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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; 61:2818-2828. [PMID: 34125519 DOI: 10.1021/acs.jcim.1c00447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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.
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Affiliation(s)
- Matthew F D Hurley
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Justin D Northrup
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Yunhui Ge
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | | | - Vincent A Voelz
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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Northrup JD, Wiener JA, Hurley MFD, Hou CFD, Keller TM, Baxter RHG, Zdilla MJ, Voelz VA, Schafmeister CE. Metal-Binding Q-Proline Macrocycles. J Org Chem 2021; 86:4867-4876. [PMID: 33635647 DOI: 10.1021/acs.joc.1c00116] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We introduce the efficient Fmoc-SPPS and peptoid synthesis of Q-proline-based, metal-binding macrocycles (QPMs), which bind metal cations and display nine functional groups. Metal-free QPMs are disordered, evidenced by NMR and a crystal structure of QPM-3 obtained through racemic crystallization. Upon addition of metal cations, QPMs adopt ordered structures. Notably, the addition of a second functional group at the hydantoin amide position (R2) converts the proline ring from Cγ-endo to Cγ-exo, due to steric interactions.
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Affiliation(s)
- Justin D Northrup
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States.,ThirdLaw Molecular, 512 Township Line Road, Blue Bell, Pennsylvania 19422, United States
| | - Jesse A Wiener
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Matthew F D Hurley
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Chun-Feng David Hou
- Department of Medical Genetics & Molecular Biochemistry, Lewis Katz School of Medicine, Temple University, 3440 North Broad Street, Philadelphia Pennsylvania 19140, United States
| | - Taylor M Keller
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Richard H G Baxter
- Department of Medical Genetics & Molecular Biochemistry, Lewis Katz School of Medicine, Temple University, 3440 North Broad Street, Philadelphia Pennsylvania 19140, United States
| | - Michael J Zdilla
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Vincent A Voelz
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Christian E Schafmeister
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States.,ThirdLaw Molecular, 512 Township Line Road, Blue Bell, Pennsylvania 19422, United States
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Pierri G, Landi A, Macedi E, Izzo I, De Riccardis F, Dinnebier RE, Tedesco C. Propyne Gas Adsorption in a Cyclic Hexapeptoid: A Combined In Situ XRPD and DFTB Study*. Chemistry 2020; 26:14320-14323. [PMID: 32618043 DOI: 10.1002/chem.202002694] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/30/2020] [Indexed: 11/06/2022]
Abstract
Cyclic peptoids are macrocyclic N-substituted oligoglycines, with remarkable structural, chemical and physical properties. The gas adsorption properties of a permanently porous hexameric cyclopeptoid decorated with four propargyl and two methoxyethyl side chains were monitored by in situ X-ray powder diffraction (XRPD). High-resolution XRPD data together with Rietveld and density functional based tight binding (DFTB) method allowed us to locate propyne guest molecules inside the host channels, even though the powder sample contains more than one phase. We were able to characterize the host-guest interactions, providing useful information on the host recognition sites and discuss host adaptiveness and host-guest chemical affinity in comparison with analogous compounds.
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Affiliation(s)
- Giovanni Pierri
- Department Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II 132, 84084, Fisciano (SA), Italy
| | - Alessandro Landi
- Department Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II 132, 84084, Fisciano (SA), Italy
| | - Eleonora Macedi
- Department of Pure and Applied Science, University of Urbino "Carlo Bo", Via della Stazione 4, 61029, Urbino, Italy
| | - Irene Izzo
- Department Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II 132, 84084, Fisciano (SA), Italy
| | - Francesco De Riccardis
- Department Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II 132, 84084, Fisciano (SA), Italy
| | - Robert E Dinnebier
- Max-Planck-Institute for Solid State Research, Heisenbergstrasse 1, Stuttgart, 70569, Germany
| | - Consiglia Tedesco
- Department Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II 132, 84084, Fisciano (SA), Italy
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Affiliation(s)
- Francesco De Riccardis
- Department of Chemistry and Biology “A. Zambelli”; University of Salerno; Via Giovani Paolo II, 132 84084 Fisciano SA Italy
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Abstract
Over the past two decades, developing medical applications for peptides has, and continues to be a highly active area of research. At present there are over 60 peptide-based drugs on the market and more than 140 in various stages of clinical trials. The interest in peptide-based therapeutics arises from their biocompatibility and their ability to form defined secondary and tertiary structures, resulting in a high selectivity for complex targets. However, there are significant challenges associated with the development of peptide-based therapeutics, namely peptides are readily metabolised in vivo. Peptoids are an emerging class of peptidomimetic and they offer an alternative to peptides. Peptoids are comprised of N-substituted glycines where side-chains are located on the nitrogen atom of the amide backbone rather than the α-carbon as is the case in peptides. This change in structure confers a high degree of resistance to proteolytic degradation but the absence of any backbone hydrogen bonding means that peptoids exhibit a high degree of conformational flexibility. Cyclisation has been explored as one possible route to rigidify peptoid structures, making them more selective, and, therefore more desirable as potential therapeutics. This review outlines the various strategies that have been developed over the last decade to access new types of macrocyclic peptoids.
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Affiliation(s)
| | - Steven L. Cobb
- Department of ChemistryDurham UniversitySouth RoadDurhamDH1 3LEUK
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