Flavonoids and related privileged scaffolds as potential urease inhibitors: a review

Synthesis, Urease Inhibition, Molecular Docking, and Optical Analysis of a Symmetrical Schiff Base and Its Selected Metal Complexes

Designing and developing small organic molecules for use as urease inhibitors is challenging due to the need for ecosystem sustainability and the requirement to prevent health risks related to the human stomach and urinary tract. Moreover, imaging analysis is widely utilized for tracking infections in intracellular and in vivo systems, which requires drug molecules with emissive potential, specifically in the low-energy region. This study comprises the synthesis of a Schiff base ligand and its selected transition metals to evaluate their UV/fluorescence properties, inhibitory activity against urease, and molecular docking. Screening of the symmetrical cage-like ligand and its metal complexes with various eco-friendly transition metals revealed significant urease inhibition potential. The IC50 value of the ligand for urease inhibition was 21.80 ± 1.88 µM, comparable to that of thiourea. Notably, upon coordination with transition metals, the ligand-nickel and ligand-copper complexes exhibited even greater potency than the reference compound, with IC50 values of 11.8 ± 1.14 and 9.31 ± 1.31 µM, respectively. The ligand-cobalt complex exhibited an enzyme inhibitory potential comparable with thiourea, while the zinc and iron complexes demonstrated the least activity, which might be due to weaker interactions with the investigated protein. Meanwhile, all the metal complexes demonstrated a pronounced optical response, which could be utilized for fluorescence-guided targeted drug delivery applications in the future. Molecular docking analysis and IC50 values from in vitro urease inhibition screening showed a trend of increasing activity from compounds 7d to 7c to 7b. Enzyme kinetics studies using the Lineweaver-Burk plot indicated mixed-type inhibition against 7c and non-competitive inhibition against 7d.

Chlorogenic acid, caffeic acid and luteolin from dandelion as urease inhibitors: insights into the molecular interactions and inhibition mechanism

BACKGROUND

Dandelion contains hundreds of active compounds capable of inhibiting urease activity, but the individual compounds have not yet been fully identified, and their effects and underlying mechanisms are not clear. The present study aimed to screen the urease inhibition active compounds of dandelion by urease inhibitory activity evaluation HPLC-tandem mass spectrometry analysis, their mechanism of urease inhibition by polyphenols was explored using enzyme kinetic studies via Lineweaver-Burk plots. Other investigations included isothermal titration calorimetry and surface plasmon resonance sensing, fluorescence quenching experiments, and single ligand molecular docking and two-ligand simultaneous docking techniques.

RESULTS

The results indicated that the ethyl acetate fraction of dandelion flower exhibited the greatest inhibition (lowest IC50 0.184 ± 0.007 mg mL-1). Chlorogenic acid, caffeic acid and luteolin could be effective urease inhibitors that acted in a non-competitive inhibition manner. Individually, chlorogenic acid could not only fast bind to urease, but also dissociate rapidly, whereas luteolin might interact with urease with the weakest affinity. The chlorogenic acid-caffeic acid combination exhibited an additive effect in urease inhibition. However, the chlorogenic acid-luteolin and caffeic acid-luteolin combinations exhibited antagonistic effects, with the caffeic acid-luteolin combination showing greater antagonism.

CONCLUSION

The present study reveals that chlorogenic acid, caffeic acid and luteolin are major bioactive compounds for urease inhibition, indicating the molecular mechanisms. The antagonistic effects were observed between luteolin and chlorogenic acid/caffeic acid, and the interactions of the catalytic site and flap may account for the antagonistic effects. © 2024 Society of Chemical Industry.

