1
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Livneh I, Fabre B, Goldhirsh G, Lulu C, Zinger A, Shammai Vainer Y, Kaduri M, Dahan A, Ziv T, Schroeder A, Ben-Neriah Y, Zohar Y, Cohen-Kaplan V, Ciechanover A. Inhibition of nucleo-cytoplasmic proteasome translocation by the aromatic amino acids or silencing Sestrin3-their sensing mediator-is tumor suppressive. Cell Death Differ 2024:10.1038/s41418-024-01370-x. [PMID: 39266717 DOI: 10.1038/s41418-024-01370-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 08/11/2024] [Accepted: 08/27/2024] [Indexed: 09/14/2024] Open
Abstract
The proteasome, the catalytic arm of the ubiquitin system, is regulated via its dynamic compartmentation between the nucleus and the cytoplasm, among other mechanisms. Under amino acid shortage, the proteolytic complex is translocated to the cytoplasm, where it stimulates proteolysis to supplement recycled amino acids for essential protein synthesis. This response is mediated via the mTOR pathway and the lack of the three aromatic amino acids Tyr, Trp, and Phe (YWF). mTOR activation by supplementation of the triad inhibits proteasome translocation, leading to cell death. We now show that tumoral inherent stress conditions result in translocation of the proteasome from the nucleus to the cytosol. We further show that the modulation of the signaling cascade governed by YWF is applicable also to non-starved cells by using higher concentration of the triad to achieve a surplus relative to all other amino acids. Based on these two phenomena, we found that the modulation of stress signals via the administration of YWF leads to nuclear proteasome sequestration and inhibition of growth of xenograft, spontaneous, and metastatic mouse tumor models. In correlation with the observed effect of YWF on tumors, we found - using transcriptomic and proteomic analyses - that the triad affects various cellular processes related to cell proliferation, migration, and death. In addition, Sestrin3-a mediator of YWF sensing upstream of mTOR-is essential for proteasome translocation, and therefore plays a pro-tumorigenic role, positioning it as a potential oncogene. This newly identified approach for hijacking the cellular "satiety center" carries therefore potential therapeutic implications for cancer.
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Affiliation(s)
- Ido Livneh
- The Rappaport Technion Integrated Cancer Center (R-TICC) and the Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, Israel.
- Institute of Pathology and Cytology, Rambam Health Care Campus, Haifa, Israel.
| | - Bertrand Fabre
- The Rappaport Technion Integrated Cancer Center (R-TICC) and the Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, Israel
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse 3, INP, CNRS, Auzeville-Tolosane, France
| | - Gilad Goldhirsh
- The Rappaport Technion Integrated Cancer Center (R-TICC) and the Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, Israel
| | - Chen Lulu
- The Rappaport Technion Integrated Cancer Center (R-TICC) and the Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, Israel
| | - Adar Zinger
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Yael Shammai Vainer
- The Louis Family Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Faculty of Chemical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Maya Kaduri
- The Louis Family Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Faculty of Chemical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Aviva Dahan
- Institute of Pathology and Cytology, Rambam Health Care Campus, Haifa, Israel
| | - Tamar Ziv
- Smoler Proteomic Center, Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Avi Schroeder
- The Louis Family Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Faculty of Chemical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Yinon Ben-Neriah
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Yaniv Zohar
- The Rappaport Technion Integrated Cancer Center (R-TICC) and the Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, Israel
- Institute of Pathology and Cytology, Rambam Health Care Campus, Haifa, Israel
| | - Victoria Cohen-Kaplan
- The Rappaport Technion Integrated Cancer Center (R-TICC) and the Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, Israel
| | - Aaron Ciechanover
- The Rappaport Technion Integrated Cancer Center (R-TICC) and the Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, Israel.
