1
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Wahl J, Ahsanullah, Zupan H, Gottschalk F, Nerlich A, Arkona C, Hocke AC, Keller BG, Rademann J. Chemically Stable Diazo Peptides as Selective Probes of Cysteine Proteases in Living Cells. Angew Chem Int Ed Engl 2024; 63:e202411006. [PMID: 39380558 DOI: 10.1002/anie.202411006] [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: 06/11/2024] [Revised: 09/04/2024] [Accepted: 09/09/2024] [Indexed: 10/10/2024]
Abstract
Diazo peptides have been described earlier, however, due to their high reactivity have not been broadly used until today. Here, we report the preparation, properties, and applications of chemically stable internal diazo peptides. Peptidyl phosphoranylidene-esters and amides were found to react with triflyl azide primarily to novel 3,4-disubstituted triazolyl-peptides. Nonaflyl azide instead furnished diazo peptides, which are chemically stable from pH 1-14 as amides and from pH 1-8 as esters. Thus, diazo peptides prepared by solid phase peptide synthesis were stable to final deprotection with 95 % trifluoroacetic acid. Diazo peptides with the recognition sequence of caspase-3 were identified as specific, covalent, and irreversible inhibitors of this enzyme at low nanomolar concentrations. A fluorescent diazo peptide entered living cells enabling microscopic imaging and quantification of apoptotic cells via flow cytometry. Thus, internal diazo peptides constitute a novel class of activity-based probes and enzyme inhibitors useful in chemical biology and medicinal chemistry.
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Affiliation(s)
- Juliane Wahl
- Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Ahsanullah
- Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Hana Zupan
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Franziska Gottschalk
- Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Andreas Nerlich
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117, Berlin, Germany
| | - Christoph Arkona
- Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Andreas C Hocke
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117, Berlin, Germany
| | - Bettina G Keller
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Jörg Rademann
- Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
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2
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Gazzi T, Brennecke B, Olikauskas V, Hochstrasser R, Wang H, Keen Chao S, Atz K, Mostinski Y, Topp A, Heer D, Kaufmann I, Ritter M, Gobbi L, Hornsperger B, Wagner B, Richter H, O'Hara F, Wittwer MB, Jul Hansen D, Collin L, Kuhn B, Benz J, Grether U, Nazaré M. Development of a Highly Selective NanoBRET Probe to Assess MAGL Inhibition in Live Cells. Chembiochem 2024:e202400704. [PMID: 39607084 DOI: 10.1002/cbic.202400704] [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: 08/27/2024] [Revised: 10/23/2024] [Indexed: 11/29/2024]
Abstract
Cell-free enzymatic assays are highly useful tools in early compound profiling due to their robustness and scalability. However, their inadequacy to reflect the complexity of target engagement in a cellular environment may lead to a significantly divergent pharmacology that is eventually observed in cells. The discrepancy that emerges from properties like permeability and unspecific protein binding may largely mislead lead compound selection to undergo further chemical optimization. We report the development of a new intracellular NanoBRET assay to assess MAGL inhibition in live cells. Based on a reverse design approach, a highly potent, reversible preclinical inhibitor was conjugated to the cell-permeable BODIPY590 acceptor fluorophore while retaining its overall balanced properties. An engineered MAGL-nanoluciferase (Nluc) fusion protein provided a suitable donor counterpart for the facile interrogation of intracellular ligand activity. Validation of assay conditions using a selection of known MAGL inhibitors set the stage for the evaluation of over 1'900 MAGL drug candidates derived from our discovery program. This evaluation enabled us to select compounds for further development based not only on target engagement, but also on favorable physicochemical parameters like permeability and protein binding. This study highlights the advantages of cell-based target engagement assays for accelerating compound profiling and progress at the early stages of drug discovery programs.
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Affiliation(s)
- Thais Gazzi
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel, 4070, Switzerland
| | - Benjamin Brennecke
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel, 4070, Switzerland
| | - Valentas Olikauskas
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel, 4070, Switzerland
| | - Remo Hochstrasser
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel, 4070, Switzerland
| | - Haiyan Wang
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel, 4070, Switzerland
| | - Suzan Keen Chao
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel, 4070, Switzerland
| | - Kenneth Atz
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel, 4070, Switzerland
| | - Yelena Mostinski
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Andreas Topp
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel, 4070, Switzerland
| | - Dominik Heer
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel, 4070, Switzerland
| | - Isabelle Kaufmann
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel, 4070, Switzerland
| | - Martin Ritter
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel, 4070, Switzerland
| | - Luca Gobbi
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel, 4070, Switzerland
| | - Benoit Hornsperger
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel, 4070, Switzerland
| | - Bjoern Wagner
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel, 4070, Switzerland
| | - Hans Richter
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel, 4070, Switzerland
| | - Fionn O'Hara
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel, 4070, Switzerland
| | - Matthias B Wittwer
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel, 4070, Switzerland
| | - Dennis Jul Hansen
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel, 4070, Switzerland
| | - Ludovic Collin
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel, 4070, Switzerland
| | - Bernd Kuhn
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel, 4070, Switzerland
| | - Joerg Benz
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel, 4070, Switzerland
| | - Uwe Grether
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel, 4070, Switzerland
| | - Marc Nazaré
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
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3
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Yin Q, Yang M. Chemoproteomics approach to elucidating biosynthetic pathway of plant natural products. FRONTIERS IN PLANT SCIENCE 2024; 15:1506569. [PMID: 39659415 PMCID: PMC11628272 DOI: 10.3389/fpls.2024.1506569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2024] [Accepted: 11/13/2024] [Indexed: 12/12/2024]
Affiliation(s)
| | - Mengquan Yang
- National Tobacco Cultivation, Physiology and Biochemistry Research Center, Flavors and Fragrance Engineering and Technology Research Center of Henan Province, College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan, China
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4
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Zhu X, Yuan Y, Wang K, Shen W, Zhu Q. Identification of Aberrant Expression of Gemcitabine-Targeting Proteins in Drug-Resistant Cells Using an Activity-Based Gemcitabine Probe. ACS Chem Biol 2024; 19:2336-2344. [PMID: 39465385 DOI: 10.1021/acschembio.4c00446] [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: 10/29/2024]
Abstract
Gemcitabine-based monotherapy or combination therapy has become the standard treatment for locally advanced and metastatic pancreatic cancer. However, the emergence of resistance within weeks of treatment severely compromises therapeutic efficacy. The intricate biological process of gemcitabine resistance in pancreatic cancer presents a complex challenge, as the underlying mechanisms remain unclear. Identifying the target protein of gemcitabine is crucial for studying its drug-resistance mechanism. An activity-based probe is a powerful tool for studying drug target proteins, but the current lack of activity-based gemcitabine probes with robust biological activity hinders research on gemcitabine. In this study, we developed three active probes based on gemcitabine, among which Gem-3 demonstrated excellent stability and labeling efficacy. We utilized Gem-3 in conjunction with chemical proteomics to identify intracellular target proteins. We identified 79 proteins that interact with gemcitabine, most of which were previously unknown and represented various functional classes. Additionally, we validated the increased expression of IFIT3 and MARCKS in drug-resistant cells, along with the activation of the NF-κB signaling pathway. These findings substantially contribute to our comprehension of gemcitabine's target proteins and further our understanding of the mechanisms driving gemcitabine resistance in pancreatic cancer cells.
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Affiliation(s)
- Xiaomei Zhu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - YuQing Yuan
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Kai Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wei Shen
- Department of Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China
| | - Qing Zhu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
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5
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Louka A, Spacho N, Korovesis D, Adamis K, Papadopoulos C, Kalaitzaki EE, Tavernarakis N, Neochoritis CG, Eleftheriadis N. Crafting Molecular Tools for 15-Lipoxygenase-1 in a Single Step. Angew Chem Int Ed Engl 2024:e202418291. [PMID: 39523872 DOI: 10.1002/anie.202418291] [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: 09/23/2024] [Revised: 10/21/2024] [Accepted: 11/08/2024] [Indexed: 11/16/2024]
Abstract
Small molecule modulators are powerful tools for selectively probing and manipulating proteins in native biological systems. However, the development of versatile modulators that exhibit desired properties is hindered by the lack of a rapid and robust synthetic strategy. Here, we develop a facile and reliable one-step methodology for the generation of multifunctional toolboxes encompassing a wide variety of chemical modulators with different desired features. These modulators bind irreversibly to the protein target via a selective warhead. Key elements are introduced onto the warhead in a single step using multi-component reactions. To illustrate the power of this new technology, we synthesized a library of diverse modulators designed to explore a highly challenging and poorly understood protein, human 15-lipoxygenase-1. Modulators made include; activity-based/photoaffinity probes, chemosensors, photocrosslinkers, as well as light-controlled and high-affinity inhibitors. The efficacy of our compounds was successfully established through the provision of on demand inhibition and labeling of our target protein in vitro, in cellulo and in vivo; thus, proving that this technology has promising potential for applications in many complex biological systems.
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Affiliation(s)
- Anastasia Louka
- Department of Chemistry, University of Crete, Voutes, 70013 Heraklion, Greece
| | - Ntaniela Spacho
- Department of Chemistry, University of Crete, Voutes, 70013 Heraklion, Greece
| | - Dimitris Korovesis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Greece
| | - Konstantinos Adamis
- Department of Chemistry, University of Crete, Voutes, 70013 Heraklion, Greece
| | | | | | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Greece
- Division of Basic Sciences, School of Medicine, University of Crete, Voutes, 70013 Heraklion, Greece
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6
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Pan X, Jiang S, Zhang X, Wang Z, Wang X, Cao L, Xiao W. Recent strategies in target identification of natural products: Exploring applications in chronic inflammation and beyond. Br J Pharmacol 2024. [PMID: 39428703 DOI: 10.1111/bph.17356] [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: 04/07/2024] [Revised: 08/01/2024] [Accepted: 08/25/2024] [Indexed: 10/22/2024] Open
Abstract
Natural products are a treasure trove for drug discovery, especially in the areas of infection, inflammation and cancer, due to their diverse bioactivities and complex, and varied structures. Chronic inflammation is closely related to many diseases, including complex diseases such as cancer and neurodegeneration. Improving target identification for natural products contributes to elucidating their mechanism of action and clinical progress. It also facilitates the discovery of novel druggable targets and the elimination of undesirable ones, thereby significantly enhancing the productivity of drug discovery and development. Moreover, the rise of polypharmacological strategies, considered promising for the treatment of complex diseases, will further increase the demand for target deconvolution. This review underscores strategies for identifying natural product targets (NPs) in the context of chronic inflammation over the past 5 years. These strategies encompass computational methodologies for early target discovery and the anticipation of compound binding sites, proteomics-driven approaches for target delineation and experimental biology techniques for target validation and comprehensive mechanistic exploration.
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Affiliation(s)
- Xian Pan
- State Key Laboratory on Technologies for Chinese Medicine Pharmaceutical Process Control and Intelligent Manufacture, Jiangning Industrial City, Economic and Technological Development Zone of Lianyungang, Lianyungang, China
- Jiangsu Kanion Pharmaceutical Co Ltd, Jiangning Industrial City, Economic and Technological Development Zone of Lianyungang, Lianyungang, China
| | - Shan Jiang
- State Key Laboratory on Technologies for Chinese Medicine Pharmaceutical Process Control and Intelligent Manufacture, Jiangning Industrial City, Economic and Technological Development Zone of Lianyungang, Lianyungang, China
- Jiangsu Kanion Pharmaceutical Co Ltd, Jiangning Industrial City, Economic and Technological Development Zone of Lianyungang, Lianyungang, China
| | - Xinzhuang Zhang
- State Key Laboratory on Technologies for Chinese Medicine Pharmaceutical Process Control and Intelligent Manufacture, Jiangning Industrial City, Economic and Technological Development Zone of Lianyungang, Lianyungang, China
- Jiangsu Kanion Pharmaceutical Co Ltd, Jiangning Industrial City, Economic and Technological Development Zone of Lianyungang, Lianyungang, China
| | - Zhenzhong Wang
- State Key Laboratory on Technologies for Chinese Medicine Pharmaceutical Process Control and Intelligent Manufacture, Jiangning Industrial City, Economic and Technological Development Zone of Lianyungang, Lianyungang, China
- Jiangsu Kanion Pharmaceutical Co Ltd, Jiangning Industrial City, Economic and Technological Development Zone of Lianyungang, Lianyungang, China
| | - Xin Wang
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Liang Cao
- State Key Laboratory on Technologies for Chinese Medicine Pharmaceutical Process Control and Intelligent Manufacture, Jiangning Industrial City, Economic and Technological Development Zone of Lianyungang, Lianyungang, China
- Jiangsu Kanion Pharmaceutical Co Ltd, Jiangning Industrial City, Economic and Technological Development Zone of Lianyungang, Lianyungang, China
- Nanjing University of Chinese Medicine, Nanjing, China
| | - Wei Xiao
- State Key Laboratory on Technologies for Chinese Medicine Pharmaceutical Process Control and Intelligent Manufacture, Jiangning Industrial City, Economic and Technological Development Zone of Lianyungang, Lianyungang, China
- Jiangsu Kanion Pharmaceutical Co Ltd, Jiangning Industrial City, Economic and Technological Development Zone of Lianyungang, Lianyungang, China
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7
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Devel L, Malgorn C, Tohon RW, Launay M, Patiniotis K, Sejalon-Cipolla M, Beau F, Thai R, Bruyat P, Bonino A, Bregant S, Subra G, Cantel S, Georgiadis D. Covalent Labeling of Matrix Metalloproteases with Affinity-Based Probes Containing Tuned Reactive N-Acyl-N-Alkyl Sulfonamide Cleavable Linkers. Chembiochem 2024:e202400441. [PMID: 39352839 DOI: 10.1002/cbic.202400441] [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: 05/17/2024] [Revised: 09/11/2024] [Accepted: 10/01/2024] [Indexed: 10/04/2024]
Abstract
Original covalent probes with an N-acyl-N-alkyl sulfonamide cleavable linker were developed to target a broad set of human Matrix Metalloproteases (MMPs). The electrophilicity of this cleavable linker was modulated to improve the selectivity of the probes as well as reduce their unspecific reactivity in complex biological matrices. We first demonstrated that targeting the S3 subsite of MMPs enables access to broad-spectrum affinity-based probes that exclusively react with the active version of these proteases. The probes were further assessed in proteomes of varying complexity, where human MMP-13 was artificially introduced at known concentration and the resulting labeled MMP was imaged by in-gel fluorescence imaging. We showed that the less reactive probe was still able to covalently modify MMP-13 while exhibiting reduced off-target unspecific reactivity. This study clearly demonstrated the importance of finely controlling the reactivity of the NASA warhead to improve the selectivity of covalent probes in complex biological systems.
