1
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Zhou S, Nishimura F, Wada K, Fujii K, Kondo T, Watanabe K, Imai Y, Ohtsuki T, Kitamatsu M. Configuration of two cysteine residues in a ring within a stapled Bim peptide affects the secondary structure and apoptotic activity. Bioorg Med Chem Lett 2024; 112:129915. [PMID: 39127242 DOI: 10.1016/j.bmcl.2024.129915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/29/2024] [Accepted: 08/04/2024] [Indexed: 08/12/2024]
Abstract
Many reports have shown that stabilization of secondary structure by stapling functional peptides enhances the intracellular bioactivity. However, no report has discussed the correlation between stabilization and biological activity based on the configuration of amino acid residues used as anchors for stapling. To clarify this, we investigated the helix content and apoptotic efficiency of an apoptosis-inducing peptide, Bim, and four stapled Bim peptides containing stapling-related Cys residues introduced with different configurations within the sequence. The results demonstrated that the configuration of Cys residues in stapled Bim peptides affected the secondary structure and intracellular activity of the peptides, and furthermore, there was a correlation between these latter two variables.
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Affiliation(s)
- Shengli Zhou
- Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, 3-1-1 Tsushimanaka, Okayama 700-8530, Japan
| | - Fuka Nishimura
- Department of Applied Chemistry, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Kazuhaya Wada
- Department of Applied Chemistry, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Kaho Fujii
- Department of Applied Chemistry, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Takeshi Kondo
- Department of Applied Chemistry, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Kazunori Watanabe
- Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, 3-1-1 Tsushimanaka, Okayama 700-8530, Japan
| | - Yoshitane Imai
- Department of Applied Chemistry, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Takashi Ohtsuki
- Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, 3-1-1 Tsushimanaka, Okayama 700-8530, Japan.
| | - Mizuki Kitamatsu
- Department of Applied Chemistry, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan.
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2
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Erckes V, Hilleke M, Isert C, Steuer C. PICKAPEP: An application for parameter calculation and visualization of cyclized and modified peptidomimetics. J Pept Sci 2024:e3646. [PMID: 39085168 DOI: 10.1002/psc.3646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 06/25/2024] [Accepted: 06/29/2024] [Indexed: 08/02/2024]
Abstract
The interest in peptides and especially in peptidomimetic structures has risen enormously in the past few years. Novel modification strategies including nonnatural amino acids, sophisticated cyclization strategies, and side chain modifications to improve the pharmacokinetic properties of peptides are continuously arising. However, a calculator tool accompanying the current development in peptide sciences towards modified peptides is missing. Herein, we present the application PICKAPEP, enabling the virtual construction and visualization of peptidomimetics ranging from well-known cyclized and modified peptides such as ciclosporin A up to fully self-designed peptide-based structures with custom amino acids. Calculated parameters include the molecular weight, the water-octanol partition coefficient, the topological polar surface area, the number of rotatable bonds, and the peptide SMILES code. To our knowledge, PICKAPEP is the first tool allowing users to add custom amino acids as building blocks and also the only tool giving the possibility to process large peptide libraries and calculate parameters for multiple peptides at once. We believe that PICKAPEP will support peptide researchers in their work and will find wide application in current as well as future peptide drug development processes. PICKAPEP is available open source for Windows and Mac operating systems (https://urldefense.com/v3/__https://www.research-collection.ethz.ch/handle/20.500.11850/681174__;!!N11eV2iwtfs!qt5f_2lNd6IZUDH1HVSVwg0zYzS8-nFazQ8c61jS5GaD5vkVS5C3igyfh3haJRnaX8ugW7o9VWUiCihPqcptmaWoqwYf9LvZTQ$).
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Affiliation(s)
- Vanessa Erckes
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Laboratory of Pharmaceutical Analytics, ETH Zurich, Zurich, Switzerland
| | - Mattis Hilleke
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Laboratory of Computer-Assisted Drug Design, ETH Zurich, Zurich, Switzerland
| | - Clemens Isert
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Laboratory of Computer-Assisted Drug Design, ETH Zurich, Zurich, Switzerland
| | - Christian Steuer
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Laboratory of Pharmaceutical Analytics, ETH Zurich, Zurich, Switzerland
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3
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Ding Y, Pedersen SS, Wang H, Xiang B, Wang Y, Yang Z, Gao Y, Morosan E, Jones MR, Xiao H, Ball ZT. Selective Macrocyclization of Unprotected Peptides with an Ex Situ Gaseous Linchpin Reagent. Angew Chem Int Ed Engl 2024; 63:e202405344. [PMID: 38753429 DOI: 10.1002/anie.202405344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Indexed: 07/16/2024]
Abstract
Peptide cyclization has dramatic effects on a variety of important properties, enhancing metabolic stability, limiting conformational flexibility, and altering cellular entry and intracellular localization. The hydrophilic, polyfunctional nature of peptides creates chemoselectivity challenges in macrocyclization, especially for natural sequences without biorthogonal handles. Herein, we describe a gaseous sulfonyl chloride derived reagent that achieves amine-amine, amine-phenol, and amine-aniline crosslinking through a minimalist linchpin strategy that affords macrocyclic urea or carbamate products. The cyclization reaction is metal-mediated and involves a novel application of sulfine species that remains unexplored in aqueous or biological contexts. The aqueous method delivers unique cyclic or bicyclic topologies directly from a variety of natural bioactive peptides without the need for protecting-group strategies.
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Affiliation(s)
- Yuxuan Ding
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| | - Simon S Pedersen
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
- Carbon Dioxide Activation Center (CADIAC), Interdisciplinary Nanoscience Center, Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Haofan Wang
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| | - Baorui Xiang
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| | - Yixian Wang
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| | - Zhi Yang
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| | - Yuxiang Gao
- Department of Physics and Astronomy, Rice University, Houston, Texas, 77005, United States
| | - Emilia Morosan
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
- Department of Physics and Astronomy, Rice University, Houston, Texas, 77005, United States
| | - Matthew R Jones
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| | - Han Xiao
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| | - Zachary T Ball
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
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4
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Das S, Pradhan TK, Samanta R. Recent Progress on Transition Metal Catalyzed Macrocyclizations Based on C-H Bond Activation at Heterocyclic Scaffolds. Chem Asian J 2024:e202400397. [PMID: 38924294 DOI: 10.1002/asia.202400397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/19/2024] [Accepted: 06/22/2024] [Indexed: 06/28/2024]
Abstract
Macrocycles are essential in protein-protein interactions and the preferential intake of bioactive scaffolds. Macrocycles are commonly synthesized by late-stage macrolactonizations, macrolactamizations, transition metal-catalyzed ring-closing metathesis, S-S bond-forming reactions, and copper-catalyzed alkyne-azide cycloaddition. Recently, transition metal-catalyzed C-H activation strategies have gained significant interest among chemists to synthesize macrocycles. This article provides a comprehensive overview of the transition metal-catalyzed macrocyclization via C-H bond functionalization of heterocycle-containing peptides, annulations, and heterocycle-ring construction through direct C-H bond functionalization. In the first part, palladium salt catalyzed coupling with indolyl C(sp3)-H and C(sp2)-H bonds for macrocyclization is reported. The second part summarizes rhodium-catalyzed macrocyclizations via site-selective C-H bond functionalization. Earth-abundant, less toxic 3d metal salt Mn-catalyzed cyclizations are reported in the latter part. This summary is expected to spark interest in emerging methods of macrocycle production among organic synthesis and chemical biology practitioners, helping to develop the discipline. We hope that this mini-review will also inspire synthetic chemists to explore new and broadly applicable C-C bond-forming strategies for macrocyclization via intramolecular C-H activation.
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Affiliation(s)
- Sarbojit Das
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Tapan Kumar Pradhan
- Department of Chemistry, Krishnath College Berhampore, Murshidabad, West Bengal, 742101
| | - Rajarshi Samanta
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
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5
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Tennett JC, Epstein SR, Sawyer N. Enhanced EphB2-Specific Peptide Inhibitors through Stabilization of Polyproline II Helical Structure. ACS Chem Biol 2024; 19:1214-1221. [PMID: 38739742 DOI: 10.1021/acschembio.3c00791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Ephrin (Eph) receptors are the largest family of receptor tyrosine kinases. Interactions between Eph receptors and their membrane-bound ephrin protein ligands are associated with many developmental processes as well as various cancers and neurodegenerative diseases. With significant crosstalk between different Eph receptors and ephrin ligands, there is an urgent need for high-affinity ligands that bind specifically to individual Eph receptors to interrogate and modulate their functions. Here, we describe the rational development of potent EphB2 receptor inhibitors derived from the EphB2 receptor-specific SNEW peptide. To improve inhibitory potency, we evaluated 20+ cross-linkers with the goal of spanning and stabilizing a single polyproline II helical turn observed when SNEW binds to the EphB2 receptor. Of the cross-linkers evaluated, an 11-atom cross-linker, composed of a rigid 2,7-dimethylnaphthyl moiety between two cysteine residues, was found to yield the most potent inhibitor. Analysis of the cyclized region of this peptide by NMR and molecular dynamics simulations suggests that cross-linking stabilizes the receptor-bound polyproline II helix structure observed in the receptor-peptide complex. Cross-linked SNEW variants retained binding specificity for EphB2 and showed cross-linker-dependent resistance to trypsin proteolysis. Beyond the discovery of more potent EphB2 receptor inhibitors, these studies illustrate a novel cyclization approach with potential to stabilize polyproline II helical structure in various peptides for specific targeting of the myriad protein-protein interactions (PPIs) mediated by polyproline II helices.
