Gyrase Research Articles

Synthesis, characterization, and biological evaluation of novel cobalt(II) complexes with β-diketonates: crystal structure determination, BSA binding properties and molecular docking study.

In order to discover a new antibiotic drug with better or similar activity of the already existing drugs, a series of novel cobalt(II) complexes with β-diketonate as ligands is synthesized and tested on four strains of bacteria and four species of fungi. All compounds showed notable antimicrobial activityagainst all tested strains. More importantly, some cobalt(II) complexes displayed greater activity than ketoconazole. It is important to notice that on the tested strains Mucor mucedo and Penicillium italicum complex 2B showed five times better activity compared to ketoconazole, while complex 2D had two times better activity on Penicillium italicum strain compared to ketoconazole. Moreover, investigations with bovine serum albumin were performed. Investigations showed that the tested complexes have an appropriate affinity for binding to bovine serum albumin. In addition, the molecular docking study was performed to investigate more specifically the sites and binding mode of the tested cobalt(II) complexes with β-diketonate as ligands to bovine serum albumin, tyrosyl-tRNA synthetase, topoisomerase II DNA gyrase, and cytochrome P450 14 alpha-sterol demethylase. In conclusion, all the results indicated the great prospective of the novel cobalt complexes for some potential clinical applications in the future.

Synthesis and computational studies of new pyridine, pyrazole, pyran, and pyranopyrimidine-based derivatives of potential antimicrobial activity as DNA gyrase and topoisomerase IV inhibitors

In this study, new derivatives based on pyridine, pyrazole, pyran, and pyranopyrimidine scaffolds 5–14 were designed and synthesized. The newly synthesized compounds were characterized using microanalytical and spectral data. Using amoxicillin and amphotericin B, two common antibacterial and antifungal medications, respectively, the antimicrobial activity of the new compounds was assessed against a variety of strains of both Gram-positive and Gram-negative bacteria as well as fungal infections. The most promising activity was achieved by pyridine-based derivatives 5, 7a, and 7b, which exhibited MIC values ranging from 0.95 to 18.04 µM against the examined bacterial strains and ranging from 4.65 to 33.16 µM against the examined fungal strains. The later derivatives were also evaluated as E. coli DNA gyrase B/topoisomerase IV inhibitors in comparison with novobiocin as a standard drug. Although the assessed candidates 5, 7a, and 7b exhibited a promising suppression impact against E. coli DNA gyrase B (IC50 = 3.11 ± 0.14, 3.85 ± 0.20, and 4.05 ± 0.10, respectively, IC50 novobiocin= 3.64 ± 0.10 µM), they showed detectable less suppression impact against Topoisomerase IV than that of the reference drug with IC50 values of 19.72 ± 1.00, 79.33 ± 0.25, 85.14 ± 0.10, and 13.42 ± 0.05 µM, respectively. Additionally, the safety profiles of 5, 7a, and 7b against WI38 cells were significantly superior to that of novobiocin (IC50 = 138 ± 0.33, 170 ± 0.40, 163.3 ± 0.17, and 86.2 ± 0.03 µM, respectively).Lastly, molecular docking was used to examine the most active derivatives 5, 7a, and 7b's binding capacity to the target DNA gyrase B/topoisomerase IV. The molecules exhibited various H-interactions with the amino acid residues Asp73, Arg76, and Val71 in E. coli DNA gyrase, where compound 5 exhibited H-bonding with the Asp1069 side chain of E. coli Topoisomerase IV. Additional in silico ADMET studies were conducted to represent their oral bioavailability and drug-likeness characteristics.

Synthesis, anti-microbial, and docking studies of functionalized chromenyl phosphonates using ionic liquid catalyst.

