1
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Li M, Li J, Lu X, Schroder R, Chandramohan A, Wuelfing WP, Templeton AC, Xu W, Gindy M, Kesisoglou F, Ling J, Sawyer T, Verma CS, Partridge AW, Su Y. Molecular Mechanism of P53 Peptide Permeation through Lipid Membranes from Solid-State NMR Spectroscopy and Molecular Dynamics Simulations. J Am Chem Soc 2024; 146:23075-23091. [PMID: 39110018 DOI: 10.1021/jacs.4c04230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2024]
Abstract
Macrocyclic peptides show promise in targeting high-value therapeutically relevant binding sites due to their high affinity and specificity. However, their clinical application is often hindered by low membrane permeability, which limits their effectiveness against intracellular targets. Previous studies focused on peptide conformations in various solvents, leaving a gap in understanding their interactions with and translocation through lipid bilayers. Addressing this, our study explores the membrane interactions of stapled peptides, a subclass of macrocyclic peptides, using solid-state nuclear magnetic resonance (ssNMR) spectroscopy and molecular dynamics (MD) simulations. We conducted ssNMR measurements on ATSP-7041M, a prototypical stapled peptide, to understand its interaction with lipid membranes, leading to an MD-informed model for peptide membrane permeation. Our findings reveal that ATSP-7041M adopts a stable α-helical structure upon membrane binding, facilitated by a cation-π interaction between its phenylalanine side chain and the lipid headgroup. This interaction makes the membrane-bound state energetically favorable, facilitating membrane affinity and insertion. The bound peptide displayed asymmetric insertion depths, with the C-terminus penetrating deeper (approximately 9 Å) than the N-terminus (approximately 4.3 Å) relative to the lipid headgroups. Contrary to expectations, peptide dynamics was not hindered by membrane binding and exhibited rapid motions similar to cell-penetrating peptides. These dynamic interactions and peptide-lipid affinity appear to be crucial for membrane permeation. MD simulations indicated a thermodynamically stable transmembrane conformation of ATSP-7041M, reducing the energy barrier for translocation. Our study offers an in silico view of ATSP-7041M's translocation from the extracellular to the intracellular region, highlighting the significance of peptide-lipid interactions and dynamics in enabling peptide transit through membranes.
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Affiliation(s)
- Mingyue Li
- Pharmaceutical Sciences and Clinical Supply, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jianguo Li
- Bioinformatics Institute at A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
- Singapore Eye Research Institute, 20 College Road Discovery Tower, Singapore 169856, Singapore
| | - Xingyu Lu
- Pharmaceutical Sciences and Clinical Supply, Merck & Co., Inc., Rahway, New Jersey 07065, United States
- Instrumentation and Service Center for Molecular Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Ryan Schroder
- Pharmaceutical Sciences and Clinical Supply, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | - W Peter Wuelfing
- Pharmaceutical Sciences and Clinical Supply, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Allen C Templeton
- Pharmaceutical Sciences and Clinical Supply, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Wei Xu
- Pharmaceutical Sciences and Clinical Supply, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Marian Gindy
- Small Molecule Science and Technology, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Filippos Kesisoglou
- Pharmaceutical Sciences and Clinical Supply, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jing Ling
- Pharmaceutical Sciences and Clinical Supply, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Tomi Sawyer
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Chandra S Verma
- Bioinformatics Institute at A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
- School of Biological Sciences, Nanyang Technological University, 50 Nanyang Drive, Singapore 637551, Singapore
| | | | - Yongchao Su
- Pharmaceutical Sciences and Clinical Supply, Merck & Co., Inc., Rahway, New Jersey 07065, United States
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2
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Qin W, Wei X, Yang D, Luo Q, Huang M, Xing S, Wei W, Liang L, Huang J, Zhou Z, Lu F. Ras-Targeting Stabilized Peptide Increases Radiation Sensitivity of Cancer Cells. Bioconjug Chem 2024; 35:737-743. [PMID: 38738511 DOI: 10.1021/acs.bioconjchem.4c00155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
Radiation therapy is one of the most common treatments for cancer. However, enhancing tumors' radiation sensitivity and overcoming tolerance remain a challenge. Previous studies have shown that the Ras signaling pathway directly influences tumor radiation sensitivity. Herein, we designed a series of Ras-targeting stabilized peptides, with satisfactory binding affinity (KD = 0.13 μM with HRas) and good cellular uptake. Peptide H5 inhibited downstream phosphorylation of ERK and increased radio-sensitivity in HeLa cells, resulting in significantly reduced clonogenic survival. The stabilized peptides, designed with an N-terminal nucleation strategy, acted as potential radio-sensitizers and broadened the applications of this kind of molecule. This is the first report of using stabilized peptides as radio-sensitizers, broadening the applications of this kind of molecule.
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Affiliation(s)
- Weirong Qin
- Pharmaceutical College, Guangxi Medical University, Nanning 530021, Guangxi, P. R. China
- Guangxi Key Laboratory of Bioactive Molecules Research and Evaluation, Guangxi Medical University, Nanning 530021, Guangxi, P. R. China
| | - Xiangzan Wei
- Education Department of Guangxi Zhuang Autonomous Region, Key Laboratory of Biological Molecular Medicine Research (Guangxi Medical University), Nanning 530021, Guangxi, P. R. China
| | - Dan Yang
- Department of Science & Technology of Shandong Province, Jinan 250101, Shandong, P. R. China
| | - Qinhong Luo
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, Guangdong, P. R. China
| | - Mingyu Huang
- Pharmaceutical College, Guangxi Medical University, Nanning 530021, Guangxi, P. R. China
| | - Shangping Xing
- Pharmaceutical College, Guangxi Medical University, Nanning 530021, Guangxi, P. R. China
| | - Wei Wei
- Pharmaceutical College, Guangxi Medical University, Nanning 530021, Guangxi, P. R. China
| | - Lin Liang
- Pharmaceutical College, Guangxi Medical University, Nanning 530021, Guangxi, P. R. China
| | - Jin Huang
- Pharmaceutical College, Guangxi Medical University, Nanning 530021, Guangxi, P. R. China
| | - Ziyuan Zhou
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, Guangdong, P. R. China
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen 518116, Guangdong, P. R. China
| | - Fei Lu
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, Guangdong, P. R. China
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3
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Chen FJ, Lin W, Chen FE. Non-symmetric stapling of native peptides. Nat Rev Chem 2024; 8:304-318. [PMID: 38575678 DOI: 10.1038/s41570-024-00591-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2024] [Indexed: 04/06/2024]
Abstract
Stapling has emerged as a powerful technique in peptide chemistry. It enables precise control over peptide conformation leading to enhanced properties such as improved stability and enhanced binding affinity. Although symmetric stapling methods have been extensively explored, the field of non-symmetric stapling of native peptides has received less attention, largely as a result of the formidable challenges it poses - in particular the complexities involved in achieving the high chemo-selectivity and site-selectivity required to simultaneously modify distinct proteinogenic residues. Over the past 5 years, there have been significant breakthroughs in addressing these challenges. In this Review, we describe the latest strategies for non-symmetric stapling of native peptides, elucidating the protocols, reaction mechanisms and underlying design principles. We also discuss current challenges and opportunities this field offers for future applications, such as ligand discovery and peptide-based therapeutics.
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Affiliation(s)
- Fa-Jie Chen
- College of Chemistry, Fuzhou University, Fuzhou, P. R. China.
| | - Wanzhen Lin
- College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, P. R. China
| | - Fen-Er Chen
- College of Chemistry, Fuzhou University, Fuzhou, P. R. China.
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai, P. R. China.
- Shanghai Engineering Research Center of Industrial Asymmetric Catalysis of Chiral Drugs, Fudan University, Shanghai, P. R. China.
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4
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Ma J, Yan L, Yang J, He Y, Wu L. Effect of Modification Strategies on the Biological Activity of Peptides/Proteins. Chembiochem 2024; 25:e202300481. [PMID: 38009768 DOI: 10.1002/cbic.202300481] [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: 06/28/2023] [Revised: 11/20/2023] [Accepted: 11/26/2023] [Indexed: 11/29/2023]
Abstract
Covalent attachment of biologically active peptides/proteins with functional moieties is an effective strategy to control their biodistribution, pharmacokinetics, enzymatic digestion, and toxicity. This review focuses on the characteristics of different modification strategies and their effects on the biological activity of peptides/proteins and illustrates their relevant applications and potential.
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Affiliation(s)
- Jian Ma
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liang Yan
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingkui Yang
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yujian He
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Li Wu
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
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5
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Dengler S, Howard RT, Morozov V, Tsiamantas C, Huang WE, Liu Z, Dobrzanski C, Pophristic V, Brameyer S, Douat C, Suga H, Huc I. Display Selection of a Hybrid Foldamer-Peptide Macrocycle. Angew Chem Int Ed Engl 2023; 62:e202308408. [PMID: 37707879 DOI: 10.1002/anie.202308408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/11/2023] [Accepted: 09/14/2023] [Indexed: 09/15/2023]
Abstract
Expanding the chemical diversity of peptide macrocycle libraries for display selection is desirable to improve their potential to bind biomolecular targets. We now have implemented a considerable expansion through a large aromatic helical foldamer inclusion. A foldamer was first identified that undergoes flexizyme-mediated tRNA acylation and that is capable of initiating ribosomal translation with yields sufficiently high to perform an mRNA display selection of macrocyclic foldamer-peptide hybrids. A hybrid macrocyclic nanomolar binder to the C-lobe of the E6AP HECT domain was selected that showed a highly converged peptide sequence. A crystal structure and molecular dynamics simulations revealed that both the peptide and foldamer are helical in an intriguing reciprocal stapling fashion. The strong residue convergence could be rationalized based on their involvement in specific interactions with the target protein. The foldamer stabilizes the peptide helix through stapling and through contacts with key residues. These results altogether represent a significant extension of the chemical space amenable to display selection and highlight possible benefits of inserting an aromatic foldamer into a peptide macrocycle for the purpose of protein recognition.
