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Zheng X, Zhu H, Zhao X, Wang J, Li Q, Zhao X. Emerging affinity methods for protein-drug interaction analysis. J Pharm Biomed Anal 2024; 249:116371. [PMID: 39047466 DOI: 10.1016/j.jpba.2024.116371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/15/2024] [Accepted: 07/15/2024] [Indexed: 07/27/2024]
Abstract
The study of protein-drug interaction plays a crucial role in understanding drug mechanisms, identifying new drug targets and biomarkers, and facilitating drug development and disease treatment. In recent years, significant progress has been made in various protein-drug interaction research methods due to the rapid development and in-depth application of mass spectrometry, nuclear magnetic resonance, Raman spectroscopy, and other technologies. The progress has enhanced the sensitivity, precision, accuracy, and applicability of analytical methods, enabling the establishment of drug-protein interaction networks. This review discusses various emerging research methods, such as native mass spectrometry, infrared spectroscopy, nuclear magnetic resonance and spectrum, biosensor technologies employing surface enhanced Raman, electrochemistry, and magneto resistive signals, as well as affinity magnetic levitation and affinity chromatography. The article also delves into the principles, applications, advantages, and limitations of these technologies.
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Affiliation(s)
- Xinxin Zheng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Huiting Zhu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Xue Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Jing Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Qian Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Xinfeng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China.
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2
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Konno S, Ishikawa F, Kakeya H, Tanabe G. Probing for optimal photoaffinity linkers of benzophenone-based photoaffinity probes for adenylating enzymes. Bioorg Med Chem 2024; 110:117815. [PMID: 38943807 DOI: 10.1016/j.bmc.2024.117815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/01/2024]
Abstract
The adenylation (A) domain of non-ribosomal peptide synthetases (NRPSs) catalyzes the adenylation reaction with substrate amino acids and ATP. Leveraging the distinct substrate specificity of A-domains, we previously developed photoaffinity probes for A-domains based on derivatization with a 5'-O-N-(aminoacyl)sulfamoyl adenosine (aminoacyl-AMS)-appended clickable benzophenone. Although our photoaffinity probes with different amino acid warheads enabled selective detection, visualization, and enrichment of target A-domains in proteomic environments, the effects of photoaffinity linkers have not been investigated. To explore the optimal benzophenone-based linker scaffold, we designed seven photoaffinity probes for the A-domains with different lengths, positions, and molecular shapes. Using probes 2-8 for the phenylalanine-activating A-domain of gramicidin S synthetase A (GrsA), we systematically investigated the binding affinity and labeling efficiency of the endogenous enzyme in a live producer cell. Our results indicated that the labeling efficiencies of probes 2-8 tended to depend on their binding affinities rather than on the linker length, flexibility, or position of the photoaffinity group. We also identified that probe 2 with a 4,4'-diaminobenzophenone linker exhibits the highest labeling efficiency for GrsA with fewer non-target labeling properties in live cells.
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Affiliation(s)
- Sho Konno
- Department of System Chemotherapy and Molecular Sciences, Division of Medicinal Frontier Sciences, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan; School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Fumihiro Ishikawa
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan.
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Medicinal Frontier Sciences, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Genzoh Tanabe
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan.
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3
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Zou M, Zhou H, Gu L, Zhang J, Fang L. Therapeutic Target Identification and Drug Discovery Driven by Chemical Proteomics. BIOLOGY 2024; 13:555. [PMID: 39194493 DOI: 10.3390/biology13080555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/07/2024] [Accepted: 07/19/2024] [Indexed: 08/29/2024]
Abstract
Throughout the human lifespan, from conception to the end of life, small molecules have an intrinsic relationship with numerous physiological processes. The investigation into small-molecule targets holds significant implications for pharmacological discovery. The determination of the action sites of small molecules provide clarity into the pharmacodynamics and toxicological mechanisms of small-molecule drugs, assisting in the elucidation of drug off-target effects and resistance mechanisms. Consequently, innovative methods to study small-molecule targets have proliferated in recent years, with chemical proteomics standing out as a vanguard development in chemical biology in the post-genomic age. Chemical proteomics can non-selectively identify unknown targets of compounds within complex biological matrices, with both probe and non-probe modalities enabling effective target identification. This review attempts to summarize methods and illustrative examples of small-molecule target identification via chemical proteomics. It delves deeply into the interactions between small molecules and human biology to provide pivotal directions and strategies for the discovery and comprehension of novel pharmaceuticals, as well as to improve the evaluation of drug safety.
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Affiliation(s)
- Mingjie Zou
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
| | - Haiyuan Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
| | - Letian Gu
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
| | - Jingzi Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
| | - Lei Fang
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
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4
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Jiang X, Shon K, Li X, Cui G, Wu Y, Wei Z, Wang A, Li X, Lu Y. Recent advances in identifying protein targets of bioactive natural products. Heliyon 2024; 10:e33917. [PMID: 39091937 PMCID: PMC11292521 DOI: 10.1016/j.heliyon.2024.e33917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 06/28/2024] [Accepted: 06/28/2024] [Indexed: 08/04/2024] Open
Abstract
Background Natural products exhibit structural complexity, diversity, and historical therapeutic significance, boasting attractive functions and biological activities that have significantly influenced drug discovery endeavors. The identification of target proteins of active natural compounds is crucial for advancing novel drug innovation. Currently, methods for identifying targets of natural products can be categorized into labeling and label-free approaches based on whether the natural bioactive constituents are modified into active probes. In addition, there is a new avenue for rapidly exploring the targets of natural products based on their innate functions. Aim This review aimed to summarize recent advancements in both labeling and label-free approaches to the identification of targets for natural products, as well as the novel target identification method based on the natural functions of natural products. Methods We systematically collected relevant articles published in recent years from PubMed, Web of Science, and ScienceDirect, focusing on methods employed for identifying protein targets of bioactive natural products. Furthermore, we systematically summarized the principles, procedures, and successful cases, as well as the advantages and limitations of each method. Results Labeling methods allow for the direct labeling of target proteins and the exclusion of indirectly targeted proteins. However, these methods are not suitable for studying post-modified compounds with abolished activity, chemically challenging synthesis, or trace amounts of natural active compounds. Label-free methods can be employed to identify targets of any natural active compounds, including trace amounts and multicomponent mixtures, but their reliability is not as high as labeling methods. The structural complementarity between natural products and their innate receptors significantly increase the opportunities for finding more promising structural analogues of the natural products, and natural products may interact with several structural analogues of receptors in humans. Conclusion Each approach presents benefits and drawbacks. In practice, a combination of methods is employed to identify targets of natural products. And natural products' innate functions-based approach is a rapid and selective strategy for target identification. This review provides valuable references for future research in this field, offering insights into techniques and methodologies.
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Affiliation(s)
- Xuan Jiang
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Kinyu Shon
- Department of Gastroenterology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xiaofeng Li
- Department of Biochemistry and Molecular Biology, School of Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Guoliang Cui
- Department of Gastroenterology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yuanyuan Wu
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Zhonghong Wei
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Aiyun Wang
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine (TCM) Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xiaoman Li
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yin Lu
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine (TCM) Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, 210023, China
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5
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Hanswillemenke A, Hofacker DT, Sorgenfrei M, Fruhner C, Franz-Wachtel M, Schwarzer D, Maček B, Stafforst T. Profiling the interactome of oligonucleotide drugs by proximity biotinylation. Nat Chem Biol 2024; 20:555-565. [PMID: 38233583 PMCID: PMC11062921 DOI: 10.1038/s41589-023-01530-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 12/17/2023] [Indexed: 01/19/2024]
Abstract
Drug-ID is a novel method applying proximity biotinylation to identify drug-protein interactions inside living cells. The covalent conjugation of a drug with a biotin ligase enables targeted biotinylation and identification of the drug-bound proteome. We established Drug-ID for two small-molecule drugs, JQ1 and SAHA, and applied it for RNaseH-recruiting antisense oligonucleotides (ASOs). Drug-ID profiles the drug-protein interactome de novo under native conditions, directly inside living cells and at pharmacologically effective drug concentrations. It requires minimal amounts of cell material and might even become applicable in vivo. We studied the dose-dependent aggregation of ASOs and the effect of different wing chemistries (locked nucleic acid, 2'-methoxyethyl and 2'-Fluoro) and ASO lengths on the interactome. Finally, we demonstrate the detection of stress-induced, intracellular interactome changes (actinomycin D treatment) with an in situ variant of the approach, which uses a recombinant biotin ligase and does not require genetic manipulation of the target cell.
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Affiliation(s)
| | | | - Michèle Sorgenfrei
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Carolin Fruhner
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Mirita Franz-Wachtel
- Interfaculty Institute of Cell Biology, University of Tübingen, Tübingen, Germany
| | - Dirk Schwarzer
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Boris Maček
- Interfaculty Institute of Cell Biology, University of Tübingen, Tübingen, Germany
| | - Thorsten Stafforst
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.
- Gene and RNA Therapy Center (GRTC), Faculty of Medicine, University of Tübingen, Tübingen, Germany.
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6
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Tabana Y, Babu D, Fahlman R, Siraki AG, Barakat K. Target identification of small molecules: an overview of the current applications in drug discovery. BMC Biotechnol 2023; 23:44. [PMID: 37817108 PMCID: PMC10566111 DOI: 10.1186/s12896-023-00815-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/22/2023] [Indexed: 10/12/2023] Open
Abstract
Target identification is an essential part of the drug discovery and development process, and its efficacy plays a crucial role in the success of any given therapy. Although protein target identification research can be challenging, two main approaches can help researchers make significant discoveries: affinity-based pull-down and label-free methods. Affinity-based pull-down methods use small molecules conjugated with tags to selectively isolate target proteins, while label-free methods utilize small molecules in their natural state to identify targets. Target identification strategy selection is essential to the success of any drug discovery process and must be carefully considered when determining how to best pursue a specific project. This paper provides an overview of the current target identification approaches in drug discovery related to experimental biological assays, focusing primarily on affinity-based pull-down and label-free approaches, and discusses their main limitations and advantages.
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Affiliation(s)
- Yasser Tabana
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Dinesh Babu
- Li Ka Shing Applied Virology Institute, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Richard Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Arno G Siraki
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Khaled Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada.