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Affiliation(s)
- Jessica C Tennett
- Department of Chemistry, Fordham University, 441 E. Fordham Rd., Bronx, New York 10458, United States
| | - Sophie R Epstein
- Department of Chemistry, Fordham University, 441 E. Fordham Rd., Bronx, New York 10458, United States
| | - Nicholas Sawyer
- Department of Chemistry, Fordham University, 441 E. Fordham Rd., Bronx, New York 10458, United States
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6
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Meisenhelter JE, Petrich NR, Blum JE, Weisen AR, Guo R, Saven JG, Pochan DJ, Kloxin CJ. Impact of Peptide Length and Solution Conditions on Tetrameric Coiled Coil Formation. Biomacromolecules 2024; 25:3775-3783. [PMID: 38717062 DOI: 10.1021/acs.biomac.4c00355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Unlike naturally derived peptides, computationally designed sequences offer programmed self-assembly and charge display. Herein, new tetrameric, coiled coil-forming peptides were computationally designed ranging from 8 to 29 amino acids in length. Experimental investigations revealed that only the sequences having three or more heptads (i.e., 21 or more amino acids) exhibited coiled coil behavior. The shortest stable coiled coil sequence had a melting temperature (Tm) of approximately 58 ± 1 °C, making it ideal for thermoreversible assembly over moderate temperatures. Effects of pH and monovalent salt were examined, revealing structural stability over a pH range of 4 to 11 and an enhancement in Tm with the addition of salt. The incorporation of the coiled coil as a hydrogel cross-linker results in a thermally and mechanically reversible hydrogel. A subsequent demonstration of the hydrogel printed through a syringe illustrated one of many potential uses from 3D printing to injectable hydrogel drug delivery.
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Affiliation(s)
- Joshua E Meisenhelter
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
| | - Nolan R Petrich
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
| | - Jacquelyn E Blum
- Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - Albree R Weisen
- Department of Materials Science and Engineering, University of Delaware, 201 DuPont Hall, Newark, Delaware 19716, United States
| | - Rui Guo
- Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - Darrin J Pochan
- Department of Materials Science and Engineering, University of Delaware, 201 DuPont Hall, Newark, Delaware 19716, United States
| | - Christopher J Kloxin
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
- Department of Materials Science and Engineering, University of Delaware, 201 DuPont Hall, Newark, Delaware 19716, United States
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7
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Hampton JT, Liu WR. Diversification of Phage-Displayed Peptide Libraries with Noncanonical Amino Acid Mutagenesis and Chemical Modification. Chem Rev 2024; 124:6051-6077. [PMID: 38686960 PMCID: PMC11082904 DOI: 10.1021/acs.chemrev.4c00004] [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: 01/02/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Abstract
Sitting on the interface between biologics and small molecules, peptides represent an emerging class of therapeutics. Numerous techniques have been developed in the past 30 years to take advantage of biological methods to generate and screen peptide libraries for the identification of therapeutic compounds, with phage display being one of the most accessible techniques. Although traditional phage display can generate billions of peptides simultaneously, it is limited to expression of canonical amino acids. Recently, several groups have successfully undergone efforts to apply genetic code expansion to introduce noncanonical amino acids (ncAAs) with novel reactivities and chemistries into phage-displayed peptide libraries. In addition to biological methods, several different chemical approaches have also been used to install noncanonical motifs into phage libraries. This review focuses on these recent advances that have taken advantage of both biological and chemical means for diversification of phage libraries with ncAAs.
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Affiliation(s)
- J. Trae Hampton
- Texas
A&M Drug Discovery Center and Department of Chemistry, College
of Arts and Sciences, Texas A&M University, College Station, Texas 77843, United States
| | - Wenshe Ray Liu
- Texas
A&M Drug Discovery Center and Department of Chemistry, College
of Arts and Sciences, Texas A&M University, College Station, Texas 77843, United States
- Institute
of Biosciences and Technology and Department of Translational Medical
Sciences, College of Medicine, Texas A&M
University, Houston, Texas 77030, United States
- Department
of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University, College Station, Texas 77843, United States
- Department
of Cell Biology and Genetics, College of Medicine, Texas A&M University, College
Station, Texas 77843, United States
- Department
of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, Texas 77843, United States
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8
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Young R, Huang T, Luo Z, Tan YS, Kaur A, Lau YH. Development of stapled NONO-associated peptides reveals unexpected cell permeability and nuclear localisation. J Pept Sci 2024; 30:e3562. [PMID: 38148630 DOI: 10.1002/psc.3562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 12/28/2023]
Abstract
The non-POU domain-containing octamer-binding protein (NONO) is a nucleic acid-binding protein with diverse functions that has been identified as a potential cancer target in cell biology studies. Little is known about structural motifs that mediate binding to NONO apart from its ability to form homodimers, as well as heterodimers and oligomers with related homologues. We report a stapling approach to macrocyclise helical peptides derived from the insulin-like growth factor binding protein (IGFBP-3) that NONO interacts with, and also from the dimerisation domain of NONO itself. Using a range of chemistries including Pd-catalysed cross-coupling, cysteine arylation and cysteine alkylation, we successfully improved the helicity and observed modest peptide binding to the NONO dimer, although binding could not be saturated at micromolar concentrations. Unexpectedly, we observed cell permeability and preferential nuclear localisation of various dye-labelled peptides in live confocal microscopy, indicating the potential for developing peptide-based tools to study NONO in a cellular context.
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Affiliation(s)
- Reginald Young
- School of Chemistry, The University of Sydney, Camperdown, Australia
| | - Tiancheng Huang
- School of Chemistry, The University of Sydney, Camperdown, Australia
| | - Zijie Luo
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Matrix, Singapore
| | - Amandeep Kaur
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Melbourne, Australia
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Camperdown, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Camperdown, Australia
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9
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Das S, Nag A. Tetrazine cyclized peptides for one-bead-one-compound library: Synthesis and sequencing. Methods Enzymol 2024; 698:141-167. [PMID: 38886030 DOI: 10.1016/bs.mie.2024.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
While most FDA-approved peptide drugs are cyclic, robust cyclization chemistry of peptides and the deconvolution of the cyclic peptide sequences using tandem mass spectrometry render cyclic peptide drug discovery difficult. In this chapter, the protocol for the successful synthesis of tetrazine-linked cyclic peptide library in solid phase, which shows both robust cyclization and easy sequence deconvolution, is described. The protocol for the linearization and cleavage of cyclic peptides from the solid phase by simple UV light irradiation, followed by accurate sequencing using tandem mass spectrometry, is described. We describe the troubleshooting for this dithiol bis-arylation reaction and for the successful cleavage of the aryl cyclic peptide into linear form. This method for efficient solid-phase macrocyclization can be used for the rapid production of loop-based peptides and screening for inhibition of protein-protein interactions, by using the covalent inverse electron-demand Diels Alder reaction to supplement the non-covalent interaction between a protein and its peptide binder, isolating highly selective peptides in the process.
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Affiliation(s)
- Samir Das
- Carlson School of Chemistry and Biochemistry, Clark University, Worcester, MA, United States
| | - Arundhati Nag
- Carlson School of Chemistry and Biochemistry, Clark University, Worcester, MA, United States.
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10
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Hartmann P, Bohdan K, Hommrich M, Juliá F, Vogelsang L, Eirich J, Zangl R, Farès C, Jacobs JB, Mukhopadhyay D, Mengeler JM, Vetere A, Sterling MS, Hinrichs H, Becker S, Morgner N, Schrader W, Finkemeier I, Dietz KJ, Griesinger C, Ritter T. Chemoselective umpolung of thiols to episulfoniums for cysteine bioconjugation. Nat Chem 2024; 16:380-388. [PMID: 38123842 PMCID: PMC10914617 DOI: 10.1038/s41557-023-01388-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 10/27/2023] [Indexed: 12/23/2023]
Abstract
Cysteine conjugation is an important tool in protein research and relies on fast, mild and chemoselective reactions. Cysteinyl thiols can either be modified with prefunctionalized electrophiles, or converted into electrophiles themselves for functionalization with selected nucleophiles in an independent step. Here we report a bioconjugation strategy that uses a vinyl thianthrenium salt to transform cysteine into a highly reactive electrophilic episulfonium intermediate in situ, to enable conjugation with a diverse set of bioorthogonal nucleophiles in a single step. The reactivity profile can connect several nucleophiles to biomolecules through a short and stable ethylene linker, ideal for introduction of infrared labels, post-translational modifications or NMR probes. In the absence of reactive exogenous nucleophiles, nucleophilic amino acids can react with the episulfonium intermediate for native peptide stapling and protein-protein ligation. Ready synthetic access to isotopologues of vinyl thianthrenium salts enables applications in quantitative proteomics. Such diverse applications demonstrate the utility of vinyl-thianthrenium-based bioconjugation as a fast, selective and broadly applicable tool for chemical biology.
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Affiliation(s)
- Philipp Hartmann
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
- Institute of Organic Chemistry, RWTH Aachen University, Aachen, Germany
| | - Kostiantyn Bohdan
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
- Institute of Organic Chemistry, RWTH Aachen University, Aachen, Germany
| | - Moritz Hommrich
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
- Institute of Organic Chemistry, RWTH Aachen University, Aachen, Germany
| | - Fabio Juliá
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | - Lara Vogelsang
- Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Jürgen Eirich
- Institute of Plant Biology and Biotechnology, University of Münster, Münster, Germany
| | - Rene Zangl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt/Main, Frankfurt/Main, Germany
| | - Christophe Farès
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | | | | | | | - Alessandro Vetere
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | | | - Heike Hinrichs
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | - Stefan Becker
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt/Main, Frankfurt/Main, Germany
| | - Wolfgang Schrader
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | - Iris Finkemeier
- Institute of Plant Biology and Biotechnology, University of Münster, Münster, Germany
| | - Karl-Josef Dietz
- Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | | | - Tobias Ritter
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany.
