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Li Y, Wu M, Fu Y, Xue J, Yuan F, Qu T, Rissanou AN, Wang Y, Li X, Hu H. Therapeutic stapled peptides: Efficacy and molecular targets. Pharmacol Res 2024; 203:107137. [PMID: 38522761 DOI: 10.1016/j.phrs.2024.107137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 03/26/2024]
Abstract
Peptide stapling, by employing a stable, preformed alpha-helical conformation, results in the production of peptides with improved membrane permeability and enhanced proteolytic stability, compared to the original peptides, and provides an effective solution to accelerate the rapid development of peptide drugs. Various reviews present peptide stapling chemistries, anchoring residues and one- or two-component cyclization, however, therapeutic stapled peptides have not been systematically summarized, especially focusing on various disease-related targets. This review highlights the latest advances in therapeutic peptide drug development facilitated by the application of stapling technology, including different stapling techniques, synthetic accessibility, applicability to biological targets, potential for solving biological problems, as well as the current status of development. Stapled peptides as therapeutic drug candidates have been classified and analysed mainly by receptor- and ligand-based stapled peptide design against various diseases, including cancer, infectious diseases, inflammation, and diabetes. This review is expected to provide a comprehensive reference for the rational design of stapled peptides for different diseases and targets to facilitate the development of therapeutic peptides with enhanced pharmacokinetic and biological properties.
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Affiliation(s)
- Yulei Li
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China.
| | - Minghao Wu
- School of Medicine, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Yinxue Fu
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Jingwen Xue
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Fei Yuan
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Tianci Qu
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Anastassia N Rissanou
- Theoretical & Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, Athens 11635, Greece
| | - Yilin Wang
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, 131 Dong'an Road, Shanghai 200032, China
| | - Xiang Li
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, China.
| | - Honggang Hu
- School of Medicine, Shanghai University, 99 Shangda Road, Shanghai 200444, China.
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2
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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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3
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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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4
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Verlinden S, Geudens N, Van Holsbeeck K, Mannes M, Martins JC, Verniest G, Ballet S. The 1,3-diyne linker as a rigid "i,i+7" staple for α-helix stabilization: Stereochemistry at work. J Pept Sci 2019; 25:e3194. [PMID: 31215108 DOI: 10.1002/psc.3194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/11/2019] [Accepted: 05/13/2019] [Indexed: 11/11/2022]
Abstract
Short alphahelical peptide sequences were stabilized through Glaser-Hay couplings of propargylated l- and/or d-serine residues at positions i and i+7. NMR analysis confirmed a full stabilization of the helical structure when a d-Ser (i), l-Ser (i+7) combination was applied. In case two l-Ser residues were involved in the cyclization, the helical conformation is disrupted outside the peptide's macrocycle.
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Affiliation(s)
- Steven Verlinden
- Research Group of Organic Chemistry, Department of Chemistry and Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Niels Geudens
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, Belgium
| | - Kevin Van Holsbeeck
- Research Group of Organic Chemistry, Department of Chemistry and Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium.,NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, Belgium
| | - Morgane Mannes
- Research Group of Organic Chemistry, Department of Chemistry and Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - José C Martins
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, Belgium
| | - Guido Verniest
- Research Group of Organic Chemistry, Department of Chemistry and Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium.,Predictive Analytics and Stability Sciences, Center of Excellence, CRS, Analytical Development, PDMS, DPDS, Janssen Research and Development, Janssen Pharmaceutical Companies of Johnson & Johnson, Beerse, Belgium
| | - Steven Ballet
- Research Group of Organic Chemistry, Department of Chemistry and Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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5
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Yuen TY, Brown CJ, Xue Y, Tan YS, Ferrer Gago FJ, Lee XE, Neo JY, Thean D, Kaan HYK, Partridge AW, Verma CS, Lane DP, Johannes CW. Stereoisomerism of stapled peptide inhibitors of the p53-Mdm2 interaction: an assessment of synthetic strategies and activity profiles. Chem Sci 2019; 10:6457-6466. [PMID: 31316744 PMCID: PMC6610352 DOI: 10.1039/c9sc01456j] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 05/19/2019] [Indexed: 12/26/2022] Open
Abstract
Staple composition can influence target binding and bioactivity of peptides. We present strategies to modulate E/Z ratios and access saturated analogues.
