1
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Chen Y, Dai C, Han J, Xing Y, Yin F, Li Z. Recent Chemical Biology Insights Towards Reversible Stapled Peptides. Chembiochem 2025; 26:e202500052. [PMID: 40011217 DOI: 10.1002/cbic.202500052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2025] [Revised: 02/25/2025] [Accepted: 02/26/2025] [Indexed: 02/28/2025]
Abstract
Peptides are increasingly recognized for their advantages over small molecules in the modulation of protein-protein interactions (PPIs), particularly in terms of potency and selectivity. "Staples" can be coupled to the amino acid residues of linear peptides to limit their conformation, improving the stability, membrane permeability, and resistance to proteolysis of peptides. However, the addition of staples can sometimes lead to the complete inactivation of the original peptide or result in extensive interactions that complicate biophysical analysis. Reversible stapled peptides provide an excellent solution to these issues. Besides, probes based on reversible stapled peptides are also indispensable tools for thoroughly investigating PPIs. Consequently, the development of diverse reversible stapling techniques for stapled peptides is crucial for broadening the applications of peptide molecules in drug discovery, drug delivery, and as tools in chemical biology research. This review aims to summarize representative chemical design strategies for reversible stapled peptides, focusing on reversible chemical stapling methods involving sulfhydryl, amino, and methylthio groups, as well as reversible modulation of the conformational states of stapled peptides. Additionally, we demonstrate some intriguing biological applications of stapled peptides and, finally, suggest future research directions in the field that will serve as references for related researchers.
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Affiliation(s)
- Ying Chen
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, P. R. China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, P. R. China
| | - Chuan Dai
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, P. R. China
| | - Jinyan Han
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, P. R. China
| | - Yun Xing
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, P. R. China
| | - Feng Yin
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, P. R. China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, P. R. China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, P. R. China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, P. R. China
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2
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Case M, Navaratna T, Vinh J, Thurber G. Rapid Evaluation of Staple Placement in Stabilized α Helices Using Bacterial Surface Display. ACS Chem Biol 2023; 18:905-914. [PMID: 37039514 PMCID: PMC10773984 DOI: 10.1021/acschembio.3c00048] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
There are a wealth of proteins involved in disease that cannot be targeted by current therapeutics because they are inside cells, inaccessible to most macromolecules, and lack small-molecule binding pockets. Stapled peptides, where two amino acids are covalently linked, form a class of macrocycles that have the potential to penetrate cell membranes and disrupt intracellular protein-protein interactions. However, their discovery relies on solid-phase synthesis, greatly limiting queries into their complex design space involving amino acid sequence, staple location, and staple chemistry. Here, we use stabilized peptide engineering by Escherichia coli display (SPEED), which utilizes noncanonical amino acids and click chemistry for stabilization, to rapidly screen staple location and linker structure to accelerate peptide design. After using SPEED to confirm hotspots in the mdm2-p53 interaction, we evaluated different staple locations and staple chemistry to identify several novel nanomolar and sub-nanomolar antagonists. Next, we evaluated SPEED in the B cell lymphoma 2 (Bcl-2) protein family, which is responsible for regulating apoptosis. We report that novel staple locations modified in the context of BIM, a high affinity but nonspecific naturally occurring peptide, improve its specificity against the highly homologous proteins in the Bcl-2 family. These compounds demonstrate the importance of screening linker location and chemistry in identifying high affinity and specific peptide antagonists. Therefore, SPEED can be used as a versatile platform to evaluate multiple design criteria for stabilized peptide engineering.
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3
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Gupta S, Azadvari N, Hosseinzadeh P. Design of Protein Segments and Peptides for Binding to Protein Targets. BIODESIGN RESEARCH 2022; 2022:9783197. [PMID: 37850124 PMCID: PMC10521657 DOI: 10.34133/2022/9783197] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/16/2022] [Indexed: 10/19/2023] Open
Abstract
Recent years have witnessed a rise in methods for accurate prediction of structure and design of novel functional proteins. Design of functional protein fragments and peptides occupy a small, albeit unique, space within the general field of protein design. While the smaller size of these peptides allows for more exhaustive computational methods, flexibility in their structure and sparsity of data compared to proteins, as well as presence of noncanonical building blocks, add additional challenges to their design. This review summarizes the current advances in the design of protein fragments and peptides for binding to targets and discusses the challenges in the field, with an eye toward future directions.
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Affiliation(s)
- Suchetana Gupta
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
| | - Noora Azadvari
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
| | - Parisa Hosseinzadeh
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
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4
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Liu Q, Sheng L, Liu YY, Gao T, Wang H, Liu Y, Cao A. A potential inhibitor of MDM2 by restoring the native conformation of the p53 α-helical peptide on gold nanoparticles. ChemMedChem 2022; 17:e202100623. [PMID: 35037401 DOI: 10.1002/cmdc.202100623] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/14/2021] [Indexed: 11/11/2022]
Abstract
Many efforts have been made to develop inhibitors of MDM2 as potential drugs for cancer therapy. In this work, we use our previous developed conformational engineering technique to stabilize the binding conformation of the p53 transcription activation domain (TAD) peptide on gold NPs (AuNPs), and create an AuNP-based anti-MDM2 artificial antibody, denoted as Goldbody, that specifically binds MDM2. Though the free TAD peptide is unstructured, circular dichroism spectra confirm that its α-helical conformation in the original p53 protein is restored on the anti-MDM2 Goldbody, and surface plasmon resonance (SPR) experiments confirm that there is strong specific interaction between the anti-MDM2 Goldbody and MDM2, demonstrating the anti-MDM2 Goldbody as a potential inhibitor of MDM2. This work demonstrates that the conformational engineering technique is not limited to the antigen-antibody systems, but can also be applied more widely in other protein-protein interfaces to create more and more artificial proteins for various biomedical applications.