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2
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Sigal M, Matsumoto S, Beattie A, Katoh T, Suga H. Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers. Chem Rev 2024; 124:6444-6500. [PMID: 38688034 PMCID: PMC11122139 DOI: 10.1021/acs.chemrev.3c00894] [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: 12/01/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
Abstract
Ribosome-dependent protein biosynthesis is an essential cellular process mediated by transfer RNAs (tRNAs). Generally, ribosomally synthesized proteins are limited to the 22 proteinogenic amino acids (pAAs: 20 l-α-amino acids present in the standard genetic code, selenocysteine, and pyrrolysine). However, engineering tRNAs for the ribosomal incorporation of non-proteinogenic monomers (npMs) as building blocks has led to the creation of unique polypeptides with broad applications in cellular biology, material science, spectroscopy, and pharmaceuticals. Ribosomal polymerization of these engineered polypeptides presents a variety of challenges for biochemists, as translation efficiency and fidelity is often insufficient when employing npMs. In this Review, we will focus on the methodologies for engineering tRNAs to overcome these issues and explore recent advances both in vitro and in vivo. These efforts include increasing orthogonality, recruiting essential translation factors, and creation of expanded genetic codes. After our review on the biochemical optimizations of tRNAs, we provide examples of their use in genetic code manipulation, with a focus on the in vitro discovery of bioactive macrocyclic peptides containing npMs. Finally, an analysis of the current state of tRNA engineering is presented, along with existing challenges and future perspectives for the field.
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Affiliation(s)
- Maxwell Sigal
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satomi Matsumoto
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Adam Beattie
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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3
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Saha A, Suga H, Brik A. Combining Chemical Protein Synthesis and Random Nonstandard Peptides Integrated Discovery for Modulating Biological Processes. Acc Chem Res 2023; 56:1953-1965. [PMID: 37312234 PMCID: PMC10357587 DOI: 10.1021/acs.accounts.3c00178] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Indexed: 06/15/2023]
Abstract
Chemical manipulation of naturally occurring peptides offers a convenient route for generating analogs to screen against different therapeutic targets. However, the limited success of the conventional chemical libraries has urged chemical biologists to adopt alternative methods such as phage and mRNA displays and create libraries of a large number of variants for the screening and selection of novel peptides. Messenger RNA (mRNA) display provides great advantages in terms of the library size and the straightforward recovery of the selected polypeptide sequences. Importantly, the integration of the flexible in vitro translation (FIT) system with the mRNA display provides the basis of the random nonstandard peptides integrated discovery (RaPID) approach for the introduction of diverse nonstandard motifs, such as unnatural side chains and backbone modifications. This platform allows the discovery of functionalized peptides with tight binding against virtually any protein of interest (POI) and therefore shows great potential in the pharmaceutical industry. However, this method has been limited to targets generated by recombinant expression, excluding its applications to uniquely modified proteins, particularly those with post-translational modifications.Chemical protein synthesis allows a wide range of changes to the protein's chemical composition to be performed, including side chain and backbone modifications and access to post-translationally modified proteins, which are often inaccessible or difficult to achieve via recombinant expression methods. Notably, d-proteins can be prepared via chemical synthesis, which has been used in mirror image phase display for the discovery of nonproteolytic d-peptide binders.Combining chemical protein synthesis with the RaPID system allows the production of a library of trillions of cyclic peptides and subsequent selection for novel cyclic peptide binders targeting a uniquely modified protein to assist in studying its unexplored biology and possibly the discovery of new drug candidates.Interestingly, the small post-translational modifier protein ubiquitin (Ub), with its various polymeric forms, regulates directly or indirectly many biochemical processes, e.g., proteasomal degradation, DNA damage repair, cell cycle regulation, etc. In this Account, we discuss combining the RaPID approach against various synthetic Ub chains for selecting effective and specific macrocyclic peptide binders. This offers an advancement in modulating central Ub pathways and provides opportunities in drug discovery areas associated with Ub signaling. We highlight experimental approaches and conceptual adaptations required to design and modulate the activity of Lys48- and Lys63-linked Ub chains by macrocyclic peptides. We also present the applications of these approaches to shed light on related biological activities and ultimately their activity against cancer. Finally, we contemplate future developments still pending in this exciting multidisciplinary field.