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Affiliation(s)
- Sebastian Dengler
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377, München, Germany
| | - Ryan T Howard
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377, München, Germany
| | - Vasily Morozov
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377, München, Germany
| | - Christos Tsiamantas
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, 113-0033, Tokyo, Japan
| | - Wei-En Huang
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, 113-0033, Tokyo, Japan
| | - Zhiwei Liu
- Department of Chemistry & Biochemistry, Rowan University, 201 Mullica Hill Road, 08028, Glassboro, New Jersey, USA
| | - Christopher Dobrzanski
- Department of Chemistry & Biochemistry, Rowan University, 201 Mullica Hill Road, 08028, Glassboro, New Jersey, USA
| | - Vojislava Pophristic
- Department of Chemistry & Biochemistry, Rowan University, 201 Mullica Hill Road, 08028, Glassboro, New Jersey, USA
| | - Sophie Brameyer
- Biozentrum, Microbiology, Ludwig-Maximilians-Universität, Großhaderner Str. 2-4, 82152, Martinsried, Germany
| | - Céline Douat
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377, München, Germany
| | - Hiroaki Suga
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, 113-0033, Tokyo, Japan
| | - Ivan Huc
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377, München, Germany
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6
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Chen B, Liu C, Cong W, Gao F, Zou Y, Su L, Liu L, Hillisch A, Lehmann L, Bierer D, Li X, Hu HG. Cyclobutane-bearing restricted anchoring residues enabled geometry-specific hydrocarbon peptide stapling. Chem Sci 2023; 14:11499-11506. [PMID: 37886087 PMCID: PMC10599482 DOI: 10.1039/d3sc04279k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
Stapled peptides are regarded as the promising next-generation therapeutics because of their improved secondary structure, membrane permeability and metabolic stability as compared with the prototype linear peptides. Usually, stapled peptides are obtained by a hydrocarbon stapling technique, anchoring from paired olefin-terminated unnatural amino acids and the consequent ring-closing metathesis (RCM). To investigate the adaptability of the rigid cyclobutane structure in RCM and expand the chemical diversity of hydrocarbon peptide stapling, we herein described the rational design and efficient synthesis of cyclobutane-based conformationally constrained amino acids, termed (E)-1-amino-3-(but-3-en-1-yl)cyclobutane-1-carboxylic acid (E7) and (Z)-1-amino-3-(but-3-en-1-yl)cyclobutane-1-carboxylic acid (Z7). All four combinations including E7-E7, E7-Z7, Z7-Z7 and Z7-E7 were proven to be applicable in RCM-mediated peptide stapling to afford the corresponding geometry-specific stapled peptides. With the aid of the combined quantum and molecular mechanics, the E7-E7 combination was proven to be optimal in both the RCM reaction and helical stabilization. With the spike protein of SARS-CoV-2 as the target, a series of cyclobutane-bearing stapled peptides were obtained. Among them, E7-E7 geometry-specific stapled peptides indeed exhibit higher α-helicity and thus stronger biological activity than canonical hydrocarbon stapled peptides. We believe that this methodology possesses great potential to expand the scope of the existing peptide stapling strategy. These cyclobutane-bearing restricted anchoring residues served as effective supplements for the existing olefin-terminated unnatural amino acids and the resultant geometry-specific hydrocarbon peptide stapling provided more potential for peptide therapeutics.
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Affiliation(s)
- Baobao Chen
- School of Medicine or Institute of Translational Medicine, Shanghai University Shanghai 200444 China
| | - Chao Liu
- School of Medicine or Institute of Translational Medicine, Shanghai University Shanghai 200444 China
| | - Wei Cong
- School of Medicine or Institute of Translational Medicine, Shanghai University Shanghai 200444 China
| | - Fei Gao
- School of Medicine or Institute of Translational Medicine, Shanghai University Shanghai 200444 China
| | - Yan Zou
- School of Pharmacy, Second Military Medical University Shanghai 200433 China
| | - Li Su
- School of Medicine or Institute of Translational Medicine, Shanghai University Shanghai 200444 China
| | - Lei Liu
- Department of Chemistry, Tsinghua University Beijing 100084 China
| | - Alexander Hillisch
- Bayer AG, Pharma Division, Drug Discovery Sciences Aprather Weg 18A Wuppertal 42096 Germany
- UCB BioSciences GmbH Alfred-Nobel-Straße 10 40789 Monheim am Rhein Germany
| | - Lutz Lehmann
- Bayer AG, Pharma Division, Drug Discovery Sciences Aprather Weg 18A Wuppertal 42096 Germany
| | - Donald Bierer
- Bayer AG, Pharma Division, Drug Discovery Sciences Aprather Weg 18A Wuppertal 42096 Germany
| | - Xiang Li
- School of Pharmacy, Second Military Medical University Shanghai 200433 China
| | - Hong-Gang Hu
- School of Medicine or Institute of Translational Medicine, Shanghai University Shanghai 200444 China
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7
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Kwok JG, Yuan Z, Arora PS. An Encodable Scaffold for Sequence-Specific Recognition of Duplex RNA. Angew Chem Int Ed Engl 2023; 62:e202308650. [PMID: 37548640 PMCID: PMC10528708 DOI: 10.1002/anie.202308650] [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: 06/19/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/08/2023]
Abstract
RNA, unlike DNA, folds into a multitude of secondary and tertiary structures. This structural diversity has impeded the development of ligands that can sequence-specifically target this biomolecule. We sought to develop ligands for double-stranded RNA (dsRNA) segments, which are ubiquitous in RNA tertiary structure. The major groove of double-stranded DNA is sequence-specifically recognized by a range of dimeric helical transcription factors, including the basic leucine zippers (bZIP) and basic helix-loop-helix (bHLH) proteins; however, such simple structural motifs are not prevalent in RNA-binding proteins. We interrogated the high-resolution structures of DNA and RNA to identify requirements for a helix fork motif to occupy dsRNA major grooves akin to dsDNA. Our analysis suggested that the rigidity and angle of approach of dimeric helices in bZIP/bHLH motifs are not ideal for the binding of dsRNA major grooves. This investigation revealed that the replacement of the leucine zipper motifs in bHLH proteins with synthetic crosslinkers would allow recognition of dsRNA. We show that a model bHLH DNA-binding motif does not bind dsRNA but can be reengineered as an RNA ligand. Based on this hypothesis, we rationally designed a miniature synthetic crosslinked helix fork (CHF) as a generalizable proteomimetic scaffold for targeting dsRNA. We evaluated several CHF constructs against a set of RNA and DNA hairpins to probe the specificity of the designed construct. Our studies reveal a new class of proteomimetics as an encodable platform for sequence-specific recognition of dsRNA.
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Affiliation(s)
- Jonathan G. Kwok
- Department of Chemistry, New York University, 29 Washington Place, New York, NY10003
| | - Zhi Yuan
- Department of Chemistry, New York University, 29 Washington Place, New York, NY10003
| | - Paramjit S. Arora
- Department of Chemistry, New York University, 29 Washington Place, New York, NY10003
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8
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Emonts J, Buyel J. An overview of descriptors to capture protein properties - Tools and perspectives in the context of QSAR modeling. Comput Struct Biotechnol J 2023; 21:3234-3247. [PMID: 38213891 PMCID: PMC10781719 DOI: 10.1016/j.csbj.2023.05.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/23/2023] [Accepted: 05/23/2023] [Indexed: 01/13/2024] Open
Abstract
Proteins are important ingredients in food and feed, they are the active components of many pharmaceutical products, and they are necessary, in the form of enzymes, for the success of many technical processes. However, production can be challenging, especially when using heterologous host cells such as bacteria to express and assemble recombinant mammalian proteins. The manufacturability of proteins can be hindered by low solubility, a tendency to aggregate, or inefficient purification. Tools such as in silico protein engineering and models that predict separation criteria can overcome these issues but usually require the complex shape and surface properties of proteins to be represented by a small number of quantitative numeric values known as descriptors, as similarly used to capture the features of small molecules. Here, we review the current status of protein descriptors, especially for application in quantitative structure activity relationship (QSAR) models. First, we describe the complexity of proteins and the properties that descriptors must accommodate. Then we introduce descriptors of shape and surface properties that quantify the global and local features of proteins. Finally, we highlight the current limitations of protein descriptors and propose strategies for the derivation of novel protein descriptors that are more informative.
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Affiliation(s)
- J. Emonts
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Germany
| | - J.F. Buyel
- University of Natural Resources and Life Sciences, Vienna (BOKU), Department of Biotechnology (DBT), Institute of Bioprocess Science and Engineering (IBSE), Muthgasse 18, 1190 Vienna, Austria
- Institute for Molecular Biotechnology, Worringerweg 1, RWTH Aachen University, 52074 Aachen, Germany
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9
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The Role of Transmembrane Proteins in Plant Growth, Development, and Stress Responses. Int J Mol Sci 2022; 23:ijms232113627. [PMID: 36362412 PMCID: PMC9655316 DOI: 10.3390/ijms232113627] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
Transmembrane proteins participate in various physiological activities in plants, including signal transduction, substance transport, and energy conversion. Although more than 20% of gene products are predicted to be transmembrane proteins in the genome era, due to the complexity of transmembrane domains they are difficult to reliably identify in the predicted protein, and they may have different overall three-dimensional structures. Therefore, it is challenging to study their biological function. In this review, we describe the typical structures of transmembrane proteins and their roles in plant growth, development, and stress responses. We propose a model illustrating the roles of transmembrane proteins during plant growth and response to various stresses, which will provide important references for crop breeding.
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10
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Cobos C, Bansal PS, Wilson DT, Jones L, Zhao G, Field MA, Eichenberger RM, Pickering DA, Ryan RYM, Ratnatunga CN, Miles JJ, Ruscher R, Giacomin PR, Navarro S, Loukas A, Daly NL. Peptides derived from hookworm anti-inflammatory proteins suppress inducible colitis in mice and inflammatory cytokine production by human cells. Front Med (Lausanne) 2022; 9:934852. [PMID: 36186812 PMCID: PMC9524151 DOI: 10.3389/fmed.2022.934852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 08/25/2022] [Indexed: 11/21/2022] Open
Abstract
A decline in the prevalence of parasites such as hookworms appears to be correlated with the rise in non-communicable inflammatory conditions in people from high- and middle-income countries. This correlation has led to studies that have identified proteins produced by hookworms that can suppress inflammatory bowel disease (IBD) and asthma in animal models. Hookworms secrete a family of abundant netrin-domain containing proteins referred to as AIPs (Anti-Inflammatory Proteins), but there is no information on the structure-function relationships. Here we have applied a downsizing approach to the hookworm AIPs to derive peptides of 20 residues or less, some of which display anti-inflammatory effects when co-cultured with human peripheral blood mononuclear cells and oral therapeutic activity in a chemically induced mouse model of acute colitis. Our results indicate that a conserved helical region is responsible, at least in part, for the anti-inflammatory effects. This helical region has potential in the design of improved leads for treating IBD and possibly other inflammatory conditions.
