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Li J, Tan YS, Verma CS. Dissecting the geometric and hydrophobic constraints of stapled peptides. Proteins 2024. [PMID: 38196284 DOI: 10.1002/prot.26662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/01/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024]
Abstract
Stapled peptides are a promising class of molecules with potential as highly specific probes of protein-protein interactions and as therapeutics. Hydrocarbon stapling affects the peptide properties through the interplay of two factors: enhancing the overall hydrophobicity and constraining the conformational flexibility. By constructing a series of virtual peptides, we study the role of each factor in modulating the structural properties of a hydrocarbon-stapled peptide PM2, which has been shown to enter cells, engage its target Mouse Double Minute 2 (MDM2), and activate p53. Hamiltonian replica exchange molecular dynamics (HREMD) simulations suggest that hydrocarbon stapling favors helical populations of PM2 through a combination of the geometric constraints and the enhanced hydrophobicity of the peptide. To further understand the conformational landscape of the stapled peptides along the binding pathway, we performed HREMD simulations by restraining the peptide at different distances from MDM2. When the peptide approaches MDM2, the binding pocket undergoes dehydration which appears to be greater in the presence of the stapled peptide compared with the linear peptide. In the binding pocket, the helicity of the stapled peptide is increased due to the favorable interactions between the peptide residues as well as the staple and the microenvironment of the binding pocket, contributing to enhanced affinity. The dissection of the multifaceted mechanism of hydrocarbon stapling into individual factors not only deepens fundamental understanding of peptide stapling, but also provides guidelines for the design of new stapled peptides.
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Affiliation(s)
- Jianguo Li
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Singapore Eye Research Institute, Singapore, Singapore
| | - Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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2
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Bluntzer MTJ, O'Connell J, Baker TS, Michel J, Hulme AN. Designing stapled peptides to inhibit
protein‐protein
interactions: An analysis of successes in a rapidly changing field. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24191] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | | | | | - Julien Michel
- EaStChem School of Chemistry The University of Edinburgh Edinburgh UK
| | - Alison N. Hulme
- EaStChem School of Chemistry The University of Edinburgh Edinburgh UK
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3
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Tan YS, Mhoumadi Y, Verma CS. Roles of computational modelling in understanding p53 structure, biology, and its therapeutic targeting. J Mol Cell Biol 2020; 11:306-316. [PMID: 30726928 PMCID: PMC6487789 DOI: 10.1093/jmcb/mjz009] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/14/2018] [Accepted: 01/31/2019] [Indexed: 12/21/2022] Open
Abstract
The transcription factor p53 plays pivotal roles in numerous biological processes, including the suppression of tumours. The rich availability of biophysical data aimed at understanding its structure–function relationships since the 1990s has enabled the application of a variety of computational modelling techniques towards the establishment of mechanistic models. Together they have provided deep insights into the structure, mechanics, energetics, and dynamics of p53. In parallel, the observation that mutations in p53 or changes in its associated pathways characterize several human cancers has resulted in a race to develop therapeutic modulators of p53, some of which have entered clinical trials. This review describes how computational modelling has played key roles in understanding structural-dynamic aspects of p53, formulating hypotheses about domains that are beyond current experimental investigations, and the development of therapeutic molecules that target the p53 pathway.
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Affiliation(s)
- Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore
| | - Yasmina Mhoumadi
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore
| | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore
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4
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Gallagher EE, Song JM, Menon A, Mishra LD, Chmiel AF, Garner AL. Consideration of Binding Kinetics in the Design of Stapled Peptide Mimics of the Disordered Proteins Eukaryotic Translation Initiation Factor 4E-Binding Protein 1 and Eukaryotic Translation Initiation Factor 4G. J Med Chem 2019; 62:4967-4978. [PMID: 31033289 PMCID: PMC6679956 DOI: 10.1021/acs.jmedchem.9b00068] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Protein disorder plays a crucial role in signal transduction and is key for many cellular processes including transcription, translation, and cell cycle. Within the intrinsically disordered protein interactome, the α-helix is commonly used for binding, which is induced via a disorder-to-order transition. Because the targeting of protein-protein interactions (PPIs) remains an important challenge in medicinal chemistry, efforts have been made to mimic this secondary structure for rational inhibitor design through the use of stapled peptides. Cap-dependent mRNA translation is regulated by two disordered proteins, 4E-BP1 and eIF4G, that inhibit or stimulate the activity of the m7G cap-binding translation initiation factor, eIF4E, respectively. Both use an α-helical motif for eIF4E binding, warranting the investigation of stapled peptide mimics for manipulating eIF4E PPIs. Herein, we describe our efforts toward this goal, resulting in the synthesis of a cell-active stapled peptide for further development in manipulating aberrant cap-dependent translation in human diseases.
