Computer-Aided Optimization of Phosphinic Inhibitors of Bacterial Ureases

Harvesting phosphorus-containing moieties for their antibacterial effects

Clinically manifested resistance of bacteria to antibiotics has emerged as a global threat to society and there is an urgent need for the development of novel classes of antibacterial agents. Recently, the use of phosphorus in antibacterial agents has been explored in quite an unprecedent manner. In this comprehensive review, we summarize the use of phosphorus-containing moieties (phosphonates, phosphonamidates, phosphonopeptides, phosphates, phosphoramidates, phosphinates, phosphine oxides, and phosphoniums) in compounds with antibacterial effect, including their use as β-lactamase inhibitors and antibacterial disinfectants. We show that phosphorus-containing moieties can serve as novel pharmacophores, bioisosteres, and prodrugs to modify pharmacodynamic and pharmacokinetic properties. We further discuss the mechanisms of action, biological activities, clinical use and highlight possible future prospects.

Rational Development of Bacterial Ureases Inhibitors

Urease, an enzyme that catalyzes the hydrolysis of urea, is a virulence factor of various pathogenic bacteria. In particular, Helicobacter pylori, that colonizes the digestive tract and Proteus spp., that can infect the urinary tract, are related to urease activity. Therefore, urease inhibitors are considered as potential therapeutics against these infections. This review describes current knowledge of the structures, activity, and biological importance of bacterial ureases. Moreover, the structure-based design of several classes of bacterial urease inhibitors is presented and discussed. Phosphinic and phosphonic acids were applied as transition-state analogues, while Michael acceptors and ebselen derivatives were applied as covalent binders of cysteine residue. This review incorporates bacterial urease inhibitors from literature published between 2008 and 2021.

Perna canaliculus as an Ecological Material in the Removal of o-Cresol Pollutants from Soil

Soil contamination with cresol is a problem of the 21st century and poses a threat to soil microorganisms, humans, animals, and plants. The lack of precise data on the potential toxicity of o-cresol in soil microbiome and biochemical activity, as well as the search for effective remediation methods, inspired the aim of this study. Soil is subjected to four levels of contamination with o-cresol: 0, 0.1, 1, 10, and 50 mg o-cresol kg-1 dry matter (DM) of soil and the following are determined: the count of eight groups of microorganisms, colony development index (CD) and ecophysiological diversity index (EP) for organotrophic bacteria, actinobacteria and fungi, and the bacterial genetic diversity. Moreover, the responses of seven soil enzymes are investigated. Perna canaliculus is a recognized biosorbent of organic pollutants. Therefore, microbial biostimulation with Perna canaliculus shells is used to eliminate the negative effect of the phenolic compound on the soil microbiome. Fungi appears to be the microorganisms most sensitive to o-cresol, while Pseudomonas sp. is the least sensitive. In o-cresol-contaminated soils, the microbiome is represented mainly by the bacteria of the Proteobacteria and Firmicutes phyla. Acid phosphatase, alkaline phosphatase and urease can be regarded as sensitive indicators of soil disturbance. Perna canaliculus shells prove to be an effective biostimulator of soil under pressure with o-cresol.

Covalent Inhibition of Bacterial Urease by Bifunctional Catechol-Based Phosphonates and Phosphinates

In this study, a new class of bifunctional inhibitors of bacterial ureases, important molecular targets for antimicrobial therapies, was developed. The structures of the inhibitors consist of a combination of a phosphonate or (2-carboxyethyl)phosphinate functionality with a catechol-based fragment, which are designed for complexation of the catalytic nickel ions and covalent bonding with the thiol group of Cys322, respectively. Compounds with three types of frameworks, including β-3,4-dihydroxyphenyl-, α-3,4-dihydroxybenzyl-, and α-3,4-dihydroxybenzylidene-substituted derivatives, exhibited complex and varying structure-dependent kinetics of inhibition. Among irreversible binders, methyl β-(3,4-dihydroxyphenyl)-β-(2-carboxyethyl)phosphorylpropionate was observed to be a remarkably reactive inhibitor of Sporosarcina pasteurii urease (k_inact/K_I = 10 420 s^-1 M^-1). The high potential of this group of compounds was also confirmed in Proteus mirabilis whole-cell-based inhibition assays. Some compounds followed slow-binding and reversible kinetics, e.g., methyl β-(3,4-dihydroxyphenyl)-β-phosphonopropionate, with K_i* = 0.13 μM, and an atypical low dissociation rate (residence time τ = 205 min).

