamic acid derivatives

Identification of novel urease inhibitors: pharmacophore modeling, virtual screening and molecular docking studies

Pharmacophore modeling and atom-based three-dimensional quantitative structure-activity relationship (3D-QSAR) have been developed on N-acylglycino- and hippurohydroxamic acid derivatives, which are known potential inhibitors of urease. This is followed by virtual screening and ADMET (absorption, distribution, metabolism, excretion and toxicity) studies on a large library of known drugs in order to get lead molecules as Helicobacter pylori urease inhibitors. A suitable three-featured pharmacophore model comprising one H-bond acceptor and two H-bond donor features (ADD.10) has been found to be the best QSAR model. An external library of compounds (∼3000 molecules), pre-filtered using Lipinski's rule of five, has been further screened using the pharmacophore model ADD.10. By analyzing the fitness of the hits with respect to the pharmacophore model and their binding interaction inside the urease active site, four molecules have been predicted to be extremely good urease inhibitors. Two of these have significant potential and should be taken up for further drug-designing process.

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.

Urease inhibitors as potential drugs for gastric and urinary tract infections: a patent review

INTRODUCTION

Urease is the enzyme that catalyzes the hydrolysis of urea, which is involved in serious infections caused by Helicobacter pylori in the gastric tract, as well as Proteus and related species in the urinary tract. The necessity to treat such infections has stimulated intensive studies on various groups of urease inhibitors.

AREAS COVERED

Patent literature on urease inhibitors with possible applications in medicine is reviewed in this paper. Hydroxamic acids, phosphoramidates, urea derivatives, quinones and heterocyclic compounds constitute the major classes of structures with such activity.

EXPERT OPINION

Until now, only one compound, acetohydroxamic acid, has been clinically used for the treatment of urinary tract infections by urease inhibition. Unfortunately, it exhibits severe side effects. Thus, it seems that the full potential of urease inhibition has not yet been fully explored. Several Japanese patents related to the use of herbal extracts as sources of polyphenolic urease inhibitors have been considered as complementary or alternative therapy; however, their accessibility is quite possibly due to reduced restrictions for the introduction of natural products to the market.

New inhibitors of Helicobacter pylori urease holoenzyme selected from phage-displayed peptide libraries

Urease is an important virulence factor for Helicobacter pylori and is critical for bacterial colonization of the human gastric mucosa. Specific inhibition of urease activity has been proposed as a possible strategy to fight this bacteria which infects billions of individual throughout the world and can lead to severe pathological conditions in a limited number of cases. We have selected peptides which specifically bind and inhibit H. pylori urease from libraries of random peptides displayed on filamentous phage in the context of pIII coat protein. Screening of a highly diverse 25-mer combinatorial library and two newly constructed random 6-mer peptide libraries on solid phase H. pylori urease holoenzyme allowed the identification of two peptides, 24-mer TFLPQPRCSALLRYLSEDGVIVPS and 6-mer YDFYWW that can bind and inhibit the activity of urease purified from H. pylori. These two peptides were chemically synthesized and their inhibition constants (Ki) were found to be 47 microM for the 24-mer and 30 microM for the 6-mer peptide. Both peptides specifically inhibited the activity of H. pylori urease but not that of Bacillus pasteurii.

Treatment options in struvite stones

Urinary calculi have plagued man over the centuries. The epidemiology and pathogenesis of infection have been studied. The curative treatment remains problematic. Without therapy, a vicious cycle of stone formation occurs. This results in renal damage and even death. Multimodality therapy is the key. Nonoperative treatment leads to progressive renal damage. The combination of maximal surgical ablation and medical therapy is synergistic. The combination of PCNL-ESWL has not appeared to produce ill effects. PCNL-ESWL is a less morbid surgical alternative than open surgical procedures. Adjunctive medical therapy, such as culture-specific antibiotics and urease inhibitors, complements surgical ablation by reducing the morbidity with persistent UTIs and stone recurrence. The urologist today must approach struvite staghorns with a vast armamentarium of surgical and medical techniques. Each patient requires a unique solution.

Molecular biology of microbial ureases

Urease (urea amidohydrolase; EC 3.5.1.5) catalyzes the hydrolysis of urea to yield ammonia and carbamate. The latter compound spontaneously decomposes to yield another molecule of ammonia and carbonic acid. The urease phenotype is widely distributed across the bacterial kingdom, and the gene clusters encoding this enzyme have been cloned from numerous bacterial species. The complete nucleotide sequence, ranging from 5.15 to 6.45 kb, has been determined for five species including Bacillus sp. strain TB-90, Klebsiella aerogenes, Proteus mirabilis, Helicobacter pylori, and Yersinia enterocolitica. Sequences for selected genes have been determined for at least 10 other bacterial species and the jack bean enzyme. Urease synthesis can be nitrogen regulated, urea inducible, or constitutive. The crystal structure of the K. aerogenes enzyme has been determined. When combined with chemical modification studies, biophysical and spectroscopic analyses, site-directed mutagenesis results, and kinetic inhibition experiments, the structure provides important insight into the mechanism of catalysis. Synthesis of active enzyme requires incorporation of both carbon dioxide and nickel ions into the protein. Accessory genes have been shown to be required for activation of urease apoprotein, and roles for the accessory proteins in metallocenter assembly have been proposed. Urease is central to the virulence of P. mirabilis and H. pylori. Urea hydrolysis by P. mirabilis in the urinary tract leads directly to urolithiasis (stone formation) and contributes to the development of acute pyelonephritis. The urease of H. pylori is necessary for colonization of the gastric mucosa in experimental animal models of gastritis and serves as the major antigen and diagnostic marker for gastritis and peptic ulcer disease in humans. In addition, the urease of Y. enterocolitica has been implicated as an arthritogenic factor in the development of infection-induced reactive arthritis. The significant progress in our understanding of the molecular biology of microbial ureases is reviewed.

Microbial ureases: significance, regulation, and molecular characterization

Microbial ureases hydrolyze urea to ammonia and carbon dioxide. Urease activity of an infectious microorganism can contribute to the development of urinary stones, pyelonephritis, gastric ulceration, and other diseases. In contrast to these harmful effects, urease activity of ruminal and gastrointestinal microorganisms can benefit both the microbe and host by recycling (thereby conserving) urea nitrogen. Microbial ureases also play an important role in utilization of environmental nitrogenous compounds and urea-based fertilizers. Urease is a high-molecular-weight, multimeric, nickel-containing enzyme. Its cytoplasmic location requires that urea enter the cell for utilization, and in some species energy-dependent urea uptake systems have been detected. Eucaryotic microorganisms possess a homopolymeric urease, analogous to the well-studied plant enzyme composed of six identical subunits. Gram-positive bacteria may also possess homopolymeric ureases, but the evidence for this is not conclusive. In contrast, ureases from gram-negative bacteria studied thus far clearly possess three distinct subunits with Mrs of 65,000 to 73,000 (alpha), 10,000 to 12,000 (beta), and 8,000 to 10,000 (gamma). Tightly bound nickel is present in all ureases and appears to participate in catalysis. Urease genes have been cloned from several species, and nickel-containing recombinant ureases have been characterized. Three structural genes are transcribed on a single messenger ribonucleic acid and translated in the order gamma, beta, and then alpha. In addition to these genes, several other peptides are encoded in the urease operon of some species. The roles for these other genes are not firmly established, but may involve regulation, urea transport, nickel transport, or nickel processing.

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.