DNA Gyrase Inhibitors Research Articles

A platform for predicting mechanism of action based on bacterial transcriptional responses identifies an unusual DNA gyrase inhibitor

In the search for much-needed new antibacterial chemical matter, a myriad of compounds have been reported in academic and pharmaceutical screening endeavors. Only a small fraction of these, however, are characterized with respect to mechanism of action (MOA). Here, we describe a pipeline that categorizes transcriptional responses to antibiotics and provides hypotheses for MOA. 3D-printed imaging hardware PFIboxes) profiles responses of Escherichia coli promoter-GFP fusions to more than 100 antibiotics. Notably, metergoline, a semi-synthetic ergot alkaloid, mimics a DNA replication inhibitor. Invitro supercoiling assays confirm this prediction, and a potent analog thereof (MLEB-1934) inhibits growth at 0.25μg/mL and is highly active against quinolone-resistant strains of methicillin-resistant Staphylococcus aureus. Spontaneous suppressor mutants map to a seldom explored allosteric binding pocket, suggesting a mechanism distinct from DNA gyrase inhibitors used in the clinic. In all, the work highlights the potential of this platform to rapidly assess MOA of new antibacterial compounds.

In vitro and in silico studies of enterobactin-inspired Ciprofloxacin and Fosfomycin first generation conjugates on the antibiotic resistant E. coli OQ866153

BackgroundThe emergence of antimicrobial resistance in bacterial pathogens is a growing concern worldwide due to its impact on the treatment of bacterial infections. The "Trojan Horse" strategy has been proposed as a potential solution to overcome drug resistance caused by permeability issues.ObjectiveThe objective of our research was to investigate the bactericidal activity and mechanism of action of the "Trojan Horse" strategy using enterobactin conjugated with Ciprofloxacin and Fosfomycin against the antibiotic-resistant Escherichia coli strain OQ866153.MethodologyEnterobactin, a mixed ligand of E. coli OQ866153, was conjugated with Ciprofloxacin and Fosfomycin individually to aid active absorption via specific enterobactin binding proteins (FepABCDG). The effectiveness of the conjugates was assessed by measuring their bactericidal activity against E. coli OQ866153, as well as their ability to inhibit DNA gyrase enzyme and biofilm formation.ResultsThe Fe+3-enterobactin-Ciprofloxacin conjugate effectively inhibited the DNA gyrase enzyme (Docking score = -8.597 kcal/mol) and resulted in a lower concentration (25 μg/ml) required to eliminate supercoiled DNA plasmids compared to the parent drug (35 μg/ml; Docking score = -6.264 kcal/mol). The Fe+3-Enterobactin-Fosfomycin conjugate showed a higher inhibition percentage (100%) of biofilm formation compared to Fosfomycin (21.58%) at a concentration of 2 mg/ml, with docking scores of -5.481 and -3.756 kcal/mol against UDP-N acetylglucosamine 1-carboxyvinyltransferase MurA.ConclusionThe findings of this study suggest that the "Trojan Horse" strategy using enterobactin conjugated with Ciprofloxacin and Fosfomycin can effectively overcome permeability issues caused by efflux proteins and enhance the bactericidal activity of these drugs against antibiotic-resistant strains of E. coli.

Antimicrobial Activity of 2-(Piperazin-1-yl)naphtho[2,3-d]thiazole-4,9-dione against Staphylococcus Strains.

There is an urgent need to discover and develop novel antibacterial agents. Accordingly, we synthesised 2-(piperazin-1-yl)naphtho[2,3-d]thiazole-4,9-dione (PNT), which exhibits antimicrobial activity. The aim of this study was to characterise PNT as an effective antimicrobial agent. Fluorescence microscopy was used to measure PNT's uptake into microbial cells (strains of Staphylococcus epidermidis, Staphylococcus aureus, and methicillin-resistant S. aureus (MRSA)), transmission electron microscopy (TEM) was used to investigate the influence of PNT on the configuration of microbial cells, and a DNA gyrase supercoiling assay was used to investigate whether PNT inhibits DNA gyrase. PNT was taken up by more than 50% of microbial cells within 30 min. Using TEM, hollowed-out bacterial cytoplasms were observed in the specimen treated with PNT, although there was no disintegration of the bacterial membrane. In the DNA gyrase supercoiling assay, a dose-dependent reduction in fluorescence intensity was observed as the concentration of PNT increased. This suggests that PNT is taken up by microbial cells, resulting in cell disruption, and it reveals that one of the mechanisms underlying the antimicrobial activity of PNT is the inhibition of DNA gyrase.