All-hydrocarbon, i, i+7 stapled peptide inhibitors of the p53-Mdm2 interaction have emerged as promising new leads for cancer therapy. Typical chemical synthesis via olefin metathesis results in the formation of both E- and Z-isomers, an observation that is rarely disclosed but may be of importance in targeting PPI. In this study, we evaluated the effect of staple geometry on the biological activity of five p53-reactivating peptides. We also present strategies for the modulation of the E/Z ratio and attainment of the hydrogenated adduct through repurposing of the metathesis catalyst.
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Affiliation(s)
- Tsz Ying Yuen
- Institute of Chemical and Engineering Sciences , Agency for Science , Technology and Research , 8 Biomedical Grove, Neuros, #07-01 , Singapore 138665 .
| | - Christopher J Brown
- P53 Laboratory , Agency for Science , Technology and Research , 8A Biomedical Grove, #06-06, Immunos , Singapore 138648
| | - Yuezhen Xue
- P53 Laboratory , Agency for Science , Technology and Research , 8A Biomedical Grove, #06-06, Immunos , Singapore 138648
| | - Yaw Sing Tan
- Bioinformatics Institute , Agency for Science , Technology and Research , 30 Biopolis Street, #07-01, Matrix , Singapore 138671
| | - Fernando J Ferrer Gago
- P53 Laboratory , Agency for Science , Technology and Research , 8A Biomedical Grove, #06-06, Immunos , Singapore 138648
| | - Xue Er Lee
- P53 Laboratory , Agency for Science , Technology and Research , 8A Biomedical Grove, #06-06, Immunos , Singapore 138648
| | - Jin Yong Neo
- Institute of Chemical and Engineering Sciences , Agency for Science , Technology and Research , 8 Biomedical Grove, Neuros, #07-01 , Singapore 138665 .
| | - Dawn Thean
- P53 Laboratory , Agency for Science , Technology and Research , 8A Biomedical Grove, #06-06, Immunos , Singapore 138648
| | - Hung Yi Kristal Kaan
- MSD Translational Medicine Research Centre , 8 Biomedical Grove #04-01, Neuros , Singapore 138665
| | - Anthony W Partridge
- MSD Translational Medicine Research Centre , 8 Biomedical Grove #04-01, Neuros , Singapore 138665
| | - Chandra S Verma
- Bioinformatics Institute , Agency for Science , Technology and Research , 30 Biopolis Street, #07-01, Matrix , Singapore 138671
| | - David P Lane
- P53 Laboratory , Agency for Science , Technology and Research , 8A Biomedical Grove, #06-06, Immunos , Singapore 138648
| | - Charles W Johannes
- Institute of Chemical and Engineering Sciences , Agency for Science , Technology and Research , 8 Biomedical Grove, Neuros, #07-01 , Singapore 138665 .
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6
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Sakaguchi I, Fukasawa T, Fujimoto K, Inouye M. Immobilization of Crosslinked Peptides that Possess High Helical Contents and Their Binding to Target DNAs on Au Surfaces. CHEM LETT 2018. [DOI: 10.1246/cl.171153] [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)
- Ikumi Sakaguchi
- Graduate School of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Toshiaki Fukasawa
- Graduate School of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Kazuhisa Fujimoto
- Department of Applied Chemistry and Biochemistry, Kyushu Sangyo University, Fukuoka 813-8503, Japan
| | - Masahiko Inouye
- Graduate School of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
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7
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Lee YJ, Han S, Lim YB. Simultaneous Stabilization and Multimerization of a Peptide α-Helix by Stapling Polymerization. Macromol Rapid Commun 2016; 37:1021-6. [PMID: 27162197 DOI: 10.1002/marc.201600179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 04/21/2016] [Indexed: 11/09/2022]
Abstract
Maintaining specific conformations of peptide ligands is crucial for improving the efficacy of biological interactions. Here, a one-pot polymerization strategy for stabilizing the α-helical conformation of peptides while simultaneously constructing multimeric ligands is presented. The new method, termed stapling polymerization, uses radical polymerization between acryloylated peptide side chains and vinylic monomers. Studies with model peptides indicate that i, i+7 crosslinking is effective for the helix stabilization, whereas i, i+4 crosslinking is not. The stapling polymerization results in the formation of peptide-polyacrylamide conjugates that include ≈3-16 peptides in a single conjugate. This stapling polymerization provides a simple but powerful methodology to fabricate multimeric α-helices that can further be developed to modulate multivalent biomacromolecular interactions.
