51
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Furukawa A, Schwochert J, Pye CR, Asano D, Edmondson QD, Turmon AC, Klein VG, Ono S, Okada O, Lokey RS. Drug‐Like Properties in Macrocycles above MW 1000: Backbone Rigidity versus Side‐Chain Lipophilicity. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004550] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Akihiro Furukawa
- Daiichi Sankyo Co., Ltd. 1-2-58, Hiromachi, Shinagawa-ku Tokyo 140-8710 Japan
| | - Joshua Schwochert
- Unnatural Products, Inc. 250 Natural Bridges Drive Santa Cruz CA 95060 USA
| | - Cameron R. Pye
- Unnatural Products, Inc. 250 Natural Bridges Drive Santa Cruz CA 95060 USA
| | - Daigo Asano
- Daiichi Sankyo Co., Ltd. 1-2-58, Hiromachi, Shinagawa-ku Tokyo 140-8710 Japan
| | - Quinn D. Edmondson
- Department of Pharmaceutical Chemistry University of California, San Francisco San Francisco California 94158 USA
| | | | - Victoria G. Klein
- Department of Chemistry & Biochemistry University of California Santa Cruz Santa Cruz CA 96064 USA
| | - Satoshi Ono
- Discovery Technology Laboratories Mitsubishi Tanabe Pharma Corporation Yokohama 227-0033 Japan
| | - Okimasa Okada
- Discovery Technology Laboratories Mitsubishi Tanabe Pharma Corporation Yokohama 227-0033 Japan
| | - R. Scott Lokey
- Department of Chemistry & Biochemistry University of California Santa Cruz Santa Cruz CA 96064 USA
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52
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Horsfall AJ, Dunning KR, Keeling KL, Scanlon DB, Wegener KL, Abell AD. A Bimane‐Based Peptide Staple for Combined Helical Induction and Fluorescent Imaging. Chembiochem 2020; 21:3423-3432. [DOI: 10.1002/cbic.202000485] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Aimee J. Horsfall
- The Department of Chemistry, School of Physical Sciences The University of Adelaide North Terrace Adelaide SA 5005 Australia
- The ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP) The University of Adelaide North Terrace Adelaide SA 5005 Australia
- Institute for Photonics and Advanced Sensing (IPAS) The University of Adelaide North Terrace Adelaide SA 5005 Australia
| | - Kylie R. Dunning
- The ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP) The University of Adelaide North Terrace Adelaide SA 5005 Australia
- Institute for Photonics and Advanced Sensing (IPAS) The University of Adelaide North Terrace Adelaide SA 5005 Australia
- Robinson Research Institute, Adelaide Medical School The University of Adelaide North Terrace Adelaide SA 5005 Australia
| | - Kelly L. Keeling
- The Department of Chemistry, School of Physical Sciences The University of Adelaide North Terrace Adelaide SA 5005 Australia
- Institute for Photonics and Advanced Sensing (IPAS) The University of Adelaide North Terrace Adelaide SA 5005 Australia
| | - Denis B. Scanlon
- The Department of Chemistry, School of Physical Sciences The University of Adelaide North Terrace Adelaide SA 5005 Australia
- Institute for Photonics and Advanced Sensing (IPAS) The University of Adelaide North Terrace Adelaide SA 5005 Australia
| | - Kate L. Wegener
- Institute for Photonics and Advanced Sensing (IPAS) The University of Adelaide North Terrace Adelaide SA 5005 Australia
- School of Biological Sciences The University of Adelaide North Terrace Adelaide SA 5005 Australia
| | - Andrew D. Abell
- The Department of Chemistry, School of Physical Sciences The University of Adelaide North Terrace Adelaide SA 5005 Australia
- The ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP) The University of Adelaide North Terrace Adelaide SA 5005 Australia
- Institute for Photonics and Advanced Sensing (IPAS) The University of Adelaide North Terrace Adelaide SA 5005 Australia
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53
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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
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54
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Xiao Q, Ashton DS, Jones ZB, Thompson KP, Price JL. Long-range PEG Stapling: Macrocyclization for Increased Protein Conformational Stability and Resistance to Proteolysis. RSC Chem Biol 2020; 1:273-280. [PMID: 33796855 PMCID: PMC8009319 DOI: 10.1039/d0cb00075b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
We previously showed that long-range stapling of two Asn-linked O-allyl PEG oligomers via olefin metathesis substantially increases the conformational stability of the WW domain through an entropic effect. The impact of stapling was more favorable when the staple connected positions that were far apart in primary sequence but close in the folded tertiary structure. Here we validate these criteria by identifying new stabilizing PEG-stapling sites within the WW domain and the SH3 domain, both β-sheet proteins. We find that stapling via olefin metathesis vs. the copper(i)-catalyzed azide/alkyne cycloaddition (CuAAC) results in similar energetic benefits, suggesting that olefin and triazole staples can be used interchangeably. Proteolysis assays of selected WW variants reveal that the observed staple-based increases in conformational stability lead to enhanced proteolytic resistance. Finally, we find that an intermolecular staple dramatically increases the quaternary structural stability of an α-helical GCN4 coiled-coil heterodimer. Long-range stapling of two Asn-linked PEG oligomers via olefin metathesis substantially increases the conformational stability of the WW and SH3 domain tertiary structures and the GCN4 coiled-coil quaternary structure.![]()
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Affiliation(s)
- Qiang Xiao
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Dallin S Ashton
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Zachary B Jones
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Katherine P Thompson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Joshua L Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
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55
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D'Ercole A, Sabatino G, Pacini L, Impresari E, Capecchi I, Papini AM, Rovero P. On‐resin microwave‐assisted copper‐catalyzed azide‐alkyne cycloaddition of H1‐relaxin B single chain ‘stapled’ analogues. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Annunziata D'Ercole
- Laboratory of Peptide and Protein Chemistry and Biology, Department of Chemistry ‘Ugo Schiff’University of Florence Sesto Fiorentino Italy
- FIS Fabbrica Italiana Sintetici S.p.A Vicenza Italy
| | - Giuseppina Sabatino
- Laboratory of Peptide and Protein Chemistry and Biology, Department of Chemistry ‘Ugo Schiff’University of Florence Sesto Fiorentino Italy
- CNR‐IC Istituto di Cristallografia Catania Italy
| | | | - Elisa Impresari
- Laboratory of Peptide and Protein Chemistry and Biology, Department of Neurosciences, Psychology, Drug Research and Child Health—Section of Pharmaceutical Sciences and NutraceuticsUniversity of Florence Sesto Fiorentino Italy
| | - Ilaria Capecchi
- Laboratory of Peptide and Protein Chemistry and Biology, Department of Neurosciences, Psychology, Drug Research and Child Health—Section of Pharmaceutical Sciences and NutraceuticsUniversity of Florence Sesto Fiorentino Italy
| | - Anna Maria Papini
- Laboratory of Peptide and Protein Chemistry and Biology, Department of Chemistry ‘Ugo Schiff’University of Florence Sesto Fiorentino Italy
- CNR‐IC Istituto di Cristallografia Catania Italy
- PeptLab@UCP and Laboratory of Chemical Biology EA4505CY Cergy Paris University Cergy‐Pontoise France
| | - Paolo Rovero
- CNR‐IC Istituto di Cristallografia Catania Italy
- Laboratory of Peptide and Protein Chemistry and Biology, Department of Neurosciences, Psychology, Drug Research and Child Health—Section of Pharmaceutical Sciences and NutraceuticsUniversity of Florence Sesto Fiorentino Italy
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56
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Kannan S, Aronica PGA, Ng S, Gek Lian DT, Frosi Y, Chee S, Shimin J, Yuen TY, Sadruddin A, Kaan HYK, Chandramohan A, Wong JH, Tan YS, Chang ZW, Ferrer-Gago FJ, Arumugam P, Han Y, Chen S, Rénia L, Brown CJ, Johannes CW, Henry B, Lane DP, Sawyer TK, Verma CS, Partridge AW. Macrocyclization of an all-d linear α-helical peptide imparts cellular permeability. Chem Sci 2020; 11:5577-5591. [PMID: 32874502 PMCID: PMC7441689 DOI: 10.1039/c9sc06383h] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/08/2020] [Indexed: 12/13/2022] Open
Abstract
Peptide-based molecules hold great potential as targeted inhibitors of intracellular protein-protein interactions (PPIs). Indeed, the vast diversity of chemical space conferred through their primary, secondary and tertiary structures allows these molecules to be applied to targets that are typically deemed intractable via small molecules. However, the development of peptide therapeutics has been hindered by their limited conformational stability, proteolytic sensitivity and cell permeability. Several contemporary peptide design strategies are aimed at addressing these issues. Strategic macrocyclization through optimally placed chemical braces such as olefinic hydrocarbon crosslinks, commonly referred to as staples, may improve peptide properties by (i) restricting conformational freedom to improve target affinities, (ii) improving proteolytic resistance, and (iii) enhancing cell permeability. As a second strategy, molecules constructed entirely from d-amino acids are hyper-resistant to proteolytic cleavage, but generally lack conformational stability and membrane permeability. Since neither approach is a complete solution, we have combined these strategies to identify the first examples of all-d α-helical stapled and stitched peptides. As a template, we used a recently reported all d-linear peptide that is a potent inhibitor of the p53-Mdm2 interaction, but is devoid of cellular activity. To design both stapled and stitched all-d-peptide analogues, we used computational modelling to predict optimal staple placement. The resultant novel macrocyclic all d-peptide was determined to exhibit increased α-helicity, improved target binding, complete proteolytic stability and, most notably, cellular activity.