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11
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Esteban JJ, Mason JR, Kaminski J, Ramachandran R, Luyt LG. A survey of stapling methods to increase affinity, activity, and stability of ghrelin analogues. RSC Med Chem 2024; 15:254-266. [PMID: 38283230 PMCID: PMC10809362 DOI: 10.1039/d3md00441d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/29/2023] [Indexed: 01/30/2024] Open
Abstract
The growth hormone secretagogue receptor (GHSR) is a G protein-coupled receptor which regulates various important physiological and pathophysiological processes in the body such as energy homeostasis, growth hormone secretion and regulation of appetite. As a result, it has been postulated as a potential therapeutic target for the treatment of cancer cachexia and other metabolic disorders, as well as a potential imaging agent target for cancers and cardiovascular diseases. Ghrelin is the primary high affinity endogenous ligand for GHSR and has limited secondary structure in solution, which makes it proteolytically unstable. This inherent instability in ghrelin can be overcome by incorporating helix-inducing staples that stabilize its structure and improve affinity and activity. We present an analysis of different stapling methods at positions 12 and 16 of ghrelin(1-20) analogues with the goal of increasing proteolytic stability and to retain or improve affinity and activity towards the GHSR. Ghrelin(1-20) analogues were modified with a wide range of chemical staples, including a lactam staple, triazole staple, hydrocarbon staple, Glaser staple, and xylene-thioether staple. Once synthesized, the receptor affinity and α-helicity were measured using competitive binding assays and circular dichroism spectroscopy, respectively. Generally, an increase in alpha-helicity using a flexible staple linker led to improved affinity towards GHSR. Ghrelin(1-20) analogues with a lactam, triazole, and hydrocarbon staple resulted in helical analogues with stronger affinity towards GHSR than unstapled ghrelin(1-20), a compound that lacks helical character. Compounds were also investigated for their agonist activity through β-arrestin 1 & 2 recruitment BRET assays and for their metabolic stability through serum stability analysis.
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Affiliation(s)
- Juan J Esteban
- Department of Chemistry, University of Western Ontario 1151 Richmond Street London Ontario N6A 3K7 Canada
| | - Julia R Mason
- Department of Chemistry, University of Western Ontario 1151 Richmond Street London Ontario N6A 3K7 Canada
| | - Jakob Kaminski
- Department of Chemistry, University of Western Ontario 1151 Richmond Street London Ontario N6A 3K7 Canada
| | - Rithwik Ramachandran
- Department of Physiology and Pharmacology, University of Western Ontario 1151 Richmond Street London Ontario N6A 5C1 Canada
| | - Leonard G Luyt
- Department of Chemistry, University of Western Ontario 1151 Richmond Street London Ontario N6A 3K7 Canada
- Departments of Medical Imaging and Oncology, University of Western Ontario 1151 Richmond Street London Ontario N6A 3K7 Canada
- London Regional Cancer Program, Lawson Health Research Institute 800 Commissioners Road East London Ontario N6A 4L6 Canada
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12
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Chau B, Liivak K, Gao J. Construction of Nonnatural Cysteine-Cross-Linked Phage Libraries. Methods Mol Biol 2024; 2738:317-332. [PMID: 37966607 DOI: 10.1007/978-1-0716-3549-0_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Phage display is a powerful technique for rapid construction and screening of peptide libraries with over 109 sequence diversity. The M13 bacteriophage genome can be edited to incorporate randomized amino acids, which will be displayed on its minor coat protein (pIII). To enable screening of nonnatural cyclic peptides on phage, the minor coat protein can be modified with a chemical cross-linker. By taking advantage of the nucleophilicity and low abundance of free cysteines on phage, a variety of cysteine cross-linkers can be installed on the pIII protein. Here, we describe the construction of a chemically modified cyclic phage library through a cysteine cross-linking reagent, 1,3-dichloroacetone (DCA).
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Affiliation(s)
- Brittney Chau
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA, USA
| | - Kristi Liivak
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA, USA
| | - Jianmin Gao
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA, USA.
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13
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Yu Q, Bai L, Jiang X. Disulfide Click Reaction for Stapling of S-terminal Peptides. Angew Chem Int Ed Engl 2023; 62:e202314379. [PMID: 37950389 DOI: 10.1002/anie.202314379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/03/2023] [Accepted: 11/10/2023] [Indexed: 11/12/2023]
Abstract
A disulfide click strategy is disclosed for stapling to enhance the metabolic stability and cellular permeability of therapeutic peptides. A 17-membered library of stapling reagents with adjustable lengths and angles was established for rapid double/triple click reactions, bridging S-terminal peptides from 3 to 18 amino acid residues to provide 18- to 48-membered macrocyclic peptides under biocompatible conditions. The constrained peptides exhibited enhanced anti-HCT-116 activity with a locked α-helical conformation (IC50 =6.81 μM vs. biological incompetence for acyclic linear peptides), which could be unstapled for rehabilitation of the native peptides under the assistance of tris(2-carboxyethyl)phosphine (TCEP). This protocol assembles linear peptides into cyclic peptides controllably to retain the diverse three-dimensional conformations, enabling their cellular uptake followed by release of the disulfides for peptide delivery.
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Affiliation(s)
- Qing Yu
- Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, P. R. China
| | - Leiyang Bai
- Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, P. R. China
| | - Xuefeng Jiang
- Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, P. R. China
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, 453007, P. R. China
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, P. R. China
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14
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Fonseca Lopez F, Miao J, Damjanovic J, Bischof L, Braun MB, Ling Y, Hartmann MD, Lin YS, Kritzer JA. Computational Prediction of Cyclic Peptide Structural Ensembles and Application to the Design of Keap1 Binders. J Chem Inf Model 2023; 63:6925-6937. [PMID: 37917529 PMCID: PMC10807374 DOI: 10.1021/acs.jcim.3c01337] [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] [Indexed: 11/04/2023]
Abstract
The Nrf2 transcription factor is a master regulator of the cellular response to oxidative stress, and Keap1 is its primary negative regulator. Activating Nrf2 by inhibiting the Nrf2-Keap1 protein-protein interaction has shown promise for treating cancer and inflammatory diseases. A loop derived from Nrf2 has been shown to inhibit Keap1 selectively, especially when cyclized, but there are no reliable design methods for predicting an optimal macrocyclization strategy. In this work, we employed all-atom, explicit-solvent molecular dynamics simulations with enhanced sampling methods to predict the relative degree of preorganization for a series of peptides cyclized with a set of bis-thioether "staples". We then correlated these predictions to experimentally measured binding affinities for Keap1 and crystal structures of the cyclic peptides bound to Keap1. This work showcases a computational method for designing cyclic peptides by simulating and comparing their entire solution-phase ensembles, providing key insights into designing cyclic peptides as selective inhibitors of protein-protein interactions.
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Affiliation(s)
| | - Jiayuan Miao
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Jovan Damjanovic
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Luca Bischof
- Department of Protein Evolution, Max Planck Institute for Biology, 72076 Tübingen, Germany
- Interfaculty Institute of Biochemistry, Tübingen University, 72076 Tübingen, Germany
| | - Michael B Braun
- Department of Protein Evolution, Max Planck Institute for Biology, 72076 Tübingen, Germany
- Interfaculty Institute of Biochemistry, Tübingen University, 72076 Tübingen, Germany
| | - Yingjie Ling
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Biology, 72076 Tübingen, Germany
- Interfaculty Institute of Biochemistry, Tübingen University, 72076 Tübingen, Germany
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
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15
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Chen B, Liu C, Cong W, Gao F, Zou Y, Su L, Liu L, Hillisch A, Lehmann L, Bierer D, Li X, Hu HG. Cyclobutane-bearing restricted anchoring residues enabled geometry-specific hydrocarbon peptide stapling. Chem Sci 2023; 14:11499-11506. [PMID: 37886087 PMCID: PMC10599482 DOI: 10.1039/d3sc04279k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
Stapled peptides are regarded as the promising next-generation therapeutics because of their improved secondary structure, membrane permeability and metabolic stability as compared with the prototype linear peptides. Usually, stapled peptides are obtained by a hydrocarbon stapling technique, anchoring from paired olefin-terminated unnatural amino acids and the consequent ring-closing metathesis (RCM). To investigate the adaptability of the rigid cyclobutane structure in RCM and expand the chemical diversity of hydrocarbon peptide stapling, we herein described the rational design and efficient synthesis of cyclobutane-based conformationally constrained amino acids, termed (E)-1-amino-3-(but-3-en-1-yl)cyclobutane-1-carboxylic acid (E7) and (Z)-1-amino-3-(but-3-en-1-yl)cyclobutane-1-carboxylic acid (Z7). All four combinations including E7-E7, E7-Z7, Z7-Z7 and Z7-E7 were proven to be applicable in RCM-mediated peptide stapling to afford the corresponding geometry-specific stapled peptides. With the aid of the combined quantum and molecular mechanics, the E7-E7 combination was proven to be optimal in both the RCM reaction and helical stabilization. With the spike protein of SARS-CoV-2 as the target, a series of cyclobutane-bearing stapled peptides were obtained. Among them, E7-E7 geometry-specific stapled peptides indeed exhibit higher α-helicity and thus stronger biological activity than canonical hydrocarbon stapled peptides. We believe that this methodology possesses great potential to expand the scope of the existing peptide stapling strategy. These cyclobutane-bearing restricted anchoring residues served as effective supplements for the existing olefin-terminated unnatural amino acids and the resultant geometry-specific hydrocarbon peptide stapling provided more potential for peptide therapeutics.