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Affiliation(s)
- Claudia Cobos
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Paramjit S. Bansal
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - David T. Wilson
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Linda Jones
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Guangzu Zhao
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Matthew A. Field
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Ramon M. Eichenberger
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Darren A. Pickering
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Rachael Y. M. Ryan
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Champa N. Ratnatunga
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - John J. Miles
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Roland Ruscher
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Paul R. Giacomin
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Severine Navarro
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Faculty of Health, Woolworths Centre for Childhood Nutrition Research, Queensland University of Technology, South Brisbane, QLD, Australia
| | - Alex Loukas
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- *Correspondence: Alex Loukas,
| | - Norelle L. Daly
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Norelle L. Daly,
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11
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Learte-Aymamí S, Martin-Malpartida P, Roldán-Martín L, Sciortino G, Couceiro JR, Maréchal JD, Macias MJ, Mascareñas JL, Vázquez ME. Controlling oncogenic KRAS signaling pathways with a Palladium-responsive peptide. Commun Chem 2022; 5:75. [PMID: 36697641 PMCID: PMC9814687 DOI: 10.1038/s42004-022-00691-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/10/2022] [Indexed: 01/28/2023] Open
Abstract
RAS oncoproteins are molecular switches associated with critical signaling pathways that regulate cell proliferation and differentiation. Mutations in the RAS family, mainly in the KRAS isoform, are responsible for some of the deadliest cancers, which has made this protein a major target in biomedical research. Here we demonstrate that a designed bis-histidine peptide derived from the αH helix of the cofactor SOS1 binds to KRAS with high affinity upon coordination to Pd(II). NMR spectroscopy and MD studies demonstrate that Pd(II) has a nucleating effect that facilitates the access to the bioactive α-helical conformation. The binding can be suppressed by an external metal chelator and recovered again by the addition of more Pd(II), making this system the first switchable KRAS binder, and demonstrates that folding-upon-binding mechanisms can operate in metal-nucleated peptides. In vitro experiments show that the metallopeptide can efficiently internalize into living cells and inhibit the MAPK kinase cascade.
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Affiliation(s)
- Soraya Learte-Aymamí
- grid.11794.3a0000000109410645Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, 15705 Spain
| | - Pau Martin-Malpartida
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, 08028 Spain
| | - Lorena Roldán-Martín
- grid.7080.f0000 0001 2296 0625Insilichem, Departament de Química, Universitat Autònoma de Barcelona, Cerdanyola, 08193 Spain
| | - Giuseppe Sciortino
- grid.7080.f0000 0001 2296 0625Insilichem, Departament de Química, Universitat Autònoma de Barcelona, Cerdanyola, 08193 Spain ,grid.473715.30000 0004 6475 7299Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Tarragona, 43007 Spain
| | - José R. Couceiro
- grid.11794.3a0000000109410645Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, 15705 Spain
| | - Jean-Didier Maréchal
- grid.7080.f0000 0001 2296 0625Insilichem, Departament de Química, Universitat Autònoma de Barcelona, Cerdanyola, 08193 Spain
| | - Maria J. Macias
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, 08028 Spain ,grid.425902.80000 0000 9601 989XInstitució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona, 08010 Spain
| | - José L. Mascareñas
- grid.11794.3a0000000109410645Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, 15705 Spain
| | - M. Eugenio Vázquez
- grid.11794.3a0000000109410645Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, 15705 Spain
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12
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Shah M, Ung Moon S, Hyun Kim J, Thanh Thao T, Goo Woo H. SARS-CoV-2 pan-variant inhibitory peptides deter S1-ACE2 interaction and neutralize delta and omicron pseudoviruses. Comput Struct Biotechnol J 2022; 20:2042-2056. [PMID: 35495107 PMCID: PMC9040525 DOI: 10.1016/j.csbj.2022.04.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 04/20/2022] [Accepted: 04/20/2022] [Indexed: 12/12/2022] Open
Abstract
Approved neutralizing antibodies that target the prototype Spike are losing their potency against the emerging variants of concern (VOCs) of SARS-CoV-2, particularly Omicron. Although SARS-CoV-2 is continuously adapting the host environment, emerging variants recognize the same ACE2 receptor for cell entry. Protein and peptide decoys derived from ACE2 or Spike proteins may hold the pan-variant inhibitory potential. Here, we deployed interactive structure- and pharmacophore-based approaches to design short and stable peptides -Coronavirus Spike Neutralizing Peptides (CSNPs)- capable of neutralizing all SARS-CoV-2 VOCs. After in silico structural stability investigation and free energies perturbation of the isolated and target-bound peptides, nine candidate peptides were evaluated for the biophysical interaction through SPR assay. CSNP1, CSNP2, and Pep1 dose-dependently bind the S1 domain of the prototype Spike, whereas CSNP4 binds both S1 and ACE2. After safety and immunocytochemistry evaluation, peptides were probed for their pan-variant inhibitory effects. CSNP1, CSNP2, and CSNP4 inhibited all VOCs dose-dependently, whereas Pep1 had a moderate effect. CSNP2 and CSNP4 could neutralize the wild-type pseudovirus up to 80 % when treated at 0.5 µM. Furthermore, CSNP4 synergize the neutralization effect of monoclonal antibody and CSNP1 in Delta variant pseudovirus assay as they target different regions on the RBD. Thus, we suggest that CSNPs are SARS-CoV-2 pan-variant inhibitory candidates for COVID-19 therapy, which may pave the way for combating the emerging immune-escaping variants. We also propose that CSNP1/2-CSNP4 peptide cocktail or CSNP1/4 mAbs cocktail with no overlapping epitopes could be effective therapeutic strategies against COVID-19.
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Affiliation(s)
- Masaud Shah
- Department of Physiology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Sung Ung Moon
- Department of Physiology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Jang Hyun Kim
- Department of Physiology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Trinh Thanh Thao
- Department of Physiology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Hyun Goo Woo
- Department of Physiology, Ajou University School of Medicine, Suwon, Republic of Korea
- Department of Biomedical Science, Graduate School, Ajou University, Suwon, Republic of Korea
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13
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Taresh AB, Hutton CA. Backbone thioamide directed macrocyclisation: lactam stapling of peptides. Org Biomol Chem 2022; 20:1488-1492. [PMID: 35103273 DOI: 10.1039/d1ob02461b] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A novel method for lactam stapling of Asp/Lys-containing peptides has been developed that does not require coupling agents. A backbone thioamide is incorporated at the N-terminal side of the aspartate residue. Ag(I)-promoted activation of the thioamide in the vicinity of the Asp carboxylate generates a cyclic isoimide intermediate that is trapped by the Lys amine to generate the macrolactam. This method is suitable for generation of i,i+2, i,i+3, and i,i+4-spaced lactam-bridged peptides.
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Affiliation(s)
- Ameer B Taresh
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Craig A Hutton
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia.
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14
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de Araujo AD, Lim J, Wu KC, Hoang HN, Nguyen HT, Fairlie DP. Landscaping macrocyclic peptides: stapling hDM2-binding peptides for helicity, protein affinity, proteolytic stability and cell uptake. RSC Chem Biol 2022; 3:895-904. [PMID: 35866171 PMCID: PMC9257625 DOI: 10.1039/d1cb00231g] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 05/19/2022] [Indexed: 12/25/2022] Open
Abstract
Surveying macrocycles for mimicking a helical tumor suppressor protein, resisting breakdown by proteases, and entering cancer cells.
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Affiliation(s)
- Aline D. de Araujo
- Division of Chemistry and Structural Biology, ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Junxian Lim
- Division of Chemistry and Structural Biology, ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kai-Chen Wu
- Division of Chemistry and Structural Biology, ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Huy N. Hoang
- Division of Chemistry and Structural Biology, ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Huy T. Nguyen
- Division of Chemistry and Structural Biology, ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology, ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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15
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Wu C, Hoang HN, Hill TA, Lim J, Kok WM, Akondi K, Liu L, Fairlie DP. Helical structure in cyclic peptides: effect of N-methyl amides versus esters. Chem Commun (Camb) 2022; 58:12475-12478. [DOI: 10.1039/d2cc05092g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cyclic peptides with esters but not N-methyl amides are the smallest known alpha helices in water and can enter cells.
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Affiliation(s)
- Chongyang Wu
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| | - Huy N. Hoang
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| | - Timothy A. Hill
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| | - Junxian Lim
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| | - W. Mei Kok
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| | - Kalyani Akondi
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| | - Ligong Liu
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| | - David P. Fairlie
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
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16
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Lendel C, Solin N. Protein nanofibrils and their use as building blocks of sustainable materials. RSC Adv 2021; 11:39188-39215. [PMID: 35492452 PMCID: PMC9044473 DOI: 10.1039/d1ra06878d] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/25/2021] [Indexed: 12/21/2022] Open
Abstract
The development towards a sustainable society requires a radical change of many of the materials we currently use. Besides the replacement of plastics, derived from petrochemical sources, with renewable alternatives, we will also need functional materials for applications in areas ranging from green energy and environmental remediation to smart foods. Proteins could, with their intriguing ability of self-assembly into various forms, play important roles in all these fields. To achieve that, the code for how to assemble hierarchically ordered structures similar to the protein materials found in nature must be cracked. During the last decade it has been demonstrated that amyloid-like protein nanofibrils (PNFs) could be a steppingstone for this task. PNFs are formed by self-assembly in water from a range of proteins, including plant resources and industrial side streams. The nanofibrils display distinct functional features and can be further assembled into larger structures. PNFs thus provide a framework for creating ordered, functional structures from the atomic level up to the macroscale. This review address how industrial scale protein resources could be transformed into PNFs and further assembled into materials with specific mechanical and functional properties. We describe what is required from a protein to form PNFs and how the structural properties at different length scales determine the material properties. We also discuss potential chemical routes to modify the properties of the fibrils and to assemble them into macroscopic structures.
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Affiliation(s)
- Christofer Lendel
- Department of Chemistry, KTH Royal Institute of Technology Teknikringen 30 SE-100 44 Stockholm Sweden
| | - Niclas Solin
- Department of Physics, Chemistry, and Biology, Electronic and Photonic Materials, Biomolecular and Organic Electronics, Linköping University Linköping 581 83 Sweden
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17
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Farley KA, Koos MRM, Che Y, Horst R, Limberakis C, Bellenger J, Lira R, Gil-Silva LF, Gil RR. Cross-Linked Poly-4-Acrylomorpholine: A Flexible and Reversibly Compressible Aligning Gel for Anisotropic NMR Analysis of Peptides and Small Molecules in Water. Angew Chem Int Ed Engl 2021; 60:26314-26319. [PMID: 34609778 DOI: 10.1002/anie.202106794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Indexed: 11/07/2022]
Abstract
Determination of the solution conformation of both small organic molecules and peptides in water remains a substantial hurdle in using NMR solution conformations to guide drug design due to the lack of easy to use alignment media. Herein we report the design of a flexible compressible chemically cross-linked poly-4-acrylomorpholine gel that can be used for the alignment of both small molecules and cyclic peptides in water. To test the new gel, residual dipolar couplings (RDCs) and J-coupling constants were used in the configurational analysis of strychnine hydrochloride, a molecule that has been studied extensively in organic solvents as well as a small cyclic peptide that is known to form an α-helix in water. The conformational ensembles for each molecule with the best fit to the data are reported. Identification of minor conformers in water that cannot easily be determined by conventional NOE measurements will facilitate the use of RDC experiments in structure-based drug design.
