DNA Gyrase Inhibitors Research Articles

Evaluation of efficacy and safety of lascufloxacin for nursing and healthcare associated pneumonia: single-arm, open-label clinical trial: A study protocol.

Lascufloxacin hydrochloride (LSFX) is a quinolone antibiotic that inhibits DNA gyrase and topoisomerase IV of bacteria, it is anticipated to minimize antibiotic resistance in bacteria. It exhibits antibacterial activity against a relatively wide range of bacterial species, including anaerobic bacteria, and its efficacy and safety against community-acquired pneumonia have been shown; however, its efficacy and safety against nursing and healthcare associated pneumonia (NHCAP) have not been verified. Here, a single-arm, open-label, uncontrolled study was conducted in which LSFX was administered to patients with NHCAP at 24 facilities. The research subjects (77 cases) were orally administered 75 mg of LSFX once a day for 7 days. The primary endpoint was the clinical efficacy at the time of test of cure (TOC) (TOC; 5-10 days after the end of LSFX administration), while the secondary endpoints were the efficacy at the time of end of treatment, early clinical efficacy, microbiological efficacy at the time of TOC and end of treatment, and safety evaluation of LSFX. NHCAP is a common pneumonia in clinical settings and a notable pneumonia whose mortality is high compared to community-acquired pneumonia. The present study showed the efficacy and safety of LSFX against NHCAP, which could lead to a larger number of therapeutic options for NHCAP.

Coumarin derivatives with potential anticancer and antibacterial activity: Design, synthesis, VEGFR-2 and DNA gyrase inhibition, and in silico studies.

A series of coumarin derivatives were designed, synthesized, and evaluated for their antiproliferative activity. Compound 3e exhibited significant antiproliferative activity and was further evaluated at five doses at the National Cancer Institute. It effectively inhibited vascular endothelial growth factor receptor-2 (VEGFR-2) with an IC50 value of 0.082 ± 0.004 µM compared with sorafenib. While compound 3e significantly downregulated total VEGFR-2 and its phosphorylation, it markedly reduced the HUVEC's migratory potential, resulting in a significant disruption in wound healing. Furthermore, compound 3e caused a 22.51-fold increment in total apoptotic level in leukemia cell line HL-60(TB) and a 6.91-fold increase in the caspase-3 level. Compound 3e also caused cell cycle arrest, mostly at the G1/S phase. Antibacterial activity was evaluated against Gram-positive and Gram-negative bacterial strains. Compound 3b was the most active derivative, with the same minimum inhibitory concentration and minimum bactericidal concentration value of 128 μg/mL against K. pneumonia and high stability in mammalian plasma. Moreover, compounds 3b and 3f inhibited Gram-negative DNA gyrase with IC50 = 0.73 ± 0.05 and 1.13 ± 0.07 µM, respectively, compared to novobiocin with an IC50 value of 0.17 ± 0.02 µM. The binding affinity and pattern of derivative 3e toward the VEGFR-2 active site and compounds 3a-c and 3f in the DNA gyrase active site were evaluated using molecular modeling. Overall, ADME studies of the synthesized coumarin derivatives displayed promising pharmacokinetic properties.

Design and synthesis of some novel hybrid molecules based on 4-thiazolidinone bearing pyridine-pyrazole scaffolds: molecular docking and molecular dynamics simulations of its major constituent onto DNA gyrase inhibition.

Due to multidrug resistance, microbial infections have become significant on a global level. As infections caused by several resistant bacteria and fungi severely harm mankind, scientists have developed new antibiotics to combat these infections. In order to develop novel antimicrobial agents, a series of 4-thiazolidinone-based 5-arylidene hybrids (5a-o) have been designed and synthesized to evaluate their antibacterial and antifungal activities. For the determination of the structure of a novel synthesized hybrid, various spectral techniques, e.g., IR, 1H NMR, 13C NMR, and Mass spectroscopy, were used. Two bacterial gram-negative (Escherichia coli and Pseudomonas aeruginosa), two gram-positive strains (Staphylococcus aureus and Streptococcus pyogenes), and one fungal strain (Candida albicans) were used to evaluate antimicrobial activity. Compounds 5c, 5g, and 5i were effective due to their MIC values of 62.5μg/mL against tested bacterial strains (S. pyogenes (5c), P. aeruginosa (5g), and E. coli (5i), respectively.) and 250μg/mL against C. albicans fungal strains, respectively. Additionally, molecular docking and 100ns molecular dynamic simulations were carried out to investigate the stability of molecular contacts and to establish how the newly synthesized inhibitors fit together in the most stable conformations.

