Multidrug efflux in Gram-negative bacteria: structural modifications in active compounds leading to efflux pump avoidance

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 analysed the activity of 73,737 compounds, recorded in the publicly accessible database CO-ADD, across three strains of E. coli – the wild-type, the efflux-deficient tolC variant, and the hyper-permeable lpxC variant, to elucidate the molecular principles of evading efflux pumps. We computationally investigated molecular features within this dataset that promote, or reduce, the propensity of being recognised by the TolC-dependent efflux systems in E. coli. 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. A comparison of our findings with inward permeability data further underscores the primary role of efflux in determining drug bioactivity in Gram-negative bacteria.