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Getting Drugs into Gram-Negative Bacteria: Rational Rules for Permeation through General Porins.

Silvia Acosta-Gutiérrez1, Luana Ferrara2, Monisha Pathania3

  • 1Department of Physics , University of Cagliari, Cittadella Universitaria di Monserrato , SP Monserrato-Sestu Km 0.8 , Monserrato , 09042 , Italy.

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Researchers determined porin structures and developed a scoring function to predict antibiotic permeability across Gram-negative bacteria outer membranes, aiding drug discovery.

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antibioticsbacteriaporins structurerational designscoring functiontransport

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Area of Science:

  • Microbiology and Structural Biology
  • Drug Discovery and Development

Background:

  • Gram-negative bacteria possess an outer membrane that restricts the entry of many hydrophilic molecules, including antibiotics.
  • Porins form water-filled channels in this outer membrane, serving as the primary pathway for small molecule transport.
  • Understanding porin-mediated transport is crucial for developing effective antibiotics against Gram-negative infections.

Purpose of the Study:

  • To elucidate the X-ray crystal structures of principal general porins from Enterobacter aerogenes, Enterobacter cloacae, and Klebsiella pneumoniae.
  • To determine the antibiotic permeability through these porins and orthologues from Escherichia coli.
  • To develop a predictive model for molecule transport through porins.

Main Methods:

  • X-ray crystallography was used to determine the three-dimensional structures of porins.
  • Antibiotic permeability assays were performed in vitro.
  • A computational scoring function was developed based on porin and molecule structures.

Main Results:

  • The X-ray crystal structures of key porins from three Enterobacteriaceae species were determined.
  • Antibiotic permeabilities were measured and correlated with structural data.
  • The developed scoring function demonstrated good agreement with experimental penetration data.

Conclusions:

  • A physical mechanism for porin-mediated transport was proposed and mathematically modeled.
  • The scoring function can efficiently screen virtual compound libraries for optimal porin permeability.
  • This approach can guide the optimization of antibiotics with poor permeation properties.