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Affiliation(s)
- Kathleen A Farley
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | - Martin R M Koos
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Ye Che
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | - Reto Horst
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | - Chris Limberakis
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | - Justin Bellenger
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | - Ricardo Lira
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | | | - Roberto R Gil
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
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18
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Farley KA, Koos MRM, Che Y, Horst R, Limberakis C, Bellenger J, Lira R, Gil‐Silva LF, Gil RR. Cross‐Linked Poly‐4‐Acrylomorpholine: A Flexible and Reversibly Compressible Aligning Gel for Anisotropic NMR Analysis of Peptides and Small Molecules in Water. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - Martin R. M. Koos
- Department of Chemistry Carnegie Mellon University 4400 Fifth Avenue Pittsburgh PA 15213 USA
| | - Ye Che
- Medicinal Sciences Pfizer Eastern Point Road Groton CT 06340 USA
| | - Reto Horst
- Medicinal Sciences Pfizer Eastern Point Road Groton CT 06340 USA
| | - Chris Limberakis
- Medicinal Sciences Pfizer Eastern Point Road Groton CT 06340 USA
| | - Justin Bellenger
- Medicinal Sciences Pfizer Eastern Point Road Groton CT 06340 USA
| | - Ricardo Lira
- Medicinal Sciences Pfizer Eastern Point Road Groton CT 06340 USA
| | | | - Roberto R. Gil
- Department of Chemistry Carnegie Mellon University 4400 Fifth Avenue Pittsburgh PA 15213 USA
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19
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Unarta IC, Xu J, Shang Y, Cheung CHP, Zhu R, Chen X, Cao S, Cheung PPH, Bierer D, Zhang M, Huang X, Li X. Entropy of stapled peptide inhibitors in free state is the major contributor to the improvement of binding affinity with the GK domain. RSC Chem Biol 2021; 2:1274-1284. [PMID: 34458841 PMCID: PMC8341669 DOI: 10.1039/d1cb00087j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/24/2021] [Indexed: 01/03/2023] Open
Abstract
Stapled peptides are promising protein–protein interaction (PPI) inhibitors that can increase the binding potency. Different from small-molecule inhibitors in which the binding mainly depends on energetic interactions with their protein targets, the binding of stapled peptides has long been suggested to be benefited from entropy. However, it remains challenging to reveal the molecular features that lead to this entropy gain, which could originate from the stabilization of the stapled peptide in solution or from the increased flexibility of the complex upon binding. This hinders the rational design of stapled peptides as PPI inhibitors. Using the guanylate kinase (GK) domain of the postsynaptic density protein 95 (PSD-95) as the target, we quantified the enthalpic and entropic contributions by combining isothermal titration calorimetry (ITC), X-ray crystallography, and free energy calculations based on all-atom molecular dynamics (MD) simulations. We successfully designed a stapled peptide inhibitor (staple 1) of the PSD-95 GK domain that led to a 25-fold increase in the binding affinity (from tens of μMs to 1.36 μM) with high cell permeability. We showed that entropy indeed greatly enhanced the binding affinity and the entropy gain was mainly due to the constrained-helix structure of the stapled peptide in solution (free state). Based on staple 1, we further designed two other stapled peptides (staple 2 and 3), which exerted even larger entropy gains compared to staple 1 because of their more flexible bound complexes (bound state). However, for staple 2 and 3, the overall binding affinities were not improved, as the loose binding in their bound states led to an enthalpic loss that largely compensated the excess entropy gain. Our work suggests that increasing the stability of the stapled peptide in free solution is an effective strategy for the rational design of stapled peptides as PPI inhibitors. The significant improvement in the binding affinity of the stapled peptide to the PSD-95 GK domain is mostly contributed by the reduction in the entropy penalty of the stapled peptide due to the restriction in the α-helical structure by stapling in the free state.![]()
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Affiliation(s)
- Ilona Christy Unarta
- Bioengineering Graduate Program, Department of Biological and Chemical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay Kowloon Hong Kong .,Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Jianchao Xu
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Hong Kong
| | - Yuan Shang
- Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong .,Division of Life Science, The Hong Kong University of Science and Technology Kowloon Hong Kong
| | - Carina Hey Pui Cheung
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Hong Kong
| | - Ruichi Zhu
- Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong .,Division of Life Science, The Hong Kong University of Science and Technology Kowloon Hong Kong
| | - Xudong Chen
- Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong .,Division of Life Science, The Hong Kong University of Science and Technology Kowloon Hong Kong
| | - Siqin Cao
- Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong .,Department of Chemistry, The Hong Kong University of Science and Technology Kowloon Hong Kong
| | - Peter Pak-Hang Cheung
- Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong .,Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Hong Kong
| | - Donald Bierer
- Department of Medicinal Chemistry, Bayer AG Aprather Weg 18A 42096 Wuppertal Germany
| | - Mingjie Zhang
- Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong .,Division of Life Science, The Hong Kong University of Science and Technology Kowloon Hong Kong
| | - Xuhui Huang
- Bioengineering Graduate Program, Department of Biological and Chemical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay Kowloon Hong Kong .,Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong .,Department of Chemistry, The Hong Kong University of Science and Technology Kowloon Hong Kong.,Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park Hong Kong
| | - Xuechen Li
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Hong Kong
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20
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Potential therapeutic applications of AKAP disrupting peptides. Clin Sci (Lond) 2021; 134:3259-3282. [PMID: 33346357 DOI: 10.1042/cs20201244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/16/2020] [Accepted: 11/30/2020] [Indexed: 11/17/2022]
Abstract
The 3'-5'-cyclic adenosine monophosphate (cAMP)/PKA pathway represents a major target for pharmacological intervention in multiple disease conditions. Although the last decade saw the concept of highly compartmentalized cAMP/PKA signaling consolidating, current means for the manipulation of this pathway still do not allow to specifically intervene on discrete cAMP/PKA microdomains. Since compartmentalization is crucial for action specificity, identifying new tools that allow local modulation of cAMP/PKA responses is an urgent need. Among key players of cAMP/PKA signaling compartmentalization, a major role is played by A-kinase anchoring proteins (AKAPs) that, by definition, anchor PKA, its substrates and its regulators within multiprotein complexes in well-confined subcellular compartments. Different tools have been conceived to interfere with AKAP-based protein-protein interactions (PPIs), and these primarily include peptides and peptidomimetics that disrupt AKAP-directed multiprotein complexes. While these molecules have been extensively used to understand the molecular mechanisms behind AKAP function in pathophysiological processes, less attention has been devoted to their potential application for therapy. In this review, we will discuss how AKAP-based PPIs can be pharmacologically targeted by synthetic peptides and peptidomimetics.
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21
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Ahangarpour M, Kavianinia I, Harris PWR, Brimble MA. Photo-induced radical thiol-ene chemistry: a versatile toolbox for peptide-based drug design. Chem Soc Rev 2021; 50:898-944. [PMID: 33404559 DOI: 10.1039/d0cs00354a] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
While the global market for peptide/protein-based therapeutics is witnessing significant growth, the development of peptide drugs remains challenging due to their low oral bioavailability, poor membrane permeability, and reduced metabolic stability. However, a toolbox of chemical approaches has been explored for peptide modification to overcome these obstacles. In recent years, there has been a revival of interest in photoinduced radical thiol-ene chemistry as a powerful tool for the construction of therapeutic peptides.
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Affiliation(s)
- Marzieh Ahangarpour
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand.
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22
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Sindhikara D, Wagner M, Gkeka P, Güssregen S, Tiwari G, Hessler G, Yapici E, Li Z, Evers A. Automated Design of Macrocycles for Therapeutic Applications: From Small Molecules to Peptides and Proteins. J Med Chem 2020; 63:12100-12115. [PMID: 33017535 DOI: 10.1021/acs.jmedchem.0c01500] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Macrocycles and cyclic peptides are increasingly attractive therapeutic modalities as they often have improved affinity, are able to bind to extended protein surfaces, and otherwise have favorable properties. Macrocyclization of a known binder may stabilize its bioactive conformation and improve its metabolic stability, cell permeability, and in certain cases oral bioavailability. Herein, we present implementation and application of an approach that automatically generates, evaluates, and proposes cyclizations utilizing a library of well-established chemical reactions and reagents. Using the three-dimensional (3D) conformation of the linear molecule in complex with a target protein as the starting point, this approach identifies attachment points, generates linkers, evaluates their geometric compatibility, and ranks the resulting molecules with respect to their predicted conformational stability and interactions with the target protein. As we show here with prospective and retrospective case studies, this procedure can be applied for the macrocyclization of small molecules and peptides and even PROteolysis TArgeting Chimeras (PROTACs) and proteins.
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Affiliation(s)
- Dan Sindhikara
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Michael Wagner
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Paraskevi Gkeka
- Integrated Drug Discovery, Sanofi R&D, 1 Avenue Pierre Brossolette, 91385 Chilly-Mazarin, France
| | - Stefan Güssregen
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Garima Tiwari
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Gerhard Hessler
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Engin Yapici
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Ziyu Li
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Andreas Evers
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
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23
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Targeting the Respiratory Syncytial Virus N 0-P Complex with Constrained α-Helical Peptides in Cells and Mice. Antimicrob Agents Chemother 2020; 64:AAC.00717-20. [PMID: 32660994 PMCID: PMC7508628 DOI: 10.1128/aac.00717-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/30/2020] [Indexed: 02/07/2023] Open
Abstract
Respiratory syncytial virus (RSV) is the main cause of severe respiratory infection in young children worldwide, and no therapies have been approved for the treatment of RSV infection. Data from recent clinical trials of fusion or L polymerase inhibitors for the treatment of RSV-infected patients revealed the emergence of escape mutants, highlighting the need for the discovery of inhibitors with novel mechanisms of action. Here we describe stapled peptides derived from the N terminus of the phosphoprotein (P) that act as replication inhibitors. Respiratory syncytial virus (RSV) is the main cause of severe respiratory infection in young children worldwide, and no therapies have been approved for the treatment of RSV infection. Data from recent clinical trials of fusion or L polymerase inhibitors for the treatment of RSV-infected patients revealed the emergence of escape mutants, highlighting the need for the discovery of inhibitors with novel mechanisms of action. Here we describe stapled peptides derived from the N terminus of the phosphoprotein (P) that act as replication inhibitors. We demonstrate that these peptides inhibit RSV replication in vitro and in vivo by preventing the formation of the N0-P complex. The present strategy provides a novel means of targeting RSV replication with constrained macrocyclic peptides or small molecules and is broadly applicable to other viruses of the Mononegavirales order.
