1
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Shao J, Lin X, Wang H, Zhao C, Yao SQ, Ge J, Zeng S, Qian L. Targeted Degradation of Cell-Surface Proteins via Chaperone-Mediated Autophagy by Using Peptide-Conjugated Antibodies. Angew Chem Int Ed Engl 2024; 63:e202319232. [PMID: 38472118 DOI: 10.1002/anie.202319232] [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: 12/29/2023] [Revised: 03/06/2024] [Accepted: 03/11/2024] [Indexed: 03/14/2024]
Abstract
Cell-surface proteins are important drug targets but historically have posed big challenges for the complete elimination of their functions. Herein, we report antibody-peptide conjugates (Ab-CMAs) in which a peptide targeting chaperone-mediated autophagy (CMA) was conjugated with commercially available monoclonal antibodies for specific cell-surface protein degradation by taking advantage of lysosomal degradation pathways. Unique features of Ab-CMAs, including cell-surface receptor- and E3 ligase-independent degradation, feasibility towards different cell-surface proteins (e.g., epidermal growth factor receptor (EGFR), programmed cell death ligand 1 (PD-L1), human epidermal growth factor receptor 2 (HER2)) by a simple change of the antibody, and successful tumor inhibition in vivo, make them attractive protein degraders for biomedical research and therapeutic applications. As the first example employing CMA to degrade proteins from the outside in, our findings may also shed new light on CMA, a degradation pathway typically targeting cytosolic proteins.
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Affiliation(s)
- Jinning Shao
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou, China, 310058
| | - Xuefen Lin
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou, China, 310058
| | - Haoting Wang
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou, China, 310058
| | - Chuhan Zhao
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou, China, 310058
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544, Singapore
| | - Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology, Zhejiang University of Technology, Hangzhou, China, 310014
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou, China, 310058
| | - Linghui Qian
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou, China, 310058
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2
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Gabizon R, Tivon B, Reddi RN, van den Oetelaar MCM, Amartely H, Cossar PJ, Ottmann C, London N. A simple method for developing lysine targeted covalent protein reagents. Nat Commun 2023; 14:7933. [PMID: 38040731 PMCID: PMC10692228 DOI: 10.1038/s41467-023-42632-5] [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: 04/13/2023] [Accepted: 10/16/2023] [Indexed: 12/03/2023] Open
Abstract
Peptide-based covalent probes can target shallow protein surfaces not typically addressable using small molecules, yet there is a need for versatile approaches to convert native peptide sequences into covalent binders that can target a broad range of residues. Here we report protein-based thio-methacrylate esters-electrophiles that can be installed easily on unprotected peptides and proteins via cysteine side chains, and react efficiently and selectively with cysteine and lysine side chains on the target. Methacrylate phosphopeptides derived from 14-3-3-binding proteins irreversibly label 14-3-3σ via either lysine or cysteine residues, depending on the position of the electrophile. Methacrylate peptides targeting a conserved lysine residue exhibit pan-isoform binding of 14-3-3 proteins both in lysates and in extracellular media. Finally, we apply this approach to develop protein-based covalent binders. A methacrylate-modified variant of the colicin E9 immunity protein irreversibly binds to the E9 DNAse, resulting in significantly higher thermal stability relative to the non-covalent complex. Our approach offers a simple and versatile route to convert peptides and proteins into potent covalent binders.
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Affiliation(s)
- Ronen Gabizon
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Barr Tivon
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Rambabu N Reddi
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Maxime C M van den Oetelaar
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB, Eindhoven, The Netherlands
| | - Hadar Amartely
- Wolfson Centre for Applied Structural Biology, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Peter J Cossar
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB, Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB, Eindhoven, The Netherlands
| | - Nir London
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel.
