1
|
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$).
Collapse
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
| |
Collapse
|
2
|
Sato N, Suetaka S, Hayashi Y, Arai M. Rational peptide design for inhibition of the KIX-MLL interaction. Sci Rep 2023; 13:6330. [PMID: 37072438 PMCID: PMC10113271 DOI: 10.1038/s41598-023-32848-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 04/03/2023] [Indexed: 05/03/2023] Open
Abstract
The kinase-inducible domain interacting (KIX) domain is an integral part of the general transcriptional coactivator CREB-binding protein, and has been associated with leukemia, cancer, and various viral diseases. Hence, the KIX domain has attracted considerable attention in drug discovery and development. Here, we rationally designed a KIX inhibitor using a peptide fragment corresponding to the transactivation domain (TAD) of the transcriptional activator, mixed-lineage leukemia protein (MLL). We performed theoretical saturation mutagenesis using the Rosetta software to search for mutants expected to bind KIX more tightly than the wild-type MLL TAD. Mutant peptides with higher helical propensities were selected for experimental characterization. We found that the T2857W mutant of the MLL TAD peptide had the highest binding affinity for KIX compared to the other 12 peptides designed in this study. Moreover, the peptide had a high inhibitory effect on the KIX-MLL interaction with a half-maximal inhibitory concentration close to the dissociation constant for this interaction. To our knowledge, this peptide has the highest affinity for KIX among all previously reported inhibitors that target the MLL site of KIX. Thus, our approach may be useful for rationally developing helical peptides that inhibit protein-protein interactions implicated in the progression of various diseases.
Collapse
Affiliation(s)
- Nao Sato
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan
| | - Shunji Suetaka
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan
| | - Yuuki Hayashi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan
- Environmental Science Center, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-0033, Japan
| | - Munehito Arai
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan.
- Department of Physics, Graduate School of Science, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan.
| |
Collapse
|
3
|
Wiedemann B, Kamps D, Depta L, Weisner J, Cvetreznik J, Tomassi S, Gentz S, Hoffmann JE, Müller MP, Koch O, Dehmelt L, Rauh D. Design and synthesis of Nrf2-derived hydrocarbon stapled peptides for the disruption of protein-DNA-interactions. PLoS One 2022; 17:e0267651. [PMID: 35731722 PMCID: PMC9216541 DOI: 10.1371/journal.pone.0267651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 04/13/2022] [Indexed: 11/29/2022] Open
Abstract
Misregulation and mutations of the transcription factor Nrf2 are involved in the development of a variety of human diseases. In this study, we employed the technology of stapled peptides to address a protein-DNA-complex and designed a set of Nrf2-based derivatives. Varying the length and position of the hydrocarbon staple, we chose the best peptide for further evaluation in both fixed and living cells. Peptide 4 revealed significant enrichment within the nucleus compared to its linear counterpart 5, indicating potent binding to DNA. Our studies suggest that these molecules offer an interesting strategy to target activated Nrf2 in cancer cells.
