The Impact of pH on Catalytically Critical Protein Conformational Changes: The Case of the Urease, a Nickel Enzyme

The Most Up-to-Date Advancements in the Design and Development of Urease Inhibitors (January 2020-March 2024)

The aim of this review is to address the most up-to-date information on the design and development, structure-activity relationship (SAR), and molecular docking study of novel and effective urease inhibitors between January 2020 and March 2024. Herein, the importance of the substituents and their effect on bioactivity of the reported compounds have been investigated. Besides, the relation between the most important residues inside the active site of the urease enzyme for interactions of the inhibitors and the active site of the enzyme has also been reviewed. This review has been classified into main reported scaffolds, namely, barbiturates, thiobarbiturates, Schiff bases, semicarbazides, thiosemcarbazides, benzimidazoles, 1,3,4-thiadiazoles, and 1,3,4-oxadiazoles, to provide better insight into the newly developed urease inhibitors.

An isothermal calorimetry assay for determining steady state kinetic and Ensitrelvir inhibition parameters for SARS-CoV-2 3CL-protease

This manuscript details the application of Isothermal Titration Calorimetry (ITC) to characterize the kinetics of 3CLpro, the main protease from the Severe Acute Respiratory Syndrome CoronaVirus-2 (SARS-CoV-2), and its inhibition by Ensitrelvir, a known non-covalent inhibitor. 3CLpro is essential for producing the proteins necessary for viral infection, which led to the COVID-19 pandemic. The ITC-based assay provided rapid and reliable measurements of 3CLpro activity, allowing for the direct derivation of the kinetic enzymatic constants KM and kcat by monitoring the thermal power required to maintain a constant temperature as the substrate is consumed. The manuscript highlights several advantages of the proposed ITC-based assay over traditional methods used to study 3CLpro, such as Förster Resonance Energy Transfer (FRET) and Liquid Chromatography-Mass Spectrometry (LC-MS) and overcomes the need for non-biological substrates or discontinuous post-reaction steps. The ease of application of the ITC method allowed for the determination of the temperature dependence of the catalytic constants, enabling the estimation of the reaction activation energy. Additionally, the assay was used to determine the inhibition mode and kinetic parameters for 3CLpro inhibition by Ensitrelvir. This molecule was revealed to act as a slow- and tight-binding inhibitor that forms an initial E•I complex (KI = 9.9 ± 0.7 nM) quickly transitioning to a tighter E•I* assembly (KI* = 1.1 ± 0.2 nM). This versatile calorimetric method is proposed for general use in the discovery and development of drugs targeting 3CLpro.

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.

Benzimidazole-acrylonitrile hybrid derivatives act as potent urease inhibitors with possible fungicidal activity

Aim: A series of benzimidazole-acrylonitrile derivatives TM1-TM53 were designed with urease inhibition approach.Materials & methods: TM1-TM53 were synthesized and characterized (1H Nuclear Magnetic Resonance (NMR), 13C NMR, Mass Spectroscopy (MS) and IR) and subjected to urease inhibition assay using commercial assay kit. A molecular docking study was also performed using Autodock tool software.Results: Except six compounds, target molecules exhibited a higher urease inhibition effect (IC50: 1.22-28.45 μM) than hydroxyurea (IC50: 100 μM). kinetic study on TM11, clarified its mode of action as a mixed inhibitor. A molecular docking study on TM6, TM11 and TM21, was performed and the results showed the main residues inside the active site of the enzyme. All TM1-TM53 were also studied in silico using molecular docking techniques to evaluate their potential to inhibit succinate dehydrogenase in comparison to fluxapyroxad as standard. Docking study revealed the high potential of TM1-TM53 as a fungicides.Conclusion: Obtained results exhibited the high activity of benzimidazole-acrylonitrile derivatives as urease inhibitors and their possible potential as fungicide agents. So, it will be beneficial to do more bioactivity investigation on this family of compounds.