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Affiliation(s)
- Erin E Gallagher
- Department of Medicinal Chemistry, College of Pharmacy , University of Michigan , 1600 Huron Parkway, NCRC B520 , Ann Arbor , Michigan 48109 , United States
| | - James M Song
- Program in Chemical Biology , University of Michigan , 210 Washtenaw Avenue , Ann Arbor , Michigan 48109 , United States
| | - Arya Menon
- Department of Medicinal Chemistry, College of Pharmacy , University of Michigan , 1600 Huron Parkway, NCRC B520 , Ann Arbor , Michigan 48109 , United States
| | - Lauren D Mishra
- Department of Medicinal Chemistry, College of Pharmacy , University of Michigan , 1600 Huron Parkway, NCRC B520 , Ann Arbor , Michigan 48109 , United States
| | - Alyah F Chmiel
- Department of Medicinal Chemistry, College of Pharmacy , University of Michigan , 1600 Huron Parkway, NCRC B520 , Ann Arbor , Michigan 48109 , United States
| | - Amanda L Garner
- Department of Medicinal Chemistry, College of Pharmacy , University of Michigan , 1600 Huron Parkway, NCRC B520 , Ann Arbor , Michigan 48109 , United States
- Program in Chemical Biology , University of Michigan , 210 Washtenaw Avenue , Ann Arbor , Michigan 48109 , United States
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5
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Trypanothione reductase inhibition and anti-leishmanial activity of all-hydrocarbon stapled α-helical peptides with improved proteolytic stability. Eur J Med Chem 2018; 149:238-247. [DOI: 10.1016/j.ejmech.2018.02.071] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/31/2018] [Accepted: 02/21/2018] [Indexed: 12/24/2022]
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6
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Lee XA, Verma C, Sim AY. Designing dual inhibitors of Mdm2/MdmX: Unexpected coupling of water with gatekeeper Y100/99. Proteins 2017; 85:1493-1506. [DOI: 10.1002/prot.25310] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 03/28/2017] [Accepted: 04/17/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Xiong An Lee
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR); Matrix 138671 Singapore
| | - Chandra Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR); Matrix 138671 Singapore
- Department of Biological Sciences; National University of Singapore; 117543 Singapore
- School of Biological Sciences; Nanyang Technological University; 637551 Singapore
| | - Adelene Y.L Sim
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR); Matrix 138671 Singapore
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7
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Stapled peptide design: principles and roles of computation. Drug Discov Today 2016; 21:1642-1653. [DOI: 10.1016/j.drudis.2016.06.012] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 05/11/2016] [Accepted: 06/13/2016] [Indexed: 12/23/2022]
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8
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Tian Y, Li J, Zhao H, Zeng X, Wang D, Liu Q, Niu X, Huang X, Xu N, Li Z. Stapling of unprotected helical peptides via photo-induced intramolecular thiol-yne hydrothiolation. Chem Sci 2016; 7:3325-3330. [PMID: 29997825 PMCID: PMC6006495 DOI: 10.1039/c6sc00106h] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 02/03/2016] [Indexed: 12/27/2022] Open
Abstract
Peptide stapling emerged as a versatile strategy to recapitulate the bioactive helical conformation of unstructured short peptides in water to improve their therapeutic properties in targeting intracellular "undruggable" targets. Here, we describe the development of photo-induced intramolecular thiol-yne macrocyclization for rapid access to short stapled peptides with enhanced biophysical properties. This new peptide stapling technique provides rapid access to conformationally constrained helices with satisfying functional group tolerance. Notably, the vinyl sulfide linkage shows distinct lipophilicity with reduced membrane toxicity compared to the corresponding all-hydrocarbon analogue. As a proof of principle, we constructed stabilized helices modulating intracellular estrogen receptor (ER)-coactivator interactions with a nanomolar binding affinity, enhanced serum stability, a diffuse cellular distribution and selective cytotoxicity towards ER-positive MCF-7 cells.
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Affiliation(s)
- Yuan Tian
- School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen , 518055 , China .
| | - Jingxu Li
- School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen , 518055 , China .
| | - Hui Zhao
- School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen , 518055 , China .
| | - Xiangze Zeng
- Department of Chemistry , Center of Systems Biology and Human Health , School of Science and Institute for Advance Study , The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon , Hong Kong , China
| | - Dongyuan Wang
- School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen , 518055 , China .
| | - Qisong Liu
- School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen , 518055 , China .
| | - Xiaogang Niu
- College of Chemistry and Molecular Engineering , Beijing Nuclear Magnetic Resonance Center , Peking University , Beijing , 100871 , China
| | - Xuhui Huang
- Department of Chemistry , Center of Systems Biology and Human Health , School of Science and Institute for Advance Study , The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon , Hong Kong , China
| | - Naihan Xu
- Key Lab in Healthy Science and Technology , Division of Life Science , Shenzhen Graduate School of Tsinghua University , Shenzhen , 518055 , China .
| | - Zigang Li
- School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen , 518055 , China .
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