title: Toward the rational design of carbapenem uptake in Pseudomonas aeruginosa.
abstract: 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.
authors.affiliation: Synlogic, 25 First Street, Cambridge, MA 02141, USA.
authors.forename: Vincent M
authors.initials: VM
authors.lastname: Isabella
authors.affiliation: Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard University, 415 Main Street, Cambridge, MA 02142, USA.
authors.forename: Arthur J
authors.initials: AJ
authors.lastname: Campbell
authors.affiliation: AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, MA 02451, USA.
authors.forename: John
authors.initials: J
authors.lastname: Manchester
authors.affiliation: AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, MA 02451, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Sylvester
authors.affiliation: AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, MA 02451, USA.
authors.forename: Asha S
authors.initials: AS
authors.lastname: Nayar
authors.affiliation: AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, MA 02451, USA.
authors.forename: Keith E
authors.initials: KE
authors.lastname: Ferguson
authors.affiliation: AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, MA 02451, USA. Electronic address: ruben.tommasi@astrazeneca.com.
authors.forename: Ruben
authors.initials: R
authors.lastname: Tommasi
authors.affiliation: AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, MA 02451, USA. Electronic address: alita.miller@astrazeneca.com.
authors.forename: Alita A
authors.initials: AA
authors.lastname: Miller
mesh_terms: D019943:Amino Acid Substitution; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D015780:Carbapenems / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology; D008826:Microbial Sensitivity Tests; D062105:Molecular Docking Simulation; D017434:Protein Structure, Tertiary; D011550:Pseudomonas aeruginosa / Q000187:drug effects / Q000378:metabolism*; D013379:Substrate Specificity
chemical_list: D001425:Bacterial Outer Membrane Proteins; D015780:Carbapenems