1
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Bavinton CE, Sternke-Hoffmann R, Yamashita T, Knipe PC, Hamilton AD, Luo J, Thompson S. Rationally designed helical peptidomimetics disrupt α-synuclein fibrillation. Chem Commun (Camb) 2022; 58:5132-5135. [PMID: 35380562 DOI: 10.1039/d2cc00212d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Misfolding of the human protein α-synuclein results in toxic fibrils and the aggregation of Lewy bodies, which are a hallmark of Parkinson's disease in brain tissue. Here we disclose a supramolecular approach where peptidomimetics are rationally designed and pre-organised to recognize the surface of native helical α-Syn by forming complementary contacts with key patches of protein surface composed of charged and hydrophobic residues. Under lipid-catalyzed conditions the mimetics slow the rate of aggregation (thioflavin-T assay) and disrupt the misfolding pathway (electron microscopy of aggregates). This hypothesis is supported by comparison with a series of negative control compounds and with circular dichroism spectroscopy. Given the approach relies on selective recognition of both amino acid sequence and conformation (helical secondary structure) there is potential to develop these compounds as tools to unravel the currently intractable structure-function relationships of (i) missense mutation, and (ii) amyloid polymorphism with disease pathogenesis.
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Affiliation(s)
- Clementine E Bavinton
- School of Chemistry and the Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| | | | - Tohru Yamashita
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Peter C Knipe
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK.,School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Belfast, BT9 5AG, UK
| | - Andrew D Hamilton
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK.,Department of Chemistry, New York University, 100 Washington Square East, NY 10003, USA
| | - Jinghui Luo
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland.
| | - Sam Thompson
- School of Chemistry and the Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK. .,Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
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2
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La Manna S, De Benedictis I, Marasco D. Proteomimetics of Natural Regulators of JAK-STAT Pathway: Novel Therapeutic Perspectives. Front Mol Biosci 2022; 8:792546. [PMID: 35047557 PMCID: PMC8762217 DOI: 10.3389/fmolb.2021.792546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 11/29/2021] [Indexed: 12/16/2022] Open
Abstract
The JAK-STAT pathway is a crucial cellular signaling cascade, including an intricate network of Protein-protein interactions (PPIs) responsible for its regulation. It mediates the activities of several cytokines, interferons, and growth factors and transduces extracellular signals into transcriptional programs to regulate cell growth and differentiation. It is essential for the development and function of both innate and adaptive immunities, and its aberrant deregulation was highlighted in neuroinflammatory diseases and in crucial mechanisms for tumor cell recognition and tumor-induced immune escape. For its involvement in a multitude of biological processes, it can be considered a valuable target for the development of drugs even if a specific focus on possible side effects associated with its inhibition is required. Herein, we review the possibilities to target JAK-STAT by focusing on its natural inhibitors as the suppressor of cytokine signaling (SOCS) proteins. This protein family is a crucial checkpoint inhibitor in immune homeostasis and a valuable target in immunotherapeutic approaches to cancer and immune deficiency disorders.
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Affiliation(s)
| | | | - Daniela Marasco
- Department of Pharmacy, University of Naples “Federico II”, Naples, Italy
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3
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Singh H, Chenna A, Gangwar U, Borah J, Goel G, Haridas V. Bispidine as a β-strand nucleator: from a β-arch to self-assembled cages and vesicles. Chem Sci 2021; 12:15757-15764. [PMID: 35003608 PMCID: PMC8654037 DOI: 10.1039/d1sc04860k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/25/2021] [Indexed: 12/23/2022] Open
Abstract
The development of synthetic scaffolds that nucleate well-folded secondary structures is highly challenging. Herein, we designed and synthesized a series of core-modified peptides (F1, F2, F3, and F4) that fold into β-strand structures. These bispidine-scaffolded peptides were studied by CD, IR, NMR, single crystal XRD, and Molecular Dynamics (MD) simulations to investigate their conformational preferences. Solid-state and solution studies revealed that bispidine is a versatile scaffold that could be placed either at the terminal or at the middle of the peptide strand for nucleating the β-strand structure. Scaffolds that nucleate an isolated β-strand conformation are rare. Bispidine placed at the C-terminus of the peptide chain could nucleate a β-strand conformation, while bispidine placed at the middle resulted in a β-arch conformation. This nucleation activity stems from the ability to restrict the psi torsion angle (ψ) through intramolecular C5 hydrogen bonding between the equatorial hydrogen(s) of bispidine and the carbonyl oxygen(s) of the amino acid close to the scaffold. Furthermore, the bispidine peptidomimetic with a super secondary structure, namely β-arch, assembled into single-hole submicron cages and spherical vesicles as evident from microscopic studies. The design logic defined here will be a significant strategy for the development of β-strand mimetics and super secondary structures.