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Affiliation(s)
- Srinivasaraghavan Kannan
- Bioinformatics Institute , Agency for Science, Technology and Research (ASTAR) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671 , Singapore . ; ; ; Tel: +65 6478 8353 ; Tel: +65 6478 8273
| | - Pietro G A Aronica
- Bioinformatics Institute , Agency for Science, Technology and Research (ASTAR) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671 , Singapore . ; ; ; Tel: +65 6478 8353 ; Tel: +65 6478 8273
| | - Simon Ng
- p53 Laboratory , Agency for Science, Technology and Research (ASTAR) , 8A Biomedical Grove, #06-04/05, Neuros/Immunos , Singapore 138648
| | - Dawn Thean Gek Lian
- p53 Laboratory , Agency for Science, Technology and Research (ASTAR) , 8A Biomedical Grove, #06-04/05, Neuros/Immunos , Singapore 138648
| | - Yuri Frosi
- p53 Laboratory , Agency for Science, Technology and Research (ASTAR) , 8A Biomedical Grove, #06-04/05, Neuros/Immunos , Singapore 138648
| | - Sharon Chee
- p53 Laboratory , Agency for Science, Technology and Research (ASTAR) , 8A Biomedical Grove, #06-04/05, Neuros/Immunos , Singapore 138648
| | - Jiang Shimin
- p53 Laboratory , Agency for Science, Technology and Research (ASTAR) , 8A Biomedical Grove, #06-04/05, Neuros/Immunos , Singapore 138648
| | - Tsz Ying Yuen
- Institute of Chemical & Engineering Science , Agency for Science, Technology and Research (ASTAR) , 8 Biomedical Grove, #07, Neuros Building , Singapore 138665
| | - Ahmad Sadruddin
- MSD International , Translation Medicine Research Centre , 8 Biomedical Grove, #04-01/05 Neuros Building , Singapore , 138665 , Singapore .
| | - Hung Yi Kristal Kaan
- MSD International , Translation Medicine Research Centre , 8 Biomedical Grove, #04-01/05 Neuros Building , Singapore , 138665 , Singapore .
| | - Arun Chandramohan
- MSD International , Translation Medicine Research Centre , 8 Biomedical Grove, #04-01/05 Neuros Building , Singapore , 138665 , Singapore .
| | - Jin Huei Wong
- Bioinformatics Institute , Agency for Science, Technology and Research (ASTAR) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671 , Singapore . ; ; ; Tel: +65 6478 8353 ; Tel: +65 6478 8273
| | - Yaw Sing Tan
- Bioinformatics Institute , Agency for Science, Technology and Research (ASTAR) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671 , Singapore . ; ; ; Tel: +65 6478 8353 ; Tel: +65 6478 8273
| | - Zi Wei Chang
- Singapore Immunology Network (SIgN) , Agency for Science, Technology and Research (ASTAR) , 8A Biomedical Grove, #03-06, Immunos , Singapore 138648
| | - Fernando J Ferrer-Gago
- p53 Laboratory , Agency for Science, Technology and Research (ASTAR) , 8A Biomedical Grove, #06-04/05, Neuros/Immunos , Singapore 138648
| | - Prakash Arumugam
- Bioinformatics Institute , Agency for Science, Technology and Research (ASTAR) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671 , Singapore . ; ; ; Tel: +65 6478 8353 ; Tel: +65 6478 8273
| | - Yi Han
- Merck & Co., Inc. , Kenilworth , New Jersey , USA
| | - Shiying Chen
- Merck & Co., Inc. , Kenilworth , New Jersey , USA
| | - Laurent Rénia
- Singapore Immunology Network (SIgN) , Agency for Science, Technology and Research (ASTAR) , 8A Biomedical Grove, #03-06, Immunos , Singapore 138648
| | - Christopher J Brown
- p53 Laboratory , Agency for Science, Technology and Research (ASTAR) , 8A Biomedical Grove, #06-04/05, Neuros/Immunos , Singapore 138648
| | - Charles W Johannes
- Institute of Chemical & Engineering Science , Agency for Science, Technology and Research (ASTAR) , 8 Biomedical Grove, #07, Neuros Building , Singapore 138665
| | - Brian Henry
- MSD International , Translation Medicine Research Centre , 8 Biomedical Grove, #04-01/05 Neuros Building , Singapore , 138665 , Singapore .
| | - David P Lane
- p53 Laboratory , Agency for Science, Technology and Research (ASTAR) , 8A Biomedical Grove, #06-04/05, Neuros/Immunos , Singapore 138648
| | | | - Chandra S Verma
- Bioinformatics Institute , Agency for Science, Technology and Research (ASTAR) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671 , Singapore . ; ; ; Tel: +65 6478 8353 ; Tel: +65 6478 8273
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551
- Department of Biological Sciences , National University of Singapore , 14 Science Drive 4 , Singapore 117543
| | - Anthony W Partridge
- MSD International , Translation Medicine Research Centre , 8 Biomedical Grove, #04-01/05 Neuros Building , Singapore , 138665 , Singapore .
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57
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Crone NS, Kros A, Boyle AL. Modulation of Coiled-Coil Binding Strength and Fusogenicity through Peptide Stapling. Bioconjug Chem 2020; 31:834-843. [PMID: 32058706 PMCID: PMC7086394 DOI: 10.1021/acs.bioconjchem.0c00009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/13/2020] [Indexed: 12/20/2022]
Abstract
Peptide stapling is a technique which has been widely employed to constrain the conformation of peptides. One of the effects of such a constraint can be to modulate the interaction of the peptide with a binding partner. Here, a cysteine bis-alkylation stapling technique was applied to generate structurally isomeric peptide variants of a heterodimeric coiled-coil forming peptide. These stapled variants differed in the position and size of the formed macrocycle. C-terminal stapling showed the most significant changes in peptide structure and stability, with calorimetric binding analysis showing a significant reduction of binding entropy for stapled variants. This entropy reduction was dependent on cross-linker size and was accompanied by a change in binding enthalpy, illustrating the effects of preorganization. The stapled peptide, along with its binding partner, were subsequently employed as fusogens in a liposome model system. An increase in both lipid- and content-mixing was observed for one of the stapled peptide variants: this increased fusogenicity was attributed to increased coiled-coil binding but not to membrane affinity, an interaction theorized to be a primary driving force in this fusion system.
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Affiliation(s)
- Niek S.
A. Crone
- Supramolecular and Biomaterials
Chemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Alexander Kros
- Supramolecular and Biomaterials
Chemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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58
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Ricardo MG, Ali AM, Plewka J, Surmiak E, Labuzek B, Neochoritis CG, Atmaj J, Skalniak L, Zhang R, Holak TA, Groves M, Rivera DG, Dömling A. Multicomponent Peptide Stapling as a Diversity‐Driven Tool for the Development of Inhibitors of Protein–Protein Interactions. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Manuel G. Ricardo
- Faculty of Chemistry, Center for Natural Product ResearchUniversity of Havana Cuba
| | - Ameena M. Ali
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
| | - Jacek Plewka
- Faculty of ChemistryJagiellonian University Krakow Poland
| | - Ewa Surmiak
- Faculty of ChemistryJagiellonian University Krakow Poland
| | - Beata Labuzek
- Faculty of ChemistryJagiellonian University Krakow Poland
| | - Constantinos G. Neochoritis
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
- Department of ChemistryUniversity of Crete Greece
| | - Jack Atmaj
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
- Faculty of ChemistryJagiellonian University Krakow Poland
| | | | - Ran Zhang
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
| | - Tad A. Holak
- Faculty of ChemistryJagiellonian University Krakow Poland
| | - Matthew Groves
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
| | - Daniel G. Rivera
- Faculty of Chemistry, Center for Natural Product ResearchUniversity of Havana Cuba
| | - Alexander Dömling
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
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59
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Ricardo MG, Ali AM, Plewka J, Surmiak E, Labuzek B, Neochoritis CG, Atmaj J, Skalniak L, Zhang R, Holak TA, Groves M, Rivera DG, Dömling A. Multicomponent Peptide Stapling as a Diversity-Driven Tool for the Development of Inhibitors of Protein-Protein Interactions. Angew Chem Int Ed Engl 2020; 59:5235-5241. [PMID: 31944488 DOI: 10.1002/anie.201916257] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Indexed: 12/12/2022]
Abstract
Stapled peptides are chemical entities in-between biologics and small molecules, which have proven to be the solution to high affinity protein-protein interaction antagonism, while keeping control over pharmacological performance such as stability and membrane penetration. We demonstrate that the multicomponent reaction-based stapling is an effective strategy for the development of α-helical peptides with highly potent dual antagonistic action of MDM2 and MDMX binding p53. Such a potent inhibitory activity of p53-MDM2/X interactions was assessed by fluorescence polarization, microscale thermophoresis, and 2D NMR, while several cocrystal structures with MDM2 were obtained. This MCR stapling protocol proved efficient and versatile in terms of diversity generation at the staple, as evidenced by the incorporation of both exo- and endo-cyclic hydrophobic moieties at the side chain cross-linkers. The interaction of the Ugi-staple fragments with the target protein was demonstrated by crystallography.
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Affiliation(s)
- Manuel G Ricardo
- Faculty of Chemistry, Center for Natural Product Research, University of Havana, Cuba
| | - Ameena M Ali
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands
| | - Jacek Plewka
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Ewa Surmiak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Beata Labuzek
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Constantinos G Neochoritis
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands.,Department of Chemistry, University of, Crete, Greece
| | - Jack Atmaj
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands.,Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Lukasz Skalniak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Ran Zhang
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands
| | - Tad A Holak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Matthew Groves
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands
| | - Daniel G Rivera
- Faculty of Chemistry, Center for Natural Product Research, University of Havana, Cuba
| | - Alexander Dömling
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands
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60
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Merritt HI, Sawyer N, Arora PS. Bent Into Shape: Folded Peptides to Mimic Protein Structure and Modulate Protein Function. Pept Sci (Hoboken) 2020; 112:e24145. [PMID: 33575525 PMCID: PMC7875438 DOI: 10.1002/pep2.24145] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 12/11/2019] [Indexed: 12/16/2022]
Abstract
Protein secondary and tertiary structure mimics have served as model systems to probe biophysical parameters that guide protein folding and as attractive reagents to modulate protein interactions. Here we review contemporary methods to reproduce loop, helix, sheet and coiled-coil conformations in short peptides.
