1
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Mi T, Gao Z, Mituta Z, Burgess K. Dual-Capped Helical Interface Mimics. J Am Chem Soc 2024; 146:10331-10341. [PMID: 38573124 PMCID: PMC11027154 DOI: 10.1021/jacs.3c11717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/25/2024] [Accepted: 03/01/2024] [Indexed: 04/05/2024]
Abstract
Disruption of protein-protein interactions is medicinally important. Interface helices may be mimicked in helical probes featuring enhanced rigidities, binding to protein targets, stabilities in serum, and cell uptake. This form of mimicry is dominated by stapling between side chains of helical residues: there has been less progress on helical N-caps, and there were no generalizable C-caps. Conversely, in natural proteins, helicities are stabilized and terminated by C- and N-caps but not staples. Bicyclic caps previously introduced by us enable interface helical mimicry featuring rigid synthetic caps at both termini in this work. An unambiguously helical dual-capped system proved to be conformationally stable, binding cyclins A and E, and showed impressive cellular uptake. In addition, the dual-capped mimic was completely resistant to proteolysis in serum over an extended period when compared with "gold standard" hydrocarbon-stapled controls. Dual-capped peptidomimetics are a new, generalizable paradigm for helical interface probe design.
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Affiliation(s)
- Tianxiong Mi
- Department
of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
| | - Zhe Gao
- Department
of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
| | - Zeynep Mituta
- ZentriForce
Pharma Research GmbH, Carl-Friedrich-Gauss-Ring 5, 69124 Heidelberg, Germany
| | - Kevin Burgess
- Department
of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
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2
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Mi T, Nguyen D, Burgess K. Bicyclic Schellman Loop Mimics (BSMs): Rigid Synthetic C-Caps for Enforcing Peptide Helicity. ACS CENTRAL SCIENCE 2023; 9:300-306. [PMID: 36844493 PMCID: PMC9951308 DOI: 10.1021/acscentsci.2c01265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Indexed: 06/18/2023]
Abstract
Macrocyclic peptides are the prevalent way to mimic interface helices for disruption of protein interactions, but current strategies to do this via synthetic C-cap mimics are underdeveloped and suboptimal. Bioinformatic studies described here were undertaken to better understand Schellman loops, the most common C-caps in proteins, to design superior synthetic mimics. An algorithm (Schellman Loop Finder) was developed, and data mining with this led to the discovery that these secondary structures are often stabilized by combinations of three hydrophobic side chains, most frequently from Leu, to form hydrophobic triangles. That insight facilitated design of synthetic mimics, bicyclic Schellman loop mimics (BSMs), where the hydrophobic triumvirate was replaced by 1,3,5-trimethylbenzene. We demonstrate that BSMs can be made quickly and efficiently, and are more rigid and helix-inducing than the best current C-cap mimics, which are rare and all monocycles.
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3
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Whisenant J, Burgess K. Synthetic helical peptide capping strategies. Chem Soc Rev 2022; 51:5795-5804. [PMID: 35786712 DOI: 10.1039/d1cs01175h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Relatively small mimics of interface secondary structures can be used to disrupt protein-protein interactions (PPIs). This strategy is valuable because many PPIs are pivotal in cell biology and contemporary medicinal chemistry. Small peptides tend to have random coil conformations in solution, so the entropy costs are high for them to order into states binding protein receptors. Consequently, peptides constrained in conformations resembling interface secondary structures are favored for enhanced affinities to PPI components. Helices are commonly found at PPI interfaces. The two general strategies that have emerged for imposing helical constraints in probes, capping and stapling, are often confused because both involve formation of macrocyclic rings. This review considers parameters that distinguish capping from stapling. Capping motifs terminate helices and project the adjacent peptide units in non-helical orientations, but stapling enforces helical motifs in ways that enable adjacent peptide fragments to extend helices. There is no evidence that stapling is more effective than capping for helix mimicry, but stapling is used more frequently. This imbalance may be because no strategies have emerged for synthetic C-capping with compact unit; if convenient and effective C-capping strategies were available then capping strategies should be more widely used.
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Affiliation(s)
- Jonathan Whisenant
- Department of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, USA.
| | - Kevin Burgess
- Department of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, USA.
