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Hurley MFD , Northrup JD , Ge Y , Schafmeister CE , Voelz VA
Metal Cation-Binding Mechanisms of Q-Proline Peptoid Macrocycles in Solution
J Chem Inf Model. 2021 Jun 28;61(6) :2818-2828
PMID: 34125519    PMCID: PMC8370751    URL: https://www.ncbi.nlm.nih.gov/pubmed/34125519
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Abstract
The rational design of foldable and functionalizable peptidomimetic scaffolds requires the concerted application of both computational and experimental methods. Recently, a new class of designed peptoid macrocycle incorporating spiroligomer proline mimics (Q-prolines) has been found to preorganize when bound by monovalent metal cations. To determine the solution-state structure of these cation-bound macrocycles, we employ a Bayesian inference method (BICePs) to reconcile enhanced-sampling molecular simulations with sparse ROESY correlations from experimental NMR studies to predict and design conformational and binding properties of macrocycles as functional scaffolds for peptidomimetics. Conformations predicted to be most populated in solution were then simulated in the presence of explicit cations to yield trajectories with observed binding events, revealing a highly preorganized all-trans amide conformation, whose formation is likely limited by the slow rate of cis/trans isomerization. Interestingly, this conformation differs from a racemic crystal structure solved in the absence of cation. Free energies of cation binding computed from distance-dependent potentials of mean force suggest Na(+) has a higher affinity to the macrocycle than K(+), with both cations binding much more strongly in acetonitrile than water. The simulated affinities are able to correctly rank the extent to which different macrocycle sequences exhibit preorganization in the presence of different metal cations and solvents, suggesting our approach is suitable for solution-state computational design.
Notes
1549-960x Hurley, Matthew F D Northrup, Justin D Ge, Yunhui Orcid: 0000-0002-3946-1440 Schafmeister, Christian E Orcid: 0000-0002-8686-7363 Voelz, Vincent A Orcid: 0000-0002-1054-2124 Journal Article United States J Chem Inf Model. 2021 Jun 28;61(6):2818-2828. doi: 10.1021/acs.jcim.1c00447. Epub 2021 Jun 14.