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Affiliation(s)
- Baobao Chen
- School of Medicine or Institute of Translational Medicine, Shanghai University Shanghai 200444 China
| | - Chao Liu
- School of Medicine or Institute of Translational Medicine, Shanghai University Shanghai 200444 China
| | - Wei Cong
- School of Medicine or Institute of Translational Medicine, Shanghai University Shanghai 200444 China
| | - Fei Gao
- School of Medicine or Institute of Translational Medicine, Shanghai University Shanghai 200444 China
| | - Yan Zou
- School of Pharmacy, Second Military Medical University Shanghai 200433 China
| | - Li Su
- School of Medicine or Institute of Translational Medicine, Shanghai University Shanghai 200444 China
| | - Lei Liu
- Department of Chemistry, Tsinghua University Beijing 100084 China
| | - Alexander Hillisch
- Bayer AG, Pharma Division, Drug Discovery Sciences Aprather Weg 18A Wuppertal 42096 Germany
- UCB BioSciences GmbH Alfred-Nobel-Straße 10 40789 Monheim am Rhein Germany
| | - Lutz Lehmann
- Bayer AG, Pharma Division, Drug Discovery Sciences Aprather Weg 18A Wuppertal 42096 Germany
| | - Donald Bierer
- Bayer AG, Pharma Division, Drug Discovery Sciences Aprather Weg 18A Wuppertal 42096 Germany
| | - Xiang Li
- School of Pharmacy, Second Military Medical University Shanghai 200433 China
| | - Hong-Gang Hu
- School of Medicine or Institute of Translational Medicine, Shanghai University Shanghai 200444 China
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16
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Dahal A, Subramanian V, Shrestha P, Liu D, Gauthier T, Jois S. Conformationally constrained cyclic grafted peptidomimetics targeting protein-protein interactions. Pept Sci (Hoboken) 2023; 115:e24328. [PMID: 38188985 PMCID: PMC10769001 DOI: 10.1002/pep2.24328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 07/03/2023] [Indexed: 01/09/2024]
Abstract
Sunflower trypsin inhibitor-1 (SFTI-1) structure is used for designing grafted peptides as a possible therapeutic agent. The grafted peptide exhibits multiple conformations in solution due to the presence of proline in the structure of the peptide. To lock the grafted peptide into a major conformation in solution, a dibenzofuran moiety (DBF) was incorporated in the peptide backbone structure, replacing the Pro-Pro sequence. NMR studies indicated a major conformation of the grafted peptide in solution. Detailed structural studies suggested that SFTI-DBF adopts a twisted beta-strand structure in solution. The surface plasmon resonance analysis showed that SFTI-DBF binds to CD58 protein. A model for the protein-SFTI-DBF complex was proposed based on docking studies. These studies suggested that SFTI-1 grafted peptide can be used to design stable peptides for therapeutic purposes by grafting organic functional groups and amino acids. However, when a similar strategy was used with another grafted peptide, the resulting peptide did not produce a single major conformation, and its biological activity was lost. Thus, conformational constraints depend on the sequence of amino acids used for SFTI-1 grafting.
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Affiliation(s)
- Achyut Dahal
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana Monroe, Monroe LA 71201
| | - Vivekanandan Subramanian
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536
| | - Prajesh Shrestha
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana Monroe, Monroe LA 71201
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge 70803
| | - Dong Liu
- AgCenter Biotechnology Laboratory, LSU Agricultural Center, Baton Rouge, LA, 70803
| | - Ted Gauthier
- AgCenter Biotechnology Laboratory, LSU Agricultural Center, Baton Rouge, LA, 70803
| | - Seetharama Jois
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana Monroe, Monroe LA 71201
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge 70803
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17
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Walther R, Westermann LM, Carmali S, Jackson SE, Brötz-Oesterhelt H, Spring DR. Identification of macrocyclic peptides which activate bacterial cylindrical proteases. RSC Med Chem 2023; 14:1186-1191. [PMID: 37360394 PMCID: PMC10285738 DOI: 10.1039/d3md00136a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/15/2023] [Indexed: 06/28/2023] Open
Abstract
The caseinolytic protease complex ClpXP is an important house-keeping enzyme in prokaryotes charged with the removal and degradation of misfolded and aggregated proteins and performing regulatory proteolysis. Dysregulation of its function, particularly by inhibition or allosteric activation of the proteolytic core ClpP, has proven to be a promising strategy to reduce virulence and eradicate persistent bacterial infections. Here, we report a rational drug-design approach to identify macrocyclic peptides which increase proteolysis by ClpP. This work expands the understanding of ClpP dynamics and sheds light on the conformational control exerted by its binding partner, the chaperone ClpX, by means of a chemical approach. The identified macrocyclic peptide ligands may, in the future, serve as a starting point for the development of ClpP activators for antibacterial applications.
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Affiliation(s)
- Raoul Walther
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road CB2 1EW Cambridge UK
| | - Linda M Westermann
- Interfaculty Institute of Microbiology and Infection Medicine, Dept. of Bioactive Compounds, University of Tübingen Auf der Morgenstelle 28 72076 Tübingen Germany
| | - Sheiliza Carmali
- School of Pharmacy, Queen's University Belfast BT9 7BL Belfast UK
| | - Sophie E Jackson
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road CB2 1EW Cambridge UK
| | - Heike Brötz-Oesterhelt
- Interfaculty Institute of Microbiology and Infection Medicine, Dept. of Bioactive Compounds, University of Tübingen Auf der Morgenstelle 28 72076 Tübingen Germany
- Cluster of Excellence Controlling Microbes to Fight Infections Germany
| | - David R Spring
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road CB2 1EW Cambridge UK
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18
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Abrigo NA, Dods KK, Makovsky CA, Lohan S, Mitra K, Newcomb KM, Le A, Hartman MCT. Development of a Cyclic, Cell Penetrating Peptide Compatible with In Vitro Selection Strategies. ACS Chem Biol 2023; 18:746-755. [PMID: 36920103 PMCID: PMC11165944 DOI: 10.1021/acschembio.2c00680] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
A key limitation for the development of peptides as therapeutics is their lack of cell permeability. Recent work has shown that short, arginine-rich macrocyclic peptides containing hydrophobic amino acids are able to penetrate cells and reach the cytosol. Here, we have developed a new strategy for developing cyclic cell penetrating peptides (CPPs) that shifts some of the hydrophobic character to the peptide cyclization linker, allowing us to do a linker screen to find cyclic CPPs with improved cellular uptake. We demonstrate that both hydrophobicity and position of the alkylation points on the linker affect uptake of macrocyclic cell penetrating peptides (CPPs). Our best peptide, 4i, is on par with or better than prototypical CPPs Arg9 (R9) and CPP12 under assays measuring total cellular uptake and cytosolic delivery. 4i was also able to carry a peptide previously discovered from an in vitro selection, 8.6, and a cytotoxic peptide into the cytosol. A bicyclic variant of 4i showed even better cytosolic entry than 4i, highlighting the plasticity of this class of peptides toward modifications. Since our CPPs are cyclized via their side chains (as opposed to head-to-tail cyclization), they are compatible with powerful technologies for peptide ligand discovery including phage display and mRNA display. Access to diverse libraries with inherent cell permeability will afford the ability to find cell permeable hits to many challenging intracellular targets.
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Affiliation(s)
- Nicolas A Abrigo
- Chemistry, Virginia Commonwealth University, 1001 W Main Street, Richmond, 23284 Virginia, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, 23219 Virginia, United States
| | - Kara K Dods
- Chemistry, Virginia Commonwealth University, 1001 W Main Street, Richmond, 23284 Virginia, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, 23219 Virginia, United States
| | - Chelsea A Makovsky
- Chemistry, Virginia Commonwealth University, 1001 W Main Street, Richmond, 23284 Virginia, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, 23219 Virginia, United States
| | - Sandeep Lohan
- Chemistry, Virginia Commonwealth University, 1001 W Main Street, Richmond, 23284 Virginia, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, 23219 Virginia, United States
| | - Koushambi Mitra
- Chemistry, Virginia Commonwealth University, 1001 W Main Street, Richmond, 23284 Virginia, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, 23219 Virginia, United States
| | - Kaylee M Newcomb
- Chemistry, Virginia Commonwealth University, 1001 W Main Street, Richmond, 23284 Virginia, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, 23219 Virginia, United States
| | - Anthony Le
- Chemistry, Virginia Commonwealth University, 1001 W Main Street, Richmond, 23284 Virginia, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, 23219 Virginia, United States
| | - Matthew C T Hartman
- Chemistry, Virginia Commonwealth University, 1001 W Main Street, Richmond, 23284 Virginia, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, 23219 Virginia, United States
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19
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Pal S. Impact of Hydrogen‐Bond Surrogate Model on Helix Stabilization and Development of Protein‐Protein Interaction Inhibitors. ChemistrySelect 2023. [DOI: 10.1002/slct.202204207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Affiliation(s)
- Sunit Pal
- Chemical Genomics Centre of the Max Planck Society Max Planck Institute of Molecular Physiology Otto-Hahn-Str. 11 44227 Dortmund Germany
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20
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Bartling CRO, Alexopoulou F, Kuschert S, Chin YKY, Jia X, Sereikaite V, Özcelik D, Jensen TM, Jain P, Nygaard MM, Harpsøe K, Gloriam DE, Mobli M, Strømgaard K. Comprehensive Peptide Cyclization Examination Yields Optimized APP Scaffolds with Improved Affinity toward Mint2. J Med Chem 2023; 66:3045-3057. [PMID: 36749163 DOI: 10.1021/acs.jmedchem.2c02017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Peptides targeting disease-relevant protein-protein interactions are an attractive class of therapeutics covering the otherwise undruggable space between small molecules and therapeutic proteins. However, peptides generally suffer from poor metabolic stability and low membrane permeability. Hence, peptide cyclization has become a valuable approach to develop linear peptide motifs into metabolically stable and potentially cell-permeable cyclic leads. Furthermore, cyclization of side chains, also known as "stapling", can stabilize particular secondary peptide structures. Here, we demonstrate that a comprehensive examination of cyclization strategies in terms of position, chemistry, and length is a prerequisite for the selection of optimal cyclic peptide scaffolds. Our systematic approach identifies cyclic APP dodecamer peptides targeting the phosphotyrosine binding domain of Mint2 with substantially improved affinity. We show that especially all-hydrocarbon stapling provides improved metabolic stability, a significantly stabilized secondary structure and membrane permeability.