Synthesis of functionalized chromenyl phosphonates by the reaction among 2-hydorxybenzaldehydes, dicyanoethane, and dialkyl phosphonates that was promoted by choline hydroxide ionic liquid catalyzes the simultaneous, Knoevenagel, Pinner, and phospha-Michael reactions, under neat condition at room temperature. Important phosphorus-containing compounds can be produced at a reasonable cost because of the mild reaction conditions and the inexpensive promoter choline hydroxide. Furthermore, the desired products can be obtained without the need for any extraction or chromatography steps. An alternate technique for the simple and high-yield synthesis of functionalized chromenyl phosphonates is offered by this protocol. The synthesized compounds were studied by anti-microbial activity and docking studies. The title compounds molecular docking investigations demonstrated their efficacy as therapeutic agents against DNA Gyrase B and Aspergillus niger endoglucanase in both antibacterial and antifungal inhibition, and they identified compounds 4a, 4d, 4l, 4p, and 4q as promising candidates for microbial treatment, with binding affinities ranging from -6.9 to -7.4kcal/mol.

Synthesis and evaluation of di-heterocyclic benzazole compounds as potential antibacterial and anti-biofilm agents against Staphylococcus aureus.

Cumulative escalation in antibiotic-resistant pathogens necessitates the quest for novel antimicrobial agents, as current options continue to diminish bacterial resistance. Herein, we report the synthesis of di-heterocyclic benzazole structures (12-19) and their invitro evaluation for some biological activities. Compounds 16 and 17 demonstrated potent antibacterial activity (MIC = 7.81 μg/mL) against Staphylococcus aureus, along with significant anti-biofilm activity. Noteworthy is the capability of Compound 17 to inhibit biofilm formation by at least 50% at sub-MIC (3.90 μg/mL) concentration. Furthermore, both compounds exhibited the potential to inhibit preformed biofilm by at least 50% at the MIC concentration (7.81 μg/mL). Additionally, Compounds 16 and 17 were examined for cytotoxic effects in HFF-1 cells, using the MTT method, and screened for binding interactions within the active site of S. aureus DNA gyrase using in silico molecular docking technique, employing AutoDock 4.2.6 and Schrödinger Glidse programs. Overall, our findings highlight Compounds 16 and 17 as promising scaffolds warranting further optimization for the development of effective antibacterial and anti-biofilm agents.

Mining and characterization of novel antimicrobial peptides from the large-scale microbiome of Shanxi aged vinegar based on metagenomics, molecular dynamics simulations and mechanism validation

The study aimed to mine and characterize novel antimicrobial peptides (AMPs) from the Shanxi aged vinegar microbiome. Utilizing machine learning techniques, AlphaFold2 structure prediction and molecular dynamics simulations, six novel AMPs were innovatively mined from 98,539 peptides based on metagenomic data, of which one peptide secreted by Lactobacillus (named La-AMP) was experimentally validated to have remarkable bactericidal effects against Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli) with high stability and no hemolytic activity. Scanning electron microscopy revealed that La-AMP caused irreversible damage to cell membranes of S. aureus and E. coli, a finding further confirmed by calcein-AM/propidium iodide staining. Additionally, La-AMP induced nucleic acid leakage and reactive oxygen species accumulation in bacterial cells. It was found to bind to DNA gyrase through salt bridges, hydrogen bonds, and hydrophobic interactions, ultimately inducing apoptosis. Thus, La-AMP exhibited encouraging promise as a valuable bioactive component for the development of natural preservatives.

Discovery of aminopiperidine based potent & novel topoisomerase inhibitor with broad spectrum anti-bacterial activity

Bacterial DNA gyrase and topoisomerase IV inhibition has emerged as a promising strategy for the cure of infections caused by antibiotic-resistant bacteria. The Novel Bacterial Topoisomerase Inhibitors (NBTIs) bind to a different site from that of the quinolones with novel mechanism of action. This evades the existing target-mediated bacterial resistance associated with quinolones. This article presents our efforts to identify in vitro potent and broad-spectrum antibacterial agent 4l.