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4
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Wiedemann B, Kamps D, Depta L, Weisner J, Cvetreznik J, Tomassi S, Gentz S, Hoffmann JE, Müller MP, Koch O, Dehmelt L, Rauh D. Design and synthesis of Nrf2-derived hydrocarbon stapled peptides for the disruption of protein-DNA-interactions. PLoS One 2022; 17:e0267651. [PMID: 35731722 PMCID: PMC9216541 DOI: 10.1371/journal.pone.0267651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 04/13/2022] [Indexed: 11/29/2022] Open
Abstract
Misregulation and mutations of the transcription factor Nrf2 are involved in the development of a variety of human diseases. In this study, we employed the technology of stapled peptides to address a protein-DNA-complex and designed a set of Nrf2-based derivatives. Varying the length and position of the hydrocarbon staple, we chose the best peptide for further evaluation in both fixed and living cells. Peptide 4 revealed significant enrichment within the nucleus compared to its linear counterpart 5, indicating potent binding to DNA. Our studies suggest that these molecules offer an interesting strategy to target activated Nrf2 in cancer cells.
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Affiliation(s)
- Bianca Wiedemann
- Faculty of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Dortmund, Germany
| | - Dominic Kamps
- Faculty of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Dortmund, Germany
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Laura Depta
- Faculty of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Dortmund, Germany
| | - Jörn Weisner
- Faculty of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Dortmund, Germany
| | - Jana Cvetreznik
- Faculty of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Dortmund, Germany
| | - Stefano Tomassi
- Department of Pharmacy, University of Naples “Federico II”, Napoli, Italy
| | - Sascha Gentz
- Protein Chemistry Facility, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Jan-Erik Hoffmann
- Protein Chemistry Facility, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Matthias P. Müller
- Faculty of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Dortmund, Germany
| | - Oliver Koch
- Institute of Pharmaceutical and Medicinal Chemistry and German Center of Infection Research, Münster, Germany
| | - Leif Dehmelt
- Faculty of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Dortmund, Germany
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Daniel Rauh
- Faculty of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Dortmund, Germany
- * E-mail:
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5
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Islam MS, Junod SL, Zhang S, Buuh ZY, Guan Y, Zhao M, Kaneria KH, Kafley P, Cohen C, Maloney R, Lyu Z, Voelz VA, Yang W, Wang RE. Unprotected peptide macrocyclization and stapling via a fluorine-thiol displacement reaction. Nat Commun 2022; 13:350. [PMID: 35039490 PMCID: PMC8763920 DOI: 10.1038/s41467-022-27995-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/19/2021] [Indexed: 12/31/2022] Open
Abstract
We report the discovery of a facile peptide macrocyclization and stapling strategy based on a fluorine thiol displacement reaction (FTDR), which renders a class of peptide analogues with enhanced stability, affinity, cellular uptake, and inhibition of cancer cells. This approach enabled selective modification of the orthogonal fluoroacetamide side chains in unprotected peptides in the presence of intrinsic cysteines. The identified benzenedimethanethiol linker greatly promoted the alpha helicity of a variety of peptide substrates, as corroborated by molecular dynamics simulations. The cellular uptake of benzenedimethanethiol stapled peptides appeared to be universally enhanced compared to the classic ring-closing metathesis (RCM) stapled peptides. Pilot mechanism studies suggested that the uptake of FTDR-stapled peptides may involve multiple endocytosis pathways in a distinct pattern in comparison to peptides stapled by RCM. Consistent with the improved cell permeability, the FTDR-stapled lead Axin and p53 peptide analogues demonstrated enhanced inhibition of cancer cells over the RCM-stapled analogues and the unstapled peptides. Strategies capable of stapling unprotected peptides in a straightforward, chemoselective, and clean manner, as well as promoting cellular uptake are of great interest. Here the authors report a peptide macrocyclization and stapling strategy which satisfies those criteria, based on a fluorine thiol displacement reaction.
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Affiliation(s)
- Md Shafiqul Islam
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Samuel L Junod
- Department of Biology, Temple University, 1900 N. 12th Street, Philadelphia, PA, 19122, USA
| | - Si Zhang
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Zakey Yusuf Buuh
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Yifu Guan
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Mi Zhao
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Kishan H Kaneria
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Parmila Kafley
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Carson Cohen
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Robert Maloney
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Zhigang Lyu
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Vincent A Voelz
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Weidong Yang
- Department of Biology, Temple University, 1900 N. 12th Street, Philadelphia, PA, 19122, USA
| | - Rongsheng E Wang
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA.