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7
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Kawamata Y, Ryu KA, Hermann GN, Sandahl A, Vantourout JC, Olow AK, Adams LTA, Rivera-Chao E, Roberts LR, Gnaim S, Nassir M, Oslund RC, Fadeyi OO, Baran PS. An electroaffinity labelling platform for chemoproteomic-based target identification. Nat Chem 2023; 15:1267-1275. [PMID: 37322100 DOI: 10.1038/s41557-023-01240-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 05/12/2023] [Indexed: 06/17/2023]
Abstract
Target identification involves deconvoluting the protein target of a pharmacologically active, small-molecule ligand, a process that is critical for early drug discovery yet technically challenging. Photoaffinity labelling strategies have become the benchmark for small-molecule target deconvolution, but covalent protein capture requires the use of high-energy ultraviolet light, which can complicate downstream target identification. Thus, there is a strong demand for alternative technologies that allow for controlled activation of chemical probes to covalently label their protein target. Here we introduce an electroaffinity labelling platform that leverages the use of a small, redox-active diazetidinone functional group to enable chemoproteomic-based target identification of pharmacophores within live cell environments. The underlying discovery to enable this platform is that the diazetidinone can be electrochemically oxidized to reveal a reactive intermediate useful for covalent modification of proteins. This work demonstrates the electrochemical platform to be a functional tool for drug-target identification.
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Affiliation(s)
- Yu Kawamata
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Keun Ah Ryu
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Gary N Hermann
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Alexander Sandahl
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Aleksandra K Olow
- Genetics and Pharmacogenomics, Merck & Co., Inc., San Francisco, CA, USA
| | | | - Eva Rivera-Chao
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Lee R Roberts
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Samer Gnaim
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Molhm Nassir
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Rob C Oslund
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA.
- InduPro Therapeutics, Cambridge, MA, USA.
| | - Olugbeminiyi O Fadeyi
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA.
- InduPro Therapeutics, Cambridge, MA, USA.
| | - Phil S Baran
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
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8
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Gordeeva AI, Valueva AA, Ershova MO, Rybakova EE, Shumov ID, Kozlov AF, Ziborov VS, Zavialova MG, Zgoda VG, Ivanov YD, Archakov AI, Pleshakova TO. Mass Spectrometric Identification of BSA Covalently Captured onto a Chip for Atomic Force Microscopy. Int J Mol Sci 2023; 24:ijms24108999. [PMID: 37240343 DOI: 10.3390/ijms24108999] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Mass spectrometry (MS) is one of the main techniques for protein identification. Herein, MS has been employed for the identification of bovine serum albumin (BSA), which was covalently immobilized on the surface of a mica chip intended for investigation by atomic force microscopy (AFM). For the immobilization, two different types of crosslinkers have been used: 4-benzoylbenzoic acid N-succinimidyl ester (SuccBB) and dithiobis(succinimidyl propionate) (DSP). According to the data obtained by using an AFM-based molecular detector, the SuccBB crosslinker was more efficient in BSA immobilization than the DSP. The type of crosslinker used for protein capturing has been found to affect the results of MS identification. The results obtained herein can be applied in the development of novel systems intended for the highly sensitive analysis of proteins with molecular detectors.
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Affiliation(s)
| | | | - Maria O Ershova
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia
| | | | - Ivan D Shumov
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia
| | - Andrey F Kozlov
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia
| | - Vadim S Ziborov
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia
| | | | - Victor G Zgoda
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia
| | - Yuri D Ivanov
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia
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9
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Petri L, Ábrányi-Balogh P, Csorba N, Keeley A, Simon J, Ranđelović I, Tóvári J, Schlosser G, Szabó D, Drahos L, Keserű GM. Activation-Free Sulfonyl Fluoride Probes for Fragment Screening. Molecules 2023; 28:molecules28073042. [PMID: 37049805 PMCID: PMC10096327 DOI: 10.3390/molecules28073042] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/14/2023] Open
Abstract
SuFEx chemistry is based on the unique reactivity of the sulfonyl fluoride group with a range of nucleophiles. Accordingly, sulfonyl fluorides label multiple nucleophilic amino acid residues, making these reagents popular in both chemical biology and medicinal chemistry applications. The reactivity of sulfonyl fluorides nominates this warhead chemotype as a candidate for an external, activation-free general labelling tag. Here, we report the synthesis and characterization of a small sulfonyl fluoride library that yielded the 3-carboxybenzenesulfonyl fluoride warhead for tagging tractable targets at nucleophilic residues. Based on these results, we propose that coupling diverse fragments to this warhead would result in a library of sulfonyl fluoride bits (SuFBits), available for screening against protein targets. SuFBits will label the target if it binds to the core fragment, which facilitates the identification of weak fragments by mass spectrometry.
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Affiliation(s)
- László Petri
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
- National Laboratory for Drug Research and Development, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
| | - Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
- National Laboratory for Drug Research and Development, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary
| | - Noémi Csorba
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
- National Laboratory for Drug Research and Development, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary
| | - Aaron Keeley
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
| | - József Simon
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
- Research Centre for Natural Sciences, MS Metabolomics Research Group, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
| | | | - József Tóvári
- Department of Experimental Pharmacology and National Tumor Biology Laboratory POB 21, National Institute of Oncology, 1525 Budapest, Hungary
| | - Gitta Schlosser
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/A, 1117 Budapest, Hungary
| | - Dániel Szabó
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
| | - László Drahos
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
- National Laboratory for Drug Research and Development, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary
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10
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Ishikawa F, Konno S, Uchiyama Y, Kakeya H, Tanabe G. Exploring a chemical scaffold for rapid and selective photoaffinity labelling of non-ribosomal peptide synthetases in living bacterial cells. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220026. [PMID: 36633280 PMCID: PMC9835605 DOI: 10.1098/rstb.2022.0026] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 06/19/2022] [Indexed: 01/13/2023] Open
Abstract
Non-ribosomal peptide synthetases (NRPSs) biosynthesize many pharmaceuticals and virulence factors. The biosynthesis of these natural peptide products from biosynthetic gene clusters depends on complex regulations in bacteria. However, our current knowledge of NRPSs is based on enzymological studies using full NRPS systems and/or a single NRPS domain in heterologous hosts. Chemical and/or biochemical strategies to capture the endogenous activities of NRPSs facilitate studies on NRPS cell biology in bacterial cells. Here, we describe a chemical scaffold for the rapid and selective photoaffinity labelling of NRPSs in purified systems, crude biological samples and living bacterial cells. We synthesized photoaffinity labelling probes coupled with 5'-O-N-(phenylalanyl)sulfamoyladenosine with clickable alkyl diazirine or trifluoromethyl phenyl diazirine. We found that a trifluoromethyl phenyl diazirine-based probe cross-linked the Phe-activating domain of a GrsA-NRPS with high selectivity and sensitivity at shorter ultraviolet (UV) irradiation times (less than 5 min) relative to a prototypical benzophenone-based probe. Our results demonstrated that this quick labelling protocol can prevent damage to proteins and cells caused by long UV irradiation times, providing a mild photoaffinity labelling method for biological samples. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Fumihiro Ishikawa
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Sho Konno
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yuko Uchiyama
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Hideaki Kakeya
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Genzoh Tanabe
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
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11
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Zhang Z, Lin J, Liu Z, Tian G, Li XM, Jing Y, Li X, Li XD. Photo-Cross-Linking To Delineate Epigenetic Interactome. J Am Chem Soc 2022; 144:20979-20997. [DOI: 10.1021/jacs.2c06135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zhuoyuan Zhang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jianwei Lin
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Zheng Liu
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Gaofei Tian
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xiao-Meng Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yihang Jing
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Xin Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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12
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Kurosawa T, Tega Y, Uchida Y, Higuchi K, Tabata H, Sumiyoshi T, Kubo Y, Terasaki T, Deguchi Y. Proteomics-Based Transporter Identification by the PICK Method: Involvement of TM7SF3 and LHFPL6 in Proton-Coupled Organic Cation Antiport at the Blood-Brain Barrier. Pharmaceutics 2022; 14:pharmaceutics14081683. [PMID: 36015309 PMCID: PMC9413594 DOI: 10.3390/pharmaceutics14081683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/07/2022] [Accepted: 08/09/2022] [Indexed: 01/20/2023] Open
Abstract
A proton-coupled organic cation (H+/OC) antiporter working at the blood–brain barrier (BBB) in humans and rodents is thought to be a promising candidate for the efficient delivery of cationic drugs to the brain. Therefore, it is important to identify the molecular entity that exhibits this activity. Here, for this purpose, we established the Proteomics-based Identification of transporter by Crosslinking substrate in Keyhole (PICK) method, which combines photo-affinity labeling with comprehensive proteomics analysis using SWATH-MS. Using preselected criteria, the PICK method generated sixteen candidate proteins. From these, knockdown screening in hCMEC/D3 cells, an in vitro BBB model, identified two proteins, TM7SF3 and LHFPL6, as candidates for the H+/OC antiporter. We synthesized a novel H+/OC antiporter substrate for functional analysis of TM7SF3 and LHFPL6 in hCMEC/D3 cells and HEK293 cells. The results suggested that both TM7SF3 and LHFPL6 are components of the H+/OC antiporter.
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Affiliation(s)
- Toshiki Kurosawa
- Laboratory of Drug Disposition and Pharmacokinetics, Faculty of Pharma-Sciences, Teikyo University, Tokyo 173-8605, Japan
| | - Yuma Tega
- Laboratory of Drug Disposition and Pharmacokinetics, Faculty of Pharma-Sciences, Teikyo University, Tokyo 173-8605, Japan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
| | - Yasuo Uchida
- Division of Membrane Transport and Drug Targeting, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
- Correspondence: (Y.U.); (Y.D.); Tel.: +81-22-795-6832 (Y.U.); +81-3-3964-8246 (Y.D.)
| | - Kei Higuchi
- Department of Biopharmaceutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan
| | - Hidetsugu Tabata
- Laboratory of Medicinal Chemistry, Faculty of Pharma-Sciences, Teikyo University, Tokyo 173-8605, Japan
| | - Takaaki Sumiyoshi
- Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, Osaka 564-8680, Japan
| | - Yoshiyuki Kubo
- Laboratory of Drug Disposition and Pharmacokinetics, Faculty of Pharma-Sciences, Teikyo University, Tokyo 173-8605, Japan
| | - Tetsuya Terasaki
- Division of Membrane Transport and Drug Targeting, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Yoshiharu Deguchi
- Laboratory of Drug Disposition and Pharmacokinetics, Faculty of Pharma-Sciences, Teikyo University, Tokyo 173-8605, Japan
- Correspondence: (Y.U.); (Y.D.); Tel.: +81-22-795-6832 (Y.U.); +81-3-3964-8246 (Y.D.)
