1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Abstract
Here, we describe a protocol for a photoaffinity labeling probe strategy for target deconvolution in live cells. We made a chemical probe by incorporation of a photoreactive group to covalently cross-link with adjacent amino acid residues upon UV irradiation. Click chemistry-based enrichment captures labeled proteins for proteomic analysis. Here, we detail specifics for finding targets of LXRβ, but the protocol has potential for application to other targets. For complete details on the use and execution of this protocol, please refer to Seneviratne et al. (2020). Protocol detailing photoaffinity probe strategy for target deconvolution in live cells Competition with parent compound demonstrates specific binding Photoaffinity label provides evidence of small-molecule binding to LXRβ Click chemistry-based enrichment captures labeled proteins for proteomic analysis
Collapse
|
3
|
Hellyer SD, Aggarwal S, Chen ANY, Leach K, Lapinsky DJ, Gregory KJ. Development of Clickable Photoaffinity Ligands for Metabotropic Glutamate Receptor 2 Based on Two Positive Allosteric Modulator Chemotypes. ACS Chem Neurosci 2020; 11:1597-1609. [PMID: 32396330 DOI: 10.1021/acschemneuro.0c00009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The metabotropic glutamate receptor 2 (mGlu2) is a transmembrane-spanning class C G protein-coupled receptor that is an attractive therapeutic target for multiple psychiatric and neurological disorders. A key challenge has been deciphering the contribution of mGlu2 relative to other closely related mGlu receptors in mediating different physiological responses, which could be achieved through the utilization of subtype selective pharmacological tools. In this respect, allosteric modulators that recognize ligand-binding sites distinct from the endogenous neurotransmitter glutamate offer the promise of higher receptor-subtype selectivity. We hypothesized that mGlu2-selective positive allosteric modulators could be derivatized to generate bifunctional pharmacological tools. Here we developed clickable photoaffinity probes for mGlu2 based on two different positive allosteric modulator scaffolds that retained similar pharmacological activity to parent compounds. We demonstrate successful probe-dependent incorporation of a commercially available clickable fluorophore using bioorthogonal conjugation. Importantly, we also show the limitations of using these probes to assess in situ fluorescence of mGlu2 in intact cells where significant nonspecific membrane binding is evident.
Collapse
Affiliation(s)
- Shane D. Hellyer
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, 399 Royal Parade, Parkville, Victoria 3052, Australia
| | - Shaili Aggarwal
- Division of Pharmaceutical Sciences, School of Pharmacy, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Amy N. Y. Chen
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, 399 Royal Parade, Parkville, Victoria 3052, Australia
| | - Katie Leach
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, 399 Royal Parade, Parkville, Victoria 3052, Australia
| | - David J. Lapinsky
- Division of Pharmaceutical Sciences, School of Pharmacy, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Karen J. Gregory
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, 399 Royal Parade, Parkville, Victoria 3052, Australia
| |
Collapse
|
4
|
Komatsu R, Sakurai K. Development of Chemical Probes for Functional Analysis of Anticancer Saponin OSW‐1. CHEM REC 2019; 19:2362-2369. [DOI: 10.1002/tcr.201900042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/17/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Rina Komatsu
- Department of Biotechnology and Life Science Faculty of EngineeringTokyo University of Agriculture and Technology 2-28-16, Nakacho, Koganei-shi Tokyo 184-8588 Japan
| | - Kaori Sakurai
- Department of Biotechnology and Life Science Faculty of EngineeringTokyo University of Agriculture and Technology 2-28-16, Nakacho, Koganei-shi Tokyo 184-8588 Japan
| |
Collapse
|
5
|
Yamada K, Ito Y. Recent Chemical Approaches for Site‐Specific Conjugation of Native Antibodies: Technologies toward Next‐Generation Antibody–Drug Conjugates. Chembiochem 2019; 20:2729-2737. [DOI: 10.1002/cbic.201900178] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Kei Yamada
- Ajinomoto Co., Inc. 1-1 Suzuki-Cho Kawasaki-Ku Kawasaki-Shi Kanagawa 210-8681 Japan
- Department of Chemistry and BioscienceGraduate School of Science and EngineeringKagoshima University 1-21-35 Korimoto Kagoshima 890-0065 Japan
| | - Yuji Ito
- Department of Chemistry and BioscienceGraduate School of Science and EngineeringKagoshima University 1-21-35 Korimoto Kagoshima 890-0065 Japan
| |
Collapse
|
6
|
Lebraud H, Surova O, Courtin A, O'Reilly M, Valenzano CR, Nordlund P, Heightman TD. Quantitation of ERK1/2 inhibitor cellular target occupancies with a reversible slow off-rate probe. Chem Sci 2018; 9:8608-8618. [PMID: 30568786 PMCID: PMC6253716 DOI: 10.1039/c8sc02754d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/15/2018] [Indexed: 11/21/2022] Open
Abstract
Target engagement is a key concept in drug discovery and its direct measurement can provide a quantitative understanding of drug efficacy and/or toxicity. Failure to demonstrate target occupancy in relevant cells and tissues has been recognised as a contributing factor to the low success rate of clinical drug development. Several techniques are emerging to quantify target engagement in cells; however, in situ measurements remain challenging, mainly due to technical limitations. Here, we report the development of a non-covalent clickable probe, based on SCH772984, a slow off-rate ERK1/2 inhibitor, which enabled efficient pull down of ERK1/2 protein via click reaction with tetrazine tagged agarose beads. This was used in a competition setting to measure relative target occupancy by selected ERK1/2 inhibitors. As a reference we used the cellular thermal shift assay, a label-free biophysical assay relying solely on ligand-induced thermodynamic stabilization of proteins. To validate the EC50 values measured by both methods, the results were compared with IC50 data for the phosphorylation of RSK, a downstream substrate of ERK1/2 used as a functional biomarker of ERK1/2 inhibition. We showed that a slow off-rate reversible probe can be used to efficiently pull down cellular proteins, significantly extending the potential of the approach beyond the need for covalent or photoaffinity warheads.
