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Bon C, Goretzki B, Flamme M, Shelton C, Davis H, Lima F, Garcia F, Brittain S, Brocklehurst CE. Oxadiazolines as Photoreleasable Labels for Drug Target Identification. J Am Chem Soc 2024; 146:26759-26765. [PMID: 39288302 DOI: 10.1021/jacs.4c06936] [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: 09/19/2024]
Abstract
Photoaffinity labeling is a widely used technique for studying ligand-protein and protein-protein interactions. Traditional photoaffinity labels utilize nonspecific C-H bond insertion reactions mediated by a highly reactive intermediate. Despite being the most widely used photoaffinity labels, diazirines exhibit limited compatibility with downstream organic reactions and suffer from storage stability concerns. This study introduces oxadiazolines as innovative and complementary photoactivatable labels for addition to the toolbox and demonstrates their application in vitro and through in cellulo labeling experiments. Oxadiazolines can be easily synthesized from ketone moieties and cleaved with 302-330 nm light to cleanly liberate a diazo reactive moiety that can covalently modify nucleophilic amino acid residues. Notably, oxadiazolines are compatible with various organic reaction conditions and functional groups, allowing for the exploration of a large chemical space. Several known inhibitors featuring the oxadiazoline functionality were prepared without affecting their binding affinity. Furthermore, we confirmed the ability of oxadiazolines to form covalent bonds with proteins upon UV-irradiation, both in vitro and in cellulo, yielding comparable results to those of the matched diazirine compounds.
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Affiliation(s)
- Corentin Bon
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4056, Switzerland
| | - Benedikt Goretzki
- Discovery Sciences, Novartis Biomedical Research, Novartis Pharma AG, Basel 4056, Switzerland
| | - Marie Flamme
- Chemical and Analytical Development, Novartis Development, Novartis Pharma AG, Basel 4056, Switzerland
| | - Claude Shelton
- Discovery Sciences, Novartis Biomedical Research, Novartis Pharma AG, Cambridge, Massachusetts 02139, United States
| | - Holly Davis
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4056, Switzerland
| | - Fabio Lima
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4056, Switzerland
| | - Francisco Garcia
- Discovery Sciences, Novartis Biomedical Research, Novartis Pharma AG, Cambridge, Massachusetts 02139, United States
| | - Scott Brittain
- Discovery Sciences, Novartis Biomedical Research, Novartis Pharma AG, Cambridge, Massachusetts 02139, United States
| | - Cara E Brocklehurst
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4056, Switzerland
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2
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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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3
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Miao Y, Yu ZQ, Xu S, Yan M. Quinone Methide Based Self-Immobilizing Molecular Fluorescent Probes for In Situ Imaging of Enzymes. Chem Asian J 2024; 19:e202400189. [PMID: 38514393 DOI: 10.1002/asia.202400189] [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: 02/20/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 03/23/2024]
Abstract
Enzymes play important roles not only in normal physiological processes but in the development of many diseases. In situ imaging of enzymes with high-resolution in living systems would helpful for clinical diagnosis and treatment. However, many molecular fluorescent probes suffer from the drawback of diffusing away from the reaction site of enzymes even out of the cells, losing the in situ information and resulting in poor imaging resolution. Quinone methide (QM) based self-immobilizing probes allow the fluorescent signal to be immobilized near the target for an extended period without deactivating the target enzymes, ensuring that it will provide amplified signals and in situ information of the target with high resolution. In this review, we summarized the recent progress of QM-based self-immobilizing probes including their design strategies, working mechanisms, classifications and applications in in situ enzyme imaging. This review calls for the development of more activatable QM-based probe with the advantages of high stability in the absence of the target but very high labeling efficiency after activation.
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Affiliation(s)
- Yeru Miao
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China
| | - Zhen-Qing Yu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China
| | - Shuai Xu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China
| | - Mei Yan
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China
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4
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Walrant A, Sachon E. Photoaffinity labeling coupled to MS to identify peptide biological partners: Secondary reactions, for better or for worse? MASS SPECTROMETRY REVIEWS 2024. [PMID: 38576378 DOI: 10.1002/mas.21880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 02/22/2024] [Accepted: 03/13/2024] [Indexed: 04/06/2024]
Abstract
Affinity photolabeling is a smart method to study noncovalent and transient interactions and provide a submolecular picture of the contacts between interacting partners. In this review, we will focus on the identification of peptide partners using photoaffinity labeling coupled to mass spectrometry in different contexts such as in vitro with a purified potential partner, in model systems such as model membranes, and with live cells using both targeted and nontargeted proteomics studies. Different biological partners will be described, among which glycoconjugates, oligonucleotides, peptides, proteins, and lipids, with the photoreactive label inserted either on the peptide of interest or on the potential partner. Particular attention will be paid to the observation and characterization of specific rearrangements following the photolabeling reaction, which can help characterize photoadducts and provide a better understanding of the interacting systems and environment.
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Affiliation(s)
- Astrid Walrant
- Laboratoire des Biomolécules, LBM, Sorbonne Université, École normale supérieure, PSL University, CNRS, Paris, France
| | - Emmanuelle Sachon
- Laboratoire des Biomolécules, LBM, Sorbonne Université, École normale supérieure, PSL University, CNRS, Paris, France
- Sorbonne Université, Mass Spectrometry Sciences Sorbonne Université, MS3U platform, Fédération de Chimie moléculaire de Paris centre, Paris, France
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5
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Malgorn C, Becher F, Bruyat P, Fruchart-Gaillard C, Beau F, Bregant S, Devel L. A New Affinity-Based Probe to Profile MMP Active Forms. Methods Mol Biol 2024; 2747:29-39. [PMID: 38038929 DOI: 10.1007/978-1-0716-3589-6_3] [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: 12/02/2023]
Abstract
A new generation of affinity-based probes (AfBPs) has been developed to label and identity matrix metalloproteinases (MMPs) under their active form in complex proteomes. First, the probe reacts with an active MMP through a proximity-driven reaction that does not require any external trigger. Following this affinity-labeling step, a streptavidin-based enrichment of the resulting biotin-tagged MMP is carried out. Finally, after on-beads proteolytic digestion by trypsin, MMP signature peptides are analyzed and identified by mass spectrometry. Such a "photoactivation-free" labeling can be applied to the detection of several MMPs in a wide variety of biological systems, including in vivo conditions.
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Affiliation(s)
- Carole Malgorn
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Gif-sur-Yvette, France
| | - François Becher
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Gif-sur-Yvette, France
| | - Pierrick Bruyat
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Gif-sur-Yvette, France
| | - Carole Fruchart-Gaillard
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Gif-sur-Yvette, France
| | - Fabrice Beau
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Gif-sur-Yvette, France
| | - Sarah Bregant
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Gif-sur-Yvette, France
| | - Laurent Devel
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Gif-sur-Yvette, France.
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6
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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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7
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Korovesis D, Gaspar VP, Beard HA, Chen S, Zahédi RP, Verhelst SHL. Mapping Peptide-Protein Interactions by Amine-Reactive Cleavable Photoaffinity Reagents. ACS OMEGA 2023; 8:25487-25495. [PMID: 37483247 PMCID: PMC10357517 DOI: 10.1021/acsomega.3c03064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/21/2023] [Indexed: 07/25/2023]
Abstract
Photoaffinity labeling followed by tandem mass spectrometry is an often used strategy to identify protein targets of small-molecule drugs or drug candidates, which, under ideal conditions, enables the identification of the actual drug binding site. In the case of bioactive peptides, however, identifying the distinct binding site is hampered because of complex fragmentation patterns during tandem mass spectrometry. We here report the development and use of small cleavable photoaffinity reagents that allow functionalization of bioactive peptides for light-induced covalent binding to their protein targets. Upon cleavage of the covalently linked peptide drug, a chemical remnant of a defined mass remains on the bound amino acid, which is then used to unambiguously identify the drug binding site. Applying our approach to known peptide-drug/protein pairs with reported crystal structures, such as the calmodulin-melittin interaction, we were able to validate the identified binding sites based on structural models. Overall, our cleavable photoaffinity labeling strategy represents a powerful tool to enable the identification of protein targets and specific binding sites of a wide variety of bioactive peptides in the future.
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Affiliation(s)
- Dimitris Korovesis
- Laboratory
of Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven−University of Leuven, Herestraat 49 Box 802, Leuven 3000, Belgium
| | - Vanessa P. Gaspar
- Segal
Cancer Proteomics Centre, Lady Davis Institute
for Medical Research and McGill University, Montreal, Quebec H3T 1E2, Canada
- Gerald
Bronfman Department of Oncology, McGill
University, Montreal, Quebec H4A 3T2, Canada
| | - Hester A. Beard
- Laboratory
of Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven−University of Leuven, Herestraat 49 Box 802, Leuven 3000, Belgium
| | - Suyuan Chen
- AG
Chemical Proteomics, Leibniz Institute for Analytical Sciences ISAS,
e.V., Otto-Hahn-Str. 6b, Dortmund 44227, Germany
| | - René P. Zahédi
- Segal
Cancer Proteomics Centre, Lady Davis Institute
for Medical Research and McGill University, Montreal, Quebec H3T 1E2, Canada
- Manitoba
Centre for Proteomics and Systems Biology, Winnipeg, Manitoba R3E 3P4, Canada
- Department
of Internal Medicine, University of Manitoba, Winnipeg, Manitoba R3E 0Z2, Canada
- Department
of Biochemistry and Medical Genetics, University
of Manitoba, Winnipeg, Manitoba R3E 3N4, Canada
- Cancer
Care Manitoba Research Institute, Winnipeg, Manitoba R3E
0V9, Canada
| | - Steven H. L. Verhelst
- Laboratory
of Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven−University of Leuven, Herestraat 49 Box 802, Leuven 3000, Belgium
- AG
Chemical Proteomics, Leibniz Institute for Analytical Sciences ISAS,
e.V., Otto-Hahn-Str. 6b, Dortmund 44227, Germany
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8
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Fan Y, Wu Y, Hou J, Wang P, Peng X, Ge G. Coumarin-based near-infrared fluorogenic probes: Recent advances, challenges and future perspectives. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2023.215020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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9
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Forrest I, Parker CG. Proteome-Wide Fragment-Based Ligand and Target Discovery. Isr J Chem 2023; 63:e202200098. [PMID: 38213795 PMCID: PMC10783656 DOI: 10.1002/ijch.202200098] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Indexed: 02/10/2023]
Abstract
Chemical probes are invaluable tools to investigate biological processes and can serve as lead molecules for the development of new therapies. However, despite their utility, only a fraction of human proteins have selective chemical probes, and more generally, our knowledge of the "chemically-tractable" proteome is limited, leaving many potential therapeutic targets unexploited. To help address these challenges, powerful chemical proteomic approaches have recently been developed to globally survey the ability of proteins to bind small molecules (i. e., ligandability) directly in native systems. In this review, we discuss the utility of such approaches, with a focus on the integration of chemoproteomic methods with fragment-based ligand discovery (FBLD), to facilitate the broad mapping of the ligandable proteome while also providing starting points for progression into lead chemical probes.