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13
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Photoaffinity labeling of benzophenone-containing salicylanilide compounds to give an insight into the mechanism in disrupting peptidoglycan formation. Bioorg Med Chem 2022; 67:116819. [PMID: 35635930 DOI: 10.1016/j.bmc.2022.116819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/05/2022] [Accepted: 05/09/2022] [Indexed: 11/20/2022]
Abstract
A series of salicylanilide compounds was previously identified as antibacterial agents that inhibit the peptidoglycan formation. To find the exact binding mode, we synthesized a benzophenone-containing salicylanilide compound (1) and used it as a photoaffinity probe to label Acinetobacter baumannii penicillin-binding protein (PBP1b). After incubation and photo-irradiation, the labeled protein was subjected to trypsin digestion, dialysis enrichment, LC-ESI-MS/MS analysis, and Mascot search to reveal an octadecapeptide sequence 364RQLRTEYQESDLTNQGLR381 that was labeled at E372. Our molecular docking experiments suggest a hydrophobic pocket surrounded by R367 and E372 is the binding site of salicylanilide 1. The pocket lies in between the transglycosylase and transpeptidase domains, thus binding of salicylanilide 1 can block the propagation pathway to disrupt the growth of peptidoglycan chain.
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14
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Lu D, Pan R, Wu W, Zhang Y, Li S, Xu H, Huang J, Xia J, Wang Q, Luan X, Lv C, Zhang W, Meng G. FL-DTD: an integrated pipeline to predict the drug interacting targets by feedback loop-based network analysis. Brief Bioinform 2022; 23:6632928. [PMID: 35794722 DOI: 10.1093/bib/bbac263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 11/12/2022] Open
Abstract
Drug target discovery is an essential step to reveal the mechanism of action (MoA) underlying drug therapeutic effects and/or side effects. Most of the approaches are usually labor-intensive while unable to identify the tissue-specific interacting targets, especially the targets with weaker drug binding affinity. In this work, we proposed an integrated pipeline, FL-DTD, to predict the drug interacting targets of novel compounds in a tissue-specific manner. This method was built based on a hypothesis that cells under a status of homeostasis would take responses to drug perturbation by activating feedback loops. Therefore, the drug interacting targets can be predicted by analyzing the network responses after drug perturbation. We evaluated this method using the expression data of estrogen stimulation, gene manipulation and drug perturbation and validated its good performance to identify the annotated drug targets. Using STAT3 as a target protein, we applied this method to drug perturbation data of 500 natural compounds and predicted five compounds with STAT3 interacting activities. Experimental assay validated the STAT3-interacting activities of four compounds. Overall, our evaluation suggests that FL-DTD predicts the drug interacting targets with good accuracy and can be used for drug target discovery.
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Affiliation(s)
- Dong Lu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun 1200, 201203, Shanghai, China
| | - Rongrong Pan
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun 1200, 201203, Shanghai, China
| | - Wenxuan Wu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun 1200, 201203, Shanghai, China
| | - Yanyan Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun 1200, 201203, Shanghai, China
| | - Shensuo Li
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun 1200, 201203, Shanghai, China
| | - Hong Xu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun 1200, 201203, Shanghai, China
| | - Jialan Huang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun 1200, 201203, Shanghai, China
| | - Jianhua Xia
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun 1200, 201203, Shanghai, China
| | - Qun Wang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun 1200, 201203, Shanghai, China
| | - Xin Luan
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun 1200, 201203, Shanghai, China
| | - Chao Lv
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun 1200, 201203, Shanghai, China
| | - Weidong Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun 1200, 201203, Shanghai, China
| | - Guofeng Meng
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun 1200, 201203, Shanghai, China
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15
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Photoaffinity labeling and bioorthogonal ligation: Two critical tools for designing "Fish Hooks" to scout for target proteins. Bioorg Med Chem 2022; 62:116721. [PMID: 35358862 DOI: 10.1016/j.bmc.2022.116721] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/14/2022] [Accepted: 03/17/2022] [Indexed: 11/21/2022]
Abstract
Small molecules remain an important category of therapeutic agents. Their binding to different proteins can lead to both desired and undesired biological effects. Identification of the proteins that a drug binds to has become an important step in drug development because it can lead to safer and more effective drugs. Parent bioactive molecules can be converted to appropriate probes that allow for visualization and identification of their target proteins. Typically, these probes are designed and synthesized utilizing some or all of five major tools; a photoactivatable group, a reporter tag, a linker, an affinity tag, and a bioorthogonal handle. This review covers two of the most challenging tools, photoactivation and bioorthogonal ligation. We provide a historical and theoretical background along with synthetic routes to prepare them. In addition, the review provides comparative analyses of the available tools that can assist decision making when designing such probes. A survey of most recent literature reports is included as well to identify recent trends in the field.
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16
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Page ACS, Scholz SO, Keenan KN, Spradlin JN, Belcher BP, Brittain SM, Tallarico JA, McKenna JM, Schirle M, Nomura DK, Toste FD. Photo-Brook rearrangement of acyl silanes as a strategy for photoaffinity probe design. Chem Sci 2022; 13:3851-3856. [PMID: 35432890 PMCID: PMC8966736 DOI: 10.1039/d2sc00426g] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/02/2022] [Indexed: 01/14/2023] Open
Abstract
Photoaffinity labeling (PAL) is a powerful tool for the identification of non-covalent small molecule–protein interactions that are critical to drug discovery and medicinal chemistry, but this approach is limited to only a small subset of robust photocrosslinkers. The identification of new photoreactive motifs capable of covalent target capture is therefore highly desirable. Herein, we report the design, synthesis, and evaluation of a new class of PAL warheads based on the UV-triggered 1,2-photo-Brook rearrangement of acyl silanes, which hitherto have not been explored for PAL workflows. Irradiation of a series of probes in cell lysate revealed an iPr-substituted acyl silane with superior photolabeling and minimal thermal background labeling compared to other substituted acyl silanes. Further, small molecule (+)-JQ1- and rapamycin-derived iPr acyl silanes were shown to selectively label recombinant BRD4-BD1 and FKBP12, respectively, with minimal background. Together, these data highlight the untapped potential of acyl silanes as a novel, tunable scaffold for photoaffinity labeling. Irradiation initiated 1,2-photo Brook rearrangement of acyl silanes generated α-siloxycarbene intermediates that were used for photoaffinity labeling. Optimization of the acyl silane group produced a probe capable of capturing small molecule–protein interactions.![]()
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Affiliation(s)
- Annika C S Page
- Department of Chemistry, University of California Berkeley California 94720 USA .,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA
| | - Spencer O Scholz
- Department of Chemistry, University of California Berkeley California 94720 USA .,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA
| | - Katherine N Keenan
- Department of Chemistry, University of California Berkeley California 94720 USA .,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA
| | - Jessica N Spradlin
- Department of Chemistry, University of California Berkeley California 94720 USA .,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA.,Innovative Genomics Institute, University of California Berkeley California 94720 USA
| | - Bridget P Belcher
- Department of Chemistry, University of California Berkeley California 94720 USA .,Innovative Genomics Institute, University of California Berkeley California 94720 USA
| | - Scott M Brittain
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA.,Novartis Institute for BioMedical Research Cambridge Massachusetts 02139 USA
| | - John A Tallarico
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA.,Novartis Institute for BioMedical Research Cambridge Massachusetts 02139 USA
| | - Jeffrey M McKenna
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA.,Novartis Institute for BioMedical Research Cambridge Massachusetts 02139 USA
| | - Markus Schirle
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA.,Novartis Institute for BioMedical Research Cambridge Massachusetts 02139 USA
| | - Daniel K Nomura
- Department of Chemistry, University of California Berkeley California 94720 USA .,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA.,Innovative Genomics Institute, University of California Berkeley California 94720 USA.,Department of Molecular and Cellular Biology, University of California Berkeley California 94720 USA
| | - F Dean Toste
- Department of Chemistry, University of California Berkeley California 94720 USA .,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA
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17
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Dai Z, An LY, Chen XY, Yang F, Zhao N, Li CC, Ren R, Li BY, Tao WY, Li P, Jiang C, Yan F, Jiang ZY, You QD, Di B, Xu LL. Target Fishing Reveals a Novel Mechanism of 1,2,4-Oxadiazole Derivatives Targeting Rpn6, a Subunit of 26S Proteasome. J Med Chem 2022; 65:5029-5043. [PMID: 35253427 DOI: 10.1021/acs.jmedchem.1c02210] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
1,2,4-Oxadiazole derivatives, a class of Nrf2-ARE activators, exert an extensive therapeutic effect on inflammation, cancer, neurodegeneration, and microbial infection. Among these analogues, DDO-7263 is the most potent Nrf2 activator and used as the core structure for bioactive probes to explore the precise mechanism. In this work, we obtained compound 7, a mimic of DDO-7263, and biotin-labeled and fluorescein-based probes, which exhibited homologous biological activities to DDO-7263, including activating Nrf2 and its downstream target genes, anti-oxidative stress, and anti-inflammatory effects. Affinity chromatography and mass analysis techniques revealed Rpn6 as the potential target protein regulating the Nrf2 signaling pathway. In vitro affinity experiments further confirmed that DDO-7263 upregulated Nrf2 through binding to Rpn6 to block the assembly of 26S proteasome and the subsequent degradation of ubiquitinated Nrf2. These results indicated that Rpn6 is a promising candidate target to activate the Nrf2 pathway for protecting cells and tissues from oxidative, electrophilic, and exogenous microbial stimulation.
