Structural properties of the nickel ions in urease: novel insights into the catalytic and inhibition mechanisms

Exploring the conformational space of the mobile flap in Sporosarcina pasteurii urease by cryo-electron microscopy

To fully understand enzymatic dynamics, it is essential to explore the complete conformational space of a biological catalyst. The catalytic mechanism of the nickel-dependent urease, the most efficient enzyme known, holds significant relevance for medical, pharmaceutical, and agro-environmental applications. A critical aspect of urease function is the conformational change of a helix-turn-helix motif that covers the active site cavity, known as the mobile flap. This motif has been observed in either an open or a closed conformation through X-ray crystallography studies and has been proposed to stabilize the coordination of a urea molecule to the essential dinuclear Ni(II) cluster in the active site, a requisite for subsequent substrate hydrolysis. This study employs cryo-electron microscopy (cryo-EM) to investigate the transient states within the conformational space of the mobile flap, devoid of the possible constraints of crystallization conditions and solid-state effects. By comparing two cryo-EM structures of Sporosarcina pasteurii urease, one in its native form and the other inhibited by N-(n-butyl) phosphoric triamide (NBPTO), we have unprecedently identified an intermediate state between the open and the catalytically efficient closed conformation of the helix-turn-helix motif, suggesting a role of its tip region in this transition between the two states.

Synergistic solidification of lead-contaminated soil by magnesium oxide and microorganisms

Although microbially induced carbonate precipitation (MICP) technology effectively promotes the remediation of heavy metal contaminated soils in low concentrations, the high concentration of heavy metals has a toxic effect on microorganisms, which leads to the decline of carbonate yield and makes the soil strength and environmental safety after remediation no up to the standard. This study describes the synergistic curing effect of MgO and microorganisms on soil contaminated with high concentrations of heavy metals. The experimental results with MgO showed 2-6 times increase in unconfined compressive strength (UCS) compared to bio-cemented samples without MgO. Toxicity characteristic leaching procedure experiments indicated that Pb-contaminated soil at 10,000 mg/kg with quantitative MgO for synergistic solidification could meet the international solid waste disposal standards, which leachable Pb²⁺ are less than 5 mg/L. In addition, the microscopic results showed that the introduction of MgO promoted the formation of magnesium calcite and dolomite, improved the solidification efficiency of heavy metal contaminants, and demonstrated the presence of Pb²⁺ in carbonate minerals. This study suggests that MgO and microorganisms have broad application prospects for synergistic solidification of Pb²⁺ soil.

Molecular dynamics simulations, molecular docking, and kinetics study of kaempferol interaction on Jack bean urease: Comparison of extended solvation model

Since the urease enzyme creates gastric cancer, peptic ulcer, hepatic coma, and urinary stones in millions of people worldwide, it is essential to find strong inhibitors to help patients. Natural products are well known for their beneficial effects on health and efforts are being made to isolate the ingredients, the so-called flavonoids. Flavonoids are now considered as an indispensable component in a variety of nutraceutical, pharmaceutical, and cosmetic applications. Kaempferol (KPF) is an antioxidant found in many fruits and vegetables. Many reports have explained the significant effects of dietary KPF in reducing the risk of chronic diseases such as cancer, ischemia, stroke, and Parkinson's. The current study aimed at investigating the inhibitory impact of KPF on Jack bean urease (JBU) using molecular dynamics (MD) simulations and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations to confirm the results obtained from isothermal titration calorimetry (ITC), extended solvation model, and docking software. In addition, UV-VIS spectrophotometry was used to study the kinetics of urease inhibition. Calorimetric and spectrophotometric determinations of the kinetic parameters of this inhibition indicate the occurrence of a reversible and noncompetitive mode. Also, the docking and MD results indicated that the urease had well adapted to the kaempferol in the binding pocket, thereby forming a stable complex. Kaempferol displayed low binding energy during MMPBSA calculations. The inhibitory potential of kaempferol was confirmed by experimental and simulation data, but in vivo investigations are also recommended to validate our results.

Flavonol morin targets host ACE2, IMP-α, PARP-1 and viral proteins of SARS-CoV-2, SARS-CoV and MERS-CoV critical for infection and survival: a computational analysis