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Affiliation(s)
- Ines Forrest
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Christopher G Parker
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
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10
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Georgiadis D, Skoulikas N, Papakyriakou A, Stratikos E. Phosphinic Peptides as Tool Compounds for the Study of Pharmacologically Relevant Zn-Metalloproteases. ACS Pharmacol Transl Sci 2022; 5:1228-1253. [PMID: 36524013 PMCID: PMC9745897 DOI: 10.1021/acsptsci.2c00183] [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: 09/12/2022] [Indexed: 11/29/2022]
Abstract
Phosphinic peptides constitute an important class of bioactive compounds that have found a wide range of applications in the field of biology and pharmacology of Zn-metalloproteases, the largest family of proteases in humans. They are designed to mimic the structure of natural substrates during their proteolysis, thus acting as mechanism-based, transition state analogue inhibitors. A combination of electrostatic interactions between the phosphinic acid group and the Zn cation as well as optimal noncovalent enzyme-ligand interactions can result in both high binding affinity for the desired target and selectivity against other proteases. Due to these unique properties, phosphinic peptides have been mainly employed as tool compounds for (a) the purposes of rational drug design by serving as ligands in X-ray crystal structures of target enzymes and allowing the identification of crucial interactions that govern optimal molecular recognition, and (b) the delineation of biological pathways where Zn-metalloproteases are key regulators. For the latter objective, inhibitors of the phosphinopeptidic type have been used either unmodified or after being transformed to probes of various types, thus expanding the arsenal of functional tools available to researchers. The aim of this review is to summarize all recent research achievements in which phosphinic peptides have played a central role as tool compounds in the understanding of the mechanism and biological functions of Zn-metalloproteases in both health and disease.
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Affiliation(s)
- Dimitris Georgiadis
- Department
of Chemistry, National and Kapodistrian
University of Athens, GR-15784 Athens, Greece
| | - Nikolaos Skoulikas
- Department
of Chemistry, National and Kapodistrian
University of Athens, GR-15784 Athens, Greece
| | - Athanasios Papakyriakou
- National
Centre for Scientific Research “Demokritos”, Agia Paraskevi GR-15341 Athens, Greece
| | - Efstratios Stratikos
- Department
of Chemistry, National and Kapodistrian
University of Athens, GR-15784 Athens, Greece
- National
Centre for Scientific Research “Demokritos”, Agia Paraskevi GR-15341 Athens, Greece
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11
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de Almeida LGN, Thode H, Eslambolchi Y, Chopra S, Young D, Gill S, Devel L, Dufour A. Matrix Metalloproteinases: From Molecular Mechanisms to Physiology, Pathophysiology, and Pharmacology. Pharmacol Rev 2022; 74:712-768. [PMID: 35738680 DOI: 10.1124/pharmrev.121.000349] [Citation(s) in RCA: 113] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The first matrix metalloproteinase (MMP) was discovered in 1962 from the tail of a tadpole by its ability to degrade collagen. As their name suggests, matrix metalloproteinases are proteases capable of remodeling the extracellular matrix. More recently, MMPs have been demonstrated to play numerous additional biologic roles in cell signaling, immune regulation, and transcriptional control, all of which are unrelated to the degradation of the extracellular matrix. In this review, we will present milestones and major discoveries of MMP research, including various clinical trials for the use of MMP inhibitors. We will discuss the reasons behind the failures of most MMP inhibitors for the treatment of cancer and inflammatory diseases. There are still misconceptions about the pathophysiological roles of MMPs and the best strategies to inhibit their detrimental functions. This review aims to discuss MMPs in preclinical models and human pathologies. We will discuss new biochemical tools to track their proteolytic activity in vivo and ex vivo, in addition to future pharmacological alternatives to inhibit their detrimental functions in diseases. SIGNIFICANCE STATEMENT: Matrix metalloproteinases (MMPs) have been implicated in most inflammatory, autoimmune, cancers, and pathogen-mediated diseases. Initially overlooked, MMP contributions can be both beneficial and detrimental in disease progression and resolution. Thousands of MMP substrates have been suggested, and a few hundred have been validated. After more than 60 years of MMP research, there remain intriguing enigmas to solve regarding their biological functions in diseases.
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Affiliation(s)
- Luiz G N de Almeida
- Departments of Physiology and Pharmacology and Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada (L.G.N.d.A., Y.E., S.C., D.Y., A.D.); Department of Physiology and Pharmacology, University of Western Ontario, London, Canada (S.G., H.T.); and Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Santé, Gif-sur-Yvette, France (L.D.)
| | - Hayley Thode
- Departments of Physiology and Pharmacology and Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada (L.G.N.d.A., Y.E., S.C., D.Y., A.D.); Department of Physiology and Pharmacology, University of Western Ontario, London, Canada (S.G., H.T.); and Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Santé, Gif-sur-Yvette, France (L.D.)
| | - Yekta Eslambolchi
- Departments of Physiology and Pharmacology and Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada (L.G.N.d.A., Y.E., S.C., D.Y., A.D.); Department of Physiology and Pharmacology, University of Western Ontario, London, Canada (S.G., H.T.); and Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Santé, Gif-sur-Yvette, France (L.D.)
| | - Sameeksha Chopra
- Departments of Physiology and Pharmacology and Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada (L.G.N.d.A., Y.E., S.C., D.Y., A.D.); Department of Physiology and Pharmacology, University of Western Ontario, London, Canada (S.G., H.T.); and Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Santé, Gif-sur-Yvette, France (L.D.)
| | - Daniel Young
- Departments of Physiology and Pharmacology and Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada (L.G.N.d.A., Y.E., S.C., D.Y., A.D.); Department of Physiology and Pharmacology, University of Western Ontario, London, Canada (S.G., H.T.); and Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Santé, Gif-sur-Yvette, France (L.D.)
| | - Sean Gill
- Departments of Physiology and Pharmacology and Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada (L.G.N.d.A., Y.E., S.C., D.Y., A.D.); Department of Physiology and Pharmacology, University of Western Ontario, London, Canada (S.G., H.T.); and Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Santé, Gif-sur-Yvette, France (L.D.)
| | - Laurent Devel
- Departments of Physiology and Pharmacology and Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada (L.G.N.d.A., Y.E., S.C., D.Y., A.D.); Department of Physiology and Pharmacology, University of Western Ontario, London, Canada (S.G., H.T.); and Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Santé, Gif-sur-Yvette, France (L.D.)
| | - Antoine Dufour
- Departments of Physiology and Pharmacology and Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada (L.G.N.d.A., Y.E., S.C., D.Y., A.D.); Department of Physiology and Pharmacology, University of Western Ontario, London, Canada (S.G., H.T.); and Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Santé, Gif-sur-Yvette, France (L.D.)
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12
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Deng H, Lei Q, Yang N, Dai S, Peng H, Yang K, Xiao Z, Wang D, Yu Z, Li N, Li W. Expanded Application of a Photoaffinity Probe to Study Epidermal Growth Factor Receptor Tyrosine Kinase with Functional Activity. Anal Chem 2022; 94:10118-10126. [PMID: 35729862 DOI: 10.1021/acs.analchem.2c01340] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The abnormal activation of the epidermal growth factor receptor (EGFR) is strongly associated with cancer invasion and metastasis. Tools and methods are required to study and visualize EGFR activation under (patho)physiological conditions. Here, we report the development of a two-step photoaffinity probe (HX101) by incorporation of a diazirine as a photoreactive group and an alkyne as a ligation handle to quantitively study EGFR kinase activity in native cellular contexts and human tissue slices. HX101 is a multifunctional probe based on the pharmacophore of the EGFR tyrosine kinase inhibitor (EGFR-TKI) and can covalently target the EGFR upon photoactivation. The incorporated alkyne serves as a versatile ligation handle and enables HX101 to introduce distinct reporter groups (e.g., fluorophore and biotin) via click chemistry. With variable reporter tags, HX101 enables visualization and target engagement studies of the active EGFR in a panel of cancer cells using flow cytometry, confocal microscopy, and mass spectrometry. Furthermore, as a proof of concept study, we applied HX101 in stochastic optical reconstruction microscopy super-resolution imaging to study EGFR activation in live cells. Importantly, HX101 was also applied to visualize EGFR mutant activity in tumor tissues from lung cancer patients for prediction of EGFR-TKI sensitivity. Altogether, our results demonstrate the wide application of a selective photoaffinity probe in multi-modal assessment/visualization of EGFR activity in both live cells and tissue slices. We anticipate that these diverse applications can facilitate the translation of a strategically functionalized probe into medical use.
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Affiliation(s)
- Hui Deng
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.,Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Qian Lei
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.,Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Na Yang
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.,Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Shengkun Dai
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, China
| | - Huipai Peng
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, China
| | - Kai Yang
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Zhaolin Xiao
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.,Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Dongpeng Wang
- Biological Science Instruments Division, Nikon Instruments (Shanghai), Chengdu, Sichuan, 610041, China
| | - Zhiyi Yu
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Nan Li
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.,Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
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13
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Mandler MD, Degnan AP, Zhang S, Aulakh D, Georges K, Sandhu B, Sarjeant A, Zhu Y, Traeger SC, Cheng PT, Ellsworth BA, Regueiro-Ren A. Structural and Thermal Characterization of Halogenated Azidopyridines: Under-Reported Synthons for Medicinal Chemistry. Org Lett 2022; 24:799-803. [PMID: 34714083 DOI: 10.1021/acs.orglett.1c03201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Owing to their participation in Click reactions, bifunctional azides are valuable intermediates in the preparation of medicines and biochemical tool compounds. Despite the privileged nature of pyridines among pharmaceutical scaffolds, reports of the synthesis and characterization of azidopyridines bearing a halogen substituent for further elaboration are almost completely unknown in the literature. As azidopyridines carry nearly equal numbers of nitrogen and carbon atoms, we hypothesized that safety concerns limited the application of these useful bifunctional building blocks in medicinal and biological chemistry. To address this concern, we prepared and characterized nine azidopyridines bearing a single fluorine, chlorine, or bromine atom. All were examined by differential scanning calorimetry (DSC), in which they demonstrated exotherms of 228-326 kJ/mol and onset temperatures between 119 and 135 °C. Selected azidopyridines were advanced to mechanical stress testing, in which impact sensitivity was noted for one regioisomer of C5H3FN4. The utility of these versatile intermediates was demonstrated through their use in a variety of Click reactions and the diversification of the halogen handles.
