Pyrrolopyrimidine inhibitors of DNA gyrase B (GyrB) and topoisomerase IV (ParE), Part II: Development of inhibitors with broad spectrum, Gram-negative antibacterial activity

The growing resistance of bacteria to many antibiotics that have been in use for several decades has generated the need to discover new antibacterial agents with structural features qualifying them to overcome the resistance mechanisms. Thus, novel pyridothienopyrimidine derivatives (2a,b–a,b) were synthesized by a series of various reactions, starting with 3-aminothieno[2,3-b]pyridine-2-carboxamides (1a,b). Condensation of compounds 1a,b with cyclohexanone gave 1’H-spiro[cyclohexane-1,2’-pyrido[3’,2’:4,5]thieno[3,2-d]pyrimidin]-4’(3’H)-ones (2a,b), which in turn were utilized to afford the target 4-substituted derivatives (3a,b–8a,b). In vitro antibacterial activity evaluations of all the new compounds (2a,b–8a,b) were performed against six strains of Gram-negative and Gram-positive bacteria. The target compounds showed significant antibacterial activity, especially against Gram-negative strains. Moreover, the compounds (2a,b; 3a,b; 4a,b; and 5a,b) that exhibited potent activity against Escherichia coli were selected to screen their inhibitory activity against Escherichia coli topoisomerase II (DNA gyrase and topoisomerase IV) enzymes. Compounds 4a and 4b showed potent dual inhibition of the two enzymes with IC50 values of 3.44 µΜ and 5.77 µΜ against DNA gyrase and 14.46 µΜ and 14.89 µΜ against topoisomerase IV, respectively. In addition, docking studies were carried out to give insight into the binding mode of the tested compounds within the E. coli DNA gyrase B active site compared with novobiocin.

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Design, Synthesis, and Antibacterial Screening of Some Novel Heteroaryl-Based Ciprofloxacin Derivatives as DNA Gyrase and Topoisomerase IV Inhibitors

Pharmaceuticals ◽

10.3390/ph14050399 ◽

2021 ◽

Vol 14 (5) ◽

pp. 399

Author(s):

Lamya H. Al-Wahaibi ◽

Amer A. Amer ◽

Adel A. Marzouk ◽

Hesham A.M. Gomaa ◽

Bahaa G. M. Youssif ◽

...

Keyword(s):

Antibacterial Activity ◽

Dna Gyrase ◽

Bacterial Strains ◽

Topoisomerase Iv ◽

Gram Positive ◽

Gram Negative ◽

E Coli ◽

Antibacterial Screening ◽

Ic50 Values

A novel series of ciprofloxacin hybrids comprising various heterocycle derivatives has been synthesized and structurally elucidated using 1H NMR, 13C NMR, and elementary analyses. Using ciprofloxacin as a reference, compounds 1–21 were screened in vitro against Gram-positive bacterial strains such as Staphylococcus aureus and Bacillus subtilis and Gram-negative strains such as Escherichia coli and Pseudomonas aeruginosa. As a result, many of the compounds examined had antibacterial activity equivalent to ciprofloxacin against test bacteria. Compounds 2–6, oxadiazole derivatives, were found to have antibacterial activity that was 88 to 120% that of ciprofloxacin against Gram-positive and Gram-negative bacteria. The findings showed that none of the compounds tested had antifungal activity against Aspergillus flavus, but did have poor activity against Candida albicans, ranging from 23% to 33% of fluconazole, with compound 3 being the most active (33% of fluconazole). The most potent compounds, 3, 4, 5, and 6, displayed an IC50 of 86, 42, 92, and 180 nM against E. coli DNA gyrase, respectively (novobiocin, IC50 = 170 nM). Compounds 4, 5, and 6 showed IC50 values (1.47, 6.80, and 8.92 µM, respectively) against E. coli topo IV in comparison to novobiocin (IC50 = 11 µM).

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In VitroandIn VivoCharacterization of the Novel Oxabicyclooctane-Linked Bacterial Topoisomerase Inhibitor AM-8722, a Selective, Potent Inhibitor of Bacterial DNA Gyrase

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00619-16 ◽

2016 ◽

Vol 60 (8) ◽

pp. 4830-4839 ◽

Cited By ~ 12

Author(s):

Christopher M. Tan ◽

Charles J. Gill ◽

Jin Wu ◽

Nathalie Toussaint ◽

Jingjun Yin ◽

...