Kinetic and structural details of urease inactivation by thiuram disulphides

This paper reports on the molecular details of the reactivity of urease, a nickel-dependent enzyme that catalyses the last step of organic nitrogen mineralization, with thiuram disulphides, a class of molecules known to inactivate the enzyme with high efficacy but for which the mechanism of action had not been yet established. IC50 values of tetramethylthiuram disulphide (TMTD or Thiram) and tetraethylthiuram disulphide (TETD or Disulfiram) in the low micromolar range were determined for plant and bacterial ureases. The X-ray crystal structure of Sporosarcina pasteurii urease inactivated by Thiram, determined at 1.68 Å resolution, revealed the presence of a covalent modification of the catalytically essential cysteine residue. This is located on the flexible flap that modulates the size of the active site channel and cavity. Formation of a Cys-S-S-C(S)-N(CH3)2 functionality responsible for enzyme inactivation was observed. Quantum-mechanical calculations carried out to rationalise the large reactivity of the active site cysteine support the view that a conserved histidine residue, adjacent to the cysteine in the active site flap, modulates the charge and electron density along the thiol SH bond by shifting electrons towards the sulphur atom and rendering the thiol proton more reactive. We speculate that this proton could be transferred to the nickel-coordinated urea amide group to yield a molecule of ammonia from the generated Curea-NH3+ functionality during catalysis.

Inhibition of Urease by Hydroquinones: A Structural and Kinetic Study

Hydroquinones are a class of organic compounds abundant in nature that result from the full reduction of the corresponding quinones. Quinones are known to efficiently inhibit urease, a NiII -containing enzyme that catalyzes the hydrolysis of urea to yield ammonia and carbonate and acts as a virulence factor of several human pathogens, in addition to decreasing the efficiency of soil organic nitrogen fertilization. Here, we report the molecular characterization of the inhibition of urease from Sporosarcina pasteurii (SPU) and Canavalia ensiformis (jack bean, JBU) by 1,4-hydroquinone (HQ) and its methyl and tert-butyl derivatives. The 1.63-Å resolution X-ray crystal structure of the SPU-HQ complex discloses that HQ covalently binds to the thiol group of αCys322, a key residue located on a mobile protein flap directly involved in the catalytic mechanism. Inhibition kinetic data obtained for the three compounds on JBU reveals the occurrence of an irreversible inactivation process that involves a radical-based autocatalytic mechanism.

Homecoming: rewinding the reductive evolution of the chloroplast genome for increasing crop yields

Developing more productive and sustainable crops will be essential to achieving food security in coming decades. A core process in plant evolution has been the transfer of chloroplast-encoded genes to the nuclear genome. We propose reverting this process as a new approach to improve plant disease resistance and photosynthesis in future crops.

Medicinal Au(I) compounds targeting urease as prospective antimicrobial agents: unveiling the structural basis for enzyme inhibition

A few gold compounds were recently found to show antimicrobial properties in vitro, holding great promise for the discovery of new drugs to overcome antibiotic resistance. Here, the inhibition of the bacterial virulence factor urease by four Au(I)-compounds, namely Au(PEt₃)Cl, Au(PEt₃)Br, Au(PEt₃)I and [Au(PEt₃)₂]Cl, obtained from the antiarthritic Au(I)-drug Auranofin and earlier reported to act as antimicrobials, is investigated. The three monophosphino Au(I) complexes showed IC₅₀ values in the 30-100 nM range, while the diphosphino Au(I) complex, though being less active, still showed a IC₅₀ value of 7 μM. The structural basis for this inhibition was provided by solving the crystal structures of urease co-crystallized with Au(PEt₃)I and [Au(PEt₃)₂]Cl: at least two Au(I) ions bind the enzyme in a flap domain involved in the catalysis, thus obliterating enzyme activity. Peculiar changes observed in the two structures reveal implications for the mechanism of soft metal binding and enzyme inactivation.

An Overview of 7α- and 7β-Hydroxysteroid Dehydrogenases: Structure, Specificity and Practical Application

7α-Hydroxysteroid dehydrogenase and 7β-hydroxysteroid dehydrogenase are key enzymes involved in bile acid metabolism. They catalyze the epimerization of a hydroxyl group through 7-keto bile acid intermediates. Basic research of the two enzymes has focused on exploring new enzymes and the structure-function relationship. The application research focused on the in vitro biosynthesis of bile acid drugs and the exploration and improvement of their catalytic ability based on molecular engineering. This article summarized the primary and advanced structural characteristics, specificities, biochemical properties, and applications of the two enzymes. The emphasis is also given to obtaining of novel 7α-hydroxysteroid dehydrogenase and 7β-hydroxysteroid dehydrogenase that are thermally stable and active in the presence of organic solvents, high substrate concentration, and extreme pH values. To achieve these goals, enzyme redesigning based on protein engineering and genomics may be the most useful approaches.