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Affiliation(s)
- Hanuman Singh
- Department of Chemistry, Indian Institute of Technology Delhi Hauz Khas New Delhi-110016 India
| | - Akshay Chenna
- Department of Chemical Engineering, Indian Institute of Technology Delhi Hauz Khas New Delhi-110016 India
| | - Upanshu Gangwar
- Department of Chemistry, Indian Institute of Technology Delhi Hauz Khas New Delhi-110016 India
| | - Julie Borah
- Department of Chemical Engineering, Indian Institute of Technology Delhi Hauz Khas New Delhi-110016 India
| | - Gaurav Goel
- Department of Chemical Engineering, Indian Institute of Technology Delhi Hauz Khas New Delhi-110016 India
| | - V Haridas
- Department of Chemistry, Indian Institute of Technology Delhi Hauz Khas New Delhi-110016 India
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4
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Rajappan SC, Vestrheim O, Sharafi M, Li J, Schneebeli ST. Carbonyl-to-Alkyne Electron Donation Effects in up to 10-nm-Long, Unimolecular Oligo( p-phenylene ethynylenes). ORGANIC MATERIALS 2021; 3:337-345. [PMID: 34505058 PMCID: PMC8425378 DOI: 10.1055/s-0041-1730899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We synthesized some of the longest unimolecular oligo(p-phenylene ethynylenes) (OPEs), which are fully substituted with electron-withdrawing ester groups. An iterative convergent/divergent (a.k.a. iterative exponential growth - IEG) strategy based on Sonogashira couplings was utilized to access these sequence-defined macromolecules with up to 16 repeating units and 32 ester substituents. The carbonyl groups of the ester substituents interact with the triple bonds of the OPEs, leading to (i) unusual, angled triple bonds with increased rotational barrier, (ii) enhanced conformational disorder, and (iii) associated broadening of the UV/Vis absorption spectrum. Our results demonstrate that fully air-stable, unimolecular OPEs with ester groups can readily be accessed with IEG chemistry, providing new macromolecular backbones with unique geometrical, conformational, and photophysical properties.
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Affiliation(s)
- Sinu C Rajappan
- University of Vermont, Departments of Chemistry and Materials Science, 82 University Place, Burlington, VT 05405, United States
| | - Olav Vestrheim
- University of Vermont, Departments of Chemistry and Materials Science, 82 University Place, Burlington, VT 05405, United States
| | - Mona Sharafi
- University of Vermont, Departments of Chemistry and Materials Science, 82 University Place, Burlington, VT 05405, United States
| | - Jianing Li
- University of Vermont, Departments of Chemistry and Materials Science, 82 University Place, Burlington, VT 05405, United States
| | - Severin T Schneebeli
- University of Vermont, Departments of Chemistry and Materials Science, 82 University Place, Burlington, VT 05405, United States
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5
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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: 26] [Impact Index Per Article: 8.7] [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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6
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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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7
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Hegedüs Z, Hóbor F, Shoemark DK, Celis S, Lian LY, Trinh CH, Sessions RB, Edwards TA, Wilson AJ. Identification of β-strand mediated protein-protein interaction inhibitors using ligand-directed fragment ligation. Chem Sci 2021; 12:2286-2293. [PMID: 34163995 PMCID: PMC8179271 DOI: 10.1039/d0sc05694d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/01/2020] [Indexed: 12/26/2022] Open
Abstract
β-Strand mediated protein-protein interactions (PPIs) represent underexploited targets for chemical probe development despite representing a significant proportion of known and therapeutically relevant PPI targets. β-Strand mimicry is challenging given that both amino acid side-chains and backbone hydrogen-bonds are typically required for molecular recognition, yet these are oriented along perpendicular vectors. This paper describes an alternative approach, using GKAP/SHANK1 PDZ as a model and dynamic ligation screening to identify small-molecule replacements for tranches of peptide sequence. A peptide truncation of GKAP functionalized at the N- and C-termini with acylhydrazone groups was used as an anchor. Reversible acylhydrazone bond exchange with a library of aldehyde fragments in the presence of the protein as template and in situ screening using a fluorescence anisotropy (FA) assay identified peptide hybrid hits with comparable affinity to the GKAP peptide binding sequence. Identified hits were validated using FA, ITC, NMR and X-ray crystallography to confirm selective inhibition of the target PDZ-mediated PPI and mode of binding. These analyses together with molecular dynamics simulations demonstrated the ligands make transient interactions with an unoccupied basic patch through electrostatic interactions, establishing proof-of-concept that this unbiased approach to ligand discovery represents a powerful addition to the armory of tools that can be used to identify PPI modulators.