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Affiliation(s)
- Young-Joo Lee
- Department of Materials Science & Engineering, Yonsei University, 50 Yonsei-ro, Seoul, 03722, South Korea
| | - Sanghun Han
- Department of Materials Science & Engineering, Yonsei University, 50 Yonsei-ro, Seoul, 03722, South Korea
| | - Yong-Beom Lim
- Department of Materials Science & Engineering, Yonsei University, 50 Yonsei-ro, Seoul, 03722, South Korea
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8
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Wang FL, Guo Y, Li SJ, Guo QX, Shi J, Li YM. Diaminodiacid-based solid-phase synthesis of all-hydrocarbon stapled α-helical peptides. Org Biomol Chem 2015; 13:6286-90. [PMID: 25966031 DOI: 10.1039/c5ob00741k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
An alternative stapling strategy is described herein using Fmoc-solid phase peptide synthesis (SPPS) that employed pre-prepared diaminodiacid building blocks to introduce all-hydrocarbon staples into peptides by on-resin cyclization. Compared to unstapled native peptides, diaminodiacid-based stapled peptides exhibited an increased α-helicity ratio and stability toward protease. Moreover, the linkage length was found to affect the bioactivity of the peptides and their ability to inhibit the Wnt pathway. Therefore, the new stapling method provides an alternative way to obtain stapled peptides with tunable linkers of diaminodiacids.
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Affiliation(s)
- Feng-Liang Wang
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China.
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9
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Ricardo MG, Morales FE, Garay H, Reyes O, Vasilev D, Wessjohann LA, Rivera DG. Bidirectional macrocyclization of peptides by double multicomponent reactions. Org Biomol Chem 2015; 13:438-46. [DOI: 10.1039/c4ob01915f] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Peptide macrocyclization by multicomponent reactions.
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Affiliation(s)
- Manuel G. Ricardo
- Center for Natural Products Research
- Faculty of Chemistry
- University of Havana
- La Habana
- Cuba
| | - Fidel E. Morales
- Center for Natural Products Research
- Faculty of Chemistry
- University of Havana
- La Habana
- Cuba
| | - Hilda Garay
- Laboratory of Peptide Synthesis
- Physical-Chemistry Division
- Center for Genetic Engineering and Biotechnology
- La Habana
- Cuba
| | - Osvaldo Reyes
- Laboratory of Peptide Synthesis
- Physical-Chemistry Division
- Center for Genetic Engineering and Biotechnology
- La Habana
- Cuba
| | - Dimitar Vasilev
- Department of Bioorganic Chemistry
- Leibniz Institute of Plant Biochemistry
- Halle/Saale
- Germany
| | - Ludger A. Wessjohann
- Department of Bioorganic Chemistry
- Leibniz Institute of Plant Biochemistry
- Halle/Saale
- Germany
| | - Daniel G. Rivera
- Center for Natural Products Research
- Faculty of Chemistry
- University of Havana
- La Habana
- Cuba
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10
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Verlinden S, Geudens N, Martins JC, Tourwé D, Ballet S, Verniest G. Oxidative α,ω-diyne coupling as an approach towards novel peptidic macrocycles. Org Biomol Chem 2015; 13:9398-404. [DOI: 10.1039/c5ob01153a] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The Glaser–Hay diyne coupling proved to be an efficient cyclisation approach towards diyne containing peptidic macrocycles.
