Multidrug Efflux in Gram-Negative Bacteria: Rationally Modifying Compounds to Avoid Efflux Pumps

Gram-negative bacteria cause the majority of critically drug-resistant infections, necessitating the rapid development of new drugs with Gram-negative activity. However, drug design is hampered by the low permeability of the Gram-negative cell envelope and the function of drug efflux pumps, which extrude foreign molecules from the cell. A better understanding of the molecular determinants of compound recognition by efflux pumps is, therefore, essential. Here, we quantitatively analyse the activity of over 73,000 compounds across three strains of E. coli – the wild-type, an efflux-deficient variant, and a hyper-permeable variant – to elucidate the molecular principles of evading efflux pumps. Our results show that, alongside a range of physicochemical features, the presence or absence of specific chemical groups in the compounds substantially increases the probability of avoiding efflux. Furthermore, comparison of our findings with inward permeability data highlights the primary role of efflux in determining drug bioactivity in Gram-negative bacteria.