Collapse
Affiliation(s)
- Honorine Lebraud
- Astex Pharmaceuticals , 436 Cambridge Science Park , Cambridge , CB4 0QA , UK . ;
| | - Olga Surova
- Astex Pharmaceuticals , 436 Cambridge Science Park , Cambridge , CB4 0QA , UK . ;
- Department of Oncology-Pathology , Karolinska Institute , CCK R8:01 , Karolinska Hospital , 171 76 Stockholm , Sweden
| | - Aurélie Courtin
- Astex Pharmaceuticals , 436 Cambridge Science Park , Cambridge , CB4 0QA , UK . ;
| | - Marc O'Reilly
- Astex Pharmaceuticals , 436 Cambridge Science Park , Cambridge , CB4 0QA , UK . ;
| | - Chiara R Valenzano
- Astex Pharmaceuticals , 436 Cambridge Science Park , Cambridge , CB4 0QA , UK . ;
| | - Pär Nordlund
- Department of Oncology-Pathology , Karolinska Institute , CCK R8:01 , Karolinska Hospital , 171 76 Stockholm , Sweden
| | - Tom D Heightman
- Astex Pharmaceuticals , 436 Cambridge Science Park , Cambridge , CB4 0QA , UK . ;
| |
Collapse
|
7
|
Murale DP, Hong SC, Haque MM, Lee JS. Photo-affinity labeling (PAL) in chemical proteomics: a handy tool to investigate protein-protein interactions (PPIs). Proteome Sci 2017; 15:14. [PMID: 28652856 PMCID: PMC5483283 DOI: 10.1186/s12953-017-0123-3] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 06/15/2017] [Indexed: 12/14/2022] Open
Abstract
Protein-protein interactions (PPIs) trigger a wide range of biological signaling pathways that are crucial for biomedical research and drug discovery. Various techniques have been used to study specific proteins, including affinity chromatography, activity-based probes, affinity-based probes and photo-affinity labeling (PAL). PAL has become one of the most powerful strategies to study PPIs. Traditional photocrosslinkers are used in PAL, including benzophenone, aryl azide, and diazirine. Upon photoirradiation, these photocrosslinkers (Pls) generate highly reactive species that react with adjacent molecules, resulting in a direct covalent modification. This review introduces recent examples of chemical proteomics study using PAL for PPIs.
Collapse
Affiliation(s)
- Dhiraj P Murale
- Molecular Recognition Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea
| | - Seong Cheol Hong
- Molecular Recognition Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea.,Department of Biological Chemistry, KIST-School UST, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea
| | - Md Mamunul Haque
- Molecular Recognition Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea
| | - Jun-Seok Lee
- Molecular Recognition Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea.,Department of Biological Chemistry, KIST-School UST, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea
| |
Collapse
|
8
|
Teruya K, Rankin GM, Chrysanthopoulos PK, Tonissen KF, Poulsen S. Characterisation of Photoaffinity‐Based Chemical Probes by Fluorescence Imaging and Native‐State Mass Spectrometry. Chembiochem 2017; 18:739-754. [DOI: 10.1002/cbic.201600598] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Indexed: 12/28/2022]
Affiliation(s)
- Kanae Teruya
- Griffith Institute for Drug Discovery Griffith University Don Young Road Nathan Queensland 4111 Australia
- School of Natural Sciences Griffith University Nathan Queensland 4111 Australia
| | - Gregory M. Rankin
- Griffith Institute for Drug Discovery Griffith University Don Young Road Nathan Queensland 4111 Australia
| | | | - Kathryn F. Tonissen
- Griffith Institute for Drug Discovery Griffith University Don Young Road Nathan Queensland 4111 Australia
- School of Natural Sciences Griffith University Nathan Queensland 4111 Australia
| | - Sally‐Ann Poulsen
- Griffith Institute for Drug Discovery Griffith University Don Young Road Nathan Queensland 4111 Australia
- School of Natural Sciences Griffith University Nathan Queensland 4111 Australia
| |
Collapse
|
9
|
Hill ZB, Pollock SB, Zhuang M, Wells JA. Direct Proximity Tagging of Small Molecule Protein Targets Using an Engineered NEDD8 Ligase. J Am Chem Soc 2016; 138:13123-13126. [PMID: 27626304 DOI: 10.1021/jacs.6b06828] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Identifying the protein targets of bioactive small molecules remains a major problem in the discovery of new chemical probes and therapeutics. While activity-based probes and photo-cross-linkers have had success in identifying protein targets of small molecules, each technique has limitations. Here we describe a method for direct proximity tagging of proteins that bind small molecules. We engineered a promiscuous ligase based on the NEDD8 conjugating enzyme, Ubc12, which can be covalently linked to a small molecule of interest. When target proteins bind the small molecule, they are directly labeled on surface lysines with a biotinylated derivative of the small ubiquitin homologue, NEDD8. This unique covalent tag can then be used to identify the small molecule binding proteins. Utilizing the drug dasatinib, we have shown that dasatinib-directed NEDDylation occurs for known endogenous protein binders in complex cell lysates. In addition, we have been able to improve NEDDylation efficiency through rational mutagenesis. Finally, we have shown that affinity-directed NEDDylation can be applied to two other protein-ligand interactions beyond kinases. Proximity tagging using this engineered ligase requires direct binding of the target and, thus, provides a useful and orthogonal approach to facilitate small molecule target identification.