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Affiliation(s)
- Christian R O Bartling
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100Copenhagen, Denmark
| | - Flora Alexopoulou
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100Copenhagen, Denmark
| | - Sarah Kuschert
- Center for Advanced Imaging, University of Queensland, St. Lucia, 4072Queensland, Australia
| | - Yanni K-Y Chin
- Center for Advanced Imaging, University of Queensland, St. Lucia, 4072Queensland, Australia
| | - Xinying Jia
- Center for Advanced Imaging, University of Queensland, St. Lucia, 4072Queensland, Australia
| | - Vita Sereikaite
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100Copenhagen, Denmark
| | - Dennis Özcelik
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100Copenhagen, Denmark
| | - Thomas M Jensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100Copenhagen, Denmark
| | - Palash Jain
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100Copenhagen, Denmark
| | - Mads M Nygaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100Copenhagen, Denmark
| | - Kasper Harpsøe
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100Copenhagen, Denmark
| | - David E Gloriam
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100Copenhagen, Denmark
| | - Mehdi Mobli
- Center for Advanced Imaging, University of Queensland, St. Lucia, 4072Queensland, Australia
| | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100Copenhagen, Denmark
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21
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Brennan A, Leech JT, Kad NM, Mason JM. The effect of helix-inducing constraints and downsizing upon a transcription block survival-derived functional cJun antagonist. CELL REPORTS. PHYSICAL SCIENCE 2022; 3:101077. [PMID: 36274790 PMCID: PMC9582194 DOI: 10.1016/j.xcrp.2022.101077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Inhibition of cJun is established as a promising therapeutic approach, particularly in cancer. We recently developed the "transcription block survival" (TBS) screening platform to derive functional peptide antagonists of transcription factor activity by ablating their ability to bind to cognate DNA. Using TBS, we screened a >131,000-member peptide library to select a 63-mer peptide that bound cJun and prevented 12-O-tetradecanoylphorbol-13-acetate response element (TRE) DNA binding. Iterative truncation was next combined with a systematic exploration of side-chain cyclization to derive a minimal active sequence. The resulting dual lactamized sequence was >40% smaller and retained low nM target affinity (equilibrium binding constant [K D ] = 0.2 versus 9.7 nM), with 8 residues at the acidic region required for functional antagonism. However, even modest C-terminal truncation resulted in functional loss. The peptide functionally antagonizes cJun (half-maximal inhibitory concentration [IC50] = 13 versus 45 μM) and is considerably more stable in human serum relative to its non-lactamized counterpart and HingeW.
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Affiliation(s)
- Andrew Brennan
- Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
| | - James T. Leech
- Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
| | - Neil M. Kad
- School of Biological Sciences, University of Kent, Canterbury, CT2 7NH, UK
| | - Jody M. Mason
- Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
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22
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Ricardo MG, Reuber EE, Yao L, Danglad-Flores J, Delbianco M, Seeberger PH. Design, Synthesis, and Characterization of Stapled Oligosaccharides. J Am Chem Soc 2022; 144:18429-18434. [PMID: 36173281 PMCID: PMC9562281 DOI: 10.1021/jacs.2c06882] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Stapling short peptides
to lock specific conformations and thereby
obtain superior pharmacological properties is well established. However,
similar concepts have not been applied to oligosaccharides. Here,
we describe the design, synthesis, and characterization of the first
stapled oligosaccharides. Automated assembly of β-(1,6)-glucans
equipped with two alkenyl side chains was followed by on-resin Grubbs
metathesis for efficient ring closure with a variety of cross-linkers
of different sizes. Oligosaccharide stapling increases enzymatic stability
and cell penetration, therefore opening new opportunities for the
use of glycans in medicinal chemistry.
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Affiliation(s)
- Manuel G Ricardo
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Emelie E Reuber
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Ling Yao
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - José Danglad-Flores
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Martina Delbianco
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
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23
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White AM, Dellsén A, Larsson N, Kaas Q, Jansen F, Plowright AT, Knerr L, Durek T, Craik DJ. Late-Stage Functionalization with Cysteine Staples Generates Potent and Selective Melanocortin Receptor-1 Agonists. J Med Chem 2022; 65:12956-12969. [PMID: 36167503 DOI: 10.1021/acs.jmedchem.2c00793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work, cysteine staples were used as a late-stage functionalization strategy to diversify peptides and build conjugates targeting the melanocortin G-protein-coupled receptors [melanocortin receptor-1 (MC1R) and MC3R-MC5R]. Monocyclic and bicyclic agonists based on sunflower trypsin inhibitor-1 were used to generate a selection of stapled peptides that were evaluated for binding (pKi) and functional activation (pEC50) of the melanocortin receptor subtypes. Stapled peptides generally had improved activity, with aromatic stapled peptides yielding selective MC1R agonists, including a xylene-stapled peptide (2) with an EC50 of 1.9 nM for MC1R and >150-fold selectivity for MC3R and MC4R. Selected stapled peptides were further functionalized with linkers and payloads, generating a series of conjugated peptides with potent MC1R activity, including one pyridazine-functionalized peptide (21) with picomolar activity at MC1R (Ki 58 pM; EC50 < 9 pM). This work demonstrates that staples can be used as modular synthetic tools to tune potency and selectivity in peptide-based drug design.
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Affiliation(s)
- Andrew M White
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Anita Dellsén
- Mechanistic Biology & Profiling, Discovery Sciences, R&D, AstraZeneca, Gothenburg 43183, Sweden
| | - Niklas Larsson
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg 43183, Sweden
| | - Quentin Kaas
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Frank Jansen
- Mechanistic Biology & Profiling, Discovery Sciences, R&D, AstraZeneca, Gothenburg 43183, Sweden
| | - Alleyn T Plowright
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43183, Sweden
| | - Laurent Knerr
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43183, Sweden
| | - Thomas Durek
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
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24
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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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25
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Extendable stapling of unprotected peptides by crosslinking two amines with o-phthalaldehyde. Nat Commun 2022; 13:311. [PMID: 35031608 PMCID: PMC8760283 DOI: 10.1038/s41467-022-27985-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 12/10/2021] [Indexed: 01/01/2023] Open
Abstract
Peptide modification methods that do not rely on the cysteine residue are underdeveloped, and their development could greatly expand the current toolbox for peptide chemistry. During the course of preliminary investigations into the classical ortho-phthalaldehyde (OPA)-amine-thiol condensation reaction, we found that in the absence of thiol, OPA readily condenses with two primary alkyl amines to form a class of underexplored isoindolin-1-imine compounds under mild aqueous conditions. From the intramolecular version of this OPA-2amines reaction, an efficient and selective methodology using mild reaction conditions has been developed for stapling unprotected peptides via crosslinking of two amino groups in both an end-to-side and side-to-side fashion. The stapling method is superfast and broadly applicable for various peptide substrates with the reacting amino groups separated by a wide range of different amino acid units. The macrocyclization reactions of selected substrates are completed within 10 seconds at 5 mM concentration and within 2 minutes at 50 μM concentration. Importantly, the resulting cyclized peptides with an isoindolinimine linkage can be extended in a one-pot sequential addition manner with several different electron-deficient π electrophiles, thereby generating more complex structures. Methods for peptide stapling, or covalently linking amino acid residues to create a non-linear structure, mostly rely on cysteine residues, which imposes a significant practical limitation. Here the authors disclose a method to chemoselectively macrocyclize two free-amine-containing residues in mild, peptide-relevant conditions, using a commercially available reagent.
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26
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Gruß H, Feiner RC, Mseya R, Schröder DC, Jewgiński M, Müller KM, Latajka R, Marion A, Sewald N. Peptide stapling by late-stage Suzuki–Miyaura cross-coupling. Beilstein J Org Chem 2022; 18:1-12. [PMID: 35047078 PMCID: PMC8744458 DOI: 10.3762/bjoc.18.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 12/09/2021] [Indexed: 12/19/2022] Open
Abstract
The development of peptide stapling techniques to stabilise α-helical secondary structure motifs of peptides led to the design of modulators of protein–protein interactions, which had been considered undruggable for a long time. We disclose a novel approach towards peptide stapling utilising macrocyclisation by late-stage Suzuki–Miyaura cross-coupling of bromotryptophan-containing peptides of the catenin-binding domain of axin. Optimisation of the linker length in order to find a compromise between both sufficient linker rigidity and flexibility resulted in a peptide with an increased α-helicity and enhanced binding affinity to its native binding partner β-catenin. An increased proteolytic stability against proteinase K has been demonstrated.
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Affiliation(s)
- Hendrik Gruß
- Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Rebecca C Feiner
- Department of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Ridhiwan Mseya
- Department of Chemistry, Middle East Technical University, 06800, Ankara, Turkey
| | - David C Schröder
- Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Michał Jewgiński
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wrocław, Poland
| | - Kristian M Müller
- Department of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Rafał Latajka
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wrocław, Poland
| | - Antoine Marion
- Department of Chemistry, Middle East Technical University, 06800, Ankara, Turkey
| | - Norbert Sewald
- Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
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27
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Xiao Q, Jones ZB, Hatfield SC, Ashton DS, Dalley NA, Dyer CD, Evangelista JL, Price JL. Structural guidelines for stabilization of α-helical coiled coils via PEG stapling. RSC Chem Biol 2022; 3:1096-1104. [PMID: 36128502 PMCID: PMC9428657 DOI: 10.1039/d1cb00237f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 07/01/2022] [Indexed: 11/24/2022] Open
Abstract
Macrocyclization or stapling is one of the most well-known and generally applicable strategies for enhancing peptide/protein conformational stability and target binding affinity. However, there are limited structure- or sequence-based guidelines for the incorporation of optimal interhelical staples within coiled coils: the location and length of an interhelical staple is either arbitrarily chosen or requires significant optimization. Here we explore the impact of interhelical PEG stapling on the conformational stability and proteolytic resistance of a model disulfide-bound heterodimeric coiled coil. We demonstrate that (1) interhelical PEG staples are more stabilizing when placed farther from an existing disulfide crosslink; (2) e/g′ staples are more stabilizing than f/b′ or b/c′ staples; (3) PEG staples between different positions have different optimal staple lengths; (4) PEG stapling tolerates variation in the structure of the PEG linker and in the mode of conjugation; and (5) the guidelines developed here enable the rational design of a stabilized PEG-stapled HER-2 affibody with enhanced conformational stability and proteolytic resistance. Here we identify key criteria for designing PEG-stapled coiled coils with increased conformational and proteolytic stability.![]()
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Affiliation(s)
- Qiang Xiao
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA
| | - Zachary B. Jones
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA
| | - Samantha C. Hatfield
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA
| | - Dallin S. Ashton
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA
| | - Nicholas A. Dalley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA
| | - Cody D. Dyer
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA
| | - Judah L. Evangelista
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Joshua L. Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA
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28
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Wang Y, Yin F, Li Z. Sulfonium-Tethered Peptide. Methods Mol Biol 2022; 2530:169-175. [PMID: 35761049 DOI: 10.1007/978-1-0716-2489-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Stapled peptides have received widespread attention in therapeutics due to the superior membrane penetration and in vivo stability. We have developed a series of methods including CIH, TD coupling, Met-Met, and Cys-Met bis-alkylation strategy to switch peptides' secondary structure and enhance their stability and cellular uptake. Here we focus on the peptide macrocyclization method of Met-Met and Cys-Met bis-alkylation strategy to generate more stable and permeable sulfonium-tethered peptides to avoid tedious synthesis, which can be utilized for drug delivery and further broad biological applications.