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Affiliation(s)
- Qi Liu
- Shanghai University, Institute of Nanochemistry and Nanobiology, CHINA
| | - Lingjie Sheng
- Shanghai University, Institute of Nanochemistry and Nanobiology, CHINA
| | - Yuan-Yuan Liu
- Shanghai University, Institute of Nanochemistry and Nanobiology, CHINA
| | - Tiange Gao
- Shanghai University, Institute of Nanochemistry and Nanobiology, CHINA
| | - Haifang Wang
- Shanghai University, Institute of Nanochemistry and Nanobiology, CHINA
| | - Yuanfang Liu
- Peking University, College of Chemistry and Molecular Engineering, CHINA
| | - Aoneng Cao
- Shanghai University, Institute of Nanochemistry and Nanobiology, No.99 Shangda Rd. Rm201, Bldg. E, 200444, Shanghai, CHINA
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5
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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: 1.2] [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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6
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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: 0.6] [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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7
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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: 13.6] [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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8
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Hetherington K, Hegedus Z, Edwards TA, Sessions RB, Nelson A, Wilson AJ. Stapled Peptides as HIF-1α/p300 Inhibitors: Helicity Enhancement in the Bound State Increases Inhibitory Potency. Chemistry 2020; 26:7638-7646. [PMID: 32307728 PMCID: PMC7318359 DOI: 10.1002/chem.202000417] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/13/2020] [Indexed: 12/17/2022]
Abstract
Protein-protein interactions (PPIs) control virtually all cellular processes and have thus emerged as potential targets for development of molecular therapeutics. Peptide-based inhibitors of PPIs are attractive given that they offer recognition potency and selectivity features that are ideal for function, yet, they do not predominantly populate the bioactive conformation, frequently suffer from poor cellular uptake and are easily degraded, for example, by proteases. The constraint of peptides in a bioactive conformation has emerged as a promising strategy to mitigate against these liabilities. In this work, using peptides derived from hypoxia-inducible factor 1 (HIF-1α) together with dibromomaleimide stapling, we identify constrained peptide inhibitors of the HIF-1α/p300 interaction that are more potent than their unconstrained sequences. Contrary to expectation, the increased potency does not correlate with an increased population of an α-helical conformation in the unbound state as demonstrated by experimental circular dichroism analysis. Rather, the ability of the peptide to adopt a bioactive α-helical conformation in the p300 bound state is better supported in the constrained variant as demonstrated by molecular dynamics simulations and circular dichroism difference spectra.
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Affiliation(s)
- Kristina Hetherington
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Zsofia Hegedus
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Thomas A. Edwards
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Richard B. Sessions
- School of BiochemistryUniversity of BristolMedical Sciences Building, University WalkBristolBS8 1TDUK
- BrisSynBioUniversity of Bristol, Life Sciences BuildingTyndall AvenueBristolBS8 1TQUK
| | - Adam Nelson
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Andrew J. Wilson
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
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9
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Identification of a Structural Determinant for Selective Targeting of HDMX. Structure 2020; 28:847-857.e5. [PMID: 32359398 DOI: 10.1016/j.str.2020.04.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/11/2020] [Accepted: 04/11/2020] [Indexed: 11/21/2022]
Abstract
p53 is a critical tumor-suppressor protein that guards the human genome against mutations by inducing cell-cycle arrest or apoptosis. Cancer cells subvert p53 by deletion, mutation, or overexpression of the negative regulators HDM2 and HDMX. For tumors that retain wild-type p53, its reactivation by pharmacologic targeting of HDM2 and/or HDMX represents a promising strategy, with a series of selective small-molecule HDM2 inhibitors and a dual HDM2/HDMX stapled-peptide inhibitor being evaluated in clinical trials. Because selective HDM2 targeting can cause hematologic toxicity, selective HDMX inhibitors could provide an alternative p53-reactivation strategy, but clinical candidates remain elusive. Here, we applied a mutation-scanning approach to uncover p53-based stapled peptides that are selective for HDMX. Crystal structures of stapled-peptide/HDMX complexes revealed a molecular mechanism for the observed specificity, which was validated by HDMX mutagenesis. Thus, we provide a blueprint for the development of HDMX-selective inhibitors to dissect and target the p53/HDMX interaction.
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10
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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: 39] [Impact Index Per Article: 7.8] [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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11
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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: 105] [Impact Index Per Article: 17.5] [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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12
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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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13
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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: 2.5] [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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14
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Design and Synthetic Strategies for Helical Peptides. Methods Mol Biol 2019; 2001:107-131. [PMID: 31134570 DOI: 10.1007/978-1-4939-9504-2_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Abnormal protein-protein interactions (PPIs) are the basis of multiple diseases, and the large and shallow PPI interfaces make the target "undruggable" for traditional small molecules. Peptides, emerging as a new therapeutic modality, can efficiently mimic PPIs with their large scaffolds. Natural peptides are flexible and usually have poor serum stability and cell permeability, features that limit their further biological applications. To satisfy the clinical application of peptide inhibitors, many strategies have been developed to constrain peptides in their bioactive conformation. In this report, we describe several classic methods used to constrain peptides into a fixed secondary structure which could significantly improve their biophysical properties.