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6
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Adpressa DA, Reibarkh M, Jiang Y, Saurí J, Makarov AA. Interrogation of solution conformation of complex macrocyclic peptides utilizing a combined SEC-HDX-MS, circular dichroism, and NMR workflow. Analyst 2021; 147:325-332. [PMID: 34927633 DOI: 10.1039/d1an01619a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Recent technological and synthetic advances have led to a resurgence in the exploration of peptides as potential therapeutics. Understanding peptide conformation in both free and protein-bound states remains one of the most critical areas for successful development of peptide drugs. In this study it was demonstrated that the combination of Size-Exclusion Chromatography with Hydrogen-Deuterium Exchange Mass Spectrometry (SEC-HDX-MS) and Circular Dichroism Spectroscopy (CD) can be used to guide the selection of peptides for further NMR analysis. Moreover, the insights from this workflow guide the choice of the best biologically relevant conditions for NMR conformational studies of peptide ligands in a free state in solution. Combined information about solution conformation character and stability across temperatures and co-solvent compositions greatly expedites selection of optimal conditions for NMR analysis. In total, the combination of SEC-HDX-MS, CD, and NMR into a single complementary workflow greatly accelerates conformational analysis of peptides in the drug discovery lead optimization process.
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Affiliation(s)
- Donovon A Adpressa
- Analytical Research & Development, Merck & Co. Inc., Boston, Massachusetts 02115, USA.
| | - Mikhail Reibarkh
- Analytical Research & Development, Merck & Co. Inc., Rahway, New Jersey 07065, USA.
| | - Yuan Jiang
- Analytical Research & Development, Merck & Co. Inc., Boston, Massachusetts 02115, USA.
| | - Josep Saurí
- Analytical Research & Development, Merck & Co. Inc., Boston, Massachusetts 02115, USA.
| | - Alexey A Makarov
- Analytical Research & Development, Merck & Co. Inc., Boston, Massachusetts 02115, USA.
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7
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Abstract
The self-assembly of foldamers into macrocycles is a simple approach to non-biological higher-order structure. Previous work on the co-assembly of ortho-phenylene foldamers with rod-shaped linkers has shown that folding and self-assembly affect each other; that is, the combination leads to new emergent behavior, such as access to otherwise unfavorable folding states. To this point this relationship has been passive. Here, we demonstrate control of self-assembly by manipulating the foldamers' conformational energy surfaces. A series of o-phenylene decamers and octamers have been assembled into macrocycles using imine condensation. Product distributions were analyzed by gel-permeation chromatography and molecular geometries extracted from a combination of NMR spectroscopy and computational chemistry. The assembly of o-phenylene decamers functionalized with alkoxy groups or hydrogens gives both [2 + 2] and [3 + 3] macrocycles. The mixture results from a subtle balance of entropic and enthalpic effects in these systems: the smaller [2 + 2] macrocycles are entropically favored but require the oligomer to misfold, whereas a perfectly folded decamer fits well within the larger [3 + 3] macrocycle that is entropically disfavored. Changing the substituents to fluoro groups, however, shifts assembly quantitatively to the [3 + 3] macrocycle products, even though the structural changes are well-removed from the functional groups directly participating in bond formation. The electron-withdrawing groups favor folding in these systems by strengthening arene–arene stacking interactions, increasing the enthalpic penalty to misfolding. The architectural changes are substantial even though the chemical perturbation is small: analogous o-phenylene octamers do not fit within macrocycles when perfectly folded, and quantitatively misfold to give small macrocycles regardless of substitution. Taken together, these results represent both a high level of structural control in structurally complex foldamer systems and the demonstration of large-amplitude structural changes as a consequence of a small structural effects. The folding propensity of ortho-phenylene foldamers dictates the outcome of their self-assembly into macrocycles.![]()
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Affiliation(s)
- Viraj C Kirinda
- Department of Chemistry & Biochemistry, Miami University Oxford OH 45056 USA
| | - C Scott Hartley
- Department of Chemistry & Biochemistry, Miami University Oxford OH 45056 USA
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8
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Crone NS, Kros A, Boyle AL. Modulation of Coiled-Coil Binding Strength and Fusogenicity through Peptide Stapling. Bioconjug Chem 2020; 31:834-843. [PMID: 32058706 PMCID: PMC7086394 DOI: 10.1021/acs.bioconjchem.0c00009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/13/2020] [Indexed: 12/20/2022]
Abstract
Peptide stapling is a technique which has been widely employed to constrain the conformation of peptides. One of the effects of such a constraint can be to modulate the interaction of the peptide with a binding partner. Here, a cysteine bis-alkylation stapling technique was applied to generate structurally isomeric peptide variants of a heterodimeric coiled-coil forming peptide. These stapled variants differed in the position and size of the formed macrocycle. C-terminal stapling showed the most significant changes in peptide structure and stability, with calorimetric binding analysis showing a significant reduction of binding entropy for stapled variants. This entropy reduction was dependent on cross-linker size and was accompanied by a change in binding enthalpy, illustrating the effects of preorganization. The stapled peptide, along with its binding partner, were subsequently employed as fusogens in a liposome model system. An increase in both lipid- and content-mixing was observed for one of the stapled peptide variants: this increased fusogenicity was attributed to increased coiled-coil binding but not to membrane affinity, an interaction theorized to be a primary driving force in this fusion system.