Collapse
Affiliation(s)
- Zachary B Hill
- Department of Pharmaceutical Chemistry and ‡Department of Cellular and Molecular Pharmacology, University of California , San Francisco, California 94158, United States
| | - Samuel B Pollock
- Department of Pharmaceutical Chemistry and ‡Department of Cellular and Molecular Pharmacology, University of California , San Francisco, California 94158, United States
| | - Min Zhuang
- Department of Pharmaceutical Chemistry and ‡Department of Cellular and Molecular Pharmacology, University of California , San Francisco, California 94158, United States
| | - James A Wells
- Department of Pharmaceutical Chemistry and ‡Department of Cellular and Molecular Pharmacology, University of California , San Francisco, California 94158, United States
| |
Collapse
|
10
|
James TD, Cardozo T, Abell LE, Hsieh ML, Jenkins LMM, Jha SS, Hinton DM. Visualizing the phage T4 activated transcription complex of DNA and E. coli RNA polymerase. Nucleic Acids Res 2016; 44:7974-88. [PMID: 27458207 PMCID: PMC5027511 DOI: 10.1093/nar/gkw656] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 07/05/2016] [Indexed: 11/13/2022] Open
Abstract
The ability of RNA polymerase (RNAP) to select the right promoter sequence at the right time is fundamental to the control of gene expression in all organisms. However, there is only one crystallized structure of a complete activator/RNAP/DNA complex. In a process called σ appropriation, bacteriophage T4 activates a class of phage promoters using an activator (MotA) and a co-activator (AsiA), which function through interactions with the σ70 subunit of RNAP. We have developed a holistic, structure-based model for σ appropriation using multiple experimentally determined 3D structures (Escherichia coli RNAP, the Thermus aquaticus RNAP/DNA complex, AsiA /σ70 Region 4, the N-terminal domain of MotA [MotANTD], and the C-terminal domain of MotA [MotACTD]), molecular modeling, and extensive biochemical observations indicating the position of the proteins relative to each other and to the DNA. Our results visualize how AsiA/MotA redirects σ, and therefore RNAP activity, to T4 promoter DNA, and demonstrate at a molecular level how the tactful interaction of transcriptional factors with even small segments of RNAP can alter promoter specificity. Furthermore, our model provides a rational basis for understanding how a mutation within the β subunit of RNAP (G1249D), which is far removed from AsiA or MotA, impairs σ appropriation.
Collapse
Affiliation(s)
- Tamara D James
- Gene Expression and Regulation Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York University School of Medicine, 180 Varick Street, Room 637, New York, NY 10014, USA
| | - Timothy Cardozo
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York University School of Medicine, 180 Varick Street, Room 637, New York, NY 10014, USA
| | - Lauren E Abell
- Gene Expression and Regulation Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Meng-Lun Hsieh
- Gene Expression and Regulation Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lisa M Miller Jenkins
- Collaborative Protein Technology Resource, Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Saheli S Jha
- Gene Expression and Regulation Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Deborah M Hinton
- Gene Expression and Regulation Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
11
|
Syeda SS, Rice D, Hook DJ, Heckert LL, Georg GI. Synthesis of Arylazide- and Diazirine-Containing CrAsH-EDT2 Photoaffinity Probes. Arch Pharm (Weinheim) 2016; 349:233-41. [PMID: 26948688 PMCID: PMC5069617 DOI: 10.1002/ardp.201500440] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/03/2016] [Accepted: 02/10/2016] [Indexed: 11/08/2022]
Abstract
Two photo-crosslinking biarsenical (CrAsH-EDT2 )-modified probes were synthesized that are expected to be useful tools for tetracysteine-labeled proteins to facilitate the co-affinity purification of their DNA binding sequences and interacting proteins. In addition, improvements for the synthesis of CrAsH-EDT2 and N(1) -(4-azido-2-nitrophenyl)hexane-1,6-diamine are reported. Both photoprobes effectively entered HeLa cells (and the nucleus) and were dependent on the tetracysteine motif in recombinant DMRT1 (doublesex and Mab3-related transcription factor) to induce fluorescence, suggesting that their crosslinking abilities can be exploited for the identification of nucleic acids and proteins associated with a protein of interest.