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Affiliation(s)
- Zsófia Hegedüs
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Fruzsina Hóbor
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Deborah K Shoemark
- School of Biochemistry, Biomedical Sciences Building, University of Bristol Bristol BS8 1TD UK
| | - Sergio Celis
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Lu-Yun Lian
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool Liverpool L69 3BX UK
| | - Chi H Trinh
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Richard B Sessions
- School of Biochemistry, Biomedical Sciences Building, University of Bristol Bristol BS8 1TD UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Andrew J Wilson
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
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8
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Peacock H, Henriques ST, Benfield AH, Elliott AG, Luo J, Luccarelli J, Nagano M, Craik DJ, Hamilton AD. Antimicrobial Peptide Mimetics Based on a Diphenylacetylene Scaffold: Synthesis, Conformational Analysis, and Activity. ChemMedChem 2020; 15:1932-1939. [DOI: 10.1002/cmdc.202000474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Indexed: 01/16/2023]
Affiliation(s)
- Hayden Peacock
- Department of Chemistry The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
- Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
- Chemistry Research Laboratory The University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Sónia Troeira Henriques
- Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
- School of Biomedical Sciences Institute of Health & Biomedical Innovation and Translational Research Institute Queensland University of Technology Brisbane QLD, 4102 Australia
| | - Aurélie H. Benfield
- Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
- School of Biomedical Sciences Institute of Health & Biomedical Innovation and Translational Research Institute Queensland University of Technology Brisbane QLD, 4102 Australia
| | - Alysha G. Elliott
- Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Jinghui Luo
- Chemistry Research Laboratory The University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
- Laboratory of Nanoscale Biology Paul Scherrer Institute 5232 Villigen Switzerland
| | - James Luccarelli
- Chemistry Research Laboratory The University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
- Department of Psychiatry Massachusetts General Hospital Boston MA 02114 USA
| | - Masanobu Nagano
- Department of Chemistry The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - David J. Craik
- Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Andrew D. Hamilton
- Department of Chemistry New York University New York NY 10003 USA
- Chemistry Research Laboratory The University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
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9
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Hong JH, Ko MS, Rao PS, Cho DG. Systematic Modifications of a Simple Tolan: Another Category of Viscosity Sensor. Org Lett 2019; 21:10085-10089. [PMID: 31808700 DOI: 10.1021/acs.orglett.9b04050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The first tolan derivative-based viscosity sensor (5d) has been synthesized, and its fluorescence intensity and lifetime increase when the viscosity of the solvent increases in methanol-glycerol mixtures. Phthalide (5d) was selected among structurally diverse tolan derivatives through systematic modifications of a simple tolan. To test 5d as a viscosity sensor, fluorescence lifetime imaging (FLIM) images of HeLa cells were obtained upon treatment with 5 μM of 5d to map the viscosity of the HeLa cells.
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Affiliation(s)
- Jung-Ho Hong
- Department of Chemistry and Chemical Engineering , Inha University , Inharo 100 , Incheon 22212 , Republic of Korea
| | - Min-Sung Ko
- Department of Chemistry and Chemical Engineering , Inha University , Inharo 100 , Incheon 22212 , Republic of Korea
| | - P Sankara Rao
- Department of Chemistry and Chemical Engineering , Inha University , Inharo 100 , Incheon 22212 , Republic of Korea
| | - Dong-Gyu Cho
- Department of Chemistry and Chemical Engineering , Inha University , Inharo 100 , Incheon 22212 , Republic of Korea
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10
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Abstract
Peptide secondary and tertiary structure motifs frequently serve as inspiration for the development of protein-protein interaction (PPI) inhibitors. While a wide variety of strategies have been used to stabilize or imitate α-helices, similar strategies for β-sheet stabilization are more limited. Synthetic scaffolds that stabilize reverse turns and cross-strand interactions have provided important insights into β-sheet stability and folding. However, these templates occupy regions of the β-sheet that might impact the β-sheet's ability to bind at a PPI interface. Here, we present the hydrogen bond surrogate (HBS) approach for stabilization of β-hairpin peptides. The HBS linkage replaces a cross-strand hydrogen bond with a covalent linkage, conferring significant conformational and proteolytic resistance. Importantly, this approach introduces the stabilizing linkage in the buried β-sheet interior, retains all side chains for further functionalization, and allows efficient solid-phase macrocyclization. We anticipate that HBS stabilization of PPI β-sheets will enhance the development of β-sheet PPI inhibitors and expand the repertoire of druggable PPIs.
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Affiliation(s)
- Nicholas Sawyer
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Paramjit S. Arora
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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11
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Shi YD, Tang Q, Jiang YF, Pei Q, Tan HW, Lu ZL, Gong B. Effective formation of stable and versatile double-stranded β-sheets templated by a hydrogen-bonded duplex. Chem Commun (Camb) 2018; 54:3719-3722. [DOI: 10.1039/c8cc01564c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
An effective approach to construct stable and versatile double-stranded β-sheets composed of tetra- and penta-peptides through a hydrogen-bonded duplex template has been explored.
