Pyrrolamide DNA Gyrase Inhibitors: Fragment-Based Nuclear Magnetic Resonance Screening To Identify Antibacterial Agents

Abstract

DNA gyrase is an essential enzyme in bacteria, and its inhibition results in the disruption of DNA synthesis and, subsequently, cell death. The pyrrolamides are a novel class of antibacterial agents targeting DNA gyrase. These compounds were identified by a fragment-based lead generation (FBLG) approach using nuclear magnetic resonance (NMR) screening to identify low-molecular-weight compounds that bind to the ATP pocket of DNA gyrase. A pyrrole hit with a binding constant of 1 mM formed the basis of the design and synthesis of a focused library of compounds that resulted in the rapid identification of a lead compound that inhibited DNA gyrase with a 50% inhibitory concentration (IC(50)) of 3 μM. The potency of the lead compound was further optimized by utilizing iterative X-ray crystallography to yield DNA gyrase inhibitors that also displayed antibacterial activity. Spontaneous mutants were isolated in Staphylococcus aureus by plating on agar plates containing pyrrolamide 4 at the MIC. The resistant variants displayed 4- to 8-fold-increased MIC values relative to the parent strain. DNA sequencing revealed two independent point mutations in the pyrrolamide binding region of the gyrB genes from these variants, supporting the hypothesis that the mode of action of these compounds was inhibition of DNA gyrase. Efficacy of a representative pyrrolamide was demonstrated against Streptococcus pneumoniae in a mouse lung infection model. These data demonstrate that the pyrrolamides are a novel class of DNA gyrase inhibitors with the potential to deliver future antibacterial agents targeting multiple clinical indications.

Optimization of Pyrrolamides as Mycobacterial GyrB ATPase Inhibitors: Structure-Activity Relationship and In Vivo Efficacy in a Mouse Model of Tuberculosis

“…Loss of this interaction may result in loss of potency against the resistant mutant. Similar type of change in potency against the mutant enzyme was observed in the case of S. aureus DNA gyrase (13).…”

“…The pyrrolamide class of compounds, identified as novel DNA gyrase inhibitors through nuclear magnetic resonance (NMR) screening and structure-guided design at AstraZeneca, were reported to have antibacterial activity (13). We describe the structure-activity relationship of pyrrolamides for inhibition of mycobacterial DNA gyrase activity and their optimization to improve anti-TB activity, followed by evaluation of in vivo efficacy in the mouse model of TB.…”

Biological evaluation and molecular modelling study of thiosemicarbazide derivatives as bacterial type IIA topoisomerases inhibitors

“…FlexX and HYDE docking algorithms as implemented in LeadIT platform of BioSolveIT program were used with default parameters. While quantitative conclusions are not possible due to the lack of consistent set of bioactivity indexes of compounds involved in comparison, similarity of scores of 7 and GSK299423, the latter being a potent inhibitor of gyrA site 32 , and significant difference from the score of 4-[4-[(3,4-dichloro-5-methyl-1H-pyrrole-2-carbonyl)amino]-1-piperidyl]quinolone-2-carboxylic acid, a potent inhibitor of gyrB site 33 , seems to indicate that 7 binds to the DNA binding pocket. This observation is opposite to the conclusion we have arrived at in our previous studies 34 and may indicate that thiosemicarbazide derivatives can inhibit both sites of gyrase.…”

New perspectives on antibacterial drug research

“…Recently, Eakin et al described initial prototypes of pyrrolamides with in vitro antibacterial activity against Gram-positive bacteria and selected Gram-negative pathogens. These compounds target the ATP-binding site of GyrB [51].…”