Collapse
Affiliation(s)
- Shameem S Syeda
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN, USA.,Interdisciplinary Center for Male Contraceptive Research and Drug Development, University of Kansas Medical Center, Kansas City, KS, USA
| | - Daren Rice
- Interdisciplinary Center for Male Contraceptive Research and Drug Development, University of Kansas Medical Center, Kansas City, KS, USA.,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Derek J Hook
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN, USA.,Interdisciplinary Center for Male Contraceptive Research and Drug Development, University of Kansas Medical Center, Kansas City, KS, USA
| | - Leslie L Heckert
- Interdisciplinary Center for Male Contraceptive Research and Drug Development, University of Kansas Medical Center, Kansas City, KS, USA.,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Gunda I Georg
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN, USA.,Interdisciplinary Center for Male Contraceptive Research and Drug Development, University of Kansas Medical Center, Kansas City, KS, USA
| |
Collapse
|
12
|
Friedman Ohana R, Kirkland TA, Woodroofe CC, Levin S, Uyeda HT, Otto P, Hurst R, Robers MB, Zimmerman K, Encell LP, Wood KV. Deciphering the Cellular Targets of Bioactive Compounds Using a Chloroalkane Capture Tag. ACS Chem Biol 2015; 10:2316-24. [PMID: 26162280 DOI: 10.1021/acschembio.5b00351] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phenotypic screening of compound libraries is a significant trend in drug discovery, yet success can be hindered by difficulties in identifying the underlying cellular targets. Current approaches rely on tethering bioactive compounds to a capture tag or surface to allow selective enrichment of interacting proteins for subsequent identification by mass spectrometry. Such methods are often constrained by ineffective capture of low affinity and low abundance targets. In addition, these methods are often not compatible with living cells and therefore cannot be used to verify the pharmacological activity of the tethered compounds. We have developed a novel chloroalkane capture tag that minimally affects compound potency in cultured cells, allowing binding interactions with the targets to occur under conditions relevant to the desired cellular phenotype. Subsequent isolation of the interacting targets is achieved through rapid lysis and capture onto immobilized HaloTag protein. Exchanging the chloroalkane tag for a fluorophore, the putative targets identified by mass spectrometry can be verified for direct binding to the compound through resonance energy transfer. Using the interaction between histone deacetylases (HDACs) and the inhibitor, Vorinostat (SAHA), as a model system, we were able to identify and verify all the known HDAC targets of SAHA as well as two previously undescribed targets, ADO and CPPED1. The discovery of ADO as a target may provide mechanistic insight into a reported connection between SAHA and Huntington's disease.
Collapse
Affiliation(s)
| | | | | | - Sergiy Levin
- Promega Biosciences LLC, San Luis Obispo, California, United States
| | - H. Tetsuo Uyeda
- Promega Biosciences LLC, San Luis Obispo, California, United States
| | - Paul Otto
- Promega Corporation, Madison, Wisconsin, United States
| | - Robin Hurst
- Promega Corporation, Madison, Wisconsin, United States
| | | | | | | | - Keith V. Wood
- Promega Corporation, Madison, Wisconsin, United States
| |
Collapse
|
13
|
Mihai DM, Hall S, Deng H, Welch CJ, Kawamura A. Benzophenone and its analogs bind to human glyoxalase 1. Bioorg Med Chem Lett 2015; 25:5349-51. [PMID: 26420066 DOI: 10.1016/j.bmcl.2015.09.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 09/10/2015] [Accepted: 09/14/2015] [Indexed: 10/23/2022]
Abstract
Benzophenone is a popular photophore for photoaffinity-labeling. It is also an important framework for drug development; many drugs contain benzophenone or analogous frameworks. The current work reports that benzophenone and its analogs bind to human glyoxalase 1. The binding, however, has little effect on the catalytic activity of this enzyme. The implications of the finding in terms of both drug development and photoaffinity-labeling are discussed.
