Gyrase Research Articles

YgiV promoter mutations cause resistance to cystobactamids and reduced virulence factor expression in Escherichia coli

Antimicrobial resistance is one of the major health threats of the modern world. Thus, new structural classes of antimicrobial compounds are needed in order to overcome existing resistance. Cystobactamids represent one such new compound class that inhibit the well-established target bacterial type II topoisomerases while exhibiting superior antibacterial and resistance-breaking properties. Understanding potential mechanisms of emerging resistances is crucial in the development of novel antibiotics as they directly impact the future therapeutic application and market success. Therefore, the frequency and molecular basis of cystobactamid resistance in Escherichia coli was analyzed. High-level resistant E. coli mutants were selected and found to harbor single nucleotide polymorphisms in the promotor region of the ygiV gene, causing an upregulation of the respective protein. These stable mutations are contrary to what was observed as a resistance genotype in the structurally related albicidins, where ygiV gene amplifications were identified as causing resistance. Overexpression of YgiV in the mutants was additionally amplified upon cystobactamid exposition, showing further adaptation to this compound class under treatment. YgiV binds cystobactamids with high binding affinity, thereby preventing their interaction with the antimicrobial targets topoisomerase IV and DNA gyrase. In addition, we observed a substantial impact of YgiV on in vitro gyrase activity by leading to increased DNA cleavage and concurrent reduction in the efficacy of cystobactamids in inhibiting gyrase supercoiling activity. Furthermore, we identified co-upregulation of membrane-modifying proteins, such as EptC, and the transcriptional regulator QseB. This presumably contributes to the observed reduced motility and fimbrial protein expression in resistant mutants, resulting in a reduced expression of virulence factors and potentially pathogenicity, associated with ygiV promotor mutations.

Design, synthesis, molecular docking, and antibacterial activity of novel amide-linked tetrahydrobenzothienopyrimidinone derivatives as potential DNA gyrase and topoisomerase IV inhibitors

Design, synthesis, molecular docking, and antibacterial activity of novel amide-linked tetrahydrobenzothienopyrimidinone derivatives as potential DNA gyrase and topoisomerase IV inhibitors

Screening for antimicrobial and antioxidant activities of quinazolinone based isoxazole and isoxazoline derivatives, synthesis and In silico studies.

Two novel series of quinazolinone based isoxazole and isoxazoline hybrid compounds were synthesized from 6-aminoquinazolinone as a key precursor. The title compounds were achieved in synthetic routes via propargylation and allylation reactions of the precursor followed by cyclization with various chloroximes. The new compounds 4a-g and 6a-g were screened for their antimicrobial activity against two Gram-positive bacteria, two Gram-negative bacteria and two fungi by employing Ampicillin and Itraconazole as standard reference. Among all, the 4-bromosubstituted analogues in isoxazole series 4d and in isoxazoline series 6d demonstrated potent activity against all bacterial and fungal strains compared to Ampicillin as well as Itraconazole. The MIC of these compounds were determined as 0.012μM. The antioxidant investigation revealed that compounds 4f and 6f with dimethyl substitution, exhibited significant activity. Their respective IC50 values were 1.28 ± 0.33, 1.39 ± 0.38µM and 1.07 ± 0.24, 1.10 ± 0.26µM, when compared to Ascorbic acid. The compounds 4g and 6g with dichloro substitution, exhibited promising results with IC50 values were 2.72 ± 0.34µM and 2.78 ± 0.41µM for 4g, and 2.24 ± 0.93µM and 2.45 ± 0.53µM for 6g, respectively. Their antimicrobial and antioxidant activities were authenticated by the molecular docking study against crystal structure of DNA gyrase and NADPH oxidase. The predicted ADME properties of these molecules progressed favourable drug-likeness properties.

Synthesis, Molecular Docking, and Biological Evaluation of Novel Indole-triazole Conjugates.