Nickel as a virulence factor in the Class I bacterial carcinogen, Helicobacter pylori

Helicobacter pylori is a human bacterial pathogen that causes peptic ulcers and has been designated a Class I carcinogen by the International Agency for Research on Cancer (IARC). Its ability to survive in the acid environment of the stomach, to colonize the stomach mucosa, and to cause cancer, are linked to two enzymes that require nickel-urease and hydrogenase. Thus, nickel is an important virulence factor and the proteins involved in nickel trafficking are potential antibiotic targets. This review summarizes the nickel biochemistry of H. pylori with a focus on the roles of nickel in virulence, nickel homeostasis, maturation of urease and hydrogenase, and the unique nickel trafficking that occurs between the hydrogenase maturation pathway and urease nickel incorporation that is mediated by the metallochaperone HypA and its partner, HypB.

Inhibition of Urease, a Ni-Enzyme: The Reactivity of a Key Thiol With Mono- and Di-Substituted Catechols Elucidated by Kinetic, Structural, and Theoretical Studies

The inhibition of urease from Sporosarcina pasteurii (SPU) and Canavalia ensiformis (jack bean, JBU) by a class of six aromatic poly-hydroxylated molecules, namely mono- and dimethyl-substituted catechols, was investigated on the basis of the inhibitory efficiency of the catechol scaffold. The aim was to probe the key step of a mechanism proposed for the inhibition of SPU by catechol, namely the sulfanyl radical attack on the aromatic ring, as well as to obtain critical information on the effect of substituents of the catechol aromatic ring on the inhibition efficacy of its derivatives. The crystal structures of all six SPU-inhibitors complexes, determined at high resolution, as well as kinetic data obtained on JBU and theoretical studies of the reaction mechanism using quantum mechanical calculations, revealed the occurrence of an irreversible inactivation of urease by means of a radical-based autocatalytic multistep mechanism, and indicate that, among all tested catechols, the mono-substituted 3-methyl-catechol is the most efficient inhibitor for urease.

Cryo-EM structure of Helicobacter pylori urease with an inhibitor in the active site at 2.0 Å resolution

Infection of the human stomach by Helicobacter pylori remains a worldwide problem and greatly contributes to peptic ulcer disease and gastric cancer. Without active intervention approximately 50% of the world population will continue to be infected with this gastric pathogen. Current eradication, called triple therapy, entails a proton-pump inhibitor and two broadband antibiotics, however resistance to either clarithromycin or metronidazole is greater than 25% and rising. Therefore, there is an urgent need for a targeted, high-specificity eradication drug. Gastric infection by H. pylori depends on the expression of a nickel-dependent urease in the cytoplasm of the bacteria. Here, we report the 2.0 Å resolution structure of the 1.1 MDa urease in complex with an inhibitor by cryo-electron microscopy and compare it to a β-mercaptoethanol-inhibited structure at 2.5 Å resolution. The structural information is of sufficient detail to aid in the development of inhibitors with high specificity and affinity.

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).

High-resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica

Urease converts urea into ammonia and carbon dioxide and makes urea available as a nitrogen source for all forms of life except animals. In human bacterial pathogens, ureases also aid in the invasion of acidic environments such as the stomach by raising the surrounding pH. Here, we report the structure of urease from the pathogen Yersinia enterocolitica at 2 Å resolution from cryo-electron microscopy. Y. enterocolitica urease is a dodecameric assembly of a trimer of three protein chains, ureA, ureB and ureC. The high data quality enables detailed visualization of the urease bimetal active site and of the impact of radiation damage. The obtained structure is of sufficient quality to support drug development efforts.

Urease is a nickel enzyme responsible for catalyzing the conversion of urea into ammonia and carbon dioxide. Here the authors report a high resolution cryo-EM structure of urease from the bacterial pathogen Yersinia enterocolitica, providing a detailed visualization of the urease bimetal active site and a basis for drug development.