Antimicrobial effects of new tetrahydrofurans

The increasing challenge of antimicrobial resistance (AMR) necessitates abrupt attention to discovering a new class of antimicrobials. In this study, we made efforts to prepare some fluoro-phenyl tetrahydrofurans-based DNA gyrase inhibitors as anti-microbial agents. To obtain the title compounds difluoro phenyl tetrahydrofurans (1-12), we used fluorophenyl-tetrahydrofuran and methyl benzenesulfonate to react with isoxazole derivatives and heterocyclic compounds bearing secondary amines in the presence of dimethylformamide (DMF) and sodium hydride (NaH) or potassium carbonate (K2CO3). The compounds were obtained in moderate to excellent yields and were characterized with FTIR, HRMS, NMR, etc. Among all compounds (1-12), compounds 1, 2, 11, and 12 were active against various Gram-positive and Gram-negative bacteria at a low concentration (MIC ranged between 1.25 and 9.75 μg/mL) and displayed low toxicity towards mammalian cells. We testified the in vitro DNA gyrase inhibitory potential for these compounds. A molecular docking study and an ADMET assessment study were carried out to understand the mode of interaction of ligand-DNA gyrase. In conclusion, we screened the compounds 1, 2, 11, and 12 for further clinical and pre-clinical studies.

Biosynthesis and Characterization of Aeonium arboreum-Derived Silver Nanoparticles: Antimicrobial Activity, Biofilm Inhibition, Antihemolytic Activity, and In Silico Studies.

Environmentally friendly biosynthesis of silver nanoparticles (AgNPs) from Aeonium arboreum (L.) Webb & Berthel is reported for the first time. The synthesized AgNPs were characterized using UV-Vis, FTIR, TEM, Zeta potential, and XRD analysis, revealing high stability (-29.1 mV), spherical shape, and an average size of 100 nm. The antimicrobial activity levels of both A. arboreum extract and biosynthesized AgNPs were evaluated against five uropathogens (Staphylococcus aureus, Enterococcus faecalis, Escherichia coli, Pseudomonas aeruginosa, and Candida albicans). Both the extract and the AgNPs exhibited significant efficacy, particularly against E. coli, with inhibition zones of 27 mm and 30 mm, respectively. LC-MS analysis tentatively identified 11 secondary metabolites in the extract, including quercetin-3-O-glucoside, quercetin-3-O-rhamnoside, myricetin 3-glucoside, and daphneresinol. In silico docking studies revealed promising binding affinities of these metabolites in relation to key enzymes involved in bacterial folate synthesis (dihydrofolate reductase (DHFR) and dihydropteroate synthase (DHPS)) and DNA replication (DNA gyrase). These findings demonstrate the potential of A. arboreum-based AgNPs and their associated metabolites as a novel therapeutic approach for combating urinary tract infections. Their antimicrobial, antihemolytic, and antibiofilm properties warrant further investigation.

Synthesis of new pyrazine-pyrazole-thiazolidin-4-one and pyrazine-triazole-thiazolidin-4-one conjugates, molecular modelling and docking as antimicrobial agents

The ever-increasing incidence of microbial resistance provide a significant peril to the scientific community. Thus, the need for the discovery and development of new antimicrobial agents is becoming critical. An effective approach to address this challenging problem is to generate hybrid molecules by combining two or more pharmacophores covalently linked to a single-molecule platform. Antimicrobial hybrids have been proposed as promising solution to overcome drug resistance and/or presumably having a broader spectrum of activity. This guided us to synthesize a new series of eight final target pyrazine-pyrazole-thiazolidin-4-one and pyrazine-triazole-thiazolidin-4-one hybrids 7, 8a-c, 12, and 13a-c and investigate their biological activities. Characterization of the designed hybrids were performed using IR, 1H NMR, 13C NMR, and mass analyses. The DFT/B3LYP approach revealed that the synthesized hybrids had a non-planar configuration. The nitrobenzylidene derivatives 8c and 13c exhibited the highest polarizability and hyperpolarizability. We examined the antimicrobial activity, DNA gyrase inhibition, molecular docking, and Swiss ADME analysis of different pyrazine-pyrazole-thiazolidin-4-one and pyrazine-triazole-thiazolidin-4-one conjugates. These compounds are effective against a number of bacterial and fungal strains, suggesting possible treatments for certain infections. DNA gyrase inhibition experiments demonstrated that conjugate 13b was more effective than novobiocin. A molecular docking study sheds light on the binding affinities and interactions of these conjugates with target proteins, revealing strong and specific bindings for numerous conjugates. Swiss ADME studies examine important pharmacokinetic parameters and show issues with bioavailability and membrane permeability in the mouth because of variations in molecular weight, lipophilicity, and hydrogen bond interactions. Swiss ADME studies have studied the drug-like qualities of these conjugates, revealing their potential in antibacterial applications.

