Folding Then Binding vs Folding through Binding in Macrocyclic Peptide Inhibitors of Human Pancreatic α-Amylase

L. Goldbach, B.J.A. Vermeulen, S. Caner, M. Liu, C. Tysoe, L. Van Gijzel, R. Yoshisada, M. Trellet, H. Van Ingen, G.D. Brayer, A.M.J.J. Bonvin, S.A.K. Jongkees

Research output: Contribution to JournalArticleAcademicpeer-review

Abstract

© 2019 American Chemical Society.De novo macrocyclic peptides, derived using selection technologies such as phage and mRNA display, present unique and unexpected solutions to challenging biological problems. This is due in part to their unusual folds, which are able to present side chains in ways not available to canonical structures such as α-helices and β-sheets. Despite much recent interest in these molecules, their folding and binding behavior remains poorly characterized. In this work, we present cocrystallization, docking, and solution NMR structures of three de novo macrocyclic peptides that all bind as competitive inhibitors with single-digit nanomolar Ki to the active site of human pancreatic α-amylase. We show that a short stably folded motif in one of these is nucleated by internal hydrophobic interactions in an otherwise dynamic conformation in solution. Comparison of the solution structures with a target-bound structure from docking indicates that stabilization of the bound conformation is provided through interactions with the target protein after binding. These three structures also reveal a surprising functional convergence to present a motif of a single arginine sandwiched between two aromatic residues in the interactions of the peptide with the key catalytic residues of the enzyme, despite little to no other structural homology. Our results suggest that intramolecular hydrophobic interactions are important for priming binding of small macrocyclic peptides to their target and that high rigidity is not necessary for high affinity.
Original languageEnglish
Pages (from-to)1751-1759
JournalACS chemical biology
Volume14
Issue number8
DOIs
Publication statusPublished - 16 Aug 2019
Externally publishedYes

Funding

A.M.J.J.B. and M.T. acknowledge financial support from the European H2020 e-Infrastructure grant BioExcel (No. 675728). H.v.I. acknowledges financial support from The Netherlands Organisation for Scientic Research (No. 723.013.010). S.C. and G.D.B. acknowledge funding from the Canadian Glycomics Network/Networks of Centres of Excellence (Project DO-2). Deglycosylated recombinant human pancreatic α-amylase was kindly provided by S. Withers (University of British Columbia, Canada). Portions of this research were carried out at the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, which is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DE-AC02-76SF00515. The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research, and by the NIH, National Institute of General Medical Sciences (including P41GM103393). The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of NIGMS or NIH.

FundersFunder number
Canadian Glycomics Network/Networks of Centres of ExcellenceDO-2
DOE Office of Biological and Environmental Research
Netherlands Organisation for Scientic Research723.013.010
Office of Basic Energy Sciences
National Institutes of Health
U.S. Department of Energy
National Institute of General Medical SciencesP41GM103393
Office of Science
H2020 European Research Council675728

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