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Affiliation(s)
- Yuena Wang
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, People's Republic of China
| | - Feng Yin
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, People's Republic of China
| | - Zigang Li
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, People's Republic of China.
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29
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de Araujo AD, Lim J, Wu KC, Hoang HN, Nguyen HT, Fairlie DP. Landscaping macrocyclic peptides: stapling hDM2-binding peptides for helicity, protein affinity, proteolytic stability and cell uptake. RSC Chem Biol 2022; 3:895-904. [PMID: 35866171 PMCID: PMC9257625 DOI: 10.1039/d1cb00231g] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 05/19/2022] [Indexed: 12/25/2022] Open
Abstract
Surveying macrocycles for mimicking a helical tumor suppressor protein, resisting breakdown by proteases, and entering cancer cells.
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Affiliation(s)
- Aline D. de Araujo
- Division of Chemistry and Structural Biology, ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Junxian Lim
- Division of Chemistry and Structural Biology, ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kai-Chen Wu
- Division of Chemistry and Structural Biology, ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Huy N. Hoang
- Division of Chemistry and Structural Biology, ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Huy T. Nguyen
- Division of Chemistry and Structural Biology, ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology, ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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30
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Dahal A, Sonju JJ, Kousoulas KG, Jois SD. Peptides and peptidomimetics as therapeutic agents for Covid-19. Pept Sci (Hoboken) 2022; 114:e24245. [PMID: 34901700 PMCID: PMC8646791 DOI: 10.1002/pep2.24245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 12/27/2022]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Covid-19 pandemic has caused high morbidity and mortality rates worldwide. Virus entry into cells can be blocked using several strategies, including inhibition of protein-protein interactions (PPIs) between the viral spike glycoprotein and cellular receptors, as well as blocking of spike protein conformational changes that are required for cleavage/activation and fusogenicity. The spike-mediated viral attachment and entry into cells via fusion of the viral envelope with cellular membranes involve PPIs mediated by short peptide fragments exhibiting particular secondary structures. Thus, peptides that can inhibit these PPIs may be used as potential antiviral agents preventing virus entry and spread. This review is focused on peptides and peptidomimetics as PPI modulators and protease inhibitors against SARS-CoV-2.
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Affiliation(s)
- Achyut Dahal
- School of Basic Pharmaceutical and Toxicological Sciences, College of PharmacyUniversity of Louisiana at MonroeMonroeLouisianaUSA
| | - Jafrin Jobayer Sonju
- School of Basic Pharmaceutical and Toxicological Sciences, College of PharmacyUniversity of Louisiana at MonroeMonroeLouisianaUSA
| | - Konstantin G. Kousoulas
- Department of Pathobiological Sciences, School of Veterinary MedicineLouisiana State UniversityBaton RougeLouisianaUSA
| | - Seetharama D. Jois
- School of Basic Pharmaceutical and Toxicological Sciences, College of PharmacyUniversity of Louisiana at MonroeMonroeLouisianaUSA
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31
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Chen XX, Tang Y, Wu M, Zhang YN, Chen K, Zhou Z, Fang GM. Helix-Constrained Peptides Constructed by Head-to-Side Chain Cross-Linking Strategies. Org Lett 2021; 23:7792-7796. [PMID: 34551517 DOI: 10.1021/acs.orglett.1c02820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Facile head-to-side chain cross-linking strategies are developed to generate helix-constrained peptides. In our strategies, a covalent cross-linker is incorporated at N, i+7 or N, i+1 positions to lock the peptide into a helical conformation. The described patterns of head-to-side chain cross-linking will provide new frameworks for constrained helical peptide.
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Affiliation(s)
- Xiao-Xu Chen
- School of Life Science, Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China
| | - Yang Tang
- Center of Minimally Invasive Treatment for Tumor, Department of Medical Ultrasound, Shanghai Tenth People's Hospital; Ultrasound Research and Education Institute, Clinical Research Center for Interventional Medicine, School of Medicine, Tongji University, Shanghai 200072, P. R. China
| | - Meng Wu
- School of Life Science, Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China
| | - Yan-Ni Zhang
- School of Life Science, Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China
| | - Kai Chen
- School of Life Science, Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China
| | - Zhaocai Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, P. R. China
| | - Ge-Min Fang
- School of Life Science, Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China
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32
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Zhao R, Shi X, Shi L, Zhao H, Yin F, Li Z. Solid phase diversity-oriented lysine modification of cyclic peptides. J Pept Sci 2021; 28:e3373. [PMID: 34643009 DOI: 10.1002/psc.3373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 11/05/2022]
Abstract
Herein, we report a novel strategy for diversity-oriented lysine modification of cyclic peptides based on the orthogonal alkylation of the lysine residues. All steps can be achieved in the solid phase with satisfying conversions. Notably, we demonstrated that the tether modification could help to improve the cellular uptake of peptides.
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Affiliation(s)
- Rongtong Zhao
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Xiaodong Shi
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Linlin Shi
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Hui Zhao
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Feng Yin
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
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33
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Horsfall AJ, Vandborg BA, Kikhtyak Z, Scanlon DB, Tilley WD, Hickey TE, Bruning JB, Abell AD. A cell permeable bimane-constrained PCNA-interacting peptide. RSC Chem Biol 2021; 2:1499-1508. [PMID: 34704055 PMCID: PMC8496261 DOI: 10.1039/d1cb00113b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/19/2021] [Indexed: 11/21/2022] Open
Abstract
The human sliding clamp protein known as proliferating cell nuclear antigen (PCNA) orchestrates DNA-replication and -repair and as such is an ideal therapeutic target for proliferative diseases, including cancer. Peptides derived from the human p21 protein bind PCNA with high affinity via a 310-helical binding conformation and are known to shut down DNA-replication. Here, we present studies on short analogues of p21 peptides (143-151) conformationally constrained with a covalent linker between i, i + 4 separated cysteine residues at positions 145 and 149 to access peptidomimetics that target PCNA. The resulting macrocycles bind PCNA with K D values ranging from 570 nM to 3.86 μM, with the bimane-constrained peptide 7 proving the most potent. Subsequent X-ray crystallography and computational modelling studies of the macrocyclic peptides bound to PCNA indicated only the high-affinity peptide 7 adopted the classical 310-helical binding conformation. This suggests the 310-helical conformation is critical to high affinity PCNA binding, however NMR secondary shift analysis of peptide 7 revealed this secondary structure was not well-defined in solution. Peptide 7 is cell permeable and localised to the cell cytosol of breast cancer cells (MDA-MB-468), revealed by confocal microscopy showing blue fluorescence of the bimane linker. The inherent fluorescence of the bimane moiety present in peptide 7 allowed it to be directly imaged in the cell uptake assay, without attachment of an auxiliary fluorescent tag. This highlights a significant benefit of using a bimane constraint to access conformationally constrained macrocyclic peptides. This study identifies a small peptidomimetic that binds PCNA with higher affinity than previous reported p21 macrocycles, and is cell permeable, providing a significant advance toward development of a PCNA inhibitor for therapeutic applications.
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Affiliation(s)
- Aimee J Horsfall
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide Adelaide South Australia 5005 Australia .,School of Physical Sciences, The University of Adelaide Adelaide South Australia 5005 Australia.,Australian Research Council Centre of Excellence for Nanoscale BioPhotonics (CNBP) Australia
| | - Beth A Vandborg
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide Adelaide South Australia 5005 Australia .,School of Biological Sciences, The University of Adelaide Adelaide South Australia 5005 Australia
| | - Zoya Kikhtyak
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide Adelaide South Australia 5005 Australia
| | - Denis B Scanlon
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide Adelaide South Australia 5005 Australia .,School of Physical Sciences, The University of Adelaide Adelaide South Australia 5005 Australia
| | - Wayne D Tilley
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide Adelaide South Australia 5005 Australia
| | - Theresa E Hickey
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide Adelaide South Australia 5005 Australia
| | - John B Bruning
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide Adelaide South Australia 5005 Australia .,School of Biological Sciences, The University of Adelaide Adelaide South Australia 5005 Australia
| | - Andrew D Abell
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide Adelaide South Australia 5005 Australia .,School of Physical Sciences, The University of Adelaide Adelaide South Australia 5005 Australia.,Australian Research Council Centre of Excellence for Nanoscale BioPhotonics (CNBP) Australia
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34
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Peptide Macrocyclization Through Palladium-Catalyzed Late-Stage C-H Activation. Methods Mol Biol 2021. [PMID: 34596842 DOI: 10.1007/978-1-0716-1689-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Cyclic peptides are an important class of bioactive compounds for the chemical biology and pharmaceutical industry. Chemical synthesis of highly constrained cyclic peptides is often challenging. Here we describe the synthetic strategy of peptide macrocyclization through late-stage palladium-catalyzed C-H activation. These methods utilize endogenous backbone amides in the peptide sequence as directing groups and are efficient in the preparation of small-to-middle size peptide macrocycles.