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Affiliation(s)
- Michael D Mandler
- Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Andrew P Degnan
- Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Shasha Zhang
- Bristol Myers Squibb Chemical and Synthetic Development, 1 Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Darpandeep Aulakh
- Bristol Myers Squibb Chemical and Synthetic Development, 1 Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Ketleine Georges
- Bristol Myers Squibb Chemical and Synthetic Development, 1 Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Bhupinder Sandhu
- Bristol Myers Squibb Chemical and Synthetic Development, 1 Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Amy Sarjeant
- Bristol Myers Squibb Chemical and Synthetic Development, 1 Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Yeheng Zhu
- Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Sarah C Traeger
- Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Peter T Cheng
- Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Bruce A Ellsworth
- Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Alicia Regueiro-Ren
- Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
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14
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Taylor MT. Photochemical protein modification in complex biological environments: recent advances and considerations for future chemical methods development. Biol Chem 2022; 403:413-420. [PMID: 35073619 PMCID: PMC10163948 DOI: 10.1515/hsz-2021-0351] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 01/12/2022] [Indexed: 12/29/2022]
Abstract
Abstract
The development of organic reactions that covalently modify biological matter in complex biological mixtures has become an invaluable asset in drug discovery. Out of the techniques developed to date, optically controlled chemistries are of particular utility owing to both the spatiotemporal control afforded by optical control as well as the impressive array of transformations that are driven by the highly reactive intermediates generated upon excitation. This minireview discusses recent advances in the development of photochemical reactions for use in complex mixtures and highlights key considerations for future photochemical reaction designs.
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Affiliation(s)
- Michael T Taylor
- Department of Chemistry, University of Wyoming, 1000 E. University Ave., Laramie, WY 82071, USA
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15
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Lü Z, Li X, Li K, Ripani P, Shi X, Xu F, Wang M, Zhang L, Brunner T, Xu P, Niu Y. Nitazoxanide and related thiazolides induce cell death in cancer cells by targeting the 20S proteasome with novel binding modes. Biochem Pharmacol 2022; 197:114913. [PMID: 35032461 DOI: 10.1016/j.bcp.2022.114913] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/08/2021] [Accepted: 01/05/2022] [Indexed: 11/02/2022]
Abstract
Nitazoxanide and related thiazolides are a novel class of anti-infectious agents against protozoan parasites, bacteria and viruses. In recent years, it is demonstrated thatthiazolides also can induced cell cycle arrest and apoptotic cell death in cancer cells. Due to their fast proliferating nature, cancer cells highly depend on the proteasome system to remove aberrant proteins. Many of these aberrant proteins are regulators of cell cycle progression and apoptosis, such as the cyclins, BCL2 family members and nuclear factor of κB (NF-κB). Here, we demonstrate at both molecular and cellular levels that the 20S proteasome is a direct target of NTZ and other thiazolides. By concurrently inhibiting the multiple catalytic subunits of 20S proteasome, NTZ promotes cell cycle arrest and triggers cell death in colon cancer cells, either directly or a sensitizer to other anti-tumor agents, especially doxorubicin. We further show that the binding mode of NTZ in the β5 subunit of the 20S proteasome is different from that of bortezomib and other existing proteasome inhibitors. These findings provide new insights in the design of novel small molecular proteasome inhibitors as anti-tumor agents suitable for solid tumor treatment in an oral dosing form.
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Affiliation(s)
- Zirui Lü
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, Xueyuan Road 38, Beijing, 100191, China
| | - Xiaona Li
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, Xueyuan Road 38, Beijing, 100191, China
| | - Kebin Li
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, Xueyuan Road 38, Beijing, 100191, China
| | - Paola Ripani
- Biochemical Pharmacology, Department of Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Xiaomeng Shi
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Xueyuan Road 38, Beijing, 100191, China
| | - Fengrong Xu
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, Xueyuan Road 38, Beijing, 100191, China
| | - Mopei Wang
- Department of Tumor Chemotherapy and Radiation Sickness, Peking University Third Hospital, Beijing, 100191, China
| | - Liangren Zhang
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, Xueyuan Road 38, Beijing, 100191, China; State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Xueyuan Road 38, Beijing, 100191, China
| | - Thomas Brunner
- Biochemical Pharmacology, Department of Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Ping Xu
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, Xueyuan Road 38, Beijing, 100191, China.
| | - Yan Niu
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, Xueyuan Road 38, Beijing, 100191, China.
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16
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McKenna SM, Fay EM, McGouran JF. Flipping the Switch: Innovations in Inducible Probes for Protein Profiling. ACS Chem Biol 2021; 16:2719-2730. [PMID: 34779621 PMCID: PMC8689647 DOI: 10.1021/acschembio.1c00572] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Over the past two
decades, activity-based probes have enabled a
range of discoveries, including the characterization of new enzymes
and drug targets. However, their suitability in some labeling experiments
can be limited by nonspecific reactivity, poor membrane permeability,
or high toxicity. One method for overcoming these issues is through
the development of “inducible” activity-based probes.
These probes are added to samples in an unreactive state and require in situ transformation to their active form before labeling
can occur. In this Review, we discuss a variety of approaches to inducible
activity-based probe design, different means of probe activation,
and the advancements that have resulted from these applications. Additionally,
we highlight recent developments which may provide opportunities for
future inducible activity-based probe innovations.
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Affiliation(s)
- Sean M. McKenna
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, Dublin 2, Ireland
- Synthesis and Solid State Pharmaceutical Centre (SSPC), Bernal Institute, Limerick V94 T9PX, Ireland
| | - Ellen M. Fay
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, Dublin 2, Ireland
| | - Joanna F. McGouran
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, Dublin 2, Ireland
- Synthesis and Solid State Pharmaceutical Centre (SSPC), Bernal Institute, Limerick V94 T9PX, Ireland
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17
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Bhukta S, Gopinath P, Dandela R. Target identification of anticancer natural products using a chemical proteomics approach. RSC Adv 2021; 11:27950-27964. [PMID: 35480761 PMCID: PMC9038044 DOI: 10.1039/d1ra04283a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/26/2021] [Indexed: 12/14/2022] Open
Abstract
In recent years, there has been a strong demand worldwide for the identification and development of potential anticancer drugs based on natural products. Natural products have been explored for their diverse biological and therapeutic applications from ancient time. In order to enhance the efficacy and selectivity and to minimize the undesired side effects of anti cancer natural products (ANPs), it is essential to understand their target proteins and their mechanistic pathway. Chemical proteomics is one of the most powerful tools to connect ANP target identification and quantification where labeling and non-labeling based approaches have been used. Herein, we have discussed the various strategies to systemically develop selective ANP based chemical probes to characterise their specific and non-specific target proteins using a chemical proteomic approach in various cancer cell lysates.
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Affiliation(s)
- Swadhapriya Bhukta
- Department of Industrial and Engineering Chemistry, Institute of Chemical Technology Indianoil Odisha Campus, Samantpuri Bhubaneswar 751013 India
| | - Pushparathinam Gopinath
- Department of Chemistry, SRM-Institute of Science and Technology Kattankulathur 603203 Chennai Tamilnadu India
| | - Rambabu Dandela
- Department of Industrial and Engineering Chemistry, Institute of Chemical Technology Indianoil Odisha Campus, Samantpuri Bhubaneswar 751013 India
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18
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Kaminska M, Bruyat P, Malgorn C, Doladilhe M, Cassar‐Lajeunesse E, Fruchart Gaillard C, De Souza M, Beau F, Thai R, Correia I, Galat A, Georgiadis D, Lequin O, Dive V, Bregant S, Devel L. Ligand‐Directed Modification of Active Matrix Metalloproteases: Activity‐based Probes with no Photolabile Group. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Monika Kaminska
- Université Paris-Saclay CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS 91191 Gif-sur-Yvette France
| | - Pierrick Bruyat
- Université Paris-Saclay CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS 91191 Gif-sur-Yvette France
| | - Carole Malgorn
- Université Paris-Saclay CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS 91191 Gif-sur-Yvette France
| | - Marion Doladilhe
- Université Paris-Saclay CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS 91191 Gif-sur-Yvette France
| | - Evelyne Cassar‐Lajeunesse
- Université Paris-Saclay CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS 91191 Gif-sur-Yvette France
| | - Carole Fruchart Gaillard
- Université Paris-Saclay CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS 91191 Gif-sur-Yvette France
| | - Mélissa De Souza
- Université Paris-Saclay CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS 91191 Gif-sur-Yvette France
| | - Fabrice Beau
- Université Paris-Saclay CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS 91191 Gif-sur-Yvette France
| | - Robert Thai
- Université Paris-Saclay CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS 91191 Gif-sur-Yvette France
| | - Isabelle Correia
- CNRS, Laboratoire des Biomolécules, LBM Sorbonne Université Ecole Normale Supérieure PSL University 75005 Paris France
| | - Andrzej Galat
- Université Paris-Saclay CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS 91191 Gif-sur-Yvette France
| | - Dimitris Georgiadis
- Department of Chemistry Laboratory of Organic Chemistry University of Athens Panepistimiopolis Zografou 15771 Athens Greece
| | - Olivier Lequin
- CNRS, Laboratoire des Biomolécules, LBM Sorbonne Université Ecole Normale Supérieure PSL University 75005 Paris France
| | - Vincent Dive
- Université Paris-Saclay CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS 91191 Gif-sur-Yvette France
| | - Sarah Bregant
- Université Paris-Saclay CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS 91191 Gif-sur-Yvette France
| | - Laurent Devel
- Université Paris-Saclay CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS 91191 Gif-sur-Yvette France
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19
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Kaminska M, Bruyat P, Malgorn C, Doladilhe M, Cassar-Lajeunesse E, Fruchart Gaillard C, De Souza M, Beau F, Thai R, Correia I, Galat A, Georgiadis D, Lequin O, Dive V, Bregant S, Devel L. Ligand-Directed Modification of Active Matrix Metalloproteases: Activity-based Probes with no Photolabile Group. Angew Chem Int Ed Engl 2021; 60:18272-18279. [PMID: 34096148 DOI: 10.1002/anie.202106117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Indexed: 12/12/2022]
Abstract
Activity-based probes enable discrimination between the active enzyme and its inactive or inactivated counterparts. Since metalloproteases catalysis is non-covalent, activity-based probes targeting them have been systematically developed by decorating reversible inhibitors with photo-crosslinkers. By exploiting two types of ligand-guided chemistry, we identified novel activity-based probes capable of covalently modifying the active site of matrix metalloproteases (MMPs) without any external trigger. The ability of these probes to label recombinant MMPs was validated in vitro and the identity of the main labelling sites within their S3 ' region unambiguously assigned. We also demonstrated that our affinity probes can react with rhMMP12 at nanogram scale (that is, at 0.07 % (w/w)) in complex proteomes. Finally, this ligand-directed chemistry was successfully applied to label active MMP-12 secreted by eukaryote cells. We believe that this approach could be transferred more widely to many other metalloproteases, thus contributing to tackle their unresolved proteomic profiling in vivo.