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Li X, Chen S, Zhang WD, Hu HG. Stapled Helical Peptides Bearing Different Anchoring Residues. Chem Rev 2020; 120:10079-10144. [DOI: 10.1021/acs.chemrev.0c00532] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Xiang Li
- School of Pharmacy, Second Military Medical University, Shanghai, China
- Insititute of Translational Medicine, Shanghai University, Shanghai, China
| | - Si Chen
- School of Medicine, Shanghai University, Shanghai, China
| | - Wei-Dong Zhang
- School of Pharmacy, Second Military Medical University, Shanghai, China
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hong-Gang Hu
- Insititute of Translational Medicine, Shanghai University, Shanghai, China
- Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
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Shah M, Kim GY, Achek A, Cho EY, Baek WY, Choi YS, Lee WH, Kim DJ, Lee SH, Kim W, Kim SS, Cheong JY, Suh CH, Choi S. The αC helix of TIRAP holds therapeutic potential in TLR-mediated autoimmune diseases. Biomaterials 2020; 245:119974. [PMID: 32220799 DOI: 10.1016/j.biomaterials.2020.119974] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 02/29/2020] [Accepted: 03/14/2020] [Indexed: 02/07/2023]
Abstract
Despite being crucial for combating microbes, paradoxical Toll-like receptors (TLRs) signaling have been associated with the aggravation of multiple immune disorders such as systemic lupus erythematosus, psoriasis, rheumatoid arthritis, and nonalcoholic steatohepatitis. The stoichiometry and precise arrangement of the interaction of adapters (via their Toll/interleukin-1 receptor [TIR] domains) are indispensable for the activation of TLRs and of downstream signaling cascades. Among adapters, plasma membrane-anchored MyD88 adaptor-like (MAL) has the potential for BB-loop-mediated self-oligomerization and interacts with other TIR domain-containing adaptors through αC and αD helices. Here, we used information on the MAL-αC interface to exploit its pharmacophores and to design a decoy peptide (MIP2) with broad-range TLR-inhibitory abilities. MIP2 abrogated MyD88- and TRIF-dependent lipopolysaccharide (LPS)-induced TLR4 signaling in murine and human cell lines and manifested a therapeutic potential in models of psoriasis, systemic lupus erythematosus, nonalcoholic steatohepatitis, and sepsis. Levels of hallmark serological and histological biomarkers were significantly restored and the disease symptoms were substantially ameliorated by MIP2 treatment of the animals. Collectively, our biophysical, in vitro, and in vivo findings suggest that MIP2 has broad specificity for TLRs and may be effective in modulating autoimmune complications caused by microbial or environmental factors.
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Affiliation(s)
- Masaud Shah
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, South Korea
| | - Gi-Young Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, South Korea
| | - Asma Achek
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, South Korea
| | - Eun-Young Cho
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, South Korea
| | - Wook-Young Baek
- Department of Rheumatology, Ajou University School of Medicine, Suwon, 16499, South Korea
| | - Yang Seon Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, South Korea
| | - Wang Hee Lee
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, South Korea
| | - Dong-Jin Kim
- Division of Nephrology, Department of Internal Medicine, Kyung Hee University Hospital at Gangdong, Seoul, 05278, South Korea
| | - Sang Ho Lee
- Division of Nephrology, Department of Internal Medicine, Kyung Hee University Hospital at Gangdong, Seoul, 05278, South Korea
| | - Wook Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, South Korea
| | - Soon Sun Kim
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, 16499, South Korea
| | - Jae Youn Cheong
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, 16499, South Korea
| | - Chang-Hee Suh
- Department of Rheumatology, Ajou University School of Medicine, Suwon, 16499, South Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, South Korea.
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Vasco AV, Moya CG, Gröger S, Brandt W, Balbach J, Pérez CS, Wessjohann LA, Rivera DG. Insights into the secondary structures of lactam N-substituted stapled peptides. Org Biomol Chem 2020; 18:3838-3842. [DOI: 10.1039/d0ob00767f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
NMR and CD studies together with molecular dynamics simulation reveal new insights into the s-cis/s-trans isomerism and the effect of the lactam bridge N-substituent on the secondary structure of stapled peptides.
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Affiliation(s)
- Aldrin V. Vasco
- Department of Bioorganic Chemistry
- Leibniz Institute of Plant Biochemistry
- Halle/Saale
- Germany
| | - Celia G. Moya
- Center for Natural Products Research
- Faculty of Chemistry
- University of Havana
- Havana
- Cuba
| | - Stefan Gröger
- Institute of Physics/Biophysics and Center for Structural and Dynamics of Proteins
- Martin Luther University Halle-Wittenberg
- Germany
| | - Wolfgang Brandt
- Department of Bioorganic Chemistry
- Leibniz Institute of Plant Biochemistry
- Halle/Saale
- Germany
| | - Jochen Balbach
- Institute of Physics/Biophysics and Center for Structural and Dynamics of Proteins
- Martin Luther University Halle-Wittenberg
- Germany
| | - Carlos S. Pérez
- Center for Natural Products Research
- Faculty of Chemistry
- University of Havana
- Havana
- Cuba
| | - Ludger A. Wessjohann
- Department of Bioorganic Chemistry
- Leibniz Institute of Plant Biochemistry
- Halle/Saale
- Germany
| | - Daniel G. Rivera
- Department of Bioorganic Chemistry
- Leibniz Institute of Plant Biochemistry
- Halle/Saale
- Germany
- Center for Natural Products Research
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27
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Hoang HN, Hill TA, Ruiz-Gómez G, Diness F, Mason JM, Wu C, Abbenante G, Shepherd NE, Fairlie DP. Twists or turns: stabilising alpha vs. beta turns in tetrapeptides. Chem Sci 2019; 10:10595-10600. [PMID: 32110345 PMCID: PMC7020788 DOI: 10.1039/c9sc04153b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 10/03/2019] [Indexed: 01/03/2023] Open
Abstract
Protein-protein interactions involve hotspots as small as 4 sequential amino acids. Corresponding tetrapeptides have no structure in water. Here we report linking side chains of amino acids X and Z to form 24 cyclic tetrapeptides, cyclo-[XAAZ]-NH2, and stabilise 14-18 membered rings that mimic different kinds of non-regular secondary structures found in protein hotspots. 2D NMR spectra allowed determination of 3D structures for 14 cyclic tetrapeptides in water. Five formed two (i, i + 3) hydrogen bonds and a beta/gamma (6, 7) or beta (9, 19, 20) turn; eight formed one (i, i + 4) hydrogen bond and twisted into a non-helical (13, 18, 21, 22, 24) or helical (5, 17, 23) alpha turn; one was less structured (15). A beta or gamma turn was favoured for Z = Dab, Orn or Glu due to a χ1 gauche (+) rotamer, while an alpha turn was favoured for Z = Dap (but not X = Dap) due to a gauche (-) rotamer. Surprisingly, an unstructured peptide ARLARLARL could be twisted into a helix when either a helical or non-helical alpha turn (5, 13, 17, 18, 21-24) with Z = Dap was attached to the N-terminus. These structural models provide insights into stability for different turns and twists corresponding to non-regular folds in protein hotspots.
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Affiliation(s)
- Huy N Hoang
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging , Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia .
| | - Timothy A Hill
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging , Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia .
| | - Gloria Ruiz-Gómez
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging , Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia .
- Structural Bioinformatics , BIOTEC , Technische Universität Dresden , Tatzberg 47-51 , 01307 Dresden , Germany
| | - Frederik Diness
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging , Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia .
- Center for Evolutionary Chemical Biology , Department of Chemistry , University of Copenhagen , 2100 Copenhagen , Denmark
| | - Jody M Mason
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging , Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia .
- Department of Biology & Biochemistry , University of Bath , Claverton Down , Bath , BA2 7AY , UK
| | - Chongyang Wu
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging , Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia .
| | - Giovanni Abbenante
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging , Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia .
| | - Nicholas E Shepherd
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging , Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia .
| | - David P Fairlie
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging , Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia .
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Jeganathan S, Wendt M, Kiehstaller S, Brancaccio D, Kuepper A, Pospiech N, Carotenuto A, Novellino E, Hennig S, Grossmann TN. Constrained Peptides with Fine-Tuned Flexibility Inhibit NF-Y Transcription Factor Assembly. Angew Chem Int Ed Engl 2019; 58:17351-17358. [PMID: 31539186 PMCID: PMC6900064 DOI: 10.1002/anie.201907901] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/19/2019] [Indexed: 12/17/2022]
Abstract
Protein complex formation depends on the interplay between preorganization and flexibility of the binding epitopes involved. The design of epitope mimetics typically focuses on stabilizing a particular bioactive conformation, often without considering conformational dynamics, which limits the potential of peptidomimetics against challenging targets such as transcription factors. We developed a peptide-derived inhibitor of the NF-Y transcription factor by first constraining the conformation of an epitope through hydrocarbon stapling and then fine-tuning its flexibility. In the initial set of constrained peptides, a single non-interacting α-methyl group was observed to have a detrimental effect on complex stability. Biophysical characterization revealed how this methyl group affects the conformation of the peptide in its bound state. Adaption of the methylation pattern resulted in a peptide that inhibits transcription factor assembly and subsequent recruitment to the target DNA.
