Identification and Structure–Activity Relationships of Novel Compounds that Potentiate the Activities of Antibiotics in Escherichia coli

Abstract

In Gram-negative bacteria, efflux pumps are able to prevent effective cellular concentrations from being achieved for a number of antibiotics. Small molecule adjuvants that act as efflux pump inhibitors (EPIs) have the potential to reinvigorate existing antibiotics that are currently ineffective due to efflux mechanisms. Through a combination of rigorous experimental screening and in silico virtual screening we recently identified novel classes of EPIs that interact with the membrane fusion protein AcrA, a critical component of the AcrAB-TolC efflux pump in E. coli. Herein, we present initial optimization efforts and structure-activity relationships around one of those previously described hits, NSC 60339 (1). From these efforts we identified two compounds, SLUPP-225 (17h) and SLUPP-417 (17o), which demonstrate favorable properties as potential EPIs in E. coli cells including the ability to penetrate the outer membrane, improved inhibition of efflux relative to 1 and potentiation of the activity of novobiocin and erythromycin.

Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance

“…For this purpose, one could test antisense oligomers (phosphorodiamidate morpholino oligomers, PPMOs), which are a promising way to inhibit the expression of a broad range of targets 79 -an approach that has been successfully used for genes encoding efflux pumps, leading to antibiotic hyper-sensitivity 60 . Targeting efflux pumps would also be possible with other small molecules [80][81][82][83] or with phages that require TolC for entry 84 . This specific approach has broader potential for gram-negative bacteria, where TolC family proteins are ubiquitous 85 .…”

Quantifying the Evolutionary Conservation of Genes Encoding Multidrug Efflux Pumps in the ESKAPE Pathogens To Identify Antimicrobial Drug Targets

“…The acrAB-tolC system in Escherichia coli has received a lot of attention as a potential drug target to treat resistant infections ( 17 , 29 ), including the use of the FDA-approved antipsychotic medication pimozide ( 30 ). This system is also found in both Enterobacter spp.…”

Repurposing Therapeutics for COVID-19: Supercomputer-Based Docking to the SARS-CoV-2 Viral Spike Protein and Viral Spike Protein-Human ACE2 Interface

“…By accounting for the conformational diversity of the receptor ensemble docking enhances the likelihood of identifying predicted hits (enrichment), which may be lost when screening against a single conformation of the target 12 . We have previously applied this technique to derive experimentally-verified hits for several protein targets to treat diseases ranging from bacterial infections to osteoporosis [14][15][16][17][18][19][20][21][22] . For this work three phases of calculations were performed: structural modeling, molecular simulations (ensemble building), and small-molecule docking (in silico ligand screening)…”