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Affiliation(s)
- Laurent Devel
- CEA, INRAE, Médicaments et Technologies pour la Santé (MTS), SIMoS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Carole Malgorn
- CEA, INRAE, Médicaments et Technologies pour la Santé (MTS), SIMoS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Regis-William Tohon
- CEA, INRAE, Médicaments et Technologies pour la Santé (MTS), SIMoS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Marie Launay
- CEA, INRAE, Médicaments et Technologies pour la Santé (MTS), SIMoS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Konstantinos Patiniotis
- Department of Chemistry, Laboratory of Organic Chemistry, University of Athens, Panepistimiopolis, Zografou, 15771, Athens, Greece
| | | | - Fabrice Beau
- CEA, INRAE, Médicaments et Technologies pour la Santé (MTS), SIMoS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Robert Thai
- CEA, INRAE, Médicaments et Technologies pour la Santé (MTS), SIMoS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Pierrick Bruyat
- CEA, INRAE, Médicaments et Technologies pour la Santé (MTS), SIMoS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Annabelle Bonino
- CEA, INRAE, Médicaments et Technologies pour la Santé (MTS), SIMoS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Sarah Bregant
- CEA, INRAE, Médicaments et Technologies pour la Santé (MTS), SIMoS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Gilles Subra
- IBMM, Univ. Montpellier, ENSCM, CNRS, Montpellier, France
| | - Sonia Cantel
- IBMM, Univ. Montpellier, ENSCM, CNRS, Montpellier, France
| | - Dimitris Georgiadis
- Department of Chemistry, Laboratory of Organic Chemistry, University of Athens, Panepistimiopolis, Zografou, 15771, Athens, Greece
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8
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Chen K, Zhang L, Ding Y, Sun Z, Meng J, Luo R, Zhou X, Liu L, Yang S. Activity-based protein profiling in drug/pesticide discovery: Recent advances in target identification of antibacterial compounds. Bioorg Chem 2024; 151:107655. [PMID: 39032407 DOI: 10.1016/j.bioorg.2024.107655] [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: 04/26/2024] [Revised: 06/18/2024] [Accepted: 07/14/2024] [Indexed: 07/23/2024]
Abstract
Given the escalating incidence of bacterial diseases and the challenge posed by pathogenic bacterial resistance, it is imperative to identify appropriate methodologies for conducting proteomic investigations on bacteria, and thereby promoting the target-based drug/pesticide discovery. Interestingly, a novel technology termed "activity-based protein profiling" (ABPP) has been developed to identify the target proteins of active molecules. However, few studies have summarized advancements in ABPP for identifying the target proteins in antibacterial-active compounds. In order to accelerate the discovery and development of new drug/agrochemical discovery, we provide a concise overview of ABPP and its recent applications in antibacterial agent discovery. Diversiform cases were cited to demonstrate the potential of ABPP for target identification though highlighting the design strategies and summarizing the reported target protein of antibacterial compounds. Overall, this review is an excellent reference for probe design towards antibacterial compounds, and offers a new perspective of ABPP in bactericide development.
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Affiliation(s)
- Kunlun Chen
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Ling Zhang
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Yue Ding
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Zhaoju Sun
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Jiao Meng
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Rongshuang Luo
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Xiang Zhou
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China.
| | - Liwei Liu
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Song Yang
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China.
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9
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Wang Q, Du T, Zhang Z, Zhang Q, Zhang J, Li W, Jiang JD, Chen X, Hu HY. Target fishing and mechanistic insights of the natural anticancer drug candidate chlorogenic acid. Acta Pharm Sin B 2024; 14:4431-4442. [PMID: 39525590 PMCID: PMC11544177 DOI: 10.1016/j.apsb.2024.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/28/2024] [Accepted: 07/01/2024] [Indexed: 11/16/2024] Open
Abstract
Chlorogenic acid (CGA) is a natural product that effectively inhibits tumor growth, demonstrated in many preclinical models, and phase II clinical trials for patients with glioma. However, its direct proteomic targets and anticancer molecular mechanisms remain unknown. Herein, we developed a novel bi-functional photo-affinity probe PAL/CGA and discovered mitochondrial acetyl-CoA acetyltransferase 1 (ACAT1) was one of the main target proteins of CGA by using affinity-based protein profiling (AfBPP) chemical proteomic approach. We performed in-depth studies on ACAT1/CGA interactions via multiple assays including SPR, ITC, and cryo-EM. Importantly, we demonstrated that CGA impaired cancer cell proliferation by inhibiting the phosphorylation of tetrameric ACAT1 on Y407 residue through a novel mode of action in vitro and in vivo. Our study highlights the use of AfBPP platforms in uncovering unique druggable modalities accessed by natural products. And identifying the molecular target of CGA sheds light on the future clinical application of CGA for cancer therapy.
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Affiliation(s)
- Qinghua Wang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Tingting Du
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Zhihui Zhang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Qingyang Zhang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jie Zhang
- Sichuan Jiuzhang Biological Science and Technology Co., Ltd., Chengdu 610041, China
| | - Wenbin Li
- Cancer Center, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Jian-Dong Jiang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xiaoguang Chen
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Hai-Yu Hu
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
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10
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den Hollander LS, Beerkens BLH, Dekkers S, van Veldhoven JPD, Ortiz Zacarías NV, van der Horst C, Sieders EG, de Valk B, Wang J, IJzerman AP, van der Es D, Heitman LH. Labeling of CC Chemokine Receptor 2 with a Versatile Intracellular Allosteric Probe. ACS Chem Biol 2024; 19:2070-2080. [PMID: 39186040 PMCID: PMC11420878 DOI: 10.1021/acschembio.4c00439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Interest in affinity-based probes (AfBPs) as novel tools to interrogate G protein-coupled receptors (GPCRs) has gained traction in recent years. AfBPs represent an interesting and more versatile alternative to antibodies. In the present study, we report the development and validation of AfBPs that target the intracellular allosteric pocket of CCR2, a GPCR of interest for the development of therapies targeting autoimmune and inflammatory diseases and also cancer. Owing to the two-step labeling process of these CCR2 AfBPs through the incorporation of a click handle, we were successful in applying our most efficient probe in a variety of in vitro experiments and making use of multiple different detection techniques, such as SDS-PAGE and LC/MS-based proteomics. Collectively, this novel probe shows high selectivity, versatility, and applicability. Hence, this is a valuable alternative for CCR2-targeting antibodies and other traditional tool compounds and could aid in target validation and engagement in drug discovery.
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Affiliation(s)
- Lisa S den Hollander
- Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, Leiden 2333 CC, The Netherlands
| | - Bert L H Beerkens
- Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, Leiden 2333 CC, The Netherlands
| | - Sebastian Dekkers
- Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, Leiden 2333 CC, The Netherlands
| | - Jacobus P D van Veldhoven
- Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, Leiden 2333 CC, The Netherlands
| | - Natalia V Ortiz Zacarías
- Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, Leiden 2333 CC, The Netherlands
| | - Cas van der Horst
- Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, Leiden 2333 CC, The Netherlands
| | - Elisabeth G Sieders
- Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, Leiden 2333 CC, The Netherlands
| | - Bert de Valk
- Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, Leiden 2333 CC, The Netherlands
| | - Jianhui Wang
- Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, Leiden 2333 CC, The Netherlands
| | - Adriaan P IJzerman
- Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, Leiden 2333 CC, The Netherlands
| | - Daan van der Es
- Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, Leiden 2333 CC, The Netherlands
| | - Laura H Heitman
- Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, Leiden 2333 CC, The Netherlands
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11
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Niphakis MJ, Cravatt BF. Ligand discovery by activity-based protein profiling. Cell Chem Biol 2024; 31:1636-1651. [PMID: 39303700 DOI: 10.1016/j.chembiol.2024.08.006] [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: 07/16/2024] [Revised: 08/15/2024] [Accepted: 08/19/2024] [Indexed: 09/22/2024]
Abstract
Genomic technologies have led to massive gains in our understanding of human gene function and disease relevance. Chemical biologists are a primary beneficiary of this information, which can guide the prioritization of proteins for chemical probe and drug development. The vast functional and structural diversity of disease-relevant proteins, however, presents challenges for conventional small molecule screening libraries and assay development that in turn raise questions about the broader "druggability" of the human proteome. Here, we posit that activity-based protein profiling (ABPP), by generating global maps of small molecule-protein interactions in native biological systems, is well positioned to address major obstacles in human biology-guided chemical probe and drug discovery. We will support this viewpoint with case studies highlighting a range of small molecule mechanisms illuminated by ABPP that include the disruption and stabilization of biomolecular (protein-protein/nucleic acid) interactions and underscore allostery as a rich source of chemical tools for historically "undruggable" protein classes.
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12
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Doleschal MN, Miller J, Jain S, Zakharov AV, Rai G, Simeonov A, Baljinnyam B, Zhuang Z. Cell-Based Covalent-Capture Deubiquitinase Assay for Inhibitor Discovery. ACS Pharmacol Transl Sci 2024; 7:2827-2839. [PMID: 39296272 PMCID: PMC11406687 DOI: 10.1021/acsptsci.4c00331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/26/2024] [Accepted: 07/31/2024] [Indexed: 09/21/2024]
Abstract
Ubiquitination is a post-translational modification that elicits a variety of cellular responses. Deubiquitinases (DUBs) remove ubiquitin moieties from proteins and modulate cellular processes by counteracting the ubiquitin ligase activities. Ubiquitination and deubiquitination processes are tightly regulated by different mechanisms and their dysregulation is associated with many diseases. Discovery of DUB inhibitors could not only lead to therapeutics but also facilitate the understanding of ubiquitination/deubiquitination processes and their regulatory mechanisms. To enable the inhibitor discovery against DUBs, we developed a cell-based DUB assay that utilizes a cell-permeable ubiquitin probe, Biotin-cR10-Ub-PA, to covalently label DUBs in their native cellular environment. Amplified luminescent proximity homogeneous assay (Alpha, specifically AlphaLISA) is utilized to quantitatively assess the capture of the target DUB by the Biotin-cR10-Ub-PA probe. We demonstrated that this new cell-based DUB assay is robust and amenable to high-throughput screening. Human USP15 was selected as a DUB of interest and screened against a library of protease inhibitors as a proof of concept. In addition to the widely adopted pan-DUB inhibitor PR-619, several other DUB inhibitors from the library were also identified as hits. This new DUB assay can be readily adapted for inhibitor discovery against many other human DUBs to identify potent and cell-permeable inhibitors.