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3
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Thomas AM, Serafini M, Grant EK, Coombs EAJ, Bluck JP, Schiedel M, McDonough MA, Reynolds JK, Lee B, Platt M, Sharlandjieva V, Biggin PC, Duarte F, Milne TA, Bush JT, Conway SJ. Mutate and Conjugate: A Method to Enable Rapid In-Cell Target Validation. ACS Chem Biol 2023; 18:2405-2417. [PMID: 37874862 PMCID: PMC10660337 DOI: 10.1021/acschembio.3c00437] [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: 07/26/2023] [Revised: 09/22/2023] [Accepted: 10/05/2023] [Indexed: 10/26/2023]
Abstract
Target validation remains a challenge in drug discovery, which leads to a high attrition rate in the drug discovery process, particularly in Phase II clinical trials. Consequently, new approaches to enhance target validation are valuable tools to improve the drug discovery process. Here, we report the combination of site-directed mutagenesis and electrophilic fragments to enable the rapid identification of small molecules that selectively inhibit the mutant protein. Using the bromodomain-containing protein BRD4 as an example, we employed a structure-based approach to identify the L94C mutation in the first bromodomain of BRD4 [BRD4(1)] as having a minimal effect on BRD4(1) function. We then screened a focused, KAc mimic-containing fragment set and a diverse fragment library against the mutant and wild-type proteins and identified a series of fragments that showed high selectivity for the mutant protein. These compounds were elaborated to include an alkyne click tag to enable the attachment of a fluorescent dye. These clickable compounds were then assessed in HEK293T cells, transiently expressing BRD4(1)WT or BRD4(1)L94C, to determine their selectivity for BRD4(1)L94C over other possible cellular targets. One compound was identified that shows very high selectivity for BRD4(1)L94C over all other proteins. This work provides a proof-of-concept that the combination of site-directed mutagenesis and electrophilic fragments, in a mutate and conjugate approach, can enable rapid identification of small molecule inhibitors for an appropriately mutated protein of interest. This technology can be used to assess the cellular phenotype of inhibiting the protein of interest, and the electrophilic ligand provides a starting point for noncovalent ligand development.
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Affiliation(s)
- Adam M. Thomas
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Marta Serafini
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Emma K. Grant
- Department
of Chemical Biology, GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Edward A. J. Coombs
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Joseph P. Bluck
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
- Department
of Biochemistry, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Matthias Schiedel
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Michael A. McDonough
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Jessica K. Reynolds
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Bernadette Lee
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Michael Platt
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Vassilena Sharlandjieva
- MRC
Molecular Haematology Unit, MRC Weatherall Institute of Molecular
Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, United
Kingdom
| | - Philip C. Biggin
- Department
of Biochemistry, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Fernanda Duarte
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Thomas A. Milne
- MRC
Molecular Haematology Unit, MRC Weatherall Institute of Molecular
Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, United
Kingdom
| | - Jacob T. Bush
- Department
of Chemical Biology, GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Stuart J. Conway
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
- Department
of Chemistry & Biochemistry, University
of California Los Angeles, 607 Charles E. Young Drive East, P.O. Box 951569, Los Angeles, California 90095-1569, United States
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4
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Yan J, Liu H, Wu Y, Niu B, Deng X, Zhang L, Dang Q, Wang Y, Lu X, Zhang B, Sun W. Recent progress of self-immobilizing and self-precipitating molecular fluorescent probes for higher-spatial-resolution imaging. Biomaterials 2023; 301:122281. [PMID: 37643487 DOI: 10.1016/j.biomaterials.2023.122281] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/12/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023]
Abstract
Flourished in the past two decades, fluorescent probe technology provides researchers with accurate and efficient tools for in situ imaging of biomarkers in living cells and tissues and may play a significant role in clinical diagnosis and treatment such as biomarker detection, fluorescence imaging-guided surgery, and photothermal/photodynamic therapy. In situ imaging of biomarkers depends on the spatial resolution of molecular probes. Nevertheless, the majority of currently available molecular fluorescent probes suffer from the drawback of diffusing from the target region. This leads to a rapid attenuation of the fluorescent signal over time and a reduction in spatial resolution. Consequently, the diffused fluorescent signal cannot accurately reflect the in situ information of the target. Self-immobilizing and self-precipitating molecular fluorescent probes can be used to overcome this problem. These probes ensure that the fluorescent signal remains at the location where the signal is generated for a long time. In this review, we introduce the development history of the two types of probes and classify them in detail according to different design strategies. In addition, we compare their advantages and disadvantages, summarize some representative studies conducted in recent years, and propose prospects for this field.
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Affiliation(s)
- Jiawei Yan
- College of Medical Laboratory, Dalian Medical University, Dalian, 116044, China
| | - Huanying Liu
- School of Mechanical and Power Engineering, Dalian Ocean University, Dalian, 116023, China
| | - Yingxu Wu
- College of Medical Laboratory, Dalian Medical University, Dalian, 116044, China
| | - Ben Niu
- College of Medical Laboratory, Dalian Medical University, Dalian, 116044, China
| | - Xiaojing Deng
- College of Medical Laboratory, Dalian Medical University, Dalian, 116044, China
| | - Linhao Zhang
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian, 116024, China
| | - Qi Dang
- College of Medical Laboratory, Dalian Medical University, Dalian, 116044, China
| | - Yubo Wang
- College of Medical Laboratory, Dalian Medical University, Dalian, 116044, China
| | - Xiao Lu
- College of Medical Laboratory, Dalian Medical University, Dalian, 116044, China
| | - Boyu Zhang
- College of Medical Laboratory, Dalian Medical University, Dalian, 116044, China.
| | - Wen Sun
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian, 116024, China.
