1
|
Tran DVH, Pham TK, Kim YW. Amine-bearing hydrocarbon cross-links: Tailoring helix stability, hydrophilicity, and synthetic adaptability in peptides. Bioorg Med Chem 2024; 112:117893. [PMID: 39197182 DOI: 10.1016/j.bmc.2024.117893] [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: 06/27/2024] [Revised: 08/16/2024] [Accepted: 08/19/2024] [Indexed: 09/01/2024]
Abstract
This study comprehensively explored the helix-stabilizing effects of amine-bearing hydrocarbon cross-links (ABXs), revealing their context-dependent nature influenced by various structural parameters. Notably, we identified a 9-atom ABX as a robust helix stabilizer, showcasing versatile synthetic adaptability while preserving peptide water solubility. Future investigations are imperative to fully exploit this system's potential and enrich our chemical toolkit for designing innovative peptide-based biomolecules.
Collapse
Affiliation(s)
- Duc V H Tran
- College of Pharmacy, Dongguk University-Seoul, Goyang 10326, Republic of Korea; Intergrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Thanh K Pham
- College of Pharmacy, Dongguk University-Seoul, Goyang 10326, Republic of Korea; Intergrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Young-Woo Kim
- College of Pharmacy, Dongguk University-Seoul, Goyang 10326, Republic of Korea; Intergrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang 10326, Republic of Korea.
| |
Collapse
|
2
|
D'Aniello A, Del Bene A, Mottola S, Mazzarella V, Cutolo R, Campagna E, Di Maro S, Messere A. The bright side of chemistry: Exploring synthetic peptide-based anticancer vaccines. J Pept Sci 2024; 30:e3596. [PMID: 38571326 DOI: 10.1002/psc.3596] [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: 12/15/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 04/05/2024]
Abstract
The present review focuses on synthetic peptide-based vaccine strategies in the context of anticancer intervention, paying attention to critical aspects such as peptide epitope selection, adjuvant integration, and nuanced classification of synthetic peptide cancer vaccines. Within this discussion, we delve into the diverse array of synthetic peptide-based anticancer vaccines, each derived from tumor-associated antigens (TAAs), including melanoma antigen recognized by T cells 1 (Melan-A or MART-1), mucin 1 (MUC1), human epidermal growth factor receptor 2 (HER-2), tumor protein 53 (p53), human telomerase reverse transcriptase (hTERT), survivin, folate receptor (FR), cancer-testis antigen 1 (NY-ESO-1), and prostate-specific antigen (PSA). We also describe the synthetic peptide-based vaccines developed for cancers triggered by oncovirus, such as human papillomavirus (HPV), and hepatitis C virus (HCV). Additionally, the potential synergy of peptide-based vaccines with common therapeutics in cancer was considered. The last part of our discussion deals with the realm of the peptide-based vaccines delivery, highlighting its role in translating the most promising candidates into effective clinical strategies. Although this discussion does not cover all the ongoing peptide vaccine investigations, it aims at offering valuable insights into the chemical modifications and the structural complexities of anticancer peptide-based vaccines.
Collapse
Affiliation(s)
- Antonia D'Aniello
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Alessandra Del Bene
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Salvatore Mottola
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Vincenzo Mazzarella
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Roberto Cutolo
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Erica Campagna
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Salvatore Di Maro
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", Caserta, Italy
- Interuniversity Research Centre on Bioactive Peptides (CIRPEB), Naples, Italy
| | - Anna Messere
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", Caserta, Italy
- Interuniversity Research Centre on Bioactive Peptides (CIRPEB), Naples, Italy
| |
Collapse
|
3
|
Ding Y, Pedersen SS, Wang H, Xiang B, Wang Y, Yang Z, Gao Y, Morosan E, Jones MR, Xiao H, Ball ZT. Selective Macrocyclization of Unprotected Peptides with an Ex Situ Gaseous Linchpin Reagent. Angew Chem Int Ed Engl 2024; 63:e202405344. [PMID: 38753429 DOI: 10.1002/anie.202405344] [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: 03/18/2024] [Indexed: 07/16/2024]
Abstract
Peptide cyclization has dramatic effects on a variety of important properties, enhancing metabolic stability, limiting conformational flexibility, and altering cellular entry and intracellular localization. The hydrophilic, polyfunctional nature of peptides creates chemoselectivity challenges in macrocyclization, especially for natural sequences without biorthogonal handles. Herein, we describe a gaseous sulfonyl chloride derived reagent that achieves amine-amine, amine-phenol, and amine-aniline crosslinking through a minimalist linchpin strategy that affords macrocyclic urea or carbamate products. The cyclization reaction is metal-mediated and involves a novel application of sulfine species that remains unexplored in aqueous or biological contexts. The aqueous method delivers unique cyclic or bicyclic topologies directly from a variety of natural bioactive peptides without the need for protecting-group strategies.
Collapse
Affiliation(s)
- Yuxuan Ding
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| | - Simon S Pedersen
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
- Carbon Dioxide Activation Center (CADIAC), Interdisciplinary Nanoscience Center, Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Haofan Wang
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| | - Baorui Xiang
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| | - Yixian Wang
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| | - Zhi Yang
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| | - Yuxiang Gao
- Department of Physics and Astronomy, Rice University, Houston, Texas, 77005, United States
| | - Emilia Morosan
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
- Department of Physics and Astronomy, Rice University, Houston, Texas, 77005, United States
| | - Matthew R Jones
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| | - Han Xiao
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| | - Zachary T Ball
- Department of Chemistry, Rice University, Houston, Texas, 77005, United States
| |
Collapse
|
4
|
Cao L, Wang L. Biospecific Chemistry for Covalent Linking of Biomacromolecules. Chem Rev 2024; 124:8516-8549. [PMID: 38913432 PMCID: PMC11240265 DOI: 10.1021/acs.chemrev.4c00066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Interactions among biomacromolecules, predominantly noncovalent, underpin biological processes. However, recent advancements in biospecific chemistry have enabled the creation of specific covalent bonds between biomolecules, both in vitro and in vivo. This Review traces the evolution of biospecific chemistry in proteins, emphasizing the role of genetically encoded latent bioreactive amino acids. These amino acids react selectively with adjacent natural groups through proximity-enabled bioreactivity, enabling targeted covalent linkages. We explore various latent bioreactive amino acids designed to target different protein residues, ribonucleic acids, and carbohydrates. We then discuss how these novel covalent linkages can drive challenging protein properties and capture transient protein-protein and protein-RNA interactions in vivo. Additionally, we examine the application of covalent peptides as potential therapeutic agents and site-specific conjugates for native antibodies, highlighting their capacity to form stable linkages with target molecules. A significant focus is placed on proximity-enabled reactive therapeutics (PERx), a pioneering technology in covalent protein therapeutics. We detail its wide-ranging applications in immunotherapy, viral neutralization, and targeted radionuclide therapy. Finally, we present a perspective on the existing challenges within biospecific chemistry and discuss the potential avenues for future exploration and advancement in this rapidly evolving field.
Collapse
Affiliation(s)
- Li Cao
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, United States
| | - Lei Wang
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, United States
| |
Collapse
|
5
|
Xue J, Fu Y, Li H, Zhang T, Cong W, Hu H, Lu Z, Yan F, Li Y. All-hydrocarbon stapling enables improvement of antimicrobial activity and proteolytic stability of peptide Figainin 2. J Pept Sci 2024; 30:e3566. [PMID: 38271799 DOI: 10.1002/psc.3566] [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: 11/23/2023] [Revised: 12/21/2023] [Accepted: 12/28/2023] [Indexed: 01/27/2024]
Abstract
Figainin 2 is a cationic, hydrophobic, α-helical host-defense peptide with 28 residues, which was isolated from the skin secretions of the Chaco tree frog. It shows potent inhibitory activity against both Gram-negative and Gram-positive pathogens and has garnered considerable interest in developing novel classes of natural antibacterial agents. However, as a linear peptide, conformational flexibility and poor proteolytic stability hindered its development as antibacterial agent. To alleviate its susceptibility to proteolytic degradation and improve its antibacterial activity, a series of hydrocarbon-stable analogs of Figainin 2 were synthesized and evaluated for their secondary structure, protease stability, antimicrobial, and hemolytic activities. Among them, F2-12 showed significant improvement in protease resistance and antimicrobial activity compared to that of the template peptide. This study provides a promising strategy for the development of antimicrobial drugs.
Collapse
Affiliation(s)
- Jingwen Xue
- School of Medicine, Weifang Medical University, Weifang, Shandong, People's Republic of China
| | - Yinxue Fu
- School of Pharmaceutical Sciences and Institute of Materia Medica, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| | - Huang Li
- School of Medicine, Shanghai University, Shanghai, People's Republic of China
| | - Ting Zhang
- School of Pharmaceutical Sciences and Institute of Materia Medica, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| | - Wei Cong
- School of Medicine, Shanghai University, Shanghai, People's Republic of China
| | - Honggang Hu
- School of Medicine, Shanghai University, Shanghai, People's Republic of China
| | - Zhiyuan Lu
- School of Pharmaceutical Sciences and Institute of Materia Medica, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| | - Fang Yan
- School of Medicine, Weifang Medical University, Weifang, Shandong, People's Republic of China
| | - Yulei Li
- School of Pharmaceutical Sciences and Institute of Materia Medica, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| |
Collapse
|
6
|
Brango-Vanegas J, Leite ML, Macedo MLR, Cardoso MH, Franco OL. Capping motifs in antimicrobial peptides and their relevance for improved biological activities. Front Chem 2024; 12:1382954. [PMID: 38873409 PMCID: PMC11169826 DOI: 10.3389/fchem.2024.1382954] [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: 02/06/2024] [Accepted: 05/13/2024] [Indexed: 06/15/2024] Open
Abstract
N-capping (N-cap) and C-capping (C-cap) in biologically active peptides, including specific amino acids or unconventional group motifs, have been shown to modulate activity against pharmacological targets by interfering with the peptide's secondary structure, thus generating unusual scaffolds. The insertion of capping motifs in linear peptides has been shown to prevent peptide degradation by reducing its susceptibility to proteolytic cleavage, and the replacement of some functional groups by unusual groups in N- or C-capping regions in linear peptides has led to optimized peptide variants with improved secondary structure and enhanced activity. Furthermore, some essential amino acid residues that, when placed in antimicrobial peptide (AMP) capping regions, are capable of complexing metals such as Cu2+, Ni2+, and Zn2+, give rise to the family known as metallo-AMPs, which are capable of boosting antimicrobial efficacy, as well as other activities. Therefore, this review presents and discusses the different strategies for creating N- and C-cap motifs in AMPs, aiming at fine-tuning this class of antimicrobials.