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Affiliation(s)
- Monika Kaminska
- Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS, 91191, Gif-sur-Yvette, France
| | - Pierrick Bruyat
- Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS, 91191, Gif-sur-Yvette, France
| | - Carole Malgorn
- Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS, 91191, Gif-sur-Yvette, France
| | - Marion Doladilhe
- Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS, 91191, Gif-sur-Yvette, France
| | - Evelyne Cassar-Lajeunesse
- Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS, 91191, Gif-sur-Yvette, France
| | - Carole Fruchart Gaillard
- Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS, 91191, Gif-sur-Yvette, France
| | - Mélissa De Souza
- Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS, 91191, Gif-sur-Yvette, France
| | - Fabrice Beau
- Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS, 91191, Gif-sur-Yvette, France
| | - Robert Thai
- Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS, 91191, Gif-sur-Yvette, France
| | - Isabelle Correia
- CNRS, Laboratoire des Biomolécules, LBM, Sorbonne Université, Ecole Normale Supérieure, PSL University, 75005, Paris, France
| | - Andrzej Galat
- Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS, 91191, Gif-sur-Yvette, France
| | - Dimitris Georgiadis
- Department of Chemistry, Laboratory of Organic Chemistry, University of Athens, Panepistimiopolis, Zografou, 15771 Athens, Greece
| | - Olivier Lequin
- CNRS, Laboratoire des Biomolécules, LBM, Sorbonne Université, Ecole Normale Supérieure, PSL University, 75005, Paris, France
| | - Vincent Dive
- Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS, 91191, Gif-sur-Yvette, France
| | - Sarah Bregant
- Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS, 91191, Gif-sur-Yvette, France
| | - Laurent Devel
- Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS, 91191, Gif-sur-Yvette, France
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20
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Zhang HW, Lv C, Zhang LJ, Guo X, Shen YW, Nagle DG, Zhou YD, Liu SH, Zhang WD, Luan X. Application of omics- and multi-omics-based techniques for natural product target discovery. Biomed Pharmacother 2021; 141:111833. [PMID: 34175822 DOI: 10.1016/j.biopha.2021.111833] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/07/2021] [Accepted: 06/14/2021] [Indexed: 02/07/2023] Open
Abstract
Natural products continue to be an unparalleled source of pharmacologically active lead compounds because of their unprecedented structures and unique biological activities. Natural product target discovery is a vital component of natural product-based medicine translation and development and is required to understand and potentially reduce mechanisms that may be associated with off-target side effects and toxicity. Omics-based techniques, including genomics, transcriptomics, proteomics, metabolomics, and bioinformatics, have become recognized as effective tools needed to construct innovative strategies to discover natural product targets. Although considerable progress has been made, the successful discovery of natural product targets remains a challenging time-consuming process that has come to increasingly rely on the effective integration of multi-omics-based technologies to create emerging panomics (a.k.a., integrative omics, pan-omics, multiomics)-based strategies. This review summarizes a series of successful studies regarding the application of integrative omics-based methods in natural product target discovery. The advantages and disadvantages of each technique are discussed, with a particular focus on the systematic integration of multi-omics strategies. Further, emerging micro-scale single-cell-based techniques are introduced, especially to deal with minute natural product samples.
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Affiliation(s)
- Hong-Wei Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Chao Lv
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Li-Jun Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xin Guo
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yi-Wen Shen
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Dale G Nagle
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Department of BioMolecular Sciences and Research Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi, University-1848, MS 38677-1848, USA
| | - Yu-Dong Zhou
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA
| | - San-Hong Liu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Wei-Dong Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; School of Pharmacy, Second Military Medical University, Shanghai 200433, China.
| | - Xin Luan
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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21
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Scinto SL, Bilodeau DA, Hincapie R, Lee W, Nguyen SS, Xu M, am Ende CW, Finn MG, Lang K, Lin Q, Pezacki JP, Prescher JA, Robillard MS, Fox JM. Bioorthogonal chemistry. NATURE REVIEWS. METHODS PRIMERS 2021; 1:30. [PMID: 34585143 PMCID: PMC8469592 DOI: 10.1038/s43586-021-00028-z] [Citation(s) in RCA: 178] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/05/2021] [Indexed: 12/11/2022]
Abstract
Bioorthogonal chemistry represents a class of high-yielding chemical reactions that proceed rapidly and selectively in biological environments without side reactions towards endogenous functional groups. Rooted in the principles of physical organic chemistry, bioorthogonal reactions are intrinsically selective transformations not commonly found in biology. Key reactions include native chemical ligation and the Staudinger ligation, copper-catalysed azide-alkyne cycloaddition, strain-promoted [3 + 2] reactions, tetrazine ligation, metal-catalysed coupling reactions, oxime and hydrazone ligations as well as photoinducible bioorthogonal reactions. Bioorthogonal chemistry has significant overlap with the broader field of 'click chemistry' - high-yielding reactions that are wide in scope and simple to perform, as recently exemplified by sulfuryl fluoride exchange chemistry. The underlying mechanisms of these transformations and their optimal conditions are described in this Primer, followed by discussion of how bioorthogonal chemistry has become essential to the fields of biomedical imaging, medicinal chemistry, protein synthesis, polymer science, materials science and surface science. The applications of bioorthogonal chemistry are diverse and include genetic code expansion and metabolic engineering, drug target identification, antibody-drug conjugation and drug delivery. This Primer describes standards for reproducibility and data deposition, outlines how current limitations are driving new research directions and discusses new opportunities for applying bioorthogonal chemistry to emerging problems in biology and biomedicine.
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Affiliation(s)
- Samuel L. Scinto
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Didier A. Bilodeau
- Department of Chemistry and Biomolecular Science, University of Ottawa, Ottawa, Ontario, Canada
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Robert Hincapie
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Wankyu Lee
- Pfizer Worldwide Research and Development, Cambridge, MA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Sean S. Nguyen
- Department of Chemistry, University of California, Irvine, CA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Minghao Xu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | | | - M. G. Finn
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kathrin Lang
- Department of Chemistry, Technical University of Munich, Garching, Germany
- Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY, USA
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Science, University of Ottawa, Ottawa, Ontario, Canada
| | - Jennifer A. Prescher
- Department of Chemistry, University of California, Irvine, CA, USA
- Molecular Biology & Biochemistry, University of California, Irvine, CA, USA
| | | | - Joseph M. Fox
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
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22
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Qi Z, Li SS, Li L, Qin Q, Yang LM, Liang YK, Kang Y, Zhang XZ, Ma AJ, Peng JB. Palladium Catalyzed Cascade Azidation/Carbonylation of Aryl Halides with Sodium Azide for the Synthesis of Amides. Chem Asian J 2021; 16:503-506. [PMID: 33470007 DOI: 10.1002/asia.202001463] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/13/2021] [Indexed: 12/11/2022]
Abstract
Amide synthesis is one of the most important transformations in organic chemistry due to their ubiquitous presence in our daily life. In this communication, a palladium catalyzed cascade azidation/carbonylation of aryl halides for the synthesis of amides was developed. Both iodo- and bromobenzene derivatives were transformed to the corresponding amides using PdCl2 /xantphos as the catalyst system and sodium azide as the nitrogen-source. The reaction proceeds via a cascade azidation/carbonylation process. A range of alkyl and halogen substituted amides were prepared in moderate to good yields.
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Affiliation(s)
- Zhuang Qi
- School of Biotechnology and Health Sciences, Wuyi University, 529020, Jiangmen, Guangdong, P. R. China
| | - Shan-Shan Li
- School of Biotechnology and Health Sciences, Wuyi University, 529020, Jiangmen, Guangdong, P. R. China
| | - Lin Li
- School of Biotechnology and Health Sciences, Wuyi University, 529020, Jiangmen, Guangdong, P. R. China
| | - Qi Qin
- School of Biotechnology and Health Sciences, Wuyi University, 529020, Jiangmen, Guangdong, P. R. China
| | - Li-Miao Yang
- School of Biotechnology and Health Sciences, Wuyi University, 529020, Jiangmen, Guangdong, P. R. China
| | - Ying-Kang Liang
- School of Biotechnology and Health Sciences, Wuyi University, 529020, Jiangmen, Guangdong, P. R. China
| | - Yun Kang
- School of Biotechnology and Health Sciences, Wuyi University, 529020, Jiangmen, Guangdong, P. R. China
| | - Xiang-Zhi Zhang
- School of Biotechnology and Health Sciences, Wuyi University, 529020, Jiangmen, Guangdong, P. R. China
| | - Ai-Jun Ma
- School of Biotechnology and Health Sciences, Wuyi University, 529020, Jiangmen, Guangdong, P. R. China
| | - Jin-Bao Peng
- School of Biotechnology and Health Sciences, Wuyi University, 529020, Jiangmen, Guangdong, P. R. China
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23
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Hamilton AJ, Payne AD, Mocerino M, Gunosewoyo H. Imaging Cannabinoid Receptors: A Brief Collection of Covalent and Fluorescent Probes for CB1 and CB2 Receptors. Aust J Chem 2021. [DOI: 10.1071/ch21007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
There has been an expanding public interest towards the notion that modulation of the sophisticated endocannabinoid system can lead to various therapeutic benefits that are yet to be fully explored. In recent years, the drug discovery paradigm in this field has been largely based on the development of selective CB2 receptor agonists, avoiding the unwanted CB1 receptor-mediated psychoactive side effects. Mechanistically, target engagement studies are crucial for confirming the ligand–receptor interaction and the subsequent biological cascades that lead to the observed therapeutic effects. Concurrently, imaging techniques for visualisation of cannabinoid receptors are increasingly reported in the literature. Small molecule imaging tools ranging from phytocannabinoids such as tetrahydrocannabinol (THC) and cannabidiol (CBD) to the endocannabinoids as well as the purely synthetic cannabimimetics, have been explored to date with varying degrees of success. This Review will cover currently known photoactivatable, electrophilic, and fluorescent ligands for both the CB1 and CB2 receptors. Structural insights from techniques such as ligand-assisted protein structure (LAPS) and the discovery of novel allosteric modulators are significant additions for better understanding of the endocannabinoid system. There has also been a plethora of fluorescent conjugates that have been assessed for their binding to cannabinoid receptors as well as their potential for cellular imaging. More recently, bifunctional probes containing either fluorophores or electrophilic tags are becoming more prevalent in the literature. Collectively, these molecular tools are invaluable in demonstrating target engagement within the human endocannabinoid system.
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24
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Curry AM, Barton E, Kang W, Mongeluzi DV, Cen Y. Development of Second Generation Activity-Based Chemical Probes for Sirtuins. Molecules 2020; 26:molecules26010011. [PMID: 33375102 PMCID: PMC7792806 DOI: 10.3390/molecules26010011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/10/2020] [Accepted: 12/18/2020] [Indexed: 12/14/2022] Open
Abstract
NAD+ (nicotinamide adenine dinucleotide)-dependent protein deacylases, namely, the sirtuins, are important cell adaptor proteins that alter cell physiology in response to low calorie conditions. They are thought to mediate the beneficial effects of calorie restriction to extend longevity and improve health profiles. Novel chemical probes are highly desired for a better understanding of sirtuin’s roles in various biological processes. We developed a group of remarkably simple activity-based chemical probes for the investigation of active sirtuin content in complex native proteomes. These probes harbor a thioacyllysine warhead, a diazirine photoaffinity tag, as well as a terminal alkyne bioorthogonal functional group. Compared to their benzophenone-containing counterparts, these new probes demonstrated improved labeling efficiency and sensitivity, shortened irradiation time, and reduced background signal. They were applied to the labeling of individual recombinant proteins, protein mixtures, and whole cell lysate. These cell permeable small molecule probes also enabled the cellular imaging of sirtuin activity change. Taken together, our study provides new chemical biology tools and future drug discovery strategies for perturbing the activity of different sirtuin isoforms.