Molecular docking, ADME-Tox, DFT and molecular dynamics simulation of butyroyl glucopyranoside derivatives against DNA gyrase inhibitors as antimicrobial agents

The emergence of antibiotic resistance highlights the critical need for novel antimicrobial agents. In this study, we investigated the synthesis of methyl α-D-glucopyranoside (1) analogs (2–6) which play vital roles in bacterial replication, in the context of DNA gyrase inhibitors. The unimolar one-step butyroylation of glucopyranoside furnished the 6-O-butyroyl derivative, which was further converted into five newer 6-O-butyroyl-2,3,4-tri-acyl-α-D-glucopyranoside analogs. The newly synthesized chemical structures were determined through physicochemical, elemental, and spectroscopic data. In vitro studies against bacteria and fungi with PASS (activity spectra for substances) prediction showed excellent antimicrobial activity of these glucopyranoside analogs. The cytotoxicity assessment indicated that the compounds exhibited less toxicity. In-depth molecular docking studies were carried out to elucidate the mechanism of action, binding energies, and interaction profiles of the synthesized compounds targeting gyrase. Additionally, a reference molecule, 4-methyl-5-[3-(methylsulfanyl)-1H-pyrazol-5-yl]-2-thiophen-2-yl-1,3-thiazole, was docked into the gyrase receptor to evaluate the inhibitory potential of the synthesized compounds. Moreover, a 100 ns molecular dynamics simulation process was performed to monitor the behavior of the complex structure, and a stable conformation and binding mode were found in the stimulating environment of the compounds. Pharmacokinetic predictions were investigated to evaluate the absorption, distribution, metabolism and toxicity of these compounds, and the combination of pharmacokinetic and drug-likeness predictions has shown promising results in silico. In summary, an integrated computational approach combining molecular docking, ADME-Tox assessment, DFT calculations, and molecular dynamics simulations highlights the promise of these derivatives as candidates for the development of new antimicrobial agents targeting DNA gyrase.

Two classes of DNA gyrase inhibitors elicit distinct evolutionary trajectories toward resistance in gram-negative pathogens

Comprehensive knowledge of mechanisms driving the acquisition of antimicrobial resistance is essential for the development of new drugs with minimized resistibility. To gain this knowledge, we combine experimental evolution in a continuous culturing device, the morbidostat, with whole genome sequencing of evolving cultures followed by characterization of drug-resistant isolates. Here, this approach was used to assess evolutionary dynamics of resistance acquisition against DNA gyrase/topoisomerase TriBE inhibitor GP6 in Escherichia coli and Acinetobacter baumannii. The evolution of GP6 resistance in both species was driven by a combination of two classes of mutational events: (i) amino acid substitutions near the ATP-binding site of the GyrB subunit of the DNA gyrase target; and (ii) various mutations and genomic rearrangements leading to upregulation of efflux pumps, species-specific (AcrAB/TolC in E. coli and AdeIJK in A. baumannii) and shared by both species (MdtK). A comparison with the experimental evolution of resistance to ciprofloxacin (CIP), previously performed using the same workflow and strains, revealed fundamental differences between these two distinct classes of compounds. Most notable were non-overlapping spectra of target mutations and distinct evolutionary trajectories that, in the case of GP6, were dominated by upregulation of efflux machinery prior to (or even in lieu) of target modification. Most of the efflux-driven GP6-resistant isolates of both species displayed a robust cross-resistance to CIP, while CIP-resistant clones showed no appreciable increase in GP6-resistance.

Investigation of bacterial DNA gyrase Inhibitor classification models and structural requirements utilizing multiple machine learning methods.