Collapse
Affiliation(s)
- José Brango-Vanegas
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
- S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
| | - Michel Lopes Leite
- Departamento de Biologia Molecular, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, Brazil
| | - Maria L. R. Macedo
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, Universidade Federal de Mato Grosso do Sul, Cidade Universitária, Campo Grande, Brazil
| | - Marlon H. Cardoso
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
- S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, Universidade Federal de Mato Grosso do Sul, Cidade Universitária, Campo Grande, Brazil
| | - Octávio Luiz Franco
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
- S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
| |
Collapse
|
7
|
Britton D, Katsara O, Mishkit O, Wang A, Pandya N, Liu C, Mao H, Legocki J, Jia S, Xiao Y, Aristizabal O, Paul D, Deng Y, Schneider R, Wadghiri YZ, Montclare JK. Engineered coiled-coil HIF1α protein domain mimic. Biomater Sci 2024; 12:2951-2959. [PMID: 38656316 PMCID: PMC11191652 DOI: 10.1039/d4bm00354c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The development of targeted anti-cancer therapeutics offers the potential for increased efficacy of drugs and diagnostics. Utilizing modalities agnostic to tumor type, such as the hypoxic tumor microenvironment (TME), may assist in the development of universal tumor targeting agents. The hypoxia-inducible factor (HIF), in particular HIF1, plays a key role in tumor adaptation to hypoxia, and inhibiting its interaction with p300 has been shown to provide therapeutic potential. Using a multivalent assembled protein (MAP) approach based on the self-assembly of the cartilage oligomeric matrix protein coiled-coil (COMPcc) domain fused to the critical residues of the C-terminal transactivation domain (C-TAD) of the α subunit of HIF1 (HIF1α), we generate HIF1α-MAP (H-MAP). The resulting H-MAP demonstrates picomolar binding affinity to p300, the ability to downregulate hypoxia-inducible genes, and in vivo tumor targeting capability.
Collapse
Affiliation(s)
- Dustin Britton
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Olga Katsara
- Department of Microbiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Orin Mishkit
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Andrew Wang
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
- Department of Biomedical Engineering, State University of New York Downstate Medical Center, Brooklyn, New York, 11203, USA
- College of Medicine, State University of New York Downstate Medical Center, Brooklyn, New York, 11203, USA
| | - Neelam Pandya
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Chengliang Liu
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Heather Mao
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Jakub Legocki
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Sihan Jia
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Yingxin Xiao
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Orlando Aristizabal
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Deven Paul
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Yan Deng
- Microscopy Laboratory, New York University Langone Health, New York, NY, 10016, USA
| | - Robert Schneider
- Department of Microbiology, New York University School of Medicine, New York, New York, 10016, USA
- Department of Radiation Oncology, New York University School of Medicine, New York, New York, 10016, USA
| | - Youssef Z Wadghiri
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Department of Chemistry, New York University, New York, New York, 10012, USA
- Department of Biomaterials, New York University College of Dentistry, New York, New York, 10010, USA
- Department of Biomedical Engineering, New York University, New York, NY, 11201, USA
| |
Collapse
|
8
|
Durukan C, Arbore F, Klintrot R, Bigiotti C, Ilie IM, Vreede J, Grossmann TN, Hennig S. Binding Dynamics of a Stapled Peptide Targeting the Transcription Factor NF-Y. Chembiochem 2024; 25:e202400020. [PMID: 38470946 DOI: 10.1002/cbic.202400020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/10/2024] [Accepted: 03/11/2024] [Indexed: 03/14/2024]
Abstract
Transcription factors (TFs) play a central role in gene regulation, and their malfunction can result in a plethora of severe diseases. TFs are therefore interesting therapeutic targets, but their involvement in protein-protein interaction networks and the frequent lack of well-defined binding pockets render them challenging targets for classical small molecules. As an alternative, peptide-based scaffolds have proven useful, in particular with an α-helical active conformation. Peptide-based strategies often require extensive structural optimization efforts, which could benefit from a more detailed understanding of the dynamics in inhibitor/protein interactions. In this study, we investigate how truncated stapled α-helical peptides interact with the transcription factor Nuclear Factor-Y (NF-Y). We identified a 13-mer minimal binding core region, for which two crystal structures with an altered C-terminal peptide conformation when bound to NF-Y were obtained. Subsequent molecular dynamics simulations confirmed that the C-terminal part of the stapled peptide is indeed relatively flexible while still showing defined interactions with NF-Y. Our findings highlight the importance of flexibility in the bound state of peptides, which can contribute to overall binding affinity.
Collapse
Affiliation(s)
- Canan Durukan
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Federica Arbore
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Rasmus Klintrot
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Carlo Bigiotti
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
- Amsterdam Center for Multiscale Modeling (ACMM), University of Amsterdam, P.O. Box, 94157, 1090 GD, Amsterdam, The Netherlands
| | - Ioana M Ilie
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
- Amsterdam Center for Multiscale Modeling (ACMM), University of Amsterdam, P.O. Box, 94157, 1090 GD, Amsterdam, The Netherlands
| | - Jocelyne Vreede
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
- Amsterdam Center for Multiscale Modeling (ACMM), University of Amsterdam, P.O. Box, 94157, 1090 GD, Amsterdam, The Netherlands
| | - Tom N Grossmann
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Sven Hennig
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| |
Collapse
|
9
|
Li Y, Wu M, Fu Y, Xue J, Yuan F, Qu T, Rissanou AN, Wang Y, Li X, Hu H. Therapeutic stapled peptides: Efficacy and molecular targets. Pharmacol Res 2024; 203:107137. [PMID: 38522761 DOI: 10.1016/j.phrs.2024.107137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 03/26/2024]
Abstract
Peptide stapling, by employing a stable, preformed alpha-helical conformation, results in the production of peptides with improved membrane permeability and enhanced proteolytic stability, compared to the original peptides, and provides an effective solution to accelerate the rapid development of peptide drugs. Various reviews present peptide stapling chemistries, anchoring residues and one- or two-component cyclization, however, therapeutic stapled peptides have not been systematically summarized, especially focusing on various disease-related targets. This review highlights the latest advances in therapeutic peptide drug development facilitated by the application of stapling technology, including different stapling techniques, synthetic accessibility, applicability to biological targets, potential for solving biological problems, as well as the current status of development. Stapled peptides as therapeutic drug candidates have been classified and analysed mainly by receptor- and ligand-based stapled peptide design against various diseases, including cancer, infectious diseases, inflammation, and diabetes. This review is expected to provide a comprehensive reference for the rational design of stapled peptides for different diseases and targets to facilitate the development of therapeutic peptides with enhanced pharmacokinetic and biological properties.
Collapse
Affiliation(s)
- Yulei Li
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China.
| | - Minghao Wu
- School of Medicine, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Yinxue Fu
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Jingwen Xue
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Fei Yuan
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Tianci Qu
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Anastassia N Rissanou
- Theoretical & Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, Athens 11635, Greece
| | - Yilin Wang
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, 131 Dong'an Road, Shanghai 200032, China
| | - Xiang Li
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, China.
| | - Honggang Hu
- School of Medicine, Shanghai University, 99 Shangda Road, Shanghai 200444, China.
| |
Collapse
|
10
|
Merz ML, Habeshian S, Li B, David JAGL, Nielsen AL, Ji X, Il Khwildy K, Duany Benitez MM, Phothirath P, Heinis C. De novo development of small cyclic peptides that are orally bioavailable. Nat Chem Biol 2024; 20:624-633. [PMID: 38155304 PMCID: PMC11062899 DOI: 10.1038/s41589-023-01496-y] [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: 03/31/2023] [Accepted: 11/02/2023] [Indexed: 12/30/2023]
Abstract
Cyclic peptides can bind challenging disease targets with high affinity and specificity, offering enormous opportunities for addressing unmet medical needs. However, as with biological drugs, most cyclic peptides cannot be applied orally because they are rapidly digested and/or display low absorption in the gastrointestinal tract, hampering their development as therapeutics. In this study, we developed a combinatorial synthesis and screening approach based on sequential cyclization and one-pot peptide acylation and screening, with the possibility of simultaneously interrogating activity and permeability. In a proof of concept, we synthesized a library of 8,448 cyclic peptides and screened them against the disease target thrombin. Our workflow allowed multiple iterative cycles of library synthesis and yielded cyclic peptides with nanomolar affinities, high stabilities and an oral bioavailability (%F) as high as 18% in rats. This method for generating orally available peptides is general and provides a promising push toward unlocking the full potential of peptides as therapeutics.
Collapse
Affiliation(s)
- Manuel L Merz
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sevan Habeshian
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Bo Li
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Jean-Alexandre G L David
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Alexander L Nielsen
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Xinjian Ji
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Khaled Il Khwildy
- Center of Phenogenomics, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Maury M Duany Benitez
- Center of Phenogenomics, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Phoukham Phothirath
- Center of Phenogenomics, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| |
Collapse
|
11
|
Mi T, Gao Z, Mituta Z, Burgess K. Dual-Capped Helical Interface Mimics. J Am Chem Soc 2024; 146:10331-10341. [PMID: 38573124 PMCID: PMC11027154 DOI: 10.1021/jacs.3c11717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/25/2024] [Accepted: 03/01/2024] [Indexed: 04/05/2024]
Abstract
Disruption of protein-protein interactions is medicinally important. Interface helices may be mimicked in helical probes featuring enhanced rigidities, binding to protein targets, stabilities in serum, and cell uptake. This form of mimicry is dominated by stapling between side chains of helical residues: there has been less progress on helical N-caps, and there were no generalizable C-caps. Conversely, in natural proteins, helicities are stabilized and terminated by C- and N-caps but not staples. Bicyclic caps previously introduced by us enable interface helical mimicry featuring rigid synthetic caps at both termini in this work. An unambiguously helical dual-capped system proved to be conformationally stable, binding cyclins A and E, and showed impressive cellular uptake. In addition, the dual-capped mimic was completely resistant to proteolysis in serum over an extended period when compared with "gold standard" hydrocarbon-stapled controls. Dual-capped peptidomimetics are a new, generalizable paradigm for helical interface probe design.
Collapse
Affiliation(s)
- Tianxiong Mi
- Department
of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
| | - Zhe Gao
- Department
of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
| | - Zeynep Mituta
- ZentriForce
Pharma Research GmbH, Carl-Friedrich-Gauss-Ring 5, 69124 Heidelberg, Germany
| | - Kevin Burgess
- Department
of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
| |
Collapse
|
12
|
Kim H, Taslakjian B, Kim S, Tirrell MV, Guler MO. Therapeutic Peptides, Proteins and their Nanostructures for Drug Delivery and Precision Medicine. Chembiochem 2024; 25:e202300831. [PMID: 38408302 DOI: 10.1002/cbic.202300831] [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: 12/08/2023] [Revised: 02/05/2024] [Accepted: 02/22/2024] [Indexed: 02/28/2024]
Abstract
Peptide and protein nanostructures with tunable structural features, multifunctionality, biocompatibility and biomolecular recognition capacity enable development of efficient targeted drug delivery tools for precision medicine applications. In this review article, we present various techniques employed for the synthesis and self-assembly of peptides and proteins into nanostructures. We discuss design strategies utilized to enhance their stability, drug-loading capacity, and controlled release properties, in addition to the mechanisms by which peptide nanostructures interact with target cells, including receptor-mediated endocytosis and cell-penetrating capabilities. We also explore the potential of peptide and protein nanostructures for precision medicine, focusing on applications in personalized therapies and disease-specific targeting for diagnostics and therapeutics in diseases such as cancer.