Indole-triazole conjugates have emerged as promising candidates for new drug development. Their distinctive structural characteristics, coupled with a wide array of biological activities, render them a captivating and promising field of research for the creation of novel pharmaceutical agents. This study aimed to synthesize indole-triazole conjugates to investigate the influence of various substituents on the functional characteristics of indole-triazole hybrids. It also aimed to study the binding modes of new hybrids with the DNA Gyrase using molecular docking studies. A new set of indole-triazole hybrids was synthesized and characterized using various physicochemical and spectral analyses. All hybrids underwent in-silico pharmacokinetic prediction studies. The antimicrobial efficacy of the hybrids was assessed using tube dilution and agar diffusion methods. Additionally, the in-vitro antioxidant activity of synthesized compounds was determined using the 1,1-diphenyl-2-picryl-hydrazyl free radical scavenging assay. Furthermore, in silico molecular docking studies were performed to enhance our comprehension of how the synthesized compounds interact at the molecular level with DNA gyrase. Pharmacokinetic predictions of synthesized hybrids indicated favourable pharmacokinetic profiles, and none of the compounds violated the Lipinski rule of five. Notably, compound 6, featuring a cyclohexanol substituent, demonstrated superior antimicrobial and antioxidant activity (EC50 value = 14.23 μmol). Molecular docking studies further supported the in vitro antioxidant and antimicrobial findings, revealing that all compounds adeptly fit into the binding pocket of DNA Gyrase and engaged in interactions with crucial amino acid residues. In summary, our research underscores the efficacy of molecular hybridization in shaping the physicochemical, pharmacokinetic, and biological characteristics of novel indole-triazole derivatives.

Efficient RhB degradation and antimicrobial activity with molecular docking study of polymers doped ZnSe nanostructure

A facile coprecipitation approach was adopted to synthesize zinc selenide (ZnSe) doped with a fixed amount (3 wt%) of cetyltrimethylammonium bromide (CTAB) and different concentrations (2 and 4 wt%) of eudragit to form ternary nanostructure (NSs). Eud and CTAB inhibit the dimension and reduce the rate of recombination of NSs to intensify catalytic performance against rhodamine B (RhB) and bactericidal action against MDR Staphylococcus aureus (S. aureus). Doped ZnSe increase active sites, porosity, and surface area to enhance the degradation of RhB dye and antimicrobial efficacy to kill pathogenic S. aureus. Assessment of 4 wt% Eud/CTAB exhibited effective performance for degradation of RhB and bactericidal potential highlights an impressive 94.3 % degradation efficiency and 8.85 ± 0.05 mm of the inhibition zone against MDR S. aureus. Computational molecular docking studies suggest that NSs, such as Eud/CTAB-doped ZnSe, have the ability to inhibit the DNA gyrase enzyme in MDR S. aureus.

How Do Gepotidacin and Zoliflodacin Stabilize DNA Cleavage Complexes with Bacterial Type IIA Topoisomerases? 1. Experimental Definition of Metal Binding Sites

One of the challenges for experimental structural biology in the 21st century is to see chemical reactions happen. Staphylococcus aureus (S. aureus) DNA gyrase is a type IIA topoisomerase that can create temporary double-stranded DNA breaks to regulate DNA topology. Drugs, such as gepotidacin, zoliflodacin and the quinolone moxifloxacin, can stabilize these normally transient DNA strand breaks and kill bacteria. Crystal structures of uncleaved DNA with a gepotidacin precursor (2.1 Å GSK2999423) or with doubly cleaved DNA and zoliflodacin (or with its progenitor QPT-1) have been solved in the same P61 space-group (a = b ≈ 93 Å, c ≈ 412 Å). This suggests that it may be possible to observe the two DNA cleavage steps (and two DNA-religation steps) in this P61 space-group. Here, a 2.58 Å anomalous manganese dataset in this crystal form is solved, and four previous crystal structures (1.98 Å, 2.1 Å, 2.5 Å and 2.65 Å) in this crystal form are re-refined to clarify crystal contacts. The structures clearly suggest a single moving metal mechanism—presented in an accompanying (second) paper. A previously published 2.98 Å structure of a yeast topoisomerase II, which has static disorder around a crystallographic twofold axis, was published as containing two metals at one active site. Re-refined coordinates of this 2.98 Å yeast structure are consistent with other type IIA topoisomerase structures in only having one metal ion at each of the two different active sites.