Infections from multidrug-resistant (MDR) bacteria have emerged as a paramount global health concern, and the therapeutic effectiveness of current treatments is swiftly diminishing. An urgent need exists to explore innovative strategies for countering drug-resistant bacteria. Bacterial DNA gyrase, functioning as an ATP-dependent enzyme, plays a pivotal role in the intricate processes of transcription, replication, and chromosome segregation within bacterial DNA. This renders it a prime target for the development of innovative antibacterial agents. However, the experimental identification of bacterial DNA gyrase inhibitors faces multifaceted challenges due to current methodological constraints. Recognizing its significance, this study developed 56 computational models designed for predicting bacterial DNA gyrase inhibitors. These models employed seven distinct molecular fingerprints and eight machine learning algorithms. Among these models, Model_2D, created using KlekotaRoth fingerprints and the SVM algorithm, stands out as the most robust performer (ACC = 0.86, MCC = 0.63, G-mean = 0.82). Moreover, given the limited exploration of structural fragments required for DNA Gyrase B inhibitors, crucial structural fingerprints influencing DNA Gyrase B inhibitors were identified through Bayesian classification. Subsequently, we conducted molecular docking to reveal the binding modes between these crucial structural fingerprints and the active site of DNA gyrase B. In conclusion, the present study aimed to develop the optimal classification model for bacterial DNA gyrase inhibitors, offering invaluable support to medicinal chemists creating innovative DNA gyrase inhibitors.

Synthesis, characterization, molecular modeling studies, and biological evaluation of metal piroxicam complexes (M = Ni(II), Pt(IV), Pd(II), Ag(I)) as antibacterial and anticancer agents.

Four piroxicam metal complexes; NiL2 , PtL2 , PdL2 , and AgL were synthesized and characterized by different techniques with enhanced antibacterial and anticancer activity. Regarding in vitro antimicrobial activity, complex NiL2 displayed potent antibacterial effect against Escherichia coli and Pseudomonas aeruginosa that was 1.9-folds higher than piroxicam (minimum inhibitory concentration [MIC] = 31.85, 65.32 µM), respectively. In case of G+ve bacteria, complex PtL2 had potent activity on Staphylococcus aureus which was 2.1-folds higher than piroxicam (MIC = 43.12 µM), while activity of complex AgL against Enterococcus faecalis was threefolds higher than piroxicam (MIC = 74.57 µM. Complexes PtL2 and PdL2 exhibited higher inhibition of DNA gyrase than piroxicam (IC50 = 6.21 µM) in the range of 1.9-1.7-folds. The in vitro antiproliferative activity depicted that all investigated complexes showed better cytotoxic effect than piroxicam, specifically Pt and Pd complexes which had lower IC50 values than piroxicam on human liver cancer cell line HepG2 by 1.8 and 1.7-folds, respectively. While Pd and Ag complexes showed 2 and 1.6-folds better effect on human colon cancer cell line HT-29 compared with piroxicam. Molecular modeling studies including docking on Stranded DNA Duplex (1juu) and DNA gyrase enzyme (1kzn) that gave good insight about interaction of complexes with target molecules, calculation of electrostatic potential map and global reactivity descriptors were performed.

Friend or Foe: Protein Inhibitors of DNA Gyrase.

DNA gyrase is essential for the successful replication of circular chromosomes, such as those found in most bacterial species, by relieving topological stressors associated with unwinding the double-stranded genetic material. This critical central role makes gyrase a valued target for antibacterial approaches, as exemplified by the highly successful fluoroquinolone class of antibiotics. It is reasonable that the activity of gyrase could be intrinsically regulated within cells, thereby helping to coordinate DNA replication with doubling times. Numerous proteins have been identified to exert inhibitory effects on DNA gyrase, although at lower doses, it can appear readily reversible and therefore may have regulatory value. Some of these, such as the small protein toxins found in plasmid-borne addiction modules, can promote cell death by inducing damage to DNA, resulting in an analogous outcome as quinolone antibiotics. Others, however, appear to transiently impact gyrase in a readily reversible and non-damaging mechanism, such as the plasmid-derived Qnr family of DNA-mimetic proteins. The current review examines the origins and known activities of protein inhibitors of gyrase and highlights opportunities to further exert control over bacterial growth by targeting this validated antibacterial target with novel molecular mechanisms. Furthermore, we are gaining new insights into fundamental regulatory strategies of gyrase that may prove important for understanding diverse growth strategies among different bacteria.