Collapse
Affiliation(s)
- Doina M Mihai
- Department of Chemistry, Hunter College and The CUNY Graduate Center, 695 Park Avenue, New York, NY 10065, USA
| | - Steven Hall
- Department of Chemistry, Hunter College and The CUNY Graduate Center, 695 Park Avenue, New York, NY 10065, USA
| | - Haiteng Deng
- School of Life Sciences, Tsinghua University, Haidian District, Beijing 100084, China
| | - Christopher J Welch
- Department of Process & Analytical Chemistry, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Akira Kawamura
- Department of Chemistry, Hunter College and The CUNY Graduate Center, 695 Park Avenue, New York, NY 10065, USA
| |
Collapse
|
14
|
Zheng W, Li G, Li X. Affinity purification in target identification: the specificity challenge. Arch Pharm Res 2015; 38:1661-85. [DOI: 10.1007/s12272-015-0635-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/07/2015] [Indexed: 12/16/2022]
|
15
|
|
16
|
Rush JS, Subramanian T, Subramanian KL, Onono FO, Waechter CJ, Spielmann HP. Novel Citronellyl-Based Photoprobes Designed to Identify ER Proteins Interacting with Dolichyl Phosphate in Yeast and Mammalian Cells. ACTA ACUST UNITED AC 2015; 9:123-141. [PMID: 27099830 DOI: 10.2174/2212796810666160216221610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
BACKGROUND Dolichyl phosphate-linked mono- and oligosaccharides (DLO) are essential intermediates in protein N-glycosylation, C- and O-mannosylation and GPI anchor biosynthesis. While many membrane proteins in the endoplasmic reticulum (ER) involved in the assembly of DLOs are known, essential proteins believed to be required for the transbilayer movement (flip-flopping) and proteins potentially involved in the regulation of DLO synthesis remain to be identified. METHODS The synthesis of a series of Dol-P derivatives composed of citronellyl-based photoprobes with benzophenone groups equipped with alkyne moieties for Huisgen "click" chemistry is now described to utilize as tools for identifying ER proteins involved in regulating the biosynthesis and transbilayer movement of lipid intermediates. In vitro enzymatic assays were used to establish that the photoprobes contain the critical structural features recognized by pertinent enzymes in the dolichol pathway. ER proteins that photoreacted with the novel probes were identified by MS. RESULTS The potential of the newly designed photoprobes, m-PAL-Cit-P and p-PAL-Cit-P, for identifying previously unidentified Dol-P-interacting proteins is supported by the observation that they are enzymatically mannosylated by Man-P-Dol synthase (MPDS) from Chinese Hamster Ovary (CHO) cells at an enzymatic rate similar to that for Dol-P. MS analyses reveal that DPM1, ALG14 and several other yeast ER proteins involved in DLO biosynthesis and lipid-mediated protein O-mannosylation photoreacted with the novel probes. CONCLUSION The newly-designed photoprobes described in this paper provide promising new tools for the identification of yet to be identified Dol-P interacting ER proteins in yeast and mammalian cells, including the Dol-P flippase required for the "re-cycling" of the glycosyl carrier lipid from the lumenal monolayer of the ER to the cytoplasmic leaflet for new rounds of DLO synthesis.
Collapse
Affiliation(s)
- Jeffrey S Rush
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Thangaiah Subramanian
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Karunai Leela Subramanian
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Fredrick O Onono
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Charles J Waechter
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, USA
| | - H Peter Spielmann
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, USA; University of Kentucky College of Medicine, Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA; Kentucky Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA; Department of Chemistry, University of Kentucky, Lexington, Kentucky 40536, USA
| |
Collapse
|
17
|
Hui JZ, Al Zaki A, Cheng Z, Popik V, Zhang H, Luning Prak ET, Tsourkas A. Facile method for the site-specific, covalent attachment of full-length IgG onto nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:3354-63. [PMID: 24729432 PMCID: PMC4142076 DOI: 10.1002/smll.201303629] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 03/20/2014] [Indexed: 05/18/2023]
Abstract
Antibodies, most commonly IgGs, have been widely used as targeting ligands in research and therapeutic applications due to their wide array of targets, high specificity and proven efficacy. Many of these applications require antibodies to be conjugated onto surfaces (e.g. nanoparticles and microplates); however, most conventional bioconjugation techniques exhibit low crosslinking efficiencies, reduced functionality due to non-site-specific labeling and random surface orientation, and/or require protein engineering (e.g. cysteine handles), which can be technically challenging. To overcome these limitations, we have recombinantly expressed Protein Z, which binds the Fc region of IgG, with an UV active non-natural amino acid benzoylphenyalanine (BPA) within its binding domain. Upon exposure to long wavelength UV light, the BPA is activated and forms a covalent link between the Protein Z and the bound Fc region of IgG. This technology was combined with expressed protein ligation (EPL), which allowed for the introduction of a fluorophore and click chemistry-compatible azide group onto the C-terminus of Protein Z during the recombinant protein purification step. This enabled the crosslinked-Protein Z-IgG complexes to be efficiently and site-specifically attached to aza-dibenzocyclooctyne-modified nanoparticles, via copper-free click chemistry.