Multidrug tolerance conferred by loss-of-function mutations in anti-sigma factor RshA of Mycobacterium abscessus.

Low-level drug resistance in noncanonical pathways can constitute steppingstones toward acquisition of high-level on-target resistance mutations in the clinic. To capture these intermediate steps in Mycobacterium abscessus (Mab), we performed classic mutant selection experiments with moxifloxacin at twofold its minimum inhibitory concentration (MIC) on solid medium. We found that low-level resistance emerged reproducibly as loss-of-function mutations in RshA (MAB_3542c), an anti-sigma factor that negatively regulates activity of SigH, which orchestrates a response to oxidative stress in mycobacteria. Since oxidative stress is generated in response to many antibiotics, we went on to show that deletion of rshA confers low to moderate resistance-by measure of MIC-to a dozen agents recommended or evaluated for the treatment of Mab pulmonary infections. Interestingly, this moderate resistance was associated with a wide range of drug tolerance, up to 1,000-fold increased survival of a ΔrshA Mab mutant upon exposure to several β-lactams and DNA gyrase inhibitors. Consistent with the putative involvement of the SigH regulon, we showed that addition of the transcription inhibitor rifabutin (RBT) abrogated the high-tolerance phenotype of ΔrshA to representatives of the β-lactam and DNA gyrase inhibitor classes. In a survey of 10,000 whole Mab genome sequences, we identified several loss-of-function mutations in rshA as well as non-synonymous polymorphisms in two cysteine residues critical for interactions with SigH. Thus, the multidrug multiform resistance phenotype we have uncovered may not only constitute a step toward canonical resistance acquisition during treatment but also contribute directly to treatment failure.

New enaminone derivatives of 6-hydroxy-4,7-dimethoxy-benzofuran-5-yl scaffold: Synthesis, antimicrobial and antioxidant activities, and molecular docking studies as potential DNA gyrase B and DHFR inhibitors

New enaminone derivatives of 6-hydroxy-4,7-dimethoxy-benzofuran-5-yl scaffold: Synthesis, antimicrobial and antioxidant activities, and molecular docking studies as potential DNA gyrase B and DHFR inhibitors

Aquificae overcomes competition by archaeal thermophiles, and crowding by bacterial mesophiles, to dominate the boiling vent-water of a Trans-Himalayan sulfur-borax spring.