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Affiliation(s)
- Abhishek Saha
- Schulich
Faculty of Chemistry, Technion-Israel Institute
of Technology, Haifa 3200008, Israel
| | - Hiroaki Suga
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - Ashraf Brik
- Schulich
Faculty of Chemistry, Technion-Israel Institute
of Technology, Haifa 3200008, Israel
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4
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Ito K, Matsuda Y, Mine A, Miyairi K, Kikuchi Y, Konishi A. Bacterially Secretable Single-Chain Tandem Macrocyclic Peptides for High Affinity and Inhibitory Activity. Chembiochem 2023; 24:e202200599. [PMID: 36409290 DOI: 10.1002/cbic.202200599] [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: 10/19/2022] [Revised: 11/21/2022] [Indexed: 11/23/2022]
Abstract
The inhibition of protein-protein interactions (PPIs) is an effective approach for therapy. Owing to their large binding surface areas to target proteins, macrocyclic peptides are suitable molecules for PPI inhibition. In this study, we developed single-chain tandem macrocyclic peptides (STaMPtides) that inhibits the vascular endothelial growth factor (VEGF) receptor 2 (VEGFR2). They were artificially designed to comprise two different VEGFR2-binding macrocyclic peptides linked in tandem by peptide linkers and secreted by Corynebacterium glutamicum. Most potent VEGFR2-inhibitory STaMPtides with length-optimized linkers exhibited >1000 times stronger inhibitory activity than their parental monomeric peptides, possibly due to the avidity effect of heterodimerization. Our approach of using STaMPtides for PPI inhibition may be used to inhibit other extracellular factors, such as growth factors and cytokines.
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Affiliation(s)
- Kenichiro Ito
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki, 210-8681, Kanagawa, Japan
| | - Yoshihiko Matsuda
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki, 210-8681, Kanagawa, Japan
| | - Ayako Mine
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki, 210-8681, Kanagawa, Japan
| | - Kyohei Miyairi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki, 210-8681, Kanagawa, Japan
| | - Yoshimi Kikuchi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki, 210-8681, Kanagawa, Japan
| | - Atsushi Konishi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki, 210-8681, Kanagawa, Japan
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5
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Yang J, Zhu Q, Wu Y, Qu X, Liu H, Jiang B, Ge D, Song X. Utilization of macrocyclic peptides to target protein-protein interactions in cancer. Front Oncol 2022; 12:992171. [PMID: 36465350 PMCID: PMC9714258 DOI: 10.3389/fonc.2022.992171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/24/2022] [Indexed: 07/30/2023] Open
Abstract
Protein-protein interactions (PPIs) play vital roles in normal cellular processes. Dysregulated PPIs are involved in the process of various diseases, including cancer. Thus, these PPIs may serve as potential therapeutic targets in cancer treatment. However, despite rapid advances in small-molecule drugs and biologics, it is still hard to target PPIs, especially for those intracellular PPIs. Macrocyclic peptides have gained growing attention for their therapeutic properties in targeting dysregulated PPIs. Macrocyclic peptides have some unique features, such as moderate sizes, high selectivity, and high binding affinities, which make them good drug candidates. In addition, some oncology macrocyclic peptide drugs have been approved by the US Food and Drug Administration (FDA) for clinical use. Here, we reviewed the recent development of macrocyclic peptides in cancer treatment. The opportunities and challenges were also discussed to inspire new perspectives.
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Affiliation(s)
- Jiawen Yang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Qiaoliang Zhu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yifan Wu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaojuan Qu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haixia Liu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Biao Jiang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Di Ge
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaoling Song
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
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6
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Selective macrocyclic peptide modulators of Lys63-linked ubiquitin chains disrupt DNA damage repair. Nat Commun 2022; 13:6174. [PMID: 36257952 PMCID: PMC9579194 DOI: 10.1038/s41467-022-33808-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
Developing an effective binder for a specific ubiquitin (Ub) chain is a promising approach for modulating various biological processes with potential applications in drug discovery. Here, we combine the Random Non-standard Peptides Integrated Discovery (RaPID) method and chemical protein synthesis to screen an extended library of macrocyclic peptides against synthetic Lys63-linked Di-Ub to discover a specific binder for this Ub chain. Furthermore, next-generation binders are generated by chemical modifications. We show that our potent cyclic peptide is cell-permeable, and inhibits DNA damage repair, leading to apoptotic cell death. Concordantly, a pulldown experiment with the biotinylated analog of our lead cyclic peptide supports our findings. Collectively, we establish a powerful strategy for selective inhibition of protein-protein interactions associated with Lys63-linked Di-Ub using cyclic peptides. This study offers an advancement in modulating central Ub pathways and provides opportunities in drug discovery areas associated with Ub signaling.