Phytochemical characterization, antimicrobial properties and in silico modeling perspectives of Anacyclus pyrethrum essential oil

Medicinal plants are used widely in the treatment of various infectious diseases. One of these medical plants is Moroccan plants such as Anacyclus pyrethrum. In this study, the essential oil isolated from the leaves of Anacyclus pyrethrum (APEO) by the hydrodistillation method was analyzed using (GC/MS) analysis. A total of forty-four compounds were identified form the oil and the oxygenated monoterpenes were the most abundant class of compounds. The major identified compound is santolina alcohol (40.7 %), followed by germacrene-D (8.9 %). The in-vitro assessment of the antimicrobial efficacy of APEO encompassed an investigation involving six microbial strains, including two Gram-positive bacteria, four Gram-negative bacteria, and three fungal strains. The findings revealed noteworthy antibacterial and antifungal properties against all examined microorganisms, with inhibitory zone diameters ranging from 25.67 ± 0.06 mm to 25.19 ± 0.03 mm for Gram-positive bacteria and from 22.34 ± 0.01 mm to 14.43 ± 0.02 mm for Gram-negative bacteria, as determined through the disc-diffusion assay. In the case of antifungal activity, inhibitory zones ranged from 24.57 ± 0.04 mm to 18.37 ± 0.06 mm. Further evaluation revealed that the MIC values of Gram-positive bacteria were at the concentration 0.25 % v/v, while MBC values ranged from 0.25 % to 1.0 % v/v. The Gram-negative bacteria exhibited MIC values spanning from 0.5 % to 2.0 % v/v, with MBC values in the range of 0.5 %–2.0 % v/v. For the fungal strains, MIC values ranged from 0.5 % to 1.0 % v/v, while the MFC consistently remained at 1.0 % for all tested fungal strains. The assessment of the MBC/MIC and MFC/MIC ratios collectively indicates that A. pyrethrum EO possesses bactericidal and fungicidal attributes. The in silico study of bioavailability predictions for compounds in APEO based on six physicochemical properties show optimal physiochemical properties including size, lipophilicity, solubility, flexibility, and saturation. α-Pinene, limonene, germacrene D, and (E)-β-farnesene are non-polar due to their lack of polar groups, and the ADME profile indicates desirable properties for considering these compounds in drug development. Molecular docking investigation indicates that all the compounds of APEO reside well into the binding site of the DNA gyrase B enzyme of Staphylococcus aureus by mediating a number of significant interactions with the binding site residues. The ADME analysis suggested that the major compounds APEO possess desirable properties for further consideration in drug development. In light of these findings, APEO could serve as a natural source for the elaboration of new and active antimicrobial drugs.

Macrolones target bacterial ribosomes and DNA gyrase and can evade resistance mechanisms.

Growing resistance toward ribosome-targeting macrolide antibiotics has limited their clinical utility and urged the search for superior compounds. Macrolones are synthetic macrolide derivatives with a quinolone side chain, structurally similar to DNA topoisomerase-targeting fluoroquinolones. While macrolones show enhanced activity, their modes of action have remained unknown. Here, we present the first structures of ribosome-bound macrolones, showing that the macrolide part occupies the macrolide-binding site in the ribosomal exit tunnel, whereas the quinolone moiety establishes new interactions with the tunnel. Macrolones efficiently inhibit both the ribosome and DNA topoisomerase in vitro. However, in the cell, they target either the ribosome or DNA gyrase or concurrently both of them. In contrast to macrolide or fluoroquinolone antibiotics alone, dual-targeting macrolones are less prone to select resistant bacteria carrying target-site mutations or to activate inducible macrolide resistance genes. Furthermore, because some macrolones engage Erm-modified ribosomes, they retain activity even against strains with constitutive erm resistance genes.

