How proteins bind macrocycles

Nat Chem Biol. 2014 Sep;10(9):723-31. doi: 10.1038/nchembio.1584. Epub 2014 Jul 20.


The potential utility of synthetic macrocycles (MCs) as drugs, particularly against low-druggability targets such as protein-protein interactions, has been widely discussed. There is little information, however, to guide the design of MCs for good target protein-binding activity or bioavailability. To address this knowledge gap, we analyze the binding modes of a representative set of MC-protein complexes. The results, combined with consideration of the physicochemical properties of approved macrocyclic drugs, allow us to propose specific guidelines for the design of synthetic MC libraries with structural and physicochemical features likely to favor strong binding to protein targets as well as good bioavailability. We additionally provide evidence that large, natural product-derived MCs can bind targets that are not druggable by conventional, drug-like compounds, supporting the notion that natural product-inspired synthetic MCs can expand the number of proteins that are druggable by synthetic small molecules.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Binding Sites / drug effects
  • Biological Availability
  • Crystallography, X-Ray
  • Drug Design
  • Macrocyclic Compounds / metabolism*
  • Mass Spectrometry
  • Models, Molecular
  • Molecular Weight
  • Pharmaceutical Preparations / metabolism
  • Protein Binding / drug effects*
  • Proteins / metabolism
  • Small Molecule Libraries


  • Macrocyclic Compounds
  • Pharmaceutical Preparations
  • Proteins
  • Small Molecule Libraries