Novel pyrazole‐biphenyl‐carboxamides for SARS‐CoV2 entry‐level restriction and microbial infections

AbstractMicrobial diseases including viral infection are big issues globally. Effective medicinal discovery for them is the need for the day. In this study, we report pyrazole‐biphenyl‐carboxamides (4a‐l) validated for their SARS‐CoV2 entry‐level restriction effect over studying the protein–protein interaction of SARS‐CoV2 with human ACE protein. Their extended antimicrobial properties were also evaluated. Online and offline software tools predicted MD simulation and ADMET druggability in silico. The antimicrobial efficacy of all compounds was also evaluated against Gram+ve Streptococcus pneumoniae (MTCC 1936), Staphylococcus aureus (MTCC 737) and Gram‐ve Escherichia coli (MTCC 443), Pseudomonas aeruginosa (MTCC 424) (bacteria). In the results, compounds 4g and 4i were evenly active against both bacteria at a low concentration range (MIC: 1.00 to 9.5 μg/mL) and displayed lesser toxicity to tested mammalian cells (EC100 = 75 μg/mL). Furthermore, it was able to kill metabolically inactive bacterial cells and eradicate established biofilms of Methicillin‐resistant Staphylococcus aureus (MRSA). Both the compounds inhibited DNA gyrase well with an IC50 0.25 μM (96% relative activity) and 0.52 μM (97% relative activity) respectively. Compounds (4a‐l) showed restrictive efficiency of SARS‐CoV2 spike protein (SC2SP) and human angiotensin‐converting enzyme 2 (hACE2) entry‐level association in COVID‐19 in silico. To assess this ability, firstly, we identified the crucial amino acid residues involved in the interface of SARS‐CoV‐2 and hACE2 virtually. We recognized the ability of 4a‐l binding to the binding interface to SARS‐CoV2; thus, the interaction of SC2SP‐hACE2 was effectively inhibited.

3+2] Cycloaddition mediated synthesis of spirooxindole pyrrolidine/piperidine fused chromene aldehyde derivatives: DFT studies, antibacterial evaluation and molecular docking investigation as DNA gyrase inhibitors

A series of diverse 2′-oxo-6b,7,8,9-tetrahydro-6H-spiro[chromeno[3,4-a]pyrrolizine-11,3′-indoline]-6a(11aH)-carbaldehyde derivatives are synthesized and antibacterial evaluation is done along with computational studies.

Identification of apigenin-4'-glucoside as bacterial DNA gyrase inhibitor by QSAR modeling, molecular docking, DFT, molecular dynamics, and in vitro confirmation studies.

It is well known that antibiotic resistance is a major health hazard. To eradicate antibiotic-resistant bacterial infections, it is essential to find a novel antibacterial agent. Hence, in this study, a quantitative structure-activity relationship (QSAR) model was developed using 43 DNA gyrase inhibitors, and 700 natural compounds were screened for their antibacterial properties. Based on molecular docking and absorption, distribution, metabolism, excretion, and toxicity (ADMET) studies, the top three leads viz., apigenin-4'-glucoside, 8-deoxygartanin, and cryptodorine were selected and structurally optimized using density functional theory (DFT) studies. The optimized structures were redocked, and molecular dynamic (MD) simulations were performed. Binding energies were calculated by molecular mechanics/Poisson-Boltzmann surface area solvation (MM-PBSA). Based on the above studies, apigenin-4'-glucoside was identified as a potent antibacterial lead. Further in vitro confirmation studies were performed using the plant Lawsonia inermis containing apigenin-4'-glucoside to confirm the antibacterial activity. For QSAR modeling, 2D descriptors were calculated by PaDEL-Descriptors v2.21 software, and the model was developed using the DTClab QSAR tool. Docking was performed using PyRx v0.8 software. ORCA v5.0.1 computational package was used to optimize the structures. The job type used in optimization was equilibrium structure search using the DFT hybrid functional ORCA method B3LYP. The basis set was 6-311G (3df, 3pd) plus four polarization functions for all atoms. Accurate docking was performed for optimized leads using the iGEMDOCK v2.1 tool with a genetic algorithm by 10 solutions each of 80 generations. Molecular dynamic simulations were performed using GROMACS 2020.04 software with CHARMM36 all-atom force field.

In silico analysis of luteolin derivatives as antibacterial agents targeting DNA gyrase and CTX-M-15 extended-spectrum β-lactamase of Escherichia coli.