Trans-Himalayan hot spring waters rich in boron, chlorine, sodium and sulfur (but poor in calcium and silicon) are known based on PCR-amplified 16S rRNA gene sequence data to harbor high diversities of infiltrating bacterial mesophiles. Yet, little is known about the community structure and functions, primary productivity, mutual interactions, and thermal adaptations of the microorganisms present in the steaming waters discharged by these geochemically peculiar spring systems. We revealed these aspects of a bacteria-dominated microbiome (microbial cell density ~8.5 × 104 mL-1; live:dead cell ratio 1.7) thriving in the boiling (85°C) fluid vented by a sulfur-borax spring called Lotus Pond, situated at 4436 m above the mean sea-level, in the Puga valley of eastern Ladakh, on the Changthang plateau. Assembly, annotation, and population-binning of >15-GB metagenomic sequence illuminated the numeral predominance of Aquificae. While members of this phylum accounted for 80% of all 16S rRNA-encoding reads within the metagenomic dataset, 14% of such reads were attributed to Proteobacteria. Post assembly, only 25% of all protein-coding genes identified were attributable to Aquificae, whereas 41% was ascribed to Proteobacteria. Annotation of metagenomic reads encoding 16S rRNAs, and/or PCR-amplified 16S rRNA genes, identified 163 bacterial genera, out of which 66 had been detected in past investigations of Lotus Pond's vent-water via 16S amplicon sequencing. Among these 66, Fervidobacterium, Halomonas, Hydrogenobacter, Paracoccus, Sulfurihydrogenibium, Tepidimonas, Thermus and Thiofaba (or their close phylogenomic relatives) were presently detected as metagenome-assembled genomes (MAGs). Remarkably, the Hydrogenobacter related MAG alone accounted for ~56% of the entire metagenome, even though only 15 out of the 66 genera consistently present in Lotus Pond's vent-water have strains growing in the laboratory at >45°C, reflecting the continued existence of the mesophiles in the ecosystem. Furthermore, the metagenome was replete with genes crucial for thermal adaptation in the context of Lotus Pond's geochemistry and topography. In terms of sequence similarity, a majority of those genes were attributable to phylogenetic relatives of mesophilic bacteria, while functionally they rendered functions such as encoding heat shock proteins, molecular chaperones, and chaperonin complexes; proteins controlling/modulating/inhibiting DNA gyrase; universal stress proteins; methionine sulfoxide reductases; fatty acid desaturases; different toxin-antitoxin systems; enzymes protecting against oxidative damage; proteins conferring flagellar structure/function, chemotaxis, cell adhesion/aggregation, biofilm formation, and quorum sensing. The Lotus Pond Aquificae not only dominated the microbiome numerically but also acted potentially as the main primary producers of the ecosystem, with chemolithotrophic sulfur oxidation (Sox) being the fundamental bioenergetic mechanism, and reductive tricarboxylic acid (rTCA) cycle the predominant carbon fixation pathway. The Lotus Pond metagenome contained several genes directly or indirectly related to virulence functions, biosynthesis of secondary metabolites including antibiotics, antibiotic resistance, and multi-drug efflux pumping. A large proportion of these genes being attributable to Aquificae, and Proteobacteria (very few were ascribed to Archaea), it could be worth exploring in the future whether antibiosis helped the Aquificae overcome niche overlap with other thermophiles (especially those belonging to Archaea), besides exacerbating the bioenergetic costs of thermal endurance for the mesophilic intruders of the ecosystem.

Spectroscopic analysis of wild medicinal desert plants from wadi sanor (beni-suef), Egypt, and their antimicrobial and antioxidant activities

Desert plants possess untapped potential for medicinal applications due to their rich phytochemical profiles. However, they need to be more explored. Thus, this study integrates advanced analytical, biochemical, and molecular techniques to investigate the phytochemical composition and biological activities (antimicrobial and antioxidant) of four desert plants (Pergularia tomentosa, Zygophyllum coccineum, Pulicaria undulata, and Ochradenus baccatus), collected from Wadi Sannor, Beni-Suef Governorate, Egypt, in March 2021. The volatile chemicals in the 70 % ethanol extracts of the selected plants were also analyzed using GC-MS. The extract exhibited strong antioxidant properties, as demonstrated by its FRAP (Ferric reducing ability of plasma) values, anti-lipid peroxidation, superoxide anion scavenging activity, and DPPH scavenging activity. Additionally, plants extracts showed high antimicrobial activities against seven pathogens, including three Gram-negative bacteria (Pseudomonas aeruginosa, Salmonella typhimurium, Escherichia coli) and four Gram-positive bacteria (Staphylococcus saprophyticus, Staphylococcus epidermidis, Enterococcus faecalis, Streptococcus salivarius). Lastly, molecular docking was conducted for cis-vaccenic acid, (E)-9-octadecenoic acid, the cyclohepta[b]furan-2-one scaffold, and URS-20(30)-en-3-ol against both the thymidylate kinase enzyme and the active sites of E. coli DNA gyrase. The results from the molecular docking studies showed a strong correlation with the biological data. Moreover, these compounds exhibited good, proposed absorption, distribution, metabolism, and excretion–toxicity (ADMET) profiles. Our study highlights the potential of P. tomentosa, Z. coccineum, P. undulata, and O. baccatus for future medical applications and the development of new pharmaceuticals derived from desert flora.