A sudden outbreak of a novel coronavirus SARS-CoV-2 in 2019 has now emerged as a pandemic threatening to efface the existence of mankind. In absence of any valid and appropriate vaccines to combat this newly evolved agent, there is need of novel resource molecules for treatment and prophylaxis. To this effect, flavonol morin which is found in fruits, vegetables and various medicinal herbs has been evaluated for its antiviral potential in the present study. PASS analysis of morin versus reference antiviral drugs baricitinib, remdesivir and hydroxychloroquine revealed that morin displayed no violations of Lipinski's rule of five and other druglikeness filters. Morin also displayed no tumorigenic, reproductive or irritant effects and exhibited good absorption and permeation through GI (clogP <5). In principal component analysis, morin appeared closest to baricitinib in 3D space. Morin displayed potent binding to spike glycoprotein, main protease 3CLPro and papain-like protease PLPro of SARS-CoV-2, SARS-CoV and MERS-CoV using molecular docking and significant binding to three viral-specific host proteins viz. human ACE2, importin-α and poly (ADP-ribose) polymerase (PARP)-1, further lending support to its antiviral efficacy. Additionally, morin displayed potent binding to pro-inflammatory cytokines IL-6, 8 and 10 also supporting its anti-inflammatory activity. MD simulation of morin with SARS-CoV-2 3CLPro and PLPro displayed strong stability at 300 K. Both complexes exhibited constant RMSDs of protein side chains and Cα atoms throughout the simulation run time. In conclusion, morin might hold considerable therapeutic potential for the treatment and management of not only COVID-19, but also SARS and MERS if studied further. Communicated by Ramaswamy H. Sarma.

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.

New acetylphenol-based acyl thioureas broaden the scope of drug candidates for urease inhibition: synthesis, in vitro screening and in silico analysis

Helicobacter pylori urease remains a validated drug target for the eradication of pervasive chronic stomach infection that leads to severe human health diseases such as gastritis and stomach cancer. The increased failure of current treatment protocols because of resistance to broadband antibiotics, severe side effects and low compliance underscore the need for a targeted eradication therapy. Therefore, in the present research, we have developed a new series of acetylphenol-based acyl thioureas that can potentially provide a new template for drug candidates to inhibit urease enzyme. Newly synthesized compounds 7a-j were evaluated for urease inhibitory strength using thiourea as a positive control. In vitro inhibitory results revealed that all the tested compounds were significantly potent than the standard drug. The most active lead 7f competitively inhibited the enzyme and displayed an IC50 value of 0.054 ± 0.002 μM, a ~413-fold strong inhibitory potential than thiourea (IC50 = 22.3 ± 0.031 μM). Various insightful structure-activity relationships were developed showing the key structural requirements for potent inhibitory effects. Molecular docking analysis of 7f inside the active pocket of urease suggested several important interactions with amino acid residues such as ILE411, MET637, ARG439, GLN635, ALA636 and ALA440. Finally, pharmacokinetic properties suggested that the tested derivatives are safe to develop as low-molecular-weight drugs to treat ureolytic bacterial infections.

Synthesis and Evaluation of 1,3,5-Triaryl-2-Pyrazoline Derivatives as Potent Dual Inhibitors of Urease and α-Glucosidase Together with Their Cytotoxic, Molecular Modeling and Drug-Likeness Studies

In the present work, a concise library of 1,3,5-triaryl-2-pyrazolines (2a-2q) was designed and synthesized by employing a multistep strategy, and the newly synthesized compounds were screened for their urease and α-glucosidase inhibitory activities. The compounds (2a-2q) were characterized using a combination of several spectroscopic techniques including FT-IR, 1H NMR, 13C NMR, and EI-MS. All the synthesized compounds, except compound 2i, were potent against urease as compared to the standard inhibitor thiourea (IC50 = 21.37 ± 0.26 μM). These analogs disclosed varying degrees of urease inhibitory activities ranging from 9.13 ± 0.25 to 18.42 ± 0.42 μM. Compounds 2b, 2g, 2m, and 2q having IC50 values of 9.36 ± 0.27, 9.13 ± 0.25, 9.18 ± 0.35, and 9.35 ± 0.35 μM, respectively, showed excellent inhibitory activity as compared to standard thiourea (IC50 = 21.37 ± 0.26 μM). A kinetic study of compound 2g revealed that compound 2g inhibited urease in a competitive mode. Among the synthesized pyrazolines, the compounds 2c, 2k, 2m, and 2o exhibited excellent α-glucosidase inhibitory activity with the lowest IC50 values of 212.52 ± 1.31, 237.26 ± 1.28, 138.35 ± 1.32, and 114.57 ± 1.35 μM, respectively, as compared to the standard acarbose (IC50 = 375.82 ± 1.76 μM). The compounds (2a-2q) showed α-glucosidase IC50 values in the range of 114.57 ± 1.35 to 462.94 ± 1.23 μM. Structure-activity relationship revealed that the size and electron-donating or -withdrawing effects of substituents influenced the activities, which led to the urease and α-glucosidase inhibiting properties. Compound 2m was a dual potent inhibitor against urease and α-glucosidase due to the presence of 2-CF3 electron-withdrawing functionality on the phenyl ring. To the best of our knowledge, these synthetic compounds were found to be the most potent dual inhibitors of urease and α-glucosidase with minimum IC50 values. The cytotoxicity of the compounds (2a-2q) was also investigated against human cell lines MCF-7 and HeLa. Compound 2l showed moderate cytotoxic activity against MCF-7 and HeLa cell lines. Moreover, in silico studies on most active compounds were also performed to understand the binding interaction of most active compounds with active sites of urease and α-glucosidase enzymes. Some compounds exhibited drug-like characteristics due to their lower cytotoxic and good ADME profiles.

