Structure-Activity Relationship and Molecular Mechanics Reveal the Importance of Ring Entropy in the Biosynthesis and Activity of a Natural Product.
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.
Hai L
0000-0003-3715-8111
HL
Tran
Katrina W
KW
Lexa
Olivier
0000-0001-7068-7299
O
Julien
Department of Biology, California Institute for Biomedical Research , La Jolla, California 92037, United States.
Travis S
TS
Young
Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University , Stanford, California 94305, United States.
Christopher T
CT
Walsh
Matthew P
0000-0001-6262-655X
MP
Jacobson
James A
JA
Wells
D001688:Biological Products / Q000737:chemistry / Q000494:pharmacology; D047028:Macrocyclic Compounds / Q000737:chemistry; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry* / Q000235:genetics / Q000494:pharmacology; D013329:Structure-Activity Relationship
D001688:Biological Products; D047028:Macrocyclic Compounds; D010455:Peptides; C012574:thiocillin