A Facile Route to Flavone-3-Carboxamides and Flavone-3-Carboxylates via Palladium-Catalyzed Amino- and Aryloxy-Carbonylation Reactions

A library of C-3 functionalized flavones was successfully provided via palladium-catalyzed amino- and aryloxycarbonylation reactions of 3-iodoflavone (1), under mild conditions. This methodology showed good functional group tolerance using a variety of amines and phenols, under an atmospheric pressure of carbon monoxide as a carbonyl source. While the flavone-3-carboxamides (2a-t) were produced in 22-79%, the flavone-3-carboxylates (4a'-l') were obtained in excellent yields (up to 88%), under identical reaction conditions, just by switching N-nucleophiles to O-nucleophiles. The convenient availability of the involved starting materials confers simplicity to this approach to design new C-3-substituted flavones of biological relevance. The solid-state structures of flavone-3-carboxamide (2r) and flavone-3-ester (4f') were further studied by single-crystal XRD analysis.

Inhibitory effect of polyphenols from sumac, pomegranate and Indian almond on urease producing bacteria and jack bean urease activity

Urinary tract infection caused by Klebsiella, Proteus and Streptococcus is a urease dependent process, hence treatment of these infections by antibacterial compounds lies in inhibition of their virulence factors. The crude methanolic extracts derived from sumac fruit, pomegranate peel and Indian almond leaves were separated into anthocyanin and non-anthocyanin fractions using solid phase cartridges. The inhibitory effect of these fractions was determined on the growth of urease producing species and jack bean urease activity. Known compounds in the fractions were also docked with ureases of different biological origins viz. K. pneumoniae (PDB ID: 8HCN), K. aerogenes (PDB ID: 2KAU), Helicobacter pylori (PDB ID:8HC1)and Canavalia ensiformis (jack bean) (PDB ID: 3LA4) to determine their binding affinities and interaction with the enzyme. All the fractions showed significant inhibition growth for P. mirabilis, S. epidermidis and K.pneumoniae. Among the samples, sumac showed greatest inhibition against all (MIC 6-25 mg.mL-1) while among the fractions, anthocyanin was found to be most active (MIC 6-12 mg/mL). Likewise, all fractions inhibited urease with lowest ICs50 shown by sumac fractions (21-116 μg.mL-1). Out of 39 compounds docked, 27 showed interaction with movable flaps and/or active site of ureases which explains their mode of inhibition.

In vitro enzymatic, in silico ADME and molecular docking based analysis for the identification of novel bis-indole containing triazine-thiazole hybrids derivatives as promising urease inhibitors

The current study details a sequence of sequential reactions for synthesizing bis-indole-based triazine bearing thiazole derivatives. Several steps were involved in the synthesis of bis-indole-based triazine bearing thiazole derivative. The synthetic reactions were monitored via thin-layer chromatography (TLC). Synthesized compounds were characterized using various spectroscopic techniques, including 1H NMR, 13C NMR, and HR-EIMS. The inhibitory activity against urease enzyme of these synthesized compounds was compared with that of thiourea, a standard drug (IC50 = 9.30 ± 0.20 µM). A range of inhibitory potencies were observed for the synthesized compounds, ranging from moderate to excellent, as follows (IC50 = 5.10 ± 0.40 µM to 29.80 ± 0.20 µM). Analyzing the structure-activity relationship (SAR) provided insight into the results, showing that different substituents had different effects on aromatic rings. Several compounds displayed outstanding inhibitory properties (among those tested were 1, 2, 4, 5, and 6 with IC50 = 6.30 ± 0.80, 5.10 ± 0.40, 5.90 ± 0.50, 8.20 ± 0.10, 8.90 ± 0.60 µM, respectively). Anti-urease evaluation of all the synthesized derivatives was conducted in which the selected compounds have shown remarkable potency compared with the standard drug thiourea (IC50 = 9.30 ± 0.20 µM). Molecular docking analysis was carried out for investigating the better binding sites and distance of the derivatives. Moreover, the drug-like properties were explored by the ADME attributes of the synthesized analogs.