Discovery of urease inhibitory effect of sulfamate derivatives: Biological and computational studies

The discovery of life-changing medicines continues to be the driving force for the rapid exploration and expansion of chemical space, enabling access to innovative small molecules of medicinal importance. These small molecules remain the backbone for modern drug discovery. In this context, the treatment of ureolytic bacterial infections inspires the identification of potent and effective inhibitors of urease, a promising and highly needed target for H. pylori eradication. The present study explores the evaluation of sulfamate derivatives for the inhibition of urease enzyme. The tested compounds showed remarkable inhibitory effect and high level of potency. Compound 1q emerged as the lead inhibitor with an IC₅₀ value of 0.062 ± 0.001 µM, ∼360-fold more potent than thiourea (IC₅₀ = 22.31 ± 0.031 µM). The assessment of various contributing factors towards the inhibition profile allowed for the establishment of diverse structure-activity relationships. Kinetics studies revealed the competitive mode of inhibition of compound 1q while molecular modeling analysis identified various crucial binding interactions with ARG609, ARG439, HIS519, HIS492, HIS593, ALA440, and ALA636 in the active pocket of the enzyme. Finally, the calculated pharmacokinetic properties suggest a promising profile of our potent sulfamate-based urease inhibitors.

Synthesis, in vitro antiurease, in vivo antinematodal activity of quinoline analogs and their in-silico study

Synthesis of quinoline analogs and their urease inhibitory activities with reference to the standard drug, thiourea (IC₅₀ = 21.86 ± 0.40 µM) are presented in this study. The inhibitory activity range is (IC₅₀ = 0.60 ± 0.01 to 24.10 ± 0.70 µM) which displayed that it is most potent class of urease inhibitor. Analog 1-9, and 11-13 emerged with many times greater antiurease potential than thiourea, in which analog 1, 2, 3, 4, 8, 9, and 11 (IC₅₀ = 3.50 ± 0.10, 7.20 ± 0.20, 1.30 ± 0.10, 2.30 ± 0.10, 0.60 ± 0.01, 1.05 ± 0.10 and 2.60 ± 0.10 µM respectively) were appeared the most potent ones among the series. In this context, most potent analogs such as 1, 3, 4, 8, and 9 were further subjected for their in vitro antinematodal study against C. elegans to examine its cytotoxicity under positive control of standard drug, Levamisole. Consequently, the cytotoxicity profile displayed that analogs 3, 8, and 9 were found with minimum cytotoxic outline at higher concentration (500 µg/mL). All analogs were characterized through ¹H NMR, ¹³C NMR and HR-EIMS. The protein-ligand binding interaction for most potent analogs was confirmed via molecular docking study.

Novel thiobarbiturates as potent urease inhibitors with potential antibacterial activity: Design, synthesis, radiolabeling and biodistribution study

Urease enzyme is a virulence factor that helps in colonization and maintenance of highly pathogenic bacteria in human. Hence, the inhibition of urease enzymes is well-established to be a promising approach for preventing deleterious effects of ureolytic bacterial infections. In this work, novel thiobarbiturate derivatives were synthesized and evaluated for their urease inhibitory activity. All tested compounds effectively inhibited the activity of urease enzyme. Compounds 1, 2a, 2b, 4 and 9 displayed remarkable anti-urease activity (IC₅₀ = 8.21-16.95 μM) superior to that of thiourea reference standard (IC₅₀ = 20.04 μM). Moreover, compounds 3a, 3g, 5 and 8 were equipotent to thiourea. Among the tested compounds, morpholine derivative 4 (IC₅₀ = 8.21 µM) was the most potent one, showing 2.5 folds the activity of thiourea. In addition, the antibacterial activity of the synthesized compounds was estimated against both standard strains and clinical isolates of urease producing bacteria. Compound 4 explored the highest potency exceeding that of cephalexin reference drug. Moreover, biodistribution study using radiolabeling approach revealed a remarked uptake of ^99mTc-compound 4 into infection induced in mice. Furthermore, a molecular docking analysis revealed proper orientation of title compounds into the urease active site rationalizing their potent anti-urease activity.