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15
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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: 6.2] [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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16
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Wu Y, Kaur A, Fowler E, Wiedmann MM, Young R, Galloway WRJD, Olsen L, Sore HF, Chattopadhyay A, Kwan TTL, Xu W, Walsh SJ, de Andrade P, Janecek M, Arumugam S, Itzhaki LS, Lau YH, Spring DR. Toolbox of Diverse Linkers for Navigating the Cellular Efficacy Landscape of Stapled Peptides. ACS Chem Biol 2019; 14:526-533. [PMID: 30702850 DOI: 10.1021/acschembio.9b00063] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Stapled peptides have great potential as modulators of protein-protein interactions (PPIs). However, there is a vast landscape of chemical features that can be varied for any given peptide, and identifying a set of features that maximizes cellular uptake and subsequent target engagement remains a key challenge. Herein, we present a systematic analysis of staple functionality on the peptide bioactivity landscape in cellular assays. Through application of a "toolbox" of diversified dialkynyl linkers to the stapling of MDM2-binding peptides via a double-click approach, we conducted a study of cellular uptake and p53 activation as a function of the linker. Minor changes in the linker motif and the specific pairing of linker with peptide sequence can lead to substantial differences in bioactivity, a finding which may have important design implications for peptide-based inhibitors of other PPIs. Given the complexity of the structure-activity relationships involved, the toolbox approach represents a generalizable strategy for optimization when progressing from in vitro binding assays to cellular efficacy studies.
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Affiliation(s)
- Yuteng Wu
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Amandeep Kaur
- European Molecular Biology Laboratory Australia Node for Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences , University of New South Wales , Sydney , NSW 2052 , Australia
| | - Elaine Fowler
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Mareike M Wiedmann
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Reginald Young
- School of Chemistry , The University of Sydney , Eastern Avenue , Sydney , NSW 2006 , Australia
| | - Warren R J D Galloway
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Lasse Olsen
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Hannah F Sore
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Anasuya Chattopadhyay
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , United Kingdom
| | - Terence T-L Kwan
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Wenshu Xu
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , United Kingdom
| | - Stephen J Walsh
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Peterson de Andrade
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Matej Janecek
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Senthil Arumugam
- European Molecular Biology Laboratory Australia Node for Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences , University of New South Wales , Sydney , NSW 2052 , Australia
| | - Laura S Itzhaki
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , United Kingdom
| | - Yu Heng Lau
- School of Chemistry , The University of Sydney , Eastern Avenue , Sydney , NSW 2006 , Australia
| | - David R Spring
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
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17
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Atangcho L, Navaratna T, Thurber GM. Hitting Undruggable Targets: Viewing Stabilized Peptide Development through the Lens of Quantitative Systems Pharmacology. Trends Biochem Sci 2019; 44:241-257. [PMID: 30563724 PMCID: PMC6661118 DOI: 10.1016/j.tibs.2018.11.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/31/2018] [Accepted: 11/22/2018] [Indexed: 01/10/2023]
Abstract
Stabilized peptide therapeutics have the potential to hit currently undruggable targets, dramatically expanding the druggable genome. However, major obstacles to their development include poor intracellular delivery, rapid degradation, low target affinity, and membrane toxicity. With the emergence of multiple stabilization techniques and screening technologies, the high efficacy of various bioactive peptides has been demonstrated in vitro, albeit with limited success in vivo. We discuss here the chemical and pharmacokinetic barriers to achieving in vivo efficacy, analyze the characteristics of FDA-approved peptide drugs, and propose a developmental tool that considers the molecular properties of stabilized peptides in a comprehensive and quantitative manner to achieve the necessary rates for in vivo delivery to the target, efficacy, and ultimately clinical translation.
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Affiliation(s)
- Lydia Atangcho
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Tejas Navaratna
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Greg M Thurber
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.
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18
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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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19
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Verhoork SJM, Jennings CE, Rozatian N, Reeks J, Meng J, Corlett EK, Bunglawala F, Noble MEM, Leach AG, Coxon CR. Tuning the Binding Affinity and Selectivity of Perfluoroaryl-Stapled Peptides by Cysteine-Editing. Chemistry 2019; 25:177-182. [PMID: 30255959 DOI: 10.1002/chem.201804163] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Indexed: 11/08/2022]
Abstract
A growing number of approaches to "staple" α-helical peptides into a bioactive conformation using cysteine cross-linking are emerging. Here, the replacement of l-cysteine with "cysteine analogues" in combinations of different stereochemistry, side chain length and beta-carbon substitution, is explored to examine the influence that the thiol-containing residue(s) has on target protein binding affinity in a well-explored model system, p53-MDM2/MDMX, which is constituted by the interaction of the tumour suppressor protein p53 and proteins MDM2 and MDMX, which regulate p53 activity. In some cases, replacement of one or more l-cysteine residues afforded significant changes in the measured binding affinity and target selectivity of the peptide. Computationally constructed homology models indicate that some modifications, such as incorporating two d-cysteine residues, favourably alter the positions of key functional amino acid side chains, which is likely to cause changes in binding affinity, in agreement with measured surface plasmon resonance data.