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Affiliation(s)
- Zhen Dai
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Lu-Yan An
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Xiao-Yi Chen
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Fan Yang
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Ni Zhao
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Cui-Cui Li
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Ren Ren
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Bing-Yan Li
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Wei-Yan Tao
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Pei Li
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Cheng Jiang
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Fang Yan
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Zheng-Yu Jiang
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Qi-Dong You
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Bin Di
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Li-Li Xu
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
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18
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19
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In Planta Labeling Using a Clickable ER-Disrupting Probe Suggests a Role for Oleosins in Arabidopsis Seedling ER Integrity. ACS Chem Biol 2021; 16:2151-2157. [PMID: 34505514 DOI: 10.1021/acschembio.1c00607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Several small-molecule perturbagens of the plant endomembrane system are known, but few selectively disrupt endoplasmic reticulum (ER) structure and function. We conducted a microscopy-based screen for small-molecule disruptors of ER structure and discovered eroonazole, a 1,2-4-triazole that induces extensive ER vesiculation in Arabidopsis seedlings. To identify eroonazole targets, we synthesized a clickable photoaffinity derivative and used it for whole-seedling labeling experiments. These reveal that the probe labels multiple oleosins, plant membrane proteins that stabilize ER-derived lipid droplets. Oleosin labeling is absent in an oleosin1234 quadruple mutant and reduced using an inactive analog. Cellular analyses of the ER in the quadruple mutant demonstrate that oleosins are required for normal ER structure during seed germination and suggest that perturbation of oleosin function by eroonazole underlies its effects on seedling ER structure.
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20
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Podvalnyy NM, Chesnov S, Nanni P, Gut M, Holland JP, Hennet T. Synthesis of photoactivable oligosaccharide derivatives from 1,2-cyclic carbamate building blocks and study of their interaction with carbohydrate-binding proteins. Carbohydr Res 2021; 508:108399. [PMID: 34298358 DOI: 10.1016/j.carres.2021.108399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 11/24/2022]
Abstract
Despite the broad occurrence of carbohydrate-protein interactions in biology, the low binding affinities of such interactions hamper the characterization of carbohydrate binding sites in the absence of three-dimensional structural models. To allow the identification of proteins interacting with specific carbohydrate epitopes, we have developed new photoactivable oligosaccharide probes. Oligosaccharides containing the 1,2-cyclic carbamate group were attached to building blocks with a primary amino group to yield the corresponding urea derivatives. Cyclic carbamates of lactose, and 3- and 2'-fucosyl lactose, were used for the conjugation with building blocks containing photoactivable diazirine, benzophenone or aryl azido groups. The resulting oligosaccharide derivatives were tested for binding to Erythrina cristagalli lectin (ECL), Aleuria aurantia lectin (AAL) and Ulex europaeus agglutinin-I (UEA I). We found that ligands containing an aryl azido photoactivable group were successfully attached to lectins. The photoactivation reaction preserved lectin integrity, as no sign of protein degradation was visible. Mass spectrometric analysis confirmed the covalent binding of between one to three oligosaccharide probes, which matched with the expected carbohydrate-binding properties of the lectins tested. The conjugation of cyclic carbamate-derivatized oligosaccharides with photoactivable aryl azido groups thus represents a convenient approach to study protein-carbohydrate interactions.
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Affiliation(s)
| | - Serge Chesnov
- Functional Genomics Center Zurich, ETH Zurich / University of Zurich, Zurich, Switzerland
| | - Paolo Nanni
- Functional Genomics Center Zurich, ETH Zurich / University of Zurich, Zurich, Switzerland
| | - Melanie Gut
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Jason P Holland
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Thierry Hennet
- Institute of Physiology, University of Zurich, Zurich, Switzerland
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21
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Ibert Q, Cauwel M, Glachet T, Tite T, Le Nahenec‐Martel P, Lohier J, Renard P, Franck X, Reboul V, Sabot C. One‐Pot Synthesis of Diazirines and
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‐Diazirines from Ketones, Aldehydes and Derivatives: Development and Mechanistic Insight. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202100679] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Quentin Ibert
- Normandie Univ ENSICAEN, UNICAEN, CNRS, LCMT 6 Boulevard du Maréchal Juin 14050 Caen Cedex
| | - Madeleine Cauwel
- Normandie Univ CNRS, UNIROUEN, INSA Rouen, COBRA 76000 Rouen France
| | - Thomas Glachet
- Normandie Univ ENSICAEN, UNICAEN, CNRS, LCMT 6 Boulevard du Maréchal Juin 14050 Caen Cedex
| | - Tony Tite
- Normandie Univ CNRS, UNIROUEN, INSA Rouen, COBRA 76000 Rouen France
| | | | - Jean‐François Lohier
- Normandie Univ ENSICAEN, UNICAEN, CNRS, LCMT 6 Boulevard du Maréchal Juin 14050 Caen Cedex
| | | | - Xavier Franck
- Normandie Univ CNRS, UNIROUEN, INSA Rouen, COBRA 76000 Rouen France
| | - Vincent Reboul
- Normandie Univ ENSICAEN, UNICAEN, CNRS, LCMT 6 Boulevard du Maréchal Juin 14050 Caen Cedex
| | - Cyrille Sabot
- Normandie Univ CNRS, UNIROUEN, INSA Rouen, COBRA 76000 Rouen France
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22
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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: 24] [Impact Index Per Article: 8.0] [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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23
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Agrahari AK, Bose P, Jaiswal MK, Rajkhowa S, Singh AS, Hotha S, Mishra N, Tiwari VK. Cu(I)-Catalyzed Click Chemistry in Glycoscience and Their Diverse Applications. Chem Rev 2021; 121:7638-7956. [PMID: 34165284 DOI: 10.1021/acs.chemrev.0c00920] [Citation(s) in RCA: 154] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Copper(I)-catalyzed 1,3-dipolar cycloaddition between organic azides and terminal alkynes, commonly known as CuAAC or click chemistry, has been identified as one of the most successful, versatile, reliable, and modular strategies for the rapid and regioselective construction of 1,4-disubstituted 1,2,3-triazoles as diversely functionalized molecules. Carbohydrates, an integral part of living cells, have several fascinating features, including their structural diversity, biocompatibility, bioavailability, hydrophilicity, and superior ADME properties with minimal toxicity, which support increased demand to explore them as versatile scaffolds for easy access to diverse glycohybrids and well-defined glycoconjugates for complete chemical, biochemical, and pharmacological investigations. This review highlights the successful development of CuAAC or click chemistry in emerging areas of glycoscience, including the synthesis of triazole appended carbohydrate-containing molecular architectures (mainly glycohybrids, glycoconjugates, glycopolymers, glycopeptides, glycoproteins, glycolipids, glycoclusters, and glycodendrimers through regioselective triazole forming modular and bio-orthogonal coupling protocols). It discusses the widespread applications of these glycoproducts as enzyme inhibitors in drug discovery and development, sensing, gelation, chelation, glycosylation, and catalysis. This review also covers the impact of click chemistry and provides future perspectives on its role in various emerging disciplines of science and technology.
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Affiliation(s)
- Anand K Agrahari
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Priyanka Bose
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Manoj K Jaiswal
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Sanchayita Rajkhowa
- Department of Chemistry, Jorhat Institute of Science and Technology (JIST), Jorhat, Assam 785010, India
| | - Anoop S Singh
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Srinivas Hotha
- Department of Chemistry, Indian Institute of Science and Engineering Research (IISER), Pune, Maharashtra 411021, India
| | - Nidhi Mishra
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Vinod K Tiwari
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
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Shukla NM, Chan M, Lao FS, Chu PJ, Belsuzarri M, Yao S, Nan J, Sato-Kaneko F, Saito T, Hayashi T, Corr M, Carson DA, Cottam HB. Structure-activity relationship studies in substituted sulfamoyl benzamidothiazoles that prolong NF-κB activation. Bioorg Med Chem 2021; 43:116242. [PMID: 34274759 DOI: 10.1016/j.bmc.2021.116242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 12/19/2022]
Abstract
In the face of emerging infectious diseases, there remains an unmet need for vaccine development where adjuvants that enhance immune responses to pathogenic antigens are highly desired. Using high-throughput screens with a cell-based nuclear factor κB (NF-κB) reporter assay, we identified a sulfamoyl benzamidothiazole bearing compound 1 that demonstrated a sustained activation of NF-κB after a primary stimulus with a Toll-like receptor (TLR)-4 agonist, lipopolysaccharide (LPS). Here, we explore systematic structure-activity relationship (SAR) studies on compound 1 that indicated the sites on the scaffold that tolerated modification and yielded more potent compounds compared to 1. The selected analogs enhanced release of immunostimulatory cytokines in the human monocytic cell line THP-1 cells and murine primary dendritic cells. In murine vaccination studies, select compounds were used as co-adjuvants in combination with the Food and Drug Administration approved TLR-4 agonistic adjuvant, monophosphoryl lipid A (MPLA) that showed significant enhancement in antigen-specific antibody titers compared to MPLA alone. Additionally, our SAR studies led to identification of a photoaffinity probe which will aid the target identification and mechanism of action studies in the future.
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Affiliation(s)
- Nikunj M Shukla
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093-0809, USA.
| | - Michael Chan
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093-0809, USA
| | - Fitzgerald S Lao
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093-0809, USA
| | - Paul J Chu
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093-0809, USA
| | - Masiel Belsuzarri
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093-0809, USA
| | - Shiyin Yao
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093-0809, USA
| | - Jason Nan
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093-0809, USA
| | - Fumi Sato-Kaneko
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093-0809, USA
| | - Tetsuya Saito
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093-0809, USA
| | - Tomoko Hayashi
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093-0809, USA
| | - Maripat Corr
- Department of Medicine, University of California San Diego, La Jolla, CA 92093-0656, USA
| | - Dennis A Carson
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093-0809, USA
| | - Howard B Cottam
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093-0809, USA
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Wu Y, Williams J, Calder EDD, Walport LJ. Strategies to expand peptide functionality through hybridisation with a small molecule component. RSC Chem Biol 2021; 2:151-165. [PMID: 34458778 PMCID: PMC8341444 DOI: 10.1039/d0cb00167h] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/09/2020] [Indexed: 02/04/2023] Open
Abstract
Combining different compound classes gives molecular hybrids that can offer access to novel chemical space and unique properties. Peptides provide ideal starting points for such molecular hybrids, which can be easily modified with a variety of molecular entities. The addition of small molecules can improve the potency, stability and cell permeability of therapeutically relevant peptides. Furthermore, they are often applied to create peptide-based tools in chemical biology. In this review, we discuss general methods that allow the discovery of this compound class and highlight key examples of peptide-small molecule hybrids categorised by the application and function of the small molecule entity.