Keyword(s):

Broad Spectrum ◽

Antibacterial Agents ◽

Cell Activity ◽

Dna Gyrase ◽

Topoisomerase Iv ◽

Bacterial Dna ◽

Whole Cell ◽

Content Type

ABSTRACTOxabicyclooctane-linked novel bacterial topoisomerase inhibitors (NBTIs) represent a new class of recently described antibacterial agents with broad-spectrum activity. NBTIs dually inhibit the clinically validated bacterial targets DNA gyrase and topoisomerase IV and have been shown to bind distinctly from known classes of antibacterial agents directed against these targets. Herein we report the molecular, cellular, andin vivocharacterization of AM-8722 as a representative N-alkylated-1,5-naphthyridone left-hand-side-substituted NBTI. Consistent with its mode of action, macromolecular labeling studies revealed a specific effect of AM-8722 to dose dependently inhibit bacterial DNA synthesis. AM-8722 displayed greater intrinsic enzymatic potency than levofloxacin versus both DNA gyrase and topoisomerase IV fromStaphylococcus aureusandEscherichia coliand displayed selectivity against human topoisomerase II. AM-8722 was rapidly bactericidal and exhibited whole-cell activity versus a range of Gram-negative and Gram-positive organisms, with no whole-cell potency shift due to the presence of DNA or human serum. Frequency-of-resistance studies demonstrated an acceptable rate of resistance emergencein vitroat concentrations 16- to 32-fold the MIC. AM-8722 displayed acceptable pharmacokinetic properties and was shown to be efficacious in mouse models of bacterial septicemia. Overall, AM-8722 is a selective and potent NBTI that displays broad-spectrum antimicrobial activityin vitroandin vivo.

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Pyrrolopyrimidine inhibitors of DNA gyrase B (GyrB) and topoisomerase IV (ParE). Part I: Structure guided discovery and optimization of dual targeting agents with potent, broad-spectrum enzymatic activity

Bioorganic & Medicinal Chemistry Letters ◽

10.1016/j.bmcl.2012.11.032 ◽

2013 ◽

Vol 23 (5) ◽

pp. 1529-1536 ◽

Cited By ~ 67

Author(s):

Leslie W. Tari ◽

Michael Trzoss ◽

Daniel C. Bensen ◽

Xiaoming Li ◽

Zhiyong Chen ◽

...

Keyword(s):

Enzymatic Activity ◽

Broad Spectrum ◽

Dna Gyrase ◽

Topoisomerase Iv ◽

Guided Discovery ◽

Dual Targeting

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Comparison of the first whole genome sequence of ‘Haemophilus quentini’ with two new strains of ‘Haemophilus quentini’ and other species ofHaemophilus

Genome ◽

10.1139/gen-2017-0195 ◽

2018 ◽

Vol 61 (5) ◽

pp. 379-385 ◽

Cited By ~ 4

Author(s):

Alasdair T.M. Hubbard ◽

Sian E.W. Davies ◽

Laura Baxter ◽

Sarah Thompson ◽

Mark M. Collery ◽

...

Keyword(s):

Sequence Variation ◽

Molecular Detection ◽

Dna Gyrase ◽

Whole Genome Sequence ◽

Human Pathogen ◽

Emerging Pathogen ◽

Topoisomerase Iv ◽

Gram Negative ◽

Unique Genes ◽

Genetic Comparison

Comparison of the genome of the Gram negative human pathogen Haemophilus quentini MP1 with other species of Haemophilus revealed that, although it is more closely related to Haemophilus haemolyticus than Haemophilus influenzae, the pathogen is in fact genetically distinct, a finding confirmed by phylogenetic analysis using the H. influenzae multilocus sequence typing genes. Further comparison with two other H. quentini strains recently identified in Canada revealed that these three genomes are more closely related than any other species of Haemophilus; however, there is still some sequence variation. There was no evidence of acquired antimicrobial resistance within the H. quentini MP1 genome nor any mutations within the DNA gyrase or topoisomerase IV genes known to confer resistance to fluoroquinolones, which has been previously identified in other H. quentini isolates. We hope by presenting the annotation and genetic comparison of the H. quentini MP1 genome it will aid the future molecular detection of this potentially emerging pathogen via the identification of unique genes that differentiate it from other species of Haemophilus.