A New Beginning to the Existing Medicines; Repurposing FDA-Approved Drugs for the Neglected Re-Emerging Disease Leptospirosis.

Leptospirosis is one of the re-emerging zoonotic diseases, especially in tropical regions. Many antibiotics are used to treat leptospirosis, but there are no scientific evidence-based guidelines or systematic clinical trials for using these drugs. A bioinformatics approach was made to shortlist some Food and Drug Administration (FDA) of the United States of America-approved and currently used drugs for leptospirosis. The existing drugs from the Drug Bank database, which are currently not used for leptospirosis, were selected to identify their target proteins and binding sites using bioinformatics methods. Orthologues of these target proteins were selected from the proteome database of Leptospira. The similar sites and their interactions with the drugs were validated and recommended for use in leptospirosis. Further, the sensitivity of recommended drugs was also validated in vitro. The sequences and structures of these proteins were compared under strictly controlled parameters and shortlisted Gatifloxacin, Imipenem, Latamoxef, Doripenem, Tigecycline, and Lactams as repurposable drugs for leptospirosis. An in vitro validation of the drugs showed significant antileptospiral activity in 12 serovars with low IC50 concentrations and also showed that the IC50 values varied across Leptospira serovars. Further, suitable proteins under the concept of "One Target, Many Drugs" identified DNA gyrase subunit A (Q72WD1), 30S ribosomal protein S9 (Q72U99), and 30S ribosomal protein S12 (Q72UA6), and these proteins were found across the pathogenic, saprophytic, and intermediate species of Leptospira. We describe a method to find repurposable drugs from the approved list that are not currently used to treat leptospirosis and validate them to be taken forward for systematic clinical trials specific to leptospirosis for recommendations in clinical use.

Development of narrow-spectrum topoisomerase-targeting antibacterials against mycobacteria

New 2-pyrrolamidobenzothiazole-based inhibitors of mycobacterial DNA gyrase were discovered. Among these, compounds 49 and 51, show excellent antibacterial activity against Mycobacterium tuberculosis and Mycobacterium abscessus with a notable preference for mycobacteria. Both compounds can penetrate infected macrophages and reduce intracellular M. tuberculosis load. Compound 51 is a potent inhibitor of DNA gyrase (M. tuberculosis DNA gyrase IC50 = 4.1 nM, Escherichia coli DNA gyrase IC50 of <10 nM), selective for bacterial topoisomerases. It displays low MIC90 values (M. tuberculosis: 0.63 μM; M. abscessus: 2.5 μM), showing specificity for mycobacteria, and no apparent toxicity. Compound 49 not only displays potent antimycobacterial activity (MIC90 values of 2.5 μM for M. tuberculosis and 0.63 μM for M. abscessus) and selectivity for mycobacteria but also exhibits favorable solubility (kinetic solubility = 55 μM) and plasma protein binding (with a fraction unbound of 2.9 % for human and 4.7 % for mouse). These findings underscore the potential of fine-tuning molecular properties to develop DNA gyrase B inhibitors that specifically target the mycobacterial chemical space, mitigating the risk of resistance development in non-target pathogens and minimizing harm to the microbiome.

Fabrication of poly (1,4-phenylene ether ether sulfone) modified with MWCNTs/reduced (GO-oxSWCNTs) NCs for enhanced antimicrobial activities

