New Antibacterial Agents Derived from the DNA Gyrase Inhibitor Cyclothialidine

Abstract

Cyclothialidine (1, Ro 09-1437) is a potent DNA gyrase inhibitor that was isolated from Streptomyces filipinensis NR0484 and is a member of a new family of natural products. It acts by competitively inhibiting the ATPase activity exerted by the B subunit of DNA gyrase but barely exhibits any growth inhibitory activity against intact bacterial cells, presumably due to insufficient permeation of the cytoplasmic membrane. To explore the antibacterial potential of 1, we developed a flexible synthetic route allowing for the systematic modification of its structure. From a first set of analogues, structure-activity relationships (SAR) were established for different substitution patterns, and the 14-hydroxylated, bicyclic core (X) of 1 seemed to be the structural prerequisite for DNA gyrase inhibitory activity. The variation of the lactone ring size, however, revealed that activity can be found among 11- to 16-membered lactones, and even seco-analogues were shown to maintain some enzyme inhibitory properties, thereby reducing the minimal structural requirements to a rather simple, hydroxylated benzyl sulfide (XI). On the basis of these "minimal structures" a modification program afforded a number of inhibitors that showed in vitro activity against Gram-positive bacteria. The best activities were displayed by 14-membered lactones, and representatives of this subclass exhibit excellent and broad in vitro antibacterial activity against Gram-positive pathogens, including Staphylococcus aureus, Streptococcus pyogenes, and Enterococcus faecalis, and overcome resistance against clinically used drugs. By improving the pharmacokinetic properties of the most active compounds (94, 97), in particular by lowering their lipophilic properties, we were able to identify congeners of cyclothialidine (1) that showed efficacy in vivo.

Lessons for fragment library design: analysis of output from multiple screening campaigns

“…However, like Abbott, the great majority of our fragment hits when crystallized with their respective protein targets bind to the sites which are known to bind small molecules as inferred from existing structural data. Among all 12 targets, high affinity (\300 nM) small-molecular ligands have been reported in the literature [14,[74][75][76][77][78][79] except for HSP70, PIN-1 and PPI-3 which correspond to the lowest hit rates observed (between 0.4 and 0.7%). For targets which yielded high hit rates ([2%), all nine proteins have potent small molecule binders known to date.…”

A practical drug discovery project at the undergraduate level

“…The various amines chosen by the students (8 a-o) are shown in Table 1. The intermediate 9 is desilylated, conveniently and rapidly, with ammonium fluoride 27 and then purified by column chromatography to give 5. Table 1 shows the analogues prepared (with screening data).…”

The challenge of developing robust drugs to overcome resistance

“…[63]), novel classes of inhibitors of the ATPase activity have been designed to circumvent the resistance observed with quinolones. Interestingly, these compounds also overcome the resistance associated with the coumarins and cyclothialidines [64,65] that bind in a region that overlaps the ATP-binding site [66,67]. These ATPase inhibitors inhibit gyrase and topoisomerase IV simultaneously, thus yielding an advantage in that the emergence of resistance would require the unlikely occurrence of simultaneous mutations.…”