Novel tricyclics (e.g., GSK945237) as potent inhibitors of bacterial type IIA topoisomerases

Miles, Timothy J.; Hennessy, Alan J.; Bax, Benjamin; Brooks, Gerald; Brown, Barry S.; Brown, Pamela; Cailleau, Nathalie; Chen, Dongzhao; Dabbs, Steven; Davies, David T.; Esken, Joel M.; Giordano, Ilaria; Hoover, Jennifer L.; Jones, Graham; Sukmar, Senthill K. Kusalakumari; Markwell, Roger E.; Minthorn, Elisabeth A.; Rittenhouse, Steve; Gwynn, Michael N.; Pearson, Neil D.

doi:10.1016/j.bmcl.2016.03.106

Cited by 43 publications

(58 citation statements)

References 51 publications

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“…In all our previous complex structures of S. aureus DNA gyrase with DNA and a variety of DNA-gate inhibitors (15,19,40), the thiophene class inhibitor-binding pocket was present. Therefore, a soakable crystal system for determining thiophene crystal structures was developed by cocrystallizing with an NBTI (namely, GSK945237) (41) and then soaking in compound 2. For crystallization, 1 μL of complex [0.047 mM GyrB27A56(GKdel) dimer, 0.072 mM 20-12p-8 DNA duplex, 0.36 mM GSK945237, 2.7 mM MnCl 2, 3.6% DMSO, 18.6 mM Hepes, 54 mM Na 2 SO 4 , pH 7.0] was mixed with 1 μL of crystallization buffer (7-11% PEG 5000 MME, 130 to 190 mM Bis-Tris, pH 6.2) and streak seeded before covering with paraffin oil.…”

Section: Methodsmentioning

confidence: 99%

Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase

Chan

Germe

Bax

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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A paucity of novel acting antibacterials is in development to treat the rising threat of antimicrobial resistance, particularly in Gram-negative hospital pathogens, which has led to renewed efforts in antibiotic drug discovery. Fluoroquinolones are broad-spectrum antibacterials that target DNA gyrase by stabilizing DNA-cleavage complexes, but their clinical utility has been compromised by resistance. We have identified a class of antibacterial thiophenes that target DNA gyrase with a unique mechanism of action and have activity against a range of bacterial pathogens, including strains resistant to fluoroquinolones. Although fluoroquinolones stabilize double-stranded DNA breaks, the antibacterial thiophenes stabilize gyrase-mediated DNA-cleavage complexes in either one DNA strand or both DNA strands. X-ray crystallography of DNA gyrase–DNA complexes shows the compounds binding to a protein pocket between the winged helix domain and topoisomerase-primase domain, remote from the DNA. Mutations of conserved residues around this pocket affect activity of the thiophene inhibitors, consistent with allosteric inhibition of DNA gyrase. This druggable pocket provides potentially complementary opportunities for targeting bacterial topoisomerases for antibiotic development.

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Section: Methodsmentioning

confidence: 99%

Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase

Chan

Germe

Bax

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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“…A number of advanced NBTI molecules have been described in the literature, including NXL101 (16), AZD9742 (17), NBTI 5463 (18), and gepotidacin (19), which recently successfully completed phase II human clinical evaluation for the treatment of uncomplicated urogenital gonorrhea caused by Neisseria gonorrhoeae (ClinicalTrials registration number NCT02294682). The NBTI pharmacophore, however, has been associated with cardiovascular and other safety liabilities (17,(20)(21)(22)(23). Therefore, a key aim in the development of NBTIs is achieving broad antibacterial potency, including against challenging Gram-negative pathogens, while maintaining satisfactory safety margins.…”

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confidence: 99%

Novel Bacterial Topoisomerase Inhibitors with Potent Broad-Spectrum Activity against Drug-Resistant Bacteria