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Affiliation(s)
- Megan N Doleschal
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, Delaware 19716, United States
| | - Jenna Miller
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Sankalp Jain
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Alexey V Zakharov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Bolormaa Baljinnyam
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Zhihao Zhuang
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, Delaware 19716, United States
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13
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Zhang B, Hong D, Qian H, Ma K, Zhu L, Jiang L, Ge J. Unveiling a new strategy for PDIA1 inhibition: Integration of activity-based probes profiling and targeted degradation. Bioorg Chem 2024; 150:107585. [PMID: 38917491 DOI: 10.1016/j.bioorg.2024.107585] [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: 02/07/2024] [Revised: 06/02/2024] [Accepted: 06/20/2024] [Indexed: 06/27/2024]
Abstract
The overexpression of PDIA1 in cancer has spurred the quest for effective inhibitors. However, existing inhibitors often bind to only one active site, limiting their efficacy. In our study, we developed a PROTAC-mimetic probe dPA by combining PACMA31 (PA) analogs with cereblon-directed pomalidomide. Through protein profiling and analysis, we confirmed dPA's specific interaction with PDIA1's active site cysteines. We further synthesized PROTAC variants with a thiophene ring and various linkers to enhance degradation efficiency. Notably, H4, featuring a PEG linker, induced significant PDIA1 degradation and inhibited cancer cell proliferation similarly to PA. The biosafety profile of H4 is comparable to that of PA, highlighting its potential for further development in cancer therapy. Our findings highlight a novel strategy for PDIA1 inhibition via targeted degradation, offering promising prospects in cancer therapeutics. This approach may overcome limitations of conventional inhibitors, presenting new avenues for advancing anti-cancer interventions.
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Affiliation(s)
- Bei Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Dawei Hong
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Hujuan Qian
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Keqing Ma
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Liquan Zhu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China; General Surgery, Department of Breast Surgery, Cancer Center, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China
| | - Linye Jiang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
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14
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Tang G, Wang X, Huang H, Xu M, Ma X, Miao F, Lu X, Zhang CJ, Gao L, Zhang ZM, Yao SQ. Small Molecule-Induced Post-Translational Acetylation of Catalytic Lysine of Kinases in Mammalian Cells. J Am Chem Soc 2024; 146:23978-23988. [PMID: 39162335 DOI: 10.1021/jacs.4c07181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
Reversible lysine acetylation is an important post-translational modification (PTM). This process in cells is typically carried out enzymatically by lysine acetyltransferases and deacetylases. The catalytic lysine in the human kinome is highly conserved and ligandable. Small-molecule strategies that enable post-translational acetylation of the catalytic lysine on kinases in a target-selective manner therefore provide tremendous potential in kinase biology. Herein, we report the first small molecule-induced chemical strategy capable of global acetylation of the catalytic lysine on kinases from mammalian cells. By surveying various lysine-acetylating agents installed on a promiscuous kinase-binding scaffold, Ac4 was identified and shown to effectively acetylate the catalytic lysine of >100 different protein kinases from live Jurkat/K562 cells. In order to demonstrate that this strategy was capable of target-selective and reversible chemical acetylation of protein kinases, we further developed six acetylating compounds on the basis of VX-680 (a noncovalent inhibitor of AURKA). Among them, Ac13/Ac14, while displaying excellent in vitro potency and sustained cellular activity against AURKA, showed robust acetylation of its catalytic lysine (K162) in a target-selective manner, leading to irreversible inhibition of endogenous kinase activity. The reversibility of this chemical acetylation was confirmed on Ac14-treated recombinant AURKA protein, followed by deacetylation with SIRT3 (a lysine deacetylase). Finally, the reversible Ac13-induced acetylation of endogenous AURKA was demonstrated in SIRT3-transfected HCT116 cells. By disclosing the first cell-active acetylating compounds capable of both global and target-selective post-translational acetylation of the catalytic lysine on kinases, our strategy could provide a useful chemical tool in kinase biology and drug discovery.
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Affiliation(s)
- Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Xuan Wang
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518000, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Huisi Huang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Manyi Xu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xingyu Ma
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Fengfei Miao
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Xiaoyun Lu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Chong-Jing Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518000, China
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
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15
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Sun D, Kang L, Chen X, Xue J, Wu X, Wong J, Wei Q, Liu S. Identification of DDX5 as a Potential Therapeutic Target of Osteosarcoma Using Thiazolone Probes. ACS Chem Biol 2024; 19:1803-1812. [PMID: 39069677 DOI: 10.1021/acschembio.4c00360] [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: 07/30/2024]
Abstract
Osteosarcoma (OS) is a rare malignant tumor that has predominantly affected children and adolescents in the past 50 years. The genomes of OS tumors exhibit a high degree of complexity, which leads to the great challenge of target identification for anti-OS. To date, no efficient therapeutic target for the treatment of OS has been validated in clinical practice. In our previous drug hunting for the treatment of OS by phenotypic screening, we found that thiazolone derivate (R)-8i was an effective and selective inhibitor against OS in MNNG/HOS cells and in vivo. However, the mechanism of action and specific molecular targets of (R)-8i remain unclear. In this study, we design and synthesize the photo-cross-linking probes based on the lead compound (R)-8i and identify DDX5 as a potential target protein using an activity-based protein profiling strategy. Further experiments including Western blot, shRNA knockdown experiments, cell colony formation, wound healing assays, and cellular thermal shift assays support that (R)-8i binds to DDX5 and induces its degradation, which affect cell proliferation and migration through the PI3K-AKT-mTOR signaling pathway. The research shows that DDX5 is a potential therapeutic target for the treatment of OS.
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Affiliation(s)
- Donghui Sun
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Li Kang
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xuwen Chen
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Jian Xue
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Xin Wu
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Qinghua Wei
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Shunying Liu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
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16
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Gao L, Ding Q, Lei X. Hunting for the Intermolecular Diels-Alderase. Acc Chem Res 2024; 57:2166-2183. [PMID: 38994670 DOI: 10.1021/acs.accounts.4c00315] [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: 07/13/2024]
Abstract
ConspectusThe Diels-Alder reaction is well known as a concerted [4 + 2] cycloaddition governed by the Woodward-Hoffmann rules. Since Prof. Otto Diels and his student Kurt Alder initially reported the intermolecular [4 + 2] cycloaddition between cyclopentadiene and quinone in 1928, it has been recognized as one of the most powerful chemical transformations to build C-C bonds and construct cyclic structures. This named reaction has been widely used in synthesizing natural products and drug molecules. Driven by the synthetic importance of the Diels-Alder reaction, identifying the enzyme that stereoselectively catalyzes the Diels-Alder reaction has become an intriguing research area in natural product biosynthesis and biocatalysis. With significant progress in sequencing and bioinformatics, dozens of Diels-Alderases have been characterized in microbial natural product biosynthesis. However, few are evolutionally dedicated to catalyzing an intermolecular Diels-Alder reaction with a concerted mechanism.This Account summarizes our endeavors to hunt for the naturally occurring intermolecular Diels-Alderase from plants. Our research journey started from the biomimetic syntheses of D-A-type terpenoids and flavonoids, showing that plants use both nonenzymatic and enzymatic intermolecular [4 + 2] cycloadditions to create complex molecules. Inspired by the biomimetic syntheses, we identify an intermolecular Diels-Alderase hidden in the biosynthetic pathway of mulberry Diels-Alder-type cycloadducts using a biosynthetic intermediate probe-based target identification strategy. This enzyme, MaDA, is an endo-selective Diels-Alderase and is then functionally characterized as a standalone intermolecular Diels-Alderase with a concerted but asynchronous mechanism. We also discover the exo-selective intermolecular Diels-Alderases in Morus plants. Both the endo- and exo-selective Diels-Alderases feature a broad substrate scope, but their mechanisms for controlling the endo/exo pathway are different. These unique intermolecular Diels-Alderases phylogenetically form a subgroup of FAD-dependent enzymes that can be found only in moraceous plants, explaining why this type of [4 + 2] cycloadduct is unique to moraceous plants. Further studies of the evolutionary mechanism reveal that an FAD-dependent oxidocyclase could acquire the Diels-Alderase activity via four critical amino acid mutations and then gradually lose its original oxidative activity to become a standalone Diels-Alderase during the natural evolution. Based on these insights, we designed new Diels-Alderases and achieved the diversity-oriented chemoenzymatic synthesis of D-A products using either naturally occurring or engineered Diels-Alderases.Overall, this Account describes our decade-long efforts to discover the intermolecular Diels-Alderases in Morus plants, particularly highlighting the importance of biomimetic synthesis and chemical proteomics in discovering new intermolecular Diels-Alderases from plants. Meanwhile, this Account also covers the evolutionary and catalytic mechanism study of intermolecular Diels-Alderases that may provide new insights into how to discover and design new Diels-Alderases as powerful biocatalysts for organic synthesis.
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Affiliation(s)
- Lei Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Qi Ding
- School of Life Science, Tsinghua University, Beijing 100084, China
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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17
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Iacobucci I, Monaco V, Hovasse A, Dupouy B, Keumoe R, Cichocki B, Elhabiri M, Meunier B, Strub JM, Monti M, Cianférani S, Blandin SA, Schaeffer-Reiss C, Davioud-Charvet E. Proteomic Profiling of Antimalarial Plasmodione Using 3-Benz(o)ylmenadione Affinity-Based Probes. Chembiochem 2024; 25:e202400187. [PMID: 38639212 DOI: 10.1002/cbic.202400187] [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: 02/29/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/20/2024]
Abstract
Understanding the mechanisms of drug action in malarial parasites is crucial for the development of new drugs to combat infection and to counteract drug resistance. Proteomics is a widely used approach to study host-pathogen systems and to identify drug protein targets. Plasmodione is an antiplasmodial early-lead drug exerting potent activities against young asexual and sexual blood stages in vitro with low toxicity to host cells. To elucidate its molecular mechanisms, an affinity-based protein profiling (AfBPP) approach was applied to yeast and P. falciparum proteomes. New (pro-) AfBPP probes based on the 3-benz(o)yl-6-fluoro-menadione scaffold were synthesized. With optimized conditions of both photoaffinity labeling and click reaction steps, the AfBPP protocol was then applied to a yeast proteome, yielding 11 putative drug-protein targets. Among these, we found four proteins associated with oxidoreductase activities, the hypothesized type of targets for plasmodione and its metabolites, and other proteins associated with the mitochondria. In Plasmodium parasites, the MS analysis revealed 44 potential plasmodione targets that need to be validated in further studies. Finally, the localization of a 3-benzyl-6-fluoromenadione AfBPP probe was studied in the subcellular structures of the parasite at the trophozoite stage.
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Affiliation(s)
- Ilaria Iacobucci
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Team Bio(IN)organic & Medicinal Chemistry, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, 25, rue Becquerel, F-67087, Strasbourg, France
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, F-67087, Strasbourg, France
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant' Angelo, Via Cintia 26, I-80126, Napoli, Italy
| | - Vittoria Monaco
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Team Bio(IN)organic & Medicinal Chemistry, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, 25, rue Becquerel, F-67087, Strasbourg, France
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, F-67087, Strasbourg, France
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant' Angelo, Via Cintia 26, I-80126, Napoli, Italy
| | - Agnès Hovasse
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, F-67087, Strasbourg, France
| | - Baptiste Dupouy
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Team Bio(IN)organic & Medicinal Chemistry, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, 25, rue Becquerel, F-67087, Strasbourg, France
| | - Rodrigue Keumoe
- Institut de Biologie Moléculaire et Cellulaire, INSERM U1257 - CNRS UPR9022 - Université de Strasbourg, 2, Allée Konrad Roentgen, -67084, Strasbourg, France
| | - Bogdan Cichocki
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Team Bio(IN)organic & Medicinal Chemistry, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, 25, rue Becquerel, F-67087, Strasbourg, France
| | - Mourad Elhabiri
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Team Bio(IN)organic & Medicinal Chemistry, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, 25, rue Becquerel, F-67087, Strasbourg, France
| | - Brigitte Meunier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-Sur-Yvette Cedex, France
| | - Jean-Marc Strub
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, F-67087, Strasbourg, France
| | - Maria Monti
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant' Angelo, Via Cintia 26, I-80126, Napoli, Italy
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, F-67087, Strasbourg, France
| | - Stéphanie A Blandin
- Institut de Biologie Moléculaire et Cellulaire, INSERM U1257 - CNRS UPR9022 - Université de Strasbourg, 2, Allée Konrad Roentgen, -67084, Strasbourg, France
| | - Christine Schaeffer-Reiss
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, F-67087, Strasbourg, France
| | - Elisabeth Davioud-Charvet
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Team Bio(IN)organic & Medicinal Chemistry, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, 25, rue Becquerel, F-67087, Strasbourg, France
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18
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Seligmann B, Liu S, Franke J. Chemical tools for unpicking plant specialised metabolic pathways. CURRENT OPINION IN PLANT BIOLOGY 2024; 80:102554. [PMID: 38820646 DOI: 10.1016/j.pbi.2024.102554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 06/02/2024]
Abstract
Elucidating the biochemical pathways of specialised metabolites in plants is key to enable or improve their sustainable biotechnological production. Chemical tools can greatly facilitate the discovery of biosynthetic genes and enzymes. Here, we summarise transdisciplinary approaches where methods from chemistry and chemical biology helped to overcome key challenges of pathway elucidation. Based on recent examples, we describe how state-of-the-art isotope labelling experiments can guide the selection of biosynthetic gene candidates, how affinity-based probes enable the identification of novel enzymes, how semisynthesis can improve the availability of elusive pathway intermediates, and how biomimetic reactions provide a better understanding of inherent chemical reactivity. We anticipate that a wider application of such chemical methods will accelerate the pace of pathway elucidation in plants.