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Affiliation(s)
- Niek S.
A. Crone
- Supramolecular and Biomaterials
Chemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Alexander Kros
- Supramolecular and Biomaterials
Chemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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9
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Baggio C, Udompholkul P, Gambini L, Jossart J, Salem AF, Håkansson M, Perry JJP, Pellecchia M. N-locking stabilization of covalent helical peptides: Application to Bfl-1 antagonists. Chem Biol Drug Des 2020; 95:412-426. [PMID: 31898401 DOI: 10.1111/cbdd.13661] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/16/2019] [Accepted: 12/23/2019] [Indexed: 12/15/2022]
Abstract
Recently, it was reported that tetrapeptides cyclized via lactam bond between the amino terminus and a glutamic residue in position 4 (termed here N-lock) can nucleate helix formation in longer peptides. We applied such strategy to derive N-locked covalent BH3 peptides that were designed to selectively target the anti-apoptotic protein Bfl-1. The resulting agents were soluble in aqueous buffer and displayed a remarkable (low nanomolar) affinity for Bfl-1 and cellular activity. The crystal structure of the complex between such N-locked covalent peptide and Bfl-1 provided insights on the geometry of the N-locking strategy and of the covalent bond between the agent and Bfl-1.
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Affiliation(s)
- Carlo Baggio
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, CA, USA
| | - Parima Udompholkul
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, CA, USA
| | - Luca Gambini
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, CA, USA
| | - Jennifer Jossart
- Department of Biochemistry, College of Natural and Agricultural Sciences, University of California Riverside, Riverside, CA, USA
| | - Ahmed F Salem
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, CA, USA
| | | | - J Jefferson P Perry
- Department of Biochemistry, College of Natural and Agricultural Sciences, University of California Riverside, Riverside, CA, USA
| | - Maurizio Pellecchia
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, CA, USA
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10
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Kinney ZJ, Kirinda VC, Hartley CS. Macrocycles of higher ortho-phenylenes: assembly and folding. Chem Sci 2019; 10:9057-9068. [PMID: 31762983 PMCID: PMC6857672 DOI: 10.1039/c9sc02975c] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 08/09/2019] [Indexed: 01/24/2023] Open
Abstract
The sizes and geometries of macrocycles assembled from ortho-phenylenes are predicted by the stabilities and bite angles of possible conformers.
Higher-order structure in abiotic foldamer systems represents an important but largely unrealized goal. As one approach to this challenge, covalent assembly can be used to assemble macrocycles with foldamer subunits in well-defined spatial relationships. Such systems have previously been shown to exhibit self-sorting, new folding motifs, and dynamic stereoisomerism, yet there remain important questions about the interplay between folding and macrocyclization and the effect of structural confinement on folding behavior. Here, we explore the dynamic covalent assembly of extended ortho-phenylenes (hexamer and decamer) with rod-shaped linkers. Characteristic 1H chemical shift differences between cyclic and acyclic systems can be compared with computational conformer libraries to determine the folding states of the macrocycles. We show that the bite angle provides a measure of the fit of an o-phenylene conformer within a shape-persistent macrocycle, affecting both assembly and ultimate folding behavior. For the o-phenylene hexamer, the bite angle and conformer stability work synergistically to direct assembly toward triangular [3 + 3] macrocycles of well-folded oligomers. For the decamer, the energetic accessibility of conformers with small bite angles allows [2 + 2] macrocycles to be formed as the predominant species. In these systems, the o-phenylenes are forced into unusual folding states, preferentially adopting a backbone geometry with distinct helical blocks of opposite handedness. The results show that simple geometric restrictions can be used to direct foldamers toward increasingly complex folds.