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Affiliation(s)
| | | | - Paramjit S. Arora
- Department of Chemistry New York University, New York, New York 10003, United States
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61
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Jeganathan S, Wendt M, Kiehstaller S, Brancaccio D, Kuepper A, Pospiech N, Carotenuto A, Novellino E, Hennig S, Grossmann TN. Constrained Peptides with Fine-Tuned Flexibility Inhibit NF-Y Transcription Factor Assembly. Angew Chem Int Ed Engl 2019; 58:17351-17358. [PMID: 31539186 PMCID: PMC6900064 DOI: 10.1002/anie.201907901] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/19/2019] [Indexed: 12/17/2022]
Abstract
Protein complex formation depends on the interplay between preorganization and flexibility of the binding epitopes involved. The design of epitope mimetics typically focuses on stabilizing a particular bioactive conformation, often without considering conformational dynamics, which limits the potential of peptidomimetics against challenging targets such as transcription factors. We developed a peptide-derived inhibitor of the NF-Y transcription factor by first constraining the conformation of an epitope through hydrocarbon stapling and then fine-tuning its flexibility. In the initial set of constrained peptides, a single non-interacting α-methyl group was observed to have a detrimental effect on complex stability. Biophysical characterization revealed how this methyl group affects the conformation of the peptide in its bound state. Adaption of the methylation pattern resulted in a peptide that inhibits transcription factor assembly and subsequent recruitment to the target DNA.
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Affiliation(s)
- Sadasivam Jeganathan
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 1544227DortmundGermany
| | - Mathias Wendt
- Department of Chemistry and Pharmaceutical SciencesVU University AmsterdamDe Boelelaan 10831081HZAmsterdamThe Netherlands
| | - Sebastian Kiehstaller
- Department of Chemistry and Pharmaceutical SciencesVU University AmsterdamDe Boelelaan 10831081HZAmsterdamThe Netherlands
| | - Diego Brancaccio
- Department of PharmacyUniversity of Naples “Federico II”Via D. Montesano49, 80131NaplesItaly
| | - Arne Kuepper
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 1544227DortmundGermany
| | - Nicole Pospiech
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 1544227DortmundGermany
| | - Alfonso Carotenuto
- Department of PharmacyUniversity of Naples “Federico II”Via D. Montesano49, 80131NaplesItaly
| | - Ettore Novellino
- Department of PharmacyUniversity of Naples “Federico II”Via D. Montesano49, 80131NaplesItaly
| | - Sven Hennig
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 1544227DortmundGermany
- Department of Chemistry and Pharmaceutical SciencesVU University AmsterdamDe Boelelaan 10831081HZAmsterdamThe Netherlands
| | - Tom N. Grossmann
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 1544227DortmundGermany
- Department of Chemistry and Pharmaceutical SciencesVU University AmsterdamDe Boelelaan 10831081HZAmsterdamThe Netherlands
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62
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Jeganathan S, Wendt M, Kiehstaller S, Brancaccio D, Kuepper A, Pospiech N, Carotenuto A, Novellino E, Hennig S, Grossmann TN. Constrained Peptides with Fine‐Tuned Flexibility Inhibit NF‐Y Transcription Factor Assembly. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Sadasivam Jeganathan
- Chemical Genomics Centre of the Max Planck Society Otto-Hahn-Strasse 15 44227 Dortmund Germany
| | - Mathias Wendt
- Department of Chemistry and Pharmaceutical SciencesVU University Amsterdam De Boelelaan 1083 1081 HZ Amsterdam The Netherlands
| | - Sebastian Kiehstaller
- Department of Chemistry and Pharmaceutical SciencesVU University Amsterdam De Boelelaan 1083 1081 HZ Amsterdam The Netherlands
| | - Diego Brancaccio
- Department of PharmacyUniversity of Naples “Federico II” Via D. Montesano 49, 80131 Naples Italy
| | - Arne Kuepper
- Chemical Genomics Centre of the Max Planck Society Otto-Hahn-Strasse 15 44227 Dortmund Germany
| | - Nicole Pospiech
- Chemical Genomics Centre of the Max Planck Society Otto-Hahn-Strasse 15 44227 Dortmund Germany
| | - Alfonso Carotenuto
- Department of PharmacyUniversity of Naples “Federico II” Via D. Montesano 49, 80131 Naples Italy
| | - Ettore Novellino
- Department of PharmacyUniversity of Naples “Federico II” Via D. Montesano 49, 80131 Naples Italy
| | - Sven Hennig
- Chemical Genomics Centre of the Max Planck Society Otto-Hahn-Strasse 15 44227 Dortmund Germany
- Department of Chemistry and Pharmaceutical SciencesVU University Amsterdam De Boelelaan 1083 1081 HZ Amsterdam The Netherlands
| | - Tom N. Grossmann
- Chemical Genomics Centre of the Max Planck Society Otto-Hahn-Strasse 15 44227 Dortmund Germany
- Department of Chemistry and Pharmaceutical SciencesVU University Amsterdam De Boelelaan 1083 1081 HZ Amsterdam The Netherlands
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Yan J, Yan S, Hou P, Lu W, Ma PX, He W, Lei B. A Hierarchical Peptide-Lanthanide Framework To Accurately Redress Intracellular Carcinogenic Protein-Protein Interaction. NANO LETTERS 2019; 19:7918-7926. [PMID: 31645103 DOI: 10.1021/acs.nanolett.9b03028] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Intracellular protein-protein interactions (PPIs) are a vital and yet underexploited class of therapeutic targets for their crucial roles in cellular processes and involvement in disease initiation and progression. Although some successful chemistry and nanotechnologies have been introduced into peptide PPI modulators to allow cell and tissue permeability, significant challenges remain with regard to the efficient and precise modulation of PPIs within specific cells of diseased tissues, such as solid tumors. Herein, an intratumoral transformable hierarchical framework, termed iPLF, was fabricated via a two-step self-assembly between peptides and lanthanide-doped nanocrystals. In this proof-of-concept study, using NanoEL effect, TME response, and tumor marker targeting, iPLF in vivo delivered the p53-MDM2 modulator DPMI into tumor cells and β-catenin-Bcl9 modulator Bcl9p into tumor stem cells. This crafted programmed nanomedicine with triple-stage delivery and responsiveness accurately modulated the specific intracellular protein-protein interactions, resulting in the suppression of tumor growth and metastasis in vivo, while maintaining a highly favorable safety profile. iPLF reached the goal of accurate, potent, and hazard-free intracellular PPI modulation, thereby providing a means to improve current knowledge of PPI networks and a novel therapeutic strategy for a great variety of diseases.
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Affiliation(s)
- Jin Yan
- Frontier Institute of Science and Technology, Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology , Xi'an Jiaotong University , Xi'an 710054 , China
| | - Siqi Yan
- The First Affiliated Hospital of Xi'an Jiaotong University , Xi'an 710061 , P.R. China
| | - Peng Hou
- The First Affiliated Hospital of Xi'an Jiaotong University , Xi'an 710061 , P.R. China
| | - Wuyuan Lu
- Institute of Human Virology and Department of Biochemistry and Molecular Biology , University of Maryland School of Medicine , Baltimore , Maryland 21201 , United States
| | - Peter X Ma
- Department of Biologic and Materials Sciences, Department of Biomedical Engineering, Macromolecular Science and Engineering Center, Department of Materials Science and Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Wangxiao He
- Department of Talent Highland , The First Affiliated Hospital of Xi'an Jiao Tong University , Xi'an 710061 , China
| | - Bo Lei
- Frontier Institute of Science and Technology, Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology , Xi'an Jiaotong University , Xi'an 710054 , China
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64
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Jing X, Jin K. A gold mine for drug discovery: Strategies to develop cyclic peptides into therapies. Med Res Rev 2019; 40:753-810. [PMID: 31599007 DOI: 10.1002/med.21639] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/05/2019] [Accepted: 09/26/2019] [Indexed: 12/19/2022]
Abstract
As a versatile therapeutic modality, peptides attract much attention because of their great binding affinity, low toxicity, and the capability of targeting traditionally "undruggable" protein surfaces. However, the deficiency of cell permeability and metabolic stability always limits the success of in vitro bioactive peptides as drug candidates. Peptide macrocyclization is one of the most established strategies to overcome these limitations. Over the past decades, more than 40 cyclic peptide drugs have been clinically approved, the vast majority of which are derived from natural products. The de novo discovered cyclic peptides on the basis of rational design and in vitro evolution, have also enabled the binding with targets for which nature provides no solutions. The current review summarizes different classes of cyclic peptides with diverse biological activities, and presents an overview of various approaches to develop cyclic peptide-based drug candidates, drawing upon series of examples to illustrate each strategy.
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Affiliation(s)
- Xiaoshu Jing
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Kang Jin
- Department of Medicinal Chemistry, School of Pharmacy, Shandong University, Jinan, Shandong, China
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65
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Montgomery JE, Donnelly JA, Fanning SW, Speltz TE, Shangguan X, Coukos JS, Greene GL, Moellering RE. Versatile Peptide Macrocyclization with Diels-Alder Cycloadditions. J Am Chem Soc 2019; 141:16374-16381. [PMID: 31523967 DOI: 10.1021/jacs.9b07578] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Macrocyclization can improve bioactive peptide ligands through preorganization of molecular topology, leading to improvement of pharmacologic properties like binding affinity, cell permeability, and metabolic stability. Here we demonstrate that Diels-Alder [4 + 2] cycloadditions can be harnessed for peptide macrocyclization and stabilization within a range of peptide scaffolds and chemical environments. Diels-Alder cyclization of diverse diene-dienophile reactive pairs proceeds rapidly, in high yield and with tunable stereochemical preferences on solid-phase or in aqueous solution. This reaction can be applied alone or in concert with other stabilization chemistries, such as ring-closing olefin metathesis, to stabilize loop, turn, and α-helical secondary structural motifs. NMR and molecular dynamics studies of model loop peptides confirmed preferential formation of endo cycloadduct stereochemistry, imparting significant structural rigidity to the peptide backbone that resulted in augmented protease resistance and increased biological activity of a Diels-Alder cyclized (DAC) RGD peptide. Separately, we demonstrated the stabilization of DAC α-helical peptides derived from the ERα-binding protein SRC2. We solved a 2.25 Å cocrystal structure of one DAC helical peptide bound to ERα, which unequivocally corroborated endo stereochemistry of the resulting Diels-Alder adduct, and confirmed that the unique architecture of stabilizing motifs formed with this chemistry can directly contribute to target binding. These data establish Diels-Alder cyclization as a versatile approach to stabilize diverse protein structural motifs under a range of chemical environments.