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Affiliation(s)
- Yuteng Wu
- Protein-Protein Interaction Laboratory, The Francis Crick Institute London UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London UK
| | - Jack Williams
- Protein-Protein Interaction Laboratory, The Francis Crick Institute London UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London UK
| | - Ewen D D Calder
- Protein-Protein Interaction Laboratory, The Francis Crick Institute London UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London UK
| | - Louise J Walport
- Protein-Protein Interaction Laboratory, The Francis Crick Institute London UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London UK
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26
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Sasaki M, Delawary M, Sakurai H, Kobayashi H, Nakao N, Tsuru H, Fukushima Y, Honzumi S, Moriyama S, Wada N, Kaneko T, Yamada K, Terasaka N, Kubota K. Novel LCAT (Lecithin:Cholesterol Acyltransferase) Activator DS-8190a Prevents the Progression of Plaque Accumulation in Atherosclerosis Models. Arterioscler Thromb Vasc Biol 2021; 41:360-376. [PMID: 33086872 DOI: 10.1161/atvbaha.120.314516] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE Enhancement of LCAT (lecithin:cholesterol acyltransferase) activity has possibility to be beneficial for atherosclerosis. To evaluate this concept, we characterized our novel, orally administered, small-molecule LCAT activator DS-8190a, which was created from high-throughput screening and subsequent derivatization. We also focused on its mechanism of LCAT activation and the therapeutic activity with improvement of HDL (high-density lipoprotein) functionality. Approach and Results: DS-8190a activated human and cynomolgus monkey but not mouse LCAT enzymes in vitro. DS-8190a was orally administered to cynomolgus monkeys and dose dependently increased LCAT activity (2.0-fold in 3 mg/kg group on day 7), resulting in HDL cholesterol elevation without drastic changes of non-HDL cholesterol. Atheroprotective effects were then evaluated using Ldl-r KO×hLcat Tg mice fed a Western diet for 8 weeks. DS-8190a treatment achieved significant reduction of atherosclerotic lesion area (48.3% reduction in 10 mg/kg treatment group). Furthermore, we conducted reverse cholesterol transport study using Ldl-r KO×hLcat Tg mice intraperitoneally injected with J774A.1 cells loaded with [3H]-cholesterol and confirmed significant increases of [3H] count in plasma (1.4-fold) and feces (1.4-fold on day 2 and 1.5-fold on day3) in the DS-8190a-treated group. With regard to the molecular mechanism involved, direct binding of DS-8190a to human LCAT protein was confirmed by 2 different approaches: affinity purification by DS-8190a-immobilized beads and thermal shift assay. In addition, the candidate binding site of DS-8190a in human LCAT protein was identified by photoaffinity labeling. CONCLUSIONS This study demonstrates the potential of DS-8190a as a novel therapeutic for atherosclerosis. In addition, this compound proves that a small-molecule direct LCAT activator can achieve HDL-C elevation in monkey and reduction of atherosclerotic lesion area with enhanced HDL function in rodent.
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Affiliation(s)
- Masato Sasaki
- Organic Synthesis Department (M.S., N.N.), Daiichi Sankyo RD Novare, Co, Ltd, Tokyo, Japan
| | - Mina Delawary
- Biological Research Laboratories (M.D., H.T., S.H., S.M., K.Y., N.T.), Daiichi Sankyo, Co, Ltd, Tokyo, Japan
| | - Hidetaka Sakurai
- Discovery Science and Technology Department (H.S., Y.F., N.W., K.K.), Daiichi Sankyo RD Novare, Co, Ltd, Tokyo, Japan
| | - Hideki Kobayashi
- Medicinal Chemistry Research Laboratories (H.K., T.K.), Daiichi Sankyo, Co, Ltd, Tokyo, Japan
| | - Naoki Nakao
- Organic Synthesis Department (M.S., N.N.), Daiichi Sankyo RD Novare, Co, Ltd, Tokyo, Japan
| | - Hiromi Tsuru
- Biological Research Laboratories (M.D., H.T., S.H., S.M., K.Y., N.T.), Daiichi Sankyo, Co, Ltd, Tokyo, Japan
| | - Yumiko Fukushima
- Discovery Science and Technology Department (H.S., Y.F., N.W., K.K.), Daiichi Sankyo RD Novare, Co, Ltd, Tokyo, Japan
| | - Shoko Honzumi
- Biological Research Laboratories (M.D., H.T., S.H., S.M., K.Y., N.T.), Daiichi Sankyo, Co, Ltd, Tokyo, Japan
| | - Sachiko Moriyama
- Biological Research Laboratories (M.D., H.T., S.H., S.M., K.Y., N.T.), Daiichi Sankyo, Co, Ltd, Tokyo, Japan
| | - Naoya Wada
- Discovery Science and Technology Department (H.S., Y.F., N.W., K.K.), Daiichi Sankyo RD Novare, Co, Ltd, Tokyo, Japan
| | - Toshio Kaneko
- Medicinal Chemistry Research Laboratories (H.K., T.K.), Daiichi Sankyo, Co, Ltd, Tokyo, Japan
| | - Keisuke Yamada
- Biological Research Laboratories (M.D., H.T., S.H., S.M., K.Y., N.T.), Daiichi Sankyo, Co, Ltd, Tokyo, Japan
| | - Naoki Terasaka
- Biological Research Laboratories (M.D., H.T., S.H., S.M., K.Y., N.T.), Daiichi Sankyo, Co, Ltd, Tokyo, Japan
| | - Kazuishi Kubota
- Discovery Science and Technology Department (H.S., Y.F., N.W., K.K.), Daiichi Sankyo RD Novare, Co, Ltd, Tokyo, Japan
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27
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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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28
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Covalent Protein Immobilization onto Muscovite Mica Surface with a Photocrosslinker. MINERALS 2020. [DOI: 10.3390/min10050464] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Muscovite mica with an amino silane-modified surface is commonly used as a substrate in atomic force microscopy (AFM) studies of biological macromolecules. Herein, the efficiency of two different protein immobilization strategies employing either (N-hydroxysuccinimide ester)-based crosslinker (DSP) or benzophenone-based photoactivatable crosslinker (SuccBB) has been compared using AFM and mass spectrometry analysis. Two proteins with different physicochemical properties—human serum albumin (HSA) and horseradish peroxidase enzyme protein (HRP)—have been used as model objects in the study. In the case of HRP, both crosslinkers exhibited high immobilization efficiency—as opposed to the case with HSA, when sufficient capturing efficiency has only been observed with SuccBB photocrosslinker. The results obtained herein can find their application in commonly employed bioanalytical systems and in the development of novel highly sensitive chip-based diagnostic platforms employing immobilized proteins. The obtained data can also be of interest for other research areas in medicine and biotechnology employing immobilized biomolecules.
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29
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Grinnell SG, Uprety R, Varadi A, Subrath J, Hunkele A, Pan YX, Pasternak GW, Majumdar S. Synthesis and Characterization of Azido Aryl Analogs of IBNtxA for Radio-Photoaffinity Labeling Opioid Receptors in Cell Lines and in Mouse Brain. Cell Mol Neurobiol 2020; 41:977-993. [PMID: 32424771 DOI: 10.1007/s10571-020-00867-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 05/05/2020] [Indexed: 10/24/2022]
Abstract
Mu opioid receptors (MOR-1) mediate the biological actions of clinically used opioids such as morphine, oxycodone, and fentanyl. The mu opioid receptor gene, OPRM1, undergoes extensive alternative splicing, generating multiple splice variants. One type of splice variants are truncated variants containing only six transmembrane domains (6TM) that mediate the analgesic action of novel opioid drugs such as 3'-iodobenzoylnaltrexamide (IBNtxA). Previously, we have shown that IBNtxA is a potent analgesic effective in a spectrum of pain models but lacks many side-effects associated with traditional opiates. In order to investigate the targets labeled by IBNtxA, we synthesized two arylazido analogs of IBNtxA that allow photolabeling of mouse mu opioid receptors (mMOR-1) in transfected cell lines and mMOR-1 protein complexes that may comprise the 6TM sites in mouse brain. We demonstrate that both allyl and alkyne arylazido derivatives of IBNtxA efficiently radio-photolabeled mMOR-1 in cell lines and MOR-1 protein complexes expressed either exogenously or endogenously, as well as found in mouse brain. In future, design and application of such radio-photolabeling ligands with a conjugated handle will provide useful tools for further isolating or purifying MOR-1 to investigate site specific ligand-protein contacts and its signaling complexes.
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Affiliation(s)
- Steven G Grinnell
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA. .,Neuroscience Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA.
| | - Rajendra Uprety
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Andras Varadi
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.,Neuroscience Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Joan Subrath
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Amanda Hunkele
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Ying Xian Pan
- Department of Neurology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.,Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Gavril W Pasternak
- Department of Neurology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.,Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.,Neuroscience Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA.,Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Susruta Majumdar
- Center for Clinical Pharmacology, St Louis College of Pharmacy and Washington University School of Medicine, St Louis, MO, USA.
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30
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Hill JR, Coll RC, Schroder K, Robertson AA. Design, synthesis and evaluation of an NLRP3 inhibitor diazirine photoaffinity probe. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.151849] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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31
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Sannino A, Gironda-Martínez A, Gorre ÉMD, Prati L, Piazzi J, Scheuermann J, Neri D, Donckele EJ, Samain F. Critical Evaluation of Photo-cross-linking Parameters for the Implementation of Efficient DNA-Encoded Chemical Library Selections. ACS COMBINATORIAL SCIENCE 2020; 22:204-212. [PMID: 32109359 DOI: 10.1021/acscombsci.0c00023] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The growing importance of DNA-encoded chemical libraries (DECLs) as tools for the discovery of protein binders has sparked an interest for the development of efficient screening methodologies, capable of discriminating between high- and medium-affinity ligands. Here, we present a systematic investigation of selection methodologies, featuring a library displayed on single-stranded DNA, which could be hybridized to a complementary oligonucleotide carrying a diazirine photoreactive group. Model experiments, performed using ligands of different affinity to carbonic anhydrase IX, revealed a recovery of preferential binders up to 10%, which was mainly limited by the highly reactive nature of carbene intermediates generated during the photo-cross-linking process. Ligands featuring acetazolamide or p-phenylsulfonamide exhibited a higher recovery compared to their counterparts based on 3-sulfamoyl benzoic acid, which had a lower affinity toward the target. A systematic evaluation of experimental parameters revealed conditions that were ideally suited for library screening, which were used for the screening of a combinatorial DECL library, featuring 669 240 combinations of two sets of building blocks. Compared to conventional affinity capture procedures on protein immobilized on solid supports, photo-cross-linking provided a better discrimination of low-affinity CAIX ligands over the background signal and therefore can be used as a tandem methodology with the affinity capture procedures.