Poly (1,4-phenylene ether ether sulfone) (PEES) is a commonly used polymer in membrane technology for water treatment applications such as water purification and blood dialyzing in hemodialysis. In this study, PEES was chemically modified by nitration, yielding nitrated Poly (1,4-phenylene ether ether sulfone) (NPEES). Following that, NPEES nanocomposites (NCs) comprise multi-walled carbon nanotubes (MWCNTs), and the process involved the synthesis of reduced graphene oxide-oxidized single-walled carbon nanotubes, abbreviated as reduced (GO-oxSWCNTs). Various characterization techniques were used on the created membranes, such as Fourier-transform infrared spectroscopy (AT-FTIR), X-ray diffraction (XRD), and scanning electron microscopy (SEM) with energy dispersive X-ray (EDX) analysis. All polymer nanocomposites were found to be amorphous, according to the XRD patterns. SEM scans revealed random crater-like features on the surface of NPEES, but MWCNTs and reduced (GO-oxSWCNTs) NCs were distributed evenly on the polymer surface. The primary goal of this study was to evaluate the antimicrobial activity of modified NPEES membranes against two Gram-positive bacteria, Staphylococcus aureus (S. aureus) and Bacillus subtilis (B. subtilis), two Gram-negative bacteria, Pseudomonas aeruginosa (P. aeruginosa) and Escherichia coli (E. coli), and a fungus, Candida albicans (C. albicans). All modified membranes, including NPEES, NPEES/MWCNTs NCs, and NPEES/MWCNTs/reduced (GO-oxSWCNTs) NCs, exhibited antibacterial activity against S. aureus and B. subtilis. Notably, when compared to NPEES/MWCNTs NCs and NPEES/MWCNTs/reduced (GO-oxSWCNTs) NCs, the NPEES membrane had higher antibacterial activity, generating a 12 mm inhibitory zone. Furthermore, molecular docking studies revealed a strong fit of the tested polymer nanocomposites into the DNA gyrase B active site (PDB ID: 4uro), which was consistent with the practical results of their antibacterial activity evaluation.

Applying UPLC-QTOF-MS/MS to profile the phytochemical constituents associated with docking studies of major components of Ziziphora capitata L as well as antimicrobial and antioxidant activity assessments of its subsequent fractions

This study aimed to investigate the phytochemical constituents, antimicrobial activity, and antioxidant effects of successive extracts of Ziziphora capitata L. aerial parts. UPLC-QTOF-MS/MS identified 79 phytoconstituents, including phenolic acids, alkaloids, flavonoids, and anthocyanins, as major phytoconstituents. Additionally, primary phytochemical investigations revealed the presence of terpenoids, steroids, flavonoids, alkaloids, tannins, and saponins in various plant fractions. The MICs of successive extracts were tested against a range of microorganisms, including gram-positive bacteria (Staphylococcus aureus, Bacillus subtilis, Streptococcus mutants, Enterococcus faecalis, Methicillin-Resistant Staphylococcus aureus (MRSA) and Staphylococcus epidermidis), gram-negative bacteria (Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Salmonella typhimurium, and Enterobacter cloacae), fungi (Aspergillus niger and Penicillium aurantiogriseum), and yeast (Candida albicans and Candida tropicalis), using the disk diffusion technique. The ethyl acetate and 95% ethanol extracts exhibited significant antibacterial activity against the tested microorganisms; however, the hexane fraction affected only P. aeruginosa. The effects of the CHCl3 and H2O fractions varied in their activities against most of the bacteria examined. Additionally, the AcOEt and 95% EtOH extracts exhibited significant antioxidant activity with IC50 = 18.6 ± 0.97 and 30.4 ± 1.86 µg/mL, respectively, compared to that of ascorbic acid (IC50 = 10.6 ± 0.8 µg/mL, reference drug). Antibacterial and antioxidant activities can be attributed to phytoconstituents, which were identified using UPLC-QTOF-MS/MS. Furthermore, docking simulations of the top ten phytochemicals of the 70% methanolic extract were carried out inside the active site of S. aureus DNA gyrase (PDB: 2XCT) and dihydropteroate synthase (DHPS) from S. pneumoniae (PDB: 2VEG) as bacterial targets and these compounds exhibited good binding modes with different types of interactions.Graphical

Antibacterial activities, PASS prediction and ADME analysis of phytochemicals from Curcubita moschata, Curcubita maxima, and Irvingia gabonensis: insights from in silico studies.