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Affiliation(s)
- S. Verlinden
- Research Group of Organic Chemistry
- Department of Chemistry and Department of Bio-engineering Sciences
- Faculty of Science and Bio-engineering Sciences
- Vrije Universiteit Brussel
- B-1050 Brussels
| | - N. Geudens
- NMR and Structure Analysis Unit
- Department of Organic and Macromolecular Chemistry
- Ghent University
- 9000 Ghent
- Belgium
| | - J. C. Martins
- NMR and Structure Analysis Unit
- Department of Organic and Macromolecular Chemistry
- Ghent University
- 9000 Ghent
- Belgium
| | - D. Tourwé
- Research Group of Organic Chemistry
- Department of Chemistry and Department of Bio-engineering Sciences
- Faculty of Science and Bio-engineering Sciences
- Vrije Universiteit Brussel
- B-1050 Brussels
| | - S. Ballet
- Research Group of Organic Chemistry
- Department of Chemistry and Department of Bio-engineering Sciences
- Faculty of Science and Bio-engineering Sciences
- Vrije Universiteit Brussel
- B-1050 Brussels
| | - G. Verniest
- Research Group of Organic Chemistry
- Department of Chemistry and Department of Bio-engineering Sciences
- Faculty of Science and Bio-engineering Sciences
- Vrije Universiteit Brussel
- B-1050 Brussels
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11
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Nogami K, Takahama K, Okushima A, Oyoshi T, Fujimoto K, Inouye M. Tailor-made designer helical peptides that induce mitochondrion-mediated cell death without necrosis. Chembiochem 2014; 15:2571-6. [PMID: 25234153 DOI: 10.1002/cbic.201402437] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Indexed: 02/02/2023]
Abstract
Managing protein-protein interactions is essential for resolving unknown biological events at the molecular level and developing drugs. We have designed and synthesized a side-chain-crosslinked helical peptides based on the binding domain of a pro-apoptotic protein (Bad) that induces programmed cell death. The peptide showed high helical content and bound to its target, Bcl-XL, more strongly than its non-crosslinked counterparts. When HeLa cells were incubated with the crosslinked peptide, the peptide entered the cytosol across the plasma membrane. The peptide formed a stable complex with Bcl-XL localized at the outer mitochondrial membrane, and this binding event caused the release of cytochrome c from the intermembrane space of mitochondria into the cytosol. This activated the caspase cascade: 70% of HeLa cells died by the apoptosis pathway (without evidence of necrosis).
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Affiliation(s)
- Kagayaki Nogami
- Graduate School of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama, 930-0194 (Japan)
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12
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Jeong WJ, Choi SJ, Choi JS, Lim YB. Chameleon-like self-assembling peptides for adaptable biorecognition nanohybrids. ACS NANO 2013; 7:6850-7. [PMID: 23844930 DOI: 10.1021/nn402025r] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We present here the development of adaptable hybrid materials in which self-assembling peptides can sense the diameter/curvature of carbon nanotubes and then adjust their overall structures from disordered states to α-helices, and vice versa. The peptides within the hybrid materials show exceptionally high thermal-induced conformational stability and molecular recognition capability for target RNA. This study shows that the context-dependent protein-folding effects can be realized in artificial nanosystems and provides a proof of principle that nanohybrid materials decorated with structured and adjustable peptide units can be fabricated using our strategy, from which smart and responsive organic/inorganic hybrid materials capable of sensing and controlling diverse biological molecular recognition events can be developed.
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Affiliation(s)
- Woo-jin Jeong
- Translational Research Center for Protein Function Control and Department of Materials Science & Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Korea
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13
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Bright SA, Brinkø A, Larsen MT, Sinning S, Williams DC, Jensen HH. Basic N-interlinked imipramines show apoptotic activity against malignant cells including Burkitt’s lymphoma. Bioorg Med Chem Lett 2013; 23:1220-4. [DOI: 10.1016/j.bmcl.2013.01.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 01/01/2013] [Accepted: 01/04/2013] [Indexed: 11/15/2022]
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14
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Fujimoto K, Kajino M, Sakaguchi I, Inouye M. Photoswitchable, DNA-binding helical peptides assembled with two independently designed sequences for photoregulation and DNA recognition. Chemistry 2012; 18:9834-40. [PMID: 22767420 DOI: 10.1002/chem.201201431] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Indexed: 11/10/2022]
Abstract
Diarylethene-bridged peptides were developed to photoregulate biomolecular interactions. The peptides are made up of diarylethene-bridged and DNA-binding regions at their N- and C termini, respectively. The two regions could be independently designed and combined as desired. The α-helicities of the peptides were photoregulated in on/off or off/on manners, and the manner depended on the positions of two ornithine (Orn) residues for cross-linking reaction at the diarylethene-bridged region. In the case of the on/off manner, when the diarylethene structure adopted the open form on the peptides, the peptides folded into stable α-helices. Upon UV irradiation, the diarylethene moiety isomerized to its closed form to destabilize the helical structures. Quartz crystal microbalance (QCM) analysis showed that the open isomer strongly associated with a target DNA, as compared with the closed one. When the closed-form peptide existing in the DNA complex was irradiated with a fluorescent lamp in the middle of the QCM monitoring, the frequency change (ΔF) was enhanced by the diarylethene photoisomerization.
