Toward the Rational Design of Carbapenem Uptake in Pseudomonas aeruginosa

Understanding how compound penetration occurs across the complex cell walls of Gram-negative bacteria is one of the greatest challenges in discovering new drugs to treat the infections they cause. A combination of next-generation transposon sequencing, computational metadynamics simulations (CMDS), and medicinal chemistry was used to define genetic and structural elements involved in facilitated carbapenem entry into Pseudomonas aeruginosa. Here we show for the first time that these compounds are taken up not only by the major outer membrane channel OccD1 (also called OprD or PA0958) but also by a closely related channel OccD3 (OpdP or PA4501). Transport-mediating molecular interactions predicted by CMDS for these channels were first confirmed genetically, then used to guide the design of carbapenem analogs with altered uptake properties. These results bring us closer to the rational design of channel transmissibility and may ultimately lead to improved permeability of compounds across bacterial outer membranes. [Display omitted] •TNseq is used to discover novel carbapenem uptake mechanisms•Pseudomonal porin OccD3 is involved in carbapenem uptake•Metadynamics simulations describe carbapenem uptake on an atomic scale•Rational carbapenem design and synthesis lead to altered uptake properties Isabella et al. utilize a multidisciplinary approach including genetics, molecular dynamics simulations, and medicinal chemistry to probe carbapenem uptake by Pseudomonas aeruginosa. A novel uptake mechanism was discovered and novel carbapenems with altered uptake properties were synthesized and characterized.