Microbial infection management and treatment are crucial as a result of the prevalent antimicrobial resistance issue. Progressive studies are being carried out on how to develop drugs that can mitigate the resistance trends of these microorganisms. Secondary metabolites of plants can also be employed and accessed for this role, as the current study examines the antibacterial activities of phytochemicals from three (3) plants (Cucubita moschata, Cucubita maxima, and Irvingia gabonesis) through computational approaches. Molecular docking studies were carried out to show the binding affinities of the phytochemicals against two target receptors (DNA gyrase and Penicillin Binding Protein 3). In addition, drug likeness analysis, bioactivity and oral-bioavailability properties, absorption, distribution, metabolism, and excretion (ADME) profiling, as well as prediction of activity spectra for substances (PASS) using online tools like SwissADME, PASS online, AdmetSAR2, and Discovery Studio, were also performed. The results obtained identified isochlorogenic acid and apigenin-7-O-glucoside for DNA gyrase (1KZN) and apigenin-7-O-glucoside for Penicillin Binding Protein 3 (4BJP), which were further subjected to molecular dynamics simulation (MDS) and therefore recommended as the lead compounds.

Development of Novel Bacterial Topoisomerase Inhibitors Assisted by Computational Screening.

Multidrug-resistant bacterial infections pose an ever-evolving threat to public health. Since the outset of the antibacterial age, bacteria have developed a multitude of diverse resistance mechanisms that suppress the effectiveness of current therapies. New drug entities, such as Novel Bacterial Topoisomerase Inhibitors (NBTIs), can circumvent this major issue. A computational docking model was employed to predict the binding to DNA gyrase of atypical NBTIs with novel pharmacophores. Synthesis of NBTIs based on computational docking and subsequent antibacterial evaluation against both Gram-positive and Gram-negative bacteria yielded congeners with outstanding anti-staphylococcal activity and varying activity against select Gram-negative pathogens.

Ligand-Based Virtual Screening for Discovery of Indole Derivatives as Potent DNA Gyrase ATPase Inhibitors Active against Mycobacterium tuberculosis and Hit Validation by Biological Assays.

Mycobacterium tuberculosis is the single most important global infectious disease killer and a World Health Organization critical priority pathogen for development of new antimicrobials. M. tuberculosis DNA gyrase is a validated target for anti-TB agents, but those in current use target DNA breakage-reunion, rather than the ATPase activity of the GyrB subunit. Here, virtual screening, subsequently validated by whole-cell and enzyme inhibition assays, was applied to identify candidate compounds that inhibit M. tuberculosis GyrB ATPase activity from the Specs compound library. This approach yielded six compounds: four carbazole derivatives (1, 2, 3, and 8), the benzoindole derivative 11, and the indole derivative 14. Carbazole derivatives can be considered a new scaffold for M. tuberculosis DNA gyrase ATPase inhibitors. IC50 values of compounds 8, 11, and 14 (0.26, 0.56, and 0.08 μM, respectively) for inhibition of M. tuberculosis DNA gyrase ATPase activity are 5-fold, 2-fold, and 16-fold better than the known DNA gyrase ATPase inhibitor novobiocin. MIC values of these compounds against growth of M. tuberculosis H37Ra are 25.0, 3.1, and 6.2 μg/mL, respectively, superior to novobiocin (MIC > 100.0 μg/mL). Molecular dynamics simulations of models of docked GyrB:inhibitor complexes suggest that hydrogen bond interactions with GyrB Asp79 are crucial for high-affinity binding of compounds 8, 11, and 14 to M. tuberculosis GyrB for inhibition of ATPase activity. These data demonstrate that virtual screening can identify known and new scaffolds that inhibit both M. tuberculosis DNA gyrase ATPase activity in vitro and growth of M. tuberculosis bacteria.

Antibacterial and Cytotoxicity of Extracts and Isolated Compounds from Artemisia abyssinica: A Combined Experimental and Computational Study.