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Affiliation(s)
- Benedikt Seligmann
- Leibniz University Hannover, Institute of Botany, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Shenyu Liu
- Leibniz University Hannover, Centre of Biomolecular Drug Research (BMWZ), Schneiderberg 38, 30167 Hannover, Germany
| | - Jakob Franke
- Leibniz University Hannover, Institute of Botany, Herrenhäuser Str. 2, 30419 Hannover, Germany; Leibniz University Hannover, Centre of Biomolecular Drug Research (BMWZ), Schneiderberg 38, 30167 Hannover, Germany.
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19
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Jiang X, Peng Z, Zhang J. Starting with screening strains to construct synthetic microbial communities (SynComs) for traditional food fermentation. Food Res Int 2024; 190:114557. [PMID: 38945561 DOI: 10.1016/j.foodres.2024.114557] [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: 03/21/2024] [Revised: 05/16/2024] [Accepted: 05/26/2024] [Indexed: 07/02/2024]
Abstract
With the elucidation of community structures and assembly mechanisms in various fermented foods, core communities that significantly influence or guide fermentation have been pinpointed and used for exogenous restructuring into synthetic microbial communities (SynComs). These SynComs simulate ecological systems or function as adjuncts or substitutes in starters, and their efficacy has been widely verified. However, screening and assembly are still the main limiting factors for implementing theoretic SynComs, as desired strains cannot be effectively obtained and integrated. To expand strain screening methods suitable for SynComs in food fermentation, this review summarizes the recent research trends in using SynComs to study community evolution or interaction and improve the quality of food fermentation, as well as the specific process of constructing synthetic communities. The potential for novel screening modalities based on genes, enzymes and metabolites in food microbial screening is discussed, along with the emphasis on strategies to optimize assembly for facilitating the development of synthetic communities.
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Affiliation(s)
- Xinyi Jiang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zheng Peng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Juan Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China.
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20
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Price S, Que EL. Probing metalloenzyme dynamics in living systems: Contemporary advances in fluorescence imaging tools and applications. Curr Opin Chem Biol 2024; 81:102475. [PMID: 38852500 DOI: 10.1016/j.cbpa.2024.102475] [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: 02/20/2024] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 06/11/2024]
Abstract
Metalloenzymes are essential to cellular function, and their overexpression or enhanced activation are potential therapeutic targets. However, the study of metalloenzymes in vitro presents various challenges, leading many to develop tools to study them in their native cellular environment. Small-molecule fluorescence probes are commonly used to monitor metalloenzyme function, activity, and distribution in situ. These include probes that are activity-based (fluorescence is mediated by enzyme activity) or binding-based (fluorescence is mediated by interactions with the enzyme upon binding its metal cofactor). We discuss recent innovations that overcome key design challenges, such as the rapid diffusion of activity-based probes, the difficulty of probing redox-active enzymes, the selectivity of binding-based probes, and the poor penetration depth of fluorescence, and describe novel applications of these tools.
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Affiliation(s)
- Sky Price
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Emily L Que
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA.
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21
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Ren X, Li H, Peng H, Yang Y, Su H, Huang C, Wang X, Zhang J, Liu Z, Wei W, Cheng K, Zhu T, Lu Z, Li Z, Zhao Q, Tang BZ, Yao SQ, Song X, Sun H. Reactivity-Tunable Fluorescent Platform for Selective and Biocompatible Modification of Cysteine or Lysine. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2402838. [PMID: 38896788 PMCID: PMC11336953 DOI: 10.1002/advs.202402838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/03/2024] [Indexed: 06/21/2024]
Abstract
Chemoselective modification of specific residues within a given protein poses a significant challenge, as the microenvironment of amino acid residues in proteins is variable. Developing a universal molecular platform with tunable chemical warheads can provide powerful tools for precisely labeling specific amino acids in proteins. Cysteine and lysine are hot targets for chemoselective modification, but current cysteine/lysine-selective warheads face challenges due to cross-reactivity and unstable reaction products. In this study, a versatile fluorescent platform is developed for highly selective modification of cysteine/lysine under biocompatible conditions. Chloro- or phenoxy-substituted NBSe derivatives effectively labeled cysteine residues in the cellular proteome with high specificity. This finding also led to the development of phenoxy-NBSe phototheragnostic for the diagnosis and activatable photodynamic therapy of GSH-overexpressed cancer cells. Conversely, alkoxy-NBSe derivatives are engineered to selectively react with lysine residues in the cellular environment, exhibiting excellent anti-interfering ability against thiols. Leveraging a proximity-driven approach, alkoxy-NBSe probes are successfully designed to demonstrate their utility in bioimaging of lysine deacetylase activity. This study also achieves integrating a small photosensitizer into lysine residues of proteins in a regioselective manner, achieving photoablation of cancer cells activated by overexpressed proteins.
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Affiliation(s)
- Xiaojie Ren
- Department of Chemistry and Centre of Super‐Diamond and Advanced Films (COSDAF)City University of Hong Kong83 Tat Chee Avenue, KowloonHong Kong999077China
- College of Chemistry & Chemical EngineeringCentral South UniversityChangshaHunan410083China
| | - Haokun Li
- Department of Chemistry and Centre of Super‐Diamond and Advanced Films (COSDAF)City University of Hong Kong83 Tat Chee Avenue, KowloonHong Kong999077China
| | - Hui Peng
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE)MOE Key Laboratory of Tumor Molecular BiologySchool of PharmacyJinan UniversityGuangzhouGuangdong510632China
| | - Yang Yang
- Department of Applied Biology and Chemical TechnologyThe Hong Kong Polytechnic UniversityHung Hom, KowloonHong Kong999077China
| | - Hang Su
- College of Chemistry & Chemical EngineeringCentral South UniversityChangshaHunan410083China
| | - Chen Huang
- Department of Chemistry and Centre of Super‐Diamond and Advanced Films (COSDAF)City University of Hong Kong83 Tat Chee Avenue, KowloonHong Kong999077China
| | - Xuan Wang
- Department of ChemistryNational University of SingaporeSingapore117543Singapore
- School of Pharmaceutical Sciences (Shenzhen)Shenzhen Campus of Sun Yat‐sen UniversityShenzhen518107China
| | - Jie Zhang
- Department of Chemistry and Centre of Super‐Diamond and Advanced Films (COSDAF)City University of Hong Kong83 Tat Chee Avenue, KowloonHong Kong999077China
| | - Zhiyang Liu
- Department of Chemistry and Centre of Super‐Diamond and Advanced Films (COSDAF)City University of Hong Kong83 Tat Chee Avenue, KowloonHong Kong999077China
| | - Wenyu Wei
- Department of Chemistry and Centre of Super‐Diamond and Advanced Films (COSDAF)City University of Hong Kong83 Tat Chee Avenue, KowloonHong Kong999077China
| | - Ke Cheng
- Department of Chemistry and Centre of Super‐Diamond and Advanced Films (COSDAF)City University of Hong Kong83 Tat Chee Avenue, KowloonHong Kong999077China
| | - Tianyang Zhu
- Department of Applied Biology and Chemical TechnologyThe Hong Kong Polytechnic UniversityHung Hom, KowloonHong Kong999077China
| | - Zhenpin Lu
- Department of Chemistry and Centre of Super‐Diamond and Advanced Films (COSDAF)City University of Hong Kong83 Tat Chee Avenue, KowloonHong Kong999077China
| | - Zhengqiu Li
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE)MOE Key Laboratory of Tumor Molecular BiologySchool of PharmacyJinan UniversityGuangzhouGuangdong510632China
| | - Qian Zhao
- Department of Applied Biology and Chemical TechnologyThe Hong Kong Polytechnic UniversityHung Hom, KowloonHong Kong999077China
| | - Ben Zhong Tang
- Department of ChemistryThe Hong Kong University of Science and TechnologyClear Water Bay, KowloonHong Kong999077China
| | - Shao Q. Yao
- Department of ChemistryNational University of SingaporeSingapore117543Singapore
| | - Xiangzhi Song
- College of Chemistry & Chemical EngineeringCentral South UniversityChangshaHunan410083China
| | - Hongyan Sun
- Department of Chemistry and Centre of Super‐Diamond and Advanced Films (COSDAF)City University of Hong Kong83 Tat Chee Avenue, KowloonHong Kong999077China
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22
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McKenna SM, Florea BI, Zisterer DM, van Kasteren SI, McGouran JF. Probing the metalloproteome: an 8-mercaptoquinoline motif enriches minichromosome maintenance complex components as significant metalloprotein targets in live cells. RSC Chem Biol 2024; 5:776-786. [PMID: 39092446 PMCID: PMC11289876 DOI: 10.1039/d4cb00053f] [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: 02/27/2024] [Accepted: 06/18/2024] [Indexed: 08/04/2024] Open
Abstract
Affinity-based probes are valuable tools for detecting binding interactions between small molecules and proteins in complex biological environments. Metalloproteins are a class of therapeutically significant biomolecules which bind metal ions as part of key structural or catalytic domains and are compelling targets for study. However, there is currently a limited range of chemical tools suitable for profiling the metalloproteome. Here, we describe the preparation and application of a novel, photoactivatable affinity-based probe for detection of a subset of previously challenging to engage metalloproteins. The probe, bearing an 8-mercaptoquinoline metal chelator, was anticipated to engage several zinc metalloproteins, including the 26S-proteasome subunit Rpn11. Upon translation of the labelling experiment to mammalian cell lysate and live cell experiments, proteomic analysis revealed that several metalloproteins were competitively enriched. The diazirine probe SMK-24 was found to effectively enrich multiple components of the minichromosome maintenance complex, a zinc metalloprotein assembly with helicase activity essential to DNA replication. Cell cycle analysis experiments revealed that HEK293 cells treated with SMK-24 experienced stalling in G0/G1 phase, consistent with inactivation of the DNA helicase complex. This work represents an important contribution to the library of cell-permeable chemical tools for studying a collection of metalloproteins for which no previous probe existed.
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Affiliation(s)
- Sean M McKenna
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin 152-160 Pearse St Dublin 2 Ireland
- Synthesis and Solid State Pharmaceutical Centre (SSPC) Ireland
| | - Bogdan I Florea
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Daniela M Zisterer
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin 152-160 Pearse St Dublin 2 Ireland
| | - Sander I van Kasteren
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Joanna F McGouran
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin 152-160 Pearse St Dublin 2 Ireland
- Synthesis and Solid State Pharmaceutical Centre (SSPC) Ireland
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23
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Wang X, Sun J, Huang H, Tang G, Chen P, Xiang M, Li L, Zhang ZM, Gao L, Yao SQ. Kinase Inhibition via Small Molecule-Induced Intramolecular Protein Cross-Linking. Angew Chem Int Ed Engl 2024; 63:e202404195. [PMID: 38695161 DOI: 10.1002/anie.202404195] [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: 02/29/2024] [Indexed: 07/02/2024]
Abstract
Remarkable progress has been made in the development of cysteine-targeted covalent inhibitors. In kinase drug discovery, covalent inhibitors capable of targeting other nucleophilic residues (i.e. lysine, or K) have emerged in recent years. Besides a highly conserved catalytic lysine, almost all human protein kinases possess an equally conserved glutamate/aspartate (e.g. E/D) that forms a K-E/D salt bridge within the enzyme's active site. Electrophilic ynamides were previously used as effective peptide coupling reagents and to develop E/D-targeting covalent protein inhibitors/probes. In the present study, we report the first ynamide-based small-molecule inhibitors capable of inducing intramolecular cross-linking of various protein kinases, leading to subsequent irreversible inhibition of kinase activity. Our strategy took advantage of the close distance between the highly conserved catalytic K and E/D residues in a targeted kinase, thus providing a conceptually general approach to achieve irreversible kinase inhibition with high specificity and desirable cellular potency. Finally, this ynamide-facilitated, ligand-induced mechanism leading to intramolecular kinase cross-linking and inhibition was unequivocally established by using recombinant ABL kinase as a representative.
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Affiliation(s)
- Xuan Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Jie Sun
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Huisi Huang
- School of Pharmacy, Jinan University, 601 West Huangpu Avenue West, Guangzhou, 510632, China
| | - Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| | - Peng Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Menghua Xiang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Lin Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen, 361005, China
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, 601 West Huangpu Avenue West, Guangzhou, 510632, China
| | - Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
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24
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Hamm P, Meinel L, Driessen MD. An Introductory Guide to Protease Sensitive Linker Design Using Matrix Metalloproteinase 13 as an Example. ACS Biomater Sci Eng 2024; 10:3693-3706. [PMID: 38813796 DOI: 10.1021/acsbiomaterials.4c00407] [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] [Indexed: 05/31/2024]
Abstract
Proteases play a crucial role, not only in physiological, but also in pathological processes, such as cancer, inflammation, arthritis, Alzheimer's, and infections, to name but a few. Their ability to cleave peptides can be harnessed for a broad range of biotechnological purposes. To do this efficiently, it is essential to find an amino acid sequence that meets the necessary requirements, including interdependent factors like specificity, selectivity, cleavage kinetics, or synthetic accessibility. Cleavage sequences from natural substrates of the protease may not be optimal in terms of specificity and selectivity, which is why these frequently require arduous and sometimes unsuccessful optimization such as by iterative exchange of single amino acids. Hence, here we describe the systematic design of protease sensitive linkers (PSLs)─peptide sequences specifically cleaved by a target protease─guided by the mass spectrometry based determination of target protease specific cleavage sites from a proteome-based peptide library. It includes a procedure for identifying bespoke PSL sequences, their optimization, synthesis, and validation and introduces a program that can indicate potential cleavage sites by hundreds of enzymes in any arbitrary amino acid sequence. Thereby, we provide an introduction to PSL design, illustrated by the example of matrix metalloproteinase 13 (MMP13). This introduction can serve as a guide and help to greatly accelerate the development and use of protease-sensitive linkers in diverse applications.