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Affiliation(s)
- You-Di Shi
- Key Laboratory of Radiopharmaceuticals
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing 100875
| | - Quan Tang
- Key Laboratory of Radiopharmaceuticals
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing 100875
| | - Ya-Fei Jiang
- Key Laboratory of Radiopharmaceuticals
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing 100875
| | - Qiang Pei
- Key Laboratory of Radiopharmaceuticals
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing 100875
| | - Hong-Wei Tan
- Key Laboratory of Radiopharmaceuticals
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing 100875
| | - Zhong-Lin Lu
- Key Laboratory of Radiopharmaceuticals
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing 100875
| | - Bing Gong
- Key Laboratory of Radiopharmaceuticals
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing 100875
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12
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Bag SS, Yashmeen A. Uracil-amino acid as a scaffold for β-sheet peptidomimetics: Study of photophysics and interaction with BSA protein. Bioorg Med Chem Lett 2017; 27:5387-5392. [PMID: 29153423 DOI: 10.1016/j.bmcl.2017.11.017] [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: 05/30/2017] [Revised: 11/05/2017] [Accepted: 11/08/2017] [Indexed: 10/18/2022]
Abstract
We report herein the uracil-di-aza-amino acid (UrAA) as a new family of molecular scaffold to induce β-hairpin structure with H-bonded β-sheet conformation in a short peptide. This has been demonstrated in two conceptual fluorescent pentapeptides wherein triazolylpyrenyl alanine and/or triazolylmethoxynapthyl alanine (TPyAlaDo and/or TMNapAlaDo) are embedded into two arms of the uracil-amino acid via an intervening leucine. Conformational analysis by CD, IR, variable temperature and 2D NMR spectroscopy reveals the β-hairpin structures for both the peptides. Study of photophysical property reveals that the pentapeptide containing fluorescent triazolyl unnatural amino acids TMNapAlaDo and TPyAlaDo at the two termini exhibits dual path entry to exciplex emission-either via FRET from TMNapAlaDo to TPyAlaDo or via direct excitation of a FRET acceptor, TPyAlaDo. The other pentapeptide with TPyAlaDo/TPyAlaDo pair shows excimer emission. Furthermore, both the peptides maintaining their fundamental photophysics are found to interact with BSA as only a test biomolecule.
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Affiliation(s)
- Subhendu Sekhar Bag
- Bioorganic Chemistry Laboratory, Department of Chemistry, Indian Institute of Technology Guwahati, North Guwhati 781039, Assam, India.
| | - Afsana Yashmeen
- Bioorganic Chemistry Laboratory, Department of Chemistry, Indian Institute of Technology Guwahati, North Guwhati 781039, Assam, India
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13
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Lamouroux A, Sebaoun L, Wicher B, Kauffmann B, Ferrand Y, Maurizot V, Huc I. Controlling Dipole Orientation through Curvature: Aromatic Foldamer Bent β-Sheets and Helix–Sheet–Helix Architectures. J Am Chem Soc 2017; 139:14668-14675. [DOI: 10.1021/jacs.7b07961] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Arthur Lamouroux
- Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Institut Européen de
Chimie Biologie, 2 Rue
Escarpit, 33600 Pessac, France
| | - Laure Sebaoun
- Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Institut Européen de
Chimie Biologie, 2 Rue
Escarpit, 33600 Pessac, France
| | - Barbara Wicher
- Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Institut Européen de
Chimie Biologie, 2 Rue
Escarpit, 33600 Pessac, France
| | - Brice Kauffmann
- Université de Bordeaux, CNRS, INSERM, Institut Européen
de Chimie Biologie (UMS3033/US001), 2 Rue Escarpit, 33600 Pessac, France
| | - Yann Ferrand
- Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Institut Européen de
Chimie Biologie, 2 Rue
Escarpit, 33600 Pessac, France
| | - Victor Maurizot
- Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Institut Européen de
Chimie Biologie, 2 Rue
Escarpit, 33600 Pessac, France
| | - Ivan Huc
- Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Institut Européen de
Chimie Biologie, 2 Rue
Escarpit, 33600 Pessac, France
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14
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Shin JH, Hong JH, Ko MS, Cho DG. Fluorescent and cooperative ion pair receptor based on tolan for Na + (or Li +) and HSO 4-: logic AND gate. Chem Commun (Camb) 2017; 53:11414-11417. [PMID: 28975165 DOI: 10.1039/c7cc06907c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A tolan derivative was synthesized as a fluorescent and cooperative ion pair receptor. As both Na+ and HSO4- ions were complexed to the receptor, only substantial fluorescence was quenched. Thus, it also acts as a logic AND gate.
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Affiliation(s)
- June-Ho Shin
- Department of Chemistry, Inha University, Incheon, 22212, Republic of Korea.