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Affiliation(s)
- Alyson M. Curry
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; (A.M.C.); (E.B.); (W.K.); (D.V.M.)
| | - Elizabeth Barton
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; (A.M.C.); (E.B.); (W.K.); (D.V.M.)
| | - Wenjia Kang
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; (A.M.C.); (E.B.); (W.K.); (D.V.M.)
| | - Daniel V. Mongeluzi
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; (A.M.C.); (E.B.); (W.K.); (D.V.M.)
| | - Yana Cen
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; (A.M.C.); (E.B.); (W.K.); (D.V.M.)
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
- Correspondence: ; Tel.: +1-804-828-7405
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25
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Verhelst SHL, Bonger KM, Willems LI. Bioorthogonal Reactions in Activity-Based Protein Profiling. Molecules 2020; 25:E5994. [PMID: 33352858 PMCID: PMC7765892 DOI: 10.3390/molecules25245994] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/27/2022] Open
Abstract
Activity-based protein profiling (ABPP) is a powerful technique to label and detect active enzyme species within cell lysates, cells, or whole animals. In the last two decades, a wide variety of applications and experimental read-out techniques have been pursued in order to increase our understanding of physiological and pathological processes, to identify novel drug targets, to evaluate selectivity of drugs, and to image probe targets in cells. Bioorthogonal chemistry has substantially contributed to the field of ABPP, as it allows the introduction of tags, which may be bulky or have unfavorable physicochemical properties, at a late stage in the experiment. In this review, we give an overview of the bioorthogonal reactions that have been implemented in ABPP, provide examples of applications of bioorthogonal chemistry in ABPP, and share some thoughts on future directions.
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Affiliation(s)
- Steven H. L. Verhelst
- Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven, Herestr. 49, Box 802, 3000 Leuven, Belgium
- AG Chemical Proteomics, Leibniz Institute for Analytical Sciences ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Kimberly M. Bonger
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Lianne I. Willems
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
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26
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Voorneveld J, Florea BI, Bakkum T, Mendowicz RJ, van der Veer MS, Gagestein B, van Kasteren SI, van der Stelt M, Overkleeft HS, Filippov DV. Olaparib-Based Photoaffinity Probes for PARP-1 Detection in Living Cells. Chembiochem 2020; 21:2431-2434. [PMID: 32282108 PMCID: PMC7496120 DOI: 10.1002/cbic.202000042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/11/2020] [Indexed: 12/31/2022]
Abstract
The poly-ADP-ribose polymerase (PARP) is a protein from the family of ADP-ribosyltransferases that catalyzes polyadenosine diphosphate ribose (ADPR) formation in order to attract the DNA repair machinery to sites of DNA damage. The inhibition of PARP activity by olaparib can cause cell death, which is of clinical relevance in some tumor types. This demonstrates that quantification of PARP activity in the context of living cells is of great importance. In this work, we present the design, synthesis and biological evaluation of photo-activatable affinity probes inspired by the olaparib molecule that are equipped with a diazirine for covalent attachment upon activation by UV light and a ligation handle for the addition of a reporter group of choice. SDS-PAGE, western blotting and label-free LC-MS/MS quantification analysis show that the probes target the PARP-1 protein and are selectively outcompeted by olaparib; this suggests that they bind in the same enzymatic pocket. Proteomics data are available via ProteomeXchange with identifier PXD018661.
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Affiliation(s)
- Jim Voorneveld
- Bio-organic Synthesis Group Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Bogdan I. Florea
- Bio-organic Synthesis Group Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Thomas Bakkum
- Bio-organic Synthesis Group Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Rafal J. Mendowicz
- Bio-organic Synthesis Group Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Miriam S. van der Veer
- Bio-organic Synthesis Group Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Berend Gagestein
- Bio-organic Synthesis Group Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Sander I. van Kasteren
- Bio-organic Synthesis Group Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Mario van der Stelt
- Bio-organic Synthesis Group Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Herman S. Overkleeft
- Bio-organic Synthesis Group Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Dmitri V. Filippov
- Bio-organic Synthesis Group Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
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27
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Basagni F, Rosini M, Decker M. Functionalized Cannabinoid Subtype 2 Receptor Ligands: Fluorescent, PET, Photochromic and Covalent Molecular Probes. ChemMedChem 2020; 15:1374-1389. [PMID: 32578963 PMCID: PMC7497013 DOI: 10.1002/cmdc.202000298] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Indexed: 01/01/2023]
Abstract
Cannabinoid subtype 2 receptors (CB2 Rs) are G protein-coupled receptors (GPCRs) belonging to the endocannabinoid system, a complex network of signalling pathways leading to the regulation of key physiological processes. Interestingly, CB2 Rs are strongly up-regulated in pathological conditions correlated with the onset of inflammatory events like cancer and neurodegenerative diseases. Therefore, CB2 Rs represent an important biological target for therapeutic as well as diagnostic purposes. No CB2 R-selective drugs are yet on the market, thus underlining a that deeper comprehension of CB2 Rs' complex activation pathways and their role in the regulation of diseases is needed. Herein, we report an overview of pharmacological and imaging tools such as fluorescent, positron emission tomography (PET), photochromic and covalent selective CB2 R ligands. These molecular probes can be used in vitro as well as in vivo to investigate and explore the unravelled role(s) of CB2 Rs, and they can help to design suitable CB2 R-targeted drugs.
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Affiliation(s)
- Filippo Basagni
- Pharmaceutical and Medicinal Chemistry Institute of Pharmacy and Food ChemistryJulius Maximilian University of WürzburgAm Hubland97074WürzburgGermany
- Department of Pharmacy and BiotechnologyUniversity of BolognaVia Belmeloro 640126BolognaItaly
| | - Michela Rosini
- Department of Pharmacy and BiotechnologyUniversity of BolognaVia Belmeloro 640126BolognaItaly
| | - Michael Decker
- Pharmaceutical and Medicinal Chemistry Institute of Pharmacy and Food ChemistryJulius Maximilian University of WürzburgAm Hubland97074WürzburgGermany
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28
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Nie P, Vartak A, Li YM. γ-Secretase inhibitors and modulators: Mechanistic insights into the function and regulation of γ-Secretase. Semin Cell Dev Biol 2020; 105:43-53. [PMID: 32249070 DOI: 10.1016/j.semcdb.2020.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 02/08/2023]
Abstract
Over two decades, γ-secretase has been the target for extensive therapeutic development due to its pivotal role in pathogenesis of Alzheimer's disease and cancer. However, it has proven to be a challenging task owing to its large set of substrates and our limited understanding of the enzyme's structural and mechanistic features. The scientific community is taking bigger strides towards solving this puzzle with recent advancement in techniques like cryogenic electron microscopy (cryo-EM) and photo-affinity labelling (PAL). This review highlights the significance of the PAL technique with multiple examples of photo-probes developed from γ-secretase inhibitors and modulators. The binding of these probes into active and/or allosteric sites of the enzyme has provided crucial information on the γ-secretase complex and improved our mechanistic understanding of this protease. Combining the knowledge of function and regulation of γ-secretase will be a decisive factor in developing novel γ-secretase modulators and biological therapeutics.
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Affiliation(s)
- Pengju Nie
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Pharmacology program, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10021, USA
| | - Abhishek Vartak
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yue-Ming Li
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Pharmacology program, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10021, USA.
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29
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Lee KM, Le P, Sieber SA, Hacker SM. Degrasyn exhibits antibiotic activity against multi-resistant Staphylococcus aureus by modifying several essential cysteines. Chem Commun (Camb) 2020; 56:2929-2932. [PMID: 32039420 DOI: 10.1039/c9cc09204h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Degrasyn inhibits deubiquitination enzymes and has anti-cancer activity. We here show that it also exhibits antimicrobial activity against multi-resistant Staphylococcus aureus. Structure activity relationship studies demonstrate an important role of the electrophilic α-cyanoacrylamide moiety as a Michael acceptor. A suite of chemical proteomic techniques unraveled binding of this moiety to various cysteine residues of essential proteins in a reversibly covalent manner.
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Affiliation(s)
- Kyu Myung Lee
- Center for Integrated Protein Science, Department of Chemistry and Chair of Organic Chemistry II, Technische Universität München, Garching bei München, Germany.
| | - Philipp Le
- Center for Integrated Protein Science, Department of Chemistry and Chair of Organic Chemistry II, Technische Universität München, Garching bei München, Germany.
| | - Stephan A Sieber
- Center for Integrated Protein Science, Department of Chemistry and Chair of Organic Chemistry II, Technische Universität München, Garching bei München, Germany.
| | - Stephan M Hacker
- Department of Chemistry, Technische Universität München, Garching bei München, Germany.
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30
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Parker CG, Pratt MR. Click Chemistry in Proteomic Investigations. Cell 2020; 180:605-632. [PMID: 32059777 PMCID: PMC7087397 DOI: 10.1016/j.cell.2020.01.025] [Citation(s) in RCA: 193] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/09/2020] [Accepted: 01/16/2020] [Indexed: 01/20/2023]
Abstract
Despite advances in genetic and proteomic techniques, a complete portrait of the proteome and its complement of dynamic interactions and modifications remains a lofty, and as of yet, unrealized, objective. Specifically, traditional biological and analytical approaches have not been able to address key questions relating to the interactions of proteins with small molecules, including drugs, drug candidates, metabolites, or protein post-translational modifications (PTMs). Fortunately, chemists have bridged this experimental gap through the creation of bioorthogonal reactions. These reactions allow for the incorporation of chemical groups with highly selective reactivity into small molecules or protein modifications without perturbing their biological function, enabling the selective installation of an analysis tag for downstream investigations. The introduction of chemical strategies to parse and enrich subsets of the "functional" proteome has empowered mass spectrometry (MS)-based methods to delve more deeply and precisely into the biochemical state of cells and its perturbations by small molecules. In this Primer, we discuss how one of the most versatile bioorthogonal reactions, "click chemistry", has been exploited to overcome limitations of biological approaches to enable the selective marking and functional investigation of critical protein-small-molecule interactions and PTMs in native biological environments.
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Affiliation(s)
- Christopher G Parker
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA.
| | - Matthew R Pratt
- Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
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31
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Deng H, Lei Q, Wu Y, He Y, Li W. Activity-based protein profiling: Recent advances in medicinal chemistry. Eur J Med Chem 2020; 191:112151. [PMID: 32109778 DOI: 10.1016/j.ejmech.2020.112151] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/04/2020] [Accepted: 02/13/2020] [Indexed: 02/05/2023]
Abstract
Activity-based protein profiling (ABPP) has become an emerging chemical proteomic approach to illustrate the interaction mechanisms between compounds and proteins. This approach has combined organic synthesis, biochemistry, cell biology, biophysics and bioinformatics to accelerate the process of drug discovery in target identification and validation, as well as in the stage of lead discovery and optimization. This review will summarize new developments and applications of ABPP in medicinal chemistry. Here, we mainly described the design principles of activity-base probes (ABPs) and general workflows of ABPP approach. Moreover, we discussed various basic and advanced ABPP strategies and their applications in medicinal chemistry, including competitive and comparative ABPP, two-step ABPP, fluorescence polarization ABPP (FluoPol-ABPP) and ABPs for visualization. In conclusion, this review will give a general overview of the applications of ABPP as a powerful and efficient technique in medicinal chemistry.
