201
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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.
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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
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202
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Zhuang S, Li Q, Cai L, Wang C, Lei X. Chemoproteomic Profiling of Bile Acid Interacting Proteins. ACS CENTRAL SCIENCE 2017; 3:501-509. [PMID: 28573213 PMCID: PMC5445530 DOI: 10.1021/acscentsci.7b00134] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Indexed: 05/04/2023]
Abstract
Bile acids (BAs) are a family of endogenous metabolites synthesized from cholesterol in liver and modified by microbiota in gut. Being amphipathic molecules, the major function of BAs is to help with dietary lipid digestion. In addition, they also act as signaling molecules to regulate lipid and glucose metabolism as well as gut microbiota composition in the host. Remarkably, recent discoveries of the dedicated receptors for BAs such as FXR and TGR5 have uncovered a number of novel actions of BAs as signaling hormones which play significant roles in both physiological and pathological conditions. Disorders in BAs' metabolism are closely related to metabolic syndrome and intestinal and neurodegenerative diseases. Though BA-based therapies have been clinically implemented for decades, the regulatory mechanism of BA is still poorly understood and a comprehensive characterization of BA-interacting proteins in proteome remains elusive. We herein describe a chemoproteomic strategy that uses a number of structurally diverse, clickable, and photoreactive BA-based probes in combination with quantitative mass spectrometry to globally profile BA-interacting proteins in mammalian cells. Over 600 BA-interacting protein targets were identified, including known endogenous receptors and transporters of BA. Analysis of these novel BA-interacting proteins revealed that they are mainly enriched in functional pathways such as endoplasmic reticulum (ER) stress response and lipid metabolism, and are predicted with strong implications with Alzheimer's disease, non-alcoholic fatty liver disease, and diarrhea. Our findings will significantly improve the current understanding of BAs' regulatory roles in human physiology and diseases.
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Affiliation(s)
- Shentian Zhuang
- Synthetic
and Functional Biomolecules Center, Beijing National Laboratory
for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and
Molecular Engineering of Ministry of Education, Department of Chemical Biology,
College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life
Sciences, Peking University, Beijing 100871, China
| | - Qiang Li
- Synthetic
and Functional Biomolecules Center, Beijing National Laboratory
for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and
Molecular Engineering of Ministry of Education, Department of Chemical Biology,
College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life
Sciences, Peking University, Beijing 100871, China
| | - Lirong Cai
- Synthetic
and Functional Biomolecules Center, Beijing National Laboratory
for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and
Molecular Engineering of Ministry of Education, Department of Chemical Biology,
College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life
Sciences, Peking University, Beijing 100871, China
| | - Chu Wang
- Synthetic
and Functional Biomolecules Center, Beijing National Laboratory
for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and
Molecular Engineering of Ministry of Education, Department of Chemical Biology,
College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life
Sciences, Peking University, Beijing 100871, China
- E-mail:
| | - Xiaoguang Lei
- Synthetic
and Functional Biomolecules Center, Beijing National Laboratory
for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and
Molecular Engineering of Ministry of Education, Department of Chemical Biology,
College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life
Sciences, Peking University, Beijing 100871, China
- E-mail:
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203
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Wang D, Du S, Cazenave-Gassiot A, Ge J, Lee JS, Wenk MR, Yao SQ. Global Mapping of Protein-Lipid Interactions by Using Modified Choline-Containing Phospholipids Metabolically Synthesized in Live Cells. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702509] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Danyang Wang
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
| | - Shubo Du
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
| | | | - Jingyan Ge
- Institute of Bioengineering; Zhejiang University of Technology; China
| | - Jun-Seok Lee
- Department of Biological Chemistry; University of Science & Technology; South Korea
| | - Markus R. Wenk
- Department of Biological Sciences; National University of Singapore; Singapore
| | - Shao Q. Yao
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
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204