The structure-based reaction mechanism of urease, a nickel dependent enzyme: tale of a long debate

This review is an attempt to retrace the chronicle that starts from the discovery of the role of nickel as the essential metal ion in urease for the enzymatic catalysis of urea, a key step in the biogeochemical cycle of nitrogen on Earth, to the most recent progress in understanding the chemistry of this historical enzyme. Data and facts are presented through the magnifying lenses of the authors, using their best judgment to filter and elaborate on the many facets of the research carried out on this metalloenzyme over the years. The tale is divided in chapters that discuss and describe the results obtained in the subsequent leaps in the knowledge that led from the discovery of a biological role for Ni to the most recent advancements in the comprehension of the relationship between the structure and function of urease. This review is intended not only to focus on the bioinorganic chemistry of this beautiful metal-based catalysis, but also, and maybe primarily, to evoke inspiration and motivation to further explore the realm of bio-based coordination chemistry.

Synthesis, Biological Evaluation and Molecular Docking of Deferasirox and Substituted 1,2,4-Triazole Derivatives as Novel Potent Urease Inhibitors: Proposing Repositioning Candidate

A series of new deferasirox derivatives were synthesized through the reaction of monosubstituted hydrazides with 2-(2-hydroxyphenyl)-4H-benzo[e][1,3]oxazin-4-one. For the first time, deferasirox and some of its derivatives were evaluated for their in vitro inhibitory activity against Jack bean urease. The potencies of the members of this class of compounds are higher than that of acetohydroxamic acid. Two compounds, bearing tetrazole and hydrazine derivatives (bioisoester of carboxylate group), represented the most potent urease inhibitory activity with IC₅₀ values of 1.268 and 3.254 μm, respectively. In silico docking studies were performed to delineate possible binding modes of the compounds with the enzyme, urease. Docking analysis suggests that the synthesized compounds were anchored well in the catalytic site and extending to the entrance of binding pocket and thus restrict the mobility of the flap by interacting with its crucial amino acid residues, CME592 and His593. The overall results of urease inhibition have shown that these target compounds can be further optimized and developed as a lead skeleton for the discovery of novel urease inhibitors.

Lead Molecules for Targeted Urease Inhibition: An Updated Review from 2010 -2018

The field of enzyme inhibition is a tremendous and quickly growing territory of research. Urease a nickel containing metalloenzyme found in bacteria, algae, fungi, and plants brings hydrolysis of urea and plays important role in environmental nitrogen cycle. Apart from this it was found to be responsible for many pathological conditions due to its presence in many microorganisms such as H. Pylori, a ureolytic bacteria having urease which elevates pH of gastric medium by hydrolyzing urea present in alimentary canal and help the bacteria to colonize and spread infection. Due to the infections caused by the various bacterial ureases such as Bacillus pasteurii, Brucella abortus, H. pylori, H. mustelae, Klebsiella aerogenes, Klebsiella tuberculosis, Mycobacterium tuberculosis, Pseudomonas putida, Sporosarcina pasteurii and Yersinia enterocolitica, it has been the current topic of today's research. About a wide range of compounds from the exhaustive literature survey has been discussed in this review which is enveloped into two expansive classes, as Inhibitors from synthetic origin and Inhibitors from natural origin. Moreover active site details of enzyme, mechanism of catalysis of substrate by enzyme, uses of plant urease and its pathogenic behavior has been included in the current review. So, overall, this review article diagrams the current landscape of the developments in the improvements in the thriving field of urease inhibitory movement in medicinal chemistry from year 2010 to 2018, with an emphasis on mechanism of action of inhibitors that may be used for more development of recent and strong urease inhibitors and open up new doors for assist examinations in a standout amongst the most lively and promising regions of research.

Structure, function, and biosynthesis of nickel-dependent enzymes

Nickel enzymes, present in archaea, bacteria, plants, and primitive eukaryotes are divided into redox and nonredox enzymes and play key functions in diverse metabolic processes, such as energy metabolism and virulence. They catalyze various reactions by using active sites of diverse complexities, such as mononuclear nickel in Ni-superoxide dismutase, glyoxylase I and acireductone dioxygenase, dinuclear nickel in urease, heteronuclear metalloclusters in [NiFe]-carbon monoxide dehydrogenase, acetyl-CoA decarbonylase/synthase and [NiFe]-hydrogenase, and even more complex cofactors in methyl-CoM reductase and lactate racemase. The presence of metalloenzymes in a cell necessitates a tight regulation of metal homeostasis, in order to maintain the appropriate intracellular concentration of nickel while avoiding its toxicity. As well, the biosynthesis and insertion of nickel active sites often require specific and elaborated maturation pathways, allowing the correct metal to be delivered and incorporated into the target enzyme. In this review, the phylogenetic distribution of nickel enzymes will be briefly described. Their tridimensional structures as well as the complexity of their active sites will be discussed. In view of the latest findings on these enzymes, a special focus will be put on the biosynthesis of their active sites and nickel activation of apo-enzymes.

