Discovery and characterization of a novel class of pyrazolopyrimidinedione tRNA synthesis inhibitors

Montgomery, Justin I.; Smith, James F.; Tomaras, Andrew P.; Zaniewski, Richard P.; McPherson, Craig J.; McAllister, Laura A.; Hartman-Neumann, Sandra; Arcari, Joel T.; Lescoe, MaryKay; Gutierrez, Jemy A.; Yuan, Ying; Limberakis, Chris; Miller, Alita A.

doi:10.1038/ja.2014.163

Cited by 15 publications

(9 citation statements)

References 21 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Thus the logD ranges observed in the AZ examples are rather similar to the range of the ChEMBL AA compounds. Recently reported antibacterial pyrazolopyrimidinedione inhibitors of tRNA synthetases also have physicochemical properties in the typical drug-like ranges [ 11 ]. Taken together, these data indicate that compounds with physicochemical property values in the typical drug range can be potent antibacterials.…”

Section: Resultsmentioning

confidence: 99%

Are the physicochemical properties of antibacterial compounds really different from other drugs?

2016

View full text Add to dashboard Cite

BackgroundIt is now widely recognized that there is an urgent need for new antibacterial drugs, with novel mechanisms of action, to combat the rise of multi-drug resistant bacteria. However, few new compounds are reaching the market. Antibacterial drug discovery projects often succeed in identifying potent molecules in biochemical assays but have been beset by difficulties in obtaining antibacterial activity. A commonly held view, based on analysis of marketed antibacterial compounds, is that antibacterial drugs possess very different physicochemical properties to other drugs, and that this profile is required for antibacterial activity.ResultsWe have re-examined this issue by performing a cheminformatics analysis of the literature data available in the ChEMBL database. The physicochemical properties of compounds with a recorded activity in an antibacterial assay were calculated and compared to two other datasets extracted from ChEMBL, marketed antibacterials and drugs marketed for other therapeutic indications. The chemical class of the compounds and Gram-negative/Gram-positive profile were also investigated. This analysis shows that compounds with antibacterial activity have physicochemical property profiles very similar to other drug classes.ConclusionsThe observation that many current antibacterial drugs lie in regions of physicochemical property space far from conventional small molecule therapeutics is correct. However, the inference that a compound must lie in one of these “outlier” regions in order to possess antibacterial activity is not supported by our analysis.Graphical abstract.Electronic supplementary materialThe online version of this article (doi:10.1186/s13321-016-0143-5) contains supplementary material, which is available to authorized users.

show abstract

Section: Resultsmentioning

confidence: 99%

Are the physicochemical properties of antibacterial compounds really different from other drugs?

2016

View full text Add to dashboard Cite

show abstract

“…Macromolecule synthesis profiling was conducted as described by Montgomery, et al [32] with minor modifications. E .…”

Section: Methodsmentioning

confidence: 99%

“…E . coli strain JL553 ( tolC , lysE ) [32] was used to measure inhibition of DNA, RNA, protein, peptidoglycan and phospholipid biosynthesis while E . coli MB5500 ( lpxC [ envA1 ], galE ; Merck & Co., Inc., Kenilworth, NJ, USA, strain collection) was used to measure inhibition of lipopolysaccharide biosynthesis.…”

Section: Methodsmentioning

confidence: 99%

“…Compound concentrations (3-fold serial dilutions) were chosen to place the minimum inhibitory concentration (see below) near the center of the dose range. Labeled cultures were incubated with compound for 25 min; stopped with trichloroacetic acid, filtered and incorporation was measured as described [32]. Percent inhibition of incorporation was calculated relative to an untreated control culture for each labeled precursor and plotted with GraphPad Prism.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Antibacterial small molecules targeting the conserved TOPRIM domain of DNA gyrase