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Affiliation(s)
- Sadasivam Jeganathan
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 1544227DortmundGermany
| | - Mathias Wendt
- Department of Chemistry and Pharmaceutical SciencesVU University AmsterdamDe Boelelaan 10831081HZAmsterdamThe Netherlands
| | - Sebastian Kiehstaller
- Department of Chemistry and Pharmaceutical SciencesVU University AmsterdamDe Boelelaan 10831081HZAmsterdamThe Netherlands
| | - Diego Brancaccio
- Department of PharmacyUniversity of Naples “Federico II”Via D. Montesano49, 80131NaplesItaly
| | - Arne Kuepper
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 1544227DortmundGermany
| | - Nicole Pospiech
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 1544227DortmundGermany
| | - Alfonso Carotenuto
- Department of PharmacyUniversity of Naples “Federico II”Via D. Montesano49, 80131NaplesItaly
| | - Ettore Novellino
- Department of PharmacyUniversity of Naples “Federico II”Via D. Montesano49, 80131NaplesItaly
| | - Sven Hennig
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 1544227DortmundGermany
- Department of Chemistry and Pharmaceutical SciencesVU University AmsterdamDe Boelelaan 10831081HZAmsterdamThe Netherlands
| | - Tom N. Grossmann
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 1544227DortmundGermany
- Department of Chemistry and Pharmaceutical SciencesVU University AmsterdamDe Boelelaan 10831081HZAmsterdamThe Netherlands
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29
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Jeganathan S, Wendt M, Kiehstaller S, Brancaccio D, Kuepper A, Pospiech N, Carotenuto A, Novellino E, Hennig S, Grossmann TN. Constrained Peptides with Fine‐Tuned Flexibility Inhibit NF‐Y Transcription Factor Assembly. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Sadasivam Jeganathan
- Chemical Genomics Centre of the Max Planck Society Otto-Hahn-Strasse 15 44227 Dortmund Germany
| | - Mathias Wendt
- Department of Chemistry and Pharmaceutical SciencesVU University Amsterdam De Boelelaan 1083 1081 HZ Amsterdam The Netherlands
| | - Sebastian Kiehstaller
- Department of Chemistry and Pharmaceutical SciencesVU University Amsterdam De Boelelaan 1083 1081 HZ Amsterdam The Netherlands
| | - Diego Brancaccio
- Department of PharmacyUniversity of Naples “Federico II” Via D. Montesano 49, 80131 Naples Italy
| | - Arne Kuepper
- Chemical Genomics Centre of the Max Planck Society Otto-Hahn-Strasse 15 44227 Dortmund Germany
| | - Nicole Pospiech
- Chemical Genomics Centre of the Max Planck Society Otto-Hahn-Strasse 15 44227 Dortmund Germany
| | - Alfonso Carotenuto
- Department of PharmacyUniversity of Naples “Federico II” Via D. Montesano 49, 80131 Naples Italy
| | - Ettore Novellino
- Department of PharmacyUniversity of Naples “Federico II” Via D. Montesano 49, 80131 Naples Italy
| | - Sven Hennig
- Chemical Genomics Centre of the Max Planck Society Otto-Hahn-Strasse 15 44227 Dortmund Germany
- Department of Chemistry and Pharmaceutical SciencesVU University Amsterdam De Boelelaan 1083 1081 HZ Amsterdam The Netherlands
| | - Tom N. Grossmann
- Chemical Genomics Centre of the Max Planck Society Otto-Hahn-Strasse 15 44227 Dortmund Germany
- Department of Chemistry and Pharmaceutical SciencesVU University Amsterdam De Boelelaan 1083 1081 HZ Amsterdam The Netherlands
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30
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Hoang HN, Wu C, Hill TA, Dantas de Araujo A, Bernhardt PV, Liu L, Fairlie DP. A Novel Long‐Range n to π* Interaction Secures the Smallest known α‐Helix in Water. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201911277] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Huy N. Hoang
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Chongyang Wu
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Timothy A. Hill
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Aline Dantas de Araujo
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Paul V. Bernhardt
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane Qld 4072 Australia
| | - Ligong Liu
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
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31
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Hoang HN, Wu C, Hill TA, Dantas de Araujo A, Bernhardt PV, Liu L, Fairlie DP. A Novel Long-Range n to π* Interaction Secures the Smallest known α-Helix in Water. Angew Chem Int Ed Engl 2019; 58:18873-18877. [PMID: 31625253 DOI: 10.1002/anie.201911277] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/10/2019] [Indexed: 12/17/2022]
Abstract
The introduction of an amide bond linking side chains of the first and fifth amino acids forms a cyclic pentapeptide that optimally stabilizes the smallest known α-helix in water. The origin of the stabilization is unclear. The observed dependence of α-helicity on the solvent and cyclization linker led us to discover a novel long-range n to π* interaction between a main-chain amide oxygen and a uniquely positioned carbonyl group in the linker of cyclic pentapeptides. CD and NMR spectra, NMR and X-ray structures, modelling, and MD simulations reveal that this first example of a synthetically incorporated long-range n to π* CO⋅⋅⋅Cγ =Ο interaction uniquely enforces an almost perfect and remarkably stable peptide α-helix in water but not in DMSO. This unusual interaction with a covalent amide bond outside the helical backbone suggests new approaches to synthetically stabilize peptide structures in water.
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Affiliation(s)
- Huy N Hoang
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Chongyang Wu
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Timothy A Hill
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Aline Dantas de Araujo
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Paul V Bernhardt
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Ligong Liu
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - David P Fairlie
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
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Jing X, Jin K. A gold mine for drug discovery: Strategies to develop cyclic peptides into therapies. Med Res Rev 2019; 40:753-810. [PMID: 31599007 DOI: 10.1002/med.21639] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/05/2019] [Accepted: 09/26/2019] [Indexed: 12/19/2022]
Abstract
As a versatile therapeutic modality, peptides attract much attention because of their great binding affinity, low toxicity, and the capability of targeting traditionally "undruggable" protein surfaces. However, the deficiency of cell permeability and metabolic stability always limits the success of in vitro bioactive peptides as drug candidates. Peptide macrocyclization is one of the most established strategies to overcome these limitations. Over the past decades, more than 40 cyclic peptide drugs have been clinically approved, the vast majority of which are derived from natural products. The de novo discovered cyclic peptides on the basis of rational design and in vitro evolution, have also enabled the binding with targets for which nature provides no solutions. The current review summarizes different classes of cyclic peptides with diverse biological activities, and presents an overview of various approaches to develop cyclic peptide-based drug candidates, drawing upon series of examples to illustrate each strategy.
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Affiliation(s)
- Xiaoshu Jing
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Kang Jin
- Department of Medicinal Chemistry, School of Pharmacy, Shandong University, Jinan, Shandong, China
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Cholesterol-conjugated stapled peptides inhibit Ebola and Marburg viruses in vitro and in vivo. Antiviral Res 2019; 171:104592. [PMID: 31473342 DOI: 10.1016/j.antiviral.2019.104592] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 08/22/2019] [Accepted: 08/25/2019] [Indexed: 02/07/2023]
Abstract
Filoviridae currently includes five official and one proposed genera. Genus Ebolavirus includes five established and one proposed ebolavirus species for Bombali virus (BOMV), Bundibugyo virus (BDBV), Ebola virus (EBOV), Reston virus (RESTV), Sudan virus (SUDV) and Taï Forest virus (TAFV), and genus Marburgvirus includes a single species for Marburg virus (MARV) and Ravn virus (RAVV). Ebola virus (EBOV) has emerged as a significant public health concern since the 2013-2016 Ebola Virus Disease outbreak in Western Africa. Currently, there are no therapeutics approved and the need for Ebola-specific therapeutics remains a gap. In search for anti-Ebola therapies we tested the idea of using inhibitory properties of peptides corresponding to the C-terminal heptad-repeat (HR2) domains of class I fusion proteins against EBOV infection. The fusion protein GP2 of EBOV belongs to class I, suggesting that a similar strategy to HIV may be applied to inhibit EBOV infection. The serum half-life of peptides was expanded by cholesterol conjugation to allow daily dosing. The peptides were further constrained to stabilize a helical structure to increase the potency of inhibition. The EC50s of lead peptides were in low micromolar range, as determined by a high-content imaging test of EBOV-infected cells. Lead peptides were tested in an EBOV lethal mouse model and efficacy of the peptides were determined following twice-daily administration of peptides for 9 days. The most potent peptide was able to protect mice from lethal challenge of mouse-adapted Ebola virus. These data show that engineered peptides coupled with cholesterol can inhibit viral production, protect mice against lethal EBOV infection, and may be used to build novel therapeutics against EBOV.
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Achek A, Shah M, Seo JY, Kwon HK, Gui X, Shin HJ, Cho EY, Lee BS, Kim DJ, Lee SH, Yoo TH, Kim MS, Choi S. Linear and Rationally Designed Stapled Peptides Abrogate TLR4 Pathway and Relieve Inflammatory Symptoms in Rheumatoid Arthritis Rat Model. J Med Chem 2019; 62:6495-6511. [PMID: 31283217 DOI: 10.1021/acs.jmedchem.9b00061] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A mounting evidence exists for the despicable role of the aberrant immune response in the pathogenesis of rheumatoid arthritis (RA), where toll-like receptor 4 (TLR4) can activate synovial fibroblasts that lead to the chronic inflammation and joint destruction, thus making TLR4 a potent drug target in RA. We report that novel TLR4-antagonizing peptide, PIP2, inhibits the induction of inflammatory biomarkers in vitro as well as in vivo. Systemically, PIP2 inhibits the lipopolysaccharide (LPS)-elicited TNF-α, IL-6, and IL-12p40 in a mouse model. The rationally designed cyclic derivative, cPIP2, is capable of inhibiting LPS-induced proinflammatory cytokines at significantly lower concentration as compared to PIP2 (PIP2 IC50 = 20 μM, cPIP2 IC50 = 5 μM). Finally, cPIP2 was able to relieve the inflammatory symptoms and synovial tissue destruction in the RA rat model. Cumulatively, these data suggest that PIP2 and cPIP2 hold strong promise for the development of peptide-based immunotherapeutics that could be of great value in curbing TLR-related immune complications including RA.
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Affiliation(s)
- Asma Achek
- Department of Molecular Science and Technology , Ajou University , Suwon 16499 , Korea
| | - Masaud Shah
- Department of Molecular Science and Technology , Ajou University , Suwon 16499 , Korea
| | - Ji Young Seo
- Department of Molecular Science and Technology , Ajou University , Suwon 16499 , Korea
| | - Hyuk-Kwon Kwon
- Department of Orthopedics and Rehabilitation , Yale University School of Medicine , New Haven , Connecticut 06520-8071 , United States
| | - Xiangai Gui
- Department of Molecular Science and Technology , Ajou University , Suwon 16499 , Korea
| | - Hyeon-Jun Shin
- Department of Molecular Science and Technology , Ajou University , Suwon 16499 , Korea
| | - Eun-Young Cho
- Department of Molecular Science and Technology , Ajou University , Suwon 16499 , Korea
| | - Byeong Sung Lee
- Department of Molecular Science and Technology , Ajou University , Suwon 16499 , Korea
| | - Dong-Jin Kim
- Division of Nephrology, Department of Internal Medicine , Kyung Hee University Hospital at Gangdong , Seoul 05278 , Korea
| | - Sang Ho Lee
- Division of Nephrology, Department of Internal Medicine , Kyung Hee University Hospital at Gangdong , Seoul 05278 , Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology , Ajou University , Suwon 16499 , Korea
| | - Moon Suk Kim
- Department of Molecular Science and Technology , Ajou University , Suwon 16499 , Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology , Ajou University , Suwon 16499 , Korea
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35
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Lathbridge A, Mason JM. Combining Constrained Heptapeptide Cassettes with Computational Design To Create Coiled-Coil Targeting Helical Peptides. ACS Chem Biol 2019; 14:1293-1304. [PMID: 31117396 DOI: 10.1021/acschembio.9b00265] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A total of 32 heptapeptides have been synthesized and characterized to establish the effect of K → D (i → i + 4) lactamization upon their ability to adopt a helical conformation. Because most parallel and dimeric coiled-coil sequences can be deconvoluted into gabcdef repeats, we have introduced fixed solvent exposed b → f (K → D) constraints into this design scaffold. Interfacial " a" hydrophobic (L/I/V/N) and " e/g" electrostatic (E/K) options (4 × 2 × 2 = 16 cassettes) were introduced as core drivers of coiled-coil stability and specificity. All present as random coils when linear but adopt a helical conformation upon lactamization. Helicity varied in magnitude from 34 to 68%, indicating different levels of constraint tolerance within the context of a sequence required to be helical for function. Using the oncogenic transcription factor cJun as an exemplar, we next utilized our bCIPA coiled-coil screening engine to select four cassettes of highest predicted affinity when paired with four gabcdef cassettes within the full-length cJun target counterpart (164 = 65 536 combinations). This information was coupled with observed helicity for each constrained cassette to select for the best balance of predicted affinity when linear and experimentally validated helicity when constrained. As a control, the same approach was taken using cassettes of high predicted target affinity but with lower experimentally validated helicity. The approach provides a novel platform of modular heptapeptide cassettes experimentally validated and separated by helical content. Appropriate cassettes can be selected and conjugated to produce longer peptides, in which constraints impart appropriate helicity such that a wide range of targets can be engaged with high affinity and selectivity.