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5
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Mohamed M, Klenke AK, Anokhin MV, Amadou H, Bothwell PJ, Conroy B, Nesterov EE, Nesterova IV. Zero-Background Small-Molecule Sensors for Near-IR Fluorescent Imaging of Biomacromolecular Targets in Cells. ACS Sens 2023; 8:1109-1118. [PMID: 36866808 PMCID: PMC10515643 DOI: 10.1021/acssensors.2c02342] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
In this study, we report a general approach to the design of a new generation of small-molecule sensors that produce a zero background but are brightly fluorescent in the near-IR spectral range upon selective interaction with a biomolecular target. We developed a fluorescence turn-on/-off mechanism based on the aggregation/deaggregation of phthalocyanine chromophores. As a proof of concept, we designed, prepared, and characterized sensors for in-cell visualization of epidermal growth factor receptor (EGFR) tyrosine kinase. We established a structure/bioavailability correlation, determined conditions for the optimal sensor uptake and imaging, and demonstrated binding specificity and applications over a wide range of treatment options involving live and fixed cells. The new approach enables high-contrast imaging and requires no in-cell chemical assembly or postexposure manipulations (i.e., washes). The general design principles demonstrated in this work can be extended toward sensors and imaging agents for other biomolecular targets.
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Affiliation(s)
- Myar Mohamed
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Anastasia K. Klenke
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Maksim V. Anokhin
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Harouna Amadou
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Paige J. Bothwell
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Brigid Conroy
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Evgueni E. Nesterov
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Irina V. Nesterova
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
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6
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Xu J, Peng L, Guo C, Xu F, Lin DS, Tang Y, Li Z. Comparison of Different Competitive Proteome Profiling Approaches in Target Identification of Covalent Inhibitors. Chembiochem 2022; 23:e202200389. [PMID: 36271784 DOI: 10.1002/cbic.202200389] [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: 07/11/2022] [Revised: 10/17/2022] [Indexed: 01/25/2023]
Abstract
Competitive proteome profiling is a powerful approach for the identification of targets of small molecules. This approach usually employs an inhibitor-derived probe or a cysteine-reactive probe such as an IA-alkyne in a comparison between inhibitor-treated and untreated samples, thus enabling distinction between genuine targets and nonspecific labeling. We have developed an active probe derived from an EGFR inhibitor, afatinib, and a cysteine reactive probe, an alkyne-containing α,β-unsaturated amide, to compare their characterization of cellular targets. In both approaches, myosin heavy chain 9 (MYH9) was identified as an off-target. Subsequent functional validation experiments suggested that MYH9 might be involved in the function of afatinib.
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Affiliation(s)
- Jiaqian Xu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Lijie Peng
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Cuiping Guo
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Fang Xu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Dong-Shi Lin
- Department of Pharmacy, Guangdong Provincial Corps Hospital of Chinese People's Armed Police Forces, Guangzhou, Guangdong, 510507, P. R. China
| | - Yi Tang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Zhengqiu Li
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou, 510632, China
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7
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Scinto SL, Reagle TR, Fox JM. Affinity Bioorthogonal Chemistry (ABC) Tags for Site-Selective Conjugation, On-Resin Protein-Protein Coupling, and Purification of Protein Conjugates. Angew Chem Int Ed Engl 2022; 61:e202207661. [PMID: 36058881 PMCID: PMC10029600 DOI: 10.1002/anie.202207661] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Indexed: 11/12/2022]
Abstract
The site-selective functionalization of proteins has broad application in chemical biology, but can be limited when mixtures result from incomplete conversion or the formation of protein containing side products. It is shown here that when proteins are covalently tagged with pyridyl-tetrazines, the nickel-iminodiacetate (Ni-IDA) resins commonly used for His-tags can be directly used for protein affinity purification. These Affinity Bioorthogonal Chemistry (ABC) tags serve a dual role by enabling affinity-based protein purification while maintaining rapid kinetics in bioorthogonal reactions. ABC-tagging works with a range of site-selective bioconjugation methods with proteins tagged at the C-terminus, N-terminus or at internal positions. ABC-tagged proteins can also be purified from complex mixtures including cell lysate. The combination of site-selective conjugation and clean-up with ABC-tagged proteins also allows for facile on-resin reactions to provide protein-protein conjugates.