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Affiliation(s)
- Prisca Hamm
- Institute for Pharmacy and Food Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Lorenz Meinel
- Institute for Pharmacy and Food Chemistry, University of Würzburg, 97074 Würzburg, Germany
- Helmholtz-Institute for RNA-Based Infection Research (HIRI), 97070 Würzburg, Germany
| | - Marc D Driessen
- Institute of Molecular Medicine I, Proteome Research, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, 40225 Düsseldorf, Germany
- Department for Oral and Craniomaxillofacial and Plastic Surgery, University Hospital Cologne and Faculty of Medicine, University of Cologne, 50937 Cologne, Germany
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25
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Ninck S, Klaus T, Kochetkova TV, Esser SP, Sewald L, Kaschani F, Bräsen C, Probst AJ, Kublanov IV, Siebers B, Kaiser M. Environmental activity-based protein profiling for function-driven enzyme discovery from natural communities. ENVIRONMENTAL MICROBIOME 2024; 19:36. [PMID: 38831353 PMCID: PMC11145796 DOI: 10.1186/s40793-024-00577-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 05/06/2024] [Indexed: 06/05/2024]
Abstract
BACKGROUND Microbial communities are important drivers of global biogeochemical cycles, xenobiotic detoxification, as well as organic matter decomposition. Their major metabolic role in ecosystem functioning is ensured by a unique set of enzymes, providing a tremendous yet mostly hidden enzymatic potential. Exploring this enzymatic repertoire is therefore not only relevant for a better understanding of how microorganisms function in their natural environment, and thus for ecological research, but further turns microbial communities, in particular from extreme habitats, into a valuable resource for the discovery of novel enzymes with potential applications in biotechnology. Different strategies for their uncovering such as bioprospecting, which relies mainly on metagenomic approaches in combination with sequence-based bioinformatic analyses, have emerged; yet accurate function prediction of their proteomes and deciphering the in vivo activity of an enzyme remains challenging. RESULTS Here, we present environmental activity-based protein profiling (eABPP), a multi-omics approach that extends genome-resolved metagenomics with mass spectrometry-based ABPP. This combination allows direct profiling of environmental community samples in their native habitat and the identification of active enzymes based on their function, even without sequence or structural homologies to annotated enzyme families. eABPP thus bridges the gap between environmental genomics, correct function annotation, and in vivo enzyme activity. As a showcase, we report the successful identification of active thermostable serine hydrolases from eABPP of natural microbial communities from two independent hot springs in Kamchatka, Russia. CONCLUSIONS By reporting enzyme activities within an ecosystem in their native state, we anticipate that eABPP will not only advance current methodological approaches to sequence homology-guided enzyme discovery from environmental ecosystems for subsequent biocatalyst development but also contributes to the ecological investigation of microbial community interactions by dissecting their underlying molecular mechanisms.
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Affiliation(s)
- Sabrina Ninck
- Chemical Biology, Centre of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany.
| | - Thomas Klaus
- Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany
| | - Tatiana V Kochetkova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Prospekt 60-Let Oktyabrya 7-2, Moscow, 117312, Russia
| | - Sarah P Esser
- Environmental Metagenomics, Research Centre One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany
| | - Leonard Sewald
- Chemical Biology, Centre of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Farnusch Kaschani
- Chemical Biology, Centre of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Christopher Bräsen
- Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany
| | - Alexander J Probst
- Environmental Metagenomics, Research Centre One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany
- Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
- Centre of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Prospekt 60-Let Oktyabrya 7-2, Moscow, 117312, Russia
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany.
| | - Markus Kaiser
- Chemical Biology, Centre of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany.
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26
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Sgroi S, Romeo E, Albanesi E, Piccardi F, Catalano F, Debellis D, Bertozzi F, Reggiani A. Combined in vivo effect of N-acylethanolamine-hydrolyzing acid amidase and glycogen synthase kinase-3β inhibition to treat multiple sclerosis. Biomed Pharmacother 2024; 175:116677. [PMID: 38701570 DOI: 10.1016/j.biopha.2024.116677] [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: 01/11/2024] [Revised: 04/19/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024] Open
Abstract
The current pharmacological approaches to multiple sclerosis (MS) target its inflammatory and autoimmune components, but effective treatments to foster remyelination and axonal repair are still lacking. We therefore selected two targets known to be involved in MS pathogenesis: N-acylethanolamine-hydrolyzing acid amidase (NAAA) and glycogen synthase kinase-3β (GSK-3β). We tested whether inhibiting these targets exerted a therapeutic effect against experimental autoimmune encephalomyelitis (EAE), an animal model of MS. The combined inhibition of NAAA and GSK-3β by two selected small-molecule compounds, ARN16186 (an NAAA inhibitor) and AF3581 (a GSK-3β inhibitor), effectively mitigated disease progression, rescuing the animals from paralysis and preventing a worsening of the pathology. The complementary activity of the two inhibitors reduced the infiltration of immune cells into the spinal cord and led to the formation of thin myelin sheaths around the axons post-demyelination. Specifically, the inhibition of NAAA and GSK-3β modulated the over-activation of NF-kB and STAT3 transcription factors in the EAE-affected mice and induced the nuclear translocation of β-catenin, reducing the inflammatory insult and promoting the remyelination process. Overall, this work demonstrates that the dual-targeting of key aspects responsible for MS progression could be an innovative pharmacological approach to tackle the pathology.
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Affiliation(s)
- Stefania Sgroi
- D3-Validation, Fondazione Istituto Italiano di Tecnologia, Genoa 16163, Italy
| | - Elisa Romeo
- Structural Biophysics Facility, Fondazione Istituto Italiano di Tecnologia, Genoa 16163, Italy
| | - Ennio Albanesi
- Department of Neuroscience and Brain Technologies, Neurofacility, Fondazione Istituto Italiano di Tecnologia, Genoa 16163, Italy
| | - Federica Piccardi
- Animal Facility, Fondazione Istituto Italiano di Tecnologia, Genoa 16163, Italy
| | - Federico Catalano
- Electron Microscopy Facility, Fondazione Istituto Italiano di Tecnologia, Genoa 16163, Italy
| | - Doriana Debellis
- Electron Microscopy Facility, Fondazione Istituto Italiano di Tecnologia, Genoa 16163, Italy
| | - Fabio Bertozzi
- D3-PharmaChemistry, Fondazione Istituto Italiano di Tecnologia, Genoa 16163, Italy
| | - Angelo Reggiani
- D3-Validation, Fondazione Istituto Italiano di Tecnologia, Genoa 16163, Italy.
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27
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Cowan DA, Albers SV, Antranikian G, Atomi H, Averhoff B, Basen M, Driessen AJM, Jebbar M, Kelman Z, Kerou M, Littlechild J, Müller V, Schönheit P, Siebers B, Vorgias K. Extremophiles in a changing world. Extremophiles 2024; 28:26. [PMID: 38683238 PMCID: PMC11058618 DOI: 10.1007/s00792-024-01341-7] [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: 10/27/2023] [Accepted: 04/02/2024] [Indexed: 05/01/2024]
Abstract
Extremophiles and their products have been a major focus of research interest for over 40 years. Through this period, studies of these organisms have contributed hugely to many aspects of the fundamental and applied sciences, and to wider and more philosophical issues such as the origins of life and astrobiology. Our understanding of the cellular adaptations to extreme conditions (such as acid, temperature, pressure and more), of the mechanisms underpinning the stability of macromolecules, and of the subtleties, complexities and limits of fundamental biochemical processes has been informed by research on extremophiles. Extremophiles have also contributed numerous products and processes to the many fields of biotechnology, from diagnostics to bioremediation. Yet, after 40 years of dedicated research, there remains much to be discovered in this field. Fortunately, extremophiles remain an active and vibrant area of research. In the third decade of the twenty-first century, with decreasing global resources and a steadily increasing human population, the world's attention has turned with increasing urgency to issues of sustainability. These global concerns were encapsulated and formalized by the United Nations with the adoption of the 2030 Agenda for Sustainable Development and the presentation of the seventeen Sustainable Development Goals (SDGs) in 2015. In the run-up to 2030, we consider the contributions that extremophiles have made, and will in the future make, to the SDGs.
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Affiliation(s)
- D A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa.
| | - S V Albers
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - G Antranikian
- Institute of Technical Biocatalysis, Hamburg University of Technology, 21073, Hamburg, Germany
| | - H Atomi
- Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - B Averhoff
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt Am Main, Germany
| | - M Basen
- Department of Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - A J M Driessen
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - M Jebbar
- Univ. Brest, CNRS, Ifremer, Laboratoire de Biologie Et d'Écologie Des Écosystèmes Marins Profonds (BEEP), IUEM, Rue Dumont d'Urville, 29280, Plouzané, France
| | - Z Kelman
- Institute for Bioscience and Biotechnology Research and the National Institute of Standards and Technology, Rockville, MD, USA
| | - M Kerou
- Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - J Littlechild
- Henry Wellcome Building for Biocatalysis, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - V Müller
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt Am Main, Germany
| | - P Schönheit
- Institute of General Microbiology, Christian Albrechts University, Kiel, Germany
| | - B Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, 45117, Essen, Germany
| | - K Vorgias
- Biology Department and RI-Bio3, National and Kapodistrian University of Athens, Athens, Greece
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Tang G, Wang W, Zhu C, Huang H, Chen P, Wang X, Xu M, Sun J, Zhang CJ, Xiao Q, Gao L, Zhang ZM, Yao SQ. Global Reactivity Profiling of the Catalytic Lysine in Human Kinome for Covalent Inhibitor Development. Angew Chem Int Ed Engl 2024; 63:e202316394. [PMID: 38248139 DOI: 10.1002/anie.202316394] [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: 10/30/2023] [Revised: 01/21/2024] [Accepted: 01/21/2024] [Indexed: 01/23/2024]
Abstract
Advances in targeted covalent inhibitors (TCIs) have been made by using lysine-reactive chemistries. Few aminophiles possessing balanced reactivity/stability for the development of cell-active TCIs are however available. We report herein lysine-reactive activity-based probes (ABPs; 2-14) based on the chemistry of aryl fluorosulfates (ArOSO2 F) capable of global reactivity profiling of the catalytic lysine in human kinome from mammalian cells. We concurrently developed reversible covalent ABPs (15/16) by installing salicylaldehydes (SA) onto a promiscuous kinase-binding scaffold. The stability and amine reactivity of these probes exhibited a broad range of tunability. X-ray crystallography and mass spectrometry (MS) confirmed the successful covalent engagement between ArOSO2 F on 9 and the catalytic lysine of SRC kinase. Chemoproteomic studies enabled the profiling of >300 endogenous kinases, thus providing a global landscape of ligandable catalytic lysines of the kinome. By further introducing these aminophiles into VX-680 (a noncovalent inhibitor of AURKA kinase), we generated novel lysine-reactive TCIs that exhibited excellent in vitro potency and reasonable cellular activities with prolonged residence time. Our work serves as a general guide for the development of lysine-reactive ArOSO2 F-based TCIs.
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Affiliation(s)
- Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| | - Wei Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Chengjun Zhu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Huisi Huang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Peng Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Xuan Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Manyi Xu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chi-nese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Jie Sun
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Chong-Jing Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chi-nese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Qicai Xiao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
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Wiest A, Kielkowski P. Cu-Catalyzed Azide-Alkyne-Thiol Reaction Forms Ubiquitous Background in Chemical Proteomic Studies. J Am Chem Soc 2024; 146:2151-2159. [PMID: 38214237 PMCID: PMC10811670 DOI: 10.1021/jacs.3c11780] [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: 10/23/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/13/2024]
Abstract
We report here a Cu-catalyzed azide-alkyne-thiol reaction forming thiotriazoles as the major byproduct under widely used bio-orthogonal protein labeling "click" conditions. The development of Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) had a tremendous impact on many biological discoveries. However, the considered chemoselectivity of CuAAC is hampered by the high reactivity of cysteine free thiols, yielding thiotriazole protein conjugates. The reaction byproducts generate false-positive protein hits in functional proteomic studies. The reported detail investigation of conjugates between chemical probes containing terminal alkynes, azide tags, and cell lysates reveals the formation of thiotriazoles, which can be readily detected by in-gel fluorescence scanning or after peptide and protein enrichment by mass spectrometry-based proteomics. In protein level identification and quantification experiments, the produced fluorescent bands or enriched proteins may not result from the important enzymatically driven reaction and can be falsely assigned as hits. This study provides a complete list of the most common background proteins. The knowledge of this previously overlooked reactivity now leads to the introduction of modified CuAAC conditions, which avoids the undesired product formation, diminishes the background, and hence improves the signal-to-noise ratio.