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Affiliation(s)
- Hui Deng
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Qian Lei
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yangping Wu
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yang He
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
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32
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Eyermann B, Meixner M, Brötz‐Oesterhelt H, Antes I, Sieber SA. Acyldepsipeptide Probes Facilitate Specific Detection of Caseinolytic Protease P Independent of Its Oligomeric and Activity State. Chembiochem 2020; 21:235-240. [PMID: 31487112 PMCID: PMC7003903 DOI: 10.1002/cbic.201900477] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Indexed: 12/21/2022]
Abstract
Caseinolytic protease P (ClpP) is a tetradecameric peptidase that assembles with chaperones such as ClpX to gain proteolytic activity. Acyldepsipeptides (ADEPs) are small-molecule mimics of ClpX that bind into hydrophobic pockets on the apical site of the complex, thereby activating ClpP. Detection of ClpP has so far been facilitated with active-site-directed probes which depend on the activity and oligomeric state of the complex. To expand the scope of ClpP labeling, we took a stepwise synthetic approach toward customized ADEP photoprobes. Structure-activity relationship studies with small fragments and ADEP derivatives paired with modeling studies revealed the design principles for suitable probe molecules. The derivatives were tested for activation of ClpP and subsequently applied in labeling studies of the wild-type peptidase as well as enzymes bearing mutations at the active site and an oligomerization sensor. Satisfyingly, the ADEP photoprobes provided a labeling readout of ClpP independent of its activity and oligomeric state.
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Affiliation(s)
- Barbara Eyermann
- Department ChemieTechnische Universität MünchenLichtenbergstrasse 485748GarchingGermany
| | - Maximilian Meixner
- Department für BiowissenschaftenTechnische Universität MünchenEmil-Erlenmeyer-Forum 885354FreisingGermany
| | - Heike Brötz‐Oesterhelt
- Interfaculty Institute of Microbiology and Infection MedicineMicrobial Bioactive CompoundsUniversity of TübingenAuf der Morgenstelle 28, E-Bau, Ebene 872076TübingenGermany
| | - Iris Antes
- Department für BiowissenschaftenTechnische Universität MünchenEmil-Erlenmeyer-Forum 885354FreisingGermany
| | - Stephan A. Sieber
- Department ChemieTechnische Universität MünchenLichtenbergstrasse 485748GarchingGermany
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33
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Xu J, Li X, Ding K, Li Z. Applications of Activity-Based Protein Profiling (ABPP) and Bioimaging in Drug Discovery. Chem Asian J 2019; 15:34-41. [PMID: 31762171 DOI: 10.1002/asia.201901500] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Indexed: 01/12/2023]
Abstract
Activity-based protein profiling (ABPP) and bioimaging have been developed in recent years as powerful technologies in drug discovery. Specifically, both approaches can be applied in critical steps of drug development, such as therapy target discovery, high-throughput drug screening and target identification of bioactive molecules. We have been focused on the development of various strategies that enable simultaneous activity-based protein profiling and bioimaging studies, thus facilitating an understanding of drug actions and potential toxicities. In this Minireview, we summarize these novel strategies and applications, with the aim of promoting these technologies in drug discovery.
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Affiliation(s)
- Jiaqian Xu
- School of Pharmacy, Jinan University, Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, 601 Huangpu Avenue West, Guangzhou, 510632, China.,Department of Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Hong Kong SAR, 999077, China
| | - Xiaoqian Li
- School of Pharmacy, Jinan University, Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Ke Ding
- School of Pharmacy, Jinan University, Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Zhengqiu Li
- School of Pharmacy, Jinan University, Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, 601 Huangpu Avenue West, Guangzhou, 510632, China
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34
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Kirsch VC, Orgler C, Braig S, Jeremias I, Auerbach D, Müller R, Vollmar AM, Sieber SA. Der zytotoxische Naturstoff Vioprolid A interagiert mit dem für die Ribosomen‐Biogenese essentiellen nukleolären Protein 14. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201911158] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Volker C. Kirsch
- Center for Integrated Protein Science (CIPSM) Department Chemie Technische Universität München (TUM) Lichtenbergstraße 4 85747 Garching Deutschland
| | - Christina Orgler
- Department für Pharmazie Pharmazeutische Biologie Ludwig-Maximilians-Universität München (LMU) Butenandtstraße 5–13 81377 München Deutschland
| | - Simone Braig
- Department für Pharmazie Pharmazeutische Biologie Ludwig-Maximilians-Universität München (LMU) Butenandtstraße 5–13 81377 München Deutschland
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt Marchioninistraße 25 81377 München Deutschland
- Dr. von Hauner Kinderkrankenhaus Ludwig-Maximilians-Universität München (LMU) Lindwurmstraße 4 80337 München Deutschland
| | - David Auerbach
- Helmholtz Institut für Pharmazeutische Forschung Saarland (HIPS) Helmholtz Center für Infektionsforschung und Department Pharmazie Universität des Saarlandes Campus Gebäude E8.1 66123 Saarbrücken Deutschland
| | - Rolf Müller
- Helmholtz Institut für Pharmazeutische Forschung Saarland (HIPS) Helmholtz Center für Infektionsforschung und Department Pharmazie Universität des Saarlandes Campus Gebäude E8.1 66123 Saarbrücken Deutschland
| | - Angelika M. Vollmar
- Department für Pharmazie Pharmazeutische Biologie Ludwig-Maximilians-Universität München (LMU) Butenandtstraße 5–13 81377 München Deutschland
| | - Stephan A. Sieber
- Center for Integrated Protein Science (CIPSM) Department Chemie Technische Universität München (TUM) Lichtenbergstraße 4 85747 Garching Deutschland
- Helmholtz Institut für Pharmazeutische Forschung Saarland (HIPS) Helmholtz Center für Infektionsforschung und Department Pharmazie Universität des Saarlandes Campus Gebäude E8.1 66123 Saarbrücken Deutschland
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35
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Kirsch VC, Orgler C, Braig S, Jeremias I, Auerbach D, Müller R, Vollmar AM, Sieber SA. The Cytotoxic Natural Product Vioprolide A Targets Nucleolar Protein 14, Which Is Essential for Ribosome Biogenesis. Angew Chem Int Ed Engl 2019; 59:1595-1600. [PMID: 31658409 PMCID: PMC7004033 DOI: 10.1002/anie.201911158] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 10/24/2019] [Indexed: 11/23/2022]
Abstract
Novel targets are needed for treatment of devastating diseases such as cancer. For decades, natural products have guided innovative therapies by addressing diverse pathways. Inspired by the potent cytotoxic bioactivity of myxobacterial vioprolides A–D, we performed in‐depth studies on their mode of action. Based on its prominent potency against human acute lymphoblastic leukemia (ALL) cells, we conducted thermal proteome profiling (TPP) and deciphered the target proteins of the most active derivative vioprolide A (VioA) in Jurkat cells. Nucleolar protein 14 (NOP14), which is essential in ribosome biogenesis, was confirmed as a specific target of VioA by a suite of proteomic and biological follow‐up experiments. Given its activity against ALL cells compared to healthy lymphocytes, VioA exhibits unique therapeutic potential for anticancer therapy through a novel mode of action.
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Affiliation(s)
- Volker C Kirsch
- Center for Integrated Protein Science (CIPSM), Department Chemie, Technische Universität München (TUM), Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Christina Orgler
- Department of Pharmacy, Pharmaceutical Biology, Ludwig-Maximilian-University of Munich (LMU), Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Simone Braig
- Department of Pharmacy, Pharmaceutical Biology, Ludwig-Maximilian-University of Munich (LMU), Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchioninistrasse 25, 81377, München, Germany.,Dr. von Hauner Children's Hospital, Ludiwg-Maximilian-University of Munich (LMU), Lindwurmstrasse 4, 80337, Munich, Germany
| | - David Auerbach
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research and Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research and Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Angelika M Vollmar
- Department of Pharmacy, Pharmaceutical Biology, Ludwig-Maximilian-University of Munich (LMU), Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Stephan A Sieber
- Center for Integrated Protein Science (CIPSM), Department Chemie, Technische Universität München (TUM), Lichtenbergstrasse 4, 85747, Garching, Germany.,Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research and Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
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36
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Singha M, Roy S, Moirangthem R, Das AK, Basak A. Naphthalimide-Based Template for Inhibitor Screening via Cross-Linking and In-Gel Fluorescence: A Case Study against HCA II. ACS OMEGA 2019; 4:11914-11920. [PMID: 31460302 PMCID: PMC6681978 DOI: 10.1021/acsomega.9b01044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 06/26/2019] [Indexed: 06/10/2023]
Abstract
We describe a rapid electrophoresis-based method for profiling of carbonic anhydrase inhibitors. In addition to the pharmacophore moiety intended for reversible interaction with a target enzyme, a fluorescent template with a built-in azide group for photoaffinity labeling is also included as a part of the inhibitor design. Following incubation and irradiation, gel electrophoresis with visualization under UV allows assessment of the efficiency of cross-linking. The relative efficiency of cross-linking of various probes can be regarded as a reflection of their inhibition potencies, an assumption supported by the trend in their IC50/K i values. The method has the advantage of being applicable to impure enzyme preparations and also can be used to screen several inhibitors including their promiscuity in parallel in a short time as has been currently demonstrated with HCA II.
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Affiliation(s)
- Monisha Singha
- Department
of Chemistry, School of Bioscience, and Department of Biotechnology Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Sayantani Roy
- Department
of Chemistry, School of Bioscience, and Department of Biotechnology Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Ravina Moirangthem
- Department
of Chemistry, School of Bioscience, and Department of Biotechnology Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Amit K. Das
- Department
of Chemistry, School of Bioscience, and Department of Biotechnology Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Amit Basak
- Department
of Chemistry, School of Bioscience, and Department of Biotechnology Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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37
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Prevet H, Collins I. Labelled chemical probes for demonstrating direct target engagement in living systems. Future Med Chem 2019; 11:1195-1224. [PMID: 31280668 DOI: 10.4155/fmc-2018-0370] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2024] Open
Abstract
Demonstrating target engagement in living systems can help drive successful drug discovery. Target engagement and occupancy studies in cells confirm direct binding of a ligand to its intended target protein and provide the binding affinity. Combined with biomarkers to measure the functional consequences of target engagement, these experiments can increase confidence in the relationship between in vitro pharmacology and observed biological effects. In this review, we focus on chemically and radioactively labelled probes as key reagents for performing such experiments. Using recent examples, we examine how the labelled probes have been employed in combination with unlabelled ligands to quantify target engagement in cells and in animals. Finally, we consider future developments of this emerging methodology.
