Structure–activity relationships of a novel pyranopyridine series of Gram-negative bacterial efflux pump inhibitors

Abstract

Recently we described a novel pyranopyridine inhibitor (MBX2319) of RND-type efflux pumps of the Enterobacteriaceae. MBX2319 (3,3-dimethyl-5-cyano-8-morpholino-6-(phenethylthio)-3,4-dihydro-1H-pyrano[3,4-c]pyridine) is structurally distinct from other known Gram-negative efflux pump inhibitors (EPIs), such as 1-(1-naphthylmethyl)-piperazine (NMP), phenylalanylarginine-β-naphthylamide (PAβN), D13-9001, and the pyridopyrimidine derivatives. Here, we report the synthesis and biological evaluation of 60 new analogs of MBX2319 that were designed to probe the structure activity relationships (SARs) of the pyranopyridine scaffold. The results of these studies produced a molecular activity map of the scaffold, which identifies regions that are critical to efflux inhibitory activities and those that can be modified to improve potency, metabolic stability and solubility. Several compounds, such as 22d–f, 22i and 22k, are significantly more effective than MBX2319 at potentiating the antibacterial activity of levofloxacin and piperacillin against Escherichia coli.

Molecular basis for inhibition of AcrB multidrug efflux pump by novel and powerful pyranopyridine derivatives

“…The accumulation of H33342 in the presence of 12.5 μM MBX3132 or MBX3135 significantly exceeded the level of H33342 accumulation over the level of H33342 accumulation of the ΔacrB strain (Fig. 4 F and G), suggesting that MBX3132 and MBX3135 inhibit additional RND family efflux pumps, because they do not perturb the inner or outer E. coli membrane (22). In the presence of 10 nM MBX3132 or MBX3135, the kinetics of AcrAB-TolCmediated nitrocefin efflux were severely affected, whereas the effect of 10 nM MBX2319 was negligible (Fig.…”

“…We systematically varied the substituents around the pyranopyridine core (22). We found that the nitrile, dimethylenesulfide, and gemdimethyl groups could not be varied without negatively affecting the activity, whereas substitutions at the phenyl and morpholinyl groups (MBX2931, MBX3132, and MBX3135) improved potency and stability (Fig.…”

“…More recently, we described new derivatives of MBX2319 with increased activity. Notably MBX3132 and MBX3135 showed full activity even at 0.1 μM, that is, at concentrations 500-fold lower than the classical inhibitors like PAβN (22). Here, we report on microbiological, crystallographic, and computational studies on the interaction of AcrB with these novel and powerful inhibitors.…”

Efflux pump inhibitors of clinically relevant multidrug resistant bacteria

“…Compounds 53 to 56 (Figure ) were shown to be the most promising in this series, reducing the MICs of levofloxacin and piperacilin against E. coli AB1157 with MPC 4 values in the range of 0.05 to 0.8 µM, which is about an order of magnitude lower than that of previously described EPIs acting on the AcrAB‐TolC efflux pump system. All of them possessed improved aqueous solubility compared to that of MBX2319 and were also more stable in a human liver microsome stability assay . The SAR was established by the following: (i) nitrile, dimethylenesulfide, and geminal dimethyl groups are important for maintaining potency; (ii) nonacidic substituents in the phenyl moiety improve potency and in vitro pharmacokinetic properties; (iii) an additional dimethyl group on the morpholine ring improves microsomal stability and replacement of the morpholinyl group with the (2‐methoxyethyl)piperazinyl moiety yields moderately stable compounds with significantly improved aqueous solubility.…”

Novel Piperazine Arylideneimidazolones Inhibit the AcrAB-TolC Pump in Escherichia coli and Simultaneously Act as Fluorescent Membrane Probes in a Combined Real-Time Influx and Efflux Assay

“…To combat MDR, efflux pump inhibitors (EPIs) are an attractive option, and several EPIs that act against the AcrAB-TolC efflux pump have already been described in the literature (4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16), among which arylpiperazine and arylmorpholine derivatives constitute some of the largest systematically examined compound classes.…”