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Affiliation(s)
- Andreas Wiest
- Department of Chemistry, LMU Munich, Würmtalstr. 201, 81375 Munich, Germany
| | - Pavel Kielkowski
- Department of Chemistry, LMU Munich, Würmtalstr. 201, 81375 Munich, Germany
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30
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Punzalan C, Wang L, Bajrami B, Yao X. Measurement and utilization of the proteomic reactivity by mass spectrometry. MASS SPECTROMETRY REVIEWS 2024; 43:166-192. [PMID: 36924435 DOI: 10.1002/mas.21837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Chemical proteomics, which involves studying the covalent modifications of proteins by small molecules, has significantly contributed to our understanding of protein function and has become an essential tool in drug discovery. Mass spectrometry (MS) is the primary method for identifying and quantifying protein-small molecule adducts. In this review, we discuss various methods for measuring proteomic reactivity using MS and covalent proteomics probes that engage through reactivity-driven and proximity-driven mechanisms. We highlight the applications of these methods and probes in live-cell measurements, drug target identification and validation, and characterizing protein-small molecule interactions. We conclude the review with current developments and future opportunities in the field, providing our perspectives on analytical considerations for MS-based analysis of the proteomic reactivity landscape.
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Affiliation(s)
- Clodette Punzalan
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Lei Wang
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
- AD Bio US, Takeda, Lexington, Massachusetts, 02421, USA
| | - Bekim Bajrami
- Chemical Biology & Proteomics, Biogen, Cambridge, Massachusetts, USA
| | - Xudong Yao
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
- Institute for Systems Biology, University of Connecticut, Storrs, Connecticut, USA
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31
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Prasch H, Wolfsgruber A, Thonhofer M, Culum A, Mandl C, Weber P, Zündel M, Nasseri SA, Gonzalez Santana A, Tegl G, Nidetzky B, Gruber K, Stütz AE, Withers SG, Wrodnigg TM. Ligand-Directed Chemistry on Glycoside Hydrolases - A Proof of Concept Study. Chembiochem 2023; 24:e202300480. [PMID: 37715738 DOI: 10.1002/cbic.202300480] [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: 07/27/2023] [Revised: 09/11/2023] [Accepted: 09/14/2023] [Indexed: 09/18/2023]
Abstract
Selective covalent labelling of enzymes using small molecule probes has advanced the scopes of protein profiling. The covalent bond formation to a specific target is the key step of activity-based protein profiling (ABPP), a method which has become an indispensable tool for measuring enzyme activity in complex matrices. With respect to carbohydrate processing enzymes, strategies for ABPP so far involve labelling the active site of the enzyme, which results in permanent loss of activity. Here, we report in a proof of concept study the use of ligand-directed chemistry (LDC) for labelling glycoside hydrolases near - but not in - the active site. During the labelling process, the competitive inhibitor is cleaved from the probe, departs the active site and the enzyme maintains its catalytic activity. To this end, we designed a building block synthetic concept for small molecule probes containing iminosugar-based reversible inhibitors for labelling of two model β-glucosidases. The results indicate that the LDC approach can be adaptable for covalent proximity labelling of glycoside hydrolases.
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Affiliation(s)
- Herwig Prasch
- Graz University of Technology, Institute of Chemistry and Technology of Biobased Systems, Stremayrgasse 9, 8010, Graz, Austria
| | - Andreas Wolfsgruber
- Graz University of Technology, Institute of Chemistry and Technology of Biobased Systems, Stremayrgasse 9, 8010, Graz, Austria
| | - Martin Thonhofer
- Graz University of Technology, Institute of Chemistry and Technology of Biobased Systems, Stremayrgasse 9, 8010, Graz, Austria
| | - André Culum
- Graz University of Technology, Institute of Chemistry and Technology of Biobased Systems, Stremayrgasse 9, 8010, Graz, Austria
| | - Christoph Mandl
- Graz University of Technology, Institute of Chemistry and Technology of Biobased Systems, Stremayrgasse 9, 8010, Graz, Austria
| | - Patrick Weber
- Graz University of Technology, Institute of Chemistry and Technology of Biobased Systems, Stremayrgasse 9, 8010, Graz, Austria
| | - Melanie Zündel
- Graz University of Technology, Institute of Chemistry and Technology of Biobased Systems, Stremayrgasse 9, 8010, Graz, Austria
| | - Seyed A Nasseri
- University of British Columbia, Department of Chemistry, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
| | - Andres Gonzalez Santana
- University of British Columbia, Department of Chemistry, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
| | - Gregor Tegl
- Graz University of Technology, Institute of Biotechnology and Biochemical Engineering, Petersgasse 10-12/I, 8010, Graz, Austria
| | - Bernd Nidetzky
- Graz University of Technology, Institute of Biotechnology and Biochemical Engineering, Petersgasse 10-12/I, 8010, Graz, Austria
| | - Karl Gruber
- University of Graz, Institute of Molecular Bioscience, Humboldtstraße 50/III, 8010, Graz, Austria
| | - Arnold E Stütz
- Graz University of Technology, Institute of Chemistry and Technology of Biobased Systems, Stremayrgasse 9, 8010, Graz, Austria
| | - Stephen G Withers
- University of British Columbia, Department of Chemistry, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
| | - Tanja M Wrodnigg
- Graz University of Technology, Institute of Chemistry and Technology of Biobased Systems, Stremayrgasse 9, 8010, Graz, Austria
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Hocking B, Armstrong A, Mann DJ. Covalent fragment libraries in drug discovery-Design, synthesis, and screening methods. PROGRESS IN MEDICINAL CHEMISTRY 2023; 62:105-146. [PMID: 37981350 DOI: 10.1016/bs.pmch.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
As the development of drugs with a covalent mode of action is becoming increasingly popular, well-validated covalent fragment-based drug discovery (FBDD) methods have been comparatively slow to keep up with the demand. In this chapter the principles of covalent fragment reactivity, library design, synthesis, and screening methods are explored in depth, focussing on literature examples with direct applications to practical covalent fragment library design and screening. Further, questions about the future of the field are explored and potential useful advances are proposed.
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Affiliation(s)
- Brad Hocking
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Alan Armstrong
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, United Kingdom
| | - David J Mann
- Department of Life Sciences, Imperial College London, London, United Kingdom.
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Tang G, Wang W, Wang X, Ding K, Ngan SC, Chen JY, Sze SK, Gao L, Yuan P, Lu X, Yao SQ. Cell-active, irreversible covalent inhibitors that selectively target the catalytic lysine of EGFR by using fluorosulfate-based SuFEx chemistry. Eur J Med Chem 2023; 259:115671. [PMID: 37499291 DOI: 10.1016/j.ejmech.2023.115671] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/09/2023] [Accepted: 07/19/2023] [Indexed: 07/29/2023]
Abstract
EGFR signaling is involved in multiple cellular processes including cell proliferation, differentiation and development, making this protein kinase one of the most valuable drug targets for the treatment of non-small cell lung carcinomas (NSCLC). Herein, we describe the design and synthesis of a series of potential covalent inhibitors targeting the catalytically conserved lysine (K745) of EGFR on the basis of Erlotinib, an FDA-approved first-generation EGFR drug. Different amine-reactive electrophiles were introduced at positions on the Erlotinib scaffold proximal to K745 in EGFR. The optimized compound 26 (as well as its close analog 30), possessing a novel arylfluorosulfate group (ArOSO2F), showed excellent in vitro potency (as low as 0.19 nM in independent IC50 determination) and selectivity against EGFR and many of its drug-resistant mutants. Both intact protein mass spectrometry (MS) and site-mapping analysis revealed that compound 26 covalently bound to EGFR at K745 through the formation of a sulfamate. In addition, compound 26 displayed good anti-proliferative potency against EGFR-overexpressing HCC827 cells by inhibiting endogenous EGFR autophosphorylation. The pharmacokinetic studies of compound 26 demonstrated the druggable potential of other ArOSO2F-containing compounds. Finally, competitive activity-based protein profiling (ABPP), cellular thermal shift assay (CETSA), as well as cellular wash-out experiments, all showed compound 26 to be the first cell-active, fluorosulfate-based targeted covalent inhibitor (TCI) of protein kinases capable of covalently engaging the catalytically conserved lysine of its target in live mammalian cells.
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Affiliation(s)
- Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| | - Wei Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518000, China
| | - Xuan Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518000, China
| | - Ke Ding
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, Guangzhou, 510632, China; State Key Laboratory of Bioorganic & Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - SoFong Cam Ngan
- Department of Health Sciences, Faculty of Applied Health Sciences, Brock University, St. Catharines, Ontario, L2S 3A1, Canada
| | - Jiao-Yu Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518000, China
| | - Siu Kwan Sze
- Department of Health Sciences, Faculty of Applied Health Sciences, Brock University, St. Catharines, Ontario, L2S 3A1, Canada
| | - Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518000, China
| | - Peiyan Yuan
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518000, China.
| | - Xiaoyun Lu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, Guangzhou, 510632, China.
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore.
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34
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Porta EOJ. Mapping the Evolution of Activity-Based Protein Profiling: A Bibliometric Review. Adv Pharm Bull 2023; 13:639-645. [PMID: 38022804 PMCID: PMC10676541 DOI: 10.34172/apb.2023.082] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/24/2023] [Accepted: 05/17/2023] [Indexed: 12/01/2023] Open
Abstract
Activity-based protein profiling (ABPP) is a chemoproteomic approach that employs small-molecule probes to directly evaluate protein functionality within complex proteomes. This technology has proven to be a potent strategy for mapping ligandable sites in organisms and has significantly impacted drug discovery processes by enabling the development of highly selective small-molecule inhibitors and the identification of new therapeutic molecular targets. Despite being nearly a quarter of a century old as a chemoproteomic tool, ABPP has yet to undergo a bibliometric analysis. In order to gauge its scholarly impact and evolution, a bibliometric analysis was performed, comparing all 1919 reported articles with the articles published in the last five years. Through a comprehensive data analysis, including a 5-step workflow, the most influential articles were identified, and their bibliometric parameters were determined. The 1919 analyzed articles span from 1999 to 2022, providing a comprehensive overview of the historical and current state of ABPP research. This analysis presents, for the first time, the characteristics of the most influential ABPP articles, offering valuable insight into the research conducted in this field and its potential future directions. The findings underscore the crucial role of ABPP in drug discovery and novel therapeutic target identification, as well as the need for continued advancements in the development of novel chemical probes and proteomic technologies to further expand the utility of ABPP.
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35
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McGary LC, Regan GL, Bearne SL. Reactive architecture profiling with a methyl acyl phosphate electrophile. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140945. [PMID: 37536394 DOI: 10.1016/j.bbapap.2023.140945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023]
Abstract
Activity-based protein profiling has facilitated the study of the activity of enzymes in proteomes, inhibitor development, and identification of enzymes that share mechanistic and active-site architectural features. Since methyl acyl phosphate monoesters act as electrostatically selective anionic electrophiles for the covalent modification of nucleophiles that reside adjacent to cationic sites in proteins, we synthesized methyl hex-5-ynoyl phosphate (MHP) to broadly target such protein architectures. After treating the soluble proteome of Paucimonas lemoignei with MHP, biotinylating the resulting acylated proteins using click chemistry, enriching the protein adducts using streptavidin, and analyzing the proteins by LC-MS/MS, a set of 240 enzymes and 132 non-enzyme proteins were identified for a wide spectrum of biological processes and from all 7 enzyme classes. Among those enzymes identified, β-hydroxybutyrate dehydrogenase (PlHBDH) and CTP synthase (E. coli orthologue, EcCTPS) were purified as recombinant enzymes and their rates of inactivation and sites of modification by MHP and methyl acetyl phosphate (MAP) were characterized. MHP reacted more slowly with these proteins than MAP but exhibited greater specificity, despite its lack of multiple binding determinants. Generally, MAP modified more surface residues than MHP. MHP specifically modified Ser 146, Lys 156, and Lys 163 at the active site of PlHBDH. MHP and MAP modified numerous residues of EcCTPS with CTP furnishing the greatest level of protection against MHP- and MAP-dependent modification and inactivation, respectively, followed by ATP and glutamine. Overall, MHP served as an effective probe to identify proteins that are potentially amenable to inhibition by methyl acyl phosphates.
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Affiliation(s)
- Laura C McGary
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Gemma L Regan
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Stephen L Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Department of Chemistry, Dalhousie University, Halifax, NS B3H 4R2, Canada.