Collapse
Affiliation(s)
- HaRam Kim
- The Pritzker School of Molecular Engineering, The University of Chicago, 5640 S. Ellis Ave., Chicago, 60637, IL, USA
| | - Boghos Taslakjian
- The Pritzker School of Molecular Engineering, The University of Chicago, 5640 S. Ellis Ave., Chicago, 60637, IL, USA
| | - Sarah Kim
- The Pritzker School of Molecular Engineering, The University of Chicago, 5640 S. Ellis Ave., Chicago, 60637, IL, USA
| | - Matthew V Tirrell
- The Pritzker School of Molecular Engineering, The University of Chicago, 5640 S. Ellis Ave., Chicago, 60637, IL, USA
| | - Mustafa O Guler
- The Pritzker School of Molecular Engineering, The University of Chicago, 5640 S. Ellis Ave., Chicago, 60637, IL, USA
| |
Collapse
|
13
|
Cheung TL, Tam LKB, Tam WS, Zhang L, Kai HY, Thor W, Wu Y, Lam PL, Yeung YH, Xie C, Chau HF, Lo WS, Zhang T, Wong KL. Facile Peptide Macrocyclization and Multifunctionalization via Cyclen Installation. SMALL METHODS 2024:e2400006. [PMID: 38593368 DOI: 10.1002/smtd.202400006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/28/2024] [Indexed: 04/11/2024]
Abstract
Cyclen-peptide bioconjugates are usually prepared in multiple steps that require individual preparation and purification of the cyclic peptide and hydrophilic cyclen derivatives. An efficient strategy is discovered for peptide cyclization and functionalization toward lanthanide probe via three components intermolecular crosslinking on solid-phase peptide synthesis with high conversion yield. Multifunctionality can be conferred by introducing different modular parts or/and metal ions on the cyclen-embedded cyclopeptide. As a proof-of-concept, a luminescent Eu3+ complex and a Gd3+-based contrasting agent for in vitro optical imaging and in vivo magnetic resonance imaging, respectively, are demonstrated through utilizing this preparation of cyclen-embedded cyclic arginylglycylaspartic acid (RGD) peptide.
Collapse
Affiliation(s)
- Tsz-Lam Cheung
- Department of Chemistry, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Kowloon, Hong Kong, China
| | - Leo K B Tam
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Wing-Sze Tam
- Department of Chemistry, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Kowloon, Hong Kong, China
| | - Leilei Zhang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, and College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Hei-Yui Kai
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Waygen Thor
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Yue Wu
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
- Department of Surgery, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China
| | - Pak-Lun Lam
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Yik-Hoi Yeung
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Chen Xie
- Department of Clinical Oncology, University of Hong Kong, Pok Fu Lam, Hong Kong Island, Hong Kong, China
| | - Ho-Fai Chau
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Wai-Sum Lo
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Tao Zhang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, and College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Ka-Leung Wong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| |
Collapse
|
14
|
Gaikwad V, Choudhury AR, Chakrabarti R. Decoding the dynamics of BCL9 triazole stapled peptide. Biophys Chem 2024; 307:107197. [PMID: 38335808 DOI: 10.1016/j.bpc.2024.107197] [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: 10/13/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024]
Abstract
BCL9 is a key protein in Wnt signaling pathway. It acts as a transcriptional co-activator to β-catenin, and dysregulation in this pathway leads to tumor growth. Inhibiting such a protein-protein interaction is considered as a therapeutic challenge. The interaction between β-catenin and BCL9 is facilitated by a 23-residue helical domain from BCL9 and a hydrophobic groove of β-catenin. To prevent this interaction, a peptide that mimics the alpha-helical domain of BCL9 can be designed. Stapling is considered a successful strategy in the pursuit of designing such peptides in which amino acids side are stitched together using chemical moieties. Among the various types of cross-linkers, triazole is the most rapid and effective one synthesized via click reaction. However, the underlying interactions behind maintaining the secondary structure of stapled peptides remain less explored. In the current work, we employed the molecular dynamics simulation to study the conformational behavior of the experimentally synthesized single and double triazole stapled BCL9 peptide. Upon the addition of a triazole staple, there is a significant reduction in the conformational space of BCL9. The helical character of the stapled peptide increases with an increase in separation between the triazole cross-linkers. Also, we encompassed the Replica Exchange with Solute Tempering (REST2) simulation to validate the high-temperature response of the stapled peptide. From REST2, the PCA and t-SNE show the reduction in distinct cluster formation on the addition of triazole staple. Our study infers further development of these triazole-stapled BCL9 peptides into effective inhibitors to target the interaction between β-catenin and BCL9.
Collapse
Affiliation(s)
- Vikram Gaikwad
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Asha Rani Choudhury
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| |
Collapse
|
15
|
de Raffele D, Ilie IM. Unlocking novel therapies: cyclic peptide design for amyloidogenic targets through synergies of experiments, simulations, and machine learning. Chem Commun (Camb) 2024; 60:632-645. [PMID: 38131333 DOI: 10.1039/d3cc04630c] [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: 12/23/2023]
Abstract
Existing therapies for neurodegenerative diseases like Parkinson's and Alzheimer's address only their symptoms and do not prevent disease onset. Common therapeutic agents, such as small molecules and antibodies struggle with insufficient selectivity, stability and bioavailability, leading to poor performance in clinical trials. Peptide-based therapeutics are emerging as promising candidates, with successful applications for cardiovascular diseases and cancers due to their high bioavailability, good efficacy and specificity. In particular, cyclic peptides have a long in vivo stability, while maintaining a robust antibody-like binding affinity. However, the de novo design of cyclic peptides is challenging due to the lack of long-lived druggable pockets of the target polypeptide, absence of exhaustive conformational distributions of the target and/or the binder, unknown binding site, methodological limitations, associated constraints (failed trials, time, money) and the vast combinatorial sequence space. Hence, efficient alignment and cooperation between disciplines, and synergies between experiments and simulations complemented by popular techniques like machine-learning can significantly speed up the therapeutic cyclic-peptide development for neurodegenerative diseases. We review the latest advancements in cyclic peptide design against amyloidogenic targets from a computational perspective in light of recent advancements and potential of machine learning to optimize the design process. We discuss the difficulties encountered when designing novel peptide-based inhibitors and we propose new strategies incorporating experiments, simulations and machine learning to design cyclic peptides to inhibit the toxic propagation of amyloidogenic polypeptides. Importantly, these strategies extend beyond the mere design of cyclic peptides and serve as template for the de novo generation of (bio)materials with programmable properties.
Collapse
Affiliation(s)
- Daria de Raffele
- University of Amsterdam, van 't Hoff Institute for Molecular Sciences, Science Park 904, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands.
- Amsterdam Center for Multiscale Modeling (ACMM), University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Ioana M Ilie
- University of Amsterdam, van 't Hoff Institute for Molecular Sciences, Science Park 904, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands.
- Amsterdam Center for Multiscale Modeling (ACMM), University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| |
Collapse
|
16
|
Abstract
Cyclic peptides are fascinating molecules abundantly found in nature and exploited as molecular format for drug development as well as other applications, ranging from research tools to food additives. Advances in peptide technologies made over many years through improved methods for synthesis and drug development have resulted in a steady stream of new drugs, with an average of around one cyclic peptide drug approved per year. Powerful technologies for screening random peptide libraries, and de novo generating ligands, have enabled the development of cyclic peptide drugs independent of naturally derived molecules and now offer virtually unlimited development opportunities. In this review, we feature therapeutically relevant cyclic peptides derived from nature and discuss the unique properties of cyclic peptides, the enormous technological advances in peptide ligand development in recent years, and current challenges and opportunities for developing cyclic peptides that address unmet medical needs.
Collapse
Affiliation(s)
- Xinjian Ji
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Alexander L Nielsen
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| |
Collapse
|
17
|
Chandramohan A, Josien H, Yuen TY, Duggal R, Spiegelberg D, Yan L, Juang YCA, Ge L, Aronica PG, Kaan HYK, Lim YH, Peier A, Sherborne B, Hochman J, Lin S, Biswas K, Nestor M, Verma CS, Lane DP, Sawyer TK, Garbaccio R, Henry B, Kannan S, Brown CJ, Johannes CW, Partridge AW. Design-rules for stapled peptides with in vivo activity and their application to Mdm2/X antagonists. Nat Commun 2024; 15:489. [PMID: 38216578 PMCID: PMC10786919 DOI: 10.1038/s41467-023-43346-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 11/06/2023] [Indexed: 01/14/2024] Open
Abstract
Although stapled α-helical peptides can address challenging targets, their advancement is impeded by poor understandings for making them cell permeable while avoiding off-target toxicities. By synthesizing >350 molecules, we present workflows for identifying stapled peptides against Mdm2(X) with in vivo activity and no off-target effects. Key insights include a clear correlation between lipophilicity and permeability, removal of positive charge to avoid off-target toxicities, judicious anionic residue placement to enhance solubility/behavior, optimization of C-terminal length/helicity to enhance potency, and optimization of staple type/number to avoid polypharmacology. Workflow application gives peptides with >292x improved cell proliferation potencies and no off-target cell proliferation effects ( > 3800x on-target index). Application of these 'design rules' to a distinct Mdm2(X) peptide series improves ( > 150x) cellular potencies and removes off-target toxicities. The outlined workflow should facilitate therapeutic impacts, especially for those targets such as Mdm2(X) that have hydrophobic interfaces and are targetable with a helical motif.
Collapse
Affiliation(s)
| | | | - Tsz Ying Yuen
- Institute of Sustainability for Chemicals, Energy and Environment, Agency for Science, Technology and Research (ASTAR), Singapore, 138665, Singapore
| | | | - Diana Spiegelberg
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Lin Yan
- Merck & Co., Inc., Kenilworth, NJ, 07033, USA
| | | | - Lan Ge
- Merck & Co., Inc., Kenilworth, NJ, 07033, USA
| | - Pietro G Aronica
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore, 138671, Singapore
| | | | - Yee Hwee Lim
- Institute of Sustainability for Chemicals, Energy and Environment, Agency for Science, Technology and Research (ASTAR), Singapore, 138665, Singapore
| | | | | | | | | | | | - Marika Nestor
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore, 138671, Singapore
| | - David P Lane
- Institute of Molecular and Cell Biology, Singapore, 138673, Singapore
| | | | | | - Brian Henry
- MSD International, Singapore, 138665, Singapore.
| | - Srinivasaraghavan Kannan
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore, 138671, Singapore.
| | | | - Charles W Johannes
- Institute of Sustainability for Chemicals, Energy and Environment, Agency for Science, Technology and Research (ASTAR), Singapore, 138665, Singapore.
- Institute of Molecular and Cell Biology, Singapore, 138673, Singapore.
- EPOC Scientific LLC, Stoneham, MA, 02180, USA.
| | - Anthony W Partridge
- MSD International, Singapore, 138665, Singapore.
- Genentech, South San Francisco, CA, 94080, USA.
| |
Collapse
|
18
|
Li J, Tan YS, Verma CS. Dissecting the geometric and hydrophobic constraints of stapled peptides. Proteins 2024. [PMID: 38196284 DOI: 10.1002/prot.26662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/01/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024]
Abstract
Stapled peptides are a promising class of molecules with potential as highly specific probes of protein-protein interactions and as therapeutics. Hydrocarbon stapling affects the peptide properties through the interplay of two factors: enhancing the overall hydrophobicity and constraining the conformational flexibility. By constructing a series of virtual peptides, we study the role of each factor in modulating the structural properties of a hydrocarbon-stapled peptide PM2, which has been shown to enter cells, engage its target Mouse Double Minute 2 (MDM2), and activate p53. Hamiltonian replica exchange molecular dynamics (HREMD) simulations suggest that hydrocarbon stapling favors helical populations of PM2 through a combination of the geometric constraints and the enhanced hydrophobicity of the peptide. To further understand the conformational landscape of the stapled peptides along the binding pathway, we performed HREMD simulations by restraining the peptide at different distances from MDM2. When the peptide approaches MDM2, the binding pocket undergoes dehydration which appears to be greater in the presence of the stapled peptide compared with the linear peptide. In the binding pocket, the helicity of the stapled peptide is increased due to the favorable interactions between the peptide residues as well as the staple and the microenvironment of the binding pocket, contributing to enhanced affinity. The dissection of the multifaceted mechanism of hydrocarbon stapling into individual factors not only deepens fundamental understanding of peptide stapling, but also provides guidelines for the design of new stapled peptides.