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66
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Botta J, Bibic L, Killoran P, McCormick PJ, Howell LA. Design and development of stapled transmembrane peptides that disrupt the activity of G-protein-coupled receptor oligomers. J Biol Chem 2019; 294:16587-16603. [PMID: 31467080 PMCID: PMC6851324 DOI: 10.1074/jbc.ra119.009160] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 08/08/2019] [Indexed: 12/23/2022] Open
Abstract
Membrane proteins can associate into larger complexes. Examples include receptor tyrosine complexes, ion channels, transporters, and G protein–coupled receptors (GPCRs). For the latter, there is abundant evidence indicating that GPCRs assemble into complexes, through both homo- and heterodimerization. However, the tools for studying and disrupting these complexes, GPCR or otherwise, are limited. Here, we have developed stabilized interference peptides for this purpose. We have previously reported that tetrahydrocannabinol-mediated cognitive impairment arises from homo- or heterooligomerization between the GPCRs cannabinoid receptor type 1 (CB1R) and 5-hydroxytryptamine 2A (5-HT2AR) receptors. Here, to disrupt this interaction through targeting CB1–5-HT2A receptor heteromers in HEK293 cells and using an array of biochemical techniques, including calcium and cAMP measurements, bimolecular fluorescence complementation assays, and CD-based helicity assessments, we developed a NanoLuc binary technology (NanoBiT)-based reporter assay to screen a small library of aryl-carbon–stapled transmembrane-mimicking peptides produced by solid-phase peptide synthesis. We found that these stapling peptides have increased α-helicity and improved proteolytic resistance without any loss of disrupting activity in vitro, suggesting that this approach may also have utility in vivo. In summary, our results provide proof of concept for using NanoBiT to study membrane protein complexes and for stabilizing disrupting peptides to target such membrane complexes through hydrocarbon-mediated stapling. We propose that these peptides could be developed to target previously undruggable GPCR heteromers.
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Affiliation(s)
- Joaquín Botta
- Centre for Endocrinology, William Harvey Research Institute, Bart's and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, United Kingdom.,School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Lucka Bibic
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Patrick Killoran
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, United Kingdom
| | - Peter J McCormick
- Centre for Endocrinology, William Harvey Research Institute, Bart's and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, United Kingdom
| | - Lesley A Howell
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
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67
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Than VT, Tran HTT, Ly DV, Dang HV, Nguyen MN, Truong AD. Bioinformatic identification and expression analysis of the chicken B cell lymphoma (BCL) gene. Genes Genomics 2019; 41:1195-1206. [PMID: 31313104 DOI: 10.1007/s13258-019-00849-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 07/03/2019] [Indexed: 01/02/2023]
Abstract
BACKGROUND B cell lymphoma (BCL) families play an important role in apoptosis as a growth factor, cell death programming, cytokine expression and immune-related genes expression. OBJECTIVES In this study, to investigate the roles of BCLs, we performed genome-wide identification, expression and functional analyses of the BCL family in chicken. METHODS Chicken BCLs genes were identified and analyzed by using bioinformatics approach. Expression profiles and Hierarchical cluster analysis of the BCLs genes in different chicken tissues were obtained from the genome-wide RNA-seq in the GEO, and Cluster and Java Treeview, respectively. RESULTS A total of 16 BCLs genes were identified from the chicken genome, which could be further classified into five distinct groups in the phylogenetic tree. On the other hand, the interaction among BCLs proteins and between BCLs proteins with NF-κB subunits are limited, indicating that the remaining the functions of BCLs protein could be investigated in chicken. Moreover, KEGG pathway analysis indicated that BCL gene family was involved in regulation of apoptotic and immune response. Finally, BCL gene family was differentially expressed in chicken tissues, pathogen infection and growth stages of early chicken early embryo. CONCLUSION This study provides significant insights into the potential functions of BCLs in chicken, including the regulation of apoptosis, cell death and expression of immune-related genes.
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Affiliation(s)
- Van Thai Than
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, 700000, Vietnam.
| | - Ha Thi Thanh Tran
- Department of Biochemistry and Immunology, National Institute of Veterinary Research, 86 Truong Chinh, Dong Da, Hanoi, 100000, Vietnam
| | - Duc Viet Ly
- Department of Biochemistry and Immunology, National Institute of Veterinary Research, 86 Truong Chinh, Dong Da, Hanoi, 100000, Vietnam
| | - Hoang Vu Dang
- Department of Biochemistry and Immunology, National Institute of Veterinary Research, 86 Truong Chinh, Dong Da, Hanoi, 100000, Vietnam
| | - Minh Nam Nguyen
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Anh Duc Truong
- Department of Biochemistry and Immunology, National Institute of Veterinary Research, 86 Truong Chinh, Dong Da, Hanoi, 100000, Vietnam.
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68
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Abstract
This Review is devoted to the chemistry of macrocyclic peptides having heterocyclic fragments in their structure. These motifs are present in many natural products and synthetic macrocycles designed against a particular biochemical target. Thiazole and oxazole are particularly common constituents of naturally occurring macrocyclic peptide molecules. This frequency of occurrence is because the thiazole and oxazole rings originate from cysteine, serine, and threonine residues. Whereas other heteroaryl groups are found less frequently, they offer many insightful lessons that range from conformational control to receptor/ligand interactions. Many options to develop new and improved technologies to prepare natural products have appeared in recent years, and the synthetic community has been pursuing synthetic macrocycles that have no precedent in nature. This Review attempts to summarize progress in this area.
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Affiliation(s)
- Ivan V Smolyar
- Department of Chemistry , Moscow State University , Leninskije Gory , 199991 Moscow , Russia
| | - Andrei K Yudin
- Davenport Research Laboratories, Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada
| | - Valentine G Nenajdenko
- Department of Chemistry , Moscow State University , Leninskije Gory , 199991 Moscow , Russia
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69
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Inhibition of β-catenin/B cell lymphoma 9 protein-protein interaction using α-helix-mimicking sulfono-γ-AApeptide inhibitors. Proc Natl Acad Sci U S A 2019; 116:10757-10762. [PMID: 31088961 DOI: 10.1073/pnas.1819663116] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The rational design of α-helix-mimicking peptidomimetics provides a streamlined approach to discover potent inhibitors for protein-protein interactions (PPIs). However, designing cell-penetrating long peptidomimetic scaffolds equipped with various functional groups necessary for interacting with large protein-binding interfaces remains challenging. This is particularly true for targeting β-catenin/BCL9 PPIs. Here we designed a series of unprecedented helical sulfono-γ-AApeptides that mimic the binding mode of the α-helical HD2 domain of B Cell Lymphoma 9 (BCL9). Our studies show that sulfono-γ-AApeptides can structurally and functionally mimic the α-helical domain of BCL9 and selectively disrupt β-catenin/BCL9 PPIs with even higher potency. More intriguingly, these sulfono-γ-AApeptides can enter cancer cells, bind with β-catenin and disrupt β-catenin/BCL9 PPIs, and exhibit excellent cellular activity, which is much more potent than the BCL9 peptide. Furthermore, our enzymatic stability studies demonstrate the remarkable stability of the helical sulfono-γ-AApeptides, with no degradation in the presence of pronase for 24 h, augmenting their biological potential. This work represents not only an example of helical sulfono-γ-AApeptides that mimic α-helix and disrupt protein-protein interactions, but also an excellent example of potent, selective, and cell-permeable unnatural foldameric peptidomimetics that disrupt the β-catenin/BCL9 PPI. The design of helical sulfono-γ-AApeptides may lead to a new strategy to modulate a myriad of protein-protein interactions.
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70
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Guarracino DA, Riordan JA, Barreto GM, Oldfield AL, Kouba CM, Agrinsoni D. Macrocyclic Control in Helix Mimetics. Chem Rev 2019; 119:9915-9949. [DOI: 10.1021/acs.chemrev.8b00623] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Danielle A. Guarracino
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Jacob A. Riordan
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Gianna M. Barreto
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Alexis L. Oldfield
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Christopher M. Kouba
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Desiree Agrinsoni
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
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71
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Kanakaveti V, Anoosha P, Sakthivel R, Rayala S, Gromiha M. Influence of Amino Acid Mutations and Small Molecules on Targeted Inhibition of Proteins Involved in Cancer. Curr Top Med Chem 2019; 19:457-466. [DOI: 10.2174/1568026619666190304143354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/19/2018] [Accepted: 12/28/2018] [Indexed: 12/23/2022]
Abstract
Background:Protein-protein interactions (PPIs) are of crucial importance in regulating the biological processes of cells both in normal and diseased conditions. Significant progress has been made in targeting PPIs using small molecules and achieved promising results. However, PPI drug discovery should be further accelerated with better understanding of chemical space along with various functional aspects.Objective:In this review, we focus on the advancements in computational research for targeted inhibition of protein-protein interactions involved in cancer.Methods:Here, we mainly focused on two aspects: (i) understanding the key roles of amino acid mutations in epidermal growth factor receptor (EGFR) as well as mutation-specific inhibitors and (ii) design of small molecule inhibitors for Bcl-2 to disrupt PPIs.Results:The paradigm of PPI inhibition to date reflect the certainty that inclination towards novel and versatile strategies enormously dictate the success of PPI inhibition. As the chemical space highly differs from the normal drug like compounds the lead optimization process has to be given the utmost priority to ensure the clinical success. Here, we provided a broader perspective on effect of mutations in oncogene EGFR connected to Bcl-2 PPIs and focused on the potential challenges.Conclusion:Understanding and bridging mutations and altered PPIs will provide insights into the alarming signals leading to massive malfunctioning of a biological system in various diseases. Finding rational elucidations from a pharmaceutical stand point will presumably broaden the horizons in future.