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36
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Malde AK, Hill TA, Iyer A, Fairlie DP. Crystal Structures of Protein-Bound Cyclic Peptides. Chem Rev 2019; 119:9861-9914. [DOI: 10.1021/acs.chemrev.8b00807] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alpeshkumar K. Malde
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Timothy A. Hill
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Abishek Iyer
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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37
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Li Y, Zhang Y, Wu M, Chang Q, Hu H, Zhao X. Improving Selectivity, Proteolytic Stability, and Antitumor Activity of Hymenochirin-1B: A Novel Glycosylated Staple Strategy. ACS Chem Biol 2019; 14:516-525. [PMID: 30789695 DOI: 10.1021/acschembio.9b00046] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
As a host defense peptide, hymenochirin-1B has attracted increasing attention for its strong cytotoxic activities. However, its poor selectivity and proteolytic stability remain major obstacles for clinical application. To solve these problems, we designed and synthesized a series of peptide analogues of hymenochirin-1B based on cationic residue substitution and stapling combined with a glycosylation strategy. Some analogues showed improvement not only in selectivity and proteolytic stability but also in antitumor activity. Among them, the glycosylated stapled peptide H-58 was identified as the most potential antitumor peptide. Flow cytometry and a competitive binding assay revealed that H-58 displayed significant antitumor selectivity. Confocal microscopy and nuclear staining with Hoechst dye demonstrated that H-58 entered the nucleus and caused DNA damage. In summary, the strategy of glycosylated stapled peptides is a promising approach for improving the antitumor selectivity, proteolytic stability, and antitumor activity of hymenochirin-1B, which can be used for other bioactive peptide modifications.
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Affiliation(s)
- Yulei Li
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Yihan Zhang
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Minghao Wu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Qi Chang
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Honggang Hu
- Translational Medicine Institute, Shanghai University, Shanghai 200436, China
| | - Xia Zhao
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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38
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Ali AM, Atmaj J, Van Oosterwijk N, Groves MR, Dömling A. Stapled Peptides Inhibitors: A New Window for Target Drug Discovery. Comput Struct Biotechnol J 2019; 17:263-281. [PMID: 30867891 PMCID: PMC6396041 DOI: 10.1016/j.csbj.2019.01.012] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 01/28/2019] [Accepted: 01/29/2019] [Indexed: 12/11/2022] Open
Abstract
Protein-protein interaction (PPI) is a hot topic in clinical research as protein networking has a major impact in human disease. Such PPIs are potential drugs targets, leading to the need to inhibit/block specific PPIs. While small molecule inhibitors have had some success and reached clinical trials, they have generally failed to address the flat and large nature of PPI surfaces. As a result, larger biologics were developed for PPI surfaces and they have successfully targeted PPIs located outside the cell. However, biologics have low bioavailability and cannot reach intracellular targets. A novel class -hydrocarbon-stapled α-helical peptides that are synthetic mini-proteins locked into their bioactive structure through site-specific introduction of a chemical linker- has shown promise. Stapled peptides show an ability to inhibit intracellular PPIs that previously have been intractable with traditional small molecule or biologics, suggesting that they offer a novel therapeutic modality. In this review, we highlight what stapling adds to natural-mimicking peptides, describe the revolution of synthetic chemistry techniques and how current drug discovery approaches have been adapted to stabilize active peptide conformations, including ring-closing metathesis (RCM), lactamisation, cycloadditions and reversible reactions. We provide an overview on the available stapled peptide high-resolution structures in the protein data bank, with four selected structures discussed in details due to remarkable interactions of their staple with the target surface. We believe that stapled peptides are promising drug candidates and open the doors for peptide therapeutics to reach currently "undruggable" space.
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Affiliation(s)
| | | | | | | | - Alexander Dömling
- Department of Drug Design, University of Groningen, Antonius Deusinglaan1, 9700AD Groningen, the Netherlands
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39
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Qin W, Xie M, Qin X, Fang Q, Yin F, Li Z. Recent advances in peptidomimetics antagonists targeting estrogen receptor α-coactivator interaction in cancer therapy. Bioorg Med Chem Lett 2018; 28:2827-2836. [DOI: 10.1016/j.bmcl.2018.05.062] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 05/25/2018] [Accepted: 05/30/2018] [Indexed: 02/07/2023]
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40
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Wuo MG, Arora PS. Engineered protein scaffolds as leads for synthetic inhibitors of protein-protein interactions. Curr Opin Chem Biol 2018; 44:16-22. [PMID: 29803113 DOI: 10.1016/j.cbpa.2018.05.013] [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] [Received: 01/31/2018] [Accepted: 05/09/2018] [Indexed: 11/18/2022]
Abstract
Rationally designed protein-protein interaction inhibitors mimic interfacial binding epitopes, specifically residues that contribute significantly to binding. However, direct mimicry often does not lead to high affinity ligands because the natural complexes themselves are functionally transient and of low affinity. The mimics typically need to be optimized for potency. Engineered proteins displaying conformationally-defined epitopes may serve as attractive alternatives to natural protein partners as they can be strictly screened for tight binding. The advantage of focused screens with conformationally-defined protein scaffolds is that conservation of the geometry of the natural binding epitopes may preserve binding site specificity while allowing direct mimicry by various synthetic secondary structure scaffolds. Here we review different classes of engineered proteins for their binding epitope geometry and as leads for synthetic secondary and tertiary structure mimics.
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Affiliation(s)
- Michael G Wuo
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, NY 10003, USA.
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41
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Wu H, Acharyya A, Wu Y, Liu L, Jo H, Gai F, DeGrado WF. Design of a Short Thermally Stable α-Helix Embedded in a Macrocycle. Chembiochem 2018; 19:902-906. [PMID: 29417711 PMCID: PMC6512792 DOI: 10.1002/cbic.201800026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Indexed: 12/12/2022]
Abstract
Although helices play key roles in peptide-protein and protein-protein interactions, the helical conformation is generally unstable for short peptides (10-15 residues) in aqueous solution in the absence of their binding partners. Thus, stabilizing the helical conformation of peptides can lead to increases in binding potency, specificity, and stability towards proteolytic degradation. Helices have been successfully stabilized by introducing side chain-to-side chain crosslinks within the central portion of the helix. However, this approach leaves the ends of the helix free, thus leading to fraying and exposure of the non-hydrogen-bonded amide groups to solvent. Here, we develop a "capped-strapped" peptide strategy to stabilize helices by embedding the entire length of the helix within a macrocycle, which also includes a semirigid organic template as well as end-capping interactions. We have designed a ten-residue capped-strapped helical peptide that behaves like a miniprotein, with a cooperative thermal unfolding transition and Tm ≈70 °C, unprecedented for helical peptides of this length. The NMR structure determination confirmed the design, and X-ray crystallography revealed a novel quaternary structure with implications for foldamer design.
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Affiliation(s)
- Haifan Wu
- Department of Pharmaceutical Chemistry, University of
California San Francisco, CA 94158 (USA)
| | - Arusha Acharyya
- Department of Chemistry, University of Pennsylvania
Philadelphia, PA 19104 (USA)
| | - Yibing Wu
- Department of Pharmaceutical Chemistry, University of
California San Francisco, CA 94158 (USA)
| | - Lijun Liu
- DLX Scientific Lawrence, KS 66049 (USA)
| | - Hyunil Jo
- Department of Pharmaceutical Chemistry, University of
California San Francisco, CA 94158 (USA)
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania
Philadelphia, PA 19104 (USA)
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry, University of
California San Francisco, CA 94158 (USA)
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42
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D de Araujo A, Lim J, Wu KC, Xiang Y, Good AC, Skerlj R, Fairlie DP. Bicyclic Helical Peptides as Dual Inhibitors Selective for Bcl2A1 and Mcl-1 Proteins. J Med Chem 2018; 61:2962-2972. [PMID: 29584430 DOI: 10.1021/acs.jmedchem.8b00010] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A 26-residue peptide BimBH3 binds indiscriminately to multiple oncogenic Bcl2 proteins that regulate apoptosis of cancer cells. Specific inhibition of the BimBH3-Bcl2A1 protein-protein interaction was obtained in vitro and in cancer cells by shortening the peptide to 14 residues, inserting two cyclization constraints to stabilize a water-stable α-helix, and incorporating an N-terminal acrylamide electrophile for selective covalent bonding to Bcl2A1. Mass spectrometry of trypsin-digested bands on electrophoresis gels established covalent bonding of an electrophilic helix to just one of the three cysteines in Bcl2A1, the one (Cys55) at the BimBH3-Bcl2A1 protein-protein interaction interface. Optimizing the helix-inducing constraints and the sequence subsequently enabled electrophile removal without loss of inhibitor potency. The bicyclic helical peptides were potent, cell permeable, plasma-stable, dual inhibitors of Bcl2A1 and Mcl-1 with high selectivity over other Bcl2 proteins. One bicyclic peptide was shown to inhibit the interaction between a pro-apoptotic protein (Bim) and either endogenous Bcl2A1 or Mcl-1, to induce apoptosis of SKMel28 human melanoma cells, and to sensitize them for enhanced cell death by the anticancer drug etoposide. These approaches look promising for chemically silencing intracellular proteins.
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Affiliation(s)
- Aline D de Araujo
- Division of Chemistry and Structural Biology, ARC Centre of Excellence in Advanced Molecular Imaging , Institute for Molecular Bioscience, The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Junxian Lim
- Division of Chemistry and Structural Biology, ARC Centre of Excellence in Advanced Molecular Imaging , Institute for Molecular Bioscience, The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Kai-Chen Wu
- Division of Chemistry and Structural Biology, ARC Centre of Excellence in Advanced Molecular Imaging , Institute for Molecular Bioscience, The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Yibin Xiang
- Noliva Therapeutics LLC , Newton , Massachusetts 02465 , United States
| | - Andrew C Good
- Noliva Therapeutics LLC , Newton , Massachusetts 02465 , United States
| | - Renato Skerlj
- Noliva Therapeutics LLC , Newton , Massachusetts 02465 , United States
| | - David P Fairlie
- Division of Chemistry and Structural Biology, ARC Centre of Excellence in Advanced Molecular Imaging , Institute for Molecular Bioscience, The University of Queensland , Brisbane , Queensland 4072 , Australia
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43
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Wu C, Hoang HN, Liu L, Fairlie DP. Glucuronic acid as a helix-inducing linker in short peptides. Chem Commun (Camb) 2018; 54:2162-2165. [PMID: 29431766 DOI: 10.1039/c7cc09785a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A new strategy is demonstrated for making peptides helical, using a carbohydrate to bridge between sidechains at each end of a pentapeptide. CD and NMR spectra establish that both an α-helix and a 310-helix structure can form depending upon the bridge.
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Affiliation(s)
- Chongyang Wu
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia.