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Affiliation(s)
| | | | | | - Luca Prati
- Philochem AG, 8112 Otelfingen, Switzerland
| | | | - Jörg Scheuermann
- Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Dario Neri
- Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zürich, Switzerland
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32
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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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33
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Humeres E, Canle M, Lopes CN, Santaballa JA, Debacher NA, Moreira RDFPM, Safin V, Pérez MIF. Photo-immobilization of proteins on carbons. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2020; 202:111675. [PMID: 31733612 DOI: 10.1016/j.jphotobiol.2019.111675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 10/16/2019] [Accepted: 10/26/2019] [Indexed: 06/10/2023]
Abstract
The photofunctionalization of three different carbons with two proteins was studied at room temperature. Water solutions of bovine serum albumin, BSA, and α-amylase, AA, were photolyzed at 21 °C in the presence of graphite microparticles (6.20 μm), MPG, graphene oxide, MPGO, and graphene oxide modified with SO2, mMPGO. The insertion of BSA on carbon matrixes occurred with a deoxygenation reaction, most likely due to a dehydration step of a water molecule. XPS, TOC and TGA, showed that the BSA photo-insertion on MPG was highly efficient with 34.9% of the weight of MPG after photolysis, with an initial concentration of 1 g∙L-1 of BSA. A high yield of AA photoinsertion on the carbons was also obtained. The calculated weight of AA inserted on MPG and MPGO after photolysis was 22.30% and 18.08%, respectively, with respect to the initial weight of carbon, when the initial concentration of AA was 60 mg∙L-1. AA immobilized on MPG was active while the enzyme on MPGO showed a smaller activity, within the experimental error. Although a certain extent of denaturalization of both proteins was observed during photolysis, the molecular weight and composition changed very little during the photolysis, which would produce mainly conformational changes and isomerization reactions.
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Affiliation(s)
- Eduardo Humeres
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil.
| | - Moisés Canle
- Universidade da Coruña, Grupo Reactividade Química e Fotorreactividade (React!), Departamento de Química, Facultade de Ciencias & CICA, E-15071 A Coruña, Spain
| | - Cristiane Nunes Lopes
- Departamento de Engenharia Química e de Alimentos, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - J Arturo Santaballa
- Universidade da Coruña, Grupo Reactividade Química e Fotorreactividade (React!), Departamento de Química, Facultade de Ciencias & CICA, E-15071 A Coruña, Spain
| | - Nito Angelo Debacher
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Regina de F P M Moreira
- Departamento de Engenharia Química e de Alimentos, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Vladimir Safin
- Universidade da Coruña, Grupo Reactividade Química e Fotorreactividade (React!), Departamento de Química, Facultade de Ciencias & CICA, E-15071 A Coruña, Spain; Department of Chemistry and Technology of Natural Energy Carriers and Carbon Materials, Siberian Federal University, Russia
| | - M Isabel Fernández Pérez
- Universidade da Coruña, Grupo Reactividade Química e Fotorreactividade (React!), Departamento de Química, Facultade de Ciencias & CICA, E-15071 A Coruña, Spain
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Raymond AC, Gao B, Girard L, Minna JD, Gomika Udugamasooriya D. Unbiased peptoid combinatorial cell screen identifies plectin protein as a potential biomarker for lung cancer stem cells. Sci Rep 2019; 9:14954. [PMID: 31628412 PMCID: PMC6802198 DOI: 10.1038/s41598-019-51004-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 09/20/2019] [Indexed: 01/16/2023] Open
Abstract
Tumors often contain a small subset of drug-resisting, self-renewing, and highly metastatic cells called tumor initiating cells or cancer stem cells (CSCs). To develop new approaches to detecting and targeting lung cancer CSCs, we applied an "unbiased" peptoid combinatorial cell screen to identify highly specific ligands that bind a CSC subpopulation of non-small cell lung cancer cells (defined by Aldefluor positivity), but not the remaining aldefluor negative cancer cells from the same preclinical model. One of the 'hit' peptoids bound to plectin, a structural protein, predominantly expressed intracellularly, but whose localization on the cell surface is linked to tumor invasion and metastasis. Our studies show both genotypic and phenotypic correlations between plectin and lung CSCs, as well as association of high plectin mRNA expression with poor patient survival in lung adenocarcinoma, potentially identifying plectin as a biomarker for lung CSCs.
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Affiliation(s)
- Aaron C Raymond
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, 4849 Calhoun Rd, Houston, TX, 77204-5037, USA
| | - Boning Gao
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX, 75390, USA
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX, 75390, USA
- Departments of Pharmacology, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - Luc Girard
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX, 75390, USA
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX, 75390, USA
- Departments of Pharmacology, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - John D Minna
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX, 75390, USA
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX, 75390, USA
- Departments of Pharmacology, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX, 75390, USA
- Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - D Gomika Udugamasooriya
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, 4849 Calhoun Rd, Houston, TX, 77204-5037, USA.
- Department of Cancer Systems Imaging, MD Anderson Cancer Center, 1881 East Road, Houston, TX, 77030-4009, USA.
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Chan M, Lao FS, Chu PJ, Shpigelman J, Yao S, Nan J, Sato-Kaneko F, Li V, Hayashi T, Corr M, Carson DA, Cottam HB, Shukla NM. Structure–Activity Relationship Studies To Identify Affinity Probes in Bis-aryl Sulfonamides That Prolong Immune Stimuli. J Med Chem 2019; 62:9521-9540. [DOI: 10.1021/acs.jmedchem.9b00870] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Michael Chan
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093-0695, United States
| | - Fitzgerald S. Lao
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093-0695, United States
| | - Paul J. Chu
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093-0695, United States
| | - Jonathan Shpigelman
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093-0695, United States
| | - Shiyin Yao
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093-0695, United States
| | - Jason Nan
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093-0695, United States
| | - Fumi Sato-Kaneko
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093-0695, United States
| | - Vicky Li
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093-0695, United States
| | - Tomoko Hayashi
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093-0695, United States
| | - Maripat Corr
- Department of Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Dennis A. Carson
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093-0695, United States
| | - Howard B. Cottam
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093-0695, United States
| | - Nikunj M. Shukla
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093-0695, United States
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Flaxman HA, Chang CF, Wu HY, Nakamoto CH, Woo CM. A Binding Site Hotspot Map of the FKBP12-Rapamycin-FRB Ternary Complex by Photoaffinity Labeling and Mass Spectrometry-Based Proteomics. J Am Chem Soc 2019; 141:11759-11764. [PMID: 31309829 DOI: 10.1021/jacs.9b03764] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Structural characterization of small molecule binding site hotspots within the global proteome is uniquely enabled by photoaffinity labeling (PAL) coupled with chemical enrichment and unbiased analysis by mass spectrometry (MS). MS-based binding site maps provide structural resolution of interaction sites in conjunction with identification of target proteins. However, binding site hotspot mapping has been confined to relatively simple small molecules to date; extension to more complex compounds would enable the structural definition of new binding modes in the proteome. Here, we extend PAL and MS methods to derive a binding site hotspot map for the immunosuppressant rapamycin, a complex macrocyclic natural product that forms a ternary complex with the proteins FKBP12 and FRB. Photo-rapamycin was developed as a diazirine-based PAL probe for rapamycin, and the FKBP12-photo-rapamycin-FRB ternary complex formed readily in vitro. Photoirradiation, digestion, and MS analysis of the ternary complex revealed a McLafferty rearrangement product of photo-rapamycin conjugated to specific surfaces on FKBP12 and FRB. Molecular modeling based on the binding site map revealed two distinct conformations of complex-bound photo-rapamycin, providing a 5.0 Å distance constraint between the conjugated residues and the diazirine carbon and a 9.0 Å labeling radius for the diazirine upon photoactivation. These measurements may be broadly useful in the interpretation of binding site measurements from PAL. Thus, in characterizing the ternary complex of photo-rapamycin by MS, we applied binding site hotspot mapping to a macrocyclic natural product and extracted precise structural measurements for interpretation of PAL products that may enable the discovery of new binding sites in the "undruggable" proteome.
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Affiliation(s)
- Hope A Flaxman
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States
| | - Chia-Fu Chang
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States
| | - Hung-Yi Wu
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States
| | - Carter H Nakamoto
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States
| | - Christina M Woo
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States
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Wang P, Li Z, Jiang L, Zhou L, Ye D. Design and Synthesis of the Diazirine-based Clickable Photo-affinity Probe Targeting Sphingomyelin Synthase 2. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570180816666181106154601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:SMS family plays a very important role in sphingolipids metabolism and is involved in the membrane mobility and signaling transduction.Methods:SMS2 subtype was related to a variety of diseases and could be regarded as a promising potential drug target. However, the uncertainty of the binding sites and the molecular mechanism of action limited the development of SMS2 inhibitors. Herein, we discovered a photo-affinity probe PAL-1 targeting SMS2.Results:The enzyme inhibitory activity and the photo-affinity labeling experiments showed that PAL-1 could be mono-labeled on SMS2.Conclusion:In summary, starting from the N-arylbenzamides core structure and the minimalist terminal alkyne-containing diazirine photo-crosslinker, we designed and synthesized a photoaffinity probe PAL-1 targeting SMS2. The enzymatic inhibitory activity study showed that PAL-1 exhibited superior selectivities for SMS2 with an IC50 of 0.37 µM over SMS1.
