New N-phenyl-4,5-dibromopyrrolamides as DNA gyrase B inhibitors

Abstract

Due to the rapid development of antimicrobial resistance, the discovery of new antibacterials is essential in the fight against potentially lethal infections. The DNA gyrase B (GyrB) subunit of bacterial DNA gyrase is an excellent target for the design of antibacterials, as it has been clinically validated by novobiocin. However, there are currently no drugs in clinical use that target GyrB. We prepared a new series of N-phenyl-4,5-dibromopyrrolamides and evaluated them against DNA gyrase and against the structurally and functionally similar enzyme, topoisomerase IV. The most active compound, 28, had an IC₅₀ of 20 nM against Escherichia coli DNA gyrase. The IC₅₀ values of 28 against Staphylococcus aureus DNA gyrase, and E. coli and S. aureus topoisomerase IV were in the low micromolar range. However, the compounds evaluated did not show significant antibacterial activities against selected Gram-positive and Gram-negative bacteria. Our results indicate that for potent inhibition of DNA gyrase, a combination of polar groups on the carboxylic end of the molecule and substituents that reach into the 'lipophilic floor' of the enzyme is required.

Fig. 1. Representative ATP-competitive DNA gyrase and topoisomerase IV inhibitors.

Fig. 2. General structures of type I and type II compounds as potential DNA gyrase B inhibitors, designed using the X-ray structure of inhibitor A bound to E. coli GyrB (PDB code: ; 4ZVI) as template.

Scheme 1. Reagents and conditions: (a) K₂CO₃, CH₃CN, rt, 15 h; (b) H₂, Pd/C, tetrahydrofuran, rt, 5 h; (c) 4,5-dibromo-pyrrole-2-carboxylic acid, TBTU, N-methylmorpholine, CH₂Cl₂, 50 °C, 15 h; (d) hydrazine monohydrate, ethanol, 80 °C, 15 h; (e) 1,1-carbonyldiimidazole, 1,4-dioxane, 101 °C, 15 h; (f) 2 M NaOH, tetrahydrofuran, rt, 15 h.

Scheme 2. Reagents and conditions: (a) Boc₂O, Et₃N, methanol, 0 °C → rt, 15 h; (b) benzyl bromide, K₂CO₃, CH₃CN, 0 °C → rt, 15 h; (c) methyl bromoacetate, K₂CO₃, CH₃CN, 0 °C → rt, 15 h; (d) HCl_(g), diethyl ether, rt, 15 h; (e) 4,5-dibromo-pyrrole-2-carboxylic acid, TBTU, N-methylmorpholine, CH₂Cl₂, 50 °C, 16 h; (f) hydrazine monohydrate, ethanol, 80 °C, 15 h; (g) 1,1-carbonyldiimidazole, 1,4-dioxane, 101 °C, 15 h; (h) 2 M NaOH, tetrahydrofuran, rt, 15 h.

Scheme 3. Reagents and conditions: (a) Boc₂O, DMAP, CH₂Cl₂/CH₃CN, 70 °C, 24 h; (b) hydroxylamine hydrochloride, Et₃N, ethanol, 65 °C, 15 h; (c) acetic anhydride, acetic acid, 85 °C, 15 h; (d) tin(ii) chloride, ethanol/ethyl acetate, 70 °C, 6 h; (e) methyl malonyl chloride, K₂CO₃, CH₃CN, 0 °C, 12 h; (f) 4 M HCl in 1,4-dioxane, rt, 15 h; (g) 4,5-dibromo-pyrrole-2-carboxylic acid, oxalyl chloride, CH₂Cl₂, 15 h, then ii) 24, pyridine, CH₂Cl₂, rt, 6 h; (h) hydrazine monohydrate, ethanol/tetrahydrofuran, 80 °C, 15 h; (i) 1,1-carbonyldiimidazole, 1,4-dioxane/dimethylformamide, 100 °C, 15 h; (j) 2 M NaOH, THF, rt, 15 h.

Fig. 3. Binding mode of compound 27 (cyan) in the E. coli GyrB (grey) (PDB code: ; 4DUH), as predicted with GOLD. The crystal water molecule is shown as a red sphere. The predicted H-bonds are given as yellow dotted lines. The fig. was prepared using PyMOL.