Urease and Nitrification Inhibitors—As Mitigation Tools for Greenhouse Gas Emissions in Sustainable Dairy Systems: A Review

Currently, nitrogen fertilizers are utilized to meet 48% of the total global food demand. The demand for nitrogen fertilizers is expected to grow as global populations continue to rise. The use of nitrogen fertilizers is associated with many negative environmental impacts and is a key source of greenhouse and harmful gas emissions. In recent years, urease and nitrification inhibitors have emerged as mitigation tools that are presently utilized in agriculture to prevent nitrogen losses and reduce greenhouse and harmful gas emissions that are associated with the use of nitrogen-based fertilizers. Both classes of inhibitor work by different mechanisms and have different physiochemical properties. Consequently, each class must be evaluated on its own merits. Although there are many benefits associated with the use of these inhibitors, little is known about their potential to enter the food chain, an event that may pose challenges to food safety. This phenomenon was highlighted when the nitrification inhibitor dicyandiamide was found as a residual contaminant in milk products in 2013. This comprehensive review aims to discuss the uses of inhibitor technologies in agriculture and their possible impacts on dairy product safety and quality, highlighting areas of concern with regards to the introduction of these inhibitor technologies into the dairy supply chain. Furthermore, this review discusses the benefits and challenges of inhibitor usage with a focus on EU regulations, as well as associated health concerns, chemical behavior, and analytical detection methods for these compounds within milk and environmental matrices.

Targeting the Protein Tunnels of the Urease Accessory Complex: A Theoretical Investigation

Urease is a nickel-containing enzyme that is essential for the survival of several and often deadly pathogenic bacterial strains, including Helicobacter pylori. Notwithstanding several attempts, the development of direct urease inhibitors without side effects for the human host remains, to date, elusive. The recently solved X-ray structure of the HpUreDFG accessory complex involved in the activation of urease opens new perspectives for structure-based drug discovery. In particular, the quaternary assembly and the presence of internal tunnels for nickel translocation offer an intriguing possibility to target the HpUreDFG complex in the search of indirect urease inhibitors. In this work, we adopted a theoretical framework to investigate such a hypothesis. Specifically, we searched for putative binding sites located at the protein–protein interfaces on the HpUreDFG complex, and we challenged their druggability through structure-based virtual screening. We show that, by virtue of the presence of tunnels, some protein–protein interfaces on the HpUreDFG complex are intrinsically well suited for hosting small molecules, and, as such, they possess good potential for future drug design endeavors.

Development of an antimicrobial bioactive paper made from bacterial cellulose

Bacterial cellulose (BC) has emerged as an attractive adsorptive material for antimicrobial agents due to its fine network structure, its large surface area, and its high porosity. In the present study, BC paper was first produced and then lysozyme was immobilized onto it by physical adsorption, obtaining a composite of lysozyme-BC paper. The morphology and the crystalline structure of the composite were similar to that of BC paper as examined by scanning electron microscopy and X-ray diffraction, respectively. Regarding operational properties, specific activities of immobilized and free lysozyme were similar. Moreover, immobilized enzyme showed a broader working temperature and higher thermal stability. The composites maintained its activity for at least 80 days without any special storage. Lysozyme-BC paper displayed antimicrobial activity against Gram-positive and Gram-negative bacteria, inhibiting their growth by 82% and 68%, respectively. Additionally, the presence of lysozyme increased the antioxidant activity of BC paper by 30%. The results indicated that BC is a suitable material to produce bioactive paper as it provides a biocompatible environment without compromising the activity of the immobilized protein. BC paper with antimicrobial and antioxidant properties may have application in the field of active packaging.

Theoretical Studies of Nickel-Dependent Enzymes

The advancements of quantum chemical methods and computer power allow detailed mechanistic investigations of metalloenzymes. In particular, both quantum chemical cluster and combined QM/MM approaches have been used, which have been proven to successfully complement experimental studies. This review starts with a brief introduction of nickel-dependent enzymes and then summarizes theoretical studies on the reaction mechanisms of these enzymes, including NiFe hydrogenase, methyl-coenzyme M reductase, nickel CO dehydrogenase, acetyl CoA synthase, acireductone dioxygenase, quercetin 2,4-dioxygenase, urease, lactate racemase, and superoxide dismutase.