The 6-fluoro-GyrB with C3, with key interactions highlighted. Crizotinib hydrochloride ParE at position 1 generates significant structural diversity in the pocket floor in the vicinity of the variable residue. Inhibitors with groups that impinge on the pocket floor in the vicinity of residue 1 generally demonstrated inferior dual-targeting activity. Diversity in residue 3 influences the volume of the interior lipophilic pocket: ParE enzymes from Gram-positive bacteria typically present a small Ala Rabbit polyclonal to JNK1 side-chain at this position, while the Gram-negative ParE enzymes present a large Ile side-chain at position 3. GyrB enzymes present intermediate Val or Ser residues at position 3. As a result, the Gram-negative ParE enzymes are the most spatially constrained in the vicinity of residue 3, and limit the size of substituents that are tolerated off the R6 position of the pyrimidoindole inhibitor scaffold. (DOCX) pone.0084409.s001.docx (394K) GUID:?A93F1EB9-808E-42E3-B8B9-65E247065758 Abstract Increasing resistance to every major class of antibiotics and a dearth of novel classes of antibacterial agents in development pipelines has created a dwindling reservoir of treatment options for serious bacterial infections. The bacterial type IIA topoisomerases, DNA gyrase and topoisomerase IV, are validated antibacterial drug targets with multiple prospective drug binding sites, including the catalytic site targeted by the fluoroquinolone antibiotics. However, growing resistance to fluoroquinolones, frequently mediated by mutations Crizotinib hydrochloride in the drug-binding site, is increasingly limiting the utility of this antibiotic class, prompting the search for other inhibitor classes that target different sites on the topoisomerase complexes. The highly conserved ATP-binding subunits of DNA gyrase (GyrB) and topoisomerase IV (ParE) have long been recognized as excellent candidates for the development of dual-targeting antibacterial agents with broad-spectrum potential. However, to date, no natural product or small molecule inhibitors targeting these sites have succeeded in the clinic, and no inhibitors of these enzymes have yet been reported with broad-spectrum antibacterial activity encompassing the majority of Gram-negative pathogens. Using structure-based drug design (SBDD), we have created a novel dual-targeting pyrimidoindole inhibitor series with exquisite potency against GyrB and ParE enzymes from a broad range of clinically important pathogens. Inhibitors from this series demonstrate potent, broad-spectrum antibacterial activity against Gram-positive and Gram-negative pathogens of clinical importance, including fluoroquinolone resistant and multidrug resistant strains. Lead compounds have been discovered with clinical potential; they are well tolerated in animals, and efficacious in Gram-negative infection models. Introduction Multidrug resistant (MDR) infections in the clinic are growing at a significant rate, largely due to the limited number of bacterial targets inhibited by the arsenal of antibiotics used for the last half-century [1-3]. Since the 1960s, the carbapenems (a Clactam natural product antibiotic class introduced in the 1980s) and the fluoroquinolones are the only new classes of antibiotics that have been developed with activity against clinically important Gram-negative pathogens. The difficulty in developing new antibacterial classes stems from the challenges of developing small molecules capable of penetrating the cell envelope and avoiding drug efflux systems . As a result, there is an alarming lack of efficacious therapeutic choices for clinicians treating these infections. To provide potential solutions to this problem, we used structure-based drug design (SBDD) to develop a novel class of broad-spectrum antibacterial agents with activity against resistant pathogens, including Gram-negative MDR strains. Advances in SBDD technology combined with a greater understanding of the factors that influence Gram-negative permeability and drug efflux has made possible the rational design of broad-spectrum antibacterial agents. Target selection is central to this process. Targets need to meet key criteria: First, the active-site of the target needs characteristics that allow for the Crizotinib hydrochloride design of highly potent enzyme inhibitors (subnanomolar inhibition.