Charrier

Salisbury

Savage

et al. 2017

Antimicrob Agents Chemother

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The novel bacterial topoisomerase inhibitor class is an investigational type of antibacterial inhibitor of DNA gyrase and topoisomerase IV that does not have cross-resistance with the quinolones. Here, we report the evaluation of the in vitro properties of a new series of this type of small molecule. Exemplar compounds selectively and potently inhibited the catalytic activities of Escherichia coli DNA gyrase and topoisomerase IV but did not block the DNA breakage-reunion step. Compounds showed broad-spectrum inhibitory activity against a wide range of Grampositive and Gram-negative pathogens, including biodefence microorganisms and Mycobacterium tuberculosis. No cross-resistance with fluoroquinolone-resistant Staphylococcus aureus and E. coli isolates was observed. Measured MIC 90 values were 4 and 8 g/ml against a panel of contemporary multidrug-resistant isolates of Acinetobacter baumannii and E. coli, respectively. In addition, representative compounds exhibited greater antibacterial potency than the quinolones against obligate anaerobic species. Spontaneous mutation rates were low, with frequencies of resistance typically Ͻ10 Ϫ8 against E. coli and A. baumannii at concentrations equivalent to 4-fold the MIC. Compound-resistant E. coli mutants that were isolated following serial passage were characterized by whole-genome sequencing and carried a single Arg38Leu amino acid substitution in the GyrA subunit of DNA gyrase. Preliminary in vitro safety data indicate that the series shows a promising therapeutic index and potential for low human ether-a-go-go-related gene (hERG) inhibition (50% inhibitory concentration [IC 50 ], Ͼ100 M). In summary, the compounds' distinct mechanism of action relative to the fluoroquinolones, whole-cell potency, low potential for resistance development, and favorable in vitro safety profile warrant their continued investigation as potential broad-spectrum antibacterial agents.

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“…For some H. influenzae, there may be little growth; however, the infection should not begin to self-resolve within a 48 or 96 h time period (Figure 2B). This lung infection model can be used during optimization of lead chemical series to support SAR, as shown in Figure 3 for representative compounds of two different series 16,17 . It provides a consistent, reproducible method for assessing PK/PD in immunocompetent animals and was used to determine that free drug area under the concentration-time curve over the minimum inhibitory concentration (fAUC/MIC) correlated with efficacy of a novel polypeptide deformylase (PDF) inhibitor against S. pneumoniae and H. influenzae (Figure 4).…”

Section: Representative Resultsmentioning

confidence: 99%

“…The multi-purpose utility of the model is demonstrated in Figures 3 and 4 and Tables 1 and 2. These studies are part of a large collection of published and unpublished data that has been generated with this model to support lead optimization efforts 16,17,[22][23][24] , for comparison and confirmation of proposed human dosing regimens 19,[25][26][27][28][29] and for PK/PD characterization It may be noted in some studies that the bacterial burden at baseline was lower than that typically targeted in other lung infection models. This is due in large part to the required dilution into agar and the small challenge volume, particularly in mice.…”

Section: Discussionmentioning

confidence: 99%

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A Robust Pneumonia Model in Immunocompetent Rodents to Evaluate Antibacterial Efficacy against S. pneumoniae, H. influenzae, K. pneumoniae, P. aeruginosa or A. baumannii

Hoover

Lewandowski

Mininger

et al. 2017

JoVE

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Efficacy of candidate antibacterial treatments must be demonstrated in animal models of infection as part of the discovery and development process, preferably in models which mimic the intended clinical indication. A method for inducing robust lung infections in immunocompetent rats and mice is described which allows for the assessment of treatments in a model of serious pneumonia caused by S. pneumoniae, H. influenzae, P. aeruginosa, K. pneumoniae or A. baumannii. Animals are anesthetized, and an agar-based inoculum is deposited deep into the lung via nonsurgical intratracheal intubation. The resulting infection is consistent, reproducible, and stable for at least 48 h and up to 96 h for most isolates. Studies with marketed antibacterials have demonstrated good correlation between in vivo efficacy and in vitro susceptibility, and concordance between pharmacokinetic/pharmacodynamic targets determined in this model and clinically accepted targets has been observed. Although there is an initial time investment when learning the technique, it can be performed quickly and efficiently once proficiency is achieved. Benefits of the model include elimination of the neutropenic requirement, increased robustness and reproducibility, ability to study more pathogens and isolates, improved flexibility in study design and establishment of a challenging infection in an immunocompetent host.

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Novel tricyclics (e.g., GSK945237) as potent inhibitors of bacterial type IIA topoisomerases

Cited by 43 publications

References 51 publications

Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase

Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase

Novel Bacterial Topoisomerase Inhibitors with Potent Broad-Spectrum Activity against Drug-Resistant Bacteria

A Robust Pneumonia Model in Immunocompetent Rodents to Evaluate Antibacterial Efficacy against <i>S. pneumoniae</i>, <i>H. influenzae</i>, <i>K. pneumoniae</i>, <em>P. aeruginosa</em> or <em>A. baumannii</em>

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