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Affiliation(s)
- Kazuhisa Fujimoto
- Department of Applied Chemistry and Biochemistry, Faculty of Engineering, Kyushu Sangyo University, Matsukadai 2-3-1, Fukuoka 813-8503, Japan.
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15
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Fujimoto K, Kajino M, Inouye M. Versatile synthesis of fluorescent, cross-linked peptides as biological probes with the advantage of high helix content. RESEARCH ON CHEMICAL INTERMEDIATES 2012. [DOI: 10.1007/s11164-012-0651-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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16
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Abstract
Many "new generation" peptidomimetics are designed to present amino acid side chains only; they do not have structural features that resemble peptide main chains. These types of molecules have frequently been presented in the literature as mimics of specific secondary structures. However, many "side-chain only" peptidomimetics do not rest in single conformational states, but exist in a limited number of freely interconverting forms. These different conformations may resemble different secondary structures, so referring to them as, for instance, turn- or helical-mimics understates the ways they could adapt to various binding situations. Sets of scaffolds that can be used to mimic aspects of nearly every secondary structure, i.e. universal peptidomimetics, can be constructed. These may assume a privileged place in library design, particularly in high throughput screening for pharmacological probes for which binding conformations, or even the target itself, is unknown at the time the library is designed (critical review, 101 references).
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Affiliation(s)
- Eunhwa Ko
- Texas A & M University, Chemistry Department, P.O. Box 30012, College Station, Texas 77842, USA
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17
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Abstract
This paper concerns peptidomimetic scaffolds that can present side chains in conformations resembling those of amino acids in secondary structures without incurring excessive entropic or enthalpic penalties. Compounds of this type are referred to here as minimalist mimics. The core hypothesis of this paper is that small sets of such scaffolds can be designed to analogue local pairs of amino acids (including noncontiguous ones) in any secondary structure; i.e., they are universal peptidomimetics. To illustrate this concept, we designed a set of four peptidomimetic scaffolds. Libraries based on them were made bearing side chains corresponding to many of the protein-derived amino acids. Modeling experiments were performed to give an indication of kinetic and thermodynamic accessibilities of conformations that can mimic secondary structures. Together, peptidomimetics based on these four scaffolds can adopt conformations that resemble almost any combination of local amino acid side chains in any secondary structure. Universal peptidomimetics of this kind are likely to be most useful in the design of libraries for high-throughput screening against diverse targets. Consequently, data arising from submission of these molecules to the NIH Molecular Libraries Small Molecule Repository (MLSMR) are outlined.