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35
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Pace JR, Lampkin BJ, Abakah C, Moyer A, Miao J, Deprey K, Cerulli RA, Lin YS, Baleja JD, Baker D, Kritzer JA. Stapled β-Hairpins Featuring 4-Mercaptoproline. J Am Chem Soc 2021; 143:15039-15044. [PMID: 34516087 DOI: 10.1021/jacs.1c04378] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptides constrained by intramolecular cross-links, especially stapled α-helices, have emerged as versatile scaffolds for drug development. However, there are fewer examples of similarly constrained scaffolds for other secondary structures. Here, we used a novel computational strategy to identify an optimal staple for antiparallel β-strands, and then we incorporated that staple within a β-hairpin peptide. The hairpin uses 4-mercaptoproline as a novel staple component, which contributes to a unique, kinked structure. The stapled hairpins show a high degree of structure in aqueous solution, excellent resistance to degradation in cell lysates, and cytosolic penetration at micromolar concentrations. They also overlay with a unique subset of kinked hairpin motifs at protein-protein interaction interfaces. Thus, these scaffolds represent promising starting points for developing inhibitors of cellular protein-protein interactions.
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Affiliation(s)
- Jennifer R Pace
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Bryan J Lampkin
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Charles Abakah
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Adam Moyer
- Molecular Engineering and Sciences Institute, University of Washington, Seattle Washington 98195, United States
| | - Jiayuan Miao
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Kirsten Deprey
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Robert A Cerulli
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts 02111, United States
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - James D Baleja
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts 02111, United States
| | - David Baker
- Molecular Engineering and Sciences Institute, University of Washington, Seattle Washington 98195, United States.,Department of Biochemistry, Institute for Protein Design, and Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, United States
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
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36
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Shabani S, Wu Y, Ryan HG, Hutton CA. Progress and perspectives on directing group-assisted palladium-catalysed C-H functionalisation of amino acids and peptides. Chem Soc Rev 2021; 50:9278-9343. [PMID: 34254063 DOI: 10.1039/d0cs01441a] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Peptide modifications can unlock a variety of compounds with structural diversity and abundant biological activity. In nature, peptide modifications, such as functionalisation at the side-chain position of amino acids, are performed using post-translational modification enzymes or incorporation of unnatural amino acids. However, accessing these modifications remains a challenge for organic chemists. During the past decades, selective C-H activation/functionalisation has attracted considerable attention in synthetic organic chemistry as a pathway to peptide modification. Various directing group strategies have been discovered that assist selective C-H activation. In particular, bidentate directing groups that enable tuneable and reversible coordination are now recognised as one of the most efficient methods for the site-selective C-H activation and functionalisation of numerous families of organic compounds. Synthetic peptide chemists have harnessed bidentate directing group strategies for selective functionalisation of the β- and γ-positions of amino acids. This method has been expanded and recognised as an effective device for the late stage macrocyclisation and total synthesis of complex peptide natural products. In this review, we discuss various β-, γ-, and δ-C(sp3)-H bond functionalisation reactions of amino acids for the formation of C-X bonds with the aid of directing groups and their application in late-stage macrocyclisation and the total synthesis of complex peptide natural products.
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Affiliation(s)
- Sadegh Shabani
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, 3010, Australia.
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37
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Wendt M, Bellavita R, Gerber A, Efrém NL, van Ramshorst T, Pearce NM, Davey PRJ, Everard I, Vazquez-Chantada M, Chiarparin E, Grieco P, Hennig S, Grossmann TN. Bicyclic β-Sheet Mimetics that Target the Transcriptional Coactivator β-Catenin and Inhibit Wnt Signaling. Angew Chem Int Ed Engl 2021; 60:13937-13944. [PMID: 33783110 PMCID: PMC8252567 DOI: 10.1002/anie.202102082] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Indexed: 12/29/2022]
Abstract
Protein complexes are defined by the three-dimensional structure of participating binding partners. Knowledge about these structures can facilitate the design of peptidomimetics which have been applied for example, as inhibitors of protein-protein interactions (PPIs). Even though β-sheets participate widely in PPIs, they have only rarely served as the basis for peptidomimetic PPI inhibitors, in particular when addressing intracellular targets. Here, we present the structure-based design of β-sheet mimetics targeting the intracellular protein β-catenin, a central component of the Wnt signaling pathway. Based on a protein binding partner of β-catenin, a macrocyclic peptide was designed and its crystal structure in complex with β-catenin obtained. Using this structure, we designed a library of bicyclic β-sheet mimetics employing a late-stage diversification strategy. Several mimetics were identified that compete with transcription factor binding to β-catenin and inhibit Wnt signaling in cells. The presented design strategy can support the development of inhibitors for other β-sheet-mediated PPIs.
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Affiliation(s)
- Mathias Wendt
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Rosa Bellavita
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Alan Gerber
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Nina-Louisa Efrém
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Thirza van Ramshorst
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Nicholas M Pearce
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Paul R J Davey
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Isabel Everard
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | | | | | - Paolo Grieco
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Sven Hennig
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Tom N Grossmann
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
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38
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Chen Z, Zhu M, Cai M, Xu L, Weng Y. Palladium-Catalyzed C(sp 3)–H Arylation and Alkynylation of Peptides Directed by Aspartic Acid (Asp). ACS Catal 2021. [DOI: 10.1021/acscatal.1c01417] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Zhuo Chen
- College of Pharmaceutical Sciences, Zhejiang University of Technology, 310014 Hangzhou, P. R. China
| | - Meijie Zhu
- College of Pharmaceutical Sciences, Zhejiang University of Technology, 310014 Hangzhou, P. R. China
| | - Mengwei Cai
- College of Pharmaceutical Sciences, Zhejiang University of Technology, 310014 Hangzhou, P. R. China
| | - Lulu Xu
- College of Pharmaceutical Sciences, Zhejiang University of Technology, 310014 Hangzhou, P. R. China
| | - Yiyi Weng
- College of Pharmaceutical Sciences, Zhejiang University of Technology, 310014 Hangzhou, P. R. China
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39
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Ricardo MG, Vázquéz-Mena Y, Iglesias-Morales Y, Wessjohann LA, Rivera DG. On the scope of the double Ugi multicomponent stapling to produce helical peptides. Bioorg Chem 2021; 113:104987. [PMID: 34022444 DOI: 10.1016/j.bioorg.2021.104987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/19/2021] [Accepted: 05/08/2021] [Indexed: 11/15/2022]
Abstract
The stabilization of helical structures by peptide stapling approaches is now a mature technology capable to provide a variety of biomedical applications. Recently, it was shown that multicomponent macrocyclization is not only an effective way to introduce conformational constraints but it also allows to incorporate additional functionalities to the staple moiety in a one-pot process. This work investigates the scope of the double Ugi multicomponent stapling approach in its capacity to produce helical peptides from unstructured sequences. For this, three different stapling combinations were implemented and the CD spectra of the cyclic peptides were measured to determine the effect of the multicomponent macrocyclization on the resulting secondary structure. A new insight into some structural factors influencing the helicity type and content is provided, along with new prospects on the utilization of this methodology to diversify the molecular tethers linking the amino acid side chains.
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Affiliation(s)
- Manuel G Ricardo
- Laboratory of Synthetic and Biomolecular Chemistry, Faculty of Chemistry, University of Havana, Zapata y G, Havana 10400, Cuba; Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Yadiel Vázquéz-Mena
- Laboratory of Synthetic and Biomolecular Chemistry, Faculty of Chemistry, University of Havana, Zapata y G, Havana 10400, Cuba
| | - Yuleidys Iglesias-Morales
- Laboratory of Synthetic and Biomolecular Chemistry, Faculty of Chemistry, University of Havana, Zapata y G, Havana 10400, Cuba
| | - Ludger A Wessjohann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Daniel G Rivera
- Laboratory of Synthetic and Biomolecular Chemistry, Faculty of Chemistry, University of Havana, Zapata y G, Havana 10400, Cuba; Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany.
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40
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Wendt M, Bellavita R, Gerber A, Efrém N, Ramshorst T, Pearce NM, Davey PRJ, Everard I, Vazquez‐Chantada M, Chiarparin E, Grieco P, Hennig S, Grossmann TN. Bicyclic β‐Sheet Mimetics that Target the Transcriptional Coactivator β‐Catenin and Inhibit Wnt Signaling. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Mathias Wendt
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | - Rosa Bellavita
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
- Department of Pharmacy University of Naples Federico II Naples Italy
| | - Alan Gerber
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | - Nina‐Louisa Efrém
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | - Thirza Ramshorst
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | - Nicholas M. Pearce
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | | | - Isabel Everard
- Mechanistic Biology and Profiling Discovery Sciences, R&D AstraZeneca Cambridge UK
| | | | | | - Paolo Grieco
- Department of Pharmacy University of Naples Federico II Naples Italy
| | - Sven Hennig
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | - Tom N. Grossmann
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
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41
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van der Zouwen AJ, Witte MD. Modular Approaches to Synthesize Activity- and Affinity-Based Chemical Probes. Front Chem 2021; 9:644811. [PMID: 33937194 PMCID: PMC8082414 DOI: 10.3389/fchem.2021.644811] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
Combinatorial and modular methods to synthesize small molecule modulators of protein activity have proven to be powerful tools in the development of new drug-like molecules. Over the past decade, these methodologies have been adapted toward utilization in the development of activity- and affinity-based chemical probes, as well as in chemoproteomic profiling. In this review, we will discuss how methods like multicomponent reactions, DNA-encoded libraries, phage displays, and others provide new ways to rapidly screen novel chemical probes against proteins of interest.
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Affiliation(s)
- Antonie J van der Zouwen
- Chemical Biology II, Stratingh Institute for Chemistry, University of Groningen, Groningen, Netherlands
| | - Martin D Witte
- Chemical Biology II, Stratingh Institute for Chemistry, University of Groningen, Groningen, Netherlands
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42
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Ceballos J, Grinhagena E, Sangouard G, Heinis C, Waser J. Cys-Cys and Cys-Lys Stapling of Unprotected Peptides Enabled by Hypervalent Iodine Reagents. Angew Chem Int Ed Engl 2021; 60:9022-9031. [PMID: 33450121 PMCID: PMC8048981 DOI: 10.1002/anie.202014511] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/22/2020] [Indexed: 12/31/2022]
Abstract
Easy access to a wide range of structurally diverse stapled peptides is crucial for the development of inhibitors of protein-protein interactions. Herein, we report bis-functional hypervalent iodine reagents for two-component cysteine-cysteine and cysteine-lysine stapling yielding structurally diverse thioalkyne linkers. This stapling method works with unprotected natural amino acid residues and does not require pre-functionalization or metal catalysis. The products are stable to purification and isolation. Post-stapling modification can be accessed via amidation of an activated ester, or via cycloaddition onto the formed thioalkyne group. Increased helicity and binding affinity to MDM2 was obtained for a i,i+7 stapled peptide.