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Affiliation(s)
- Hugues Prevet
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Ian Collins
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP, UK
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38
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Halloran MW, Lumb JP. Recent Applications of Diazirines in Chemical Proteomics. Chemistry 2019; 25:4885-4898. [PMID: 30444029 DOI: 10.1002/chem.201805004] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/12/2018] [Indexed: 02/06/2023]
Abstract
The elucidation of substrate-protein interactions is an important component of the drug development process. Due to the complexity of native cellular environments, elucidating these fundamental biochemical interactions remains challenging. Photoaffinity labeling (PAL) is a versatile technique that can provide insight into ligand-target interactions. By judicious modification of substrates with a photoreactive group, PAL creates a covalent crosslink between a substrate and its biological target following UV-irradiation. Among the commonly employed photoreactive groups, diazirines have emerged as the gold standard. In this Minireview, recent developments in the field of diazirine-based photoaffinity labeling will be discussed, with emphasis being placed on their applications in chemical proteomic studies.
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Affiliation(s)
- Matthew W Halloran
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
| | - Jean-Philip Lumb
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
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39
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Van Kersavond T, Konopatzki R, Chakrabarty S, Blank-Landeshammer B, Sickmann A, Verhelst SHL. Short Peptides with Uncleavable Peptide Bond Mimetics as Photoactivatable Caspase-3 Inhibitors. Molecules 2019; 24:E206. [PMID: 30626051 PMCID: PMC6337261 DOI: 10.3390/molecules24010206] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 12/28/2018] [Accepted: 01/03/2019] [Indexed: 12/31/2022] Open
Abstract
Chemical probes that covalently interact with proteases have found increasing use for the study of protease function and localization. The design and synthesis of such probes is still a bottleneck, as the strategies to target different families are highly diverse. We set out to design and synthesize chemical probes based on protease substrate specificity with inclusion of an uncleavable peptide bond mimic and a photocrosslinker for covalent modification of the protease target. With caspase-3 as a model target protease, we designed reduced amide and triazolo peptides as substrate mimetics, whose sequences can be conveniently constructed by modified solid phase peptide synthesis. We found that these probes inhibited the caspase-3 activity, but did not form a covalent bond. It turned out that the reduced amide mimics, upon irradiation with a benzophenone as photosensitizer, are oxidized and form low concentrations of peptide aldehydes, which then act as inhibitors of caspase-3. This type of photoactivation may be utilized in future photopharmacology experiments to form protease inhibitors at a precise time and location.
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Affiliation(s)
- Tim Van Kersavond
- Leibniz-Institut für Analytische Wissenschaften ISAS, Otto-Hahn-Str. 6b, 44227 Dortmund, Germany.
| | - Raphael Konopatzki
- Leibniz-Institut für Analytische Wissenschaften ISAS, Otto-Hahn-Str. 6b, 44227 Dortmund, Germany.
| | - Suravi Chakrabarty
- Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, KU Leuven-University of Leuven, Herestraat 49 Box 802, 3000 Leuven, Belgium.
| | | | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften ISAS, Otto-Hahn-Str. 6b, 44227 Dortmund, Germany.
| | - Steven H L Verhelst
- Leibniz-Institut für Analytische Wissenschaften ISAS, Otto-Hahn-Str. 6b, 44227 Dortmund, Germany.
- Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, KU Leuven-University of Leuven, Herestraat 49 Box 802, 3000 Leuven, Belgium.
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40
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Chen Y, Topp EM. Photolytic Labeling and Its Applications in Protein Drug Discovery and Development. J Pharm Sci 2018; 108:791-797. [PMID: 30339867 DOI: 10.1016/j.xphs.2018.10.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 11/19/2022]
Abstract
In this mini-review, the major types of photolytic labeling reagents are presented together with their reaction mechanisms. The applications of photolytic labeling in protein drug discovery and development are then discussed; these have expanded from studies of protein-protein interactions in vivo to protein-matrix interactions in lyophilized solids. The mini-review concludes with recommendations for further development of the approach, which include the need for new and more chemically diverse photo-reactive reagents and better understanding of the mechanisms of photolytic labeling reactions in various media.
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Affiliation(s)
- Yuan Chen
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907
| | - Elizabeth M Topp
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907.
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41
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Wang Y, Fang Z, Chen X, Wang Y. Mild Dirhodium(II)-Catalyzed Chemo- and Regioselective Azidation of Arenes. Org Lett 2018; 20:5732-5736. [DOI: 10.1021/acs.orglett.8b02446] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Yi Wang
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Zaixiang Fang
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Xiaochuan Chen
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Yuanhua Wang
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
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42
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Tomlinson MJ, Krout D, Pramod AB, Lever JR, Newman AH, Henry LK, Vaughan RA. Identification of the benztropine analog [ 125I]GA II 34 binding site on the human dopamine transporter. Neurochem Int 2018; 123:34-45. [PMID: 30125594 DOI: 10.1016/j.neuint.2018.08.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/10/2018] [Accepted: 08/14/2018] [Indexed: 12/21/2022]
Abstract
The dopamine transporter (DAT) is a neuronal membrane protein that is responsible for reuptake of dopamine (DA) from the synapse and functions as a major determinant in control of DA neurotransmission. Cocaine and many psychostimulant drugs bind to DAT and block reuptake, inducing DA overflow that forms the neurochemical basis for euphoria and addiction. Paradoxically, however, some ligands such as benztropine (BZT) bind to DAT and inhibit reuptake but do not produce these effects, and it has been hypothesized that differential mechanisms of binding may stabilize specific transporter conformations that affect downstream neurochemical or behavioral outcomes. To investigate the binding mechanisms of BZT on DAT we used the photoaffinity BZT analog [125I]N-[n-butyl-4-(4‴-azido-3‴-iodophenyl)]-4',4″-difluoro-3α-(diphenylmethoxy)tropane ([125I]GA II 34) to identify the site of cross-linking and predict the binding pose relative to that of previously-examined cocaine photoaffinity analogs. Biochemical findings show that adduction of [125I]GA II 34 occurs at residues Asp79 or Leu80 in TM1, with molecular modeling supporting adduction to Leu80 and a pharmacophore pose in the central S1 site similar to that of cocaine and cocaine analogs. Substituted cysteine accessibility method protection analyses verified these findings, but identified some differences in structural stabilization relative to cocaine that may relate to BZT neurochemical outcomes.
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Affiliation(s)
- Michael J Tomlinson
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, United States
| | - Danielle Krout
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, United States
| | - Akula Bala Pramod
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, United States
| | - John R Lever
- Research Service, Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, 65201, United States; Department of Radiology and Radiopharmaceutical Sciences Institute, University of Missouri, Columbia, MO 65211, United States
| | - Amy Hauck Newman
- Medicinal Chemistry Section, National Institute on Drug Abuse - Intramural Research Program, Baltimore, MD 21224, United States
| | - L Keith Henry
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, United States.
| | - Roxanne A Vaughan
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, United States.
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43
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Ge SS, Chen B, Wu YY, Long QS, Zhao YL, Wang PY, Yang S. Current advances of carbene-mediated photoaffinity labeling in medicinal chemistry. RSC Adv 2018; 8:29428-29454. [PMID: 35547988 PMCID: PMC9084484 DOI: 10.1039/c8ra03538e] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/07/2018] [Indexed: 12/21/2022] Open
Abstract
Photoaffinity labeling (PAL) in combination with a chemical probe to covalently bind its target upon UV irradiation has demonstrated considerable promise in drug discovery for identifying new drug targets and binding sites. In particular, carbene-mediated photoaffinity labeling (cmPAL) has been widely used in drug target identification owing to its excellent photolabeling efficiency, minimal steric interference and longer excitation wavelength. Specifically, diazirines, which are among the precursors of carbenes and have higher carbene yields and greater chemical stability than diazo compounds, have proved to be valuable photolabile reagents in a diverse range of biological systems. This review highlights current advances of cmPAL in medicinal chemistry, with a focus on structures and applications for identifying small molecule-protein and macromolecule-protein interactions and ligand-gated ion channels, coupled with advances in the discovery of targets and inhibitors using carbene precursor-based biological probes developed in recent decades.
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Affiliation(s)
- Sha-Sha Ge
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Biao Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Yuan-Yuan Wu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Qing-Su Long
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Yong-Liang Zhao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Pei-Yi Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Song Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
- College of Pharmacy, East China University of Science & Technology Shanghai 200237 China
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44
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Hofbauer B, Vomacka J, Stahl M, Korotkov VS, Jennings MC, Wuest WM, Sieber SA. Dual Inhibitor of Staphylococcus aureus Virulence and Biofilm Attenuates Expression of Major Toxins and Adhesins. Biochemistry 2018; 57:1814-1820. [PMID: 29451388 DOI: 10.1021/acs.biochem.7b01271] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Staphylococcus aureus is a major bacterial pathogen that invades and damages host tissue by the expression of devastating toxins. We here performed a phenotypic screen of 35 molecules that were structurally inspired by previous hydroxyamide-based S. aureus virulence inhibitors compiled from commercial sources or designed and synthesized de novo. One of the most potent compounds, AV73, not only reduced hemolytic alpha-hemolysin production in S. aureus but also impeded in vitro biofilm formation. The effect of AV73 on bacterial proteomes and extracellular protein levels was analyzed by quantitative proteomics and revealed a significant down-regulation of major virulence and biofilm promoting proteins. To elucidate the mode of action of AV73, target identification was performed using affinity-based protein profiling (AfBPP), where among others YidC was identified as a target.
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Affiliation(s)
- Barbara Hofbauer
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Institute of Advanced Studies (IAS) , Technische Universität München (TUM) , Lichtenbergstraße 4 , D-85747 Garching , Germany
| | - Jan Vomacka
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Institute of Advanced Studies (IAS) , Technische Universität München (TUM) , Lichtenbergstraße 4 , D-85747 Garching , Germany
| | - Matthias Stahl
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Institute of Advanced Studies (IAS) , Technische Universität München (TUM) , Lichtenbergstraße 4 , D-85747 Garching , Germany
| | - Vadim S Korotkov
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Institute of Advanced Studies (IAS) , Technische Universität München (TUM) , Lichtenbergstraße 4 , D-85747 Garching , Germany
| | - Megan C Jennings
- Department of Chemistry , Temple University , 1910 North 13th Street , Philadelphia , Pennsylvania 19122 , United States
| | - William M Wuest
- Department of Chemistry , Temple University , 1910 North 13th Street , Philadelphia , Pennsylvania 19122 , United States
| | - Stephan A Sieber
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Institute of Advanced Studies (IAS) , Technische Universität München (TUM) , Lichtenbergstraße 4 , D-85747 Garching , Germany
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45
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Soethoudt M, Stolze SC, Westphal MV, van Stralen L, Martella A, van Rooden EJ, Guba W, Varga ZV, Deng H, van Kasteren SI, Grether U, IJzerman AP, Pacher P, Carreira EM, Overkleeft HS, Ioan-Facsinay A, Heitman LH, van der Stelt M. Selective Photoaffinity Probe That Enables Assessment of Cannabinoid CB 2 Receptor Expression and Ligand Engagement in Human Cells. J Am Chem Soc 2018; 140:6067-6075. [PMID: 29420021 PMCID: PMC5958339 DOI: 10.1021/jacs.7b11281] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
![]()
Chemical
tools and methods that report on G protein-coupled receptor
(GPCR) expression levels and receptor occupancy by small molecules
are highly desirable. We report the development of LEI121 as a photoreactive
probe to study the type 2 cannabinoid receptor (CB2R),
a promising GPCR to treat tissue injury and inflammatory diseases.