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In VitroActivity of AZD0914, a Novel Bacterial DNA Gyrase/Topoisomerase IV Inhibitor, against Clinically Relevant Gram-Positive and Fastidious Gram-Negative Pathogens

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01016-15 ◽

2015 ◽

Vol 59 (10) ◽

pp. 6053-6063 ◽

Cited By ~ 12

Author(s):

Douglas J. Biedenbach ◽

Michael D. Huband ◽

Meredith Hackel ◽

Boudewijn L. M. de Jonge ◽

Daniel F. Sahm ◽

...

Keyword(s):

Bacterial Species ◽

Dna Gyrase ◽

Species Group ◽

Coagulase Negative Staphylococci ◽

Topoisomerase Iv ◽

Gram Positive ◽

Bacterial Dna ◽

Gram Negative ◽

Content Type

ABSTRACTAZD0914, a new spiropyrimidinetrione bacterial DNA gyrase inhibitor with a novel mode of inhibition, has activity against bacterial species commonly cultured from patient infection specimens, including fluoroquinolone-resistant isolates. This study assessed thein vitroactivity of AZD0914 against key Gram-positive and fastidious Gram-negative clinical isolates collected globally in 2013. AZD0914 demonstrated potent activity, with MIC90s for AZD0914 of 0.25 mg/liter againstStaphylococcus aureus(n= 11,680), coagulase-negative staphylococci (n= 1,923), streptococci (n= 4,380), andMoraxella catarrhalis(n= 145), 0.5 mg/liter againstStaphylococcus lugdunensis(n= 120) andHaemophilus influenzae(n= 352), 1 mg/liter againstEnterococcus faecalis(n= 1,241), and 2 mg/liter againstHaemophilus parainfluenzae(n= 70). The activity againstEnterococcus faeciumwas more limited (MIC90, 8 mg/liter). The spectrum and potency of AZD0914 included fluoroquinolone-resistant isolates in each species group, including methicillin-resistant staphylococci, penicillin-resistant streptococci, vancomycin-resistant enterococci, β-lactamase-producingHaemophilusspp., andM. catarrhalis. Based on thesein vitrofindings, AZD0914 warrants further investigation for its utility against a variety of Gram-positive and fastidious Gram-negative bacterial species.

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In VitroAntibacterial Activity of AZD0914, a New Spiropyrimidinetrione DNA Gyrase/Topoisomerase Inhibitor with Potent Activity against Gram-Positive, Fastidious Gram-Negative, and Atypical Bacteria

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.04124-14 ◽

2014 ◽

Vol 59 (1) ◽

pp. 467-474 ◽

Cited By ~ 44

Author(s):

Michael D. Huband ◽

Patricia A. Bradford ◽

Linda G. Otterson ◽

Gregory S. Basarab ◽

Amy C. Kutschke ◽

...

Keyword(s):

Antibacterial Activity ◽

Legionella Pneumophila ◽

Bacterial Species ◽

Dna Gyrase ◽

Cross Resistance ◽

Gram Positive ◽

Gram Negative ◽

Content Type ◽

Topoisomerase Inhibitor

ABSTRACTAZD0914 is a new spiropyrimidinetrione bacterial DNA gyrase/topoisomerase inhibitor with potentin vitroantibacterial activity against key Gram-positive (Staphylococcus aureus,Staphylococcus epidermidis,Streptococcus pneumoniae,Streptococcus pyogenes, andStreptococcus agalactiae), fastidious Gram-negative (Haemophilus influenzaeandNeisseria gonorrhoeae), atypical (Legionella pneumophila), and anaerobic (Clostridium difficile) bacterial species, including isolates with known resistance to fluoroquinolones. AZD0914 works via inhibition of DNA biosynthesis and accumulation of double-strand cleavages; this mechanism of inhibition differs from those of other marketed antibacterial compounds. AZD0914 stabilizes and arrests the cleaved covalent complex of gyrase with double-strand broken DNA under permissive conditions and thus blocks religation of the double-strand cleaved DNA to form fused circular DNA. Whereas this mechanism is similar to that seen with fluoroquinolones, it is mechanistically distinct. AZD0914 exhibited low frequencies of spontaneous resistance inS. aureus, and if mutants were obtained, the mutations mapped togyrB. Additionally, no cross-resistance was observed for AZD0914 against recent bacterial clinical isolates demonstrating resistance to fluoroquinolones or other drug classes, including macrolides, β-lactams, glycopeptides, and oxazolidinones. AZD0914 was bactericidal in both minimum bactericidal concentration andin vitrotime-kill studies. Inin vitrocheckerboard/synergy testing with 17 comparator antibacterials, only additivity/indifference was observed. The potentin vitroantibacterial activity (including activity against fluoroquinolone-resistant isolates), low frequency of resistance, lack of cross-resistance, and bactericidal activity of AZD0914 support its continued development.