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Affiliation(s)
- Penghui Wang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, China
| | - Zhining Li
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, China
| | - Lulu Jiang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, China
| | - Lu Zhou
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, China
| | - Deyong Ye
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, China
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38
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Abstract
Identification of the protein targets of bioactive small molecules is a routine challenge in chemical biology and phenotype-based drug discovery. Recent years have seen an explosion of approaches to meeting this challenge, but the traditional method of affinity pulldowns remains a practical choice in many contexts. This technique can be used as long as an affinity probe can be synthesized, usually with a crosslinking moiety to enable photo-affinity pulldowns. It can be applied to varied tissue types and can be performed with minimal specialized equipment. Here, we provide our protocol for photo-affinity pulldown experiments, with notes on making this method generally applicable to varied target identification challenges.
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Affiliation(s)
- Seung-Yong Seo
- College of Pharmacy, Gachon University, Incheon, South Korea
| | - Timothy W Corson
- Indiana University School of Medicine, Indianapolis, IN, United States.
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Kögler LM, Stichel J, Kaiser A, Beck-Sickinger AG. Cell-Free Expression and Photo-Crosslinking of the Human Neuropeptide Y 2 Receptor. Front Pharmacol 2019; 10:176. [PMID: 30881304 PMCID: PMC6405639 DOI: 10.3389/fphar.2019.00176] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 02/11/2019] [Indexed: 12/15/2022] Open
Abstract
G protein-coupled receptors (GPCRs) represent a large family of different proteins, which are involved in physiological processes throughout the entire body. Furthermore, they represent important drug targets. For rational drug design, it is important to get further insights into the binding mode of endogenous ligands as well as of therapeutic agents at the respective target receptors. However, structural investigations usually require homogenous, solubilized and functional receptors, which is still challenging. Cell-free expression methods have emerged in the last years and many different proteins are successfully expressed, including hydrophobic membrane proteins like GPCRs. In this work, an Escherichia coli based cell-free expression system was used to express the neuropeptide Y2 receptor (Y2R) for structural investigations. This GPCR was expressed in two different variants, a C-terminal enhanced green fluorescent fusion protein and a cysteine deficient variant. In order to obtain soluble receptors, the expression was performed in the presence of mild detergents, either Brij-35 or Brij-58, which led to high amounts of soluble receptor. Furthermore, the influence of temperature, pH value and additives on protein expression and solubilization was tested. For functional and structural investigations, the receptors were expressed at 37°C, pH 7.4 in the presence of 1 mM oxidized and 5 mM reduced glutathione. The expressed receptors were purified by ligand affinity chromatography and functionality of Y2R_cysteine_deficient was verified by a homogenous binding assay. Finally, photo-crosslinking studies were performed between cell-free expressed Y2R_cysteine_deficient and a neuropeptide Y (NPY) analog bearing the photoactive, unnatural amino acid p-benzoyl-phenylalanine at position 27 and biotin at position 22 for purification. After enzymatic digestion, fragments of crosslinked receptor were identified by mass spectrometry. Our findings demonstrate that, in contrast to Y1R, NPY position 27 remains flexible when bound to Y2R. These results are in agreement with the suggested binding mode of NPY at Y2R.
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Affiliation(s)
- Lisa Maria Kögler
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Leipzig, Germany
| | - Jan Stichel
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Leipzig, Germany
| | - Anette Kaiser
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Leipzig, Germany
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Müskens FM, Ward RJ, Herkt D, van de Langemheen H, Tobin AB, Liskamp RMJ, Milligan G. Design, Synthesis, and Evaluation of a Diazirine Photoaffinity Probe for Ligand-Based Receptor Capture Targeting G Protein-Coupled Receptors. Mol Pharmacol 2019; 95:196-209. [PMID: 30514721 PMCID: PMC6324650 DOI: 10.1124/mol.118.114249] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/27/2018] [Indexed: 12/21/2022] Open
Abstract
Chemoproteomic approaches to identify ligand-receptor interactions have gained popularity. However, identifying transmembrane receptors remains challenging. A new trifunctional probe to aid the nonbiased identification of such receptors was developed and synthesized using a convenient seven-step synthesis. This probe contained three functional groups: 1) an N-hydroxysuccinimide ester for ligand-coupling through free amines, 2) a diazirine moiety to capture the receptor of interest upon irradiation with UV light, and 3) a biotin group which allowed affinity purification of the final adduct using streptavidin. The interaction between the G protein-coupled tachykinin neurokinin 1 (NK1) receptor, expressed in an inducible manner, and the peptidic ligand substance P was used as a test system. Liquid chromatography-mass spectrometry analysis confirmed successful coupling of the probe to substance P, while inositol monophosphate accumulation assays demonstrated that coupling of the probe did not interfere substantially with the substance P-NK1 receptor interaction. Confocal microscopy and western blotting provided evidence of the formation of a covalent bond between the probe and the NK1 receptor upon UV activation. As proof of concept, the probe was used in full ligand-based receptor-capture experiments to identify the substance P-binding receptor via liquid chromatography-tandem mass spectrometry, resulting in the successful identification of only the NK1 receptor. This provides proof of concept toward general utilization of this probe to define interactions between ligands and previously unidentified plasma-membrane receptors.
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Affiliation(s)
- Frederike M Müskens
- School of Chemistry, College of Science and Engineering (F.M.M., D.H., H.L., R.M.J.L.) and Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences (F.M.M., R.J.W., A.B.T., G.M.), University of Glasgow, Glasgow, United Kingdom
| | - Richard J Ward
- School of Chemistry, College of Science and Engineering (F.M.M., D.H., H.L., R.M.J.L.) and Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences (F.M.M., R.J.W., A.B.T., G.M.), University of Glasgow, Glasgow, United Kingdom
| | - Dominik Herkt
- School of Chemistry, College of Science and Engineering (F.M.M., D.H., H.L., R.M.J.L.) and Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences (F.M.M., R.J.W., A.B.T., G.M.), University of Glasgow, Glasgow, United Kingdom
| | - Helmus van de Langemheen
- School of Chemistry, College of Science and Engineering (F.M.M., D.H., H.L., R.M.J.L.) and Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences (F.M.M., R.J.W., A.B.T., G.M.), University of Glasgow, Glasgow, United Kingdom
| | - Andrew B Tobin
- School of Chemistry, College of Science and Engineering (F.M.M., D.H., H.L., R.M.J.L.) and Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences (F.M.M., R.J.W., A.B.T., G.M.), University of Glasgow, Glasgow, United Kingdom
| | - Rob M J Liskamp
- School of Chemistry, College of Science and Engineering (F.M.M., D.H., H.L., R.M.J.L.) and Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences (F.M.M., R.J.W., A.B.T., G.M.), University of Glasgow, Glasgow, United Kingdom
| | - Graeme Milligan
- School of Chemistry, College of Science and Engineering (F.M.M., D.H., H.L., R.M.J.L.) and Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences (F.M.M., R.J.W., A.B.T., G.M.), University of Glasgow, Glasgow, United Kingdom
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41
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Letham DS, Zhang XD, Hocart CH. The Synthesis of ³H-Labelled 8-Azido-N⁶-Benzyladenine and Related Compounds for Photoaffinity Labelling of Cytokinin-Binding Proteins. Molecules 2019; 24:E349. [PMID: 30669410 PMCID: PMC6359637 DOI: 10.3390/molecules24020349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/07/2019] [Accepted: 01/17/2019] [Indexed: 11/20/2022] Open
Abstract
The biology of the group of plant hormones termed cytokinins is reviewed to reveal areas where further studies of cytokinin-binding proteins could be significant. Such areas include: inhibition of human tumour cell growth by cytokinin ribosides, the role of cytokinins in the development of diverse micro-organisms including the cyanobacteria and Mycobacterium tuberculosis, the very rapid responses of plant cells to exogenous cytokinins, and other aspects of cytokinin plant biology. Photoaffinity labelling (PAL) coupled to the recent advances in HPLC of proteins and mass spectral analysis and sequencing of proteins, may have relevance to these areas. To facilitate PAL, we present experimental details for two methods for synthesis of 8-azido-N⁶-benzyladenine, which has the azido affinity group in the preferred position of the purine ring. Synthesis from [2-³H]adenosine yielded the above-mentioned PAL reagent with ³H in the purine ring and also gave labelled 9-riboside and 8-azido-N⁶,9-dibenzyladenine. 8-Azido-N⁶-benzyladenine was also prepared from 6,8-dichloropurine by a facile synthesis, which would allow a label to be sited in the benzyl group where substituents can also be introduced to vary cytokinin activity. The use of inactive cytokinin analogues in assessing the significance of PAL is discussed.
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Affiliation(s)
- David S Letham
- Research School of Biology, Australian National University, Canberra ACT 0200, Australia.
| | - Xue-Dong Zhang
- Research School of Biology, Australian National University, Canberra ACT 0200, Australia.
| | - Charles H Hocart
- Research School of Biology, Australian National University, Canberra ACT 0200, Australia.
- School of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Long Shuo Rd, Wei Yang District, Shaanxi 710021, China.
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42
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Hosoya T, Watanabe K, Tsuda J, Ochiai H, Niwa T. Divergent Synthesis of Photoaffinity Probe Candidates by Click Reactions of Azido-Substituted Aryltrifluoromethyldiazirines. HETEROCYCLES 2019. [DOI: 10.3987/com-18-s(f)76] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Hosoya T, Yoshida S, Nishiyama Y, Misawa Y, Hazama Y, Oya K. Synthesis of Diverse 3-Azido-5-(azidomethyl)benzene Derivatives via Formal C–H Azidation and Functional Group-Selective Transformations. HETEROCYCLES 2019. [DOI: 10.3987/com-18-s(f)72] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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44
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Procacci B, Roy SS, Norcott P, Turner N, Duckett SB. Unlocking a Diazirine Long-Lived Nuclear Singlet State via Photochemistry: NMR Detection and Lifetime of an Unstabilized Diazo-Compound. J Am Chem Soc 2018; 140:16855-16864. [PMID: 30407809 PMCID: PMC6300312 DOI: 10.1021/jacs.8b10923] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Diazirines
are important for photoaffinity labeling, and their
photoisomerization is relatively well-known. This work shows how hyperpolarized
NMR spectroscopy can be used to characterize an unstable diazo-compound
formed via photoisomerization of a 15N2-labeled
silyl-ether-substituted diazirine. This diazirine is prepared in a
nuclear spin singlet state via catalytic transfer of spin order from para-hydrogen. The active hyperpolarization catalyst is
characterized to provide insight into the mechanism. The photochemical
isomerization of the diazirine into the diazo-analogue allows the
NMR invisible nuclear singlet state of the parent compound to be probed.