Developments in Non-Intercalating Bacterial Topoisomerase Inhibitors: Allosteric and ATPase Inhibitors of DNA Gyrase and Topoisomerase IV.

Increases in antibiotic usage and antimicrobial resistance occurrence have caused a dramatic reduction in the effectiveness of many frontline antimicrobial treatments. Topoisomerase inhibitors including fluoroquinolones are broad-spectrum antibiotics used to treat a range of infections, which stabilise a topoisomerase-DNA cleavage complex via intercalation of the bound DNA. However, these are subject to bacterial resistance, predominantly in the form of single-nucleotide polymorphisms in the active site. Significant research has been undertaken searching for novel bioactive molecules capable of inhibiting bacterial topoisomerases at sites distal to the fluoroquinolone binding site. Notably, researchers have undertaken searches for anti-infective agents that can inhibit topoisomerases through alternate mechanisms. This review summarises work looking at the inhibition of topoisomerases predominantly through non-intercalating agents, including those acting at a novel allosteric site, ATPase domain inhibitors, and those offering unique binding modes and mechanisms of action.

Computational and Preclinical Prediction of the Antimicrobial Properties of an Agent Isolated from Monodora myristica: A Novel DNA Gyrase Inhibitor

The African nutmeg (Monodora myristica) is a medically useful plant. We, herein, aimed to critically examine whether bioactive compounds identified in the extracted oil of Monodora myristica could act as antimicrobial agents. To this end, we employed the Schrödinger platform as the computational tool to screen bioactive compounds identified in the oil of Monodora myristica. Our lead compound displayed the highest potency when compared with levofloxacin based on its binding affinity. The hit molecule was further subjected to an Absorption, Distribution, Metabolism, Excretion (ADME) prediction, and a Molecular Dynamics (MD) simulation was carried out on molecules with PubChem IDs 529885 and 175002 and on three standards (levofloxacin, cephalexin, and novobiocin). The MD analysis results demonstrated that two molecules are highly compact when compared to the native protein; thereby, this suggests that they could affect the protein on a structural and a functional level. The employed computational approach demonstrates that conformational changes occur in DNA gyrase after the binding of inhibitors; thereby, this resulted in structural and functional changes. These findings expand our knowledge on the inhibition of bacterial DNA gyrase and could pave the way for the discovery of new drugs for the treatment of multi-resistant bacterial infections.

Re-evaluation of critical concentrations of antituberculosis fluoroquinolones in the Mycobacteria Growth Indicator Tube 960 system.

Fluoroquinolones (FQs) have substantial activity against the Mycobacterium tuberculosis complex (MTBc) by preventing bacterial DNA synthesis through DNA gyrase inhibition. The reference standard for FQ-resistance testing is phenotypic drug-susceptibility testing (pDST) based on growth inhibition of MTBc in drug-containing Mycobacteria Growth Indicator Tube system (MGIT) media at a critical concentration (CC) that differentiates phenotypically wild-type from nonwild-type MTBc and at a clinical breakpoint that identifies strains that will likely still respond to treatment at higher doses. Despite the recent introduction of powerful new TB drugs, highly sensitive detection of clinically defined FQ resistance remains key. In this study, we re-evaluated the current WHO-recommended CCs of Lfx (1.0 mg/ml), Mfx (0.25 mg/ml), Gfx (0.25 μg/ml), and the nowadays, obsolete CC of Ofx (2.0 mg/ml) for MGIT, using 147 MTBc isolates with known gyrA and gyrB sequences including both high-and low-level FQ resistance-conferring mutants. We tested a wide range of drug concentrations covering the current and former/obsolete WHO-recommended CCs for FQs and some intermediate concentrations to challenge the current WHO-recommended CCs. The specificity of all four CCs was 100%. The sensitivities varied: 92.4% for Ofx and Lfx, 85.7% for Mfx, and 83.2% for Gfx. Lowering the CC of Mfx to 0.125 mg/ml would allow to correctly classify all wild-type and mutant isolates while lowering the CC of Gfx to 0.125 mg/ml would still misclassify some gyrA/gyrB mutants as susceptible. Based on our findings, a minimal inhibitory concentration of 0.125 mg/ml on MGIT medium is a more appropriate CC for Mfx and probably also as a surrogate for overall FQ resistance in the MTBc.

