Design and synthesis of thiobarbituric acid analogues as potent urease inhibitors

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.

Antiurease Activity of Antibiotics: In Vitro, In Silico, Structure Activity Relationship, and MD Simulations of Cephalosporins and Fluoroquinolones

Helicobacter pylori infection is widespread in 50% of the world's population and is associated with gastric ulcers and related disorders that ultimately culminate in gastric cancer. Levofloxacin-based, or clarithromycin-based, triple therapy is frequently used to inhibit the bacterial urease enzyme for the eradication of H. pylori. A comprehensive investigation based on the urease inhibitory profiles of antibiotics and their computational implications is lacking in the scientific literature. The present study was aimed specifically to determine the antiurease activities within the realms of cephalosporins and fluoroquinolones by in vitro methods supported with in silico investigations. The results demonstrate the jack bean urease inhibitory activity of cephalosporins, wherein cefadroxil, cefpodoxime, cefotaxime, and cefaclor displayed inhibitions (IC50 21.35 ± 0.64 to 62.86 ± 0.78 μM) compared with the standard thiourea (IC50 21.25 ± 0.15 μM). Among fluoroquinolones, levofloxacin, ofloxacin, and gemifloxacin (IC50 7.24 ± 0.29 to 16.53 ± 0.85 μM) unveiled remarkable inhibitory profiles. Levofloxacin and ofloxacin exhibited competitive inhibition against the said enzyme. Ciprofloxacin and moxifloxacin displayed weak urease inhibitions. During molecular docking studies, Asp362, Gly279, Arg338, Asn168, Asp223, Gln364, and Met366 were involved in hydrogen bonding in fluoroquinolones, and hydrogen bonding was established with Arg338, His248, Asn168 residues, and metal Ni601 and Ni602 of the enzyme. MD simulations and MMPBSA results demonstrated the existence of significant protein-ligand binding. Overall, these results warrant further investigations into the significance of these active molecules in relation to their inhibitory potential against the targeted urease enzyme.

Anti-enzymatic and DNA docking studies of montelukast: A multifaceted molecular scaffold with in vitro investigations, molecular expression analysis and molecular dynamics simulations

Montelukast, an approved leukotriene receptor 1 (Cys-LT 1) antagonist with anti-inflammatory properties is used for the treatment of asthma and allergic rhinitis. In the present studies, montelukast was subjected to in vitro inhibitory assays followed by kinetic and in silico investigations. Montelukast demonstrated inhibitory activity against yeast α-glucosidase (IC50 44.31 ± 1.21 μM), jack bean urease (JB urease, IC50 8.72 ± 0.23 μM), human placental alkaline phosphatase (hPAP, IC50 17.53 ± 0.19 μM), bovine intestinal alkaline phosphatase (bIAP, IC50 15.18 ± 0.23 μM) and soybean 15-lipoxygenase (15-LOX, IC50 2.41 ± 0.13 μM). Kinetic studies against α-glucosidase and urease enzymes revealed its competitive mode of inhibition. Molecular expression analysis of montelukast in breast cancer cell line MCF-7 down-regulated AP by a factor of 0.27 (5 μM) compared with the 0.26 value for standard inhibitor levamisole (10 μM). Molecular docking estimated a binding affinity ranging -8.82 to -15.65 kcal/mol for the enzymes. Docking against the DNA dodecamer (ID: 1BNA) observed -9.13 kcal/mol via minor groove binding. MD simulations suggested stable binding between montelukast and the target proteins predicting strong inhibitory potential of the ligand. Montelukast features a chloroquinoline, phenyl ring, a cyclopropane group, a carboxylic group and a sulfur atom all of which collectively enhance its inhibitory potential against the said enzymes. These in vitro and computational investigations demonstrate that it is possible and suggested that the interactions of montelukast with more than one targets presented herein may be linked with the side effects presented by this drug and necessitate additional work. The results altogether suggest montelukast as an important structural scaffold possessing multitargeted features and warrant further investigations in repurposing beyond its traditional pharmacological use.

An overview of the privileged synthetic heterocycles as urease enzyme inhibitors: Structure-activity relationship

Urease is a metalloenzyme including two Ni2+ ions, found in some plants, bacteria, fungi, microorganisms, invertebrate animals, and animal tissues. Urease acts as a significant virulence factor, mainly in catheter blockage and infective urolithiasis as well as in the pathogenesis of gastric infection. Therefore, studies on urease lead to novel synthetic inhibitors. In this review, the synthesis and antiurease activities of a collection of privileged synthetic heterocycles such as (thio)barbiturate, (thio)urea, dihydropyrimidine, and triazol derivatives were described and discussed according to structure-activity relationship findings in search of the best moieties and substituents that are answerable for encouraging the desired activity even more potent than the standard. It was found that linking substituted phenyl and benzyl rings to the heterocycles led to potent urease inhibitors.