A Synthetic Route Towards Spiro Indanone Fused Pyrano[2,3‐c]Chromene Derivatives via Oxa–Diels–Alder Reaction: Computational Investigation, Antibacterial Evaluation and Molecular Docking Studies as Potential DNA Gyrase Inhibitors

ABSTRACTA highly efficient method for the synthesis of 2′H‐spiro[indene‐2,3′‐pyrano[2,3‐c]chromene] derivatives 20(a–s) has been developed involving oxa–Diels–Alder reaction as the key step under conventional conditions in good to excellent yields. The compounds were all characterized using 1H, 13C NMR, HRMS, and X‐ray crystallography. The present study employs DFT to validate the reaction pathway. In vitro antibacterial assay of all the synthesized derivatives was evaluated against Gram‐negative Escherichia coli and Gram‐positive Staphylococcus aureus bacterial strains. Compound 20e was found to be the most potent molecule with ZI of 19 mm and MIC of 16 μg mL−1 in E. coli and ZI of 14 mm and MIC of 32 μg mL−1 in S. aureus. Additionally, 20e demonstrated a strong inhibition of DNA gyrase in silico, with a binding affinity of −9.3 and − 9.0 kcal/mol in E. coli and S. aureus respectively. Also, significant pharmacokinetic, physicochemical, and drug‐like properties of the spirocyclic compounds were further corroborated by ADME investigations. Hence, these new series of spiro indanone fused pyrano[2,3‐c]chromene derivatives may be potent druggable antibacterial agents in future.

The leaf essential oils of Meiogyne virgata (Blume) Miq., M. vietnamica Jaikhamseub, T.A.Le & Chaowasku, and Orophea polycarpa A.DC.: Chemical composition, antimicrobial activity, molecular docking, and toxicity profiling

The present study aims to describe the chemical composition of essential oils from three Vietnamese Annonaceae species, Meiogyne virgata, M. vietnamica, and Orophea polycarpa, and their antimicrobial activity. Essential oils were extracted by hydro-distillation. From the GC-FID/MS (gas chromatography-flame ionization detection and mass spectrometry) analysis, the leaf essential oil of M. virgata was reported to contain the major compound germacrene D (42.48%). Spathulenol (24.51%), bicyclogermacrene (18.58%), β-selinene (11.14%), and germacrene D (8.20%) can be seen as the main compound in M. vietnamica leaf essential oil. α-Phellandrene (39.35%), bicyclogermacrene (13.07%), β-phellandrene (10.87%), and limonene (8.27%) represented O. polycarpa leaf essential oil. Essential oil of M. virgata leaves exhibited strong antimicrobial activity against the Gram (+) bacterium Bacillus subtilis ATCC 5230, the Gram (-) bacterium Escherichia coli ATCC 8739, and the fungus Aspergillus niger ATCC 9587 with the same MIC value of 16 μg/mL. The docking method showed that germacrene D has the ΔGbinding (binding affinity) values of –6.68, –5.265, and –5.602 kcal/mol with the proteins E. coli DNA gyrase, B. subtilis TasA, and A. niger PhyA, respectively. Alkyl and pi-alkyl interactions are the main contributors to the binding affinity between the studied proteins and ligands. Furthermore, germacrene D is predicted to have low toxicity and is not active against any of the considered organ targets.

In-vitro and in-silico studies based discovery of 2-aryl-N-(4-morpholinophenyl)thiazol-4-amines as promising DNA gyrase inhibitors

