Getting drugs into gram-negative bacteria: rational rules for permeation through general porins

Silvia Acosta-gutiérrez, Luana Ferrara, Monisha Pathania, Muriel Masi, Jiajun Wang, Igor Bodrenko, Michael Zahn, Mathias Winterhalter, Robert A. Stavenger, Jean-Marie Pagès, James H. Naismith, Bert van den Berg, Malcolm G. P. Page, Matteo Ceccarelli

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Small, hydrophilic molecules, including most important antibiotics in clinical use, cross the Gram-negative outer membrane through the water-filled channels provided by porins. We have determined the X-ray crystal structures of the principal general porins from three species of Enterobacteriaceae, namely Enterobacter aerogenes, Enterobacter cloacae, and Klebsiella pneumoniae, and determined their antibiotic permeabilities as well as those of the orthologues from Escherichia coli. Starting from the structure of the porins and molecules, we propose a physical mechanism underlying transport and condense it in a computationally efficient scoring function. The scoring function shows good agreement with in vitro penetration data and will enable the screening of virtual databases to identify molecules with optimal permeability through porins and help to guide the optimization of antibiotics with poor permeation.
Original languageEnglish
Pages (from-to)1487-1498
Number of pages12
JournalACS Infectious Diseases
Issue number10
Early online date2 Jul 2018
Publication statusPublished - 12 Oct 2018


  • bacteria
  • antibiotics
  • rational design
  • porins structure
  • transport
  • scoring function


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