Anti-breast Adenocarcinoma and Anti-urease Anti-tyrosinase Properties of 5-Pentylresorcinol as Natural Compound with Molecular Docking Studies

5-Pentylresorcinol is a type of the group of resorcinol compounds that is resorcinol in that has hydrogen atom at position 5 is replaced by a pentyl group. It has a role as a lichen metabolite. This compound showed excellent to good inhibitory activities against studied these enzymes with IC₅₀ values of 65.96 µM for urease and 34.81 µM for tyrosinase. Standard compounds for enzymes had IC₅₀ values of 1.94±0.24 µM against urease and 84.36±5.17 µM against tyrosinase. The IC₅₀ of 5-pentylresorcinol against MCF7 cell line was 165.72 µg/mL; against Hs 578Bst cell line was 102.14 µg/mL; against Hs 319.T cell line was 12.34 µg/mL; and against UACC-3133 cell line was 73.07 µg/mL, respectively. The chemical activities of 5-pentylresorcinol against urease and tyrosinase were evaluated using the molecular modeling study. The anti-cancer activity of 5-pentylresorcinol was also investigated by treating the compound on the BRCT repeat region from the breast cancer-associated protein (BRCA1), and their interactions were assessed utilizing the molecular docking calculations. The results revealed the probable interactions and their characteristics at an atomic level. The docking scores of 5-pentylresorcinol against urease, tyrosinase, and BRCA1 are -3.073, -5.262, and -3.238 (kcal/mol), respectively.

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.

A pH-responsive fluorometric and colorimetric system based on silicon quantum dots and 4-nitrophenol for urease activity detection

In this paper, we proposed a dual-signal fluorometric and colorimetric system based on silicon quantum dots (SiQDs) and 4-nitrophenol (4-NP) for pH and urease sensing. SiQDs with fluorescence emission of 460 nm were prepared via aqueous-phase synthesis. As the pH of the system gradually increased, the absorption band of 4-NP at 400 nm increased and a color reaction from colorless to yellow occurred. The absorption of 4-NP overlapped quiet well with the fluorescence excitation spectrum of SiQDs, which can effectively quench the fluorescence of SiQDs. Therefore, the change of fluorescence and absorption intensities could be used to quantify pH value. The fluorometric and colorimetric pH-sensing systems both exhibited a linear respond to pH ranging from 6.0 to 7.8 with an interval of 0.2 pH unit. Urease could specifically hydrolyze urea to generate carbon dioxide and ammonia, causing an obvious increase of the pH value. Thus, urease could also be detected quantitatively by the above dual-signal pH sensing system. The linear ranges of the fluorometric and colorimetric methods for urease detection were both 2-40 U L-1. The limits of detection were 1.67 and 1.07 U L-1, respectively. More importantly, this established dual-signal system has been successfully exploited in the detection of urease in real samples with satisfactory recoveries. Compared with other traditional single-signal assay strategies, the results obtained by dual-signal methods are more accurate and reliable.

Synthesis, biological evaluation and in silico studies of new pyrazoline derivatives bearing benzo[d]thiazol-2(3H)-one moiety as potential urease inhibitors

Novel pyrazoline derivatives containing benzo[d]thiazol-2(3H)-one moiety were synthesized and screened for their inhibitory properties against to urease, a clinically important metabolic enzyme. In vitro enzyme inhibition studies revealed that all pyrazolines (7.21-87.77 µM) were more potent than the standard inhibitor acetohydroxamic acid (251.74 µM) against the urease enzyme. Most notably, compound 2m , which is more active than the other compounds in in vitro and molecular docking studies, showed a significant inhibition potential and efficient IC 50 values (7.21±0.09 µM) and in silico inhibition constant (0.11 µM). Furthermore, molecular dynamics (MD) simulation analysis suggests that the binding stability of urease enzyme and compound 2m were stably maintained during the 100 ns simulation time. Compound 2m also exhibited good physicochemical and pharmacokinetic parameters. The overall results of urease inhibition have indicated that these pyrazoline derivative compounds can be further optimized and developed for the discovery of novel urease inhibitors.

Homo pair formations of thiobarbituric acid: DFT calculations and QTAIM analysis

Homo pair formations of thiobarbituric acid (TBA) were investigated in this work by performing density functional theory (DFT) calculations and the quantum theory of atoms in molecule (QTAIM) analysis. Different types of interactions including N–H . . . O, N–H . . . S, C–H . . . O, and C–H . . . S were involved in formations of five models of homo pair of TBA. In this regard, the results of energy strength and QTAIM features indicated that the model with two N–H . . . O interacting bond (D1) was placed at the highest stability and the model with one N–H . . . O and one C–H . . . S interacting bonds (D5) was placed at the lowest stability. Existence of hydrogen bond (HB) interactions in the models were confirmed based on the obtained results. As a consequence, self-interaction of TBA, as an initiator of pharmaceutical compounds production, was investigated in this work in addition to recognition of existence of different types of interactions.

Recent Efforts in the Discovery of Urease Inhibitor Identifications

Urease is an attractive drug target for designing anti-infective agents against pathogens such as Helicobacter pylori, Proteus mirabilis, and Ureaplasma urealyticum. In the past century, hundreds of medicinal chemists focused their efforts on explorations of urease inhibitors. Despite the FDA's approval of acetohydroxamic acid as a urease inhibitor for the treatment of struvite nephrolithiasis and the widespread use of N-(n-butyl)thiophosphoric triamide as a soil urease inhibitor as nitrogen fertilizer synergists in agriculture, urease inhibitors with high potency and safety are urgently needed. Exploration of novel urease inhibitors has therefore become a hot research topic recently. Herein, inhibitors identified worldwide from 2016 to 2021 have been reviewed. They structurally belong to more than 20 classes of compounds such as urea/thioure analogues, hydroxamic acids, sulfonamides, metal complexes, and triazoles. Some inhibitors showed excellent potency with IC50 values lower than 10 nM, having 10000-fold higher potency than the positive control thiourea.