Nandan Haloi, Archit Kumar Vasan, Emily Jane Geddes, Arjun Prasanna, Po-Chao
Wen, William W. Metcalf, Paul J Hergenrother, and Emad Tajkhorshid.
Rationalizing generation of broad spectrum antibiotics with the
addition of a positive charge.
Chemical Science, 12:15028-15044, 2021.
HALO2021A-ET
Antibiotic resistance of Gram-negative bacteria is largely attributed to the low permeability of their outer membrane (OM). Recently,
we disclosed the eNTRy rules, a key lesson of which is that the introduction of a primary amine enhances OM permeation in certain
contexts. To understand the molecular basis for this finding, we perform an extensive set of molecular dynamics (MD) simulations and
free energy calculations comparing the permeation of aminated and amine-free antibiotic derivatives through the most abundant OM porin
of E. coli, OmpF. To improve sampling of conformationally flexible drugs in MD simulations, we developed a novel, Monte Carlo and
graph theory based algorithm to probe more efficiently the rotational and translational degrees of freedom visited during the
permeation of the antibiotic molecule through OmpF. The resulting pathways were then used for free-energy calculations, revealing a
lower barrier against the permeation of the aminated compound, substantiating its greater OM permeability. Further analysis revealed
that the amine facilitates permeation by enabling the antibiotic to align its dipole to the luminal electric field of the porin and
while forming favorable electrostatic interactions with specific, highly-conserved charged residues. The importance of these
interactions in permeation was further validated with experimental mutagenesis and whole cell accumulation assays. Overall, this study
provides insights on the importance of the primary amine for antibiotic permeation into Gram-negative pathogens that could help the
design of future antibiotics. We also offer a new computational approach for calculating free-energy of processes where relevant
molecular conformations cannot be efficiently captured.