Robust therapeutic potential of carbazole-triazine hybrids as a new class of urease inhibitors: A distinctive combination of nitrogen-containing heterocycles

The inhibition of urease enzyme is very important as it plays a key role in the treatment of several urinary and gastrointestinal tract infections. This enzyme provides a suitable environment for Helicobacter pylori at the low pH of the stomach, a causative agent of gastric and peptic ulcer that may lead to cancer. In agriculture, the high urease content causes environmental and economic problems. In this pursuit, given the well-established importance of integrated pharmacophores in medicinal chemistry and to explore new inhibitors of urease featuring two distinct heterocyclic functionalities, we herein report a facile synthesis of carbazole-triazine hybrids (3a-j). These new propeller-shaped chemical scaffolds were evaluated for their urease inhibitory potential in order to identify suitable leads. The initial structure-activity survey work guided through in vitro bioactivity results recognized 3e and 3f as new starting point hits incorporating bulky iodo (3e) and strong electron-withdrawing nitro (3f) groups at the para-position of aryl amine component. The potent compounds (3e &3f) exhibited the highest activity with IC₅₀ values of 5.6 and 6.7 µM, respectively. In the molecular docking analysis, these compounds depicted excellent binding interactions with the active site residues. The key interactions observed include hydrogen bonding, π-π interactions, π-cation and nickel atom coordination to the triazine nitrogen of both inhibitors.

Molecular Docking of Natural Phenolic Compounds for the Screening of Urease Inhibitors

BACKGROUND

Bacterial ureases have been the cause of various human and animal pathogenicity including hepatic encephalopathy, hepatic coma urolithiasis, gastric and peptic ulcers, pyelonephritis, and urinary catheter encrustation by the production of ammonia. Hence, in view of the side effects of existing drugs, there is a strong need to discover, more safe, effective and potent compounds for the treatment of infections caused by urease.

METHODS

For this purpose, several natural phenolic compounds have been screened by molecular modelling techniques, wherein the phenolic compounds were docked to the active site of Jack bean urease (PDB ID 3LA4) using the Schrodinger docking software.

RESULTS

The lead compounds were identified via in-silico screening technique where docking score, binding energy, ADME and toxicity data were considered to screen the lead compounds as compared with the available standard drugs. From the docking study of screened natural phenolic compounds, five compounds diosmin, morin, chlorogenic acid, capsaicin and resveratrol were selected based upon their better affinity towards the receptor and were considered for further wet lab studies.

CONCLUSION

The in-silico results were confirmed by in vitro experiments by use of the Jack bean urease using Weatherburn method.

The Maturation Pathway of Nickel Urease

Maturation of urease involves post-translational insertion of nickel ions to form an active site with a carbamylated lysine ligand and is assisted by urease accessory proteins UreD, UreE, UreF and UreG. Here, we review our current understandings on how these urease accessory proteins facilitate the urease maturation. The urease maturation pathway involves the transfer of Ni2+ from UreE → UreG → UreF/UreD → urease. To avoid the release of the toxic metal to the cytoplasm, Ni2+ is transferred from one urease accessory protein to another through specific protein–protein interactions. One central theme depicts the role of guanosine triphosphate (GTP) binding/hydrolysis in regulating the binding/release of nickel ions and the formation of the protein complexes. The urease and [NiFe]-hydrogenase maturation pathways cross-talk with each other as UreE receives Ni2+ from hydrogenase maturation factor HypA. Finally, the druggability of the urease maturation pathway is reviewed.

Utility of anthranilic acid and diethylacetylenedicarboxylate for the synthesis of nitrogenous organo/organometallic compounds as urease inhibitors

Fumarate diester 3 was synthesized upon reacting anthranilic acid with diethylacetylenedicarboxylate. Compound 3 was reacted with different nucleophiles in mild reaction conditions. Selected reaction routes that afforded products 6, 9, 10, 11, and 12 were explained. The estimated mechanism for the reaction of 3 with ethylenediamine to afford 9 was proved by X-ray single-crystal and retro-synthetic reaction. Acetyl anthranilic acid was utilized with zinc and copper to afford the organometallic compounds 14a and 14b, respectively. Three single crystals were afforded for 3, 9 and the organocopper complex 14b. Target compounds were screened for their inhibitory potential against urease enzyme. Most compounds were more potent than thiourea as standard inhibitor, considering that oxopiperazine 9 exhibited double the activity: IC₅₀ = 8.16 ± 0.65 µM (thiourea IC₅₀ = 20.04 ± 0.33 µM). Docking studies were in agreement with the in vitro enzyme assay.