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Affiliation(s)
- Samuel L Scinto
- Department of Chemistry and Biochemistry, University of Delaware, Ammon Pinizzotto Biopharmaceutical Innovation Center, Newark, DE 19713, USA
| | - Tyler R Reagle
- Department of Chemistry and Biochemistry, University of Delaware, Ammon Pinizzotto Biopharmaceutical Innovation Center, Newark, DE 19713, USA
| | - Joseph M Fox
- Department of Chemistry and Biochemistry, University of Delaware, Ammon Pinizzotto Biopharmaceutical Innovation Center, Newark, DE 19713, USA
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8
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Zhu Y, Shuai W, Zhao M, Pan X, Pei J, Wu Y, Bu F, Wang A, Ouyang L, Wang G. Unraveling the Design and Discovery of c-Jun N-Terminal Kinase Inhibitors and Their Therapeutic Potential in Human Diseases. J Med Chem 2022; 65:3758-3775. [PMID: 35200035 DOI: 10.1021/acs.jmedchem.1c01947] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
c-Jun N-terminal kinases (JNKs), members of the mitogen-activated protein kinase (MAPK) family, are encoded by three genes: jnk1, jnk2, and jnk3. JNKs are involved in the pathogenesis and development of many diseases, such as neurodegenerative diseases, inflammation, and cancers. Therefore, JNKs have become important therapeutic targets. Many JNK inhibitors have been discovered, and some have been introduced into clinical trials. However, the study of isoform-selective JNK inhibitors is still a challenging task. To further develop novel JNK inhibitors with clinical value, a comprehensive understanding of JNKs and their corresponding inhibitors is required. In this Perspective, we introduced the JNK signaling pathways and reviewed different chemical types of JNK inhibitors, focusing on their structure-activity relationships and biological activities. The challenges and strategies for the development of JNK inhibitors are also discussed. It is hoped that this Perspective will provide valuable references for the development of novel selective JNK inhibitors.
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Affiliation(s)
- Yumeng Zhu
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Wen Shuai
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Min Zhao
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Xiaoli Pan
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Junping Pei
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Yongya Wu
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Faqian Bu
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Aoxue Wang
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Liang Ouyang
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Guan Wang
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
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9
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Fang H, Peng B, Ong SY, Wu Q, Li L, Yao SQ. Recent advances in activity-based probes (ABPs) and affinity-based probes (A fBPs) for profiling of enzymes. Chem Sci 2021; 12:8288-8310. [PMID: 34221311 PMCID: PMC8221178 DOI: 10.1039/d1sc01359a] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/11/2021] [Indexed: 12/14/2022] Open
Abstract
Activity-based protein profiling (ABPP) is a technique that uses highly selective active-site targeted chemical probes to label and monitor the state of proteins. ABPP integrates the strengths of both chemical and biological disciplines. By utilizing chemically synthesized or modified bioactive molecules, ABPP is able to reveal complex physiological and pathological enzyme-substrate interactions at molecular and cellular levels. It is also able to provide critical information of the catalytic activity changes of enzymes, annotate new functions of enzymes, discover new substrates of enzymes, and allow real-time monitoring of the cellular location of enzymes. Based on the mechanism of probe-enzyme interaction, two types of probes that have been used in ABPP are activity-based probes (ABPs) and affinity-based probes (AfBPs). This review highlights the recent advances in the use of ABPs and AfBPs, and summarizes their design strategies (based on inhibitors and substrates) and detection approaches.
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Affiliation(s)
- Haixiao Fang
- Key Laboratory of Flexible Electronics (KLOFE), Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Bo Peng
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE), Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University 127 West Youyi Road Xi'an 710072 P. R. China
| | - Sing Yee Ong
- Department of Chemistry, National University of Singapore 4 Science Drive 2 117544 Singapore
| | - Qiong Wu
- Key Laboratory of Flexible Electronics (KLOFE), Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE), Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore 4 Science Drive 2 117544 Singapore
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10
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Lang W, Yuan C, Zhu L, Du S, Qian L, Ge J, Yao SQ. Recent advances in construction of small molecule-based fluorophore-drug conjugates. J Pharm Anal 2020; 10:434-443. [PMID: 33133727 PMCID: PMC7591808 DOI: 10.1016/j.jpha.2020.08.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 08/08/2020] [Accepted: 08/12/2020] [Indexed: 12/11/2022] Open
Abstract
As a powerful tool to advance drug discovery, molecular imaging may provide new insights into the process of drug effect and therapy at cellular and molecular levels. When compared with other detection methods, fluorescence-based strategies are highly attractive and can be used to illuminate pathways of drugs' transport, with multi-color capacity, high specificity and good sensitivity. The conjugates of fluorescent molecules and therapeutic agents create exciting avenues for real-time monitoring of drug delivery and distribution, both in vitro and in vivo. In this short review, we discuss recent developments of small molecule-based fluorophore-drug conjugates, including non-cleavable and cleavable ones, that are capable of visualizing drug delivery.