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Affiliation(s)
- V. Kanakaveti
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai - 600036, Tamil Nadu, India
| | - P. Anoosha
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai - 600036, Tamil Nadu, India
| | - R. Sakthivel
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai - 600036, Tamil Nadu, India
| | - S.K. Rayala
- Molecular Oncology Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai - 600036, Tamil Nadu, India
| | - M.M. Gromiha
- Advanced Computational Drug Discovery Unit (ACDD), Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
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72
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Feng M, Jin JQ, Xia L, Xiao T, Mei S, Wang X, Huang X, Chen J, Liu M, Chen C, Rafi S, Zhu AX, Feng YX, Zhu D. Pharmacological inhibition of β-catenin/BCL9 interaction overcomes resistance to immune checkpoint blockades by modulating T reg cells. SCIENCE ADVANCES 2019; 5:eaau5240. [PMID: 31086813 PMCID: PMC6506245 DOI: 10.1126/sciadv.aau5240] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 03/27/2019] [Indexed: 06/09/2023]
Abstract
The Wnt/β-catenin (β-cat) pathway plays a critical role in cancer. Using hydrocarbon-stapled peptide technologies, we aim to develop potent, selective inhibitors targeting this pathway by disrupting the interaction of β-cat with its coactivators B-cell lymphoma 9 (BCL9) and B-cell lymphoma 9-like (B9L). We identified a set of peptides, including hsBCL9CT-24, that robustly inhibits the activity of β-cat and suppresses cancer cell growth. In animal models, these peptides exhibit potent anti-tumor effects, favorable pharmacokinetic profiles, and minimal toxicities. Markedly, these peptides promote intratumoral infiltration of cytotoxic T cells by reducing regulatory T cells (Treg) and increasing dendritic cells (DCs), therefore sensitizing cancer cells to PD-1 inhibitors. Given the strong correlation between Treg infiltration and APC mutation in colorectal cancers, it indicates our peptides can reactivate anti-cancer immune response suppressed by the oncogenic Wnt pathway. In summary, we report a promising strategy for cancer therapy by pharmacological inhibition of the Wnt/β-cat signaling.
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MESH Headings
- Animals
- Antineoplastic Agents, Immunological/metabolism
- Antineoplastic Agents, Immunological/pharmacology
- Cell Line, Tumor
- Cell Proliferation/drug effects
- Chemokine CCL20/antagonists & inhibitors
- Chemokine CCL20/metabolism
- Chemokine CCL22/antagonists & inhibitors
- Chemokine CCL22/metabolism
- Colorectal Neoplasms/metabolism
- Colorectal Neoplasms/pathology
- Female
- Humans
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- Peptides/metabolism
- Peptides/pharmacology
- T-Lymphocytes, Cytotoxic/cytology
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
- T-Lymphocytes, Regulatory/cytology
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/metabolism
- Transcription Factors/antagonists & inhibitors
- Transcription Factors/chemistry
- Transcription Factors/metabolism
- Transplantation, Heterologous
- Wnt Signaling Pathway/drug effects
- beta Catenin/antagonists & inhibitors
- beta Catenin/metabolism
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Affiliation(s)
- M. Feng
- School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - J. Q. Jin
- Harvard College, Harvard University, Cambridge, MA 02138, USA
| | - L. Xia
- School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - T. Xiao
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02145, USA
| | - S. Mei
- Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - X. Wang
- School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - X. Huang
- School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - J. Chen
- School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - M. Liu
- Harvard College, Harvard University, Cambridge, MA 02138, USA
| | - C. Chen
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02145, USA
| | - S. Rafi
- Schrödinger, LLC, Cambridge, MA 02142, USA
| | - A. X. Zhu
- Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA
| | - Y.-X. Feng
- The First Affiliated Hospital, Zhejiang University School of Medicine, Institute of Translational Medicine, Zhejiang University, Hangzhou 310029, China
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - D. Zhu
- School of Pharmacy, Fudan University, Shanghai, 201203, China
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73
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Reguera L, Rivera DG. Multicomponent Reaction Toolbox for Peptide Macrocyclization and Stapling. Chem Rev 2019; 119:9836-9860. [PMID: 30990310 DOI: 10.1021/acs.chemrev.8b00744] [Citation(s) in RCA: 188] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In the past decade, multicomponent reactions have experienced a renaissance as powerful peptide macrocyclization tools enabling the rapid creation of skeletal complexity and diversity with low synthetic cost. This review provides both a historical and modern overview of the development of the peptide multicomponent macrocyclization as a strategy capable to compete with the classic peptide cyclization methods in terms of chemical efficiency and synthetic scope. We prove that the utilization of multicomponent reactions for cyclizing peptides by either their termini or side chains provides a key advantage over those more established methods; that is, the possibility to explore the cyclic peptide chemotype space not only at the amino acid sequence but also at the ring-forming moiety. Owing to its multicomponent nature, this type of peptide cyclization process is well-suited to generate diversity at both the endo- and exo-cyclic fragments formed during the ring-closing step, which stands as a distinctive and useful characteristic for the creation and screening of cyclic peptide libraries. Examples of the novel multicomponent peptide stapling approach and heterocycle ring-forming macrocyclizations are included, along with multicomponent methods incorporating macrocyclization handles and the one-pot syntheses of macromulticyclic peptide cages. Interesting applications of this strategy in the field of drug discovery and chemical biology are provided.
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Affiliation(s)
- Leslie Reguera
- Center for Natural Product Research, Faculty of Chemistry , University of Havana , Zapata y G , Havana 10400 , Cuba
| | - Daniel G Rivera
- Center for Natural Product Research, Faculty of Chemistry , University of Havana , Zapata y G , Havana 10400 , Cuba
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74
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Ojo OS, Nardone B, Musolino SF, Neal AR, Wilson L, Lebl T, Slawin AMZ, Cordes DB, Taylor JE, Naismith JH, Smith AD, Westwood NJ. Synthesis of the natural product descurainolide and cyclic peptides from lignin-derived aromatics. Org Biomol Chem 2019; 16:266-273. [PMID: 29242868 DOI: 10.1039/c7ob02697h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Alternative sources of potential feedstock chemicals are of increasing importance as the availability of oil decreases. The biopolymer lignin is viewed as a source of useful mono-aromatic compounds as exemplified by the industrial scale production of vanillin from this biomass. Alternative lignin-derived aromatics are available in pure form but to date examples of the use of these types of compounds are rare. Here we address this issue by reporting the conversion of an aromatic keto-alcohol to the anti- and syn-isomers of Descurainolide A. The key step involves a rhodium-catalyzed allylic substitution reaction. Enantio-enriched allylic alcohols were generated via an isothiourea-catalyzed kinetic resolution enabling access to both the (2R,3R) and (2S,3S) enantiomers of anti-Descurainolide A. In addition we show that the lignin-derived keto-alcohols can be converted into unnatural amino acid derivatives of tyrosine. Finally, these amino acids were incorporated into cyclic peptide scaffolds through the use of both chemical and an enzyme-mediated macrocylisation.
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Affiliation(s)
- O Stephen Ojo
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St Andrews, Fife, Scotland, KY16 9ST, UK
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75
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Masuda S, Tsuda S, Yoshiya T. Ring-closing metathesis of unprotected peptides in water. Org Biomol Chem 2019; 16:9364-9367. [PMID: 30516782 DOI: 10.1039/c8ob02778a] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Ring-closing metathesis (RCM) is an attractive reaction for the preparation of artificially designed peptides. Until now, RCM has been used for fully or partially protected peptides. Herein, the first RCM of unprotected peptides in water was achieved using a water-soluble Ru catalyst.
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Affiliation(s)
- Shun Masuda
- Peptide Institute, Inc., Ibaraki, Osaka 567-0085, Japan.
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76
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Vinogradov AA, Yin Y, Suga H. Macrocyclic Peptides as Drug Candidates: Recent Progress and Remaining Challenges. J Am Chem Soc 2019; 141:4167-4181. [PMID: 30768253 DOI: 10.1021/jacs.8b13178] [Citation(s) in RCA: 412] [Impact Index Per Article: 82.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Peptides as a therapeutic modality attract much attention due to their synthetic accessibility, high degree of specific binding, and the ability to target protein surfaces traditionally considered "undruggable". Unfortunately, at the same time, other pharmacological properties of a generic peptide, such as metabolic stability and cell permeability, are quite poor, which limits the success of de novo discovered biologically active peptides as drug candidates. Here, we review how macrocyclization as well as the incorporation of nonproteogenic amino acids and various conjugation strategies may be utilized to improve on these characteristics to create better drug candidates. We analyze recent progress and remaining challenges in improving individual pharmacological properties of bioactive peptides, and offer our opinion on interfacing these, often conflicting, considerations, to create balanced drug candidates as a potential way to make further progress in this area.
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Affiliation(s)
- Alexander A Vinogradov
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
| | - Yizhen Yin
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
| | - Hiroaki Suga
- 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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77
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Ali AM, Atmaj J, Van Oosterwijk N, Groves MR, Dömling A. Stapled Peptides Inhibitors: A New Window for Target Drug Discovery. Comput Struct Biotechnol J 2019; 17:263-281. [PMID: 30867891 PMCID: PMC6396041 DOI: 10.1016/j.csbj.2019.01.012] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 01/28/2019] [Accepted: 01/29/2019] [Indexed: 12/11/2022] Open
Abstract
Protein-protein interaction (PPI) is a hot topic in clinical research as protein networking has a major impact in human disease. Such PPIs are potential drugs targets, leading to the need to inhibit/block specific PPIs. While small molecule inhibitors have had some success and reached clinical trials, they have generally failed to address the flat and large nature of PPI surfaces. As a result, larger biologics were developed for PPI surfaces and they have successfully targeted PPIs located outside the cell. However, biologics have low bioavailability and cannot reach intracellular targets. A novel class -hydrocarbon-stapled α-helical peptides that are synthetic mini-proteins locked into their bioactive structure through site-specific introduction of a chemical linker- has shown promise. Stapled peptides show an ability to inhibit intracellular PPIs that previously have been intractable with traditional small molecule or biologics, suggesting that they offer a novel therapeutic modality. In this review, we highlight what stapling adds to natural-mimicking peptides, describe the revolution of synthetic chemistry techniques and how current drug discovery approaches have been adapted to stabilize active peptide conformations, including ring-closing metathesis (RCM), lactamisation, cycloadditions and reversible reactions. We provide an overview on the available stapled peptide high-resolution structures in the protein data bank, with four selected structures discussed in details due to remarkable interactions of their staple with the target surface. We believe that stapled peptides are promising drug candidates and open the doors for peptide therapeutics to reach currently "undruggable" space.