Molecular docking, synthesis, kinetics study, structure-activity relationship and ADMET analysis of morin analogous as Helicobacter pylori urease inhibitors

Background

Urease are responsible for several pathogenic states in human as well as in animals and its inhibition is utmost urgent. Clinically used drugs are associated with many side effects; recently several researches have shown that flavonoids have good urease inhibition properties. Morin, a natural flavonoid has been investigated for urease inhibition studies which includes designing of library of morin analogues and their in-silico evaluation with the help of Schrodinger’s maestro package of molecular docking software against crystallographic complex of plant enzyme Jack bean urease (PDB ID: 3LA4) followed by synthesis and in vitro evaluation.

Results

Best thirteen derivatives of morin were selected on the basis of their interaction energy and dock score for synthesis and further investigated for in-vitro antioxidant, urease inhibitory and Anti-H. Pylori activity. In-vitro results revealed that a large number of synthesized compounds were found to possess excellent antioxidant and urease Inhibition properties.

Conclusions

Among the synthesized compounds, N-(2-chlorophenyl)-N-((4E)-2-(2,4-dihydroxyphenyl)-3,5,7-trihydroxy-4H-chromen-4-ylidene)thiourea (M2b) and N-(4-bromophenyl)-N-((4E)-2-(2,4-dihydroxyphenyl)-3,5,7-trihydroxy-4H-chromen-4-ylidene)thiourea (M2i) were found to be most potent urease inhibitor and antioxidant with IC₅₀ value 10.74 ± 0.018, 11.12 ± 0.033 and 7.37 ± 0.024, 7.73 ± 0.015and 7.795 ± 0.003 µM. Derivative M2i exhibited good anti-H. pylori activity having MIC = 500 μg/ml and zone of inhibition 15.00 ± 0.00 mm as compared to standard AHA having MIC = 1000 μg/ml and zone of inhibition 9.00 ± 0.50 mm determined against H. Pylori bacterium (ATCC 43504, DSM 4867) by well diffusion technique. Furthermore, molecular docking study explained the binding pattern of synthesized ligand within active cavity of jack bean protein and drug similarity was explained by ADME studies by quikprop module of molecular docking software.

Electronic supplementary material

The online version of this article (10.1186/s13065-019-0562-2) contains supplementary material, which is available to authorized users.

Insights into Urease Inhibition by N-( n-Butyl) Phosphoric Triamide through an Integrated Structural and Kinetic Approach

The nickel-dependent enzyme urease represents a negative element for the efficiency of soil nitrogen fertilization as well as a virulence factor for a large number of pathogenic and antibiotic-resistant bacteria. The development of ever more efficient urease inhibitors demands knowledge of their modes of action at the molecular level. N-( n-Butyl)-phosphoric triamide (NBPTO) is the oxo-derivative of N-( n-butyl)-thiophosphoric triamide (NBPT), which is extensively employed in agriculture to increase the efficiency of urea-based fertilizers. The 1.45 Å resolution structure of the enzyme-inhibitor complex obtained upon incubation of Sporosarcina pasteurii urease (SPU) with NBPTO shows the presence of diamido phosphoric acid (DAP), generated upon enzymatic hydrolysis of NBPTO with the release of n-butyl amine. DAP is bound in a tridentate binding mode to the two Ni(II) ions in the active site of urease via two O atoms and an amide NH₂ group, whereas the second amide group of DAP points away from the metal center into the active-site channel. The mobile flap modulating the size of the active-site cavity is found in a disordered closed-open conformation. A kinetic characterization of the NBPTO-based inhibition of both bacterial (SPU) and plant ( Canavalia ensiformis or jack bean, JBU) ureases, carried out by calorimetric measurements, indicates the occurrence of a reversible slow-inhibition mode of action. The latter is characterized by a very small value of the equilibrium dissociation constant of the urease-DAP complex caused, in turn, by the large rate constant for the formation of the enzyme-inhibitor complex. The much greater capability of NBPTO to inhibit urease, as compared with that of NBPT, is thus not caused by the presence of a P═O moiety versus a P═S moiety, as previously suggested, but rather by the readiness of NBPTO to react with urease without the need to convert one of the P-NH₂ amide moieties to its P-OH acid derivative, as in the case of NBPT. The latter process is indeed characterized by a very small equilibrium constant that reduces drastically the concentration of the active form of the inhibitor in the case of NBPT. This indicates that high-efficiency phosphoramide-based urease inhibitors must have at least one O atom bound to the central P atom in order for the molecule to efficiently and rapidly bind to the dinickel center of the enzyme.

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.