Collapse
Affiliation(s)
- Jianguo Li
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Singapore Eye Research Institute, Singapore, Singapore
| | - Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| |
Collapse
|
19
|
Paquette AR, Boddy CN. Double Stranded DNA Binding Stapled Peptides: An Emerging Tool for Transcriptional Regulation. Chembiochem 2023; 24:e202300594. [PMID: 37750576 DOI: 10.1002/cbic.202300594] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 09/27/2023]
Abstract
Stapled peptides have rapidly established themselves as a powerful technique to mimic α-helical interactions with a short peptide sequence. There are many examples of stapled peptides that successfully disrupt α-helix-mediated protein-protein interactions, with an example currently in clinical trials. DNA-protein interactions are also often mediated by α-helices and are involved in all transcriptional regulation processes. Unlike DNA-binding small molecules, which typically lack DNA sequence selectivity, DNA-binding proteins bind with high affinity and high selectivity. These are ideal candidates for the design DNA-binding stapled peptides. Despite the parallel to protein-protein interaction disrupting stapled peptides and the need for sequence specific DNA binders, there are very few DNA-binding stapled peptides. In this review we examine all the known DNA-binding stapled peptides. Their design concepts are compared to stapled peptides that disrupt protein-protein interactions and based on the few examples in the literature, DNA-binding stapled peptide trends are discussed.
Collapse
Affiliation(s)
- André R Paquette
- Department of Chemistry and Biomolecular Sciences, The University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Christopher N Boddy
- Department of Chemistry and Biomolecular Sciences, The University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| |
Collapse
|
20
|
Liu XY, Cai W, Ronceray N, Radenovic A, Fierz B, Waser J. Synthesis of Fluorescent Cyclic Peptides via Gold(I)-Catalyzed Macrocyclization. J Am Chem Soc 2023; 145:26525-26531. [PMID: 38035635 PMCID: PMC10722513 DOI: 10.1021/jacs.3c09261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 12/02/2023]
Abstract
Rapid and efficient cyclization methods that form structurally novel peptidic macrocycles are of high importance for medicinal chemistry. Herein, we report the first gold(I)-catalyzed macrocyclization of peptide-EBXs (ethynylbenziodoxolones) via C2-Trp C-H activation. This reaction was carried out in the presence of protecting group free peptide sequences and is enabled by a simple commercial gold catalyst (AuCl·Me2S). The method displayed a rapid reaction rate (within 10 min), wide functional group tolerance (27 unprotected peptides were cyclized), and up to 86% isolated yield. The obtained highly conjugated cyclic peptide linker, formed through C-H alkynylation, can be directly applied to live-cell imaging as a fluorescent probe without further attachment of fluorophores.
Collapse
Affiliation(s)
- Xing-Yu Liu
- Laboratory
of Catalysis and Organic Synthesis, École
Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCSO, 1015 Lausanne, Switzerland
| | - Wei Cai
- Laboratory
of Biophysical Chemistry of Macromolecules, Institute of Chemical
Sciences and Engineering, École Polytechnique
Fédérale de Lausanne, EPFL SB ISIC LCBM, 1015 Lausanne, Switzerland
| | - Nathan Ronceray
- Laboratory
of Nanoscale Biology, School of Engineering, Institute of Bioengineering, EPFL STI IBI LBEN, 1015 Lausanne, Switzerland
| | - Aleksandra Radenovic
- Laboratory
of Nanoscale Biology, School of Engineering, Institute of Bioengineering, EPFL STI IBI LBEN, 1015 Lausanne, Switzerland
| | - Beat Fierz
- Laboratory
of Biophysical Chemistry of Macromolecules, Institute of Chemical
Sciences and Engineering, École Polytechnique
Fédérale de Lausanne, EPFL SB ISIC LCBM, 1015 Lausanne, Switzerland
| | - Jerome Waser
- Laboratory
of Catalysis and Organic Synthesis, École
Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCSO, 1015 Lausanne, Switzerland
| |
Collapse
|
21
|
Mi T, Siriwibool S, Burgess K. Streamlined Protein-Protein Interface Loop Mimicry. Angew Chem Int Ed Engl 2023; 62:e202307092. [PMID: 37849440 DOI: 10.1002/anie.202307092] [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: 06/01/2023] [Revised: 10/12/2023] [Accepted: 10/17/2023] [Indexed: 10/19/2023]
Abstract
Cyclic peptides comprising endocyclic organic fragments, "cyclo-organopeptides", can be probes for perturbing protein-protein interactions (PPIs). Finding loop mimics is difficult because of high conformational variability amongst targets. Backbone Matching (BM), introduced here, helps solve this problem in the illustrative cases by facilitating efficient evaluation of virtual cyclo-organopeptide core-structure libraries. Thus, 86 rigid organic fragments were selected to build a library of 602 cyclo-organopeptides comprising Ala and organic parts: "cyclo-{-(Ala)n -organo-}". The central hypothesis is "hit" library members have accessible low energy conformers corresponding to backbone structures of target protein loops, while library members which cannot attain this conformation are probably unworthy of further evaluation. BM thereby prioritizes candidate loop mimics, so that less than 10 cyclo-organopeptides are needed to be prepared to find leads for two illustrative PPIs: iNOS ⋅ SPSB2, and uPA ⋅ uPAR.
Collapse
Affiliation(s)
- Tianxiong Mi
- Department of Chemistry, Texas A & M University, 77842, College Station, TX, USA
| | - Siriwalee Siriwibool
- School of Chemistry, Institute of Science, Suranaree University of Technology, 30000, Nakhon Ratchasima, Thailand
| | - Kevin Burgess
- Department of Chemistry, Texas A & M University, 77842, College Station, TX, USA
| |
Collapse
|
22
|
Jelinska C, Kannan S, Frosi Y, Ramlan SR, Winnerdy F, Lakshminarayanan R, Johannes CW, Brown CJ, Phan AT, Rhodes D, Verma CS. Stitched peptides as potential cell permeable inhibitors of oncogenic DAXX protein. RSC Chem Biol 2023; 4:1096-1110. [PMID: 38033728 PMCID: PMC10685803 DOI: 10.1039/d3cb00149k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 09/25/2023] [Indexed: 12/02/2023] Open
Abstract
DAXX (Death Domain Associated Protein 6) is frequently upregulated in various common cancers, and its suppression has been linked to reduced tumor progression. Consequently, DAXX has gained significant interest as a therapeutic target in such cancers. DAXX is known to function in several critical biological pathways including chromatin remodelling, transcription regulation, and DNA repair. Leveraging structural information, we have designed and developed a novel set of stapled/stitched peptides that specifically target a surface on the N-terminal helical bundle domain of DAXX. This surface serves as the anchor point for binding to multiple interaction partners, such as Rassf1C, p53, Mdm2, and ATRX, as well as for the auto-regulation of the DAXX N-terminal SUMO interaction motif (SIM). Our experiments demonstrate that these peptides effectively bind to and inhibit DAXX with a higher affinity than the known interaction partners. Furthermore, these peptides release the auto-inhibited SIM, enabling it to interact with SUMO-1. Importantly, we have developed stitched peptides that can enter cells, maintaining their intracellular concentrations at nanomolar levels even after 24 hours, without causing any membrane perturbation. Collectively, our findings suggest that these stitched peptides not only serve as valuable tools for probing the molecular interactions of DAXX but also hold potential as precursors to the development of therapeutic interventions.
Collapse
Affiliation(s)
- Clare Jelinska
- NTU Institute of Structural Biology, Experimental Medicine Building Level 06-01, 59 Nanyang Drive 636921 Singapore
- NTU School of Biological Sciences, 60 Nanyang Drive 637551 Singapore
- NTU Lee Kong Chian School of Medicine, Experimental Medicine Building, 59 Nanyang Drive 636921 Singapore
| | | | - Yuri Frosi
- DITL, Institute of Cellular and Molecular Biology (A*STAR), 8a Biomedical Grove 138648 Singapore
| | - Siti Radhiah Ramlan
- DITL, Institute of Cellular and Molecular Biology (A*STAR), 8a Biomedical Grove 138648 Singapore
| | - Fernaldo Winnerdy
- NTU Institute of Structural Biology, Experimental Medicine Building Level 06-01, 59 Nanyang Drive 636921 Singapore
| | - Rajamani Lakshminarayanan
- Ocular Infections and Anti-Microbials Research Group, Singapore Eye Research Institute, The Academia, 20 College Road Singapore 169856 Singapore
- Department of Pharmacy, National University of Singapore Singapore 117543 Singapore
- Academic Clinical Program in Ophthalmology and Visual Sciences Academic Clinical Program, Duke-NUS Medical School 169857 Singapore
| | - Charles W Johannes
- DITL, Institute of Cellular and Molecular Biology (A*STAR), 8a Biomedical Grove 138648 Singapore
| | - Christopher J Brown
- DITL, Institute of Cellular and Molecular Biology (A*STAR), 8a Biomedical Grove 138648 Singapore
| | - Anh-Tuan Phan
- NTU Institute of Structural Biology, Experimental Medicine Building Level 06-01, 59 Nanyang Drive 636921 Singapore
- NTU School of Physical and Mathematical Sciences. 21 Nanyang link 637371 Singapore
| | - Daniela Rhodes
- NTU Institute of Structural Biology, Experimental Medicine Building Level 06-01, 59 Nanyang Drive 636921 Singapore
- NTU School of Biological Sciences, 60 Nanyang Drive 637551 Singapore
- NTU Lee Kong Chian School of Medicine, Experimental Medicine Building, 59 Nanyang Drive 636921 Singapore
| | - Chandra S Verma
- NTU School of Biological Sciences, 60 Nanyang Drive 637551 Singapore
- Bioinformatics institute (A*STAR), 30 Biopolis Street, Matrix Level 07-01 138671 Singapore
- Department of Biological Sciences, National University of Singapore Block S3 #05-01 16 Science Drive 4 117558 Singapore
| |
Collapse
|
23
|
McLoughlin NM, Albers MA, Collado Camps E, Paulus J, Ran YA, Neubacher S, Hennig S, Brock R, Grossmann TN. Environment-Responsive Peptide Dimers Bind and Stabilize Double-Stranded RNA. Angew Chem Int Ed Engl 2023; 62:e202308028. [PMID: 37603459 DOI: 10.1002/anie.202308028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 08/23/2023]
Abstract
Double-stranded RNAs (dsRNA) possess immense potential for biomedical applications. However, their therapeutic utility is limited by low stability and poor cellular uptake. Different strategies have been explored to enhance the stability of dsRNA, including the incorporation of modified nucleotides, and the use of diverse carrier systems. Nevertheless, these have not resulted in a broadly applicable approach thereby preventing the wide-spread application of dsRNA for therapeutic purposes. Herein, we report the design of dimeric stapled peptides based on the RNA-binding protein TAV2b. These dimers are obtained via disulfide formation and mimic the natural TAV2b assembly. They bind and stabilize dsRNA in the presence of serum, protecting it from degradation. In addition, peptide binding also promotes cellular uptake of dsRNA. Importantly, peptide dimers monomerize under reducing conditions which results in a loss of RNA binding. These findings highlight the potential of peptide-based RNA binders for the stabilization and protection of dsRNA, representing an appealing strategy towards the environment-triggered release of RNA. This can broaden the applicability of dsRNA, such as short interfering RNAs (siRNA), for therapeutic applications.