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Kim Y, Li H, Choi J, Boo J, Jo H, Hyun JY, Shin I. Glycosidase-targeting small molecules for biological and therapeutic applications. Chem Soc Rev 2023; 52:7036-7070. [PMID: 37671645 DOI: 10.1039/d3cs00032j] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Glycosidases are ubiquitous enzymes that catalyze the hydrolysis of glycosidic linkages in oligosaccharides and glycoconjugates. These enzymes play a vital role in a wide variety of biological events, such as digestion of nutritional carbohydrates, lysosomal catabolism of glycoconjugates, and posttranslational modifications of glycoproteins. Abnormal glycosidase activities are associated with a variety of diseases, particularly cancer and lysosomal storage disorders. Owing to the physiological and pathological significance of glycosidases, the development of small molecules that target these enzymes is an active area in glycoscience and medicinal chemistry. Research efforts carried out thus far have led to the discovery of numerous glycosidase-targeting small molecules that have been utilized to elucidate biological processes as well as to develop effective chemotherapeutic agents. In this review, we describe the results of research studies reported since 2018, giving particular emphasis to the use of fluorescent probes for detection and imaging of glycosidases, activity-based probes for covalent labelling of these enzymes, glycosidase inhibitors, and glycosidase-activatable prodrugs.
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Affiliation(s)
- Yujun Kim
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Hui Li
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Joohee Choi
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Jihyeon Boo
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Hyemi Jo
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
- Department of Drug Discovery, Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea.
| | - Ji Young Hyun
- Department of Drug Discovery, Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea.
| | - Injae Shin
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
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37
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Zhu S, Deen MC, Zhu Y, Gilormini PA, Chen X, Davis OB, Chin MY, Henry AG, Vocadlo DJ. A Fixable Fluorescence-Quenched Substrate for Quantitation of Lysosomal Glucocerebrosidase Activity in Both Live and Fixed Cells. Angew Chem Int Ed Engl 2023; 62:e202309306. [PMID: 37582679 DOI: 10.1002/anie.202309306] [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: 06/30/2023] [Revised: 08/10/2023] [Accepted: 08/15/2023] [Indexed: 08/17/2023]
Abstract
Fluorogenic substrates are emerging tools that enable studying enzymatic processes within their native cellular environments. However, fluorogenic substrates that function within live cells are generally incompatible with cellular fixation, preventing their tandem application with fundamental cell biology methods such as immunocytochemistry. Here we report a simple approach to enable the chemical fixation of a dark-to-light substrate, LysoFix-GBA, which enables quantification of glucocerebrosidase (GCase) activity in both live and fixed cells. LysoFix-GBA enables measuring responses to both chemical and genetic perturbations to lysosomal GCase activity. Further, LysoFix-GBA permits simple multiplexed co-localization studies of GCase activity with subcellular protein markers. This tool will aid studying the role of GCase activity in Parkinson's Disease, creating new therapeutic approaches targeting the GCase pathway. This approach also lays the foundation for an approach to create fixable substrates for other lysosomal enzymes.
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Affiliation(s)
- Sha Zhu
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Matthew C Deen
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Yanping Zhu
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Pierre-André Gilormini
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Xi Chen
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Oliver B Davis
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA
| | - Marcus Y Chin
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA
| | - Anastasia G Henry
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA
| | - David J Vocadlo
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
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38
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Zhang J, Lin C, Jin S, Wang H, Wang Y, Du X, Hutchinson MR, Zhao H, Fang L, Wang X. The pharmacology and therapeutic role of cannabidiol in diabetes. EXPLORATION (BEIJING, CHINA) 2023; 3:20230047. [PMID: 37933286 PMCID: PMC10582612 DOI: 10.1002/exp.20230047] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 05/31/2023] [Indexed: 11/08/2023]
Abstract
In recent years, cannabidiol (CBD), a non-psychotropic cannabinoid, has garnered substantial interest in drug development due to its broad pharmacological activity and multi-target effects. Diabetes is a chronic metabolic disease that can damage multiple organs in the body, leading to the development of complications such as abnormal kidney function, vision loss, neuropathy, and cardiovascular disease. CBD has demonstrated significant therapeutic potential in treating diabetes mellitus and its complications owing to its various pharmacological effects. This work summarizes the role of CBD in diabetes and its impact on complications such as cardiovascular dysfunction, nephropathy, retinopathy, and neuropathy. Strategies for discovering molecular targets for CBD in the treatment of diabetes and its complications are also proposed. Moreover, ways to optimize the structure of CBD based on known targets to generate new CBD analogues are explored.
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Affiliation(s)
- Jin Zhang
- Department of GeriatricsThe First Hospital of Jilin UniversityChangchunPeople's Republic of China
- State Key Laboratory of Natural and Biomimetic DrugsPeking UniversityBeijingPeople's Republic of China
- Laboratory of Chemical Biology, Changchun Institute of Applied ChemistryChinese Academy of SciencesChangchunPeople's Republic of China
| | - Cong Lin
- Laboratory of Chemical Biology, Changchun Institute of Applied ChemistryChinese Academy of SciencesChangchunPeople's Republic of China
| | - Sha Jin
- Laboratory of Chemical Biology, Changchun Institute of Applied ChemistryChinese Academy of SciencesChangchunPeople's Republic of China
- School of Applied Chemistry and EngineeringUniversity of Science and Technology of ChinaHefeiPeople's Republic of China
| | - Hongshuang Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied ChemistryChinese Academy of SciencesChangchunPeople's Republic of China
| | - Yibo Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied ChemistryChinese Academy of SciencesChangchunPeople's Republic of China
| | - Xiubo Du
- Shenzhen Key Laboratory of Marine Biotechnology and EcologyCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenPeople's Republic of China
| | - Mark R. Hutchinson
- Discipline of PhysiologyAdelaide Medical SchoolUniversity of AdelaideThe Commonwealth of AustraliaAdelaideAustralia
- ARC Centre for Nanoscale BioPhotonicsUniversity of AdelaideThe Commonwealth of AustraliaAdelaideAustralia
| | - Huiying Zhao
- Department of GeriatricsThe First Hospital of Jilin UniversityChangchunPeople's Republic of China
| | - Le Fang
- Department of NeurologyThe China‐Japan Union Hospital of Jilin UniversityChangchunPeople's Republic of China
| | - Xiaohui Wang
- State Key Laboratory of Natural and Biomimetic DrugsPeking UniversityBeijingPeople's Republic of China
- Laboratory of Chemical Biology, Changchun Institute of Applied ChemistryChinese Academy of SciencesChangchunPeople's Republic of China
- School of Applied Chemistry and EngineeringUniversity of Science and Technology of ChinaHefeiPeople's Republic of China
- Beijing National Laboratory for Molecular SciencesBeijingPeople's Republic of China
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39
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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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40
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Porta EO, Steel PG. Activity-based protein profiling: A graphical review. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2023; 5:100164. [PMID: 37692766 PMCID: PMC10484978 DOI: 10.1016/j.crphar.2023.100164] [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: 04/17/2023] [Revised: 08/06/2023] [Accepted: 08/23/2023] [Indexed: 09/12/2023] Open
Abstract
Activity-based protein profiling (ABPP) is a chemoproteomic technology that employs small chemical probes to directly interrogate protein function within complex proteomes. Since its initial application almost 25 years ago, ABPP has proven to be a powerful and versatile tool for addressing numerous challenges in drug discovery, including the development of highly selective small-molecule inhibitors, the discovery of new therapeutic targets, and the illumination of target proteins in tissues and organisms. This graphical review provides an overview of the rapid evolution of ABPP strategies, highlighting the versatility of the approach with selected examples of its successful application.
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Affiliation(s)
| | - Patrick G. Steel
- Department of Chemistry, Durham University, Durham, DH1 3LE, United Kingdom
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41
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Lourenço AL. Editorial: Mapping enzyme activity: from novel diagnostics to target-based therapeutics, how activity-based probes are improving our understanding of biological catalysts. Front Pharmacol 2023; 14:1271247. [PMID: 37675044 PMCID: PMC10478076 DOI: 10.3389/fphar.2023.1271247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 08/16/2023] [Indexed: 09/08/2023] Open
Affiliation(s)
- André Luiz Lourenço
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, San Francisco, CA, United States
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42
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Nicolau I, Hădade ND, Matache M, Funeriu DP. Synthetic Approaches of Epoxysuccinate Chemical Probes. Chembiochem 2023; 24:e202300157. [PMID: 37096389 DOI: 10.1002/cbic.202300157] [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: 02/26/2023] [Revised: 04/21/2023] [Accepted: 04/23/2023] [Indexed: 04/26/2023]
Abstract
Synthetic chemical probes are powerful tools for investigating biological processes. They are particularly useful for proteomic studies such as activity-based protein profiling (ABPP). These chemical methods initially used mimics of natural substrates. As the techniques gained prominence, more and more elaborate chemical probes with increased specificity towards given enzyme/protein families and amenability to various reaction conditions were used. Among the chemical probes, peptidyl-epoxysuccinates represent one of the first types of compounds used to investigate the activity of the cysteine protease papain-like family of enzymes. Structurally derived from the natural substrate, a wide body of inhibitors and activity- or affinity-based probes bearing the electrophilic oxirane unit for covalent labeling of active enzymes now exists. Herein, we review the literature regarding the synthetic approaches to epoxysuccinate-based chemical probes together with their reported applications, from biological chemistry and inhibition studies to supramolecular chemistry and the formation of protein arrays.
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Affiliation(s)
- Ioana Nicolau
- University of Bucharest, Faculty of Chemistry, Department of Organic Chemistry, Biochemistry and Catalysis, Research Centre of Applied Organic Chemistry, 90 Panduri Street, 050663, Bucharest, Romania
| | - Niculina D Hădade
- Babes-Bolyai University, Faculty of Chemistry and Chemical Engineering, Supramolecular and Organometallic Chemistry Centre, 11 Arany Janos Street, 400028, Cluj-Napoca, Romania
| | - Mihaela Matache
- University of Bucharest, Faculty of Chemistry, Department of Organic Chemistry, Biochemistry and Catalysis, Research Centre of Applied Organic Chemistry, 90 Panduri Street, 050663, Bucharest, Romania
| | - Daniel P Funeriu
- University of Bucharest, Faculty of Chemistry, Department of Organic Chemistry, Biochemistry and Catalysis, Research Centre of Applied Organic Chemistry, 90 Panduri Street, 050663, Bucharest, Romania
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43
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Pan S, Ding A, Li Y, Sun Y, Zhan Y, Ye Z, Song N, Peng B, Li L, Huang W, Shao H. Small-molecule probes from bench to bedside: advancing molecular analysis of drug-target interactions toward precision medicine. Chem Soc Rev 2023; 52:5706-5743. [PMID: 37525607 DOI: 10.1039/d3cs00056g] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Over the past decade, remarkable advances have been witnessed in the development of small-molecule probes. These molecular tools have been widely applied for interrogating proteins, pathways and drug-target interactions in preclinical research. While novel structures and designs are commonly explored in probe development, the clinical translation of small-molecule probes remains limited, primarily due to safety and regulatory considerations. Recent synergistic developments - interfacing novel chemical probes with complementary analytical technologies - have introduced and expedited diverse biomedical opportunities to molecularly characterize targeted drug interactions directly in the human body or through accessible clinical specimens (e.g., blood and ascites fluid). These integrated developments thus offer unprecedented opportunities for drug development, disease diagnostics and treatment monitoring. In this review, we discuss recent advances in the structure and design of small-molecule probes with novel functionalities and the integrated development with imaging, proteomics and other emerging technologies. We further highlight recent applications of integrated small-molecule technologies for the molecular analysis of drug-target interactions, including translational applications and emerging opportunities for whole-body imaging, tissue-based measurement and blood-based analysis.
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Affiliation(s)
- Sijun Pan
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Aixiang Ding
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yisi Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yaxin Sun
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yueqin Zhan
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Zhenkun Ye
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Ning Song
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Bo Peng
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Lin Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Wei Huang
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Huilin Shao
- Institute for Health Innovation & Technology, National University of Singapore, Singapore 117599, Singapore.
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore 117583, Singapore
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44
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Lucero B, Francisco KR, Liu LJ, Caffrey CR, Ballatore C. Protein-protein interactions: developing small-molecule inhibitors/stabilizers through covalent strategies. Trends Pharmacol Sci 2023; 44:474-488. [PMID: 37263826 PMCID: PMC11003449 DOI: 10.1016/j.tips.2023.04.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/15/2023] [Accepted: 04/26/2023] [Indexed: 06/03/2023]
Abstract
The development of small-molecule inhibitors or stabilizers of selected protein-protein interactions (PPIs) of interest holds considerable promise for the development of research tools as well as candidate therapeutics. In this context, the covalent modification of selected residues within the target protein has emerged as a promising mechanism of action to obtain small-molecule modulators of PPIs with appropriate selectivity and duration of action. Different covalent labeling strategies are now available that can potentially allow for a rational, ground-up discovery and optimization of ligands as PPI inhibitors or stabilizers. This review article provides a synopsis of recent developments and applications of such tactics, with a particular focus on site-directed fragment tethering and proximity-enabled approaches.
