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

Abstract

Moxifloxacin has shown excellent activity against drug-sensitive as well as drug-resistant tuberculosis (TB), thus confirming DNA gyrase as a clinically validated target for discovering novel anti-TB agents. We have identified novel inhibitors in the pyrrolamide class which kill Mycobacterium tuberculosis through inhibition of ATPase activity catalyzed by the GyrB domain of DNA gyrase. A homology model of the M. tuberculosis H37Rv GyrB domain was used for deciphering the structure-activity relationship and binding interactions of inhibitors with mycobacterial GyrB enzyme. Proposed binding interactions were later confirmed through cocrystal structure studies with the Mycobacterium smegmatis GyrB ATPase domain. The most potent compound in this series inhibited supercoiling activity of DNA gyrase with a 50% inhibitory concentration (IC 50 ) of <5 nM, an MIC of 0.03 g/ml against M. tuberculosis H37Rv, and an MIC 90 of <0.25 g/ml against 99 drug-resistant clinical isolates of M. tuberculosis. The frequency of isolating spontaneous resistant mutants was ϳ10 ؊6 to 10 ؊8 , and the point mutation mapped to the M. tuberculosis GyrB domain (Ser208 Ala), thus confirming its mode of action. The best compound tested for in vivo efficacy in the mouse model showed a 1.1-log reduction in lung CFU in the acute model and a 0.7-log reduction in the chronic model. This class of GyrB inhibitors could be developed as novel anti-TB agents. In 2010, the World Health Organization estimated that ϳ11.1 million people across the globe were infected with Mycobacterium tuberculosis, with an associated mortality rate of 1.3 million (1). Patients with drug-sensitive tuberculosis (TB) are treated with an intensive regimen consisting of a 2-month, once-daily combination therapy of isoniazid, rifampin, pyrazinamide, and ethambutol. This is followed by a 4-month continuation regimen with isoniazid and rifampin (2).These anti-TB drugs were discovered in the period spanning 1945 to 1965. The reemergence of TB due to HIV and multiple-drug-resistant (MDR) strains of TB has created a global epidemic. Therefore, there is an urgent need to discover new drugs with a novel mode of action (3-6).The clinical efficacy of fluoroquinolone drugs demonstrated over the past 20 to 30 years has validated DNA gyrase as a target in the area of broad-spectrum antibacterials (7). DNA gyrase is essential for growth in all bacteria, including mycobacteria. Due to the absence of topoisomerase IV, DNA gyrase is essential for DNA supercoiling as well as decatenation activities in M. tuberculosis (8). In addition, this enzyme is essential for DNA replication and repair as well as transcription. Therefore, we believed that a novel class of DNA gyrase inhibitors would be effective anti-TB agents.DNA gyrase is a heterotetramer comprising of GyrA and GyrB subunits (A 2 B 2 ). GyrA contains the DNA breakage-reunion site, while GyrB hydrolyzes ATP (9). This enzyme introduces negative supercoils into circular DNA following ATP hydrolysis. DNA gyrase also catalyzes the interconversion...

Pharmacokinetic and Pharmacodynamic Evaluation of AZD5847 in a Mouse Model of Tuberculosis

“…In the dose fractionation (DF) study, blood samples were collected from 8 out of 14 dose groups on day 18 in the 4-week study and 12 out of 13 dose groups on day 37 in the 8-week study. For the lung epithelial lining fluid (ELF) PK in healthy mice, bronchoalveolar lavage (BAL) was performed on healthy mice after the oral administration of AZD5847 at 250 mg/kg by previously described methods (14). Blood and BAL fluid samples were collected at 5 min, 15 min, 30 min, 1 h, 2 h, 4 h, 8 h, 16 h, 24 h, and 48 h after dosing.…”

New Structural Templates for Clinically Validated and Novel Targets in Antimicrobial Drug Research and Development

“…Furthermore, the 2-pyridinyl urea 35 (Basarab et al 2013), the 2-aminopyrimidine 36 (Uria-Nickelsen et al 2013), aminobenzimidazols 37 (Finn 2013) and 38 (Chopra et al 2012), the pyrrolamide 39 (Shahul et al 2014) and the thiazolopyridone 40 (Kale et al 2013;Kale et al 2014) were reported as efficient ATPsite inhibitors against Gram-positive bacteria, and, for some of them (38, 39 and 40) also moderate activities against M. tuberculosis were revealed. The first catalytic-site inhibitor of the DNA gyrase was nalidixic acid 41 (Scheme 16), introducing the antibacterial class of quinolones.…”

In Vitro and In Vivo Activities of DS-2969b, a Novel GyrB Inhibitor, and Its Water-Soluble Prodrug, DS11960558, against Methicillin-Resistant Staphylococcus aureus

“…Bacterial DNA gyrase and topoisomerase IV are highly conserved type II topoisomerases that play essential roles in DNA replication and transcription. They are established antibacterial drug targets (19,20) and have been used for the discovery of inhibitors with a novel scaffold (21,22,23). DNA gyrase is a heterotetramer comprising two GyrA and two GyrB subunits, whereas topoisomerase IV is a heterotetramer comprising two ParC and two ParE subunits.…”