Recognition of AMP, ADP and ATP through Cooperative Binding by Cu(II) and Zn(II) Complexes Containing Urea and/or Phenylboronic-Acid Moieties

We report a series of Cu(II) and Zn(II) complexes with different ligands containing a dipicolyl unit functionalized with urea groups that may contain or not a phenylboronic acid function. These complexes were designed for the recognition of phosphorylated anions through coordination to the metal ion reinforced by hydrogen bonds involving the anion and NH groups of urea. The complexes were isolated and several adducts with pyrophosphate were characterized using X-ray diffraction measurements. Coordination of one of the urea nitrogen atoms to the metal ion promoted the hydrolysis of the ligands containing 1,3-diphenylurea units, while ligands bearing 1-ethyl-3-phenylurea groups did not hydrolyze significantly at room temperature. Spectrophotometric titrations, combined with ¹H and ³¹P NMR studies, were used in investigating the binding of phosphate, pyrophosphate (PPi), and nucleoside 5′-polyphosphates (AMP, ADP, ATP, CMP, and UMP). The association constants determined in aqueous solution (pH 7.0, 0.1 M MOPS) point to a stronger association with PPi, ADP, and ATP as compared with the anions containing a single phosphate unit. The [CuL⁴]²⁺ complex shows important selectivity for pyrophosphate (PPi) over ADP and ATP.

Effect of different ammonia sources on aceticlastic and hydrogenotrophic methanogens

Ammonium chloride (NH₄Cl) was usually used as a model ammonia source to simulate ammonia inhibition during anaerobic digestion (AD) of nitrogen-rich feedstocks. However, ammonia in AD originates mainly from degradation of proteins, urea and nucleic acids, which is distinct from NH₄Cl. Thus, in this study, the inhibitory effect of a "natural" ammonia source (urea) and NH₄Cl, on four pure methanogenic strains (aceticlastic: Methanosarcina thermophila, Methanosarcina barkeri; hydrogenotrophic: Methanoculleus bourgensis, Methanoculleus thermophilus), was assessed under mesophilic (37 °C) and thermophilic (55 °C) conditions. The results showed that urea hydrolysis increased pH significantly to unsuitable levels for methanogenic growth, while NH₄Cl had a negligible effect on pH. After adjusting initial pH to 7 and 8, urea was significantly stronger inhibitor with longer lag phases to methanogenesis compared to NH₄Cl. Overall, urea seems to be more toxic on both aceticlastic and hydrogenotrophic methanogens compared to NH₄Cl under the same total and free ammonia levels.

Metal complexes of a novel heterocyclic benzimidazole ligand formed by rearrangement-cyclization of the corresponding Schiff base. Electrosynthesis, structural characterization and antimicrobial activity

One-pot electrochemical synthesis of metal complexes containing a novel heterocyclic benzimidazole ligand is reported and characterized.

Urea stabilisation and concentration for urine-diverting dry toilets: Urine dehydration in ash

Human excreta contain the same nitrogen, phosphorus and potassium (N-P-K) as the fertilisers used to produce the food consumed. However, human excreta are considered unwanted waste throughout the world, creating humanitarian and environmental problems. In order to replace the nutrients removed from fields during crop harvesting, more fertilisers are manufactured, in processes contributing to environmental changes at global level. The limitation of human urine as a fertiliser is its low nutrient concentration compared with commercial fertilisers. This study developed a technique to increase the N concentration (from 0.6% to >6%) through urine dehydration to produce a dry fertiliser of monetary value and avoid the need for liquid disposal from the toilet. The technique is intended for a container-based sanitation system that collects, contains, treats and reduces the volume of urine within the container. In tests, fresh human urine was added at various intervals to wood ash at 35°C and 65°C, to alkalise and thus inhibit the enzyme urease from catalysing hydrolysis of urea to ammonia. Mass balance calculations demonstrated a 95% reduction during dehydration, while preserving up to 90% of the N. Such a system would greatly simplify the logistics and costs of storage, transportation and application of urine as a fertiliser. The truly innovative feature is the final product: a dry powder with 7.8% N, 2.5% P and 10.9% K by weight, i.e. equivalent to commercial fertiliser.

Inactivation of urease by 1,4-benzoquinone: chemistry at the protein surface

The high activity of urease, a Ni(ii) enzyme, has several adverse effects on human health and agriculture, and its modulation needs the use of inhibitors.

Andrographolide sodium bisulphite-induced inactivation of urease: inhibitory potency, kinetics and mechanism

BACKGROUND

The inhibitory effect of andrographolide sodium bisulphite (ASB) on jack bean urease (JBU) and Helicobacter pylori urease (HPU) was performed to elucidate the inhibitory potency, kinetics and mechanism of inhibition in 20 mM phosphate buffer, pH 7.0, 2 mM EDTA, 25 °C.

METHODS

The ammonia formations, indicator of urease activity, were examined using modified spectrophotometric Berthelot (phenol-hypochlorite) method. The inhibitory effect of ASB was characterized with IC50 values. Lineweaver-Burk and Dixon plots for JBU inhibition of ASB was constructed from the kinetic data. SH-blocking reagents and competitive active site Ni2+ binding inhibitors were employed for mechanism study. Molecular docking technique was used to provide some information on binding conformations as well as confirm the inhibition mode.