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Wang D, Du S, Cazenave-Gassiot A, Ge J, Lee JS, Wenk MR, Yao SQ. Global Mapping of Protein-Lipid Interactions by Using Modified Choline-Containing Phospholipids Metabolically Synthesized in Live Cells. Angew Chem Int Ed Engl 2017; 56:5829-5833. [DOI: 10.1002/anie.201702509] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Indexed: 01/19/2023]
Affiliation(s)
- Danyang Wang
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
| | - Shubo Du
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
| | | | - Jingyan Ge
- Institute of Bioengineering; Zhejiang University of Technology; China
| | - Jun-Seok Lee
- Department of Biological Chemistry; University of Science & Technology; South Korea
| | - Markus R. Wenk
- Department of Biological Sciences; National University of Singapore; Singapore
| | - Shao Q. Yao
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
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205
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Parker CG, Galmozzi A, Wang Y, Correia BE, Sasaki K, Joslyn CM, Kim AS, Cavallaro CL, Lawrence RM, Johnson SR, Narvaiza I, Saez E, Cravatt BF. Ligand and Target Discovery by Fragment-Based Screening in Human Cells. Cell 2017; 168:527-541.e29. [PMID: 28111073 DOI: 10.1016/j.cell.2016.12.029] [Citation(s) in RCA: 285] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/14/2016] [Accepted: 12/20/2016] [Indexed: 01/28/2023]
Abstract
Advances in the synthesis and screening of small-molecule libraries have accelerated the discovery of chemical probes for studying biological processes. Still, only a small fraction of the human proteome has chemical ligands. Here, we describe a platform that marries fragment-based ligand discovery with quantitative chemical proteomics to map thousands of reversible small molecule-protein interactions directly in human cells, many of which can be site-specifically determined. We show that fragment hits can be advanced to furnish selective ligands that affect the activity of proteins heretofore lacking chemical probes. We further combine fragment-based chemical proteomics with phenotypic screening to identify small molecules that promote adipocyte differentiation by engaging the poorly characterized membrane protein PGRMC2. Fragment-based screening in human cells thus provides an extensive proteome-wide map of protein ligandability and facilitates the coordinated discovery of bioactive small molecules and their molecular targets.
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Affiliation(s)
- Christopher G Parker
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Andrea Galmozzi
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yujia Wang
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bruno E Correia
- École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Kenji Sasaki
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Christopher M Joslyn
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Arthur S Kim
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Cullen L Cavallaro
- Research and Development, Bristol-Myers Squibb Company, Princeton, NJ 08648, USA
| | - R Michael Lawrence
- Research and Development, Bristol-Myers Squibb Company, Princeton, NJ 08648, USA
| | - Stephen R Johnson
- Research and Development, Bristol-Myers Squibb Company, Princeton, NJ 08648, USA
| | - Iñigo Narvaiza
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Enrique Saez
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Benjamin F Cravatt
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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206
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Ravasco JMJM, Monteiro CM, Trindade AF. Cyclopropenes: a new tool for the study of biological systems. Org Chem Front 2017. [DOI: 10.1039/c7qo00054e] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cyclopropenes have become an important mini-tag tool in chemical biology, participating in fast inverse electron demand Diels–Alder and photoclick reactions in biological settings.
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Affiliation(s)
- João M. J. M. Ravasco
- Instituto de Investigação do Medicamento (iMed.ULisboa)
- Faculdade de Farmácia
- Universidade de Lisboa
- 1649-003 Lisboa
- Portugal
| | - Carlos M. Monteiro
- Instituto de Investigação do Medicamento (iMed.ULisboa)
- Faculdade de Farmácia
- Universidade de Lisboa
- 1649-003 Lisboa
- Portugal
| | - Alexandre F. Trindade
- Instituto de Investigação do Medicamento (iMed.ULisboa)
- Faculdade de Farmácia
- Universidade de Lisboa
- 1649-003 Lisboa
- Portugal
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207
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Chiba K, Asanuma M, Ishikawa M, Hashimoto Y, Dodo K, Sodeoka M, Yamaguchi T. Specific fluorescence labeling of target proteins by using a ligand–4-azidophthalimide conjugate. Chem Commun (Camb) 2017; 53:8751-8754. [DOI: 10.1039/c7cc03252h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two distinct model studies demonstrate that the ligand–4-azidophthalimide conjugate strategy is useful for specific fluorescence labeling of target proteins.