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15
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Sawyer N, Watkins AM, Arora PS. Protein Domain Mimics as Modulators of Protein-Protein Interactions. Acc Chem Res 2017; 50:1313-1322. [PMID: 28561588 DOI: 10.1021/acs.accounts.7b00130] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Protein-protein interactions (PPIs) are ubiquitous in biological systems and often misregulated in disease. As such, specific PPI modulators are desirable to unravel complex PPI pathways and expand the number of druggable targets available for therapeutic intervention. However, the large size and relative flatness of PPI interfaces make them challenging molecular targets. This Account describes our systematic approach using secondary and tertiary protein domain mimics (PDMs) to specifically modulate PPIs. Our strategy focuses on mimicry of regular secondary and tertiary structure elements from one of the PPI partners to inspire rational PDM design. We have compiled three databases (HIPPDB, SIPPDB, and DIPPDB) of secondary and tertiary structures at PPI interfaces to guide our designs and better understand the energetics of PPI secondary and tertiary structures. Our efforts have focused on three of the most common secondary and tertiary structures: α-helices, β-strands, and helix dimers (e.g., coiled coils). To mimic α-helices, we designed the hydrogen bond surrogate (HBS) as an isosteric PDM and the oligooxopiperazine helix mimetic (OHM) as a topographical PDM. The nucleus of the HBS approach is a peptide macrocycle in which the N-terminal i, i + 4 main-chain hydrogen bond is replaced with a covalent carbon-carbon bond. In mimicking a main-chain hydrogen bond, the HBS approach stabilizes the α-helical conformation while leaving all helical faces available for functionalization to tune binding affinity and specificity. The OHM approach, in contrast, envisions a tetrapeptide to mimic one face of a two-turn helix. We anticipated that placement of ethylene bridges between adjacent amides constrains the tetrapeptide backbone to mimic the i, i + 4, and i + 7 side chains on one face of an α-helix. For β-strands, we developed triazolamers, a topographical PDM where the peptide bonds are replaced by triazoles. The triazoles simultaneously stabilize the extended, zigzag conformation of β-strands and transform an otherwise ideal protease substrate into a stable molecule by replacement of the peptide bonds. We turned to a salt bridge surrogate (SBS) approach as a means for stabilizing very short helix dimers. As with the HBS approach, the SBS strategy replaces a noncovalent interaction with a covalent bond. Specifically, we used a bis-triazole linkage that mimics a salt bridge interaction to drive helix association and folding. Using this approach, we were able to stabilize helix dimers that are less than half of the length required to form a coiled coil from two independent strands. In addition to demonstrating the stabilization of desired structures, we have also shown that our designed PDMs specifically modulate target PPIs in vitro and in vivo. Examples of PPIs successfully targeted include HIF1α/p300, p53/MDM2, Bcl-xL/Bak, Ras/Sos, and HIV gp41. The PPI databases and designed PDMs created in these studies will aid development of a versatile set of molecules to probe complex PPI functions and, potentially, PPI-based therapeutics.
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Affiliation(s)
- Nicholas Sawyer
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Andrew M. Watkins
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Paramjit S. Arora
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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16
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Tashiro S, Chiba M, Shionoya M. Arrangement of Proteinogenic α-Amino Acids on a Cyclic Peptide Comprising Alternate Biphenyl-Cored ζ-Amino Acids. Chem Asian J 2017; 12:1087-1094. [DOI: 10.1002/asia.201700203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 03/25/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Shohei Tashiro
- Department of Chemistry; Graduate School of Science; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Masayuki Chiba
- Department of Chemistry; Graduate School of Science; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry; Graduate School of Science; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
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17
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Busschaert N, Thompson S, Hamilton AD. An α-helical peptidomimetic scaffold for dynamic combinatorial library formation. Chem Commun (Camb) 2017; 53:313-316. [DOI: 10.1039/c6cc07787k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A novel oligobenzamide-based α-helix mimetic was designed and synthesised with either imine or hydrazone functionalities that serve both to pre-organise the side-chain vectors to mimic the i, i + 4 and i + 7 residues of an α-helix, and to allow for the facile creation of dynamic libraries.
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Affiliation(s)
- Nathalie Busschaert
- Department of Chemistry
- New York University
- New York
- USA
- Chemistry Research Laboratory
| | - Sam Thompson
- Chemistry Research Laboratory
- University of Oxford
- UK
- Chemistry
- University of Southampton
| | - Andrew D. Hamilton
- Department of Chemistry
- New York University
- New York
- USA
- Chemistry Research Laboratory
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18
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Watkins AM, Bonneau R, Arora PS. Modeling and Design of Peptidomimetics to Modulate Protein-Protein Interactions. Methods Mol Biol 2017; 1561:291-307. [PMID: 28236245 DOI: 10.1007/978-1-4939-6798-8_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We describe a modular approach to identify and inhibit protein-protein interactions (PPIs) that are mediated by protein secondary and tertiary structures with rationally designed peptidomimetics. Our analysis begins with entries of high-resolution complexes in the Protein Data Bank and utilizes conformational sampling, scoring, and design capabilities of advanced biomolecular modeling software to develop peptidomimetics.
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Affiliation(s)
| | - Richard Bonneau
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
- Computer Science Department, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
| | - Paramjit S Arora
- Department of Chemistry, New York University, 29 Washington Place, Brown Bldg., Room 360, New York, NY, USA.
