New Understanding for New Antibiotics: Bacterial Nutrient Stress and Drug Efflux

Abstract

The dramatic decline in the discovery and development of novel antibiotics has been met with an exponential increase in antibiotic-resistant pathogenic bacteria. Calls for new chemical matter have been paradoxically answered with the withdrawal of multinational pharmaceutical companies from the field of antibiotic discovery and development. Nevertheless, scientific challenges have also been a major contributor to a lean antibiotic pipeline. Renewed efforts to gain a deeper understanding of the bacterial physiology, which governs growth and survival, are urgently needed. To this end, I have examined two important avenues with relevance to the field of new antibiotic discovery using Escherichia coli as a model: 1) a systems analysis of the interactions of essential functions under nutrient stress and 2) a physicochemical and structural analysis of small molecules to identify properties that influence Gram-negative activity and efflux susceptibility. I tackled the first aim by systematically combining 45 chemical probes that target essential cellular processes. I revealed a highly connected network of 186 interactions, of which 81 were synergistic and 105 were antagonistic. The network highlighted new connectivity between housekeeping functions and nutrient metabolism. I approached the second aim by screening ~314,000 diverse synthetic compounds for inhibitors of an efflux-deficient E. coli strain. I identified about 4,500 actives, of which approximately 84% showed high susceptibility to efflux. Using a machine learning approach, I assessed the physicochemical space occupied by these 4,500 inhibitors and determined that hydrophobic and planar small molecules with low molecular stability exhibited antibacterial activity only in efflux-compromised E. coli. Further, compounds with reduced branching and compactness showed increased susceptibility to efflux. Within this dataset, I also identified some compound series highlighting structural variations that have a large impact on efflux susceptibility. In all, the work provides new insights into an emerging target in antibiotic drug discovery, namely nutrient stress, and uncovers some physicochemical properties and structural motifs that contribute to antibacterial activity and efflux susceptibility of small molecules.