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Affiliation(s)
- Wenjie Lang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Chaonan Yuan
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Liquan Zhu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Shubo Du
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Linghui Qian
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Shao Q. Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
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Ducharme GT, LaCasse Z, Sheth T, Nesterova IV, Nesterov EE. Design of Turn‐On Near‐Infrared Fluorescent Probes for Highly Sensitive and Selective Monitoring of Biopolymers. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Gerard T. Ducharme
- Department of Chemistry Louisiana State University Baton Rouge LA 70803 USA
| | - Zane LaCasse
- Department of Chemistry and Biochemistry Northern Illinois University DeKalb IL 60115 USA
| | - Tanya Sheth
- Department of Chemistry and Biochemistry Northern Illinois University DeKalb IL 60115 USA
| | - Irina V. Nesterova
- Department of Chemistry and Biochemistry Northern Illinois University DeKalb IL 60115 USA
| | - Evgueni E. Nesterov
- Department of Chemistry Louisiana State University Baton Rouge LA 70803 USA
- Department of Chemistry and Biochemistry Northern Illinois University DeKalb IL 60115 USA
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Ducharme GT, LaCasse Z, Sheth T, Nesterova IV, Nesterov EE. Design of Turn‐On Near‐Infrared Fluorescent Probes for Highly Sensitive and Selective Monitoring of Biopolymers. Angew Chem Int Ed Engl 2020; 59:8440-8444. [DOI: 10.1002/anie.202000108] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/03/2020] [Indexed: 11/05/2022]
Affiliation(s)
- Gerard T. Ducharme
- Department of Chemistry Louisiana State University Baton Rouge LA 70803 USA
| | - Zane LaCasse
- Department of Chemistry and Biochemistry Northern Illinois University DeKalb IL 60115 USA
| | - Tanya Sheth
- Department of Chemistry and Biochemistry Northern Illinois University DeKalb IL 60115 USA
| | - Irina V. Nesterova
- Department of Chemistry and Biochemistry Northern Illinois University DeKalb IL 60115 USA
| | - Evgueni E. Nesterov
- Department of Chemistry Louisiana State University Baton Rouge LA 70803 USA
- Department of Chemistry and Biochemistry Northern Illinois University DeKalb IL 60115 USA
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Backus KM, Cao J, Maddox SM. Opportunities and challenges for the development of covalent chemical immunomodulators. Bioorg Med Chem 2019; 27:3421-3439. [PMID: 31204229 DOI: 10.1016/j.bmc.2019.05.050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/24/2019] [Accepted: 05/31/2019] [Indexed: 02/06/2023]
Abstract
Compounds that react irreversibly with cysteines have reemerged as potent and selective tools for altering protein function, serving as chemical probes and even clinically approved drugs. The exquisite sensitivity of human immune cell signaling pathways to oxidative stress indicates the likely, yet still underexploited, general utility of covalent probes for selective chemical immunomodulation. Here, we provide an overview of immunomodulatory cysteines, including identification of electrophilic compounds available to label these residues. We focus our discussion on three protein classes essential for cell signaling, which span the 'druggability' spectrum from amenable to chemical probes (kinases), somewhat druggable (proteases), to inaccessible (phosphatases). Using existing inhibitors as a guide, we identify general strategies to guide the development of covalent probes for selected undruggable classes of proteins and propose the application of such compounds to alter immune cell functions.
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Affiliation(s)
- Keriann M Backus
- Departments of Biological Chemistry and Chemistry and Biochemistry, University of California Los Angeles, USA.
| | - Jian Cao
- Departments of Biological Chemistry and Chemistry and Biochemistry, University of California Los Angeles, USA
| | - Sean M Maddox
- Departments of Biological Chemistry and Chemistry and Biochemistry, University of California Los Angeles, USA
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