Collapse
Affiliation(s)
- Bianca Wiedemann
- Faculty of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Dortmund, Germany
| | - Dominic Kamps
- Faculty of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Dortmund, Germany
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Laura Depta
- Faculty of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Dortmund, Germany
| | - Jörn Weisner
- Faculty of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Dortmund, Germany
| | - Jana Cvetreznik
- Faculty of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Dortmund, Germany
| | - Stefano Tomassi
- Department of Pharmacy, University of Naples “Federico II”, Napoli, Italy
| | - Sascha Gentz
- Protein Chemistry Facility, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Jan-Erik Hoffmann
- Protein Chemistry Facility, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Matthias P. Müller
- Faculty of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Dortmund, Germany
| | - Oliver Koch
- Institute of Pharmaceutical and Medicinal Chemistry and German Center of Infection Research, Münster, Germany
| | - Leif Dehmelt
- Faculty of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Dortmund, Germany
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Daniel Rauh
- Faculty of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Dortmund, Germany
- * E-mail:
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Sun P, Zhang Z, Li L, Wang X, Xiong L, Yang N, Li Y, Li Z. Design, synthesis, and insecticidal evaluation of novel anthranilic diamides of
N
‐pyridylpyrazole
derivatives containing
3‐thioethers. J Heterocycl Chem 2021. [DOI: 10.1002/jhet.4422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Pengwei Sun
- State Key Laboratory of Elemento‐Organic Chemistry Research Institute of Elemento‐Organic Chemistry, College of Chemistry, Nankai University Tianjin China
| | - Ze Zhang
- State Key Laboratory of Elemento‐Organic Chemistry Research Institute of Elemento‐Organic Chemistry, College of Chemistry, Nankai University Tianjin China
| | - Linshan Li
- State Key Laboratory of Elemento‐Organic Chemistry Research Institute of Elemento‐Organic Chemistry, College of Chemistry, Nankai University Tianjin China
| | - Xinyao Wang
- State Key Laboratory of Elemento‐Organic Chemistry Research Institute of Elemento‐Organic Chemistry, College of Chemistry, Nankai University Tianjin China
| | - Lixia Xiong
- State Key Laboratory of Elemento‐Organic Chemistry Research Institute of Elemento‐Organic Chemistry, College of Chemistry, Nankai University Tianjin China
| | - Na Yang
- State Key Laboratory of Elemento‐Organic Chemistry Research Institute of Elemento‐Organic Chemistry, College of Chemistry, Nankai University Tianjin China
| | - Yuxin Li
- State Key Laboratory of Elemento‐Organic Chemistry Research Institute of Elemento‐Organic Chemistry, College of Chemistry, Nankai University Tianjin China
| | - Zhengming Li
- State Key Laboratory of Elemento‐Organic Chemistry Research Institute of Elemento‐Organic Chemistry, College of Chemistry, Nankai University Tianjin China
| |
Collapse
|
6
|
de Araujo AD, Nguyen HT, Fairlie DP. Late-Stage Hydrocarbon Conjugation and Cyclisation in Synthetic Peptides and Proteins. Chembiochem 2021; 22:1784-1789. [PMID: 33506598 DOI: 10.1002/cbic.202000796] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/07/2021] [Indexed: 12/26/2022]
Abstract
The conventional S-alkylation of cysteine relies upon using activated electrophiles. Here we demonstrate high-yielding and selective S-alkylation and S-lipidation of cysteines in unprotected synthetic peptides and proteins by using weak electrophiles and a Zn2+ promoter. Linear or branched iodoalkanes can S-alkylate cysteine in an unprotected 38-residue Myc peptide fragment and in a 91-residue miniprotein Omomyc, thus highlighting selective late-stage synthetic modifications. Metal-assisted cysteine alkylation is also effective for incorporating dehydroalanine into unprotected peptides and for peptide cyclisation via aliphatic thioether crosslinks, including customising macrocycles to stabilise helical peptides for enhanced uptake and delivery to proteins inside cells. Chemoselective and efficient late-stage Zn2+ -promoted cysteine alkylation in unprotected peptides and proteins promises many useful applications.
Collapse
Affiliation(s)
- Aline D de Araujo
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Huy T Nguyen
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David P Fairlie
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| |
Collapse
|
7
|
Lindsey‐Crosthwait A, Rodriguez‐Lema D, Walko M, Pask CM, Wilson AJ. Structural optimization of reversible dibromomaleimide peptide stapling. Pept Sci (Hoboken) 2021; 113:e24157. [PMID: 34938942 PMCID: PMC8650577 DOI: 10.1002/pep2.24157] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/29/2020] [Accepted: 03/02/2020] [Indexed: 01/05/2023]
Abstract
Methods to constrain peptides in a bioactive α-helical conformation for inhibition of protein-protein interactions represent an ongoing area of investigation in chemical biology. Recently, the first example of a reversible "stapling" methodology was described which exploits native cysteine or homocysteine residues spaced at the i and i + 4 positions in a peptide sequence together with the thiol selective reactivity of dibromomaleimides (a previous study). This manuscript reports on the optimization of the maleimide based constraint, focusing on the kinetics of macrocyclization and the extent to which helicity is promoted with different thiol containing amino acids. The study identified an optimal stapling combination of X 1 = L-Cys and X 5 = L-hCys in the context of the model peptide Ac-X1AAAX5-NH2, which should prove useful in implementing the dibromomaleimide stapling strategy in peptidomimetic ligand discovery programmes.