The identity of the diazo-species is confirmed by trapping with N-phenyl maleimide via a cycloaddition reaction to afford
bicyclic pyrazolines that also show singlet state character. The presence
of singlet states in the diazirine and the diazo-compound is validated
by comparison of experimental nutation behavior with theoretical simulation.
The magnetic state lifetime of the diazo-compound is determined as
12 ± 1 s in CD3OD solution at room temperature, whereas
its chemical lifetime is measured as 100 ± 5 s by related hyperpolarized
NMR studies. Indirect evidence for the generation of the photoproduct para-N2 is presented.
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Affiliation(s)
- Barbara Procacci
- Centre for Hyperpolarisation in Magnetic Resonance, Department of Chemistry, York Science Park , University of York , York YO10 5NY , United Kingdom
| | - Soumya S Roy
- Centre for Hyperpolarisation in Magnetic Resonance, Department of Chemistry, York Science Park , University of York , York YO10 5NY , United Kingdom
| | - Philip Norcott
- Centre for Hyperpolarisation in Magnetic Resonance, Department of Chemistry, York Science Park , University of York , York YO10 5NY , United Kingdom
| | - Norman Turner
- Accelerator Research Group, University of Huddersfield , Queensgate, Huddersfield HD1 3DH , United Kingdom
| | - Simon B Duckett
- Centre for Hyperpolarisation in Magnetic Resonance, Department of Chemistry, York Science Park , University of York , York YO10 5NY , United Kingdom
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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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46
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Beiroth F, Koudelka T, Overath T, Knight SD, Tholey A, Lindhorst TK. Diazirine-functionalized mannosides for photoaffinity labeling: trouble with FimH. Beilstein J Org Chem 2018; 14:1890-1900. [PMID: 30112094 PMCID: PMC6071696 DOI: 10.3762/bjoc.14.163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/27/2018] [Indexed: 12/27/2022] Open
Abstract
Photoaffinity labeling is frequently employed for the investigation of ligand–receptor interactions in solution. We have employed an interdisciplinary methodology to achieve facile photolabeling of the lectin FimH, which is a bacterial protein, crucial for adhesion, colonization and infection. Following our earlier work, we have here designed and synthesized diazirine-functionalized mannosides as high-affinity FimH ligands and performed an extensive study on photo-crosslinking of the best ligand (mannoside 3) with a series of model peptides and FimH. Notably, we have employed high-performance mass spectrometry to be able to detect radiation results with the highest possible accuracy. We are concluding from this study that photolabeling of FimH with sugar diazirines has only very limited success and cannot be regarded a facile approach for covalent modification of FimH.
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Affiliation(s)
- Femke Beiroth
- Otto Diels Institute of Organic Chemistry, Christiana Albertina University of Kiel, Otto-Hahn-Platz 3/4, 24118 Kiel, Germany
| | - Tomas Koudelka
- Systematic Proteomics & Bioanalytics, Institute for Experimental Medicine, Christiana Albertina University of Kiel, Niemannsweg 11, D-24105 Kiel, Germany
| | - Thorsten Overath
- Systematic Proteomics & Bioanalytics, Institute for Experimental Medicine, Christiana Albertina University of Kiel, Niemannsweg 11, D-24105 Kiel, Germany
| | - Stefan D Knight
- Department of Cell and Molecular Biology, Uppsala University, Uppsala Biomedical Centre, P.O. Box 596, S-751 24 Uppsala, Sweden
| | - Andreas Tholey
- Systematic Proteomics & Bioanalytics, Institute for Experimental Medicine, Christiana Albertina University of Kiel, Niemannsweg 11, D-24105 Kiel, Germany
| | - Thisbe K Lindhorst
- Otto Diels Institute of Organic Chemistry, Christiana Albertina University of Kiel, Otto-Hahn-Platz 3/4, 24118 Kiel, Germany
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47
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Desrochers GF, Cornacchia C, McKay CS, Pezacki JP. Activity-Based Phosphatidylinositol Kinase Probes Detect Changes to Protein-Protein Interactions During Hepatitis C Virus Replication. ACS Infect Dis 2018; 4:752-757. [PMID: 29509402 DOI: 10.1021/acsinfecdis.8b00047] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Protein-protein interactions are integral to host-virus interactions and can contribute significantly to enzyme regulation by changing the localization of both host and viral enzymes within the cell, inducing conformational change relevant to enzyme activity or recruiting other additional proteins to form functional complexes. Identifying the interactors of active enzymes using an activity-based protein profiling probe has allowed us to characterize both normal enzyme activation mechanisms and the manner by which these mechanisms are hijacked and altered by the hepatitis C virus (HCV). Here, we report use of a novel activity-based probe, PIKBPyne, which labels phosphatidylinositol kinases (PIKs) in an activity-based manner, to investigate HCV-dependent changes in protein-protein interactions for PI4KB. Herein, we report the synthesis of new variations on PIKBPyne, compare their ability to label the interacting partners of PI4KB, and demonstrate the utility of our approach in characterizing virus-mediated changes to host function.
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Affiliation(s)
- Geneviève F. Desrochers
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Pvt., Ottawa, Ontario K1N 6N5, Canada
| | - Christina Cornacchia
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Pvt., Ottawa, Ontario K1N 6N5, Canada
| | - Craig S. McKay
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Pvt., Ottawa, Ontario K1N 6N5, Canada
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Pvt., Ottawa, Ontario K1N 6N5, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Rd., Ottawa, Ontario K1H 8M5, Canada
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48
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Hill JR, Robertson AAB. Fishing for Drug Targets: A Focus on Diazirine Photoaffinity Probe Synthesis. J Med Chem 2018; 61:6945-6963. [PMID: 29683660 DOI: 10.1021/acs.jmedchem.7b01561] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Target identification is a high-priority, albeit challenging, aspect of drug discovery. Diazirine-based photoaffinity probes (PAPs) can facilitate the process by covalently capturing transient molecular interactions. This can help identify target proteins and map the ligand's interactome. Diazirine probes have even been incorporated by cellular machinery into proteins. Embarking on the synthesis of customized PAPs, containing either an aliphatic or trifluoromethyl phenyl diazirine, can be a considerable endeavor, particularly for medicinal chemists and chemical biologists new to the field. This review takes a synthetic focus, aiming to summarize available routes, propose new avenues, and illuminate recent advances in diazirine synthesis. Select examples of diazirine photoaffinity labeling applications have been included throughout to provide instructive definition of the advantages and limitations of the technology while simultaneously highlighting how these reagents can be applied in a practical sense.
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Affiliation(s)
- James R Hill
- Institute for Molecular Bioscience , The University of Queensland , St. Lucia , Queensland 4072 , Australia
| | - Avril A B Robertson
- Institute for Molecular Bioscience , The University of Queensland , St. Lucia , Queensland 4072 , Australia.,School of Chemistry and Molecular Biosciences , The University of Queensland , St. Lucia QLD4072 , Australia
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49
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Graham E, Rymarchyk S, Wood M, Cen Y. Development of Activity-Based Chemical Probes for Human Sirtuins. ACS Chem Biol 2018; 13:782-792. [PMID: 29385333 DOI: 10.1021/acschembio.7b00754] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Sirtuins consume stoichiometric amounts of nicotinamide adenine dinucleotide (NAD+) to remove an acetyl group from lysine residues. These enzymes have been implicated in regulating various cellular events and have also been suggested to mediate the beneficial effects of calorie restriction (CR). However, controversies on sirtuin biology also peaked during the past few years because of conflicting results from different research groups. This is partly because these enzymes have been discovered recently and the intricate interaction loops between sirtuins and other proteins make the characterization of them extremely difficult. Current molecular biology and proteomics techniques report protein abundance rather than active sirtuin content. Innovative chemical tools that can directly probe the functional state of sirtuins are desperately needed. We have obtained a set of powerful activity-based chemical probes that are capable of assessing the active content of sirtuins in model systems. These probes consist of a chemical "warhead" that binds to the active site of active enzyme and a handle that can be used for the visualization of these enzymes by fluorescence. In complex native proteome, the probes can selectively "highlight" the active sirtuin components. Furthermore, these probes were also able to probe the dynamic change of sirtuin activity in response to cellular stimuli. These chemical probes and the labeling strategies will provide transformative technology to allow the direct linking of sirtuin activity to distinct physiological processes. They will create new opportunities to investigate how sirtuins provide health benefits in adapting cells to environmental cues and provide critical information to dissect sirtuin regulatory networks.
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Affiliation(s)
- Elysian Graham
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, Vermont 05446, United States
| | - Stacia Rymarchyk
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, Vermont 05446, United States
| | - Marci Wood
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, Vermont 05446, United States
| | - Yana Cen
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, Vermont 05446, United States
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50
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Woll KA, Dailey WP, Eckenhoff RG. Identification of General Anesthetic Target Protein-Binding Sites by Photoaffinity Labeling and Mass Spectrometry. Methods Enzymol 2018; 602:231-246. [PMID: 29588031 DOI: 10.1016/bs.mie.2018.01.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
General anesthetics are unique in that they represent a diverse range of chemical structures. Therefore, it is not surprising that the desired and undesired molecular targets, and binding sites therein, are as equally diverse and unique. Photoaffinity labeling has proven to be a valuable strategy for the identification of anesthetic molecular targets, as well as binding sites within those targets. In combination with the advances in mass spectrometry-based proteomics, along with the ability to comprehensively map posttranslational modifications, the method is likely to undergo continued improvement. Here, we provide the fundamentals for the design and development of an anesthetic photolabel. We also outline a protocol for the identification of photolabeled residues by mass spectrometry. The major steps include the photolabeling experiment, sample preparation, high-resolution mass spectrometry, and data analysis. The protocol can be used as a foundation for further optimization for the specific protein of interest and conditions of an experiment. The use of photoaffinity labeling adds an advantageous alternative and/or complementary approach to increase understanding of anesthetic molecular mechanisms.
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Affiliation(s)
- Kellie A Woll
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - William P Dailey
- University of Pennsylvania School of Arts and Sciences, Philadelphia, PA, United States
| | - Roderic G Eckenhoff
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States.
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