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Affiliation(s)
| | | | | | | | - Alexander Dömling
- Department of Drug Design, University of Groningen, Antonius Deusinglaan1, 9700AD Groningen, the Netherlands
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78
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Affiliation(s)
- Xiao Hu
- School of Pharmacy, Jiangsu University, 301 Xuefu Road Zhenjiang Jiangsu 212013 China
| | - Bo Wu
- School of Pharmacy, Jiangsu University, 301 Xuefu Road Zhenjiang Jiangsu 212013 China
| | - Weiping Zheng
- School of Pharmacy, Jiangsu University, 301 Xuefu Road Zhenjiang Jiangsu 212013 China
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79
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Abstract
Click chemistry is a powerful tool in constraining peptides into their active conformations. This chapter presents recent advancements involving the use of copper-catalyzed [3 + 2] azide-alkyne cycloaddition (CuAAC), better known as "click reaction" in the design and synthesis of cyclic peptide and cyclic peptidomimetic compounds. The usage of "click chemistry" reactions includes various topics: (a) mimicking peptide bonds; (b) synthesis of ordered structures; (c) ligation of peptidomimetic scaffolds; and most importantly in this chapter (d) cyclization of peptidomimetic scaffolds using the triazole ring as constraint of conformation.
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80
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Roy S, Ghosh P, Ahmed I, Chakraborty M, Naiya G, Ghosh B. Constrained α-Helical Peptides as Inhibitors of Protein-Protein and Protein-DNA Interactions. Biomedicines 2018; 6:E118. [PMID: 30567318 PMCID: PMC6315407 DOI: 10.3390/biomedicines6040118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 02/06/2023] Open
Abstract
Intracellular regulatory pathways are replete with protein-protein and protein-DNA interactions, offering attractive targets for therapeutic interventions. So far, most drugs are targeted toward enzymes and extracellular receptors. Protein-protein and protein-DNA interactions have long been considered as "undruggable". Protein-DNA interactions, in particular, present a difficult challenge due to the repetitive nature of the B-DNA. Recent studies have provided several breakthroughs; however, a design methodology for these classes of inhibitors is still at its infancy. A dominant motif of these macromolecular interactions is an α-helix, raising possibilities that an appropriate conformationally-constrained α-helical peptide may specifically disrupt these interactions. Several methods for conformationally constraining peptides to the α-helical conformation have been developed, including stapling, covalent surrogates of hydrogen bonds and incorporation of unnatural amino acids that restrict the conformational space of the peptide. We will discuss these methods and several case studies where constrained α-helices have been used as building blocks for appropriate molecules. Unlike small molecules, the delivery of these short peptides to their targets is not straightforward as they may possess unfavorable cell penetration and ADME properties. Several methods have been developed in recent times to overcome some of these problems. We will discuss these issues and the prospects of this class of molecules as drugs.
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Affiliation(s)
- Siddhartha Roy
- Department of Biophysics, Bose Institute, P1/12 CIT Scheme VII M, Kolkata 700054, India.
| | - Piya Ghosh
- Department of Biophysics, Bose Institute, P1/12 CIT Scheme VII M, Kolkata 700054, India.
| | - Israr Ahmed
- Department of Biophysics, Bose Institute, P1/12 CIT Scheme VII M, Kolkata 700054, India.
| | - Madhumita Chakraborty
- Department of Biophysics, Bose Institute, P1/12 CIT Scheme VII M, Kolkata 700054, India.
| | - Gitashri Naiya
- Department of Biophysics, Bose Institute, P1/12 CIT Scheme VII M, Kolkata 700054, India.
| | - Basusree Ghosh
- Department of Biophysics, Bose Institute, P1/12 CIT Scheme VII M, Kolkata 700054, India.
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81
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Bruyat P, Gautier A, Jean L, Renard PY. Use of an Air-Stable Cu(I)-NHC Catalyst for the Synthesis of Peptidotriazoles. J Org Chem 2018; 83:13515-13522. [PMID: 30280899 DOI: 10.1021/acs.joc.8b01490] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We report the use of air-stable Cu(I)-NHC complex 4a as a catalyst for the efficient microwave-assisted synthesis of peptidotriazoles on solid phase. Compared with the usual conditions (CuI or CuSO4/NaAsc), catalyst 4a allowed the preparation of a series of peptidomimetic compounds containing a 1,2,3-triazole ring in their backbone without the oxidation of common side-chains. Overall, the peptidotriazoles were obtained in good yields (61-87%), in excellent purity (higher than 94%) and with low copper contamination.
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Affiliation(s)
- Pierrick Bruyat
- Normandie Univ , UNIROUEN, INSA Rouen, CNRS, COBRA (UMR 6014) , 76000 Rouen , France
| | - Arnaud Gautier
- Université Clermont Auvergne , CNRS, Sigma Clermont, ICCF , F-63000 Clermont-Ferrand , France
| | - Ludovic Jean
- Normandie Univ , UNIROUEN, INSA Rouen, CNRS, COBRA (UMR 6014) , 76000 Rouen , France
| | - Pierre-Yves Renard
- Normandie Univ , UNIROUEN, INSA Rouen, CNRS, COBRA (UMR 6014) , 76000 Rouen , France
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82
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Decoene KW, Vannecke W, Passioura T, Suga H, Madder A. Pyrrole-Mediated Peptide Cyclization Identified through Genetically Reprogrammed Peptide Synthesis. Biomedicines 2018; 6:biomedicines6040099. [PMID: 30380792 PMCID: PMC6315747 DOI: 10.3390/biomedicines6040099] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/23/2018] [Accepted: 10/24/2018] [Indexed: 12/11/2022] Open
Abstract
Flexible in vitro translation (FIT) was used as a screening method to uncover a new methodology for peptide constraining based on the attack of a nucleophilic side-chain functionality onto an oxidized furylalanine side chain. A set of template peptides, each containing furylalanine as furan-modified amino acid and a nucleophilic residue (Cys, His, Lys, Arg, Ser, or Tyr), was produced through FIT. The translation mixtures were treated with N-bromosuccinimide (NBS) to achieve selective furan oxidation and subsequent MALDI analysis demonstrated Lys and Ser as promising residues for cyclisation. Solid-phase peptide synthesis (SPPS) was used to synthesize suitable amounts of material for further in-depth analysis and characterisation. It was found that in the case of the peptide containing lysine next to a furylalanine residue, a one-pot oxidation and reduction reaction leads to the generation of a cyclic peptide featuring a pyrrole moiety as cyclisation motif, resulting from the attack of the lysine side chain onto the oxidized furylalanine side chain. Structural evidence was provided via NMR and the generality of the methodology was explored. We hereby expand the scope of our previously developed furan-based peptide labeling and crosslinking strategy.
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Affiliation(s)
- Klaas W Decoene
- Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, 9000 Ghent, Belgium.
| | - Willem Vannecke
- Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, 9000 Ghent, Belgium.
| | - Toby Passioura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Annemieke Madder
- Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, 9000 Ghent, Belgium.
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83
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Skowron KJ, Speltz TE, Moore TW. Recent structural advances in constrained helical peptides. Med Res Rev 2018; 39:749-770. [PMID: 30307621 DOI: 10.1002/med.21540] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 09/05/2018] [Accepted: 09/06/2018] [Indexed: 12/20/2022]
Abstract
Given the ubiquity of the ⍺-helix in the proteome, there has been much research in developing mimics of ⍺-helices, and most of this study has been toward developing protein-protein interaction inhibitors. A common strategy for mimicking ⍺-helices has been through the use of constrained, helical peptides. The addition of a constraint typically provides for conformational and proteolytic stability and, in some cases, cell permeability. Some of the most well-known strategies included are lactam formation and hydrocarbon "stapling." Beyond those strategies, there have been many recent advances in developing constrained peptides. The purpose of this review is to highlight recent advances in the development of new helix-stabilizing technologies, constraint diversification strategies, tether diversification strategies, and combination strategies that create new bicyclic helical peptides.
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Affiliation(s)
- Kornelia J Skowron
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
| | - Thomas E Speltz
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
| | - Terry W Moore
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois.,Translational Oncology Program, University of Illinois Cancer Center, Chicago, Illinois
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84
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Tsuchie R, Shimosato M, Hamasaki K. Hydrophobic Association of a Side Chains Induces Reversible Helix Folding in a Dual Aromatic Ring Tagged Short Peptide. CHEM LETT 2018. [DOI: 10.1246/cl.180601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ryusuke Tsuchie
- Department of Applied Chemistry, Shibaura Institute of Technology, 3-5-7 Toyosu, Koto-ku, Tokyo 135-8548, Japan
| | - Mayu Shimosato
- Department of Applied Chemistry, Shibaura Institute of Technology, 3-5-7 Toyosu, Koto-ku, Tokyo 135-8548, Japan
| | - Keita Hamasaki
- Department of Applied Chemistry, Shibaura Institute of Technology, 3-5-7 Toyosu, Koto-ku, Tokyo 135-8548, Japan
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85
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Hou Z, Sun C, Geng H, Hu K, Xie M, Ma Y, Jiang F, Yin F, Li Z. Facile Chemoselective Modification of Thio-Ethers Generates Chiral Center-Induced Helical Peptides. Bioconjug Chem 2018; 29:2904-2908. [PMID: 30193458 DOI: 10.1021/acs.bioconjchem.8b00624] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A precisely positioned sulfimide chiral center on-tether of a thio-ether tethered peptide determines the peptide secondary structure by chemoselective oxaziridine modification. This method provides a facile way to tune peptides' secondary structures and biophysical properties.