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Nybomycin Inhibits both Fluoroquinolone-Sensitive and Fluoroquinolone-Resistant Escherichia coli DNA Gyrase

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00777-20 ◽

2021 ◽

Vol 65 (5) ◽

Author(s):

Dmitrii I. Shiriaev ◽

Alina A. Sofronova ◽

Ekaterina A. Berdnikovich ◽

Dmitrii A. Lukianov ◽

Ekaterina S. Komarova ◽

...

Keyword(s):

Escherichia Coli ◽

Bacterial Species ◽

Dna Gyrase ◽

Resistant Bacteria ◽

Mutant Form ◽

Wild Type ◽

Topoisomerase Iv ◽

Gram Positive ◽

Gram Negative ◽

Content Type

ABSTRACT Bacterial type II topoisomerases, DNA gyrase and topoisomerase IV, are targets of many antibiotics, including fluoroquinolones (FQs). Unfortunately, a number of bacterial species easily acquire resistance to FQs by mutations in either DNA gyrase or topoisomerase IV genes. The emergence of resistant pathogenic strains is a global problem in health care; therefore, identifying alternative pathways to thwart their persistence is the current frontier in drug discovery. Nybomycins are an attractive class of compounds, reported to be “reverse antibiotics” that selectively inhibit growth of some Gram-positive FQ-resistant bacteria by targeting the mutant form of DNA gyrase while being inactive against wild-type strains with FQ-sensitive gyrases. The strong “reverse” effect was demonstrated only for a few Gram-positive organisms resistant to FQs due to the S83L/I mutation in the GyrA subunit of DNA gyrase. However, the activity of nybomycins has not been extensively explored among Gram-negative species. Here, we observed that in a ΔtolC strain of the Gram-negative Escherichia coli with enhanced permeability, wild-type gyrase and a GyrA S83L mutant, resistant to fluoroquinolones, are similarly sensitive to nybomycin.

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Contributions of the 8-Methoxy Group of Gatifloxacin to Resistance Selectivity, Target Preference, and Antibacterial Activity against Streptococcus pneumoniae

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.45.6.1649-1653.2001 ◽

2001 ◽

Vol 45 (6) ◽

pp. 1649-1653 ◽

Cited By ~ 55

Author(s):

Hideyuki Fukuda ◽

Ryuta Kishii ◽

Masaya Takei ◽

Masaki Hosaka

Keyword(s):

Antibacterial Activity ◽

Streptococcus Pneumoniae ◽

Type Strain ◽

Methoxy Group ◽

Wild Type Strain ◽

Dna Gyrase ◽

Wild Type ◽

Topoisomerase Iv ◽

Mutant Strains

ABSTRACT Gatifloxacin (8-methoxy, 7-piperazinyl-3′-methyl) at the MIC selected mutant strains that possessed gyrA mutations at a low frequency (3.7 × 10−9) from wild-type strainStreptococcus pneumoniae IID553. AM-1147 (8-methoxy, 7-piperazinyl-3′-H) at the MIC or higher concentrations selected no mutant strains. On the other hand, the respective 8-H counterparts of these two compounds, AM-1121 (8-H, 7-piperazinyl-3′-methyl) and ciprofloxacin (8-H, 7-piperazinyl-3′-H), at one and two times the MIC selected mutant strains that possessed parC mutations at a high frequency (>2.4 × 10−6). The MIC of AM-1147 increased for the gyrA mutant strains but not for theparC mutant strains compared with that for the wild-type strain. These results suggest that fluoroquinolones that harbor 8-methoxy groups select mutant strains less frequently and prefer DNA gyrase, as distinct from their 8-H counterparts. The in vitro activities of gatifloxacin and AM-1147 are twofold higher against the wild-type strain, eight- and twofold higher against the first-stepparC and gyrA mutant strains, respectively, and two- to eightfold higher against the second-step gyrA andparC double mutant strains than those of their 8-H counterparts. These results indicate that the 8-methoxy group contributes to enhancement of antibacterial activity against target-altered mutant strains as well as the wild-type strain. It is hypothesized that the 8-methoxy group of gatifloxacin increases the level of target inhibition, especially against DNA gyrase, so that it is nearly the same as that for topoisomerase IV inhibition in the bacterial cell, leading to potent antibacterial activity and a low level of resistance selectivity.

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