Collapse
Affiliation(s)
- Ayanna Lindsey‐Crosthwait
- School of Chemistry, University of LeedsLeedsUK
- Astbury Centre for Structural Molecular Biology, University of LeedsLeedsUK
| | - Diana Rodriguez‐Lema
- School of Chemistry, University of LeedsLeedsUK
- Astbury Centre for Structural Molecular Biology, University of LeedsLeedsUK
| | - Martin Walko
- School of Chemistry, University of LeedsLeedsUK
- Astbury Centre for Structural Molecular Biology, University of LeedsLeedsUK
| | | | - Andrew J. Wilson
- School of Chemistry, University of LeedsLeedsUK
- Astbury Centre for Structural Molecular Biology, University of LeedsLeedsUK
| |
Collapse
|
8
|
Li X, Chen S, Zhang WD, Hu HG. Stapled Helical Peptides Bearing Different Anchoring Residues. Chem Rev 2020; 120:10079-10144. [DOI: 10.1021/acs.chemrev.0c00532] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Xiang Li
- School of Pharmacy, Second Military Medical University, Shanghai, China
- Insititute of Translational Medicine, Shanghai University, Shanghai, China
| | - Si Chen
- School of Medicine, Shanghai University, Shanghai, China
| | - Wei-Dong Zhang
- School of Pharmacy, Second Military Medical University, Shanghai, China
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hong-Gang Hu
- Insititute of Translational Medicine, Shanghai University, Shanghai, China
- Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| |
Collapse
|
9
|
Bednar TN, Resnikoff AR, Gavenonis J. Microwave-assisted cleavage of cysteine perfluoroaryl thioethers. Amino Acids 2020; 52:841-845. [PMID: 32350627 DOI: 10.1007/s00726-020-02846-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/23/2020] [Indexed: 11/28/2022]
Abstract
The cysteine- perfluoroarene SNAr reaction allows for the sequence-specific attachment of dyes and affinity tags to peptides and proteins. However, while many methods exist for the desulfuration of native and functionalized cysteine residues, there are no reports of their application to perfluoroarylated cysteines. Herein we report both the hydrogenolysis of a perfluoroarylated cysteine to alanine and elimination to dehydroalanine, reactions that are both accelerated by microwave irradiation.
Collapse
Affiliation(s)
- Taylor N Bednar
- Department of Chemistry, Dickinson College, 28 North College Street, Carlisle, PA, 17013, USA.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Alissa R Resnikoff
- Department of Chemistry, Dickinson College, 28 North College Street, Carlisle, PA, 17013, USA.,Chicago Medical School, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, North Chicago, IL, 60064, USA
| | - Jason Gavenonis
- Department of Chemistry, Dickinson College, 28 North College Street, Carlisle, PA, 17013, USA.
| |
Collapse
|
10
|
Moiola M, Memeo MG, Quadrelli P. Stapled Peptides-A Useful Improvement for Peptide-Based Drugs. Molecules 2019; 24:molecules24203654. [PMID: 31658723 PMCID: PMC6832507 DOI: 10.3390/molecules24203654] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/24/2019] [Accepted: 10/01/2019] [Indexed: 12/24/2022] Open
Abstract
Peptide-based drugs, despite being relegated as niche pharmaceuticals for years, are now capturing more and more attention from the scientific community. The main problem for these kinds of pharmacological compounds was the low degree of cellular uptake, which relegates the application of peptide-drugs to extracellular targets. In recent years, many new techniques have been developed in order to bypass the intrinsic problem of this kind of pharmaceuticals. One of these features is the use of stapled peptides. Stapled peptides consist of peptide chains that bring an external brace that force the peptide structure into an α-helical one. The cross-link is obtained by the linkage of the side chains of opportune-modified amino acids posed at the right distance inside the peptide chain. In this account, we report the main stapling methodologies currently employed or under development and the synthetic pathways involved in the amino acid modifications. Moreover, we report the results of two comparative studies upon different kinds of stapled-peptides, evaluating the properties given from each typology of staple to the target peptide and discussing the best choices for the use of this feature in peptide-drug synthesis.