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Affiliation(s)
- Sanne J M Verhoork
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom St, Liverpool, L3 3AF, UK
| | - Claire E Jennings
- Northern Institute for Cancer Research, Newcastle University, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Neshat Rozatian
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE, UK
| | - Judith Reeks
- Northern Institute for Cancer Research, Newcastle University, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Jieman Meng
- Northern Institute for Cancer Research, Newcastle University, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Emily K Corlett
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE, UK
| | - Fazila Bunglawala
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom St, Liverpool, L3 3AF, UK
| | - Martin E M Noble
- Northern Institute for Cancer Research, Newcastle University, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Andrew G Leach
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom St, Liverpool, L3 3AF, UK
| | - Christopher R Coxon
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom St, Liverpool, L3 3AF, UK
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20
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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: 2.7] [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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21
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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: 3.1] [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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22
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Li X, Zou Y, Hu HG. Different stapling-based peptide drug design: Mimicking α-helix as inhibitors of protein–protein interaction. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2018.01.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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23
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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: 74] [Impact Index Per Article: 10.6] [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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24
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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: 5.6] [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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25
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Grison CM, Burslem GM, Miles JA, Pilsl LKA, Yeo DJ, Imani Z, Warriner SL, Webb ME, Wilson AJ. Double quick, double click reversible peptide "stapling". Chem Sci 2017; 8:5166-5171. [PMID: 28970902 PMCID: PMC5618791 DOI: 10.1039/c7sc01342f] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/11/2017] [Indexed: 12/23/2022] Open
Abstract
A versatile, rapid and reversible approach to constrain peptides in a bioactive helical conformation and bearing a functional handle for inhibition of protein–protein interactions is described.
The development of constrained peptides for inhibition of protein–protein interactions is an emerging strategy in chemical biology and drug discovery. This manuscript introduces a versatile, rapid and reversible approach to constrain peptides in a bioactive helical conformation using BID and RNase S peptides as models. Dibromomaleimide is used to constrain BID and RNase S peptide sequence variants bearing cysteine (Cys) or homocysteine (hCys) amino acids spaced at i and i + 4 positions by double substitution. The constraint can be readily removed by displacement of the maleimide using excess thiol. This new constraining methodology results in enhanced α-helical conformation (BID and RNase S peptide) as demonstrated by circular dichroism and molecular dynamics simulations, resistance to proteolysis (BID) as demonstrated by trypsin proteolysis experiments and retained or enhanced potency of inhibition for Bcl-2 family protein–protein interactions (BID), or greater capability to restore the hydrolytic activity of the RNAse S protein (RNase S peptide). Finally, use of a dibromomaleimide functionalized with an alkyne permits further divergent functionalization through alkyne–azide cycloaddition chemistry on the constrained peptide with fluorescein, oligoethylene glycol or biotin groups to facilitate biophysical and cellular analyses. Hence this methodology may extend the scope and accessibility of peptide stapling.
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Affiliation(s)
- Claire M Grison
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - George M Burslem
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Jennifer A Miles
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Ludwig K A Pilsl
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - David J Yeo
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Zeynab Imani
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Stuart L Warriner
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Michael E Webb
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Andrew J Wilson
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
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26
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Tran PT, Larsen CØ, Røndbjerg T, De Foresta M, Kunze MBA, Marek A, Løper JH, Boyhus LE, Knuhtsen A, Lindorff-Larsen K, Pedersen DS. Diversity-Oriented Peptide Stapling: A Third Generation Copper-Catalysed Azide-Alkyne Cycloaddition Stapling and Functionalisation Strategy. Chemistry 2017; 23:3490-3495. [DOI: 10.1002/chem.201700128] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Phuong Thu Tran
- Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Christian Ørnbøl Larsen
- Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Tobias Røndbjerg
- Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Martina De Foresta
- Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Micha B. A. Kunze
- Structural Biology and NMR Laboratory; Department of Biology; University of Copenhagen; Ole Maaloes Vej 5 2200 Copenhagen Denmark
| | - Ales Marek
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; 16610 Prague 6 Czech Republic
| | - Jacob Hartvig Løper
- Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Lotte-Emilie Boyhus
- Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Astrid Knuhtsen
- Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory; Department of Biology; University of Copenhagen; Ole Maaloes Vej 5 2200 Copenhagen Denmark
| | - Daniel Sejer Pedersen
- Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
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27
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Wiedmann MM, Tan YS, Wu Y, Aibara S, Xu W, Sore HF, Verma CS, Itzhaki L, Stewart M, Brenton JD, Spring DR. Development of Cell-Permeable, Non-Helical Constrained Peptides to Target a Key Protein-Protein Interaction in Ovarian Cancer. Angew Chem Int Ed Engl 2017; 56:524-529. [PMID: 27918136 PMCID: PMC5291322 DOI: 10.1002/anie.201609427] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 10/18/2016] [Indexed: 02/04/2023]
Abstract
There is a lack of current treatment options for ovarian clear cell carcinoma (CCC) and the cancer is often resistant to platinum-based chemotherapy. Hence there is an urgent need for novel therapeutics. The transcription factor hepatocyte nuclear factor 1β (HNF1β) is ubiquitously overexpressed in CCC and is seen as an attractive therapeutic target. This was validated through shRNA-mediated knockdown of the target protein, HNF1β, in five high- and low-HNF1β-expressing CCC lines. To inhibit the protein function, cell-permeable, non-helical constrained proteomimetics to target the HNF1β-importin α protein-protein interaction were designed, guided by X-ray crystallographic data and molecular dynamics simulations. In this way, we developed the first reported series of constrained peptide nuclear import inhibitors. Importantly, this general approach may be extended to other transcription factors.