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Affiliation(s)
- Eunhwa Ko
- Department of Chemistry and Laboratory for Molecular Simulation, Texas A&M University, Box 30012, College Station, Texas 77842, United States
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18
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Kajino M, Fujimoto K, Inouye M. Side-Chain Cross-Linked Short α-Helices That Behave like Original Proteins in Biomacromolecular Interactions. J Am Chem Soc 2010; 133:656-9. [DOI: 10.1021/ja106821x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Masaoki Kajino
- Graduate School of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
| | - Kazuhisa Fujimoto
- Graduate School of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
| | - Masahiko Inouye
- Graduate School of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
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19
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Helix Induction by Dirhodium: Access to Biocompatible Metallopeptides with Defined Secondary Structure. Chemistry 2010; 16:6651-9. [DOI: 10.1002/chem.200903092] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Bich C, Maedler S, Chiesa K, DeGiacomo F, Bogliotti N, Zenobi R. Reactivity and applications of new amine reactive cross-linkers for mass spectrometric detection of protein-protein complexes. Anal Chem 2010; 82:172-9. [PMID: 19994840 DOI: 10.1021/ac901651r] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chemical cross-linking of proteins permits the stabilization of noncovalent complexes through introduction of covalent bonds. A crucial challenge is to find the fastest and most efficient cross-linkers in order to minimize reaction times and to handle delicate complexes. New cross-linkers were synthesized by introducing N-hydroxyphthalimide, hydroxybenzotriazole, and 1-hydroxy-7-azabenzotriazole as leaving groups instead of the commonly used N-hydroxysuccimidyl moiety. With the use of matrix-assisted laser desorption ionization (MALDI) mass spectrometry, these new cross-linkers were then compared with the commercially available disuccinimidyl suberate (DSS) for covalent stabilization of the gluthatione-S-transferase (GST) dimer and of an antibody-antigen complex. They showed a better efficiency, generated about 30% more cross-linked complex, and reacted about 10 times faster than DSS. The reaction with the GST dimer was utilized to get information about their reaction efficiency and kinetics. Their ability to stabilize only specific protein complexes was verified by incubating them with a mixture of the proteins GST and ubiquitin. Finally, the cross-linkers were incubated with synthetic peptides to study the selectivity of the binding with various amino acid side chains. Not only lysine but also tyrosine was found to react with the newly synthesized cross-linker containing 1-hydroxy-7-azabenzotriazole as the reactive group.
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Affiliation(s)
- Claudia Bich
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
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21
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Madden MM, Vera CIR, Song W, Lin Q. Facile synthesis of stapled, structurally reinforced peptide helices via a photoinduced intramolecular 1,3-dipolar cycloaddition reaction. Chem Commun (Camb) 2009:5588-90. [PMID: 19753366 PMCID: PMC2765658 DOI: 10.1039/b912094g] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We report the first use of a photoinduced 1,3-dipolar cycloaddition reaction in "stapling" peptide sidechains to reinforce a model peptide helical structure with moderate to excellent yields; the resulting pyrazoline "staplers" exhibit unique fluorescence useful in a cell permeability study.
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Affiliation(s)
- Michael M. Madden
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260 USA
| | - Claudia I. Rivera Vera
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260 USA
| | - Wenjiao Song
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260 USA
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260 USA
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22
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Electroorganic synthesis in oil-in-water (O/W) nanoemulsion: TEMPO-mediated electrooxidation of amphiphilic alcohols in water. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.06.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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23
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Kutchukian PS, Yang JS, Verdine GL, Shakhnovich EI. All-atom model for stabilization of alpha-helical structure in peptides by hydrocarbon staples. J Am Chem Soc 2009; 131:4622-7. [PMID: 19334772 DOI: 10.1021/ja805037p] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent work has shown that the incorporation of an all-hydrocarbon "staple" into peptides can greatly increase their alpha-helix propensity, leading to an improvement in pharmaceutical properties such as proteolytic stability, receptor affinity, and cell permeability. Stapled peptides thus show promise as a new class of drugs capable of accessing intractable targets such as those that engage in intracellular protein-protein interactions. The extent of alpha-helix stabilization provided by stapling has proven to be substantially context dependent, requiring cumbersome screening to identify the optimal site for staple incorporation. In certain cases, a staple encompassing one turn of the helix (attached at residues i and i+4) furnishes greater helix stabilization than one encompassing two turns (i,i+7 staple), which runs counter to expectation based on polymer theory. These findings highlight the need for a more thorough understanding of the forces that underlie helix stabilization by hydrocarbon staples. Here we report all-atom Monte Carlo folding simulations comparing unmodified peptides derived from RNase A and BID BH3 with various i,i+4 and i,i+7 stapled versions thereof. The results of these simulations were found to be in quantitative agreement with experimentally determined helix propensities. We also discovered that staples can stabilize quasi-stable decoy conformations, and that the removal of these states plays a major role in determining the helix stability of stapled peptides. Finally, we critically investigate why our method works, exposing the underlying physical forces that stabilize stapled peptides.