Discovery and Hit-to-Lead Optimization of Benzothiazole Scaffold-Based DNA Gyrase Inhibitors with Potent Activity against Acinetobacter baumannii and Pseudomonas aeruginosa

We have developed compounds with a promising activity against Acinetobacter baumannii and Pseudomonas aeruginosa, which are both on the WHO priority list of antibiotic-resistant bacteria. Starting from DNA gyrase inhibitor 1, we identified compound 27, featuring a 10-fold improved aqueous solubility, a 10-fold improved inhibition of topoisomerase IV from A. baumannii and P. aeruginosa, a 10-fold decreased inhibition of human topoisomerase IIα, and no cross-resistance to novobiocin. Cocrystal structures of 1 in complex with Escherichia coli GyrB24 and (S)-27 in complex with A. baumannii GyrB23 and P. aeruginosa GyrB24 revealed their binding to the ATP-binding pocket of the GyrB subunit. In further optimization steps, solubility, plasma free fraction, and other ADME properties of 27 were improved by fine-tuning of lipophilicity. In particular, analogs of 27 with retained anti-Gram-negative activity and improved plasma free fraction were identified. The series was found to be nongenotoxic, nonmutagenic, devoid of mitochondrial toxicity, and possessed no ion channel liabilities.

Computer-aided structure-based optimization of 4,5,6,7-tetrahydrobenzo[d]thiazole-2,6-diamine derivatives as DNA gyrase B inhibitors

Here we report a theoretical-experimental study of 4,5,6,7-tetrahydrobenzo[d]thiazole-2,6-diamine derivatives that act as inhibitors of bacterial DNA gyrase B (GyrB).

Catalytic performance and antibacterial behaviour with molecular docking analysis of silver and polyacrylic acid doped graphene quantum dots.

In this research, a fixed concentration (3 wt%) of Ag/PAA and PAA/Ag doped graphene quantum dots (GQDs) were synthesized using the co-precipitation technique. A variety of characterization techniques were employed to synthesize samples to investigate their optical, morphological, structural, and compositional analyses, antimicrobial efficacy, and dye degradation potential with molecular docking analysis. GQDs have high solubility, narrow band gaps, and are suitable for electron acceptors and donors but show less adsorption and catalytic behavior. Incorporating polyacrylic acid (PAA) into GQDs increases the catalytic and antibacterial activities due to the carboxylic group (-COOH). Furthermore, introducing silver (Ag) increased the degradation of dye and microbes as it had a high surface-to-volume ratio. In addition, molecular docking studies were used to decipher the mechanism underlying the bactericidal action of silver and polyacrylic acid-doped graphene quantum dots and revealed inhibition of β-lactamase and DNA gyrase.

Virtual screening of novel pyridine derivatives as effective inhibitors of DNA gyrase (GyrA) of salmonella typhi

In a bid to discovering novel antibiotics to combat growing trend of multi-drug resistance strains of Salmonella typhi, 48 new pyridine derivatives with significant inhibitory activities against the aforementioned bacterium were subjected to molecular docking against DNA gyrase protease of the bacterium, drug likeness evaluation and pharmacokinetics profiling. All the 48 leads displayed better binding affinity values when compared with Amoxicillin, Ciprofloxacin, Ceftriaxone, Ampicillin, and chloramphenicol, the standard antibiotics used herein for quality assurance. Furthermore, the majority of the compounds were, however, screened out due to their poor pharmacokinetics profiles and drug-likeness. Only five compounds emerged as the most promising leads and they include C4 with binding affinity of -8.0 kcal/mol, C8 (-8.6 kcal/mol), C9 (-8.1 kcal/mol), C26 (-8.3 kcal/mol), and C27 (-8.0 kcal/mol). These compounds not only displayed better binding affinity when compared with the reference antibiotics but also exhibit different modes of interactions with the target protease of the bacterium making them more potent and drug like. Toxicity evaluation of the leads also revealed that the compounds are neither tumorigenic nor mutagenic. In view of the excellent binding affinity, high pharmacokinetics profile and positive drug-likeness of the novel ligands, we recommend these promising compounds for in vitro and in vivo studies in order to discover novel antibiotics that could curb the dangerous trend of multiple drug resistance by Salmonella typhi.