Luteolin exhibited antibacterial activity against Escherichia coli and its chemical structure similar to that of ciprofloxacin (CPF) which works by inhibiting DNA gyrase. Filtrate from passion fruit extract containing luteolin and its derivatives could inhibit extended-spectrum β-lactamase (ESBL)-producing E. coli. Antibacterial compounds that can also inhibit ESBL will be valuable compounds to overcome the problem of resistant bacteria. This study aimed to ensure the potency of luteolin and luteolin derivatives targeting DNA gyrase and ESBL by in silico approach. Docking simulation of ligands L1-L14 was performed using AutoDock Vina, and pharmacokinetics and toxicity (absorption, distribution, metabolism, excretion, and toxicity) profiles were predicted by pKCSM online. The docking result revealed higher binding affinity on DNA gyrase (PDB.1KZN) of 12 luteolin derivatives (energy <-7.6 kcal/mol) compared to CPF and higher affinity (energy <-6.27 kcal/mol) of all compounds than clavulanic acid against ESBL CTX-M-15 (PDB.4HBU). The compounds could be absorbed through the human intestine moderately, which showed low permeability to blood-brain barrier, nontoxic and nonhepatotoxic. The most active luteolin glycoside (L6) is capable to inhibit DNA gyrase and ESBL from E. coli which provided the potential against resistant bacteria and was promoted as lead compounds to be developed further.

New quinazolin-2,4-dione derivatives incorporating acylthiourea, pyrazole and/or oxazole moieties as antibacterial agents via DNA gyrase inhibition.

This article contributes to the search for new therapeutic agents for treatment of diseases caused by bacterial pathogens. In this study, a new series of compounds incorporating numerous bioactive moieties such as quinazolin-2,4-dione, acylthiourea linkage, and/or five membered nitrogen heterocycles (pyrazole and oxazole) 2-5a-c was described to identify new antibacterial drug candidates via inhibition of DNA gyrase enzyme. The precursor N-[N'-(2-cyano-acetyl)-hydrazinocarbothioyl]-4-(2,4-dioxo-1,4-dihydro-2H-quinazolin-3-yl)-benzamide 2 was prepared by treatment of compound 1 with ammonium thiocyanate and cyanoacetic acid hydrazide through multicomponent reaction (MCR). In addition, compounds 3a-d and 4a-b were synthesized by treatment of 2 with aromatic aldehydes and/or ketones through Knoevenagel reaction, affording high purity products in satisfactory yields. Moreover, new heterocyclic moieties such as pyrazole and/or oxazole attached to quinazolin-2,4-dione core 5a-c were synthesized by treatment of 3c with different nucleophilic reagents like hydrazine, phenyl hydrazine and hydroxyl amine, respectively. Subsequently, the obtained products were structurally characterized by IR, 1H-, 13C-NMR, and MS analyses. The minimum inhibitory concentration (MIC) and antibacterial potency of all compounds were estimated against two G-ve (E. coli and P. aeruginosa), and two G+ve bacteria (B. subtilis and S. aureus). Encouragingly, compound 3c demonstrated the best antibacterial activity against all the strains of the tested pathogenic bacteria at low concentrations compared with the standard drug, Ciprofloxacin. Electron withdrawing groups such as -NO2 and -Cl enhance the antibacterial activity. Next, a molecular docking study between the synthesized derivatives and the target enzyme, DNA gyrase enzyme (PDB: 2xct) was undertaken to investigate intermolecular interactions between the compounds and target enzyme.

Multimodal antibacterial potency of newly designed and synthesized Schiff's/Mannich based coumarin derivatives: potential inhibitors of bacterial DNA gyrase and biofilm production.

