Fragment-guided design of subnanomolar β-lactamase inhibitors active in vivo

Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):17448-53. doi: 10.1073/pnas.1208337109. Epub 2012 Oct 5.


Fragment-based design was used to guide derivatization of a lead series of β-lactamase inhibitors that had heretofore resisted optimization for in vivo activity. X-ray structures of fragments overlaid with the lead suggested new, unanticipated functionality and points of attachment. Synthesis of three derivatives improved affinity over 20-fold and improved efficacy in cell culture. Crystal structures were consistent with the fragment-based design, enabling further optimization to a K(i) of 50 pM, a 500-fold improvement that required the synthesis of only six derivatives. One of these, compound 5, was tested in mice. Whereas cefotaxime alone failed to cure mice infected with β-lactamase-expressing Escherichia coli, 65% were cleared of infection when treated with a cefotaxime:5 combination. Fragment complexes offer a path around design hurdles, even for advanced molecules; the series described here may provide leads to overcome β-lactamase-based resistance, a key clinical challenge.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Bacterial Agents / chemistry*
  • Anti-Bacterial Agents / pharmacology
  • Bacteria / drug effects
  • Drug Design*
  • Enzyme Inhibitors / chemistry*
  • Enzyme Inhibitors / pharmacology
  • Microbial Sensitivity Tests
  • Models, Molecular
  • X-Ray Diffraction
  • beta-Lactamase Inhibitors*


  • Anti-Bacterial Agents
  • Enzyme Inhibitors
  • beta-Lactamase Inhibitors

Associated data

  • PDB/4E3I
  • PDB/4E3J
  • PDB/4E3K
  • PDB/4E3L
  • PDB/4E3M
  • PDB/4E3N
  • PDB/4E3O