Artemisia abyssinica is a widely cultivated hedge plant in Ethiopia. Traditionally, they have been used to treat a variety of health conditions, including intestinal problems, infectious diseases, tonsillitis, and leishmaniasis. Silica gel chromatographic separation of the methanol and ethyl acetate extracts of the leaves, roots, and stem barks of A. abyssinica led to the isolation of 12 compounds, labeled as 1-12. Among these, compounds 1, 3, 4, 5, and 7-11 are reported as new to the genus Artemisia. The extracts and isolated compounds from A. abyssinica were evaluated for their in vitro antibacterial activity against four bacterial strains: Streptococcus pyogenes, Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli, using the disc diffusion assay. All of the extracts displayed weak antibacterial activity, with inhibition zone diameters (IZDs) ranging from 6.10 ± 0.3 to 9.30 ± 0.20 mm. The isolated compounds, on the other hand, exhibited weak to moderate antibacterial activity, with IZDs ranging from 6.00 ± 0.300 to 13.50 ± 0.50 mm. The most potent antibacterial activity was observed for compound 6, which showed an IZD of 13.30 ± 0.50 mm against E. coli and 13.50 ± 0.50 mm against P. aeruginosa. This activity was comparable to that of the positive control ceftriaxone, which had IZDs of 14.1 ± 0.3 and 13.8 ± 0.5 mm against E. coli and P. aeruginosa, respectively. The in silico molecular docking analysis against DNA gyrase B revealed that compound 5 showed a higher binding affinity (-6.9 kcal/mol), followed by compound 10 (-6.7 kcal/mol) and compound 12 (-6.3 kcal/mol), whereas ciprofloxacin showed -7.3 kcal/mol. The binding affinities of compounds 5, 11, 10, and 9 were found to be -5.0, -4.3, -4.2, and -4.0 kcal/mol against S. aureus Pyruvate kinase, respectively, whereas ciprofloxacin showed a binding affinity of -4.9 kcal/mol, suggesting that compound 5 had a better binding affinity compared with ciprofloxacin. The effect of extracts of A. abyssinica was evaluated for cytotoxic activity against the breast cancer cell line (MCF-7) by the MTT assay. The extracts induced a decrease in cell viability and exerted a cytotoxic effect at a concentration of 20 μg/mL. The highest percent cell viability was observed for the methanol extract of the stem (92.9%), whereas the least was observed for the methanol extract of the root (34.5%). The result of the latter was significant compared with the positive control. The binding affinities of the isolated compounds were also assessed against human topoisomerase inhibitors IIβ. Results showed that compound 5 showed a binding affinity of -6.0 kcal/mol, followed by 11 (-5.4 kcal/mol), 10 (-5.0 kcal/mol), and 11 (-4.9 kcal/mol). Similar to ciprofloxacin, compounds 4, 5, 6, 9, 10, and 12 comply with Lipinski's rule of five. Overall, the comprehensive investigation of the chemical constituents and their biological activities reinforces the traditional medicinal applications of A. abyssinica and warrants further exploration of this plant as a source of novel therapeutic agents.

Molecular Docking and Molecular Dynamics Simulations of Synthesized Thiazole-Isatin-1,2,3-triazole Hybrids as Promising Inhibitors for DNA Gyrase and Sterol 14α-Demethylase.

In the present work, a new class of thiazole-isatin-1,2,3-triazole hybrids (5 a-5 p) and precursor alkyne hybrids (6 a-6 d) has been reported with their in-silico studies. After structural identifications using different spectroscopic technique such as FTIR, 1H and 13C NMR and HRMS, the synthesized hybrids were explored for their biological potential using molecular docking and molecular dynamics calculations. Molecular docking results revealed that compound 5 j showed maximum binding energy i. e. -10.3 and -12.6 kcal/mol against antibacterial and antifungal enzymes; 1KZN (E. coli) and 5TZ1 (C. albicans), respectively. Molecular dynamics simulations for the best molecule (100 ns) followed by PBSA calculations suggested a stable complex of 5 j with 5TZ1 with binding energy of -118.760 kJ/mol as compared to 1KZN (-94.593 kJ/mol). The mean RMSD values for the 1KZN with 5 j complex remained approximately 0.175 nm throughout all the time span of 100 ns in the production stages and is in the acceptable range. Whereas, 5TZ1 with 5 j complex, RMSD values exhibited variability within the range of 0.15-0.25 nm.