The briskened urge to develop potential antibacterial candidates against multidrug-resistant pathogens has motivated the present research study. Herein, newly synthesized coumarin derivatives with azomethine and amino-methylated as the functional groups have been focused on their antibacterial efficacy. The study proposed two distinct series: 3-acetyl substituted coumarin derivatives, followed by the Schiff base approach (5a-5i), and formaldehyde-secondary cyclic amine-based derivatives (7a-7g), using the Mannich base approach, further the compounds have been confirmed through various spectral studies. Further, target-specific binding affinity has been affirmed via in silico study. In vitro antibacterial study suggested compounds 5d and 5f to be most effective against S. aureus and multidrug-resistant K. pneumoniae, with MIC values of 8 and 16 μg mL-1. Among them, the compounds 5d and 5f showed excellent binding scores against different bacterial gyrase compared to the standard novobiocin. Based on RMRS, RMSF, Rg, and H-bond plots, MD simulation study at 100 ns also suggested better stability of 5d inside gyraseB of E. coli than the complex of E. coli-GyrB-novobiocin. The toxicity and pharmacokinetic profiles showed favorable drug-likeness. Overall, systematic in vitro and in silico assessment suggested that multimodal antibacterial derivatives 5d and 5f strongly inhibit both bacterial DNA gyrase and biofilm formation of drug-resistant pathogens, suggesting their potency in mainstream antibacterial therapy.

Benzothiazole DNA gyrase inhibitors and their conjugates with siderophore mimics: design, synthesis and evaluation.

Benzothiazole-based bacterial DNA gyrase and topoisomerase IV inhibitors are promising new antibacterial agents with potent activity against Gram-positive and Gram-negative bacterial strains. The aim of this study was to improve the uptake of these inhibitors into the cytoplasm of Gram-negative bacteria by conjugating them to the small siderophore mimics. The best conjugate 18b displayed potent Escherichia coli DNA gyrase and topoisomerase IV inhibition. The interaction analysis of molecular dynamics simulation trajectory showed the important contribution of the siderophore mimic moiety to binding affinity. By NMR spectroscopy, we demonstrated that the hydroxypyridinone moiety alone was responsible for the chelation of iron(iii). Moreover, 18b showed an enhancement of antibacterial activity against E. coli JW5503 in an iron-depleted medium, clearly indicating an increased uptake of 18b in this bacterial strain.

Novel 4,5-dibromo-N-phenyl-1H-pyrrole-2-carboxamide Hybrids as Promising DNA Gyrase Inhibitors: Design, synthesis and antimicrobial evaluation

Bacterial DNA gyrase remains a prominent and vital target in discovering new antibacterial drugs. In the present research work, we designed and synthesized a series of novel 4,5-dibromo-N-phenyl-1H-pyrrole-2-carboxamide hybrids containing substituted 1,2,3-triazole and isoxazole moieties which could serve as potential E. coli DNA gyrase inhibitors. The title compounds were synthesized with a good to excellent yield, and all the newly synthesized compounds were characterized by physicochemical and spectral analysis (FTIR, 1H NMR, and 13C NMR). The DNA gyrase (E. coli) inhibitory assay was performed for all synthesized compounds. Results showed that four compounds, 11a (IC50 = 0.90 µM), 11b (IC50 = 0.28 µM), 17a (IC50 = 0.72 µM) and 17b (IC50 = 0.43 µM), exhibited good DNA gyrase inhibitory activity. In-silico molecular docking study was performed to understand the mode of interaction of compounds with the target enzyme. A docking study on the E. coli DNA gyrase protein revealed that compounds 11b (-7.011 kcal/mol) and 17b (-6.60 kcal/mol) interact with ARG136 and ASP73, two key amino acid residues, with docking scores of −7.01 and −6.60, respectively. The MD simulation was further employed to elucidate the thermodynamic binding energy, RMSD, and RMSF of compounds 11b and 17b. They exhibited binding energies of -47.598 kcal/mol and -41.682 kcal/mol, respectively. This provides valuable information on the binding mode and structure-activity relationship of these new hybrids of 4,5-dibromo-N-phenyl-1H-pyrrole-2-carboxamides as promising E. coli DNA gyrase B inhibitors. In addition, these hybrid derivatives showed more prominent antibacterial action on Gram-negative rather than Gram-positive organisms. Surprisingly, compounds 11b (MIC = 1.56 µg/mL) and 17b (MIC = 3.125 µg/mL) also displayed promising anti-mycobacterial activity.

Virtual Screening and ADMET Prediction to Uncover the Potency of Flavonoids from Genus Erythrina as Antibacterial Agent through Inhibition of Bacterial ATPase DNA Gyrase B.