LEI121 is the first CB2R-selective bifunctional probe that
covalently captures CB2R upon photoactivation. An incorporated
alkyne serves as ligation handle for the introduction of reporter
groups. LEI121 enables target engagement studies and visualization
of endogenously expressed CB2R in HL-60 as well as primary
human immune cells using flow cytometry. Our findings show that strategically
functionalized probes allow monitoring of endogenous GPCR expression
and engagement in human cells using tandem photoclick chemistry and
hold promise as biomarkers in translational drug discovery.
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Affiliation(s)
| | | | - Matthias V Westphal
- Laboratorium für Organische Chemie , Eidgenössische Technische Hochschule Zürich , Vladimir-Prelog-Weg 3 , Zürich 8093 , Switzerland
| | - Luuk van Stralen
- Department of Rheumatology , Leiden University Medical Center , Albinusdreef 2 , Leiden 2333 ZA , The Netherlands
| | | | | | - Wolfgang Guba
- Roche Innovation Center Basel , F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124 , Basel 4070 , Switzerland
| | - Zoltan V Varga
- Laboratory of Cardiovascular Physiology and Tissue Injury , National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health , 5625 Fishers Lane , Rockville , Maryland 20852 , United States
| | | | | | - Uwe Grether
- Roche Innovation Center Basel , F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124 , Basel 4070 , Switzerland
| | | | - Pal Pacher
- Laboratory of Cardiovascular Physiology and Tissue Injury , National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health , 5625 Fishers Lane , Rockville , Maryland 20852 , United States
| | - Erick M Carreira
- Laboratorium für Organische Chemie , Eidgenössische Technische Hochschule Zürich , Vladimir-Prelog-Weg 3 , Zürich 8093 , Switzerland
| | | | - Andreea Ioan-Facsinay
- Department of Rheumatology , Leiden University Medical Center , Albinusdreef 2 , Leiden 2333 ZA , The Netherlands
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Atzrodt J, Derdau V, Kerr WJ, Reid M. Deuterium- und tritiummarkierte Verbindungen: Anwendungen in den modernen Biowissenschaften. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201704146] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jens Atzrodt
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry; Industriepark Höchst, G876 65926 Frankfurt Deutschland
| | - Volker Derdau
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry; Industriepark Höchst, G876 65926 Frankfurt Deutschland
| | - William J. Kerr
- Department of Pure and Applied Chemistry, WestCHEM; University of Strathclyde; 295 Cathedral Street Glasgow Scotland G1 1XL Großbritannien
| | - Marc Reid
- Department of Pure and Applied Chemistry, WestCHEM; University of Strathclyde; 295 Cathedral Street Glasgow Scotland G1 1XL Großbritannien
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47
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Atzrodt J, Derdau V, Kerr WJ, Reid M. Deuterium- and Tritium-Labelled Compounds: Applications in the Life Sciences. Angew Chem Int Ed Engl 2018; 57:1758-1784. [PMID: 28815899 DOI: 10.1002/anie.201704146] [Citation(s) in RCA: 407] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 07/27/2017] [Indexed: 12/19/2022]
Abstract
Hydrogen isotopes are unique tools for identifying and understanding biological and chemical processes. Hydrogen isotope labelling allows for the traceless and direct incorporation of an additional mass or radioactive tag into an organic molecule with almost no changes in its chemical structure, physical properties, or biological activity. Using deuterium-labelled isotopologues to study the unique mass-spectrometric patterns generated from mixtures of biologically relevant molecules drastically simplifies analysis. Such methods are now providing unprecedented levels of insight in a wide and continuously growing range of applications in the life sciences and beyond. Tritium (3 H), in particular, has seen an increase in utilization, especially in pharmaceutical drug discovery. The efforts and costs associated with the synthesis of labelled compounds are more than compensated for by the enhanced molecular sensitivity during analysis and the high reliability of the data obtained. In this Review, advances in the application of hydrogen isotopes in the life sciences are described.
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Affiliation(s)
- Jens Atzrodt
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry, Industriepark Höchst, G876, 65926, Frankfurt, Germany
| | - Volker Derdau
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry, Industriepark Höchst, G876, 65926, Frankfurt, Germany
| | - William J Kerr
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow, Scotland, G1 1XL, UK
| | - Marc Reid
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow, Scotland, G1 1XL, UK
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48
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Krout D, Pramod AB, Dahal RA, Tomlinson MJ, Sharma B, Foster JD, Zou MF, Boatang C, Newman AH, Lever JR, Vaughan RA, Henry LK. Inhibitor mechanisms in the S1 binding site of the dopamine transporter defined by multi-site molecular tethering of photoactive cocaine analogs. Biochem Pharmacol 2017; 142:204-215. [PMID: 28734777 DOI: 10.1016/j.bcp.2017.07.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 07/17/2017] [Indexed: 10/19/2022]
Abstract
Dopamine transporter (DAT) blockers like cocaine and many other abused and therapeutic drugs bind and stabilize an inactive form of the transporter inhibiting reuptake of extracellular dopamine (DA). The resulting increases in DA lead to the ability of these drugs to induce psychomotor alterations and addiction, but paradoxical findings in animal models indicate that not all DAT antagonists induce cocaine-like behavioral outcomes. How this occurs is not known, but one possibility is that uptake inhibitors may bind at multiple locations or in different poses to stabilize distinct conformational transporter states associated with differential neurochemical endpoints. Understanding the molecular mechanisms governing the pharmacological inhibition of DAT is therefore key for understanding the requisite interactions for behavioral modulation and addiction. Previously, we leveraged complementary computational docking, mutagenesis, peptide mapping, and substituted cysteine accessibility strategies to identify the specific adduction site and binding pose for the crosslinkable, photoactive cocaine analog, RTI 82, which contains a photoactive azide attached at the 2β position of the tropane pharmacophore. Here, we utilize similar methodology with a different cocaine analog N-[4-(4-azido-3-I-iodophenyl)-butyl]-2-carbomethoxy-3-(4-chlorophenyl)tropane, MFZ 2-24, where the photoactive azide is attached to the tropane nitrogen. In contrast to RTI 82, which crosslinked into residue Phe319 of transmembrane domain (TM) 6, our findings show that MFZ 2-24 adducts to Leu80 in TM1 with modeling and biochemical data indicating that MFZ 2-24, like RTI 82, occupies the central S1 binding pocket with the (+)-charged tropane ring nitrogen coordinating with the (-)-charged carboxyl side chain of Asp79. The superimposition of the tropane ring in the three-dimensional binding poses of these two distinct ligands provides strong experimental evidence for cocaine binding to DAT in the S1 site and the importance of the tropane moiety in competitive mechanisms of DA uptake inhibition. These findings set a structure-function baseline for comparison of typical and atypical DAT inhibitors and how their interactions with DAT could lead to the loss of cocaine-like behaviors.
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Affiliation(s)
- Danielle Krout
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, USA
| | - Akula Bala Pramod
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, USA
| | - Rejwi Acharya Dahal
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, USA
| | - Michael J Tomlinson
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, USA
| | - Babita Sharma
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, USA
| | - James D Foster
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, USA
| | - Mu-Fa Zou
- Medicinal Chemistry Section, National Institute on Drug Abuse - Intramural Research Program, Baltimore, MD 21224, USA
| | - Comfort Boatang
- Medicinal Chemistry Section, National Institute on Drug Abuse - Intramural Research Program, Baltimore, MD 21224, USA
| | - Amy Hauck Newman
- Medicinal Chemistry Section, National Institute on Drug Abuse - Intramural Research Program, Baltimore, MD 21224, USA
| | - John R Lever
- Research Service, Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, 65201, USA; Department of Radiology and Radiopharmaceutical Sciences Institute, University of Missouri, Columbia, MO 65211, USA
| | - Roxanne A Vaughan
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, USA.
| | - L Keith Henry
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, USA.
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49
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Fetzer C, Korotkov VS, Thänert R, Lee KM, Neuenschwander M, von Kries JP, Medina E, Sieber SA. Verringerung der Virulenz von multiresistentem Staphylococcus aureus
mithilfe eines chemischen Disruptors des ClpX-Chaperon-Komplexes. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Christian Fetzer
- Center for Integrated Protein Science am Department Chemie; Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Vadim S. Korotkov
- Center for Integrated Protein Science am Department Chemie; Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Robert Thänert
- Infektionsimmunologie, Helmholtz-Zentrum für Infektionsforschung; Inhoffenstraße 7 38124 Braunschweig Deutschland
| | - Kyu Myung Lee
- Center for Integrated Protein Science am Department Chemie; Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Martin Neuenschwander
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie; Robert-Roessle-Straße 10 13125 Berlin Deutschland
| | - Jens Peter von Kries
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie; Robert-Roessle-Straße 10 13125 Berlin Deutschland
| | - Eva Medina
- Infektionsimmunologie, Helmholtz-Zentrum für Infektionsforschung; Inhoffenstraße 7 38124 Braunschweig Deutschland
| | - Stephan A. Sieber
- Center for Integrated Protein Science am Department Chemie; Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
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50
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Fetzer C, Korotkov VS, Thänert R, Lee KM, Neuenschwander M, von Kries JP, Medina E, Sieber SA. A Chemical Disruptor of the ClpX Chaperone Complex Attenuates the Virulence of Multidrug-Resistant Staphylococcus aureus. Angew Chem Int Ed Engl 2017; 56:15746-15750. [DOI: 10.1002/anie.201708454] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 09/08/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Christian Fetzer
- Center for Integrated Protein Science at the Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85747 Garching Germany
| | - Vadim S. Korotkov
- Center for Integrated Protein Science at the Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85747 Garching Germany
| | - Robert Thänert
- Infection Immunology Research Group; Helmholtz Centre for Infection Research; Inhoffenstrasse 7 38124 Braunschweig Germany
| | - Kyu Myung Lee
- Center for Integrated Protein Science at the Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85747 Garching Germany
| | - Martin Neuenschwander
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie; Robert-Roessle-Strasse 10 13125 Berlin Germany
| | - Jens Peter von Kries
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie; Robert-Roessle-Strasse 10 13125 Berlin Germany
| | - Eva Medina
- Infection Immunology Research Group; Helmholtz Centre for Infection Research; Inhoffenstrasse 7 38124 Braunschweig Germany
| | - Stephan A. Sieber
- Center for Integrated Protein Science at the Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85747 Garching Germany
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