Structure-Activity Relationship and Molecular Mechanics Reveal the Importance of Ring Entropy in the Biosynthesis and Activity of a Natural Product

J Am Chem Soc. 2017 Feb 22;139(7):2541-2544. doi: 10.1021/jacs.6b10792. Epub 2017 Feb 13.


Macrocycles are appealing drug candidates due to their high affinity, specificity, and favorable pharmacological properties. In this study, we explored the effects of chemical modifications to a natural product macrocycle upon its activity, 3D geometry, and conformational entropy. We chose thiocillin as a model system, a thiopeptide in the ribosomally encoded family of natural products that exhibits potent antimicrobial effects against Gram-positive bacteria. Since thiocillin is derived from a genetically encoded peptide scaffold, site-directed mutagenesis allows for rapid generation of analogues. To understand thiocillin's structure-activity relationship, we generated a site-saturation mutagenesis library covering each position along thiocillin's macrocyclic ring. We report the identification of eight unique compounds more potent than wild-type thiocillin, the best having an 8-fold improvement in potency. Computational modeling of thiocillin's macrocyclic structure revealed a striking requirement for a low-entropy macrocycle for activity. The populated ensembles of the active mutants showed a rigid structure with few adoptable conformations while inactive mutants showed a more flexible macrocycle which is unfavorable for binding. This finding highlights the importance of macrocyclization in combination with rigidifying post-translational modifications to achieve high-potency binding.

Publication types

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

MeSH terms

  • Biological Products* / chemistry
  • Biological Products* / pharmacology
  • Macrocyclic Compounds / chemistry
  • Molecular Conformation
  • Molecular Dynamics Simulation
  • Peptides / chemistry*
  • Peptides / genetics
  • Peptides / pharmacology
  • Structure-Activity Relationship


  • Biological Products
  • Macrocyclic Compounds
  • Peptides
  • thiocillin