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Affiliation(s)
- Kosuke Chiba
- Institute of Molecular and Cellular Biosciences
- The University of Tokyo
- Tokyo 113-0032
- Japan
| | - Miwako Asanuma
- Synthetic Organic Chemistry Laboratory
- RIKEN
- Wako
- Japan
- AMED-CREST
| | - Minoru Ishikawa
- Institute of Molecular and Cellular Biosciences
- The University of Tokyo
- Tokyo 113-0032
- Japan
| | - Yuichi Hashimoto
- Institute of Molecular and Cellular Biosciences
- The University of Tokyo
- Tokyo 113-0032
- Japan
| | - Kosuke Dodo
- Synthetic Organic Chemistry Laboratory
- RIKEN
- Wako
- Japan
- AMED-CREST
| | - Mikiko Sodeoka
- Synthetic Organic Chemistry Laboratory
- RIKEN
- Wako
- Japan
- AMED-CREST
| | - Takao Yamaguchi
- Institute of Molecular and Cellular Biosciences
- The University of Tokyo
- Tokyo 113-0032
- Japan
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208
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Zhou Y, Di Z, Li X, Shan Y, Li W, Zhang H, Xiao Y. Chemical proteomics reveal CD147 as a functional target of pseudolaric acid B in human cancer cells. Chem Commun (Camb) 2017; 53:8671-8674. [DOI: 10.1039/c7cc04345g] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Pseudolaric acid B targets CD147 in human cancer cells.
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Affiliation(s)
- Yiqing Zhou
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
| | - Zhengao Di
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
| | - Xiaoming Li
- Institute for Nutritional Sciences
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
- Shanghai 200032
- China
| | - Yuanhong Shan
- Core Facility Centre of the Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
- Shanghai 200032
- China
| | - Weichao Li
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
| | - Haibing Zhang
- Institute for Nutritional Sciences
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
- Shanghai 200032
- China
| | - Youli Xiao
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
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209
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Kanoh N, Okamura T, Suzuki T, Iwabuchi Y. A mild two-step propargylation of aromatic bioactive small molecules. Org Biomol Chem 2017; 15:7190-7195. [DOI: 10.1039/c7ob01587a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A mild 2-step propargylation strategy for aromatic bioactive small molecules has been developed.
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Affiliation(s)
- Naoki Kanoh
- Graduate School of Pharmaceutical Sciences
- Tohoku University
- Sendai 980-8578
- Japan
| | - Toshitaka Okamura
- Graduate School of Pharmaceutical Sciences
- Tohoku University
- Sendai 980-8578
- Japan
| | - Takahiro Suzuki
- Graduate School of Pharmaceutical Sciences
- Tohoku University
- Sendai 980-8578
- Japan
| | - Yoshiharu Iwabuchi
- Graduate School of Pharmaceutical Sciences
- Tohoku University
- Sendai 980-8578
- Japan
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210
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Guo H, Xu J, Hao P, Ding K, Li Z. Competitive affinity-based proteome profiling and imaging to reveal potential cellular targets of betulinic acid. Chem Commun (Camb) 2017; 53:9620-9623. [DOI: 10.1039/c7cc04190j] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Affinity-based proteome profiling (AfBP) coupled with bioimaging to uncover cellular targets of betulinic acid.
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Affiliation(s)
- Haijun Guo
- College of Pharmacy
- Jinan University
- Guangzhou
- China
| | - Jiaqian Xu
- College of Pharmacy
- Jinan University
- Guangzhou
- China
| | - Piliang Hao
- School of Life Science and Technology
- ShanghaiTech University
- Shanghai 201210
- China
| | - Ke Ding
- College of Pharmacy
- Jinan University
- Guangzhou
- China
| | - Zhengqiu Li
- College of Pharmacy
- Jinan University
- Guangzhou
- China
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211
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Kleiner P, Heydenreuter W, Stahl M, Korotkov VS, Sieber SA. Eine Gesamtproteom‐basierte Auflistung der Hintergrundbinder von Photovernetzern. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605993] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Philipp Kleiner
- Center for Integrated Protein Science an der Fakultät für Chemie Technische Universität München Lichtenbergstraße 4 85747 Garching Deutschland
| | - Wolfgang Heydenreuter
- Center for Integrated Protein Science an der Fakultät für Chemie Technische Universität München Lichtenbergstraße 4 85747 Garching Deutschland
| | - Matthias Stahl
- Center for Integrated Protein Science an der Fakultät für Chemie Technische Universität München Lichtenbergstraße 4 85747 Garching Deutschland
| | - Vadim S. Korotkov
- Center for Integrated Protein Science an der Fakultät für Chemie Technische Universität München Lichtenbergstraße 4 85747 Garching Deutschland
| | - Stephan A. Sieber