Collapse
Affiliation(s)
- James Zhe Hui
- Department of Bioengineering, University of Pennsylvania, 210 S. 33 Street, 240 Skirkanich Hall, Philadelphia, PA 19104, USA
| | - Ajlan Al Zaki
- Department of Bioengineering, University of Pennsylvania, 210 S. 33 Street, 240 Skirkanich Hall, Philadelphia, PA 19104, USA
| | - Zhiliang Cheng
- Department of Bioengineering, University of Pennsylvania, 210 S. 33 Street, 240 Skirkanich Hall, Philadelphia, PA 19104, USA
| | - Vladimir Popik
- Department of Chemistry, University of Georgia, Athens, GA 30602, USA
| | - Hongtao Zhang
- Department of Pathology and Lab Medicine, University of Pennsylvania, PA 19104, USA
| | - Eline T. Luning Prak
- Department of Pathology and Lab Medicine, University of Pennsylvania, PA 19104, USA
| | - Andrew Tsourkas
- Department of Bioengineering, University of Pennsylvania, 210 S. 33 Street, 240 Skirkanich Hall, Philadelphia, PA 19104, USA
| |
Collapse
|
18
|
Sakurai K, Ozawa S, Yamada R, Yasui T, Mizuno S. Comparison of the Reactivity of Carbohydrate Photoaffinity Probes with Different Photoreactive Groups. Chembiochem 2014; 15:1399-403. [DOI: 10.1002/cbic.201402051] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Indexed: 01/12/2023]
|
19
|
Perols A, Karlström AE. Site-specific photoconjugation of antibodies using chemically synthesized IgG-binding domains. Bioconjug Chem 2014; 25:481-8. [PMID: 24520805 DOI: 10.1021/bc400440u] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Site-specific labeling of antibodies can be performed using the immunoglobulin-binding Z domain, derived from staphylococcal protein A (SpA), which has a well-characterized binding site in the Fc region of antibodies. By introducing a photoactivable probe in the Z domain, a covalent bond can be formed between the Z domain and the antibody by irradiation with UV light. The aim of this study was to improve the conjugation yield for labeling of different subclasses of IgG having different sequence composition, using a photoactivated Z domain variant. Four different variants of the Z domain (Z5BPA, Z5BBA, Z32BPA, and Z32BBA) were synthesized to investigate the influence of the position of the photoactivable probe and the presence of a flexible linker between the probe and the protein. For two of the variants, the photoreactive benzophenone group was introduced as part of an amino acid side chain by incorporation of the unnatural amino acid benzoylphenylalanine (BPA) during peptide synthesis. For the other two variants, the photoreactive benzophenone group was attached via a flexible linker by coupling of benzoylbenzoic acid (BBA) to the ε-amino group of a selectively deprotected lysine residue. Photoconjugation experiments using human IgG1, mouse IgG1, and mouse IgG2A demonstrated efficient conjugation for all antibodies. It was shown that differences in linker length had a large impact on the conjugation efficiency for labeling of mouse IgG1, whereas the positioning of the photoactivable probe in the sequence of the protein had a larger effect for mouse IgG2A. Conjugation to human IgG1 was only to a minor extent affected by position or linker length. For each subclass of antibody, the best variant tested using a standard conjugation protocol resulted in conjugation efficiencies of 41-66%, which corresponds to on average approximately one Z domain attached to each antibody. As a combination of the two best performing variants, Z5BBA and Z32BPA, a Z domain variant with two photoactivable probes (Z5BBA32BPA) was also synthesized with the aim of targeting a wider panel of antibody subclasses and species. This new reagent could efficiently couple to all antibody subclasses that were targeted by the single benzophenone-labeled Z domain variants, with conjugation efficiencies of 26-41%.
Collapse
Affiliation(s)
- Anna Perols
- KTH Royal Institute of Technology, School of Biotechnology, Division of Protein Technology, AlbaNova University Center , SE - 106 91 Stockholm, Sweden
| | | |
Collapse
|
20
|
Sakurai K, Yamada R, Okada A, Tawa M, Ozawa S, Inoue M. Selective Fluorescence Detection of Small-Molecule-Binding Proteins by Using a Dual Photoaffinity Labeling System. Chembiochem 2013; 14:421-5. [DOI: 10.1002/cbic.201200758] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Indexed: 01/01/2023]
|
21
|
Sakurai K, Tawa M, Okada A, Yamada R, Sato N, Inahara M, Inoue M. Active/Inactive Dual‐Probe System for Selective Photoaffinity Labeling of Small Molecule‐Binding Proteins. Chem Asian J 2012; 7:1567-71. [DOI: 10.1002/asia.201200085] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 03/02/2012] [Indexed: 12/19/2022]
Affiliation(s)
- Kaori Sakurai
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2‐24‐16 Naka‐cho, Koganei‐shi, Tokyo 184‐8588 (Japan), Fax: (+81) 42‐388‐7374
| | - Masaki Tawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2‐24‐16 Naka‐cho, Koganei‐shi, Tokyo 184‐8588 (Japan), Fax: (+81) 42‐388‐7374
| | - Ayumi Okada
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2‐24‐16 Naka‐cho, Koganei‐shi, Tokyo 184‐8588 (Japan), Fax: (+81) 42‐388‐7374
| | - Rika Yamada
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2‐24‐16 Naka‐cho, Koganei‐shi, Tokyo 184‐8588 (Japan), Fax: (+81) 42‐388‐7374
| | - Noriyuki Sato
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2‐24‐16 Naka‐cho, Koganei‐shi, Tokyo 184‐8588 (Japan), Fax: (+81) 42‐388‐7374
| | - Masahiro Inahara
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2‐24‐16 Naka‐cho, Koganei‐shi, Tokyo 184‐8588 (Japan), Fax: (+81) 42‐388‐7374
| | - Maia Inoue
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2‐24‐16 Naka‐cho, Koganei‐shi, Tokyo 184‐8588 (Japan), Fax: (+81) 42‐388‐7374
| |
Collapse
|
22
|
Abstract
Benzophenone photoprobes represent powerful tools for chemical proteomics. Upon UV irradiation, a benzophenone photoprobe can selectively form a covalent bond with its target protein in complex protein mixtures. Thus, photoprobes can be used to profile a wide variety of proteins in complex proteomes. This chapter describes simple protocols to derivatize fluorenylmethyloxycarbonyl (Fmoc)-protected peptide-nucleic-acid adenine (PNA adenine) into a benzophenone photoprobe and its application in photolabeling its target proteins. The method as described does not require specialized equipment for probe synthesis and photolabeling. In addition, the strategy is applicable to recognition motifs other than PNA adenine, such as peptides, to profile their target proteins in complex proteomes.