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19
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Xin D, Burgess K. Anthranilic acid-containing cyclic tetrapeptides: at the crossroads of conformational rigidity and synthetic accessibility. Org Biomol Chem 2016; 14:5049-58. [PMID: 27173439 PMCID: PMC4916954 DOI: 10.1039/c6ob00693k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Each amino acid in a peptide contributes three atom units to main-chains, hence natural cyclic peptides can be 9, 12, 15, …. i.e. 3n membered-rings, where n is the number of amino acids. Cyclic peptides that are 9 or 12-membered ring compounds tend to be hard to prepare because of strain, while their one amino acid homologs (15-membered cyclic pentapeptides) are not conformationally homogeneous unless constrained by strategically placed proline or d-amino acid residues. We hypothesized that replacing one genetically encoded amino acid in a cyclic tetrapeptide with a rigid β-amino acid would render peptidomimetic designs that rest at a useful crossroads between synthetic accessibility and conformational rigidity. Thus this research explored non-proline containing 13-membered ring peptides 1 featuring one anthranilic acid (Anth) residue. Twelve cyclic peptides of this type were prepared, and in doing so the viability of both solution- and solid-phase methods was demonstrated. The library produced contained a complete set of four diastereoisomers of the sequence 1aaf (i.e. cyclo-AlaAlaPheAnth). Without exception, these four diastereoisomers each adopted one predominant conformation in solution; basically these conformations feature amide N-H vectors puckering above and below the equatorial plane, and approximately oriented their N-H[combining low line] atoms towards the polar axis. Moreover, the shapes of these conformers varied in a logical and predictable way (NOE, temperature coefficient, D/H exchange, circular dichroism). Comparisons were made of the side-chain orientations presented by compounds 1aaa in solution with ideal secondary structures and protein-protein interaction interfaces. Various 1aaa stereoisomers in solution present side-chains in similar orientations to regular and inverse γ-turns, and to the most common β-turns (types I and II). Consistent with this, compounds 1aaa have a tendency to mimic various turns and bends at protein-protein interfaces. Finally, proteolytic- and hydrolytic stabilities of the compounds at different pHs indicate they are robust relative to related linear peptides, and rates of permeability through an artificial membrane indicate their structures are conducive to cell permeability.
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Affiliation(s)
- Dongyue Xin
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX 77842, USA.
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20
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Modell AE, Blosser SL, Arora PS. Systematic Targeting of Protein-Protein Interactions. Trends Pharmacol Sci 2016; 37:702-713. [PMID: 27267699 DOI: 10.1016/j.tips.2016.05.008] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 05/14/2016] [Accepted: 05/16/2016] [Indexed: 12/22/2022]
Abstract
Over the past decade, protein-protein interactions (PPIs) have gone from being neglected as 'undruggable' to being considered attractive targets for the development of therapeutics. Recent advances in computational analysis, fragment-based screening, and molecular design have revealed promising strategies to address the basic molecular recognition challenge: how to target large protein surfaces with specificity. Several systematic and complementary workflows have been developed to yield successful inhibitors of PPIs. Here we review the major contemporary approaches utilized for the discovery of inhibitors and focus on a structure-based workflow, from the selection of a biological target to design.
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Affiliation(s)
- Ashley E Modell
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Sarah L Blosser
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, NY 10003, USA
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21
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1,4-Bis[(N-acetyl-l-phenylalanyl-glycyl-l-alanyl)aminomethyl]benzene. MOLBANK 2016. [DOI: 10.3390/m893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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22
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Shugrue CR, DeFrancisco JR, Metrano AJ, Brink BD, Nomoto RS, Linton BR. Detection of weak hydrogen bonding to fluoro and nitro groups in solution using H/D exchange. Org Biomol Chem 2016; 14:2223-7. [PMID: 26782121 DOI: 10.1039/c5ob02360b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrogen/deuterium (H/D) exchange can be a sensitive technique for measuring the strength of hydrogen bonding to neutral organic nitro and fluoro groups. The slower rates of reaction in comparison to suitable controls suggest that hydrogen bonding is present, albeit rather weak.
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Affiliation(s)
- C R Shugrue
- Department of Chemistry, College of the Holy Cross, Worcester, MA, USA.
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23
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Nissinkorn Y, Lahav‐Mankovski N, Rabinkov A, Albeck S, Motiei L, Margulies D. Sensing Protein Surfaces with Targeted Fluorescent Receptors. Chemistry 2015; 21:15981-7. [DOI: 10.1002/chem.201502069] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Indexed: 12/11/2022]
Affiliation(s)
- Yael Nissinkorn
- Department of Organic Chemistry, Weizmann Institute of Science, 76100, Rehovot (Israel)
| | - Naama Lahav‐Mankovski
- Department of Organic Chemistry, Weizmann Institute of Science, 76100, Rehovot (Israel)
| | - Aharon Rabinkov
- Department of Biological Services, Weizmann Institute of Science, 76100, Rehovot (Israel)
| | - Shira Albeck
- Israel Structural Proteomics Center, Weizmann Institute of Science, 76100, Rehovot (Israel)
| | - Leila Motiei
- Department of Organic Chemistry, Weizmann Institute of Science, 76100, Rehovot (Israel)
| | - David Margulies
- Department of Organic Chemistry, Weizmann Institute of Science, 76100, Rehovot (Israel)
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24
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Lanning ME, Fletcher S. Multi-Facial, Non-Peptidic α-Helix Mimetics. BIOLOGY 2015; 4:540-55. [PMID: 26404384 PMCID: PMC4588149 DOI: 10.3390/biology4030540] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 08/11/2015] [Accepted: 08/14/2015] [Indexed: 01/13/2023]
Abstract
α-Helices often recognize their target proteins at protein–protein interfaces through more than one recognition face. This review describes the state-of-the-art in the design of non-peptidic α-helix mimetics that reproduce functionality from multiple faces of an α-helix.