Synthesis, molecular simulation studies, in vitro biological assessment of 2-substituted benzoxazole derivatives as promising antimicrobial agents.

The 2-substituted benzoxazole derivatives are known to exhibit a wide spectrum of biological potential. Two series of novel benzoxazole derivatives containing 2-phenyl and 2-N-phenyl groups were synthesized, by following the green chemistry approach. All the newly synthesized derivatives were screened against gram-positive bacteria (Streptococcus pyogenes, Staphylococcus aureus), gram-negative bacteria (Pseudomonas aeruginosa, Escherichia coli) and the fungus (Aspergillus clavatus and Candida albicans). Most of these compounds have demonstrated potent antibacterial activities, especially against E. coli at 25 μg/mL, along with moderate antifungal activity. Among these, two compounds, 21 and 18, showed interesting antibacterial profile. Molecular docking studies suggested that the antibacterial activity can be linked to the inhibition of DNA gyrase. Overall, the study proposes that these biologically potent compounds can be considered for developing the next generation antimicrobial agents.

Synthesis and pharmacological evaluation of 1,3-diaryl substituted pyrazole based (thio)urea derivatives as potent antimicrobial agents against multi-drug resistant Staphylococcus aureus and Mycobacterium tuberculosis.

The urgent development of newer alternatives has been deemed a panacea for tackling emerging antimicrobial resistance effectively. Herein, we report the design, synthesis, and biological evaluation of 1,3-diaryl substituted pyrazole-based urea and thiourea derivatives as antimicrobial agents. Preliminary screening results revealed that compound 7a (3,4-dichlorophenyl derivative) exhibited potent activity against S. aureus (MIC = 0.25 μg mL-1) and compound 7j (2,4-difluorophenyl derivative) against Mycobacterium tuberculosis (MIC = 1 μg mL-1). Compounds 7a and 7j were non-toxic to Vero cells with a favorable selectivity index of 40 and 200, respectively, and demonstrated good microsomal stability. Compound 7a exhibited equipotent activity (MIC = 0.25 μg mL-1) against various multidrug-resistant strains of S. aureus, which include various strains of MRSA and VRSA, and elicited bacteriostatic properties. In an enzymatic assay, 7a effectively inhibited DNA gyrase supercoiling activity at a concentration of 8 times MIC. Further, molecular modeling studies suggested that compound 7a binds at the active site of DNA gyrase with good affinity.

Insight into DNA Gyrase Inhibition Using Quantitative Structure-Activity ‎Relationships and Structure-Based Drug Design Approaches

The emergence of certain bacterial strains resistant ‎to antibiotics has become a major public health ‎problem, hence the need to develop new antibiotic ‎molecules. Bacterial DNA gyrase, a type II DNA ‎topoisomerase found in all bacteria is a proven ‎target for antibacterial chemotherapy. Our objective ‎is designing novel DNA Gyrase inhibitors using ‎Quantitative Structure-Activity Relationships and ‎Structure-Based Drug Design Approaches. We used ‎bioinformatics tools, biological databases like PDB ‎‎(Protein DataBank), Binding Databases and ‎software’s like, MarvinView, MarvinSketch, PyMOL, ‎AutoDockTools-1.5.6. The 3D crystal structure of ‎DNA Gyrase was extracted from PDB (code: 4DHU) ‎and we characterized the active site. Using 83 ‎compounds with different Ki were extracted from ‎Binding Databases, we built and validated a QSAR ‎Model (PLS regression) and we confirmed the ‎interesting correlation between predicted and ‎experimental Ki (R2=0,843). Four molecules were ‎chosen to be docked into DNA Gyrase active site ‎using AutoDockTools. The compound which has the ‎low Ki (Benzimidazole urea analogue 5) shows more ‎binding affinity with score value of ΔG= -8,6 kcal/mol ‎than the others compounds. So, it would be very ‎interesting to synthesis this promising compound ‎and to test in vitro its antibacterial properties.‎

Synthesis, Structural Characterization and Biological Activity Evaluation of Novel Cu(II) Complexes with 3-(trifluoromethyl)phenylthiourea Derivatives.