Background: DNA gyrase is an important enzyme for the survival of bacteria. Many DNA gyrase inhibitors are in clinical practice. However, these inhibitors also encompass certain toxic and drug/food interactions. This warrants the development of a new template as DNA gyrase inhibitors. Therefore, this study aimed to deliver morpholine-based thiazoles (5a-5l) as safer DNA gyrase inhibitors.Methods: The 5a-5l were prepared by reacting compound 3 with various aryl thioamides. The structures of 5a-5l were ascertained by their spectral records. The 5a-5l were subjected to their antibacterial activity potential (serial plate dilution method), DNA gyrase inhibiting activity, and toxicity analysis (MTT assay) against HepG2 & Vero cell lines. The in-silico studies (pharmacokinetic parameters and molecular docking) of 5a-5l were likewise performed.Results: It was surprisingly observed that the MIC values of 5a-5l were equal to the MIC values of ciprofloxacin (12.5 µg/ml) against the tested bacteria, whereas the DNA gyrase inhibitory activity (IC50 in µg/ml) of 5h (3.52), 5g (3.76), 5f (3.88), 5e (4.08), 5l (4.11), 5b (4.28), 5k (4.28), 5i (4.30), and 5d (4.32) was equal/better than ciprofloxacin (4.32). The MTT assay also implied the non-cytotoxic nature of 5a-5l against HepG2 & Vero cell lines up to 200 µg/ml concentration. The docking outcomes indicated a similar binding pattern of 5a-5l and ciprofloxacin at the active site of DNA gyrase, wherein 5a-5l displayed a better binding affinity for the active site. The in-silico toxicity data employing the ProTox-II web server indicated no hepatotoxicity, carcinogenicity, immunotoxicity, mutagenicity, or cytotoxic effect of 5a-5l. Also, the SwissADME software supported the drug-likeliness properties and high gastrointestinal absorption of 5a-5l.Conclusion: Compounds 5h, 5g, 5f, 5e, 5l, 5b, 5k, 5i, and 5d are potent DNA gyrase inhibitors with promising safety profiles.Keywords: Discovery; Morpholine; Thiazole; DNA gyrase; MTT assay; Docking

Ligand-based pharmacophore modeling targeting the fluoroquinolone antibiotics to identify potential antimicrobial compounds

Antibiotic resistance presents a serious challenge to global healthcare, making the discovery of new therapeutic agents crucial. In this study, we used pharmacophore modeling and virtual screening to identify potential lead compounds against drug-resistant bacteria. We developed a shared feature pharmacophore (SFP) map using four antibiotics—Ciprofloxacin, Delafloxacin, Levofloxacin, and Ofloxacin—and generated a drug library of 160,000 compounds from ZINCPharmer based on these features, which included hydrophobic areas, hydrogen bond acceptors (HBA), hydrogen bond donors (HBD), and aromatic moieties (Ar). Through virtual screening, we identified 25 potential drug compounds as hits, with fit scores ranging from 97.85 to 116 and RMSD values from 0.28 to 0.63. These hits were then subjected to molecular docking against the DNA gyrase subunit A protein (PDB ID: 4DDQ), with ciprofloxacin as a control. The top five compounds—ZINC09133461, ZINC03791737, ZINC21983587, ZINC26469742, and ZINC26740199—achieved the highest docking scores, ranging from − 7.3 to − 7.4 kcal/mol and ciprofloxacin − 7.3 kcal/mol. After evaluating the drug-likeness of these compounds using Lipinski’s rule and analyzing their physicochemical properties, ZINC26740199 emerged as the most promising lead, offering hope in the fight against antibiotic resistance. Furthermore, molecular scaffold analysis revealed key similarities between ZINC26740199 and Ciprofloxacin, particularly in aromatic rings, hydrophobic regions, and hydrogen bond acceptors. These features suggest its potential as an effective antimicrobial agent, though further laboratory studies are needed to confirm its efficacy.

Synthesis, Biological Evaluation, andMolecular Docking Studies of Indole-Based Heterocyclic Scaffolds as Potential Antibacterial Agents.

This study aimed to synthesize C3-indole derivatives linked to various heterocyclic scaffolds, including thiophenes, thiazolidine-4-ones, and 1,3,4-thiadiazoles, via the reaction of ethylthioacetanilide 2 with different α-haloketones.The structures of the target compounds were established using 1H and 13C nuclear magnetic resonance spectroscopy, mass spectrometry, infrared spectroscopy, and elemental analysis. The synthesized compounds were tested for antimicrobial activity against different microbes: S. aureus ATCC 6538 (Gram-positive bacteria), E. coli ATCC 25933 (Gram-negative bacteria), C. albicans ATCC 10231 (yeast), and fungi (A. niger NRRL-A326). Thiophene 6a, thiazolidine-4-one 8, and compound 10d exhibited the highest antimicrobial activities. The molecular docking study showed that compounds 2, 4, 6a, and 6c had good binding energy and favorable binding modes of interactions with the DNA gyrase B enzymes (PDB: 3U2D) and (PDB: 1S14). The results showed that the NH group of the indole in compounds 2 and 4, together with the nitrile group (CN), played an important role in inhibiting DNA gyrase B of S. aureus, PDB: 3U2D. Furthermore, the NH of the indole ring, together with the ethylamino group of compound 2, was crucial in inhibiting DNA gyrase B of E. coli, PDB: 1S14. These results could inspire further development of indole derivatives as antimicrobial drugs.