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Affiliation(s)
- Zhanfeng Hou
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen , 518055 , China
| | - Chengjie Sun
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen , 518055 , China
| | - Hao Geng
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen , 518055 , China
| | - Kuan Hu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen , 518055 , China
| | - Mingsheng Xie
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen , 518055 , China
| | - Yue Ma
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen , 518055 , China
| | - Fan Jiang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen , 518055 , China
| | - Feng Yin
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen , 518055 , China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen , 518055 , China
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86
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Szałaj N, Lu L, Benediktsdottir A, Zamaratski E, Cao S, Olanders G, Hedgecock C, Karlén A, Erdélyi M, Hughes D, Mowbray SL, Brandt P. Boronic ester-linked macrocyclic lipopeptides as serine protease inhibitors targeting Escherichia coli type I signal peptidase. Eur J Med Chem 2018; 157:1346-1360. [DOI: 10.1016/j.ejmech.2018.08.086] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/22/2018] [Accepted: 08/29/2018] [Indexed: 12/22/2022]
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87
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Přibylka A, Krchňák V. An Alkyne Rod to Constrain a Peptide Backbone in an Extended Conformation. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800979] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Adam Přibylka
- Department of Organic Chemistry; Palacký University; 17. listopadu 12 771 46 Olomouc Czech Republic
| | - Viktor Krchňák
- Department of Organic Chemistry; Palacký University; 17. listopadu 12 771 46 Olomouc Czech Republic
- Department of Organic Chemistry and Biochemistry; University of Notre Dame; 46556 Notre Dame IN United States
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88
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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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89
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Iegre J, Gaynord JS, Robertson NS, Sore HF, Hyvönen M, Spring DR. Two-Component Stapling of Biologically Active and Conformationally Constrained Peptides: Past, Present, and Future. ADVANCED THERAPEUTICS 2018. [DOI: 10.1002/adtp.201800052] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jessica Iegre
- Department of Chemistry; University of Cambridge; Cambridge CB2 1EW UK
| | | | | | - Hannah F. Sore
- Department of Chemistry; University of Cambridge; Cambridge CB2 1EW UK
| | - Marko Hyvönen
- Department of Biochemistry; University of Cambridge; Cambridge CB2 1GA UK
| | - David R. Spring
- Department of Chemistry; University of Cambridge; Cambridge CB2 1EW UK
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90
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Jiang Y, Long H, Zhu Y, Zeng Y. Macrocyclic peptides as regulators of protein-protein interactions. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2018.05.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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91
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Ran X, Gestwicki JE. Inhibitors of protein-protein interactions (PPIs): an analysis of scaffold choices and buried surface area. Curr Opin Chem Biol 2018; 44:75-86. [PMID: 29908451 DOI: 10.1016/j.cbpa.2018.06.004] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/04/2018] [Indexed: 12/17/2022]
Abstract
Protein-protein interactions (PPI) were once considered 'undruggable', but clinical successes, driven by advanced methods in drug discovery, have challenged that notion. Here, we review the last three years of literature on PPI inhibitors to understand what is working and why. From the 66 recently reported PPI inhibitors, we found that the average molecular weight was significantly greater than 500Da, but that this trend was driven, in large part, by the contribution of peptide-based compounds. Despite differences in average molecular weight, we found that compounds based on small molecules or peptides were almost equally likely to be potent inhibitors (KD<1μM). Finally, we found PPIs with buried surface area (BSA) less than 2000Å2 were more likely to be inhibited by small molecules, while PPIs with larger BSA values were typically inhibited by peptides. PPIs with BSA values over 4000Å2 seemed to create a particular challenge, especially for orthosteric small molecules. Thus, it seems important to choose the inhibitor scaffold based on the properties of the target interaction. Moreover, this survey suggests a (more nuanced) conclusion to the question of whether PPIs are good drug targets; namely, that some PPIs are readily 'druggable' given the right choice of scaffold, while others still seem to deserve the 'undruggable' moniker.
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Affiliation(s)
- Xu Ran
- Institute for Neurodegenerative Diseases and Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, United States
| | - Jason E Gestwicki
- Institute for Neurodegenerative Diseases and Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, United States.
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92
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Cistrone PA, Silvestri AP, Hintzen JCJ, Dawson PE. Rigid Peptide Macrocycles from On-Resin Glaser Stapling. Chembiochem 2018; 19:1031-1035. [PMID: 29516601 PMCID: PMC6097620 DOI: 10.1002/cbic.201800121] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Indexed: 12/31/2022]
Abstract
Peptide macrocycles are widely utilized in the development of high affinity ligands, including stapled α-helices. The linear rigidity of a 1,3-diynyl linkage provides an optimal distance (7 Å) between β-carbons of the i,i+4 amino acid side chains, thus suggesting its utility in stabilizing α-helical structures. Here, we report the development of an on-resin strategy for an intramolecular Glaser reaction between two alkyne-terminated side chains by using copper chloride, an essential bpy-diol ligand, and diisopropylethylamine at room temperature. The efficiency of this ligation was illustrated by the synthesis of (i,i+4)-, (i,i+5)-, (i,i+6)-, and (i,i+7)-stapled BCL-9 α-helical peptides using the unnatural amino acid propargyl serine. Overall, this procedurally simple method relies on inexpensive and widely available reagents to generate low molecular weight 23-, 26-, 29-, and 32-membered peptide macrocycles.
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Affiliation(s)
- Philip A. Cistrone
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037 (United States),
| | - Anthony P. Silvestri
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037 (United States),
| | - Jordi C. J. Hintzen
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037 (United States),
| | - Philip E. Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037 (United States),
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93
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Robertson NS, Spring DR. Using Peptidomimetics and Constrained Peptides as Valuable Tools for Inhibiting Protein⁻Protein Interactions. Molecules 2018; 23:molecules23040959. [PMID: 29671834 PMCID: PMC6017787 DOI: 10.3390/molecules23040959] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 04/16/2018] [Accepted: 04/18/2018] [Indexed: 02/07/2023] Open
Abstract
Protein–protein interactions (PPIs) are tremendously important for the function of many biological processes. However, because of the structure of many protein–protein interfaces (flat, featureless and relatively large), they have largely been overlooked as potential drug targets. In this review, we highlight the current tools used to study the molecular recognition of PPIs through the use of different peptidomimetics, from small molecules and scaffolds to peptides. Then, we focus on constrained peptides, and in particular, ways to constrain α-helices through stapling using both one- and two-component techniques.
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Affiliation(s)
- Naomi S Robertson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - David R Spring
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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94
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Ran X, Burchfiel ET, Dong B, Rettko NJ, Dunyak BM, Shao H, Thiele DJ, Gestwicki JE. Rational design and screening of peptide-based inhibitors of heat shock factor 1 (HSF1). Bioorg Med Chem 2018; 26:5299-5306. [PMID: 29661622 DOI: 10.1016/j.bmc.2018.04.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 03/31/2018] [Accepted: 04/06/2018] [Indexed: 01/09/2023]
Abstract
Heat shock factor 1 (HSF1) is a stress-responsive transcription factor that regulates expression of protein chaperones and cell survival factors. In cancer, HSF1 plays a unique role, hijacking the normal stress response to drive a cancer-specific transcriptional program. These observations suggest that HSF1 inhibitors could be promising therapeutics. However, HSF1 is activated through a complex mechanism, which involves release of a negative regulatory domain, leucine zipper 4 (LZ4), from a masked oligomerization domain (LZ1-3), and subsequent binding of the oligomer to heat shock elements (HSEs) in HSF1-responsive genes. Recent crystal structures have suggested that HSF1 oligomers are held together by extensive, buried contact surfaces, making it unclear whether there are any possible binding sites for inhibitors. Here, we have rationally designed a series of peptide-based molecules based on the LZ4 and LZ1-3 motifs. Using a plate-based, fluorescence polarization (FP) assay, we identified a minimal region of LZ4 that suppresses binding of HSF1 to the HSE. Using this information, we converted this peptide into a tracer and used it to understand how binding of LZ4 to LZ1-3 suppresses HSF1 activation. Together, these results suggest a previously unexplored avenue in the development of HSF1 inhibitors. Furthermore, the findings highlight how native interactions can inspire the design of inhibitors for even the most challenging protein-protein interactions (PPIs).
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Affiliation(s)
- Xu Ran
- Institute for Neurodegenerative Disease, University of California at San Francisco, San Francisco, CA 94143, United States
| | - Eileen T Burchfiel
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, United States
| | - Bushu Dong
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, United States
| | - Nicholas J Rettko
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94143, United States
| | - Bryan M Dunyak
- Institute for Neurodegenerative Disease, University of California at San Francisco, San Francisco, CA 94143, United States
| | - Hao Shao
- Institute for Neurodegenerative Disease, University of California at San Francisco, San Francisco, CA 94143, United States
| | - Dennis J Thiele
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, United States; Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, United States; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, United States
| | - Jason E Gestwicki
- Institute for Neurodegenerative Disease, University of California at San Francisco, San Francisco, CA 94143, United States; Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94143, United States.
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95
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Zhang M, Wang Z, Zhang Y, Guo W, Ji H. Structure-Based Optimization of Small-Molecule Inhibitors for the β-Catenin/B-Cell Lymphoma 9 Protein-Protein Interaction. J Med Chem 2018; 61:2989-3007. [PMID: 29566337 DOI: 10.1021/acs.jmedchem.8b00068] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Structure-based optimization was conducted to improve the potency, selectivity, and cell-based activities of β-catenin/B-cell lymphoma 9 (BCL9) inhibitors based on the 4'-fluoro- N-phenyl-[1,1'-biphenyl]-3-carboxamide scaffold, which was designed to mimic the side chains of the hydrophobic α-helical hot spots at positions i, i + 3, and i + 7. Compound 29 was found to disrupt the β-catenin/BCL9 protein-protein interaction (PPI) with a Ki of 0.47 μM and >1900-fold selectivity for β-catenin/BCL9 over β-catenin/E-cadherin PPIs. The proposed binding mode of new inhibitors was consistent with the results of site-directed mutagenesis and structure-activity relationship studies. Cell-based studies indicated that 29 disrupted the β-catenin/BCL9 interaction without affecting the β-catenin/E-cadherin interaction, selectively suppressed transactivation of Wnt/β-catenin signaling, downregulated expression of Wnt target genes, and inhibited viability of Wnt/β-catenin-dependent cancer cells in dose-dependent manners. A comparison of the biochemical and cell-based assay results offered the directions for future inhibitor optimization.