Copper complexes with 1,3-disubstituted thiourea derivatives, all containing 3-(trifluoromethyl)phenyl tail and 1-alkyl/halogen-phenyl substituent, were synthesized. The experimental spectroscopic studies and theoretical calculation revealed that two ligands coordinate to Cu(II) in a bidentate fashion via thiocarbonyl S and deprotonated N atoms of thiourea moiety. Such monomers are characteristic of alkylphenylthiourea complexes, whereas the formation of a sandwich-type dimer is observed for halogeno derivatives. For the first time, the structural identifications of CuN2S2-based complexes using experimental and theoretical X-ray absorption near edge structure are demonstrated. The dimeric halogeno derivatives showed higher antimicrobial activity in comparison with alkylphenylthiourea complexes. The Cu(II) complex of 1-(4-chloro-3-nitrophenyl)-3-[3-(trifluoromethyl)phenyl]thiourea was active against 19 strains of methicillin-resistant Staphylococci (MIC = 2 µg/mL). This derivative acted as a dual inhibitor of DNA gyrase and topoisomerase IV isolated from Staphylococcus aureus. Additionally, complexes of halogenphenylthiourea strongly inhibited the growth of mycobacteria isolated from tuberculosis patients, even fourfold stronger than the reference isoniazid. The complexes exerted weak to moderate antitumor activity (towards SW480, SW620, and PC3) being non-toxic towards normal HaCaT cells.

An In-Silico Evaluation of Anthraquinones as Potential Inhibitors of DNA Gyrase B of Mycobacterium tuberculosis.

The World Health Organization reported that tuberculosis remains on the list of the top ten threats to public health worldwide. Among the main causes is the limited effectiveness of treatments due to the emergence of resistant strains of Mycobacterium tuberculosis. One of the main drug targets studied to combat M. tuberculosis is DNA gyrase, the only enzyme responsible for regulating DNA topology in this specie and considered essential in all bacteria. In this context, the present work tested the ability of 2824 anthraquinones retrieved from the PubChem database to act as competitive inhibitors through interaction with the ATP-binding pocket of DNA gyrase B of M. tuberculosis. Virtual screening results based on molecular docking identified 7122772 (N-(2-hydroxyethyl)-9,10-dioxoanthracene-2-sulfonamide) as the best-scored ligand. From this anthraquinone, a new derivative was designed harbouring an aminotriazole moiety, which exhibited higher binding energy calculated by molecular docking scoring and free energy calculation from molecular dynamics simulations. In addition, in these last analyses, this ligand showed to be stable in complex with the enzyme and further predictions indicated a low probability of cytotoxic and off-target effects, as well as an acceptable pharmacokinetic profile. Taken together, the presented results show a new synthetically accessible anthraquinone with promising potential to inhibit the GyrB of M. tuberculosis.

Development of pharmacophore model to identify potential DNA gyrase inhibitors

There is great concern in the medical community due to rapid increase in antibiotic resistance, causing 700,000 deaths annually worldwide. Therefore, there is paramount need to develop novel and innovative antibacterial agents active against resistant bacterial strains. DNA gyrase is a crucial enzyme in bacterial replication that is absent in eukaryotes, making it effective curative target for antibacterials. To identify potential DNA gyrase inhibitors by virtual screening of NCI database using a 3-step approach. A total of 271 compounds with known IC50 values against Escherichia coli DNA GyrA were selected to develop a pharmacophore model for dual screening approach to identify new potential hits from the NCI database. In the second step, the NCI database was also screened using in-house built NN-QSAR model. Molecular docking of common 5298 compounds screened from both methods were performed against E. coli DNA GyrA (PDB id- 6RKU), and 3004 compounds are reported to exhibit lower binding energies than ciprofloxacin (−6.77 Kcal/mol). The top three compounds (NCI371878, NCI371876 and NCI142159) reported with binding energy of −13.5, −13.19 and −13.03 Kcal/mol were further subjected to MD simulation studies for 100 ns supporting the stability of the docked complexes.