Collapse
Affiliation(s)
- Mattia Moiola
- Department of Chemistry, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy.
| | - Misal G Memeo
- Department of Chemistry, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy.
| | - Paolo Quadrelli
- Department of Chemistry, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy.
| |
Collapse
|
11
|
Bakail M, Rodriguez‐Marin S, Hegedüs Z, Perrin ME, Ochsenbein F, Wilson AJ. Recognition of ASF1 by Using Hydrocarbon-Constrained Peptides. Chembiochem 2019; 20:891-895. [PMID: 30512234 PMCID: PMC6468270 DOI: 10.1002/cbic.201800633] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Indexed: 12/20/2022]
Abstract
Inhibiting the histone H3-ASF1 (anti-silencing function 1) protein-protein interaction (PPI) represents a potential approach for treating numerous cancers. As an α-helix-mediated PPI, constraining the key histone H3 helix (residues 118-135) is a strategy through which chemical probes might be elaborated to test this hypothesis. In this work, variant H3118-135 peptides bearing pentenylglycine residues at the i and i+4 positions were constrained by olefin metathesis. Biophysical analyses revealed that promotion of a bioactive helical conformation depends on the position at which the constraint is introduced, but that the potency of binding towards ASF1 is unaffected by the constraint and instead that enthalpy-entropy compensation occurs.
Collapse
Affiliation(s)
- May Bakail
- Institute for Integrative Biology of the Cell (I2BC)IBITECSCEACNRSUniversité Paris–SudUniversité Paris–Saclay91198Gif-sur-Yvette CedexFrance
- Present address: Inserm, U1016Institut CochinCNRSUMR8104Université Paris Descartes27, rue du Faubourg Saint-Jacques75014ParisFrance
| | - Silvia Rodriguez‐Marin
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Zsófia Hegedüs
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Marie E. Perrin
- Institute for Integrative Biology of the Cell (I2BC)IBITECSCEACNRSUniversité Paris–SudUniversité Paris–Saclay91198Gif-sur-Yvette CedexFrance
| | - Françoise Ochsenbein
- Institute for Integrative Biology of the Cell (I2BC)IBITECSCEACNRSUniversité Paris–SudUniversité Paris–Saclay91198Gif-sur-Yvette CedexFrance
| | - Andrew J. Wilson
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| |
Collapse
|
12
|
Zhang G, Barragan F, Wilson K, Levy N, Herskovits A, Sapozhnikov M, Rodríguez Y, Kelmendi L, Alkasimi H, Korsmo H, Chowdhury M, Gerona‐Navarro G. A Solid‐Phase Approach to Accessing Bisthioether‐Stapled Peptides Resulting in a Potent Inhibitor of PRC2 Catalytic Activity. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201810007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Gan Zhang
- Department of Chemistry Brooklyn College of The City University of New York 2900 Bedford Avenue Brooklyn NY 11210 USA
- Ph.D. Program in Chemistry The Graduate Center of The City University of New York New York NY USA
| | - Flavia Barragan
- Department of Chemistry Brooklyn College of The City University of New York 2900 Bedford Avenue Brooklyn NY 11210 USA
| | - Khadija Wilson
- Department of Chemistry Brooklyn College of The City University of New York 2900 Bedford Avenue Brooklyn NY 11210 USA
| | - Nissim Levy
- Department of Chemistry Brooklyn College of The City University of New York 2900 Bedford Avenue Brooklyn NY 11210 USA
| | - Adam Herskovits
- Department of Chemistry Brooklyn College of The City University of New York 2900 Bedford Avenue Brooklyn NY 11210 USA
| | - Milana Sapozhnikov
- Department of Chemistry Brooklyn College of The City University of New York 2900 Bedford Avenue Brooklyn NY 11210 USA
| | - Yoel Rodríguez
- Department of Chemistry Brooklyn College of The City University of New York 2900 Bedford Avenue Brooklyn NY 11210 USA
- Department of Natural Sciences Hostos Community College of The City University of New York 475 Grand Concourse Bronx NY 10451 USA
| | - Leutrim Kelmendi
- Department of Chemistry Brooklyn College of The City University of New York 2900 Bedford Avenue Brooklyn NY 11210 USA
| | - Haleem Alkasimi
- Department of Chemistry Brooklyn College of The City University of New York 2900 Bedford Avenue Brooklyn NY 11210 USA
| | - Hunter Korsmo
- Department of Chemistry Brooklyn College of The City University of New York 2900 Bedford Avenue Brooklyn NY 11210 USA
| | - Maisha Chowdhury
- Department of Chemistry Brooklyn College of The City University of New York 2900 Bedford Avenue Brooklyn NY 11210 USA