Collapse
Affiliation(s)
- Niall M McLoughlin
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Marvin A Albers
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Estel Collado Camps
- Department of Medical BioSciences, Radboud University, Nijmegen Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Jannik Paulus
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Youri A Ran
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Saskia Neubacher
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Incircular B.V., De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Sven Hennig
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Roland Brock
- Department of Medical BioSciences, Radboud University, Nijmegen Medical Center, 6525 GA, Nijmegen, The Netherlands
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, 293, Bahrain
| | - Tom N Grossmann
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| |
Collapse
|
24
|
Lourenço ALP, Rios TB, da Silva ÁP, Franco OL, Ramada MHS. Peptide Stapling Applied to Antimicrobial Peptides. Antibiotics (Basel) 2023; 12:1400. [PMID: 37760697 PMCID: PMC10525709 DOI: 10.3390/antibiotics12091400] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Antimicrobial peptides (AMPs) are considered a promising therapeutic approach against multi-drug resistant microorganisms. Besides their advantages, there are limitations to be overcome so that these molecules can become market competitive. One of the biggest limitations is proteolytic susceptibility, which could be overcome by structural modifications such as cyclization, especially for helix-constraining strategies. Over the years, many helix stabilization techniques have arisen, such as lactam-bridging, triazole-based, N-alkylation and all-hydrocarbon stapling. All-hydrocarbon stapling takes advantage of modified amino acid residues and olefinic cross-linking to constrain peptide helices. Despite being a well-established strategy and presenting efficient stability results, there are different limitations especially related to toxicity. In this review, recent studies on stapled AMPs for antimicrobial usage are explored with the aim of understanding the future of these molecules as putative antimicrobial agents.
Collapse
Affiliation(s)
- Ana Laura Pereira Lourenço
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília 71966-700, Brazil
| | - Thuanny Borba Rios
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília 71966-700, Brazil
- S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande 79117-900, Brazil
| | - Állan Pires da Silva
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília 71966-700, Brazil
| | - Octávio Luiz Franco
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília 71966-700, Brazil
- S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande 79117-900, Brazil
| | - Marcelo Henrique Soller Ramada
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília 71966-700, Brazil
- Programa de Pós-Graduação em Gerontologia, Universidade Católica de Brasília, Brasília 71966-700, Brazil
| |
Collapse
|
25
|
Schmeing S, Amrahova G, Bigler K, Chang JY, Openy J, Pal S, Posada L, Gasper R, 't Hart P. Rationally designed stapled peptides allosterically inhibit PTBP1-RNA-binding. Chem Sci 2023; 14:8269-8278. [PMID: 37564416 PMCID: PMC10411625 DOI: 10.1039/d3sc00985h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/28/2023] [Indexed: 08/12/2023] Open
Abstract
The diverse role of the splicing factor PTBP1 in human cells has been widely studied and was found to be a driver for several diseases. PTBP1 binds RNA through its RNA-recognition motifs which lack obvious pockets for inhibition. A unique transient helix has been described to be part of its first RNA-recognition motif and to be important for RNA binding. In this study, we further confirmed the role of this helix and envisioned its dynamic nature as a unique opportunity to develop stapled peptide inhibitors of PTBP1. The peptides were found to be able to inhibit RNA binding via fluorescence polarization assays and directly occupy the helix binding site as observed by protein crystallography. These cell-permeable inhibitors were validated in cellulo to alter the regulation of alternative splicing events regulated by PTBP1. Our study demonstrates transient secondary structures of a protein can be mimicked by stapled peptides to inhibit allosteric mechanisms.
Collapse
Affiliation(s)
- Stefan Schmeing
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Gulshan Amrahova
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Katrin Bigler
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Jen-Yao Chang
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Joseph Openy
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Sunit Pal
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Laura Posada
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Raphael Gasper
- Crystallography and Biophysics Unit, Max-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Peter 't Hart
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| |
Collapse
|
26
|
Kriegesmann J, Schlatzer T, Che K, Altdorf C, Huhmann S, Kählig H, Kurzbach D, Breinbauer R, Becker CFW. Constraining and Modifying Peptides Using Pd-Mediated Cysteine Allylation. Chembiochem 2023; 24:e202300098. [PMID: 36917494 PMCID: PMC10947015 DOI: 10.1002/cbic.202300098] [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: 02/06/2023] [Revised: 03/14/2023] [Accepted: 03/14/2023] [Indexed: 03/16/2023]
Abstract
Over the past decades, several strategies for inducing and stabilizing secondary structure formation in peptides have been developed to increase their proteolytic stability and their binding affinity to specific interaction partners. Here, we report how our recently introduced chemoselective Pd-catalyzed cysteine allylation reaction can be extended to stapling and how the resulting alkene-containing staples themselves can be further modified to introduce additional probes into such stabilized peptides. The latter is demonstrated by introducing a fluorophore as well as a PEG moiety into different stapled peptides using bioorthogonal thiol-ene and Diels-Alder reactions. Furthermore, we investigated structural implications of our allyl staples when used to replace conformationally relevant disulfide bridges. To this end, we chose a selective binder of integrin α3 β1 (LXY3), which is only active in its cyclic disulfide form. We replaced the disulfide bridge by different stapling reagents in order to increase stability and binding affinity towards integrin α3 β1 .
Collapse
Affiliation(s)
- Julia Kriegesmann
- Institute of Biological ChemistryFaculty of ChemistryUniversity of Vienna1090ViennaAustria
| | - Thomas Schlatzer
- Institute of Organic ChemistryGraz University of Technology8010GrazAustria
| | - Kateryna Che
- Institute of Biological ChemistryFaculty of ChemistryUniversity of Vienna1090ViennaAustria
| | - Claudia Altdorf
- Syntab Therapeutics GmbHPauwelstrasse 17post code?AachenGermany
| | - Susanne Huhmann
- Institute of Biological ChemistryFaculty of ChemistryUniversity of Vienna1090ViennaAustria
| | - Hanspeter Kählig
- Department of Organic ChemistryFaculty of ChemistryUniversity of Vienna1090ViennaAustria
| | - Dennis Kurzbach
- Institute of Biological ChemistryFaculty of ChemistryUniversity of Vienna1090ViennaAustria
| | - Rolf Breinbauer
- Institute of Organic ChemistryGraz University of Technology8010GrazAustria
| | - Christian F. W. Becker
- Institute of Biological ChemistryFaculty of ChemistryUniversity of Vienna1090ViennaAustria
| |
Collapse
|
27
|
Settelmeier S, Varasteh Z, Staniszewska M, Beerlage AL, Zarrad F, Fendler WP, Rischpler C, Notni J, Totzeck M, Herrmann K, Rassaf T, Hendgen-Cotta UB. Demonstration of the Early Cardiac Bioavailability of a Non-Specific Cell-Targeted Peptide Using Radionuclide-Based Imaging In Vivo. Pharmaceuticals (Basel) 2023; 16:824. [PMID: 37375771 DOI: 10.3390/ph16060824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/23/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023] Open
Abstract
The cardiac bioavailability of peptide drugs that inhibit harmful intracellular protein-protein interactions in cardiovascular diseases remains a challenging task in drug development. This study investigates whether a non-specific cell-targeted peptide drug is available in a timely manner at its intended biological destination, the heart, using a combined stepwise nuclear molecular imaging approach. An octapeptide (heart8P) was covalently coupled with the trans-activator of transcription (TAT) protein transduction domain residues 48-59 of human immunodeficiency virus-1 (TAT-heart8P) for efficient internalization into mammalian cells. The pharmacokinetics of TAT-heart8P were evaluated in dogs and rats. The cellular internalization of TAT-heart8P-Cy(5.5) was examined on cardiomyocytes. The real-time cardiac delivery of 68Ga-NODAGA-TAT-heart8P was tested in mice under physiological and pathological conditions. Pharmacokinetic studies of TAT-heart8P in dogs and rats revealed a fast blood clearance, high tissue distribution, and high extraction by the liver. TAT-heart-8P-Cy(5.5) was rapidly internalized in mouse and human cardiomyocytes. Correspondingly, organ uptake of hydrophilic 68Ga-NODAGA-TAT-heart8P occurred rapidly after injection with an initial cardiac bioavailability already 10 min post-injection. The saturable cardiac uptake was revailed by the pre-injection of the unlabeled compound. The cardiac uptake of 68Ga-NODAGA-TAT-heart8P did not change in a model of cell membrane toxicity. This study provides a sequential stepwise workflow to evaluate the cardiac delivery of a hydrophilic, non-specific cell-targeting peptide. 68Ga-NODAGA-TAT-heart8P showed rapid accumulation in the target tissue early after injection. The implementation of PET/CT radionuclide-based imaging methodology as a means to assess effective and temporal cardiac uptake represents a useful and critical application in drug development and pharmacological research and can be extended to the evaluation of comparable drug candidates.
Collapse
Affiliation(s)
- Stephan Settelmeier
- Department of Cardiology and Vascular Medicine, West German Heart and Vascular Center, Medical Faculty, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Zohreh Varasteh
- Department of Nuclear Medicine, Medical Faculty, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
- Department of Nuclear Medicine, Klinikum rechts der Isar der TUM, 81675 Munich, Germany
| | - Magdalena Staniszewska
- Department of Nuclear Medicine, Medical Faculty, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Anna-Lena Beerlage
- Department of Cardiology and Vascular Medicine, West German Heart and Vascular Center, Medical Faculty, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Fadi Zarrad
- Department of Nuclear Medicine, Medical Faculty, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Wolfgang P Fendler
- Department of Nuclear Medicine, Medical Faculty, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Christoph Rischpler
- Department of Nuclear Medicine, Medical Faculty, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Johannes Notni
- Department of Nuclear Medicine, Medical Faculty, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
- TRIMT GmbH, 01454 Radeberg, Germany
| | - Matthias Totzeck
- Department of Cardiology and Vascular Medicine, West German Heart and Vascular Center, Medical Faculty, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Ken Herrmann
- Department of Nuclear Medicine, Medical Faculty, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Tienush Rassaf
- Department of Cardiology and Vascular Medicine, West German Heart and Vascular Center, Medical Faculty, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Ulrike B Hendgen-Cotta
- Department of Cardiology and Vascular Medicine, West German Heart and Vascular Center, Medical Faculty, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| |
Collapse
|
28
|
Ghareeb H, Metanis N. Enhancing the gastrointestinal stability of salmon calcitonin through peptide stapling. Chem Commun (Camb) 2023; 59:6682-6685. [PMID: 37186112 DOI: 10.1039/d3cc01140b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Salmon calcitonin (sCT) is a polypeptide hormone available in the clinic. sCT is degraded in the gastrointestinal tract in minutes. In this work, a stapled analogue of salmon calcitonin, KaY-1(R24Q), was developed using the cooperative stapling between Lys and Tyr, with R24Q substitution. The analogue exhibited an improved stability in simulated gastric and intestinal fluid and retained the ability to activate the calcitonin receptor. This work will serve as a starting point for the development of an oral sCT drug.