Phytochemicals: a promising approach to control infectious bursal disease

Infectious bursal disease (IBD) is one of the dangerous diseases of poultry that affects the bursa of Fabricius, which is an important organ of the bird's immune system. IBD virus is resistant to many drugs, making its control difficult. Vaccination of IBD is in practice for a long time worldwide to control IBD, but secondary issues like vaccine failure and lower efficacy lead to their reduced use in the field. Multiple medicines are currently used, but the phytochemicals have emerged as promising agents for controlling IBD. The drugs to be developed should possess direct antiviral properties by targeting viral entry mechanisms, enhancing the host immune response, and inhibiting viral protein synthesis. Phytochemicals have potential to contribute to food security by minimizing the possibility of disease outbreaks and ensuring that consumers worldwide obtain healthy poultry products. It has been now claimed that direct and indirect activities of phytochemicals can be effective in the control of IBDV. Although available evidence suggest that the phytochemicals can contribute in controlling occurrence IBDV, there is a definite need of focused studies to gain more insight and develop rational strategies for their practical use. This review highlights the disease caused by IBDV, inhibition of viral replication, boosting the immune system, disruption of viral membrane, and important phytochemicals showing antiviral activities against IBDV.

Exploration of morpholine-thiophene hybrid thiosemicarbazones for the treatment of ureolytic bacterial infections via targeting urease enzyme: Synthesis, biochemical screening and computational analysis

An important component of the pathogenicity of potentially pathogenic bacteria in humans is the urease enzyme. In order to avoid the detrimental impact of ureolytic bacterial infections, the inhibition of urease enzyme appears to be an appealing approach. Therefore, in the current study, morpholine-thiophene hybrid thiosemicarbazone derivatives (5a-i) were designed, synthesized and characterized through FTIR, 1H NMR, 13C NMR spectroscopy and mass spectrometry. A range of substituents including electron-rich, electron-deficient and inductively electron-withdrawing groups on the thiophene ring was successfully tolerated. The synthesized derivatives were evaluated in vitro for their potential to inhibit urease enzyme using the indophenol method. The majority of compounds were noticeably more potent than the conventional inhibitor, thiourea. The lead inhibitor, 2-(1-(5-chlorothiophen-2-yl)ethylidene)-N-(2-morpholinoethyl)hydrazinecarbothioamide (5g) inhibited the urease in an uncompetitive manner with an IC50 value of 3.80 ± 1.9 µM. The findings of the docking studies demonstrated that compound 5g has a strong affinity for the urease active site. Significant docking scores and efficient binding free energies were displayed by the lead inhibitor. Finally, the ADME properties of lead inhibitor (5g) suggested the druglikeness behavior with zero violation.

Photoprotective Effects of Two New Morin-Schiff Base Derivatives on UVB-Irradiated HaCaT Cells

Ultraviolet (UV) radiation harms the skin, causing oxidative damage, inflammation, and disruption of the skin's barrier function. There is considerable interest in identifying new natural ingredients with antioxidant and anti-inflammatory properties to serve as adjuvants in sunscreens. The flavonoid morin (1) can undergo structural modifications to enhance its biological properties. The aim of this study was to synthesize two new morin-Schiff base derivatives, morin oxime (2) and morin semicarbazone (3), comparing their photoprotective effects with that of the parent compound on UVB-exposed HaCaT keratinocytes. The chemical structure of the novel compounds was revealed based on spectroscopic data analysis. Our findings demonstrated that derivatives 2 and 3 enhanced the light absorption capability in the UV-visible (vis) range compared to 1. Tested compounds exhibited a higher scavenger capacity than Trolox. Moreover, pre-treatment with all compounds protected HaCaT cells from UVB-induced cell death. Compound 3 demonstrated the strongest antioxidant effect, reducing reactive oxygen species (ROS) generation and, subsequently, malondialdehyde (MDA) levels. Additionally, compounds 2 and 3 exhibited greater anti-inflammatory effects than compound 1, significantly reducing interleukin (IL)-6 production levels at all tested concentrations. These findings have demonstrated, for the first time, a promising photoprotective activity of two new Schiff base derivatives and suggest their use as natural sunscreen ingredients.