| | - Guillermo Gerona‐Navarro
- Department of Chemistry Brooklyn College of The City University of New York 2900 Bedford Avenue Brooklyn NY 11210 USA
- Ph.D. Program in Chemistry The Graduate Center of The City University of New York New York NY USA
- Ph.D. Program in Biochemistry The Graduate Center of The City University of New York New York NY USA
| |
Collapse
|
13
|
Surur AS, Schulig L, Link A. Interconnection of sulfides and sulfoxides in medicinal chemistry. Arch Pharm (Weinheim) 2018; 352:e1800248. [DOI: 10.1002/ardp.201800248] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/29/2018] [Accepted: 10/30/2018] [Indexed: 12/17/2022]
Affiliation(s)
| | - Lukas Schulig
- Institute of Pharmacy; University of Greifswald; Greifswald Germany
| | - Andreas Link
- Institute of Pharmacy; University of Greifswald; Greifswald Germany
| |
Collapse
|
14
|
Li X, Tolbert WD, Hu HG, Gohain N, Zou Y, Niu F, He WX, Yuan W, Su JC, Pazgier M, Lu W. Dithiocarbamate-inspired side chain stapling chemistry for peptide drug design. Chem Sci 2018; 10:1522-1530. [PMID: 30809370 PMCID: PMC6357863 DOI: 10.1039/c8sc03275k] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/23/2018] [Indexed: 02/06/2023] Open
Abstract
A novel peptide stapling strategy based on the dithiocarbamate chemistry linking the side chains of residues Lys(i) and Cys(i + 4) of unprotected peptides is developed.
Two major pharmacological hurdles severely limit the widespread use of small peptides as therapeutics: poor proteolytic stability and membrane permeability. Importantly, low aqueous solubility also impedes the development of peptides for clinical use. Various elaborate side chain stapling chemistries have been developed for α-helical peptides to circumvent this problem, with considerable success in spite of inevitable limitations. Here we report a novel peptide stapling strategy based on the dithiocarbamate chemistry linking the side chains of residues Lys(i) and Cys(i + 4) of unprotected peptides and apply it to a series of dodecameric peptide antagonists of the p53-inhibitory oncogenic proteins MDM2 and MDMX. Crystallographic studies of peptide–MDM2/MDMX complexes structurally validated the chemoselectivity of the dithiocarbamate staple bridging Lys and Cys at (i, i + 4) positions. One dithiocarbamate-stapled PMI derivative, DTCPMI, showed a 50-fold stronger binding to MDM2 and MDMX than its linear counterpart. Importantly, in contrast to PMI and its linear derivatives, the DTCPMI peptide actively traversed the cell membrane and killed HCT116 tumor cells in vitro by activating the tumor suppressor protein p53. Compared with other known stapling techniques, our solution-based DTC stapling chemistry is simple, cost-effective, regio-specific and environmentally friendly, promising an important new tool for the development of peptide therapeutics with improved pharmacological properties including aqueous solubility, proteolytic stability and membrane permeability.
Collapse
Affiliation(s)
- Xiang Li
- School of Pharmacy , Second Military Medical University , Shanghai 200433 , China.,Institute of Human Virology and Department of Biochemistry and Molecular Biology , University of Maryland , School of Medicine , Baltimore , MD , USA . ;
| | - W David Tolbert
- Institute of Human Virology and Department of Biochemistry and Molecular Biology , University of Maryland , School of Medicine , Baltimore , MD , USA . ;
| | - Hong-Gang Hu
- School of Pharmacy , Second Military Medical University , Shanghai 200433 , China
| | - Neelakshi Gohain
- Institute of Human Virology and Department of Biochemistry and Molecular Biology , University of Maryland , School of Medicine , Baltimore , MD , USA . ;
| | - Yan Zou
- School of Pharmacy , Second Military Medical University , Shanghai 200433 , China
| | - Fan Niu
- Institute of Human Virology and Department of Biochemistry and Molecular Biology , University of Maryland , School of Medicine , Baltimore , MD , USA . ;
| | - Wang-Xiao He
- Institute of Human Virology and Department of Biochemistry and Molecular Biology , University of Maryland , School of Medicine , Baltimore , MD , USA . ;
| | - Weirong Yuan
- Institute of Human Virology and Department of Biochemistry and Molecular Biology , University of Maryland , School of Medicine , Baltimore , MD , USA . ;
| | - Jia-Can Su
- Changhai Hospital , Second Military Medical University , Shanghai 200433 , China .