Collapse
Affiliation(s)
- Hiba Ghareeb
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
| | - Norman Metanis
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
- Casali Center for Applied Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| |
Collapse
|
29
|
Calugi L, Sautariello G, Lenci E, Mattei ML, Coppa C, Cini N, Contini A, Trabocchi A. Identification of a short ACE2-derived stapled peptide targeting the SARS-CoV-2 spike protein. Eur J Med Chem 2023; 249:115118. [PMID: 36682293 PMCID: PMC9842534 DOI: 10.1016/j.ejmech.2023.115118] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 01/04/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023]
Abstract
The design and synthesis of a series of peptide derivatives based on a short ACE2 α-helix 1 epitope and subsequent [i - i+4] stapling of the secondary structure resulted in the identification of a 9-mer peptide capable to compete with recombinant ACE2 towards Spike RBD in the micromolar range. Specifically, SARS-CoV-2 Spike inhibitor screening based on colorimetric ELISA assay and structural studies by circular dichroism showed the ring-closing metathesis cyclization being capable to stabilize the helical structure of the 9-mer 34HEAEDLFYQ42 epitope better than the triazole stapling via click chemistry. MD simulations showed the stapled peptide being able not only to bind the Spike RBD, sterically interfering with ACE2, but also showing higher affinity to the target as compared to parent epitope.
Collapse
Affiliation(s)
- Lorenzo Calugi
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 13, 50019, Sesto Fiorentino, Florence, Italy
| | - Giulia Sautariello
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 13, 50019, Sesto Fiorentino, Florence, Italy
| | - Elena Lenci
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 13, 50019, Sesto Fiorentino, Florence, Italy
| | - Mauro Leucio Mattei
- General Laboratory, Careggi University Hospital, Largo Brambilla 3, 50134, Florence, Italy
| | - Crescenzo Coppa
- Department of Pharmaceutical Sciences, University of Milan, Via Venezian 21, 20133, Milan, Italy
| | - Nicoletta Cini
- General Laboratory, Careggi University Hospital, Largo Brambilla 3, 50134, Florence, Italy
| | - Alessandro Contini
- Department of Pharmaceutical Sciences, University of Milan, Via Venezian 21, 20133, Milan, Italy
| | - Andrea Trabocchi
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, 50019, Sesto Fiorentino, Florence, Italy.
| |
Collapse
|
30
|
Zhang P, Walko M, Wilson A. Maleimide constrained BAD BH3 domain peptides as BCL-xL Inhibitors: A Versatile Approach to Rapidly Identify Sites Compatible with Peptide Constraining. Bioorg Med Chem Lett 2023; 87:129260. [PMID: 36997005 DOI: 10.1016/j.bmcl.2023.129260] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023]
Abstract
Development of protein-protein interaction (PPI) inhibitors remains a major challenge. A significant number of PPIs are mediated by helical recognition epitopes; although peptides derived from such epitopes are attractive templates for inhibitor design, they may not readily adopt a bioactive conformation, are susceptible to proteolysis and rarely elicit optimal cell uptake properties. Constraining peptides has therefore emerged as a useful method to mitigate against these liabilities in the development of PPI inhibitors. Building on our recently reported method for constraining peptides by reaction of dibromomaleimide derivatives with two cysteines positioned in an i and i + 4 relationship, in this study, we showcase the power of the method for rapid identification of ideal constraining positions using a maleimide-staple scan based on a 19-mer sequence derived from the BAD BH3 domain. We found that the maleimide constraint had little or a detrimental impact on helicity and potency in most sequences, but successfully identified i, i + 4 positions where the maleimide constraint was tolerated. Analyses using modelling and molecular dynamics (MD) simulations revealed that the inactive constrained peptides likely lose interactions with the protein as a result of introducing the constraint.
Collapse
|
31
|
You Y, Liu H, Zhu Y, Zheng H. Rational design of stapled antimicrobial peptides. Amino Acids 2023; 55:421-442. [PMID: 36781451 DOI: 10.1007/s00726-023-03245-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 01/30/2023] [Indexed: 02/15/2023]
Abstract
The global increase in antimicrobial drug resistance has dramatically reduced the effectiveness of traditional antibiotics. Structurally diverse antibiotics are urgently needed to combat multiple-resistant bacterial infections. As part of innate immunity, antimicrobial peptides have been recognized as the most promising candidates because they comprise diverse sequences and mechanisms of action and have a relatively low induction rate of resistance. However, because of their low chemical stability, susceptibility to proteases, and high hemolytic effect, their usage is subject to many restrictions. Chemical modifications such as D-amino acid substitution, cyclization, and unnatural amino acid modification have been used to improve the stability of antimicrobial peptides for decades. Among them, a side-chain covalent bridge modification, the so-called stapled peptide, has attracted much attention. The stapled side-chain bridge stabilizes the secondary structure, induces protease resistance, and increases cell penetration and biological activity. Recent progress in computer-aided drug design and artificial intelligence methods has also been used in the design of stapled antimicrobial peptides and has led to the successful discovery of many prospective peptides. This article reviews the possible structure-activity relationships of stapled antimicrobial peptides, the physicochemical properties that influence their activity (such as net charge, hydrophobicity, helicity, and dipole moment), and computer-aided methods of stapled peptide design. Antimicrobial peptides under clinical trial: Pexiganan (NCT01594762, 2012-05-07). Omiganan (NCT02576847, 2015-10-13).
Collapse
Affiliation(s)
- YuHao You
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
| | - HongYu Liu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
| | - YouZhuo Zhu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
| | - Heng Zheng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, People's Republic of China.
| |
Collapse
|
32
|
Cho THS, Pick K, Raivio TL. Bacterial envelope stress responses: Essential adaptors and attractive targets. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119387. [PMID: 36336206 DOI: 10.1016/j.bbamcr.2022.119387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 10/05/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022]
Abstract
Millions of deaths a year across the globe are linked to antimicrobial resistant infections. The need to develop new treatments and repurpose of existing antibiotics grows more pressing as the growing antimicrobial resistance pandemic advances. In this review article, we propose that envelope stress responses, the signaling pathways bacteria use to recognize and adapt to damage to the most vulnerable outer compartments of the microbial cell, are attractive targets. Envelope stress responses (ESRs) support colonization and infection by responding to a plethora of toxic envelope stresses encountered throughout the body; they have been co-opted into virulence networks where they work like global positioning systems to coordinate adhesion, invasion, microbial warfare, and biofilm formation. We highlight progress in the development of therapeutic strategies that target ESR signaling proteins and adaptive networks and posit that further characterization of the molecular mechanisms governing these essential niche adaptation machineries will be important for sparking new therapeutic approaches aimed at short-circuiting bacterial adaptation.
Collapse
Affiliation(s)
- Timothy H S Cho
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Kat Pick
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Tracy L Raivio
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.
| |
Collapse
|
33
|
Zhang Y, Guo J, Cheng J, Zhang Z, Kang F, Wu X, Chu Q. High-Throughput Screening of Stapled Helical Peptides in Drug Discovery. J Med Chem 2023; 66:95-106. [PMID: 36580278 DOI: 10.1021/acs.jmedchem.2c01541] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Therapeutic peptides have revolutionized treatment for a number of human diseases. In particular, the past two decades have witnessed rapid progress of stapled helical peptides in drug discovery. Stapled helical peptides are chemically modified and constrained in their bioactive α-helical conformation. Compared to unstabilized linear peptides, stapled helical peptides exhibit superior binding affinity and selectivity, enhanced membrane permeability, and improved metabolic stability, presenting exciting promise for targeting otherwise challenging protein-protein interfaces. In this Perspective, we summarize recent applications of high-throughput screening technologies for identification of potent stapled helical peptides with optimized binding properties. We expect to provide a broad reference to accelerate the development of stapled helical peptides as the next generation of therapeutic peptides for various human diseases.
Collapse
Affiliation(s)
- Yiwei Zhang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Jiabei Guo
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Jiongjia Cheng
- Key Laboratory of Advanced Functional Materials of Nanjing, Nanjing Xiaozhuang University, Nanjing 211171, China
| | - Zhenghua Zhang
- Department of Chemistry, School of Science, China Pharmaceutical University, Nanjing 211198, China
| | - Fenghua Kang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
| | - Xiaoxing Wu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Qian Chu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China.,Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| |
Collapse
|
34
|
Paulussen FM, Grossmann TN. Peptide-based covalent inhibitors of protein-protein interactions. J Pept Sci 2023; 29:e3457. [PMID: 36239115 PMCID: PMC10077911 DOI: 10.1002/psc.3457] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 12/13/2022]
Abstract
Protein-protein interactions (PPI) are involved in all cellular processes and many represent attractive therapeutic targets. However, the frequently rather flat and large interaction areas render the identification of small molecular PPI inhibitors very challenging. As an alternative, peptide interaction motifs derived from a PPI interface can serve as starting points for the development of inhibitors. However, certain proteins remain challenging targets when applying inhibitors with a competitive mode of action. For that reason, peptide-based ligands with an irreversible binding mode have gained attention in recent years. This review summarizes examples of covalent inhibitors that employ peptidic binders and have been tested in a biological context.
Collapse
Affiliation(s)
- Felix M Paulussen
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Molecular Microbiology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Tom N Grossmann
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
35
|
Escobedo A, Piccirillo J, Aranda J, Diercks T, Mateos B, Garcia-Cabau C, Sánchez-Navarro M, Topal B, Biesaga M, Staby L, Kragelund BB, García J, Millet O, Orozco M, Coles M, Crehuet R, Salvatella X. A glutamine-based single α-helix scaffold to target globular proteins. Nat Commun 2022; 13:7073. [PMID: 36400768 PMCID: PMC9674830 DOI: 10.1038/s41467-022-34793-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 11/04/2022] [Indexed: 11/19/2022] Open
Abstract
The binding of intrinsically disordered proteins to globular ones can require the folding of motifs into α-helices. These interactions offer opportunities for therapeutic intervention but their modulation with small molecules is challenging because they bury large surfaces. Linear peptides that display the residues that are key for binding can be targeted to globular proteins when they form stable helices, which in most cases requires their chemical modification. Here we present rules to design peptides that fold into single α-helices by instead concatenating glutamine side chain to main chain hydrogen bonds recently discovered in polyglutamine helices. The resulting peptides are uncharged, contain only natural amino acids, and their sequences can be optimized to interact with specific targets. Our results provide design rules to obtain single α-helices for a wide range of applications in protein engineering and drug design.
Collapse
Affiliation(s)
- Albert Escobedo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain.
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
| | - Jonathan Piccirillo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Juan Aranda
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Tammo Diercks
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, 48160, Derio, Spain
| | - Borja Mateos
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Carla Garcia-Cabau
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Macarena Sánchez-Navarro
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina López Neyra (IPBLN-CSIC), Armilla, Granada, Spain
| | - Busra Topal
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Mateusz Biesaga
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Lasse Staby
- REPIN and Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Birthe B Kragelund
- REPIN and Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Jesús García
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Oscar Millet
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, 48160, Derio, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
- Department of Biochemistry and Biomedicine, University of Barcelona, Avinguda Diagonal 645, 08028, Barcelona, Spain
| | - Murray Coles
- Department of Protein Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tubingen, Germany
| | - Ramon Crehuet
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain.
- ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Spain.
| |
Collapse
|
36
|
Ricardo MG, Reuber EE, Yao L, Danglad-Flores J, Delbianco M, Seeberger PH. Design, Synthesis, and Characterization of Stapled Oligosaccharides. J Am Chem Soc 2022; 144:18429-18434. [PMID: 36173281 PMCID: PMC9562281 DOI: 10.1021/jacs.2c06882] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Stapling short peptides
to lock specific conformations and thereby
obtain superior pharmacological properties is well established. However,
similar concepts have not been applied to oligosaccharides. Here,
we describe the design, synthesis, and characterization of the first
stapled oligosaccharides. Automated assembly of β-(1,6)-glucans
equipped with two alkenyl side chains was followed by on-resin Grubbs
metathesis for efficient ring closure with a variety of cross-linkers
of different sizes. Oligosaccharide stapling increases enzymatic stability
and cell penetration, therefore opening new opportunities for the
use of glycans in medicinal chemistry.
Collapse
Affiliation(s)
- Manuel G Ricardo
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Emelie E Reuber
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Ling Yao
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - José Danglad-Flores
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Martina Delbianco
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| |
Collapse
|
37
|
Cui J, Ogasawara Y, Kurata I, Matoba K, Fujioka Y, Noda NN, Shibasaki M, Watanabe T. Targeting the ATG5-ATG16L1 Protein–Protein Interaction with a Hydrocarbon-Stapled Peptide Derived from ATG16L1 for Autophagy Inhibition. J Am Chem Soc 2022; 144:17671-17679. [DOI: 10.1021/jacs.2c07648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Jin Cui
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, 3-14-23 Kamiosaki Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Yuta Ogasawara
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, 3-14-23 Kamiosaki Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Ikuko Kurata
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, 3-14-23 Kamiosaki Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Kazuaki Matoba
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, 3-14-23 Kamiosaki Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Yuko Fujioka
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, 3-14-23 Kamiosaki Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Nobuo N. Noda
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, 3-14-23 Kamiosaki Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Masakatsu Shibasaki
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, 3-14-23 Kamiosaki Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Takumi Watanabe
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, 3-14-23 Kamiosaki Shinagawa-ku, Tokyo, 141-0021, Japan
| |
Collapse
|
38
|
Paulussen FM, Schouten GK, Moertl C, Verheul J, Hoekstra I, Koningstein GM, Hutchins GH, Alkir A, Luirink RA, Geerke DP, van Ulsen P, den Blaauwen T, Luirink J, Grossmann TN. Covalent Proteomimetic Inhibitor of the Bacterial FtsQB Divisome Complex. J Am Chem Soc 2022; 144:15303-15313. [PMID: 35945166 PMCID: PMC9413201 DOI: 10.1021/jacs.2c06304] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The use of antibiotics is threatened by the emergence
and spread
of multidrug-resistant strains of bacteria. Thus, there is a need
to develop antibiotics that address new targets. In this respect,
the bacterial divisome, a multi-protein complex central to cell division,
represents a potentially attractive target. Of particular interest
is the FtsQB subcomplex that plays a decisive role in divisome assembly
and peptidoglycan biogenesis in E. coli. Here, we report the structure-based design of
a macrocyclic covalent inhibitor derived from a periplasmic region
of FtsB that mediates its binding to FtsQ. The bioactive conformation
of this motif was stabilized by a customized cross-link resulting
in a tertiary structure mimetic with increased affinity for FtsQ.
To increase activity, a covalent handle was incorporated, providing
an inhibitor that impedes the interaction between FtsQ and FtsB irreversibly. The covalent inhibitor reduced the growth of an outer
membrane-permeable E. coli strain,
concurrent with the expected loss of FtsB localization, and also affected
the infection of zebrafish larvae by a clinical E.
coli strain. This first-in-class inhibitor of a divisome
protein–protein interaction highlights the potential of proteomimetic
molecules as inhibitors of challenging targets. In particular, the
covalent mode-of-action can serve as an inspiration for future antibiotics
that target protein–protein interactions.
Collapse
Affiliation(s)
- Felix M Paulussen
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands.,Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands.,Department of Molecular Microbiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands
| | - Gina K Schouten
- Medical Microbiology and Infection Control (MMI), Amsterdam UMC Location VUmc, De Boelelaan 1108, Amsterdam 1081 HZ, Netherlands
| | - Carolin Moertl
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands.,Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands
| | - Jolanda Verheul
- Department of Bacterial Cell Biology and Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Sciencepark 904, Amsterdam 1098 XH, Netherlands
| | - Irma Hoekstra
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands
| | - Gregory M Koningstein
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands.,Department of Molecular Microbiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands
| | - George H Hutchins
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands.,Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands
| | - Aslihan Alkir
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands
| | - Rosa A Luirink
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands.,Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands
| | - Daan P Geerke
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands.,Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands
| | - Peter van Ulsen
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands.,Department of Molecular Microbiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands
| | - Tanneke den Blaauwen
- Department of Bacterial Cell Biology and Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Sciencepark 904, Amsterdam 1098 XH, Netherlands
| | - Joen Luirink
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands.,Department of Molecular Microbiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands
| | - Tom N Grossmann
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands.,Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands
| |
Collapse
|
39
|
Yang L, Yang G, Bing Z, Tian Y, Huang L, Niu Y, Yang L. Accelerating the discovery of anticancer peptides targeting lung and breast cancers with the Wasserstein autoencoder model and PSO algorithm. Brief Bioinform 2022; 23:6658854. [PMID: 35945135 DOI: 10.1093/bib/bbac320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 06/14/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
In the development of targeted drugs, anticancer peptides (ACPs) have attracted great attention because of their high selectivity, low toxicity and minimal non-specificity. In this work, we report a framework of ACPs generation, which combines Wasserstein autoencoder (WAE) generative model and Particle Swarm Optimization (PSO) forward search algorithm guided by attribute predictive model to generate ACPs with desired properties. It is well known that generative models based on Variational AutoEncoder (VAE) and Generative Adversarial Networks (GAN) are difficult to be used for de novo design due to the problems of posterior collapse and difficult convergence of training. Our WAE-based generative model trains more successfully (lower perplexity and reconstruction loss) than both VAE and GAN-based generative models, and the semantic connections in the latent space of WAE accelerate the process of forward controlled generation of PSO, while VAE fails to capture this feature. Finally, we validated our pipeline on breast cancer targets (HIF-1) and lung cancer targets (VEGR, ErbB2), respectively. By peptide-protein docking, we found candidate compounds with the same binding sites as the peptides carried in the crystal structure but with higher binding affinity and novel structures, which may be potent antagonists that interfere with these target-mediated signaling.
Collapse
Affiliation(s)
- Lijuan Yang
- Institute of modern physics, Chinese Academy of Science, Lanzhou 730000, China.,School of Physics and Technology, Lanzhou University, Lanzhou 730000, China.,School of Physics, University of Chinese Academy of Science, Beijing 100049, China.,Advanced Energy Science and Technology Guangdong Laboratory, Huizhou 516000, China
| | - Guanghui Yang
- Institute of modern physics, Chinese Academy of Science, Lanzhou 730000, China.,Advanced Energy Science and Technology Guangdong Laboratory, Huizhou 516000, China
| | - Zhitong Bing
- Institute of modern physics, Chinese Academy of Science, Lanzhou 730000, China.,Advanced Energy Science and Technology Guangdong Laboratory, Huizhou 516000, China
| | - Yuan Tian
- Institute of modern physics, Chinese Academy of Science, Lanzhou 730000, China.,School of Information Science and Engineering, Lanzhou University, Lanzhou 730000, China
| | - Liang Huang
- School of Physics and Technology, Lanzhou University, Lanzhou 730000, China
| | - Yuzhen Niu
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences, Shandong University of Technology, Zibo 255000, China
| | - Lei Yang
- Institute of modern physics, Chinese Academy of Science, Lanzhou 730000, China.,Advanced Energy Science and Technology Guangdong Laboratory, Huizhou 516000, China
| |
Collapse
|
40
|
Joaquin D, Mansfield SA, Chanthakhoun JC, LeSueur AK, Blackburn TA, Castle SL. Synthesis and Studies of Bulky Cycloalkyl α,β-Dehydroamino Acids that Enhance Proteolytic Stability. Org Lett 2022; 24:5329-5333. [PMID: 35839437 PMCID: PMC10243721 DOI: 10.1021/acs.orglett.2c01962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Three new bulky cycloalkyl α,β-dehydroamino acids (ΔAAs) have been designed and synthesized. Each residue enhances the rigidity of model peptides and their stability to proteolysis, with larger ring sizes exhibiting greater effects. Peptides containing bulky cycloalkyl ΔAAs are inert to conjugate addition by a nucleophilic thiol. The results suggest that these residues will be effective tools for improving the proteolytic stability of bioactive peptides.
Collapse
Affiliation(s)
- Daniel Joaquin
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Samuel A Mansfield
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Joseph C Chanthakhoun
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Austin K LeSueur
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Tiffani A Blackburn
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Steven L Castle
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| |
Collapse
|
41
|
Koelman EMR, Yeste-Vázquez A, Grossmann TN. Targeting the interaction of β-catenin and TCF/LEF transcription factors to inhibit oncogenic Wnt signaling. Bioorg Med Chem 2022; 70:116920. [PMID: 35841828 DOI: 10.1016/j.bmc.2022.116920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 11/02/2022]
Abstract
The Wnt/β-catenin signaling pathway is crucially involved in embryonic development, stem cell maintenance and tissue renewal. Hyperactivation of this pathway is associated with the development and progression of various types of cancers. The transcriptional coactivator β-catenin represents a pivotal component of the pathway and its interaction with transcription factors of the TCF/LEF family is central to pathway activation. Inhibition of this crucial protein-protein interaction via direct targeting of β-catenin is considered a promising strategy for the inactivation of oncogenic Wnt signaling. This review summarizes advances in the development of Wnt antagonists that have been shown to directly bind β-catenin.
Collapse
Affiliation(s)
- Emma M R Koelman
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, NL, The Netherlands
| | - Alejandro Yeste-Vázquez
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, NL, The Netherlands; Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, Amsterdam, NL, The Netherlands
| | - Tom N Grossmann
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, NL, The Netherlands; Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, Amsterdam, NL, The Netherlands.
| |
Collapse
|
42
|
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.
Collapse
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
| |
Collapse
|
43
|
Franco HEO, Chaloux BT, Hartman MCT. Spontaneous, co-translational peptide macrocyclization using p-cyanoacetylene-phenylalanine. Chem Commun (Camb) 2022; 58:6737-6740. [PMID: 35607950 DOI: 10.1039/d2cc01148d] [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
Peptide macrocycles (PMCs) are increasingly popular for the development of inhibitors of protein-protein interactions (PPIs). Large libraries of PMCs are accessible using display technologies like mRNA display and phage display. These technologies require macrocyclization chemistries to be compatible with biological milieu, severely limiting the types of technologies available for cyclization. Here, we introduce the novel non-canonical amino acid (ncAA) p-cyanoacetylene-L-Phe (pCAF), which facilitates spontaneous, co-translational cyclization through Michael addition with cysteine under physiological conditions. This new, robust chemistry creates stable macrocycles of a wide variety of ring sizes including bicyclic structures.