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7
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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.
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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
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8
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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.
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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
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9
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Vanjari R, Eid E, Vamisetti GB, Mandal S, Brik A. Highly Efficient Cyclization Approach of Propargylated Peptides via Gold(I)-Mediated Sequential C-N, C-O, and C-C Bond Formation. ACS CENTRAL SCIENCE 2021; 7:2021-2028. [PMID: 34966846 PMCID: PMC8711126 DOI: 10.1021/acscentsci.1c00969] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Indexed: 05/02/2023]
Abstract
A rapid and efficient cyclization of unprotected N-propargylated peptides using the Au(I) organometallic complex is reported. The method relies on the activation of the propargyl functionality using gold(I) to produce a new linkage with the N-terminus amine at the cyclization site. The presented method features a fast reaction rate (within 20 min), mild conditions, chemoselectivity, wide sequence scope, and high yields (up to 87%). The strategy was successfully tested on a wide variety of 30 unprotected peptides having various sequences and lengths, thus providing access to structurally distinct cyclic peptides. The practical usefulness of this method was demonstrated in producing peptides that bind efficiently to Lys48-linked di- and tetra-ubiquitin chains. The new cyclic peptide modulators exhibited high permeability to living cells and promoted apoptosis via binding with the endogenous Lys48-linked ubiquitin chains.
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10
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Taguchi S, Suga H. Targeting of extracellular protein-protein interactions with macrocyclic peptides. Curr Opin Chem Biol 2021; 62:82-89. [PMID: 33774472 DOI: 10.1016/j.cbpa.2021.02.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/23/2021] [Accepted: 02/23/2021] [Indexed: 12/16/2022]
Abstract
Targeting of extracellular protein-protein interactions (PPI) is emerging as a major application for de novo discovered macrocyclic peptides. Modern discovery platforms can routinely identify macrocyclic peptide ligands capable of highly selective modulation of extracellular signaling pathways; amenability to chemical synthesis and natural modularity of peptides additionally provides an avenue for their further structural elaboration, while the challenge of cell internalization can be minimized. Here, we discuss the recent progress in targeting extracellular PPIs with macrocyclic peptides by focusing on a number of recent case studies. We analyze the scope and potential limitations of the discovery systems in identifying functional macrocyclic ligands. We also highlight the recent technical advancements allowing for a more streamlined discovery pipeline and our brief perspective in this field.
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Affiliation(s)
- Shota Taguchi
- Department of Advanced Interdisciplinary, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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11
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Vamisetti GB, Meledin R, Nawatha M, Suga H, Brik A. The Development of a Fluorescence-Based Competitive Assay Enabled the Discovery of Dimeric Cyclic Peptide Modulators of Ubiquitin Chains. Angew Chem Int Ed Engl 2021; 60:7018-7023. [PMID: 33326152 PMCID: PMC8048552 DOI: 10.1002/anie.202013392] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/13/2020] [Indexed: 12/15/2022]
Abstract
Development of modulators targeting specific interactions of ubiquitin-based conjugates with their partners is a formidable task since it requires a suitable screening assay and homogeneous ubiquitin conjugates. We developed a novel high-throughput strategy for screening ligands for Lys48-linked tetraubiquitin chain in a relatively simple, fast, and affordable manner. This approach combined with a state-of-the-art toolbox of chemical protein synthesis and a specially optimized Cys deprotection protocol enabled us to design highly potent, Lys48-linked tetraubiquitin chain selective "next generation" dimeric peptide modulators. The dimeric peptide exhibited cancer cell permeability and induced cell death with higher efficiency compared to its monocyclic analogue. These features make our dimeric peptide a promising candidate for further studies using in vivo models. Our assay can be adopted for other various ubiquitin chains in their free or anchored forms as well as conjugates for Ub-like modifiers.