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Affiliation(s)
- Maryanna E Lanning
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N. Pine St., Baltimore, MD 21201, USA.
| | - Steven Fletcher
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N. Pine St., Baltimore, MD 21201, USA.
- University of Maryland Greenebaum Cancer Center, 22 S. Greene St., Baltimore, MD 21201, USA.
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25
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Ross JE, Knipe PC, Thompson S, Hamilton AD. Hybrid Diphenylalkyne-Dipeptide Oligomers Induce Multistrand β-Sheet Formation. Chemistry 2015; 21:13518-21. [DOI: 10.1002/chem.201502690] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Indexed: 12/14/2022]
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26
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Pelay-Gimeno M, Glas A, Koch O, Grossmann TN. Structure-Based Design of Inhibitors of Protein-Protein Interactions: Mimicking Peptide Binding Epitopes. Angew Chem Int Ed Engl 2015; 54:8896-927. [PMID: 26119925 PMCID: PMC4557054 DOI: 10.1002/anie.201412070] [Citation(s) in RCA: 491] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions (PPIs) are involved at all levels of cellular organization, thus making the development of PPI inhibitors extremely valuable. The identification of selective inhibitors is challenging because of the shallow and extended nature of PPI interfaces. Inhibitors can be obtained by mimicking peptide binding epitopes in their bioactive conformation. For this purpose, several strategies have been evolved to enable a projection of side chain functionalities in analogy to peptide secondary structures, thereby yielding molecules that are generally referred to as peptidomimetics. Herein, we introduce a new classification of peptidomimetics (classes A-D) that enables a clear assignment of available approaches. Based on this classification, the Review summarizes strategies that have been applied for the structure-based design of PPI inhibitors through stabilizing or mimicking turns, β-sheets, and helices.
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Affiliation(s)
- Marta Pelay-Gimeno
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
| | - Adrian Glas
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
| | - Oliver Koch
- TU Dortmund University, Department of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6, 44227 Dortmund (Germany)
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
- TU Dortmund University, Department of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6, 44227 Dortmund (Germany)
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27
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Pelay-Gimeno M, Glas A, Koch O, Grossmann TN. Strukturbasierte Entwicklung von Protein-Protein-Interaktionsinhibitoren: Stabilisierung und Nachahmung von Peptidliganden. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201412070] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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28
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Methyl 2-[(2-{2-[(2-acetamidophenyl)ethynyl]benzamido} phenyl)ethynyl]benzoate. MOLBANK 2015. [DOI: 10.3390/m854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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29
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Vijayadas KN, Kotmale AS, Thorat SH, Gonnade RG, Nair RV, Rajamohanan PR, Sanjayan GJ. Reversal of H-bonding direction by N-sulfonation in a synthetic reverse-turn peptide motif. Org Biomol Chem 2015; 13:3064-9. [PMID: 25624112 DOI: 10.1039/c4ob02438a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This communication depicts an intriguing example of hydrogen-bonding reversal upon introduction of a sulfonamide linkage at the N-terminus of a synthetic reverse-turn peptide motif. The ready availability of two sulfonyl oxygen atoms, as hydrogen-bonding acceptors, combined with the inherent twisted conformation of sulfonamides are seen to act as switches that engage/disengage the hydrogen-bond at the sticky ends/termini.
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Affiliation(s)
- Kuruppanthara N Vijayadas
- Division of Organic Chemistry, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India.
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30
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Zhang YC, Zhang DW, Wang H, Zhou Y, Li ZT. Bipyridinium radical cation dimerization-driven polymeric pleated foldamers and a homoduplex that undergo ion-tuned interconversion. Polym Chem 2015. [DOI: 10.1039/c5py00419e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Radical cation dimerization induces bipyridinium-derived polymers to form pleated secondary structures and a homoduplex which can be tuned by ammonium to interconvert.