- Center for Integrated Protein Science an der Fakultät für Chemie Technische Universität München Lichtenbergstraße 4 85747 Garching Deutschland
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212
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Kleiner P, Heydenreuter W, Stahl M, Korotkov VS, Sieber SA. A Whole Proteome Inventory of Background Photocrosslinker Binding. Angew Chem Int Ed Engl 2016; 56:1396-1401. [DOI: 10.1002/anie.201605993] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/15/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Philipp Kleiner
- Center for Integrated Protein Science at the Department of Chemistry Technische Universität München Lichtenbergstrasse 4 85747 Garching Germany
| | - Wolfgang Heydenreuter
- Center for Integrated Protein Science at the Department of Chemistry Technische Universität München Lichtenbergstrasse 4 85747 Garching Germany
| | - Matthias Stahl
- Center for Integrated Protein Science at the Department of Chemistry Technische Universität München Lichtenbergstrasse 4 85747 Garching Germany
| | - Vadim S. Korotkov
- Center for Integrated Protein Science at the Department of Chemistry Technische Universität München Lichtenbergstrasse 4 85747 Garching Germany
| | - Stephan A. Sieber
- Center for Integrated Protein Science at the Department of Chemistry Technische Universität München Lichtenbergstrasse 4 85747 Garching Germany
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213
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Wang L, Ishida A, Hashidoko Y, Hashimoto M. Dehydrogenation of the NH−NH Bond Triggered by Potassium
tert
‐Butoxide in Liquid Ammonia. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201610371] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Lei Wang
- Division of Applied Bioscience Graduate School of Agriculture Hokkaido University Kita 9, Nishi 9, Kita-ku Sapporo 060-8589 Japan
| | - Akiko Ishida
- Division of Applied Bioscience Graduate School of Agriculture Hokkaido University Kita 9, Nishi 9, Kita-ku Sapporo 060-8589 Japan
| | - Yasuyuki Hashidoko
- Division of Applied Bioscience Graduate School of Agriculture Hokkaido University Kita 9, Nishi 9, Kita-ku Sapporo 060-8589 Japan
| | - Makoto Hashimoto
- Division of Applied Bioscience Graduate School of Agriculture Hokkaido University Kita 9, Nishi 9, Kita-ku Sapporo 060-8589 Japan
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214
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Wang L, Ishida A, Hashidoko Y, Hashimoto M. Dehydrogenation of the NH-NH Bond Triggered by Potassium tert-Butoxide in Liquid Ammonia. Angew Chem Int Ed Engl 2016; 56:870-873. [PMID: 27936299 DOI: 10.1002/anie.201610371] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Indexed: 12/24/2022]
Abstract
A novel strategy for the dehydrogenation of the NH-NH bond is disclosed using potassium tert-butoxide (tBuOK) in liquid ammonia (NH3 ) under air at room temperature. Its synthetic value is well demonstrated by the highly efficient synthesis of aromatic azo compounds (up to 100 % yield, 3 min), heterocyclic azo compounds, and dehydrazination of phenylhydrazine. The broad application of this strategy and its benefit to chemical biology is proved by a novel, convenient, one-pot synthesis of aliphatic diazirines, which are important photoreactive agents for photoaffinity labeling.
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Affiliation(s)
- Lei Wang
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, 060-8589, Japan
| | - Akiko Ishida
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, 060-8589, Japan
| | - Yasuyuki Hashidoko
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, 060-8589, Japan
| | - Makoto Hashimoto
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, 060-8589, Japan
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215
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Peng B, Thorsell A, Karlberg T, Schüler H, Yao SQ. Small Molecule Microarray Based Discovery of PARP14 Inhibitors. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201609655] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Bo Peng
- Department of Chemistry National University of Singapore 3 Science Drive Singapore 117543 Singapore
| | - Ann‐Gerd Thorsell
- Karolinska Institute Department of Medical Biochemistry & Biophysics Scheeles väg 2 17177 Stockholm Sweden
| | - Tobias Karlberg
- Karolinska Institute Department of Medical Biochemistry & Biophysics Scheeles väg 2 17177 Stockholm Sweden
| | - Herwig Schüler
- Karolinska Institute Department of Medical Biochemistry & Biophysics Scheeles väg 2 17177 Stockholm Sweden
| | - Shao Q. Yao
- Department of Chemistry National University of Singapore 3 Science Drive Singapore 117543 Singapore
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216
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Peng B, Thorsell AG, Karlberg T, Schüler H, Yao SQ. Small Molecule Microarray Based Discovery of PARP14 Inhibitors. Angew Chem Int Ed Engl 2016; 56:248-253. [DOI: 10.1002/anie.201609655] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 11/22/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Bo Peng