Utilizing the drug repurposing strategy on current drugs: new leads for peptic ulcers via biochemical and biomolecular dynamics studies

The hyperactivity of urease enzymes plays a crucial role in the development of hepatic coma, hepatic encephalopathy, urolithiasis, gastric and peptic ulcers. Additionally, these enzymes adversely impact the soil's nitrogen efficiency for crop production. In the current study 100 known drugs were tested against Jack Bean urease and Proteus mirabilis urease and identified three inhibitors i.e. terbutaline (compound 1), Ketoprofen (compound 2) and norepinephrine bitartrate (compound 3). As a result, these compounds showed excellent inhibition against Jack Bean urease i.e. (IC50 = 2.1-11.3 µM), and Proteus mirabilis urease (4.8-11.9 µM). Moreover, in silico studies demonstrate maximum interactions of compounds in the enzyme's active site. Furthermore, intermolecular interactions between compounds and enzyme atoms were examined using STD-NMR spectrophotometry. In parallel, molecular dynamics simulation was carried out to study compounds dynamic behavior within the urease binding region. Urease remained stable during most of the simulation time and ligands were bound in the protein active pocket as observed from the Root mean square deviation (RMSD) and ligand RMSD analyses. Furthermore, these compounds display interactions with the crucial residues, including His492 and Asp633, in 100 ns simulations. In the binding energy analysis, norepinephrine bitartrate exhibited the highest binding energy (-76.32 kcal/mol) followed by Ketoprofen (-65.56 kcal/mol) and terbutaline (-62.15 kcal/mol), as compared to acetohydroxamic acid (-52.86 kcal/mol). The current findings highlight the potential of drug repurposing as an effective approach for identifying novel anti-urease compounds.Communicated by Ramaswamy H. Sarma.

Clodronic Acid has Strong Inhibitory Interactions with the Urease Enzyme of Helicobacter pylori: Computer-aided Design and in vitro Confirmation

BACKGROUND

Helicobacter pylori (HP) infection could lead to various gastrointestinal diseases. Urease is the most important virulence factor of HP. It protects the bacterium against gastric acid.

OBJECTIVE

Therefore, we aimed to design urease inhibitors as drugs against HP infection.

METHODS

The DrugBank-approved library was assigned with 3D conformations and the structure of the urease was prepared. Using a re-docking strategy, the proper settings were determined for docking by PyRx and GOLD software. Virtual screening was performed to select the best inhibitory drugs based on binding affinity, FitnessScore, and binding orientation to critical amino acids of the active site. The best inhibitory drug was then evaluated by IC50 and the diameter of the zone of inhibition for bacterial growth.

RESULTS

The structures of prepared drugs were screened against urease structure using the determined settings. Clodronic acid was determined to be the best-identified drug, due to higher PyRx binding energy, better GOLD FitnessScore, and interaction with critical amino acids of urease. In vitro results were also in line with the computational data. IC50 values of Clodronic acid and Acetohydroxamic Acid (AHA) were 29.78 ± 1.13 and 47.29 ± 2.06 μg/ml, respectively. Diameters of the zones of inhibition were 18 and 15 mm for Clodronic acid and AHA, respectively.

CONCLUSION

Clodronic acid has better HP urease inhibition potential than AHA. Given its approved status, the development of a repurposed drug based on Clodronic acid would require less time and cost. Further, in vivo studies would unveil the efficacy of Clodronic acid as a urease inhibitor.

Computational Advancement towards the Identification of Natural Inhibitors for Dengue Virus: A Brief Review

Viral infectious illnesses represent a severe hazard to human health due to their widespread incidence worldwide. Among these ailments, the dengue virus (DENV) infection stands out. World Health Organization (WHO) estimates that DENV infection affects ~400 million people each year, with potentially fatal symptoms showing up in 1% of the cases. In several instances, academic and pharmaceutical researchers have conducted several pilot and clinical studies on a variety of topics, including viral epidemiology, structure and function analyses, infection source and route, therapeutic targets, vaccinations, and therapeutic drugs. Amongst Takeda, TAK-003, Sanofi, Dengvaxia®, and Butantan/NIH/Merck, Dengvaxia® (CYD-TDV) is the only licensed vaccination yet; however, the potential inhibitors are under development. The biology and evolution of DENVs are briefly discussed in this review, which also compiles the most recent studies on prospective antiviral targets and antiviral candidates. In conclusion, the triumphs and failures have influenced the development of anti-DENV medications, and the findings in this review article will stimulate more investigation.