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Affiliation(s)
- Mareike M. Wiedmann
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Cancer Research UK Cambridge InstituteUniversity of CambridgeLi Ka Shing Centre, Robinson WayCambridgeCB2 0REUK
| | - Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and ResearchA*STAR30 Biopolis Street, #07-01 MatrixSingapore138671Singapore
| | - Yuteng Wu
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Shintaro Aibara
- SciLifeLabTomtebodavägen 23A171 65 SolnaStockholmSweden
- MRC Laboratory of Molecular BiologyFrancis Crick Avenue, Cambridge Biomedical CampusCambridgeCB2 0QHUK
| | - Wenshu Xu
- Department of PharmacologyTennis Court RoadCambridgeCB2 1PDUK
| | - Hannah F. Sore
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Chandra S. Verma
- Bioinformatics Institute, Agency for Science, Technology and ResearchA*STAR30 Biopolis Street, #07-01 MatrixSingapore138671Singapore
- School of Biological SciencesNanyang Technological University60 Nanyang DriveSingapore637551Singapore
- Department of Biological SciencesNational University of Singapore14 Science Drive 4Singapore117543Singapore
| | - Laura Itzhaki
- Department of PharmacologyTennis Court RoadCambridgeCB2 1PDUK
| | - Murray Stewart
- MRC Laboratory of Molecular BiologyFrancis Crick Avenue, Cambridge Biomedical CampusCambridgeCB2 0QHUK
| | - James D. Brenton
- Cancer Research UK Cambridge InstituteUniversity of CambridgeLi Ka Shing Centre, Robinson WayCambridgeCB2 0REUK
| | - David R. Spring
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
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28
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Wiedmann MM, Tan YS, Wu Y, Aibara S, Xu W, Sore HF, Verma CS, Itzhaki L, Stewart M, Brenton JD, Spring DR. Development of Cell-Permeable, Non-Helical Constrained Peptides to Target a Key Protein-Protein Interaction in Ovarian Cancer. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201609427] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Mareike M. Wiedmann
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
- Cancer Research UK Cambridge Institute; University of Cambridge; Li Ka Shing Centre, Robinson Way Cambridge CB2 0RE UK
| | - Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and Research; A*STAR; 30 Biopolis Street, #07-01 Matrix Singapore 138671 Singapore
| | - Yuteng Wu
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Shintaro Aibara
- SciLifeLab; Tomtebodavägen 23A 171 65 Solna Stockholm Sweden
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge Biomedical Campus Cambridge CB2 0QH UK
| | - Wenshu Xu
- Department of Pharmacology; Tennis Court Road Cambridge CB2 1PD UK
| | - Hannah F. Sore
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Chandra S. Verma
- Bioinformatics Institute, Agency for Science, Technology and Research; A*STAR; 30 Biopolis Street, #07-01 Matrix Singapore 138671 Singapore
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
- Department of Biological Sciences; National University of Singapore; 14 Science Drive 4 Singapore 117543 Singapore
| | - Laura Itzhaki
- Department of Pharmacology; Tennis Court Road Cambridge CB2 1PD UK
| | - Murray Stewart
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge Biomedical Campus Cambridge CB2 0QH UK
| | - James D. Brenton
- Cancer Research UK Cambridge Institute; University of Cambridge; Li Ka Shing Centre, Robinson Way Cambridge CB2 0RE UK
| | - David R. Spring
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
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29
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Lin H, Jiang Y, Zhang Q, Hu K, Li Z. An in-tether sulfilimine chiral center induces helicity in short peptides. Chem Commun (Camb) 2016; 52:10389-10391. [PMID: 27480995 DOI: 10.1039/c6cc04508a] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A precisely positioned sulfilimine chiral center in the tether of a stabilized peptide would determine the peptide's secondary structure. Peptide sulfilimines could be prepared by a facile chloramine T oxidation and the two resulting peptide diastereomers showed significant differences in their secondary structures, which were supported by circular dichroism spectroscopy and NMR.