Recent developments in the synthesis and applications of phosphinic peptide analogs

Synthetic pseudopeptides that fit well with the active site architecture allow the most effective binding to enzymes, similar to native substrates in high-energy transition states. Phosphinic acid peptide analogs that comprise the tetrahedral phosphorus moiety introduced to replace an internal amide bond exert such an isosteric or isoelectronic resemblance, combined with providing other advantageous features, for example, metal complexing properties. Accordingly, they are capable of inhibiting metal-dependent enzymes involved in biological functions in eukaryotic and prokaryotic cells. These enzymes are associated with notorious human diseases, such as cancer, e.g., matrix metalloproteinases, or are etiological factors of protozoal and bacterial infections, e.g., metalloaminopeptidases. The affinity and selectivity of these compounds can be conveniently adjusted, either by structural modification of dedicated side chains or by backbone elongation to enhance specific interactions with the corresponding binding pockets. Recent approaches to the synthesis of these compounds are illustrated by examples of the preparation of rationally designed structures of inhibitors of particular enzymes. Activity against appealing enzymatic targets is presented, along with the molecular mechanisms of action and therapeutic implications. Innovative aspects of phosphinic peptide application, e.g., as activity-based probes, and ligands of complexes of radioisotopes for nuclear medicine are also outlined.

Recent advances in design of new urease inhibitors: A review

Urease is a nickel-dependent metalloenzyme found in plants, some bacteria, and fungi. Bacterial enzyme is of special importance since it has been demonstrated as a potent virulence factor for some species. Especially it is central to Helicobacter pylori metabolism and virulence being necessary for its colonization of the gastric mucosa, and is a potent immunogen that elicits a vigorous immune response. Therefore, it is not surprising that efforts to design, synthesize and evaluate of new inhibitors of urease are and active field of medicinal chemistry. In this paper recent advances on this field are reviewed.

Ureases: Historical aspects, catalytic, and non-catalytic properties - A review

Urease (urea amidohydrolase, EC 3.5.1.5) is a nickel-containing enzyme produced by plants, fungi, and bacteria that catalyzes the hydrolysis of urea into ammonia and carbamate. Urease is of historical importance in Biochemistry as it was the first enzyme ever to be crystallized (1926). Finding nickel in urease's active site (1975) was the first indication of a biological role for this metal. In this review, historical and structural features, kinetics aspects, activation of the metallocenter and inhibitors of the urea hydrolyzing activity of ureases are discussed. The review also deals with the non-enzymatic biological properties, whose discovery 40 years ago started a new chapter in the study of ureases. Well recognized as virulence factors due to the production of ammonia and alkalinization in diseases by urease-positive microorganisms, ureases have pro-inflammatory, endocytosis-inducing and neurotoxic activities that do not require ureolysis. Particularly relevant in plants, ureases exert insecticidal and fungitoxic effects. Data on the jack bean urease and on jaburetox, a recombinant urease-derived peptide, have indicated that interactions with cell membrane lipids may be the basis of the non-enzymatic biological properties of ureases. Altogether, with this review we wanted to invite the readers to take a second look at ureases, very versatile proteins that happen also to catalyze the breakdown of urea into ammonia and carbamate.

Aminophosphinates against Helicobacter pylori ureolysis-Biochemical and whole-cell inhibition characteristics

Urease is an important virulence factor from Helicobacter pylori that enables bacterial colonization of human gastric mucosa. Specific inhibition of urease activity can be regarded as a promising adjuvant strategy for eradication of this pathogen. A group of organophosphorus inhibitors of urease, namely, aminophosphinic acid and aminophosphonic acid derivatives, were evaluated in vitro against H. pylori urease. The kinetic characteristics of recombinant enzyme activity demonstrated a competitive reversible mode of inhibition with K_i values ranging from 0.294 to 878 μM. N-n-Hexylaminomethyl-P-aminomethylphosphinic acid and N-methylaminomethyl-P-hydroxymethylphosphinic acid were the most effective inhibitors (K_i = 0.294 μM and 1.032 μM, respectively, compared to K_i = 23 μM for the established urease inhibitor acetohydroxamic acid).

The biological relevance of the inhibitors was verified in vitro against a ureolytically active Escherichia coli Rosetta host that expressed H. pylori urease and against a reference strain, H. pylori J99 (CagA⁺/VacA⁺). The majority of the studied compounds exhibited urease-inhibiting activity in these whole-cell systems. Bis(N-methylaminomethyl)phosphinic acid was found to be the most effective inhibitor in the susceptibility profile studies of H. pylori J99. The cytotoxicity of nine structurally varied inhibitors was evaluated against four normal human cell lines and was found to be negligible.

Polarity and structure of derivatives of bis(2-phenylethyl)selenophosphinic acid

Conformational analysis of derivatives of bis(2-phenylethyl)selenophosphinic acid was carried out by the method of dipole moments and density functional theory calculations. The conformations of the examined compounds fit into the overall conformational picture for the PIV compounds: these derivatives exist as conformational equilibrium of non-eclipsed gauche and trans forms with propeller arrangement of the substituents relative to the P=Se bond. We stipulate that the eclipsed cis orientation of substituent may be caused by the formation of H-contact.