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Affiliation(s)
- Peter S Kutchukian
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
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24
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Diana D, Ziaco B, Colombo G, Scarabelli G, Romanelli A, Pedone C, Fattorusso R, D'Andrea L. Structural Determinants of the Unusual Helix Stability of a De Novo Engineered Vascular Endothelial Growth Factor (VEGF) Mimicking Peptide. Chemistry 2008; 14:4164-6. [DOI: 10.1002/chem.200800180] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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25
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Fujimoto K, Kajino M, Inouye M. Development of a series of cross-linking agents that effectively stabilize alpha-helical structures in various short peptides. Chemistry 2008; 14:857-63. [PMID: 17969217 DOI: 10.1002/chem.200700843] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A series of cross-linking agents of varying rigidity and length were designed to stabilize helical structures in short peptides and were then synthesized. The sequences of the short peptides employed in this study each include two X residues (X=Dap, Dab, Orn, and Lys) at the i/i+4, i/i+7, or i/i+11 positions to provide the sites for cross-linking. These peptides were subjected to reaction with the synthesized cross-linking agents, and the helical content of the resulting cross-linked peptides were analyzed in detail by circular dichroism. For each of the peptide classes we found combinations with the cross-linking agents suitable for the construction of stable helical structures up to >95 % helicity at 5 degrees C. Our method could also be applied to biologically related sequences seen in native proteins such as Rev.
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Affiliation(s)
- Kazuhisa Fujimoto
- Graduate School of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan.
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26
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Che Y, Marshall GR. Privileged scaffolds targeting reverse-turn and helix recognition. Expert Opin Ther Targets 2008; 12:101-14. [PMID: 18076374 DOI: 10.1517/14728222.12.1.101] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Protein-protein interactions dominate molecular recognition in biologic systems. One major challenge for drug discovery arises from the very large surfaces that are characteristic of many protein-protein interactions. OBJECTIVES To identify 'drug-like' small molecule leads capable of modulating protein-protein interactions based on common protein-recognition motifs, such as alpha-helices, beta-strands, reverse-turns and polyproline motifs for example. OVERVIEW Many proteins/peptides are unstructured under physiologic conditions and only fold into ordered structures on binding to their cellular targets. Therefore, preorganization of an inhibitor into its protein-bound conformation reduces the entropy of binding and enhances the relative affinity of the inhibitor. Accordingly, this review describes a general strategy to address the challenge based on the 'privileged structure hypothesis' [Che, PhD thesis, Washington University, 2003] that chemical templates capable of mimicking surfaces of protein-recognition motifs are potential privileged scaffolds as small-molecule inhibitors of protein-protein interactions. The authors highlight recent advances in the design of privileged scaffolds targeting reverse-turn and helical recognition. CONCLUSIONS Privileged scaffolds targeting common protein-recognition motifs are useful to help elucidate the receptor-bound conformation and to provide non-peptidic, bioavailable substructures suitable for optimization to modulate protein-protein interactions.
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Affiliation(s)
- Ye Che
- Washington University, Center for Computational Biology and Department of Biochemistry and Molecular Biophysics, St. Louis, MO 63110, USA
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27
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Che Y, Brooks BR, Marshall GR. Development of small molecules designed to modulate protein-protein interactions. J Comput Aided Mol Des 2006; 20:109-30. [PMID: 16622794 DOI: 10.1007/s10822-006-9040-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2005] [Accepted: 02/13/2006] [Indexed: 01/25/2023]
Abstract
Protein-protein interactions are ubiquitous, essential to almost all known biological processes, and offer attractive opportunities for therapeutic intervention. Developing small molecules that modulate protein-protein interactions is challenging, owing to the large size of protein-complex interface, the lack of well-defined binding pockets, etc. We describe a general approach based on the "privileged-structure hypothesis" [Che, Ph.D. Thesis, Washington University, 2003] - that any organic templates capable of mimicking surfaces of protein-recognition motifs are potential privileged scaffolds as protein-complex antagonists--to address the challenges inherent in the discovery of small-molecule inhibitors of protein-protein interactions.
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Affiliation(s)
- Ye Che
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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