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Affiliation(s)
- Javier Ceballos
- Laboratory of Catalysis and Organic SynthesisEcole Polytechnique Fédérale de LausanneEPFL SB ISIC LCSO, BCH 14021015LausanneSwitzerland
| | - Elija Grinhagena
- Laboratory of Catalysis and Organic SynthesisEcole Polytechnique Fédérale de LausanneEPFL SB ISIC LCSO, BCH 14021015LausanneSwitzerland
| | - Gontran Sangouard
- Laboratory of Therapeutic Proteins and PeptidesEcole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LPPT, BCH 53051015LausanneSwitzerland
| | - Christian Heinis
- Laboratory of Therapeutic Proteins and PeptidesEcole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LPPT, BCH 53051015LausanneSwitzerland
| | - Jerome Waser
- Laboratory of Catalysis and Organic SynthesisEcole Polytechnique Fédérale de LausanneEPFL SB ISIC LCSO, BCH 14021015LausanneSwitzerland
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43
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Ceballos J, Grinhagena E, Sangouard G, Heinis C, Waser J. Cys–Cys and Cys–Lys Stapling of Unprotected Peptides Enabled by Hypervalent Iodine Reagents. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014511] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Javier Ceballos
- Laboratory of Catalysis and Organic Synthesis Ecole Polytechnique Fédérale de Lausanne EPFL SB ISIC LCSO, BCH 1402 1015 Lausanne Switzerland
| | - Elija Grinhagena
- Laboratory of Catalysis and Organic Synthesis Ecole Polytechnique Fédérale de Lausanne EPFL SB ISIC LCSO, BCH 1402 1015 Lausanne Switzerland
| | - Gontran Sangouard
- Laboratory of Therapeutic Proteins and Peptides Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LPPT, BCH 5305 1015 Lausanne Switzerland
| | - Christian Heinis
- Laboratory of Therapeutic Proteins and Peptides Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LPPT, BCH 5305 1015 Lausanne Switzerland
| | - Jerome Waser
- Laboratory of Catalysis and Organic Synthesis Ecole Polytechnique Fédérale de Lausanne EPFL SB ISIC LCSO, BCH 1402 1015 Lausanne Switzerland
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44
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A versatile resin for the generation of thioether-bonded head-to-tail cyclized peptides. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2021.152867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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45
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Zhu HY, Wu M, Yu FQ, Zhang YN, Xi TK, Chen K, Fang GM. Chemical synthesis of thioether-bonded bicyclic peptides using tert-butylthio and Trt-protected cysteines. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2021.152875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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46
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Besenius P, Zengerling L, Kemper B, Hellmich UA. Synthesis and Structural Stability of α-Helical Gold(I)-Metallopeptidesy. Synlett 2021. [DOI: 10.1055/a-1290-8412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractThe synthesis of hexa- and dodecapeptides functionalized with two Au(I)–phosphine complexes is reported. The high stability of the Au(I)–phosphine bond allowed orthogonal peptide-protecting-group chemistry, even when using hard Lewis acids like boron tribromide. This enabled the preparation of an Fmoc-protected lysine derivative carrying the Au(I) complex in a side chain, which was used in standard Fmoc-based solid-phase peptide synthesis protocols. Alanine and leucine repeats in the metallododecapeptide formed α-helical secondary structures in 2,2,2-trifluoroethanol–H2O and 1,1,1,3,3,3-hexafluoroisopropanol–H2O mixtures with high thermal stability, as shown by temperature-dependent CD spectroscopy studies.
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Affiliation(s)
- Pol Besenius
- Department of Chemistry, Johannes Gutenberg-University Mainz
| | | | - Benedict Kemper
- Department of Chemistry, Johannes Gutenberg-University Mainz
| | - Ute A. Hellmich
- Department of Chemistry, Johannes Gutenberg-University Mainz
- Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt
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47
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Li B, Tang H, Turlik A, Wan Z, Xue X, Li L, Yang X, Li J, He G, Houk KN, Chen G. Cooperative Stapling of Native Peptides at Lysine and Tyrosine or Arginine with Formaldehyde. Angew Chem Int Ed Engl 2021; 60:6646-6652. [DOI: 10.1002/anie.202016267] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Bo Li
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Hong Tang
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Aneta Turlik
- Department of Chemistry and Biochemistry University of California Los Angeles CA 90095 USA
| | - Zhao Wan
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Xiao‐Song Xue
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
- Department of Chemistry and Biochemistry University of California Los Angeles CA 90095 USA
| | - Li Li
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation Institute of Materia Medica Chinese Academy of Medical Sciences Peking Union Medical College Beijing 100050 China
| | - Xiaoxiao Yang
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation Institute of Materia Medica Chinese Academy of Medical Sciences Peking Union Medical College Beijing 100050 China
| | - Jiuyuan Li
- Asymchem Life Science Co., Ltd. TEDA Tianjin 300457 China
| | - Gang He
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Kendall N. Houk
- Department of Chemistry and Biochemistry University of California Los Angeles CA 90095 USA
| | - Gong Chen
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
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48
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Li B, Tang H, Turlik A, Wan Z, Xue X, Li L, Yang X, Li J, He G, Houk KN, Chen G. Cooperative Stapling of Native Peptides at Lysine and Tyrosine or Arginine with Formaldehyde. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Bo Li
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Hong Tang
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Aneta Turlik
- Department of Chemistry and Biochemistry University of California Los Angeles CA 90095 USA
| | - Zhao Wan
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Xiao‐Song Xue
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
- Department of Chemistry and Biochemistry University of California Los Angeles CA 90095 USA
| | - Li Li
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation Institute of Materia Medica Chinese Academy of Medical Sciences Peking Union Medical College Beijing 100050 China
| | - Xiaoxiao Yang
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation Institute of Materia Medica Chinese Academy of Medical Sciences Peking Union Medical College Beijing 100050 China
| | - Jiuyuan Li
- Asymchem Life Science Co., Ltd. TEDA Tianjin 300457 China
| | - Gang He
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Kendall N. Houk
- Department of Chemistry and Biochemistry University of California Los Angeles CA 90095 USA
| | - Gong Chen
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
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49
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Kandler R, Das S, Nag A. Copper-ligand clusters dictate size of cyclized peptide formed during alkyne-azide cycloaddition on solid support. RSC Adv 2021; 11:4842-4852. [PMID: 34377440 PMCID: PMC8351437 DOI: 10.1039/d0ra07491h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Peptide and peptidomimetic cyclization by copper-catalyzed alkyne-azide cycloaddition (CuAAC) reaction have been used to mimic disulfide bonds, alpha helices, amide bonds, and for one-bead-one-compound (OBOC) library development. A limited number of solid-supported CuAAC cyclization methods resulting in monomeric cyclic peptide formation have been reported for specific peptide sequences, but there exists no general study on monocyclic peptide formation using CuAAC cyclization. Since several cyclic peptides identified from an OBOC CuAAC cyclized library has been shown to have important biological applications, we discuss here an efficient method of alkyne-azide 'click' catalyzed monomeric cyclic peptide formation on a solid support. The reason behind the efficiency of the method is explored. CuAAC cyclization of a peptide sequence with azidolysine and propargylglycine is performed under various reaction conditions, with different catalysts, in the presence or absence of an organic base. The results indicate that piperidine plays a critical role in the reaction yield and monomeric cycle formation by coordinating to Cu and forming Cu-ligand clusters. A previously synthesized copper compound containing piperidine, [Cu4I4(pip)4], is found to catalyze the CuAAC cyclization of monomeric peptide effectively. The use of 1.5 equivalents of CuI and the use of DMF as solvent is found to give optimal CuAAC cyclized monomer yields. The effect of the peptide sequence and peptide length on monomer formation are also investigated by varying either parameter systemically. Peptide length is identified as the determining factor for whether the monomeric or dimeric cyclic peptide is the major product. For peptides with six, seven, or eight amino acids, the monomer is the major product from CuAAC cyclization. Longer and shorter peptides on cyclization show less monomer formation. CuAAC peptide cyclization of non-optimal peptide lengths such as pentamers is affected significantly by the amino acid sequence and give lower yields.
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Affiliation(s)
- Rene Kandler
- Carlson School of Chemistry and Biochemistry, Clark University, Worcester, MA 01610, USA
| | - Samir Das
- Carlson School of Chemistry and Biochemistry, Clark University, Worcester, MA 01610, USA
| | - Arundhati Nag
- Carlson School of Chemistry and Biochemistry, Clark University, Worcester, MA 01610, USA
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50
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Hart P', Hommen P, Noisier A, Krzyzanowski A, Schüler D, Porfetye AT, Akbarzadeh M, Vetter IR, Adihou H, Waldmann H. Structure Based Design of Bicyclic Peptide Inhibitors of RbAp48. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202009749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Peter 't Hart
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Chemical Genomics Centre of the Max Planck Society Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Pascal Hommen
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Chemical Genomics Centre of the Max Planck Society Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Anaïs Noisier
- Medicinal Chemistry, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceutical R&D AstraZeneca Gothenburg Sweden
| | - Adrian Krzyzanowski
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Darijan Schüler
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Arthur T. Porfetye
- Department of Mechanistic Cell Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Mohammad Akbarzadeh
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Ingrid R. Vetter
- Department of Mechanistic Cell Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Hélène Adihou
- Medicinal Chemistry, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceutical R&D AstraZeneca Gothenburg Sweden
- AstraZeneca MPI Satellite Unit Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Herbert Waldmann
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
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