Fragment-to-Hit-to-Lead Discovery of a Novel Pyridylurea Scaffold of ATP Competitive Dual Targeting Type II Topoisomerase Inhibiting Antibacterial Agents

Abstract

The discovery and optimization of a new class of bacterial topoisomerase (DNA gyrase and topoisomerase IV) inhibitors binding in the ATP domain are described. A fragment molecule, 1-ethyl-3-(2-pyridyl)urea, provided sufficiently potent enzyme inhibition (32 μM) to prompt further analogue work. Acids and acid isosteres were incorporated at the 5-pyridyl position of this fragment, bridging to a key asparagine residue, improving enzyme inhibition, and leading to measurable antibacterial activity. A CF3-thiazole substituent at the 4-pyridyl position improved inhibitory potency due to a favorable lipophilic interaction. Promising antibacterial activity was seen versus the Gram-positive pathogens Staphylococcus aureus and Streptococcus pneumoniae and the Gram-negative pathogens Haemophilus influenzae and Moraxella catarrhalis . Precursor metabolite incorporation and mutant analysis studies support the mode-of-action, blockage of DNA synthesis by dual target topoisomerase inhibition. Compound 35 was efficacious in a mouse S. aureus disease model, where a 4.5-log reduction in colony forming units versus control was demonstrated.

Pyridine-3-carboxamide-6-yl-ureas as novel inhibitors of bacterial DNA gyrase: Structure based design, synthesis, SAR and antimicrobial activity

“…[7,8,10,11]. Notably, benzimidazol-2-yl-ureas (1), benzathiazol-2-yl-ureas (2), imidazopyridin-2-yl-ureas (3), triazolopyridine-5-carboxamides (4), isoquinolin-3-yl-ureas (5) and pyridin-3-yl-ureas (6) reported by groups at Vertex [7], Prolysis 11 , Pfizer [10], Evotec [8], Actelion [12] and AstraZeneca [13] respectively, exemplify the prevalence of this moiety amongst antibacterial GyrB / ParE inhibitors ( Fig. 1).…”

A Novel Inhibitor of Gyrase B Is a Potent Drug Candidate for Treatment of Tuberculosis and Nontuberculosis Mycobacterial Infections

“…The catalytic subunits (GyrA/ParC) are clinically validated drug targets of the fluoroquinolones, such as moxifloxacin (MXF) (2), while the ATPase subunits (GyrB/ParE) have not been as extensively exploited and may present a new option for treating DR strains of M. tuberculosis (3). Furthermore, several different chemical classes have been described as inhibitors of gyrase B with potent activity against DR bacteria, including M. tuberculosis (4)(5)(6)(7)(8)(9)(10).…”

A Novel High-Throughput Cell-Based Assay Aimed at Identifying Inhibitors of DNA Metabolism in Bacteria

“…3). The screen identified known inhibitors of DNA metabolism that were present in the compound library, such as quinolones (9) and other inhibitors of DNA gyrase (GyrA) (39), as well as ATPase inhibitors of GyrB (40)(41)(42)(43), DNA ligase (44,45), and thymidylate kinase (46,47). Given that the assay identified a wide variety of inhibitors, rather than inhibitors of just a single target, the assay was validated as a useful probe to identify inhibitors of DNA metabolism (Fig.…”