Enhancing antibacterial efficacy through macrocyclic host complexation of fluoroquinolone antibiotics for overcoming resistance

The use of supramolecular assemblies in pharmaceuticals has garnered significant interest. Recent studies have shown that the activities of antibacterial agents can be enhanced through complexation with cyclic oligomers and metal ions. Notably, these complexes sometimes possess greater therapeutic properties than the parent drugs. To develop microbiologically potent supramolecular drugs, the complexation of macrocyclic hosts with fluoroquinolone (FQ) antibiotics was investigated. FQs are a successful family of antibiotics that target the bacterial enzymes DNA gyrase and DNA topoisomerase IV, leading to bacterial cell death through the inhibition of DNA synthesis. However, antibiotic resistance resulting from the repeated use of FQs over time has limited their effectiveness against resistant pathogens. To overcome this issue, the encapsulation of FQs in polyphenolic macrocycles was investigated. This study highlights resorcinarene, a polyphenolic host with antibacterial properties, and its ability to chemically interact with FQs. The inclusion complexation process was analyzed using NMR and FTIR techniques. The binding constants determined by 1H-NMR titration revealed that levofloxacin forms more stable complexes with resorcinarene than with β-cyclodextrin, which aligned with MD simulations. Assessment of the geometric characteristics of the inclusion complexes using 2D NMR analysis confirmed that different moieties of various FQs can fit into a single host cavity and improve activity against gram-negative bacteria. Overall, these findings suggest that encapsulation in polyphenolic macrocycles is a promising strategy for utilizing FQs against antibiotic-resistant bacteria.

Revolutionizing Quinolone Development for DNA Gyrase Targeting; Discovering the Promising Approach to Fighting Microbial Infections

Abstract: DNA gyrase is a type II topoisomerase enzyme that can cause negative supercoiling in DNA by using the energy produced by ATP hydrolysis. There are two main types of topoi-somerases: type I and type II. Type I enzymes cut a single strand of DNA and are further clas-sified as type IA if they connect to a 5′ phosphate of DNA, or type IB if they link to a 3′ phos-phate. Type II topoisomerases break both strands, creating a staggered double-strand break. Antimicrobial resistance is a major concern for the global healthcare system. Resistance is the ability of microorganisms to neutralize and withstand antimicrobial drugs previously used to treat microbial infections. Some known classes of DNA gyrase inhibitors are coumarins, cyclo-thialidines, and quinolones. Antimicrobial medicines such as quinolones have been widely used to treat microbiological diseases. However, the increased use of quinolones has led to the emer-gence of quinolone-resistant bacteria, which poses a serious risk to public health. Microorgan-isms can cause resistance due to changes in the target enzymes, DNA gyrase, and topoisomerase IV, which are responsible for transcription and DNA replication. Additionally, differences in drug entry and efflux may also play a role in resistance. Plasmids that produce the Qnr protein can mediate resistance to quinolones by protecting the quinolone targets from inhibition. This review aims to revolutionize the discovery of quinolone-based antibiotics, specifically targeting DNA gyrase, a critical enzyme in bacterial DNA replication, to enhance the efficacy and spec-ificity of anti-microbail agents against microbial infections.

Role of DNA Double-Strand Break Formation in Gyrase Inhibitor-Mediated Killing of Nonreplicating Persistent Mycobacterium tuberculosis in Caseum.