Collapse
|
23
|
Biochemical analysis with the expanded genetic lexicon. Anal Bioanal Chem 2012; 403:2089-102. [PMID: 22322380 DOI: 10.1007/s00216-012-5784-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 01/17/2012] [Accepted: 01/23/2012] [Indexed: 02/02/2023]
Abstract
The information used to build proteins is stored in the genetic material of every organism. In nature, ribosomes use 20 native amino acids to synthesize proteins in most circumstances. However, laboratory efforts to expand the genetic repertoire of living cells and organisms have successfully encoded more than 80 nonnative amino acids in E. coli, yeast, and other eukaryotic systems. The selectivity, fidelity, and site-specificity provided by the technology have enabled unprecedented flexibility in manipulating protein sequences and functions in cells. Various biophysical probes can be chemically conjugated or directly incorporated at specific residues in proteins, and corresponding analytical techniques can then be used to answer diverse biological questions. This review summarizes the methodology of genetic code expansion and its recent progress, and discusses the applications of commonly used analytical methods.
Collapse
|
24
|
Konrad A, Karlström AE, Hober S. Covalent immunoglobulin labeling through a photoactivable synthetic Z domain. Bioconjug Chem 2011; 22:2395-403. [PMID: 22026370 DOI: 10.1021/bc200052h] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Traditionally, labeling of antibodies has been performed by covalent conjugation to amine or carboxyl groups. These methods are efficient but suffer from nonspecificity, since all free and available amine/carboxyl groups have the possibility to react. This drawback may lead to uncontrolled levels and locations of the labeling. Hence, the labeled molecules might behave differently and, possibly, the binding site of the antibody will also be affected. In this project, we have developed a highly stringent method for labeling of antibodies by utilizing an immunoglobulin-binding domain from protein A, the Z domain. Domain Z has been synthesized with an amino acid analogue, benzoylphenylalanine, capable of forming covalent attachment to other amino acids upon UV-exposure. This feature has been used for directed labeling of immunoglobulins and subsequent use of these in different assays.
Collapse
Affiliation(s)
- Anna Konrad
- Division of Proteomics, AlbaNova University Center, Stockholm, Sweden
| | | | | |
Collapse
|
25
|
Park IH, Li C. Characterization of molecular recognition of STAT3 SH2 domain inhibitors through molecular simulation. J Mol Recognit 2011; 24:254-65. [PMID: 21360612 DOI: 10.1002/jmr.1047] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Signal transducer and activator of transcription 3 (STAT3) is an anti-cancer target protein due to its over-activation in tumor cells. The Tyr705-phosphorylated (pTyr) STAT3 binds to the pTyr-recognition site of its Src Homology 2 (SH2) domain of another STAT3 monomer to form a homo-dimer, which then causes cellular anti-apoptosis, proliferation, and tumor invasion. Recently, many STAT3 SH2 dimerization inhibitors have been discovered via both computational and experimental methods. To systematically assess their binding affinities and specificities, for eight representative inhibitors, we utilized molecular docking, molecular dynamics simulation, and ensuing energetic analysis to compare their binding characteristics. The inhibitors' binding free energies were calculated via MMPB(GB)SA, and the STAT3 SH2 binding "hot spots" were evaluated through binding energy decomposition and hydrogen bond (H-bond) distribution analysis. Several conclusions can be drawn: (1) the overall enthalpy-entropy compensation paradigm is preserved for the STAT3 SH2/ligand binding thermodynamics; (2) at one end of the binding spectrum, two compounds bind to SH2 due to their minimum entropic penalties that result from their relative rigidities and increased dynamics of SH2 upon their binding; at the other end of the binding spectrum, one compound shows a typical weak binder behavior due to its loose binding in the SH2's strongest enthalpy-contributing binding subsite; (3) hydrogen bonding seems a strong indicator to evaluate the SH2/ligand binding potency, which echoes a finding that CH/π non-classical H-bond is responsible for some pTyr peptides binding to their corresponding SH2 domains; (4) STAT3 SH2 domain possesses three binding "hot spots": pTyr705-binding pocket with polar residues and contributing the largest binding enthalpy (two-thirds); Leu706 subsite which is the most dynamic and hardest to target; a hydrophobic side pocket which is unique to STAT3 and very targetable, which may offer unique opportunity to design STAT3-specific inhibitors, particularly with fragment-based approach.