Whole-cell Proteus mirabilis urease inhibition by aminophosphinates for the control of struvite formation

The study evaluated the in vitro impact of a series of aminophosphinic urease inhibitors on Proteusmirabilis. The group of compounds comprised structurally diverse analogues of diamidophosphate built on an N-C-P scaffold. The influence of urease inhibition on urea-splitting activity was assessed by whole-cell pH-static kinetic measurements. The potential to prevent struvite formation was determined by monitoring changes in pH and ionic composition of artificial urine medium during P. mirabilis growth. The most active compounds exhibited stronger positive effect on urine stability than the acknowledged inhibitor acetohydroxamic acid. The high anti-ureolytic and pH-stabilizing effect of urease inhibitors 4 and 14 was well correlated with their reported kinetic properties against pure urease from P. mirabilis (Ki values of 0.62±0.09 and 0.202±0.057 µM, respectively, compared to 5.7±0.4 µM for acetohydroxamic acid). The effect of repressed ureolysis upon the viability of Proteus cells was studied using MTT [3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide] metabolic efficiency assay and LIVE/DEAD fluorescent staining. Most of the compounds caused whole-cell dehydrogenase activity loss; four structures (1, 2, 4 and 14) reduced the culture viability by nearly 70 % at 1 mM concentration. Results of dual fluorescent staining suggested that besides urea-splitting prevention, the structures additionally exerted an outer-membrane-destabilizing effect.

Bis(aminomethyl)phosphinic Acid, a Highly Promising Scaffold for the Development of Bacterial Urease Inhibitors

Inhibitors of bacterial ureases are considered to be promising compounds in the treatment of infections caused by Helicobacter pylori in the gastric tract and/or by urealytic bacteria (e.g., Proteus species) in the urinary tract. A new, extended transition state scaffold, bis(aminomethyl)phosphinic acid, was successfully explored for the construction of effective enzyme inhibitors. A reliable methodology for the synthesis of phosphinate analogues in a three-component Mannich-type reaction was elaborated. The obtained molecules were assayed against ureases purified from Sporosarcina pasteurii and Proteus mirabilis, and aminomethyl(N-n-hexylaminomethyl)phosphinic acid was found to be the most potent inhibitor, with a K i = 108 nM against the S. pasteurii enzyme.

Synthesis, characterization and urease inhibition, in vitro anticancer and antileishmanial studies of Ni(II) complexes with N,N,N'-trisubstituted thioureas

A series of N,N,N'-trisubstituted thioureas (1-12) and their Ni(II) complexes (1a-12a) were synthesized and characterized by multinuclear ((1)H and (13)C) NMR, FT-IR spectroscopy and LC-MS techniques in combination with elemental analysis. The crystal structures of both ligands and Ni(II) chelates of type Ni(L-O, S)2 were determined by single crystal X-ray diffraction analysis. All the complexes were adopted to have square planar geometry, where the N,N,N'-trisubstituted thioureas showed bidentate mode of coordination at nickel centre through oxygen and sulfur atoms. The synthesized complexes were screened for potential inhibitors of Jack bean urease. Compounds 1a and 3a were observed as most potent inhibitors of urease exhibiting IC50 values of 1.17 ± 0.12 and 1.19 ± 0.41 µM, respectively. Cytotoxicity assay on lung carcinoma (H-157) and kidney fibroblast (BHK-21) cell showed that compounds were significant anticancer agents. Additionally, the complexes were tested against Leishmania major and found to be potent antileishmanial agents.

N-substituted aminomethanephosphonic and aminomethane-P-methylphosphinic acids as inhibitors of ureases

Small unextended molecules based on the diamidophosphate structure with a covalent carbon-to-phosphorus bond to improve hydrolytic stability were developed as a novel group of inhibitors to control microbial urea decomposition. Applying a structure-based inhibitor design approach using available crystal structures of bacterial urease, N-substituted derivatives of aminomethylphosphonic and P-methyl-aminomethylphosphinic acids were designed and synthesized. In inhibition studies using urease from Bacillus pasteurii and Canavalia ensiformis, the N,N-dimethyl derivatives of both lead structures were most effective with dissociation constants in the low micromolar range (Ki=13±0.8 and 0.62±0.09 μM, respectively). Whole-cell studies on a ureolytic strain of Proteus mirabilis showed the high efficiency of N,N-dimethyl and N-methyl derivatives of aminomethane-P-methylphosphinic acids for urease inhibition in pathogenic bacteria. The high hydrolytic stability of selected inhibitors was confirmed over a period of 30 days using NMR technique.

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.