RESULTS

The IC50 of ASB against JBU and HPU was 3.28±0.13 mM and 3.17±0.34 mM, respectively. The inhibition proved to be competitive and concentration- dependent in a slow-binding progress. The rapid formation of initial ASB-JBU complex with an inhibition constant of Ki=2.86×10(-3) mM was followed by a slow isomerization into the final complex with an overall inhibition constant of Ki*=1.33×10(-4) mM. The protective experiment proved that the urease active site is involved in the binding of ASB. Thiol reagents (L-cysteine and dithiothreithol) strongly protect the enzyme from the loss of enzymatic activity, while boric acid and fluoride show weaker protection, indicating that the active-site sulfhydryl group of JBU was potentially involved in the blocking process. Moreover, inhibition of ASB proved to be reversible since ASB-inactivated JBU could be reactivated by dithiothreitol application. Molecular docking assay suggested that ASB made contacts with the important sulfhydryl group Cys-592 residue and restricted the mobility of the active-site flap.

CONCLUSIONS

ASB was a competitive inhibitor targeting thiol groups of urease in a slow-binding manner both reversibly and concentration-dependently, serving as a promising urease inhibitor for the treatment of urease-related diseases.

Design and synthesis of new barbituric- and thiobarbituric acid derivatives as potent urease inhibitors: Structure activity relationship and molecular modeling studies

In this study 36 new compounds were synthesized by condensing barbituric acid or thiobarbituric acid and respective anilines (bearing different substituents) in the presence of triethyl orthoformate in good yields. In vitro urease inhibition studies against jack bean urease revealed that barbituric acid derived compounds (1-9 and 19-27) were found to exhibit low to moderate activity however thiobarbituric acid derived compounds (10-18 and 28-36) showed significant inhibition activity at low micro-molar concentrations. Among the synthesized compounds, compounds (15), (12), (10), (36), (16) and (35) showed excellent urease inhibition with IC50 values 8.53 ± 0.027, 8.93 ± 0.027, 12.96 ± 0.13, 15 ± 0.098, 18.9 ± 0.027 and 19.7 ± 0.63 μM, respectively, even better than the reference compound thiourea (IC50 = 21 ± 0.011). The compound (11) exhibited comparable activity to the standard with IC50 value 21.83 ± 0.19 μM. In silico molecular docking studies for most active compounds (10), (12), (15), (16), (35) and (36) and two inactive compounds (3) and (6) were performed to predict the binding patterns.

In vitro screening and evaluation of some Indian medicinal plants for their potential to inhibit Jack bean and bacterial ureases causing urinary infections

CONTEXT

Bacterial ureases play an important role in pathogenesis of urinary infections. Selection of plants was done on the basis of their uses by the local people for the treatment of various bacterial and urinary infections.

OBJECTIVE

Our investigation screens and evaluates 15 Indian medicinal plants for their possible urease inhibitory activity as well as their ability to inhibit bacteria causing urinary infections.

MATERIALS AND METHODS

Plant extracts in three different solvents (methanol, aqueous, and cow urine) were screened for their effect on Jack-bean urease using the phenol-hypochlorite method. Subsequently, seven bacterial strains were screened for their ability to release urease and further antimicrobial-linked urease inhibition activity and minimum inhibitory concentration of the tested extracts were evaluated by the agar well diffusion and microdilution method, respectively.

RESULTS

Five plants out of 15 crude extracts revealed good urease inhibitory activity (≥ 20% at 1 mg/ml conc.) and IC50 values for these extracts ranged from 2.77 to 0.70 mg/ml. Further testing of these extracts on urease-producing bacterial strains (Staphylococcus aureus NCDC 109, S. aureus MTCC 3160, Proteus vulgaris MTCC 426, Klebsiella pneumoniae MTCC 4030, and Pseudomonas aeruginosa MTCC 7453) showed good anti-urease potency with an MIC ranging from 500 to 7.3 µg/ml.

DISCUSSION AND CONCLUSION

The results of screening as well as susceptibility assay clearly revealed a strong urease inhibitory effect of Acacia nilotica L. (Fabaceae), Emblica officinalis Gaertn. (Phyllanthaceae), Psidium guajava L. (Myrtaceae), Rosa indica L. (Rosaceae), and Terminalia chebula Retz. (Combretaceae). Our findings may help to explain the beneficial effect of these plants against infections associated with the urease enzyme.

Hydrolytically active tetranuclear [NiII2]2 complexes: synthesis, structure, spectroscopy and phosphoester hydrolysis

Hydrolytically active three tetranuclear nickel(ii) complexes of a new symmetrical μ-bis(tetradentate) ligand, H₅chdp were prepared and their catalytic activity toward the phosphoester hydrolysis was examined.