Investigation of a set of flavonoid compounds as Helicobacter pylori urease inhibitors: insights from in silico studies

Helicobacter pylori (H. pylori) is a spiral, microaerophilic gram-negative bacterium, which is associated with the destruction of the lining of the stomach, leads to chronic inflammation of the stomach, which can cause stomach and duodenal ulcers. The problems caused by the treatment with antibiotics have caused researchers to use new approaches to treat infections caused by H. pylori, among them specific treatments with flavonoids. Urease enzyme, as one of the most important pathogenic and antigenic factors of this bacterium, is a suitable target for this purpose. In this study, the inhibitory effect of flavonoid compounds compared to acetohydroxamic acid on H. pylori urease enzyme was evaluated using molecular modeling methods. First, the interaction of flavonoids with urease enzyme compared with acetohydroxamic acid was investigated by molecular docking method to produce efficient docking poses. Then the physicochemical properties and toxicity of the best flavonoid compounds were analyzed using the swissadme server. Also, molecular dynamics calculations were performed to precisely understand the interactions between ligands and protein. The results of this study show that all the investigated flavonoid compounds are capable of inhibiting H. pylori urease. Among these compounds, six compounds chrysin, galangin, kaempferol, luteolin, morin and quercetin showed a greater tendency to bind to urease, compared to the acetohydroxamic acid inhibitor. These compounds are desirable in terms of physicochemical properties. This study also revealed that the flavonoids with their hydroxyl groups (-OH) play an important role during bond formation with amino acids Ala278, Ala169, His314, Asp362 and Asn168. Therefore, flavonoid compounds, due to their suitable location in the active site of the urease, create a more effective inhibition than the chemical drug acetohydroxamic acid and can be suitable candidates for the treatment of Helicobacter pylori under in vitro and in vivo investigations.Communicated by Ramaswamy H. Sarma.

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.

Exploring the potential of propanamide-sulfonamide based drug conjugates as dual inhibitors of urease and cyclooxygenase-2: biological and their in silico studies

Derivative synthesis has been a crucial method for altering the effects of already-approved medications, especially to lessen adverse effects and enhance results. Making use of this multi-target approach, a series of naproxen-sulfa drug conjugates was designed and synthesized. The newly designed conjugates were confirmed by spectroscopic techniques like IR, 1HNMR, 13CNMR, and elemental analysis. The conjugates were screened for anti-inflammatory, urease, and cyclooxygenase-2 (COX-2) inhibition. Naproxen conjugated with sulfanilamide, sulfathiazole, and sulfaguanidine was found potent and showed a competitive mode of urease inhibition, with IC50 (µM) values 6.69 ± 0.11, 5.82 ± 0.28, 5.06 ± 0.29, respectively. When compared to other screened conjugates, the naproxen-sulfamethoxazole conjugation showed better anti-inflammatory action by inhibiting induced edema by 82.8%, which is comparable to the medication indomethacin (86.8% inhibition). Whereas it exhibited 75.4% inhibition of COX-2 at 10 µM concentration which is comparable with the reference drug (celecoxib, 77.1% inhibition). Moreover, the binding modes of competitive inhibitors with the urease and COX-2 receptor were predicted through molecular docking studies and their stability analysis through MD simulations showed that these compounds made stable complexes with the respective targets and there were no conformational changes that occurred during simulation. The obtained results showed that the conjugates of approved therapeutic molecules may lead to the development of novel types of pharmacological agents in the treatment of several pathological disorders where urease and COX-2 enzymes are involved.