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Affiliation(s)
- Zacharias J Kinney
- Department of Chemistry & Biochemistry , Miami University , Oxford , OH 45056 , USA .
| | - Viraj C Kirinda
- Department of Chemistry & Biochemistry , Miami University , Oxford , OH 45056 , USA .
| | - C Scott Hartley
- Department of Chemistry & Biochemistry , Miami University , Oxford , OH 45056 , USA .
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11
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Affiliation(s)
- Alanna Schepartz
- Department of Chemistry, Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, USA.
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12
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Acharyya A, Ge Y, Wu H, DeGrado WF, Voelz VA, Gai F. Exposing the Nucleation Site in α-Helix Folding: A Joint Experimental and Simulation Study. J Phys Chem B 2019; 123:1797-1807. [PMID: 30694671 DOI: 10.1021/acs.jpcb.8b12220] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
One of the fundamental events in protein folding is α-helix formation, which involves sequential development of a series of helical hydrogen bonds between the backbone C═O group of residues i and the -NH group of residues i + 4. While we now know a great deal about α-helix folding dynamics, a key question that remains to be answered is where the productive helical nucleation event occurs. Statistically, a helical nucleus (or the first helical hydrogen-bond) can form anywhere within the peptide sequence in question; however, the one that leads to productive folding may only form at a preferred location. This consideration is based on the fact that the α-helical structure is inherently asymmetric, due to the specific alignment of the helical hydrogen bonds. While this hypothesis is plausible, validating it is challenging because there is not an experimental observable that can be used to directly pinpoint the location of the productive nucleation process. Therefore, in this study we combine several techniques, including peptide cross-linking, laser-induced temperature-jump infrared spectroscopy, and molecular dynamics simulations, to tackle this challenge. Taken together, our experimental and simulation results support an α-helix folding mechanism wherein the productive nucleus is formed at the N-terminus, which propagates toward the C-terminal end of the peptide to yield the folded structure. In addition, our results show that incorporation of a cross-linker can lead to formation of differently folded conformations, underscoring the need for all-atom simulations to quantitatively assess the proposed cross-linking design.
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Affiliation(s)
- Arusha Acharyya
- Department of Chemistry , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Yunhui Ge
- Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Haifan Wu
- Department of Pharmaceutical Chemistry , University of California , San Francisco , California 94158 , United States
| | - William F DeGrado
- Department of Pharmaceutical Chemistry , University of California , San Francisco , California 94158 , United States
| | - Vincent A Voelz
- Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Feng Gai
- Department of Chemistry , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
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13
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Skowron KJ, Speltz TE, Moore TW. Recent structural advances in constrained helical peptides. Med Res Rev 2018; 39:749-770. [PMID: 30307621 DOI: 10.1002/med.21540] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 09/05/2018] [Accepted: 09/06/2018] [Indexed: 12/20/2022]
Abstract
Given the ubiquity of the ⍺-helix in the proteome, there has been much research in developing mimics of ⍺-helices, and most of this study has been toward developing protein-protein interaction inhibitors. A common strategy for mimicking ⍺-helices has been through the use of constrained, helical peptides. The addition of a constraint typically provides for conformational and proteolytic stability and, in some cases, cell permeability. Some of the most well-known strategies included are lactam formation and hydrocarbon "stapling." Beyond those strategies, there have been many recent advances in developing constrained peptides. The purpose of this review is to highlight recent advances in the development of new helix-stabilizing technologies, constraint diversification strategies, tether diversification strategies, and combination strategies that create new bicyclic helical peptides.
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Affiliation(s)
- Kornelia J Skowron
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
| | - Thomas E Speltz
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
| | - Terry W Moore
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois.,Translational Oncology Program, University of Illinois Cancer Center, Chicago, Illinois
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14
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Arthur C. Cope Scholar Awards: E. P. Balskus, N. Chatani, W. F. DeGrado, F. Glorius, R. R. Knowles, D. Ma, H. D. Maynard, J. P. Morken, G. K. S. Prakash, K. A. Woerpel / Priestley-Medaille: K. B. Sharpless. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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15
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Arthur C. Cope Scholar Awards: E. P. Balskus, N. Chatani, W. F. DeGrado, F. Glorius, R. R. Knowles, D. Ma, H. D. Maynard, J. P. Morken, G. K. S. Prakash, K. A. Woerpel / Priestley Medal: K. B. Sharpless. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/anie.201807888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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