| | - Marzena Pazgier
- Institute of Human Virology and Department of Biochemistry and Molecular Biology , University of Maryland , School of Medicine , Baltimore , MD , USA . ;
| | - Wuyuan Lu
- Institute of Human Virology and Department of Biochemistry and Molecular Biology , University of Maryland , School of Medicine , Baltimore , MD , USA . ;
| |
Collapse
|
15
|
Zhang G, Barragan F, Wilson K, Levy N, Herskovits A, Sapozhnikov M, Rodríguez Y, Kelmendi L, Alkasimi H, Korsmo H, Chowdhury M, Gerona-Navarro G. A Solid-Phase Approach to Accessing Bisthioether-Stapled Peptides Resulting in a Potent Inhibitor of PRC2 Catalytic Activity. Angew Chem Int Ed Engl 2018; 57:17073-17078. [PMID: 30339297 DOI: 10.1002/anie.201810007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/05/2018] [Indexed: 12/11/2022]
Abstract
Stapled peptides have emerged as a new class of therapeutics to effectively target intractable protein-protein interactions. Thus, efficient and versatile methods granting easy access to this class of compounds and expanding the scope(s) of the currently available ones are of great interest. Now, a solid phase approach is described for the synthesis of bisthioether stapled peptides with multiple architectures, including single-turn, double-turn, and double-stapled macrocycles. This method allows for ligation with all-hydrocarbon linkers of various lengths, avoiding the use of unnatural amino acids and expensive catalysts, and affords cyclopeptides with remarkable resistance to proteolytic degradation. The potential of this procedure is demonstrated by applying it to generate a stapled peptide that shows potent in vitro inhibition of methyltransferase activity of the polycomb repressive complex 2 (PRC2) of proteins.
Collapse
Affiliation(s)
- Gan Zhang
- Department of Chemistry, Brooklyn College of The City University of New York, 2900 Bedford Avenue, Brooklyn, NY, 11210, USA.,Ph.D. Program in Chemistry, The Graduate Center of The City University of New York, New York, NY, USA
| | - Flavia Barragan
- Department of Chemistry, Brooklyn College of The City University of New York, 2900 Bedford Avenue, Brooklyn, NY, 11210, USA
| | - Khadija Wilson
- Department of Chemistry, Brooklyn College of The City University of New York, 2900 Bedford Avenue, Brooklyn, NY, 11210, USA
| | - Nissim Levy
- Department of Chemistry, Brooklyn College of The City University of New York, 2900 Bedford Avenue, Brooklyn, NY, 11210, USA
| | - Adam Herskovits
- Department of Chemistry, Brooklyn College of The City University of New York, 2900 Bedford Avenue, Brooklyn, NY, 11210, USA
| | - Milana Sapozhnikov
- Department of Chemistry, Brooklyn College of The City University of New York, 2900 Bedford Avenue, Brooklyn, NY, 11210, USA
| | - Yoel Rodríguez
- Department of Chemistry, Brooklyn College of The City University of New York, 2900 Bedford Avenue, Brooklyn, NY, 11210, USA.,Department of Natural Sciences, Hostos Community College of The City University of New York, 475 Grand Concourse, Bronx, NY, 10451, USA
| | - Leutrim Kelmendi
- Department of Chemistry, Brooklyn College of The City University of New York, 2900 Bedford Avenue, Brooklyn, NY, 11210, USA
| | - Haleem Alkasimi
- Department of Chemistry, Brooklyn College of The City University of New York, 2900 Bedford Avenue, Brooklyn, NY, 11210, USA
| | - Hunter Korsmo
- Department of Chemistry, Brooklyn College of The City University of New York, 2900 Bedford Avenue, Brooklyn, NY, 11210, USA
| | - Maisha Chowdhury
- Department of Chemistry, Brooklyn College of The City University of New York, 2900 Bedford Avenue, Brooklyn, NY, 11210, USA
| | - Guillermo Gerona-Navarro
- Department of Chemistry, Brooklyn College of The City University of New York, 2900 Bedford Avenue, Brooklyn, NY, 11210, USA.,Ph.D. Program in Chemistry, The Graduate Center of The City University of New York, New York, NY, USA.,Ph.D. Program in Biochemistry, The Graduate Center of The City University of New York, New York, NY, USA
| |
Collapse
|
16
|