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Affiliation(s)
- Ganga B. Vamisetti
- SchulichFaculty of ChemistryTechnion-Israel Institute of TechnologyHaifa3200008Israel
| | - Roman Meledin
- SchulichFaculty of ChemistryTechnion-Israel Institute of TechnologyHaifa3200008Israel
| | - Mickal Nawatha
- SchulichFaculty of ChemistryTechnion-Israel Institute of TechnologyHaifa3200008Israel
| | - Hiroaki Suga
- Department of ChemistrySchool of ScienceThe University of TokyoTokyo113-0033Japan
| | - Ashraf Brik
- SchulichFaculty of ChemistryTechnion-Israel Institute of TechnologyHaifa3200008Israel
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12
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Vamisetti GB, Meledin R, Nawatha M, Suga H, Brik A. The Development of a Fluorescence‐Based Competitive Assay Enabled the Discovery of Dimeric Cyclic Peptide Modulators of Ubiquitin Chains. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ganga B. Vamisetti
- Schulich Faculty of Chemistry Technion-Israel Institute of Technology Haifa 3200008 Israel
| | - Roman Meledin
- Schulich Faculty of Chemistry Technion-Israel Institute of Technology Haifa 3200008 Israel
| | - Mickal Nawatha
- Schulich Faculty of Chemistry Technion-Israel Institute of Technology Haifa 3200008 Israel
| | - Hiroaki Suga
- Department of Chemistry School of Science The University of Tokyo Tokyo 113-0033 Japan
| | - Ashraf Brik
- Schulich Faculty of Chemistry Technion-Israel Institute of Technology Haifa 3200008 Israel
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13
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Rogers JM, Nawatha M, Lemma B, Vamisetti GB, Livneh I, Barash U, Vlodavsky I, Ciechanover A, Fushman D, Suga H, Brik A. In vivo modulation of ubiquitin chains by N-methylated non-proteinogenic cyclic peptides. RSC Chem Biol 2020; 2:513-522. [PMID: 34179781 PMCID: PMC8232551 DOI: 10.1039/d0cb00179a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cancer and other disease states can change the landscape of proteins post-translationally tagged with ubiquitin (Ub) chains. Molecules capable of modulating Ub chains are potential therapeutic agents, but their discovery represents a significant challenge. Recently, it was shown that de novo cyclic peptides, selected from trillion-member random libraries, are capable of binding particular Ub chains. However, these peptides were overwhelmingly proteinogenic, so the prospect of in vivo activity was uncertain. Here, we report the discovery of small, non-proteinogenic cyclic peptides, rich in non-canonical features like N-methylation, which can tightly and specifically bind Lys48-linked Ub chains. These peptides engage three Lys48-linked Ub units simultaneously, block the action of deubiquitinases and the proteasome, induce apoptosis in vitro, and attenuate tumor growth in vivo. This highlights the potential of non-proteinogenic cyclic peptide screening to rapidly find in vivo-active leads, and the targeting of ubiquitin chains as a promising anti-cancer mechanism of action.
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Affiliation(s)
- Joseph M Rogers
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Mickal Nawatha
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200008, Israel
| | - Betsegaw Lemma
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Ganga B Vamisetti
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200008, Israel
| | - Ido Livneh
- The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Uri Barash
- The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Israel Vlodavsky
- The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Aaron Ciechanover
- The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200008, Israel
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Katoh T, Suga H. Ribosomal Elongation of Aminobenzoic Acid Derivatives. J Am Chem Soc 2020; 142:16518-16522. [DOI: 10.1021/jacs.0c05765] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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15
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Rogers JM. Peptide Folding and Binding Probed by Systematic Non-canonical Mutagenesis. Front Mol Biosci 2020; 7:100. [PMID: 32671094 PMCID: PMC7326784 DOI: 10.3389/fmolb.2020.00100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/04/2020] [Indexed: 12/20/2022] Open
Abstract
Many proteins and peptides fold upon binding another protein. Mutagenesis has proved an essential tool in the study of these multi-step molecular recognition processes. By comparing the biophysical behavior of carefully selected mutants, the concert of interactions and conformational changes that occur during folding and binding can be separated and assessed. Recently, this mutagenesis approach has been radically expanded by deep mutational scanning methods, which allow for many thousands of mutations to be examined in parallel. Furthermore, these high-throughput mutagenesis methods have been expanded to include mutations to non-canonical amino acids, returning peptide structure-activity relationships with unprecedented depth and detail. These developments are timely, as the insights they provide can guide the optimization of de novo cyclic peptides, a promising new modality for chemical probes and therapeutic agents.
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Affiliation(s)
- Joseph M Rogers
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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