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Affiliation(s)
- Bobby Lucero
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Karol R Francisco
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Lawrence J Liu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Conor R Caffrey
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Carlo Ballatore
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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45
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Capela R, Félix R, Clariano M, Nunes D, Perry MDJ, Lopes F. Target Identification in Anti-Tuberculosis Drug Discovery. Int J Mol Sci 2023; 24:10482. [PMID: 37445660 DOI: 10.3390/ijms241310482] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/17/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is the etiological agent of tuberculosis (TB), a disease that, although preventable and curable, remains a global epidemic due to the emergence of resistance and a latent form responsible for a long period of treatment. Drug discovery in TB is a challenging task due to the heterogeneity of the disease, the emergence of resistance, and uncomplete knowledge of the pathophysiology of the disease. The limited permeability of the cell wall and the presence of multiple efflux pumps remain a major barrier to achieve effective intracellular drug accumulation. While the complete genome sequence of Mtb has been determined and several potential protein targets have been validated, the lack of adequate models for in vitro and in vivo studies is a limiting factor in TB drug discovery programs. In current therapeutic regimens, less than 0.5% of bacterial proteins are targeted during the biosynthesis of the cell wall and the energetic metabolism of two of the most important processes exploited for TB chemotherapeutics. This review provides an overview on the current challenges in TB drug discovery and emerging Mtb druggable proteins, and explains how chemical probes for protein profiling enabled the identification of new targets and biomarkers, paving the way to disruptive therapeutic regimens and diagnostic tools.
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Affiliation(s)
- Rita Capela
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Rita Félix
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Marta Clariano
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Diogo Nunes
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Maria de Jesus Perry
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Francisca Lopes
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
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46
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Finin P, Khan RMN, Oh S, Boshoff HIM, Barry CE. Chemical approaches to unraveling the biology of mycobacteria. Cell Chem Biol 2023; 30:420-435. [PMID: 37207631 PMCID: PMC10201459 DOI: 10.1016/j.chembiol.2023.04.014] [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: 02/06/2023] [Revised: 04/07/2023] [Accepted: 04/27/2023] [Indexed: 05/21/2023]
Abstract
Mycobacterium tuberculosis (Mtb), perhaps more than any other organism, is intrinsically appealing to chemical biologists. Not only does the cell envelope feature one of the most complex heteropolymers found in nature1 but many of the interactions between Mtb and its primary host (we humans) rely on lipid and not protein mediators.2,3 Many of the complex lipids, glycolipids, and carbohydrates biosynthesized by the bacterium still have unknown functions, and the complexity of the pathological processes by which tuberculosis (TB) disease progress offers many opportunities for these molecules to influence the human response. Because of the importance of TB in global public health, chemical biologists have applied a wide-ranging array of techniques to better understand the disease and improve interventions.
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Affiliation(s)
- Peter Finin
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - R M Naseer Khan
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - Sangmi Oh
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - Helena I M Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - Clifton E Barry
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA.
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47
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Châtre R, Blochouse E, Eid R, Djago F, Lange J, Tarighi M, Renoux B, Sobilo J, Le Pape A, Clarhaut J, Geffroy C, Opalinski I, Tuo W, Papot S, Poinot P. Induced-volatolomics for the design of tumour activated therapy. Chem Sci 2023; 14:4697-4703. [PMID: 37181780 PMCID: PMC10171039 DOI: 10.1039/d2sc06797h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 04/07/2023] [Indexed: 05/16/2023] Open
Abstract
The discovery of tumour-associated markers is of major interest for the development of selective cancer chemotherapy. Within this framework, we introduced the concept of induced-volatolomics enabling to monitor simultaneously the dysregulation of several tumour-associated enzymes in living mice or biopsies. This approach relies on the use of a cocktail of volatile organic compound (VOC)-based probes that are activated enzymatically for releasing the corresponding VOCs. Exogenous VOCs can then be detected in the breath of mice or in the headspace above solid biopsies as specific tracers of enzyme activities. Our induced-volatolomics modality highlighted that the up-regulation of N-acetylglucosaminidase was a hallmark of several solid tumours. Having identified this glycosidase as a potential target for cancer therapy, we designed an enzyme-responsive albumin-binding prodrug of the potent monomethyl auristatin E programmed for the selective release of the drug in the tumour microenvironment. This tumour activated therapy produced a remarkable therapeutic efficacy on orthotopic triple-negative mammary xenografts in mice, leading to the disappearance of tumours in 66% of treated animals. Thus, this study shows the potential of induced-volatolomics for the exploration of biological processes as well as the discovery of novel therapeutic strategies.
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Affiliation(s)
- Rémi Châtre
- University of Poitiers, UMR CNRS 7285, Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), Equipe Labellisée Ligue Contre le Cancer 4 Rue Michel-Brunet, TSA 51106 86073 Poitiers Cedex 9 France
| | - Estelle Blochouse
- University of Poitiers, UMR CNRS 7285, Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), Equipe Labellisée Ligue Contre le Cancer 4 Rue Michel-Brunet, TSA 51106 86073 Poitiers Cedex 9 France
| | - Rony Eid
- University of Poitiers, UMR CNRS 7285, Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), Equipe Labellisée Ligue Contre le Cancer 4 Rue Michel-Brunet, TSA 51106 86073 Poitiers Cedex 9 France
| | - Fabiola Djago
- University of Poitiers, UMR CNRS 7285, Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), Equipe Labellisée Ligue Contre le Cancer 4 Rue Michel-Brunet, TSA 51106 86073 Poitiers Cedex 9 France
| | - Justin Lange
- University of Poitiers, UMR CNRS 7285, Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), Equipe Labellisée Ligue Contre le Cancer 4 Rue Michel-Brunet, TSA 51106 86073 Poitiers Cedex 9 France
| | - Mehrad Tarighi
- University of Poitiers, UMR CNRS 7285, Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), Equipe Labellisée Ligue Contre le Cancer 4 Rue Michel-Brunet, TSA 51106 86073 Poitiers Cedex 9 France
| | - Brigitte Renoux
- University of Poitiers, UMR CNRS 7285, Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), Equipe Labellisée Ligue Contre le Cancer 4 Rue Michel-Brunet, TSA 51106 86073 Poitiers Cedex 9 France
| | - Julien Sobilo
- UAR No. 44 PHENOMIN TAAM-Imagerie In Vivo, CNRS 3B Rue de la Férollerie F-45071 Orléans France
| | - Alain Le Pape
- UAR No. 44 PHENOMIN TAAM-Imagerie In Vivo, CNRS 3B Rue de la Férollerie F-45071 Orléans France
| | - Jonathan Clarhaut
- University of Poitiers, UMR CNRS 7285, Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), Equipe Labellisée Ligue Contre le Cancer 4 Rue Michel-Brunet, TSA 51106 86073 Poitiers Cedex 9 France
- CHU de Poitiers 2 Rue de la Miléterie, CS 90577 F-86021 Poitiers France
| | - Claude Geffroy
- University of Poitiers, UMR CNRS 7285, Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), Equipe Labellisée Ligue Contre le Cancer 4 Rue Michel-Brunet, TSA 51106 86073 Poitiers Cedex 9 France
| | - Isabelle Opalinski
- University of Poitiers, UMR CNRS 7285, Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), Equipe Labellisée Ligue Contre le Cancer 4 Rue Michel-Brunet, TSA 51106 86073 Poitiers Cedex 9 France
| | - Wei Tuo
- University of Poitiers, UMR CNRS 7285, Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), Equipe Labellisée Ligue Contre le Cancer 4 Rue Michel-Brunet, TSA 51106 86073 Poitiers Cedex 9 France
| | - Sébastien Papot
- University of Poitiers, UMR CNRS 7285, Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), Equipe Labellisée Ligue Contre le Cancer 4 Rue Michel-Brunet, TSA 51106 86073 Poitiers Cedex 9 France
- Seekyo SA 2 Avenue Galilée, BP 30153 86961 Futuroscope France
| | - Pauline Poinot
- University of Poitiers, UMR CNRS 7285, Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), Equipe Labellisée Ligue Contre le Cancer 4 Rue Michel-Brunet, TSA 51106 86073 Poitiers Cedex 9 France
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48
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Zhu L, Hu S, Yan X, Zeng Q, Zhang B, Jiang L, Yao SQ, Ge J. Ugi reaction-assisted assembly of covalent PROTACs against glutathione peroxidase 4. Bioorg Chem 2023; 134:106461. [PMID: 36924654 DOI: 10.1016/j.bioorg.2023.106461] [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: 09/16/2022] [Revised: 12/06/2022] [Accepted: 03/07/2023] [Indexed: 03/12/2023]
Abstract
Inducing cell ferroptosis by inactivating glutathione peroxidase 4 (GPX4) is a popular cancer treatment strategy. However, only few GPX4 inhibitors have been developed to date. PROteolysis Targeting Chimera (PROTAC) is a promising approach to provide new opportunities to overcome limitations of traditional therapeutics. Herein, a PROTAC-like activity-based probe PD-Q2 was first assembled using Ugi reaction, consisting of a known GPX4 inhibitor ML-162 homolog to the E3 ligase cereblon ligand-pomalidomide. Pull-down and immunoblotting analysis revealed that GPX4 was a covalent target of PD-Q2, but the degradation efficiency was weak. Therefore, a series of degraders was further synthesized by varying the linkers of heterofunctional PROTACs. Among these degraders, PD-4 and PD-P2 were found to promote effective GPX4 degradation via the ubiquitin-proteasome system and cause lipid ROS accumulation. PD-4 and PD-P2 showed potent inhibitory of colony formation and cell growth. Furthermore, we found that with pomalidomide, the degraders exhibit a high fluorescent signal that is mostly localized in the lysosome, which may affect the effectiveness of anti-cell proliferation. Overall, we provide GPX4 degraders for further exploring therapeutic potential of regulating ferroptosis.
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Affiliation(s)
- Liquan Zhu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Shiqi Hu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Xiaoqiao Yan
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Qian Zeng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Bei Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Linye Jiang
- 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, 4 Science Drive 2, Singapore 117544, Singapore.
| | - Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China.
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49
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Nickel GA, Diehl KL. Chemical Biology Approaches to Identify and Profile Interactors of Chromatin Modifications. ACS Chem Biol 2023; 18:1014-1026. [PMID: 35238546 PMCID: PMC9440160 DOI: 10.1021/acschembio.1c00794] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In eukaryotes, DNA is packaged with histone proteins in a complex known as chromatin. Both the DNA and histone components of chromatin can be chemically modified in a wide variety of ways, resulting in a complex landscape often referred to as the "epigenetic code". These modifications are recognized by effector proteins that remodel chromatin and modulate transcription, translation, and repair of the underlying DNA. In this Review, we examine the development of methods for characterizing proteins that interact with these histone and DNA modifications. "Mark first" approaches utilize chemical, peptide, nucleosome, or oligonucleotide probes to discover interactors of a specific modification. "Reader first" approaches employ arrays of peptides, nucleosomes, or oligonucleotides to profile the binding preferences of interactors. These complementary strategies have greatly enhanced our understanding of how chromatin modifications effect changes in genomic regulation, bringing us ever closer to deciphering this complex language.
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Affiliation(s)
- Garrison A. Nickel
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, United States
| | - Katharine L. Diehl
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, United States
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50
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Mons E, Kim RQ, Mulder MPC. Technologies for Direct Detection of Covalent Protein-Drug Adducts. Pharmaceuticals (Basel) 2023; 16:547. [PMID: 37111304 PMCID: PMC10146396 DOI: 10.3390/ph16040547] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
In the past two decades, drug candidates with a covalent binding mode have gained the interest of medicinal chemists, as several covalent anticancer drugs have successfully reached the clinic. As a covalent binding mode changes the relevant parameters to rank inhibitor potency and investigate structure-activity relationship (SAR), it is important to gather experimental evidence on the existence of a covalent protein-drug adduct. In this work, we review established methods and technologies for the direct detection of a covalent protein-drug adduct, illustrated with examples from (recent) drug development endeavors. These technologies include subjecting covalent drug candidates to mass spectrometric (MS) analysis, protein crystallography, or monitoring intrinsic spectroscopic properties of the ligand upon covalent adduct formation. Alternatively, chemical modification of the covalent ligand is required to detect covalent adducts by NMR analysis or activity-based protein profiling (ABPP). Some techniques are more informative than others and can also elucidate the modified amino acid residue or bond layout. We will discuss the compatibility of these techniques with reversible covalent binding modes and the possibilities to evaluate reversibility or obtain kinetic parameters. Finally, we expand upon current challenges and future applications. Overall, these analytical techniques present an integral part of covalent drug development in this exciting new era of drug discovery.
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Affiliation(s)
- Elma Mons
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (E.M.)
- Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Robbert Q. Kim
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (E.M.)
| | - Monique P. C. Mulder
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (E.M.)
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