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Affiliation(s)
- Yun-Chang Zhang
- Department of Chemistry
- Collaborative Innovation Center of Chemistry for Energy Materials (iChEM)
- Fudan University
- Shanghai 200433
- China
| | - Dan-Wei Zhang
- Department of Chemistry
- Collaborative Innovation Center of Chemistry for Energy Materials (iChEM)
- Fudan University
- Shanghai 200433
- China
| | - Hui Wang
- Department of Chemistry
- Collaborative Innovation Center of Chemistry for Energy Materials (iChEM)
- Fudan University
- Shanghai 200433
- China
| | - Yaming Zhou
- Department of Chemistry
- Collaborative Innovation Center of Chemistry for Energy Materials (iChEM)
- Fudan University
- Shanghai 200433
- China
| | - Zhan-Ting Li
- Department of Chemistry
- Collaborative Innovation Center of Chemistry for Energy Materials (iChEM)
- Fudan University
- Shanghai 200433
- China
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31
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Robinson CW, Rye CS, Chessum NEA, Jones K. A model β-sheet interaction and thermodynamic analysis of β-strand mimetics. Org Biomol Chem 2015; 13:7402-7. [DOI: 10.1039/c5ob00886g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Two novel β-strand mimetics are synthesized and their binding to a model peptide is studied in detail by 1H NMR.
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Affiliation(s)
- Colin W. Robinson
- Cancer Research UK Cancer Therapeutics Unit
- Institute of Cancer Research
- Haddow Laboratories
- London
- UK
| | - Carl S. Rye
- Cancer Research UK Cancer Therapeutics Unit
- Institute of Cancer Research
- Haddow Laboratories
- London
- UK
| | - Nicola E. A. Chessum
- Cancer Research UK Cancer Therapeutics Unit
- Institute of Cancer Research
- Haddow Laboratories
- London
- UK
| | - Keith Jones
- Cancer Research UK Cancer Therapeutics Unit
- Institute of Cancer Research
- Haddow Laboratories
- London
- UK
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32
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Kheria S, Nair RV, Kotmale AS, Rajamohanan PR, Sanjayan GJ. The role of N-terminal proline in stabilizing the Ant–Pro zipper motif. NEW J CHEM 2015. [DOI: 10.1039/c4nj02151g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper deals with the role of N-terminal proline in stabilizing the Ant–Pro zipper structure by the co-operative contribution of competing forces viz. hydrogen bonding, aromatic stacking and backbone chirality.
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Affiliation(s)
- Sanjeev Kheria
- Division of Organic Chemistry
- National Chemical Laboratory
- Pune 411 008
- India
| | - Roshna V. Nair
- Division of Organic Chemistry
- National Chemical Laboratory
- Pune 411 008
- India
| | - Amol S. Kotmale
- Central NMR Facility
- National Chemical Laboratory
- Pune 411 008
- India
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33
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Structure-based inhibition of protein-protein interactions. Eur J Med Chem 2014; 94:480-8. [PMID: 25253637 DOI: 10.1016/j.ejmech.2014.09.047] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 09/03/2014] [Accepted: 09/12/2014] [Indexed: 12/24/2022]
Abstract
Protein-protein interactions (PPIs) are emerging as attractive targets for drug design because of their central role in directing normal and aberrant cellular functions. These interactions were once considered "undruggable" because their large and dynamic interfaces make small molecule inhibitor design challenging. However, landmark advances in computational analysis, fragment screening and molecular design have enabled development of a host of promising strategies to address the fundamental molecular recognition challenge. An attractive approach for targeting PPIs involves mimicry of protein domains that are critical for complex formation. This approach recognizes that protein subdomains or protein secondary structures are often present at interfaces and serve as organized scaffolds for the presentation of side chain groups that engage the partner protein(s). Design of protein domain mimetics is in principle rather straightforward but is enabled by a host of computational strategies that provide predictions of important residues that should be mimicked. Herein we describe a workflow proceeding from interaction network analysis, to modeling a complex structure, to identifying a high-affinity sub-structure, to developing interaction inhibitors. We apply the design procedure to peptidomimetic inhibitors of Ras-mediated signaling.
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Abstract
The development of inhibitors for protein-protein interactions frequently involves the mimicry of secondary structure motifs. While helical protein-protein interactions have been heavily targeted, a similar level of success for the inhibition of β-strand and β-sheet rich interfaces has been elusive. We describe an assessment of the full range of β-strand interfaces whose high-resolution structures are available in the Protein Data Bank. This analysis identifies complexes where a β-stand or β-sheet contributes significantly to binding. The results highlight the molecular recognition complexity in strand-mediated interactions relative to helical interfaces and offer guidelines for the construction of β-strand and β-sheet mimics as ligands for protein receptors. The online data set will potentially serve as an entry-point to new classes of protein-protein interaction inhibitors.
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Affiliation(s)
- Andrew M. Watkins
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Paramjit S. Arora
- Department of Chemistry, New York University, New York, New York 10003, United States
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35
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36
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Chua KCH, Pietsch M, Zhang X, Hautmann S, Chan HY, Bruning JB, Gütschow M, Abell AD. Macrocyclic Protease Inhibitors with Reduced Peptide Character. Angew Chem Int Ed Engl 2014; 53:7828-31. [DOI: 10.1002/anie.201404301] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Indexed: 01/14/2023]
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