Synthetic transformation of 6-Fluoroimidazo[1,2-a]Pyridine-3-carbaldehyde into 6-Fluoroimidazo[1,2-a]Pyridine-Oxazole Derivatives: In vitro urease inhibition and in silico study

Purpose

Ulcer is a serious disease that is caused due to different bacteria and over usage of various NSAIDs which caused to reduce the defensive system of stomach. Therefore, some novel series are needed to overcome these issues.

Methods

Oxazole-based imidazopyridine scaffolds (4a-p) were designed and synthesized by two step reaction protocol and then subjected to urease inhibition profile (in vitro). All the newly afforded analogs (4a-p) were found potent and demonstrated moderate to significant inhibition profile.

Results

Particularly, the analogs 4i (IC₅₀ = 5.68 ± 1.66 μM), 4o (IC₅₀ = 7.11 ± 1.24 μM), 4 g (IC₅₀ = 9.41 ± 1.19 μM) and 4 h (IC₅₀ = 10.45 ± 2.57 μM) were identified to be more potent than standard thiourea drug (IC₅₀ = 21.37 ± 1.76 μM). Additionally, the variety of spectroscopic tools such as ¹H NMR, ¹³C NMR and HREI-MS analysis were employed to confirm the precise structures of all the newly afforded analogs.

Discussion

The structure-activity relationship (SAR) studies showed that analogs possess the substitution either capable of furnishing strong HB like -OH or had strong EW nature such as -CF₃ & -NO₂ groups displayed superior inhibitory potentials than the standard thiourea drug. A good PLI (protein-ligand interaction) profile was shown by most active analogs when subjected to molecular study against corresponding target with key significant interactions such as pi-pi stacking, pi-pi T shaped and hydrogen bonding.

Current status of N-, O-, S-heterocycles as potential alkaline phosphatase inhibitors: a medicinal chemistry overview

Heterocycles are a class of compounds that have been found to be potent inhibitors of alkaline phosphatase (AP), an enzyme that plays a critical role in various physiological processes such as bone metabolism, cell growth and differentiation, and has been linked to several diseases such as cancer and osteoporosis. AP is a widely distributed enzyme, and its inhibition has been considered as a therapeutic strategy for the treatment of these diseases. Heterocyclic compounds have been found to inhibit AP by binding to the active site of the enzyme, thereby inhibiting its activity. Heterocyclic compounds such as imidazoles, pyrazoles, and pyridines have been found to be potent AP inhibitors and have been studied as potential therapeutics for the treatment of cancer, osteoporosis, and other diseases. However, the development of more potent and selective inhibitors that can be used as therapeutics for the treatment of various diseases is an ongoing area of research. Additionally, the study of the mechanism of action of heterocyclic AP inhibitors is an ongoing area of research, which could lead to the identification of new targets and new therapeutic strategies. The enzyme known as AP has various physiological functions and is present in multiple tissues and organs throughout the body. This article presents an overview of the different types of AP isoforms, their distribution, and physiological roles. It also discusses the structure and mechanism of AP, including the hydrolysis of phosphate groups. Furthermore, the importance of AP as a clinical marker for liver disease, bone disorders, and cancer is emphasized, as well as its use in the diagnosis of rare inherited disorders such as hypophosphatasia. The potential therapeutic applications of AP inhibitors for different diseases are also explored. The objective of this literature review is to examine the function of alkaline phosphatase in various physiological conditions and diseases, as well as analyze the structure-activity relationships of recently reported inhibitors. The present review summarizes the structure-activity relationship (SAR) of various heterocyclic compounds as AP inhibitors. The SAR studies of these compounds have revealed that the presence of a heterocyclic ring, particularly a pyridine, pyrimidine, or pyrazole ring, in the molecule is essential for inhibitory activity. Additionally, the substitution pattern and stereochemistry of the heterocyclic ring also play a crucial role in determining the potency of the inhibitor.