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Affiliation(s)
- Huacan Lin
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Yixiang Jiang
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Qingzhou Zhang
- 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.
| | - Zigang Li
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
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30
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Zhang L, Navaratna T, Thurber GM. A Helix-Stabilizing Linker Improves Subcutaneous Bioavailability of a Helical Peptide Independent of Linker Lipophilicity. Bioconjug Chem 2016; 27:1663-72. [PMID: 27327034 DOI: 10.1021/acs.bioconjchem.6b00209] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Stabilized peptides address several limitations to peptide-based imaging agents and therapeutics such as poor stability and low affinity due to conformational flexibility. There is also active research in developing these compounds for intracellular drug targeting, and significant efforts have been invested to determine the effects of helix stabilization on intracellular delivery. However, much less is known about the impact on other pharmacokinetic parameters such as plasma clearance and bioavailability. We investigated the effect of different fluorescent helix-stabilizing linkers with varying lipophilicity on subcutaneous (sc) bioavailability using the glucagon-like peptide-1 (GLP-1) receptor ligand exendin as a model system. The stabilized peptides showed significantly higher protease resistance and increased bioavailability independent of linker hydrophilicity, and all subcutaneously delivered conjugates were able to successfully target the islets of Langerhans with high specificity. The lipophilic peptide variants had slower absorption and plasma clearance than their respective hydrophilic conjugates, and the absolute bioavailability was also lower likely due to the longer residence times in the skin. Their ease and efficiency make double-click helix stabilization chemistries a useful tool for increasing the bioavailability of peptide therapeutics, many of which suffer from rapid in vivo protease degradation. Helix stabilization using linkers of varying lipophilicity can further control sc absorption and clearance rates to customize plasma pharmacokinetics.
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Affiliation(s)
- Liang Zhang
- Department of Chemical Engineering, and ‡Department of Biomedical Engineering University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Tejas Navaratna
- Department of Chemical Engineering, and ‡Department of Biomedical Engineering University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Greg M Thurber
- Department of Chemical Engineering, and ‡Department of Biomedical Engineering University of Michigan , Ann Arbor, Michigan 48109, United States
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31
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Aronica P, Verma C, Popovic B, Leatherbarrow R, Gould IR. The Parasol Protocol for computational mutagenesis. Protein Eng Des Sel 2016; 29:253-61. [DOI: 10.1093/protein/gzw009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 03/15/2016] [Indexed: 11/12/2022] Open
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32
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Wang ZA, Ding XZ, Tian CL, Zheng JS. Protein/peptide secondary structural mimics: design, characterization, and modulation of protein–protein interactions. RSC Adv 2016. [DOI: 10.1039/c6ra13976k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This review discusses general aspects of novel artificial peptide secondary structure mimics for modulation of PPIs, their therapeutic applications and future prospects.
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Affiliation(s)
- Zhipeng A. Wang
- School of Life Sciences
- University of Science and Technology of China
- Hefei 230026
- China
- Department of Chemistry
| | - Xiaozhe Z. Ding
- School of Life Sciences
- Tsinghua University
- Beijing 100084
- China
- Department of Bioengineering
| | - Chang-Lin Tian
- School of Life Sciences
- University of Science and Technology of China
- Hefei 230026
- China
| | - Ji-Shen Zheng
- School of Life Sciences
- University of Science and Technology of China
- Hefei 230026
- China
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33
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Lau YH, Wu Y, Rossmann M, Tan BX, de Andrade P, Tan YS, Verma C, McKenzie GJ, Venkitaraman AR, Hyvönen M, Spring DR. Double Strain-Promoted Macrocyclization for the Rapid Selection of Cell-Active Stapled Peptides. Angew Chem Int Ed Engl 2015; 54:15410-3. [PMID: 26768531 PMCID: PMC5868729 DOI: 10.1002/anie.201508416] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Indexed: 12/11/2022]
Abstract
Peptide stapling is a method for designing macrocyclic alpha-helical inhibitors of protein-protein interactions. However, obtaining a cell-active inhibitor can require significant optimization. We report a novel stapling technique based on a double strain-promoted azide-alkyne reaction, and exploit its biocompatibility to accelerate the discovery of cell-active stapled peptides. As a proof of concept, MDM2-binding peptides were stapled in parallel, directly in cell culture medium in 96-well plates, and simultaneously evaluated in a p53 reporter assay. This in situ stapling/screening process gave an optimal candidate that showed improved proteolytic stability and nanomolar binding to MDM2 in subsequent biophysical assays. α-Helicity was confirmed by a crystal structure of the MDM2-peptide complex. This work introduces in situ stapling as a versatile biocompatible technique with many other potential high-throughput biological applications.
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Affiliation(s)
- Yu Heng Lau
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW (UK)
| | - Yuteng Wu
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW (UK)
| | - Maxim Rossmann
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA (UK)
| | - Ban Xiong Tan
- p53Lab, A*STAR, 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648 (Singapore)
| | - Peterson de Andrade
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW (UK)
| | - Yaw Sing Tan
- Bioinformatics Institute, A*STAR, 30 Biopolis St, #07-01 Matrix, Singapore 138671 (Singapore)
| | - Chandra Verma
- Bioinformatics Institute, A*STAR, 30 Biopolis St, #07-01 Matrix, Singapore 138671 (Singapore)
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
- School of Biological Sciences, Nanyang Technological University, 50 Nanyang Drive, Singapore 637551
| | | | | | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA (UK)
| | - David R Spring
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW (UK).
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34
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Nevola L, Giralt E. Modulating protein-protein interactions: the potential of peptides. Chem Commun (Camb) 2015; 51:3302-15. [PMID: 25578807 DOI: 10.1039/c4cc08565e] [Citation(s) in RCA: 208] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Protein-protein interactions (PPIs) have emerged as important and challenging targets in chemical biology and medicinal chemistry. The main difficulty encountered in the discovery of small molecule modulators derives from the large contact surfaces involved in PPIs when compared with those that participate in protein-small molecule interactions. Because of their intrinsic features, peptides can explore larger surfaces and therefore represent a useful alternative to modulate PPIs. The use of peptides as therapeutics has been held back by their instability in vivo and poor cell internalization. However, more than 200 peptide drugs and homologous compounds (proteins or antibodies) containing peptide bonds are (or have been) on the market, and many alternatives are now available to tackle these limitations. This review will focus on the latest progress in the field, spanning from "lead" identification methods to binding evaluation techniques, through an update of the most successful examples described in the literature.