The emergence of antimicrobial resistance due to the widespread and inappropriate use of antibiotics has now become the global health challenge. Flavonoids have long been reported to be a potent antimicrobial agent against a wide range of pathogenic microorganisms in vitro. Therefore, new antibiotics development based on flavonoid structures could be a potential strategy to fight against antibiotic-resistant infections. This research aims to screen the potency of flavonoids of the genus Erythrina as an inhibitor of bacterial ATPase DNA gyrase B. From the 378 flavonoids being screened, 49 flavonoids show potential as an inhibitor of ATPase DNA gyrase B due to their lower binding affinity compared to the inhibitor and ATP. Further screening for their toxicity, we identified 6 flavonoids from these 49 flavonoids, which are predicted to have low toxicity. Among these flavonoids, erystagallin B (334) is predicted to have the best pharmacokinetic properties, and therefore, could be further developed as new antibacterial agent.

Norfloxacin derivatives as DNA gyrase and urease inhibitors: synthesis, biological evaluation and molecular docking.

Background: DNA gyrase and urease enzymes are important targets for the treatment of gastroenteritis, appendicitis, tuberculosis, urinary tract infectionsand Crohn's disease. Materials & methods: Esterification of norfloxacin was performed to enhance DNA gyrase and urease enzyme inhibition potential. Structure elucidation and chemical characterization were done through spectral (1H NMR, Fourier transformIR, 13C NMR) and carbon, hydrogen, nitrogenand sulfur analysis along with molecular docking. Results & conclusion: The majority of derivatives exhibited significant results but the 3e derivative showed maximum bactericidal, DPPH scavenging (96%), DNA gyrase and urease enzyme inhibitory activity with IC50 of 0.15±0.24and 1.14±0.11μM respectively which was further supported by molecular docking studies. So, the active derivatives can serve as a lead compound for the treatment of various pathological conditions.

Catalytic action and bactericidal behavior of samarium/carbon spheres-doped manganese oxide nanostructures and their molecular docking analysis

The co-precipitation technique was adapted to synthesize different concentrations (2 % and 4 %) of samarium (Sm) doped constant equates of carbon spheres (Cs) and manganese oxide (MnO2). The principal objective of this investigation is to demonstrate confirmation that Sm/Cs-doped MnO2 nanostructures (NSs) owned antibacterial and catalytic attributes. Reduction in surface area manifested to agglomeration, NSs faces become inaccessible to initiate a reaction, can be overcome upon doping of Sm. Sm has the potential to increase the activity of metal oxide ascribed to its electron trapping effect. The structural morphologies, optical properties, functional groups, elemental composition, and d-spacing were determined by applying various characterizations. With the incorporation of CS and Sm, UV–vis spectra shifted towards lower wavelength and band gap energy (Eg) was reduced. MnO2 possessed orthorhombic structure, according to the XRD pattern and TEM exhibited long Burr-like morphology of undoped MnO2. SAED image illustrated that MnO2 is polycrystalline. 4 % Sm/CS doped MnO2 revealed the highest degradation (91 %) in a neutral environment. Furthermore, 4 % Sm/Cs doped-MnO2 revealed an inhibitory zone of 2.85 mm against Escherichia coli (E. coli). Additionally, an analysis of molecular docking revealed a binding interface with NRs and the functional domains of certain cellular proteins. Results indicated that Cs-doped MnO2 and Cs/Sm-doped MnO2 NRs are the most potent DNA gyrase and FabB enzyme inhibitors.

In silico Study on Structural Inhibition of Bacterial DNA Gyrase by Major Secondary Metabolites Found in Grape Seed Extract

In the early 20th century, during the era of investigating and identifying essential “vitamins”, scientific research focused on grape seed extracts and their bioactive components, particularly polyphenols. Extensive studies have demonstrated that grape seed extract, rich in proanthocyanidins, offers protection against a wide spectrum of diseases, encompassing inflammation, cardiac ailments, peptic ulcers, hypertension, diabetes, cancer, and microbial infections. To explore potential secondary metabolites within grape seed extract that could serve as structural inhibitors of bacterial DNA Gyrase, molecular docking studies were performed. The docking results revealed that two phytochemicals, namely (-)-catechin and Procyanidin-B2, exhibited the highest potency in inhibiting DNA gyrase subunit B. Subsequent in silico physicochemical and pharmacokinetic parameter predictions were conducted using specialized web servers for the examined phytochemicals. Notably, (-)-catechin displayed superior inhibitory and ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) characteristics, suggesting its potential for utilization in synthesizing novel antibacterial compounds.