et al. 2017

View full text Add to dashboard Cite

To combat the threat of antibiotic-resistant Gram-negative bacteria, novel agents that circumvent established resistance mechanisms are urgently needed. Our approach was to focus first on identifying bioactive small molecules followed by chemical lead prioritization and target identification. Within this annotated library of bioactives, we identified a small molecule with activity against efflux-deficient Escherichia coli and other sensitized Gram-negatives. Further studies suggested that this compound inhibited DNA replication and selection for resistance identified mutations in a subunit of E. coli DNA gyrase, a type II topoisomerase. Our initial compound demonstrated weak inhibition of DNA gyrase activity while optimized compounds demonstrated significantly improved inhibition of E. coli and Pseudomonas aeruginosa DNA gyrase and caused cleaved complex stabilization, a hallmark of certain bactericidal DNA gyrase inhibitors. Amino acid substitutions conferring resistance to this new class of DNA gyrase inhibitors reside exclusively in the TOPRIM domain of GyrB and are not associated with resistance to the fluoroquinolones, suggesting a novel binding site for a gyrase inhibitor.

show abstract

“…During a high-throughput phenotypic screen, a pyrazolopyrimidinedione compound series was identified as a LysRS inhibitor by a group at Pfizer Worldwide Research and Development. 28 This compound was also shown to be an ATP competitor, but additional work has not been published. Three compounds were identified as inhibitors of LysRS in this study, and additional structure-activity relationship studies to enhance potency will be required to determine if these compounds have the potential for development as antibacterial agents.…”

Section: Discussionmentioning

confidence: 99%

Lysyl-tRNA Synthetase from Pseudomonas aeruginosa: Characterization and Identification of Inhibitory Compounds

Balboa

Dean

et al. 2020

SLAS Discovery

View full text Add to dashboard Cite

Pseudomonas aeruginosa is an opportunistic pathogen that causes nosocomial infections and has highly developed systems for acquiring resistance against numerous antibiotics. The gene ( lysS) encoding P. aeruginosa lysyl-tRNA synthetase (LysRS) was cloned and overexpressed, and the resulting protein was purified to 98% homogeneity. LysRS was kinetically evaluated, and the Km values for the interaction with lysine, adenosine triphosphate (ATP), and tRNALys were determined to be 45.5, 627, and 3.3 µM, respectively. The kcatobs values were calculated to be 13, 22.8, and 0.35 s−1, resulting in kcatobs/ KM values of 0.29, 0.036, and 0.11 s−1µM−1, respectively. Using scintillation proximity assay technology, natural product and synthetic compound libraries were screened to identify inhibitors of function of the enzyme. Three compounds (BM01D09, BT06F11, and BT08F04) were identified with inhibitory activity against LysRS. The IC50 values were 17, 30, and 27 µM for each compound, respectively. The minimum inhibitory concentrations were determined against a panel of clinically important pathogens. All three compounds were observed to inhibit the growth of gram-positive organisms with a bacteriostatic mode of action. However, two compounds (BT06F11 and BT08F04) were bactericidal against cultures of gram-negative bacteria. When tested against human cell cultures, BT06F11 was not toxic at any concentration tested, and BM01D09 was toxic only at elevated levels. However, BT08F04 displayed a CC50 of 61 µg/mL. In studies of the mechanism of inhibition, BM01D09 inhibited LysRS activity by competing with ATP for binding, and BT08F04 was competitive with ATP and uncompetitive with the amino acid. BT06F11 inhibited LysRS activity by a mechanism other than substrate competition.

show abstract

Discovery and characterization of a novel class of pyrazolopyrimidinedione tRNA synthesis inhibitors

Cited by 15 publications

References 21 publications

Are the physicochemical properties of antibacterial compounds really different from other drugs?

Are the physicochemical properties of antibacterial compounds really different from other drugs?

Antibacterial small molecules targeting the conserved TOPRIM domain of DNA gyrase

Lysyl-tRNA Synthetase from Pseudomonas aeruginosa: Characterization and Identification of Inhibitory Compounds

Contact Info

Product

Resources

About