Collapse
Affiliation(s)
- H Estheban Osorio Franco
- Massey Cancer Center, Virginia Commonwealth University, 401 College St, Richmond, 23219, Virginia, USA. .,Department of Chemistry, Virginia Commonwealth University, 1001 W Main Street, Richmond, 23284, VA, USA
| | - Brennan T Chaloux
- Massey Cancer Center, Virginia Commonwealth University, 401 College St, Richmond, 23219, Virginia, USA. .,Department of Chemistry, Virginia Commonwealth University, 1001 W Main Street, Richmond, 23284, VA, USA
| | - Matthew C T Hartman
- Massey Cancer Center, Virginia Commonwealth University, 401 College St, Richmond, 23219, Virginia, USA. .,Department of Chemistry, Virginia Commonwealth University, 1001 W Main Street, Richmond, 23284, VA, USA
| |
Collapse
|
44
|
Abstract
Being able to effectively target RNA with potent ligands will open up a large number of potential therapeutic options. The knowledge on how to achieve this is ever expanding but an important question that remains open is what chemical matter is suitable to achieve this goal. The high flexibility of an RNA as well as its more limited chemical diversity and featureless binding sites can be difficult to target selectively but can be addressed by well-designed cyclic peptides. In this review we will provide an overview of reported cyclic peptide ligands for therapeutically relevant RNA targets and discuss the methods used to discover them. We will also provide critical insights into the properties required for potent and selective interaction and suggestions on how to assess these parameters. The use of cyclic peptides to target RNA is still in its infancy but the lessons learned from past examples can be adopted for the development of novel potent and selective ligands.
Collapse
Affiliation(s)
- Sunit Pal
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Peter 't Hart
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| |
Collapse
|
45
|
Vanjari R, Panda D, Mandal S, Vamisetti GB, Brik A. Gold(I)-Mediated Rapid Cyclization of Propargylated Peptides via Imine Formation. J Am Chem Soc 2022; 144:4966-4976. [PMID: 35258952 PMCID: PMC8949771 DOI: 10.1021/jacs.1c12906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Indexed: 12/15/2022]
Abstract
In fundamental research and drug discovery, there is still a need for effective and straightforward chemical approaches for generating cyclic peptides. The divergent synthesis of cyclic peptides remains a challenge, in particular when cyclization is carried out in the presence of unprotected side chains and a nonpeptidic component within the cycle is needed. Herein, we describe a novel and efficient strategy based on Au(I)-mediated cyclization of unprotected peptides through rapid (30-60 min) amine addition on a propargyl group to generate an imine linkage. Mechanistic insights reveal that the reaction proceeds via regioselective Markovnikov's addition of the amine on the Au(I)-activated propargyl. This strategy was successfully applied to prepare efficiently (56-94%) over 35 diverse cyclic peptides having different sequences and lengths. We have also achieved stereoselective reduction of cyclic imines employing chiral ligands. The practicality of our method was extended for the synthesis of cyclic peptides that bind Lys48-linked di-ubiquitin chains with high affinity, leading to apoptosis of cancer cells.
Collapse
Affiliation(s)
- Rajeshwer Vanjari
- Schulich Faculty of Chemistry, Technion − Israel Institute of Technology, Haifa 3200008, Israel
| | - Deepanjan Panda
- Schulich Faculty of Chemistry, Technion − Israel Institute of Technology, Haifa 3200008, Israel
| | - Shaswati Mandal
- Schulich Faculty of Chemistry, Technion − Israel Institute of Technology, Haifa 3200008, Israel
| | - Ganga B. Vamisetti
- Schulich Faculty of Chemistry, Technion − Israel Institute of Technology, Haifa 3200008, Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion − Israel Institute of Technology, Haifa 3200008, Israel
| |
Collapse
|
46
|
Mohapatra S, An J, Gómez-Bombarelli R. Chemistry-informed macromolecule graph representation for similarity computation, unsupervised and supervised learning. MACHINE LEARNING: SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1088/2632-2153/ac545e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Abstract
The near-infinite chemical diversity of natural and artificial macromolecules arises from the vast range of possible component monomers, linkages, and polymers topologies. This enormous variety contributes to the ubiquity and indispensability of macromolecules but hinders the development of general machine learning methods with macromolecules as input. To address this, we developed a chemistry-informed graph representation of macromolecules that enables quantifying structural similarity, and interpretable supervised learning for macromolecules. Our work enables quantitative chemistry-informed decision-making and iterative design in the macromolecular chemical space.
Collapse
|
47
|
Stapling of Peptides Potentiates: The Antibiotic Treatment of Acinetobacter baumannii In Vivo. Antibiotics (Basel) 2022; 11:antibiotics11020273. [PMID: 35203875 PMCID: PMC8868297 DOI: 10.3390/antibiotics11020273] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/15/2022] [Accepted: 02/18/2022] [Indexed: 11/21/2022] Open
Abstract
The rising incidence of multidrug resistance in Gram-negative bacteria underlines the urgency for novel treatment options. One promising new approach is the synergistic combination of antibiotics with antimicrobial peptides. However, the use of such peptides is not straightforward; they are often sensitive to proteolytic degradation, which greatly limits their clinical potential. One approach to increase stability is to apply a hydrocarbon staple to the antimicrobial peptide, thereby fixing them in an α-helical conformation, which renders them less exposed to proteolytic activity. In this work we applied several different hydrocarbon staples to two previously described peptides shown to act on the outer membrane, L6 and L8, and tested their activity in a zebrafish embryo infection model using a clinical isolate of Acinetobacter baumannii as a pathogen. We show that the introduction of such a hydrocarbon staple to the peptide L8 improves its in vivo potentiating activity on antibiotic treatment, without increasing its in vivo antimicrobial activity, toxicity or hemolytic activity.
Collapse
|
48
|
Ueda A, Makura Y, Kakazu S, Kato T, Umeno T, Hirayama K, Doi M, Oba M, Tanaka M. E-Selective Ring-Closing Metathesis in α-Helical Stapled Peptides Using Carbocyclic α,α-Disubstituted α-Amino Acids. Org Lett 2022; 24:1049-1054. [PMID: 35073100 DOI: 10.1021/acs.orglett.1c04256] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present an E-selective ring-closing metathesis reaction in α-helical stapled peptides at positions i and i + 4. The use of two chiral carbocyclic α,α-disubstituted α-amino acids, (1S,3S)-Ac5c3OAll and (1R,3S)-Ac5c3OAll, provides a high E-selectivity of a ≤59:1 E:Z ratio, while mixtures with E:Z ratios of 2.1-0.5:1 were produced with standard acyclic (S)-(4-pentenyl)alanine amino acids. A stapled octapeptide composed of (1S,3S)- and (1R,3S)-Ac5c3OAll amino acids showed a right-handed α-helical crystal structure.
Collapse
Affiliation(s)
- Atsushi Ueda
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Yui Makura
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Sana Kakazu
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Takuma Kato
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka 569-1094, Japan
| | - Tomohiro Umeno
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Kazuhiro Hirayama
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Mitsunobu Doi
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka 569-1094, Japan
| | - Makoto Oba
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
- Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto 606-0823, Japan
| | - Masakazu Tanaka
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| |
Collapse
|
49
|
Luong HX, Bui HTP, Tung TT. Application of the All-Hydrocarbon Stapling Technique in the Design of Membrane-Active Peptides. J Med Chem 2022; 65:3026-3045. [PMID: 35112864 DOI: 10.1021/acs.jmedchem.1c01744] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The threats of drug resistance and new emerging pathogens have led to an urgent need to develop alternative treatment therapies. Recently, considerable research efforts have focused on membrane-active peptides (MAPs), a category of peptides in drug discovery with antimicrobial, anticancer, and cell penetration activities that have demonstrated their potential to be multifunctional agents. Nonetheless, natural MAPs have encountered various disadvantages, which mainly include poor bioavailability, the lack of a secondary structure in short peptides, and high production costs for long peptide sequences. Hence, an "all-hydrocarbon stapling system" has been applied to these peptides and proven to effectively stabilize the helical conformations, improving proteolytic resistance and increasing both the potency and the cell permeability. In this review, we summarized and categorized the advances made using this powerful technique in the development of stapled MAPs. Furthermore, outstanding issues and suggestions for future design within each subcategory were thoroughly discussed.
Collapse
Affiliation(s)
- Huy Xuan Luong
- Faculty of Pharmacy, PHENIKAA University, Hanoi 12116, Vietnam.,PHENIKAA Institute for Advanced Study (PIAS), PHENIKAA University, Hanoi 12116, Vietnam
| | | | - Truong Thanh Tung
- Faculty of Pharmacy, PHENIKAA University, Hanoi 12116, Vietnam.,PHENIKAA Institute for Advanced Study (PIAS), PHENIKAA University, Hanoi 12116, Vietnam
| |
Collapse
|
50
|
Islam MS, Junod SL, Zhang S, Buuh ZY, Guan Y, Zhao M, Kaneria KH, Kafley P, Cohen C, Maloney R, Lyu Z, Voelz VA, Yang W, Wang RE. Unprotected peptide macrocyclization and stapling via a fluorine-thiol displacement reaction. Nat Commun 2022; 13:350. [PMID: 35039490 PMCID: PMC8763920 DOI: 10.1038/s41467-022-27995-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/19/2021] [Indexed: 12/31/2022] Open
Abstract
We report the discovery of a facile peptide macrocyclization and stapling strategy based on a fluorine thiol displacement reaction (FTDR), which renders a class of peptide analogues with enhanced stability, affinity, cellular uptake, and inhibition of cancer cells. This approach enabled selective modification of the orthogonal fluoroacetamide side chains in unprotected peptides in the presence of intrinsic cysteines. The identified benzenedimethanethiol linker greatly promoted the alpha helicity of a variety of peptide substrates, as corroborated by molecular dynamics simulations. The cellular uptake of benzenedimethanethiol stapled peptides appeared to be universally enhanced compared to the classic ring-closing metathesis (RCM) stapled peptides. Pilot mechanism studies suggested that the uptake of FTDR-stapled peptides may involve multiple endocytosis pathways in a distinct pattern in comparison to peptides stapled by RCM. Consistent with the improved cell permeability, the FTDR-stapled lead Axin and p53 peptide analogues demonstrated enhanced inhibition of cancer cells over the RCM-stapled analogues and the unstapled peptides. Strategies capable of stapling unprotected peptides in a straightforward, chemoselective, and clean manner, as well as promoting cellular uptake are of great interest. Here the authors report a peptide macrocyclization and stapling strategy which satisfies those criteria, based on a fluorine thiol displacement reaction.
Collapse
Affiliation(s)
- Md Shafiqul Islam
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Samuel L Junod
- Department of Biology, Temple University, 1900 N. 12th Street, Philadelphia, PA, 19122, USA
| | - Si Zhang
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Zakey Yusuf Buuh
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Yifu Guan
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Mi Zhao
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Kishan H Kaneria
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Parmila Kafley
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Carson Cohen
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Robert Maloney
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Zhigang Lyu
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Vincent A Voelz
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Weidong Yang
- Department of Biology, Temple University, 1900 N. 12th Street, Philadelphia, PA, 19122, USA
| | - Rongsheng E Wang
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA.
| |
Collapse
|