Tuberculosis is the leading cause of mortality by infectious agents worldwide. The necrotic debris, known as caseum, which accumulates in the center of pulmonary lesions and cavities is home to nonreplicating drug-tolerant Mycobacterium tuberculosis that presents a significant hurdle to achieving a fast and durable cure. Fluoroquinolones such as moxifloxacin are highly effective at killing this nonreplicating persistent bacterial population and boosting TB lesion sterilization. Fluoroquinolones target bacterial DNA gyrase, which catalyzes the negative supercoiling of DNA and relaxes supercoils ahead of replication forks. In this study, we investigated the potency of several other classes of gyrase inhibitors against M. tuberculosis in different states of replication. In contrast to fluoroquinolones, many other gyrase inhibitors kill only replicating bacterial cultures but produce negligible cidal activity against M. tuberculosis in ex vivo rabbit caseum. We demonstrate that while these inhibitors are capable of inhibiting M. tuberculosis gyrase DNA supercoiling activity, fluoroquinolones are unique in their ability to cleave double-stranded DNA at low micromolar concentrations. We hypothesize that double-strand break formation is an important driver of gyrase inhibitor-mediated bactericidal potency against nonreplicating persistent M. tuberculosis populations in the host. This study provides general insight into the lesion sterilization potential of different gyrase inhibitor classes and informs the development of more effective chemotherapeutic options against persistent mycobacterial infections.

Screening of synthesized perimidine compounds for the assessment of antimicrobial potential: in-vitro and in-silico molecular docking and molecular dynamics simulation studies

Presently, antimicrobial resistance is a major and worldwide concern due to high rate of mutation in microorganisms, widespread use, lack of efficacy of drugs, and low drug discovery rate. Considering the importance of N-heterocycles as antibiotics, perimidine derivatives 3(a–v) have been synthesized via cyclocondensation reaction of 1,8-diaminonaphthalene and aryl aldehydes. Further, the synthesized perimidines 3(a–v) were screened as potent antimicrobial agents via in-vitro, in-silico, ADME and MD simulation studies. All 22 derivatives 3(a–v) were studied against two-gram +ve (E. coli and P. aeruginosa), two-gram −ve (S. aureus and B. subtilis), and two fungal (A. niger and S. cerevisiae) strains using ciprofloxacin and fluconazole as reference drugs. The in-vitro study results showed that compounds 3e, 3h, 3l, and 3m were the most potent against S. aureus and 3(a–d), 3(g–i), and 3s were the most active against B. subtilis as compared to the standard. Furthermore, molecular docking studies were performed against Dihydrofolate reductase (PDB Id: 3SRW) from S. aureus, DNA gyrase (PDB Id: 4DUH) from E. coli, and ERG11 gene (PDB Id: 4LXJ). Compounds 3f, 3f/3m, and 3o were found to bind efficiently with the highest binding energy − 10.6, − 9.6, and − 11.3kcal/mol depicting the potential inhibitor of 3SRW, 4DUH, and 4LXJ receptor protein, respectively. The drug-likeness properties of compounds were studied using SwissADME program. To further validate these findings, molecular dynamics simulations were conducted to evaluate their binding stability. From simulation studies, it was observed that all the shortlisted compounds displayed stable binding within the active site of the selected proteins.Graphical abstract

Phyto-mediated fabrication of cerium oxide nanoparticles using Mollugo oppositifolia L aqueous leaf extract: Antibacterial, antitonicity, and molecular docking studies

The use of bio-processes for synthesizing metal oxide nanoparticles represents a forefront area of research in nanotechnology. This study introduces a rapid and eco-friendly approach for producing cerium oxide nanoparticles (CeO2 NPs) utilizing the aqueous extract of Mollugo oppositifolia L leaves as a catalyst. The synthesized CeO2 NPs underwent comprehensive characterization through scanning electron microscopy (SEM), X-ray diffraction (XRD), ultraviolet–visible spectroscopy (UV–Vis), and Fourier transform infrared spectroscopy (FT-IR). Furthermore, the antimicrobial activity of the CeO2 NPs was assessed in vitro against various bacterial strains, demonstrating a concentration-dependent inhibition zone when exposed to concentrations ranging from 25 to 100 μg/mL. Antitonicity activity results of the synthesized CeO2 NPs revealed significant activity. Further molecular docking studies also revealed that the synthesized CeO2 NPs have better docking ability compared to control Streptomycin in E. coli topoisomerase II DNA gyrase B (PDB ID:1KZN).