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Affiliation(s)
- Laura Nevola
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, 08028 Barcelona, Spain.
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35
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Lau YH, Wu Y, Rossmann M, Tan BX, de Andrade P, Tan YS, Verma C, McKenzie GJ, Venkitaraman AR, Hyvönen M, Spring DR. Double Strain-Promoted Macrocyclization for the Rapid Selection of Cell-Active Stapled Peptides. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508416] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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36
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Micewicz ED, Sharma S, Waring AJ, Luong HT, McBride WH, Ruchala P. Bridged Analogues for p53-Dependent Cancer Therapy Obtained by S-Alkylation. Int J Pept Res Ther 2015; 22:67-81. [PMID: 26957954 DOI: 10.1007/s10989-015-9487-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A small library of anticancer, cell-permeating, stapled peptides based on potent dual-specific antagonist of p53-MDM2/MDMX interactions, PMI-N8A, was synthesized, characterized and screened for anticancer activity against human colorectal cancer cell line, HCT-116. Employed synthetic modifications included: S-alkylation-based stapling, point mutations increasing hydrophobicity in key residues as well as improvement of cell-permeability by introduction of polycationic sequence(s) that were woven into the sequence of parental peptide. Selected analogue, ArB14Co, was also tested in vivo and exhibited potent anticancer bioactivity at the low dose (3.0 mg/kg). Collectively, our findings suggest that application of stapling in combination with rational design of polycationic short analogues may be a suitable approach in the development of physiologically active p53-MDM2/MDMX peptide inhibitors.
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Affiliation(s)
- Ewa D Micewicz
- Department of Radiation Oncology, University of California at Los Angeles, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
| | - Shantanu Sharma
- Materials and Process Simulation Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Alan J Waring
- Department of Medicine, Los Angeles Biomedical Research Institute at Harbor-UCLA, Medical Center, 1000 West Carson Street, Torrance, CA 90502, USA
| | - Hai T Luong
- Department of Analytical Operations, Gilead Sciences, Inc., 4049 Avenida de la Plata, Oceanside CA, 92056, USA
| | - William H McBride
- Department of Radiation Oncology, University of California at Los Angeles, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
| | - Piotr Ruchala
- Department of Psychiatry and Biobehavioral Sciences, University of California at Los Angeles, 760 Westwood Plaza, Los Angeles, CA 90024, USA
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37
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Pelay-Gimeno M, Glas A, Koch O, Grossmann TN. Structure-Based Design of Inhibitors of Protein-Protein Interactions: Mimicking Peptide Binding Epitopes. Angew Chem Int Ed Engl 2015; 54:8896-927. [PMID: 26119925 PMCID: PMC4557054 DOI: 10.1002/anie.201412070] [Citation(s) in RCA: 537] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions (PPIs) are involved at all levels of cellular organization, thus making the development of PPI inhibitors extremely valuable. The identification of selective inhibitors is challenging because of the shallow and extended nature of PPI interfaces. Inhibitors can be obtained by mimicking peptide binding epitopes in their bioactive conformation. For this purpose, several strategies have been evolved to enable a projection of side chain functionalities in analogy to peptide secondary structures, thereby yielding molecules that are generally referred to as peptidomimetics. Herein, we introduce a new classification of peptidomimetics (classes A-D) that enables a clear assignment of available approaches. Based on this classification, the Review summarizes strategies that have been applied for the structure-based design of PPI inhibitors through stabilizing or mimicking turns, β-sheets, and helices.
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Affiliation(s)
- Marta Pelay-Gimeno
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
| | - Adrian Glas
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
| | - Oliver Koch
- TU Dortmund University, Department of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6, 44227 Dortmund (Germany)
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
- TU Dortmund University, Department of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6, 44227 Dortmund (Germany)
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38
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Tan BX, Brown CJ, Ferrer FJ, Yuen TY, Quah ST, Chan BH, Jansson AE, Teo HL, Nordlund P, Lane DP. Assessing the Efficacy of Mdm2/Mdm4-Inhibiting Stapled Peptides Using Cellular Thermal Shift Assays. Sci Rep 2015; 5:12116. [PMID: 26159518 PMCID: PMC4498326 DOI: 10.1038/srep12116] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 06/19/2015] [Indexed: 12/26/2022] Open
Abstract
Previous publications on stapled peptide inhibitors against Mdm2/Mdm4-p53 interactions have established that this new class of drugs have the potential to be easily optimised to attain high binding affinity and specificity, but the mechanisms controlling their cellular uptake and target engagement remain elusive and controversial. To aid in understanding the rules of peptide and staple design, and to enable rapid optimisation, we employed the newly-developed cellular thermal shift assay (CETSA). CETSA was able to validate stapled peptide binding to Mdm2 and Mdm4, and the method was also used to determine the extent of cellular uptake, cellular availability, and intracellular binding of the endogenous target proteins in its native environment. Our data suggest that while the stapled peptides engage their targets intracellularly, more work is needed to improve their cellular entry and target engagement efficiency in vivo. CETSA now provides a valuable tool to optimize such in vivo properties of stapled peptides.