Discovery of novel 1,3,5-triazines as potent antibacterial agent against urinary tract infection-causing clinical isolates of Escherichia coli via inhibition of DNA Gyrase.

A novel series of 1,3,5-triazine-phenylthiazole-pyrazole derivatives were synthesized and subsequently tested for Escherichia coli DNA Gyrase inhibitory activity where they showed excellent inhibitory activity. The top-three ranked DNA gyrase inhibitor (4e, 4g and 4h) were further subjected to antibacterial and anti-biofilm activity against clinical isolates of resistant E.coli strains obtained from Urinary Tract Infection (UTI) patients (CREC81, CREC106, CREC163). Compound 4h was identified as most potent antibacterial agent in the above study. The compound 4h was further evaluated in murine model of E.coli UTI in BALB/c mice infected by transurethral injection of CREC106 strain. Results of the study suggest that compound 4h reduces bacterial load of CREC106 in the treated mice and found approximately equipotent to Novobiocin as standard.

Molecular Docking and Pharmacokinetic Studies of Some New pyridyl and hydrazinyl bearing thiazole Derivatives as Potential DNA gyrase Inhibitors

Molecular Docking and Pharmacokinetic Studies of Some New pyridyl and hydrazinyl bearing thiazole Derivatives as Potential DNA gyrase Inhibitors

A short hydrophobic peptide conjugated 3,5- disubstituted pyrazoles as antibacterial agents with DNA gyrase inhibition

Antimicrobial peptides (AMP) are found in majority of living organisms. Their mode of action is unique and different from the conventional antibiotics. Though several classes of antimicrobial peptides have been studied, their mechanism of action against microbes is not yet clearly understood, otherwise it would open up a solid background for further development of new pharmaceutical compounds. The present work describes the synthesis and evaluation of antimicrobial activity of peptide-pyrazole conjugates. The antibacterial potency of these conjugates was evaluated against both Gram positive and Gram negative bacterial strains, increased antibacterial efficacy was found in peptide-pyrazole conjugates compared to peptides alone and simple pyrazole compounds. A molecular docking study revealed that the ligand PH3, PH4, and PH10 is very potent against key proteins. Compounds PH3, PH4, and PH10 bind near the putative binding site of DNA gyrase with the docking score of -6.54, -8.2, and -7.09 kcal/mol.

Genomic potential of Streptomyces roseochromogenes NRRL 3504 for the production of specialized metabolites: analysis in silico

Streptomyces roseochromogenes NRRL 3504 is the only known producer of aminocoumarin antibiotic clorobiocin – an inhibitor of bacterial DNA-gyrase and topoisomerase IV. Sequencing of NRRL 3504 genome revealed a plethora of specialized metabolite biosynthetic gene clusters (BGCs) within the latter, attesting to the significant potential of this species for the production of various as-yet-unknown bioactive compounds. Here we report bioinformatic analysis of NRRL 3504 genome aimed to better understand what kind of small molecules this strain could produce and genetic mechanisms that may limit their production. In addition to the most commonly applied bioinformatic service for BGCs detection antiSMASH, we turned to alternative tools for secondary metabolome in silico analysis such as PRISM, DeepBGC, ARTS, SEMPI and GECCO. While different genome mining applications pointed to a common core set of BGCs within the NRRL 3504, each tool having its own algorithm of BGCs detection also discovered certain number of non-overlapping clusters. This was especially true for machine learning tool DeepBGC that unearthed the biggest number of BGCs. To summarize the obtained results we used BGCViz tool, which visualizes and integrates BGC annotations from various sources by using genomic coordinates. We discuss the genetic and structural diversity of the BGCs and outline the most interesting, in opinion, targets for further investigations. Most of the described BGCs are most likely silent due to very low or zero transcription. Therefore, it might be needed to find the ways to activate the transcription of the BGCs of interest. To this end, we mined NRRL 3504 genome for the orthologs of global regulatory genes known to be involved in regulation of specialized metabolism of S. coelicolor A3(2). We were able to identify almost all plausible global regulators of interest in NRRL 3504, implying that overall scheme of regulation of specialized metabolism in A3(2) and NRRL 3504 might be similar. Results of our work set the stage for a more detailed experimental scrutiny of silent specialized metabolome of NRRL 3504.