Skowron KJ, Speltz TE, Moore TW. Recent structural advances in constrained helical peptides. Med Res Rev 2018; 39:749-770. [PMID: 30307621 DOI: 10.1002/med.21540] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 09/05/2018] [Accepted: 09/06/2018] [Indexed: 12/20/2022]
Abstract
Given the ubiquity of the ⍺-helix in the proteome, there has been much research in developing mimics of ⍺-helices, and most of this study has been toward developing protein-protein interaction inhibitors. A common strategy for mimicking ⍺-helices has been through the use of constrained, helical peptides. The addition of a constraint typically provides for conformational and proteolytic stability and, in some cases, cell permeability. Some of the most well-known strategies included are lactam formation and hydrocarbon "stapling." Beyond those strategies, there have been many recent advances in developing constrained peptides. The purpose of this review is to highlight recent advances in the development of new helix-stabilizing technologies, constraint diversification strategies, tether diversification strategies, and combination strategies that create new bicyclic helical peptides.
Collapse
Affiliation(s)
- Kornelia J Skowron
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
| | - Thomas E Speltz
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
| | - Terry W Moore
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois.,Translational Oncology Program, University of Illinois Cancer Center, Chicago, Illinois
| |
Collapse
|
17
|
Perell GT, Mishra NK, Sudhamalla B, Ycas PD, Islam K, Pomerantz WCK. Specific Acetylation Patterns of H2A.Z Form Transient Interactions with the BPTF Bromodomain. Biochemistry 2017; 56:4607-4615. [PMID: 28771339 PMCID: PMC5779092 DOI: 10.1021/acs.biochem.7b00648] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Post-translational lysine acetylation of histone tails affects both chromatin accessibility and recruitment of multifunctional bromodomain-containing proteins for modulating transcription. The bromodomain- and PHD finger-containing transcription factor (BPTF) regulates transcription but has also been implicated in high gene expression levels in a variety of cancers. In this report, the histone variant H2A.Z, which replaces H2A in chromatin, is evaluated for its affinity for BPTF with a specific recognition pattern of acetylated lysine residues of the N-terminal tail region. Although BPTF immunoprecipitates H2A.Z-containing nucleosomes, a direct interaction with its bromodomain has not been reported. Using protein-observed fluorine nuclear magnetic resonance (PrOF NMR) spectroscopy, we identified a diacetylation of H2A.Z on lysine residues 4 and 11, with the highest affinity for BPTF with a Kd of 780 μM. A combination of subsequent 1H NMR Carr-Purcell-Meiboom-Gill experiments and photo-cross-linking further confirmed the specificity of the diacetylation pattern at lysines 4 and 11. Because of an adjacent PHD domain, this transient interaction may contribute to a higher-affinity bivalent interaction. Further evaluation of specificity toward a set of bromodomains, including two BET bromodomains (Brd4 and BrdT) and two Plasmodium falciparum bromodomains, resulted in one midmicromolar affinity binder, PfGCN5 (Kd = 650 μM). With these biochemical experiments, we have identified a direct interaction of histone H2A.Z with bromodomains with a specific acetylation pattern that further supports the role of H2A.Z in epigenetic regulation.
Collapse
Affiliation(s)
- Gabriella T. Perell
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Neeraj K. Mishra
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Babu Sudhamalla
- Department of Chemistry, University of Pittsburgh, 1307 Chevron Science Center, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Peter D. Ycas
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Kabirul Islam
- Department of Chemistry, University of Pittsburgh, 1307 Chevron Science Center, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - William C. K. Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| |
Collapse
|