Collapse
Affiliation(s)
- In-Hee Park
- Chemical Physics Program, The Ohio State University, Columbus, OH 43210, USA
| | | |
Collapse
|
26
|
Geurink PP, Prely LM, van der Marel GA, Bischoff R, Overkleeft HS. Photoaffinity labeling in activity-based protein profiling. Top Curr Chem (Cham) 2011; 324:85-113. [PMID: 22028098 DOI: 10.1007/128_2011_286] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Activity-based protein profiling has come to the fore in recent years as a powerful strategy for studying enzyme activities in their natural surroundings. Substrate analogs that bind covalently and irreversibly to an enzyme active site and that are equipped with an identification or affinity tag can be used to unearth new enzyme activities, to establish whether and at what subcellular location the enzymes are active, and to study the inhibitory effects of small compounds. A specific class of activity-based protein probes includes those that employ a photo-activatable group to create the covalent bond. Such probes are targeted to those enzymes that do not employ a catalytic nucleophile that is part of the polypeptide backbone. An overview of the various photo-activatable groups that are available to chemical biology researchers is presented, with a focus on their (photo)chemistry and their application in various research fields. A number of comparative studies are described in which the efficiency of various photo-activatable groups are compared.
Collapse
Affiliation(s)
- Paul P Geurink
- Leiden Institute of Chemistry and the Netherlands Proteomics Centre, Leiden University, The Netherlands
| | | | | | | | | |
Collapse
|
27
|
Arsenault J, Cabana J, Fillion D, Leduc R, Guillemette G, Lavigne P, Escher E. Temperature dependent photolabeling of the human angiotensin II type 1 receptor reveals insights into its conformational landscape and its activation mechanism. Biochem Pharmacol 2010; 80:990-9. [DOI: 10.1016/j.bcp.2010.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 06/07/2010] [Accepted: 06/07/2010] [Indexed: 11/15/2022]
|
28
|
Nakamaru-Ogiso E, Han H, Matsuno-Yagi A, Keinan E, Sinha SC, Yagi T, Ohnishi T. The ND2 subunit is labeled by a photoaffinity analogue of asimicin, a potent complex I inhibitor. FEBS Lett 2010; 584:883-8. [PMID: 20074573 DOI: 10.1016/j.febslet.2010.01.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2009] [Revised: 01/07/2010] [Accepted: 01/07/2010] [Indexed: 10/20/2022]
Abstract
NADH:ubiquinone oxidoreductase (complex I) is the entry enzyme of mitochondrial oxidative phosphorylation. To obtain the structural information on inhibitor/quinone binding sites, we synthesized [3H]benzophenone-asimicin ([3H]BPA), a photoaffinity analogue of asimicin, which belongs to the acetogenin family known as the most potent complex I inhibitor. We found that [3H]BPA was photo-crosslinked to ND2, ND1 and ND5 subunits, by the three dimensional separation (blue-native/doubled SDS-PAGE) of [3H]BPA-treated bovine heart submitochondrial particles. The cross-linking was blocked by rotenone. This is the first finding that ND2 was photo-crosslinked with a potent complex I inhibitor, suggesting its involvement in the inhibitor/quinone-binding.
Collapse
Affiliation(s)
- Eiko Nakamaru-Ogiso
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | | | | | | | | | | | | |
Collapse
|
29
|
Wright K, Moretto A, Crisma M, Wakselman M, Mazaleyrat JP, Formaggio F, Toniolo C. A new tool for photoaffinity labeling studies: a partially constrained, benzophenone based, α-amino acid. Org Biomol Chem 2010; 8:3281-6. [DOI: 10.1039/c003943h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
30
|
van Scherpenzeel M, Moret EE, Ballell L, Liskamp RMJ, Nilsson UJ, Leffler H, Pieters RJ. Synthesis and Evaluation of New Thiodigalactoside-Based Chemical Probes to Label Galectin-3. Chembiochem 2009; 10:1724-33. [DOI: 10.1002/cbic.200900198] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
31
|
Abu-Farha M, Elisma F, Zhou H, Tian R, Zhou H, Asmer MS, Figeys D. Proteomics: From Technology Developments to Biological Applications. Anal Chem 2009; 81:4585-99. [DOI: 10.1021/ac900735j] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Mohamed Abu-Farha
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, Ontario, Canada, and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Fred Elisma
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, Ontario, Canada, and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Houjiang Zhou
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, Ontario, Canada, and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Ruijun Tian
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, Ontario, Canada, and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Hu Zhou
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, Ontario, Canada, and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Mehmet Selim Asmer
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, Ontario, Canada, and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, Ontario, Canada, and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| |
Collapse
|