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Affiliation(s)
| | | | | | - Tsz Ying Yuen
- Institute of Chemical and Engineering Sciences, A*STAR
| | | | | | - Anna E Jansson
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Hsiang Ling Teo
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Pär Nordlund
- School of Biological Sciences, Nanyang Technological University, Singapore
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Marine JE, Liang X, Song S, Rudick JG. Azide-rich peptides via an on-resin diazotransfer reaction. Biopolymers 2015; 104:419-26. [PMID: 25753459 PMCID: PMC4516611 DOI: 10.1002/bip.22634] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 02/23/2015] [Accepted: 02/24/2015] [Indexed: 12/19/2022]
Abstract
Azide-containing amino acids are valuable building blocks in peptide chemistry, because azides are robust partners in several bioorthogonal reactions. Replacing polar amino acids with apolar, azide-containing amino acids in solid-phase peptide synthesis can be tricky, especially when multiple azide residues are to be introduced in the amino acid sequence. We present a strategy for effectively incorporating multiple azide-containing residues site-specifically.
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Affiliation(s)
- Jeannette E. Marine
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, United States
| | - Xiaoli Liang
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, United States
| | - Shuang Song
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, United States
| | - Jonathan G. Rudick
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, United States
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40
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Pelay-Gimeno M, Glas A, Koch O, Grossmann TN. Strukturbasierte Entwicklung von Protein-Protein-Interaktionsinhibitoren: Stabilisierung und Nachahmung von Peptidliganden. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201412070] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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41
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He Y, Chen D, Zheng W. An enhanced functional interrogation/manipulation of intracellular signaling pathways with the peptide ‘stapling’ technology. Oncogene 2015; 34:5685-98. [DOI: 10.1038/onc.2015.37] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Revised: 01/16/2015] [Accepted: 01/16/2015] [Indexed: 12/13/2022]
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42
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Lau YH, Wu Y, de Andrade P, Galloway WRJD, Spring DR. A two-component 'double-click' approach to peptide stapling. Nat Protoc 2015; 10:585-94. [PMID: 25763835 DOI: 10.1038/nprot.2015.033] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Peptide cyclization is a useful strategy for the stabilization of short flexible peptides into well-defined bioactive conformations, thereby enhancing their ability to interact with proteins and other important biomolecules. We present an optimized procedure for the stabilization of linear diazido peptides in an α-helical conformation upon reaction with dialkynyl linkers under Cu(I) catalysis. As this procedure generates side chain-cyclized peptides bearing a bis-triazole linkage, it is referred to as 'double-click' stapling. Double-click stapling can enhance the binding affinity, proteolytic stability and cellular activity of a peptide inhibitor. A distinguishing feature of double-click stapling is the efficiency with which peptides bearing different staple linkages can be synthesized, thus allowing for modular control over peptide bioactivity. This protocol describes the double-click reaction between a 1,3-dialkynylbenzene linker and peptides that contain azidoornithine. Subsequent peptide purification and confirmation steps are also described. The entire double-click stapling protocol can be completed in ∼48 h, including two overnight lyophilization steps.
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Affiliation(s)
- Yu Heng Lau
- University Chemical Laboratory, University of Cambridge, Cambridge, UK
| | - Yuteng Wu
- University Chemical Laboratory, University of Cambridge, Cambridge, UK
| | | | | | - David R Spring
- University Chemical Laboratory, University of Cambridge, Cambridge, UK
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43
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Lau YH, de Andrade P, McKenzie GJ, Venkitaraman AR, Spring DR. Linear aliphatic dialkynes as alternative linkers for double-click stapling of p53-derived peptides. Chembiochem 2014; 15:2680-3. [PMID: 25354189 DOI: 10.1002/cbic.201402374] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Indexed: 02/02/2023]
Abstract
We investigated linear aliphatic dialkynes as a new structural class of i,i+7 linkers for the double-click stapling of p53-based peptides. The optimal combination of azido amino acids and dialkynyl linker length for MDM2 binding was determined. In a direct comparison between aliphatic and aromatic staple scaffolds, the aliphatic staples resulted in superior binding to MDM2 in vitro and superior p53-activating capability in cells when using a diazidopeptide derived from phage display. This work demonstrates that the nature of the staple scaffold is an important factor that can affect peptide bioactivity in cells.
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Affiliation(s)
- Yu Heng Lau
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (UK)
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44
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Lau YH, de Andrade P, Wu Y, Spring DR. Peptide stapling techniques based on different macrocyclisation chemistries. Chem Soc Rev 2014; 44:91-102. [PMID: 25199043 DOI: 10.1039/c4cs00246f] [Citation(s) in RCA: 440] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Peptide stapling is a strategy for constraining short peptides typically in an alpha-helical conformation. Stapling is carried out by covalently linking the side-chains of two amino acids, thereby forming a peptide macrocycle. There is an expanding repertoire of stapling techniques based on different macrocyclisation chemistries. In this tutorial review, we categorise and analyse key examples of peptide stapling in terms of their synthesis and applicability to biological systems.
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Affiliation(s)
- Yu Heng Lau
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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