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Affiliation(s)
- Min Zhang
- Drug Discovery Department , H. Lee Moffitt Cancer Center and Research Institute , Tampa , Florida 33612 , United States.,Departments of Oncologic Sciences and Chemistry , University of South Florida , Tampa , Florida 33620 , United States
| | - Zhen Wang
- Drug Discovery Department , H. Lee Moffitt Cancer Center and Research Institute , Tampa , Florida 33612 , United States.,Departments of Oncologic Sciences and Chemistry , University of South Florida , Tampa , Florida 33620 , United States
| | - Yongqiang Zhang
- Drug Discovery Department , H. Lee Moffitt Cancer Center and Research Institute , Tampa , Florida 33612 , United States.,Departments of Oncologic Sciences and Chemistry , University of South Florida , Tampa , Florida 33620 , United States
| | - Wenxing Guo
- Drug Discovery Department , H. Lee Moffitt Cancer Center and Research Institute , Tampa , Florida 33612 , United States.,Departments of Oncologic Sciences and Chemistry , University of South Florida , Tampa , Florida 33620 , United States
| | - Haitao Ji
- Drug Discovery Department , H. Lee Moffitt Cancer Center and Research Institute , Tampa , Florida 33612 , United States.,Departments of Oncologic Sciences and Chemistry , University of South Florida , Tampa , Florida 33620 , United States
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96
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Larionov VA, Adonts HV, Gugkaeva ZT, Smol'yakov AF, Saghyan AS, Miftakhov MS, Kuznetsova SA, Maleev VI, Belokon YN. The Elaboration of a General Approach to the Asymmetric Synthesis of 1,4-Substituted 1,2,3-Triazole Containing Amino Acids via
Ni(II) Complexes. ChemistrySelect 2018. [DOI: 10.1002/slct.201800228] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Vladimir A. Larionov
- Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences; Vavilov Str. 28 119991 Moscow Russian Federation
- Department of Inorganic Chemistry; People's Friendship University of Russia (RUDN University); Miklukho-Maklaya Str. 6 117198 Moscow Russian Federation
| | - Hovhannes V. Adonts
- Institute of Pharmacy of the Yerevan State University; Alex Manoogian Str. 1 0025 Yerevan Armenia
| | - Zalina T. Gugkaeva
- Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences; Vavilov Str. 28 119991 Moscow Russian Federation
| | - Alexander F. Smol'yakov
- Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences; Vavilov Str. 28 119991 Moscow Russian Federation
- Department of Inorganic Chemistry; People's Friendship University of Russia (RUDN University); Miklukho-Maklaya Str. 6 117198 Moscow Russian Federation
| | - Ashot S. Saghyan
- Institute of Pharmacy of the Yerevan State University; Alex Manoogian Str. 1 0025 Yerevan Armenia
- SPC “Armbiotechnology” SNPO NAS RA; Gyurjyan Str. 14 0056 Yerevan Armenia
| | - Mansur S. Miftakhov
- Ufa Institute of Chemistry of Russian Academy of Sciences; Prospect Oktyabrya 71 450054 Ufa Russian Federation
| | - Svetlana A. Kuznetsova
- Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences; Vavilov Str. 28 119991 Moscow Russian Federation
| | - Victor I. Maleev
- Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences; Vavilov Str. 28 119991 Moscow Russian Federation
| | - Yuri N. Belokon
- Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences; Vavilov Str. 28 119991 Moscow Russian Federation
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97
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Jiang Y, Hu K, Shi X, Tang Q, Wang Z, Ye X, Li Z. Switching substitution groups on the in-tether chiral centre influences backbone peptides' permeability and target binding affinity. Org Biomol Chem 2018; 15:541-544. [PMID: 27929189 DOI: 10.1039/c6ob02289h] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Different substitution groups on the in-tether chiral centre of chirality-induced helical peptides (CIH peptides) showed distinguishable effects on the peptides' cellular uptakes and binding affinities with the estrogen receptor α(ER-α). This study proves that in-tether chiral centres are a valuable modification site for constructing peptide ligands with preferable biophysical properties.
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Affiliation(s)
- Yixiang Jiang
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Kuan Hu
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Xiaodong Shi
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Qingzhuang Tang
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - ZiChen Wang
- Shenzhen Middle School, Shenzhen 518001, China
| | - Xiyang Ye
- Department of Gynecology, Shenzhen People's Hospital, Shenzhen 518055, China
| | - Zigang Li
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
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98
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Sawyer TK, Partridge AW, Kaan HYK, Juang YC, Lim S, Johannes C, Yuen TY, Verma C, Kannan S, Aronica P, Tan YS, Sherborne B, Ha S, Hochman J, Chen S, Surdi L, Peier A, Sauvagnat B, Dandliker PJ, Brown CJ, Ng S, Ferrer F, Lane DP. Macrocyclic α helical peptide therapeutic modality: A perspective of learnings and challenges. Bioorg Med Chem 2018; 26:2807-2815. [PMID: 29598901 DOI: 10.1016/j.bmc.2018.03.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 03/03/2018] [Accepted: 03/06/2018] [Indexed: 12/20/2022]
Abstract
Macrocyclic α-helical peptides have emerged as a compelling new therapeutic modality to tackle targets confined to the intracellular compartment. Within the scope of hydrocarbon-stapling there has been significant progress to date, including the first stapled α-helical peptide to enter into clinical trials. The principal design concept of stapled α-helical peptides is to mimic a cognate (protein) ligand relative to binding its target via an α-helical interface. However, it was the proclivity of such stapled α-helical peptides to exhibit cell permeability and proteolytic stability that underscored their promise as unique macrocyclic peptide drugs for intracellular targets. This perspective highlights key learnings as well as challenges in basic research with respect to structure-based design, innovative chemistry, cell permeability and proteolytic stability that are essential to fulfill the promise of stapled α-helical peptide drug development.
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99
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Wang C, Xia S, Zhang P, Zhang T, Wang W, Tian Y, Meng G, Jiang S, Liu K. Discovery of Hydrocarbon-Stapled Short α-Helical Peptides as Promising Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Fusion Inhibitors. J Med Chem 2018; 61:2018-2026. [PMID: 29442512 PMCID: PMC7075646 DOI: 10.1021/acs.jmedchem.7b01732] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The hexameric α-helical coiled-coil formed between the C-terminal and N-terminal heptad repeat (CHR and NHR) regions of class I viral fusion proteins plays an important role in mediating the fusion of the viral and cellular membranes and provides a clear starting point for molecular mimicry that drives viral fusion inhibitor design. Unfortunately, such peptide mimicry of the short α-helical region in the CHR of Middle East respiratory syndrome coronavirus (MERS-CoV) spike protein has been thwarted by the loss of the peptide's native α-helical conformation when taken out of the parent protein structure. Here, we describe that appropriate all-hydrocarbon stapling of the short helical portion-based peptide to reinforce its bioactive secondary structure remarkably improves antiviral potency. The resultant stapled peptide P21S10 could effectively inhibit infection by MERS-CoV pseudovirus and its spike protein-mediated cell-cell fusion; additionally, P21S10 exhibits improved pharmacokinetic properties than HR2P-M2, suggesting strong potential for development as an anti-MERS-CoV therapeutic.
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Affiliation(s)
- Chao Wang
- State Key Laboratory of Toxicology and Medical Countermeasures , Beijing Institute of Pharmacology and Toxicology , 27 Tai-Ping Road , Beijing 100850 , China
| | - Shuai Xia
- Key Laboratory of Medical Molecular Virology of MOE/MOH, School of Basic Medical Sciences and Shanghai Public Health Clinical Center , Fudan University , 130 Dong An Road , Shanghai 200032 , China
| | - Peiyu Zhang
- Key Laboratory of Structure-Based Drug Design and Discovery of the Ministry of Education , Shenyang Pharmaceutical University , Shenyang 110016 , China
| | - Tianhong Zhang
- State Key Laboratory of Toxicology and Medical Countermeasures , Beijing Institute of Pharmacology and Toxicology , 27 Tai-Ping Road , Beijing 100850 , China
| | - Weicong Wang
- Pharmaceutical Preparation Section, Plastic Surgery Hospital , Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100144 , China
| | - Yangli Tian
- State Key Laboratory of Toxicology and Medical Countermeasures , Beijing Institute of Pharmacology and Toxicology , 27 Tai-Ping Road , Beijing 100850 , China
| | - Guangpeng Meng
- Key Laboratory of Structure-Based Drug Design and Discovery of the Ministry of Education , Shenyang Pharmaceutical University , Shenyang 110016 , China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology of MOE/MOH, School of Basic Medical Sciences and Shanghai Public Health Clinical Center , Fudan University , 130 Dong An Road , Shanghai 200032 , China.,Lindsley F. Kimball Research Institute , New York Blood Center , New York , New York 10065 , United States
| | - Keliang Liu
- State Key Laboratory of Toxicology and Medical Countermeasures , Beijing Institute of Pharmacology and Toxicology , 27 Tai-Ping Road , Beijing 100850 , China.,Key Laboratory of Structure-Based Drug Design and Discovery of the Ministry of Education , Shenyang Pharmaceutical University , Shenyang 110016 , China
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100
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Dantas de Araujo A, Perry SR, Fairlie DP. Chemically Diverse Helix-Constrained Peptides Using Selenocysteine Crosslinking. Org Lett 2018; 20:1453-1456. [DOI: 10.1021/acs.orglett.8b00233] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Aline Dantas de Araujo
- Division of Chemistry and
Structural Biology, ARC Centre of Excellence in Advanced Molecular
Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Samuel R. Perry
- Division of Chemistry and
Structural Biology, ARC Centre of Excellence in Advanced Molecular
Imaging, 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 in Advanced Molecular
Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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