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44
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Dantas de Araujo A, Perry SR, Fairlie DP. Chemically Diverse Helix-Constrained Peptides Using Selenocysteine Crosslinking. Org Lett 2018; 20:1453-1456. [DOI: 10.1021/acs.orglett.8b00233] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Aline Dantas de Araujo
- Division of Chemistry and
Structural Biology, ARC Centre of Excellence in Advanced Molecular
Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Samuel R. Perry
- Division of Chemistry and
Structural Biology, ARC Centre of Excellence in Advanced Molecular
Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David P. Fairlie
- Division of Chemistry and
Structural Biology, ARC Centre of Excellence in Advanced Molecular
Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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45
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Shepherd NE, Harrison RS, Ruiz-Gomez G, Abbenante G, Mason JM, Fairlie DP. Downsizing the BAD BH3 peptide to small constrained α-helices with improved ligand efficiency. Org Biomol Chem 2018; 14:10939-10945. [PMID: 27819377 DOI: 10.1039/c6ob02185a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bcl2 Homology (BH) proteins can either trigger or prevent programmed cell death or apoptosis. Deregulation of the BH protein family network leads to evasion of apoptosis, uncontrolled proliferation and is a hallmark of cancer. Inhibition of pro-survival BH proteins is a promising chemotherapeutic strategy for certain cancers. We have examined whether helix-constrained peptides based on the BAD BH3 domain (residues 103-127) can be downsized to much smaller more drug-like peptides. We report the preparation, structural characterisation, in vitro Bcl-xL inhibition and leukemic T-cell killing ability of 45 linear, mono-, bi- and tricyclic helical peptidomimetics between 8- and 19-residues in length. We show that the BAD BH3 can be downsized to 8-14 residues and still maintain appreciable affinity for Bcl-xL. In addition, the binding efficiency indices (BEI) of the downsized mimetics are significantly higher than the BAD BH3 and similar stapled BH3 mimetics, approaching drug-like molecules. This suggests that bicyclic and monocyclic mimetics based on BH3 domains are much more efficient binding ligands than the longer peptides which they mimic.
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Affiliation(s)
- Nicholas E Shepherd
- Centre of Excellence in Advanced Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia.
| | - Rosemary S Harrison
- Centre of Excellence in Advanced Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia.
| | - Gloria Ruiz-Gomez
- Centre of Excellence in Advanced Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia. and Structural Bioinformatics, BIOTEC, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Giovanni Abbenante
- Centre of Excellence in Advanced Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia.
| | - Jody M Mason
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - David P Fairlie
- Centre of Excellence in Advanced Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia.
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46
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Haney CM, Werner HM, McKay JJ, Horne WS. Thermodynamic origin of α-helix stabilization by side-chain cross-links in a small protein. Org Biomol Chem 2018; 14:5768-73. [PMID: 27006192 DOI: 10.1039/c6ob00475j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Peptide cross-linking has been widely explored as a means of constraining short sequences into stable folded conformations, most commonly α-helices. The prevailing hypothesis for the origin of helix stabilization is an entropic effect resulting from backbone pre-organization; however, obtaining direct evidence bearing on this hypothesis is challenging. Here, we compare the folding thermodynamics of a small helix-rich protein domain and analogues containing one of three common cross-linking motifs. Analysis of the folding free energy landscapes of linear vs. cyclized species reveal consistent trends in the effect of cyclization on folding energetics, as well as subtle differences based on the chemistry of the cross link. Stabilization in all three systems arises entirely from a reduction in the entropic penalty of folding that more than compensates for an enthalpic destabilization of the folded state.
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Affiliation(s)
- Conor M Haney
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave., Pittsburgh, PA 15260, USA.
| | - Halina M Werner
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave., Pittsburgh, PA 15260, USA.
| | - James J McKay
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave., Pittsburgh, PA 15260, USA.
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave., Pittsburgh, PA 15260, USA.
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47
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Perry SR, Hill TA, de Araujo AD, Hoang HN, Fairlie DP. Contiguous hydrophobic and charged surface patches in short helix-constrained peptides drive cell permeability. Org Biomol Chem 2018; 16:367-371. [DOI: 10.1039/c7ob02952g] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Different ways to get peptides into cells.
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Affiliation(s)
- Samuel R. Perry
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging
- Institute for Molecular Bioscience
- University of Queensland
- Brisbane
- Australia
| | - Timothy A. Hill
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging
- Institute for Molecular Bioscience
- University of Queensland
- Brisbane
- Australia
| | - Aline D. de Araujo
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging
- Institute for Molecular Bioscience
- University of Queensland
- Brisbane
- Australia
| | - Huy N. Hoang
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging
- Institute for Molecular Bioscience
- University of Queensland
- Brisbane
- Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging
- Institute for Molecular Bioscience
- University of Queensland
- Brisbane
- Australia
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48
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Li Y, Wu M, Chang Q, Zhao X. Stapling strategy enables improvement of antitumor activity and proteolytic stability of host-defense peptide hymenochirin-1B. RSC Adv 2018; 8:22268-22275. [PMID: 35541711 PMCID: PMC9081086 DOI: 10.1039/c8ra03446j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 05/14/2018] [Indexed: 12/18/2022] Open
Abstract
Hymenochirin-1B is a cationic, amphipathic, α-helical host-defense peptide with 29 residues, which was isolated from skin secretions of the Congo clawed frog and showed potent cytotoxic activities against a range of tumor cell lines. However, the application of hymenochirin-1B as a drug is limited due to its conformational flexibility and poor proteolytic stability. In this research, a series of hydrocarbon-stapled analogs of hymenochirin-1B were designed, synthesized, and tested. Some analogs showed remarkable improvement not only in α-helicity, but also in antitumor activity and protease resistance when compared to the parent peptide. The results indicated that most stapled peptide analogues possessed improved activities against a series of tumor cells; in particular, the bicyclic stapled peptide H-10 showed promising prospects for novel anti-tumor drug development. Our data demonstrated the important impacts of the all-hydrocarbon crosslink stapling strategy on the biological activity, proteolytic stability and helicity of hymenochirin-1B. A series of stapled peptide analogs of hymenochirin-1B were efficiently prepared by an Fmoc-SPPS procedure. The peptide stapling strategy can improve the helicity, proteolytic stability and tumor cell-killing activity of linear peptide hymenochirin-1B.![]()
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Affiliation(s)
- Yulei Li
- Key Laboratory of Marine Drugs
- Ministry of Education
- School of Medicine and Pharmacy
- Ocean University of China
- Qingdao 266003
| | - Minghao Wu
- Key Laboratory of Marine Drugs
- Ministry of Education
- School of Medicine and Pharmacy
- Ocean University of China
- Qingdao 266003
| | - Qi Chang
- Key Laboratory of Marine Drugs
- Ministry of Education
- School of Medicine and Pharmacy
- Ocean University of China
- Qingdao 266003
| | - Xia Zhao
- Key Laboratory of Marine Drugs
- Ministry of Education
- School of Medicine and Pharmacy
- Ocean University of China
- Qingdao 266003
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49
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Wang SH, Yu J. Structure-based design for binding peptides in anti-cancer therapy. Biomaterials 2017; 156:1-15. [PMID: 29182932 DOI: 10.1016/j.biomaterials.2017.11.024] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 10/30/2017] [Accepted: 11/21/2017] [Indexed: 12/18/2022]
Abstract
The conventional anticancer therapeutics usually lack cancer specificity, leading to damage of normal tissues that patients find hard to tolerate. Ideally, anticancer therapeutics carrying payloads of drugs equipped with cancer targeting peptides can act like "guided missiles" with the capacity of targeted delivery toward many types of cancers. Peptides are amenable for conjugation to nano drugs for functionalization, thereby improving drug delivery and cellular uptake in cancer-targeting therapies. Peptide drugs are often more difficult to design through molecular docking and in silico analysis than small molecules, because peptide structures are more flexible, possess intricate molecular conformations, and undergo complex interactions. In this review, the development and application of strategies for structure-based design of cancer-targeting peptides against GRP78 are discussed. This Review also covers topics related to peptide pharmacokinetics and targeting delivery, including molecular docking studies, features that provide advantages for in vivo use, and properties that influence the cancer-targeting ability. Some advanced technologies and special peptides that can overcome the pharmacokinetic challenges have also been included.
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Affiliation(s)
- Sheng-Hung Wang
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, Chang Gung University, Taoyuan 333, Taiwan
| | - John Yu
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, Chang Gung University, Taoyuan 333, Taiwan; Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.
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50
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Xie M, Zhao H, Liu Q, Zhu Y, Yin F, Liang Y, Jiang Y, Wang D, Hu K, Qin X, Wang Z, Wu Y, Xu N, Ye X, Wang T, Li Z. Structural Basis of Inhibition of ERα-Coactivator Interaction by High-Affinity N-Terminus Isoaspartic Acid Tethered Helical Peptides. J Med Chem 2017; 60:8731-8740. [PMID: 29045135 DOI: 10.1021/acs.jmedchem.7b00732] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Direct inhibition of the protein-protein interaction of ERα and its endogenous coactivators with a cell permeable stabilized peptide may offer a novel, promising strategy for combating ERα positive breast cancers. Here, we report the co-crystal structure of a helical peptide stabilized by a N-terminal unnatural cross-linked aspartic acid (TD) in complex with the ERα ligand binding domain (LBD). We designed a series of peptides and peptide 6 that showed direct and high-affinity binding to ERα with selective antiproliferative activity in ERα positive breast cancer cells. The co-crystal structure of the TD-stabilized peptide 6 in complex with ERα LBD further demonstrates that it forms an α helical conformation and directly binds at the coactivator binding site of ERα. Further studies showed that peptide 6W could potently inhibit cellular ERα's transcriptional activity. This approach demonstrates the potential of TD stabilized peptides to modulate various intracellular protein-protein interactions involved in a range of disorders.
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Affiliation(s)
- Mingsheng Xie
- 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
| | - Qisong Liu
- Shenzhen Key Lab of Tissue Engineering, The Second People's Hospital of Shenzhen , Shenzhen 518035, China
| | - Yujia Zhu
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center , Guangzhou 510060, Guangdong, China
| | - Feng Yin
- School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University , Shenzhen 518055, China
| | - Yujie Liang
- School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University , Shenzhen 518055, China
| | - Yanhong Jiang
- School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University , Shenzhen 518055, China
| | - Dongyuan Wang
- School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University , Shenzhen 518055, China
| | - Kuan Hu
- School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University , Shenzhen 518055, China
| | - Xuan Qin
- School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University , Shenzhen 518055, China
| | - Zichen Wang
- Shenzhen Middle School , Shenzhen 518001, China
| | - Yujie Wu
- Department of Biology, Southern University of Science and Technology , Shenzhen 518055, China
| | - Naihan Xu
- Key Lab in Healthy Science and Technology, Division of Life Science, Shenzhen Graduate School of Tsinghua University , Shenzhen 518055, China
| | - Xiyang Ye
- Department of Gynecology, Shenzhen People's Hospital , Shenzhen 518020, China
| | - Tao Wang
- Department of Biology, Southern University of Science and Technology , Shenzhen 518055, China
| | - Zigang Li
- School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University , Shenzhen 518055, China
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