- Department of Chemistry; National University of Singapore; 3 Science Drive Singapore 117543 Singapore
| | - Ann-Gerd Thorsell
- Karolinska Institute; Department of Medical Biochemistry & Biophysics; Scheeles väg 2 17177 Stockholm Sweden
| | - Tobias Karlberg
- Karolinska Institute; Department of Medical Biochemistry & Biophysics; Scheeles väg 2 17177 Stockholm Sweden
| | - Herwig Schüler
- Karolinska Institute; Department of Medical Biochemistry & Biophysics; Scheeles väg 2 17177 Stockholm Sweden
| | - Shao Q. Yao
- Department of Chemistry; National University of Singapore; 3 Science Drive Singapore 117543 Singapore
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217
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Xie Y, Ge J, Lei H, Peng B, Zhang H, Wang D, Pan S, Chen G, Chen L, Wang Y, Hao Q, Yao SQ, Sun H. Fluorescent Probes for Single-Step Detection and Proteomic Profiling of Histone Deacetylases. J Am Chem Soc 2016; 138:15596-15604. [DOI: 10.1021/jacs.6b07334] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yusheng Xie
- Department
of Biology and Chemistry, City University of Hong Kong, 83 Tat
Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
- Key
Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, People’s Republic of China
| | - Jingyan Ge
- College
of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People’s Republic of China
| | - Haipeng Lei
- Department
of Biology and Chemistry, City University of Hong Kong, 83 Tat
Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
- Key
Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, People’s Republic of China
| | - Bo Peng
- Department
of Chemistry, National University of Singapore, Singapore 119077
| | - Huatang Zhang
- Department
of Biology and Chemistry, City University of Hong Kong, 83 Tat
Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
- Key
Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, People’s Republic of China
| | - Danyang Wang
- Department
of Chemistry, National University of Singapore, Singapore 119077
| | - Sijun Pan
- Department
of Chemistry, National University of Singapore, Singapore 119077
| | - Ganchao Chen
- Department
of Biology and Chemistry, City University of Hong Kong, 83 Tat
Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
- Key
Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, People’s Republic of China
| | - Lanfang Chen
- Department
of Physiology, University of Hong Kong, Pok Fu Lam, Hong Kong, People’s Republic of China
| | - Yi Wang
- Department
of Physiology, University of Hong Kong, Pok Fu Lam, Hong Kong, People’s Republic of China
| | - Quan Hao
- Department
of Physiology, University of Hong Kong, Pok Fu Lam, Hong Kong, People’s Republic of China
| | - Shao Q. Yao
- Department
of Chemistry, National University of Singapore, Singapore 119077
| | - Hongyan Sun
- Department
of Biology and Chemistry, City University of Hong Kong, 83 Tat
Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
- Key
Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, People’s Republic of China
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218
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Liu X, Dong T, Zhou Y, Huang N, Lei X. Exploring the Binding Proteins of Glycolipids with Bifunctional Chemical Probes. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Xiaohui Liu
- School of Pharmaceutical Science and Technology; Tianjin University; Tianjin 300072 China
| | - Ting Dong
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
| | - Yu Zhou
- National Institute of Biological Sciences (NIBS); Changping District Beijing 102206 China
| | - Niu Huang
- National Institute of Biological Sciences (NIBS); Changping District Beijing 102206 China
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
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219
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Liu X, Dong T, Zhou Y, Huang N, Lei X. Exploring the Binding Proteins of Glycolipids with Bifunctional Chemical Probes. Angew Chem Int Ed Engl 2016; 55:14330-14334. [DOI: 10.1002/anie.201608827] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Indexed: 01/06/2023]
Affiliation(s)
- Xiaohui Liu
- School of Pharmaceutical Science and Technology; Tianjin University; Tianjin 300072 China
| | - Ting Dong
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
| | - Yu Zhou
- National Institute of Biological Sciences (NIBS); Changping District Beijing 102206 China
| | - Niu Huang
- National Institute of Biological Sciences (NIBS); Changping District Beijing 102206 China
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
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220
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Horning BD, Suciu RM, Ghadiri DA, Ulanovskaya OA, Matthews ML, Lum KM, Backus KM, Brown SJ, Rosen H, Cravatt BF. Chemical Proteomic Profiling of Human Methyltransferases. J Am Chem Soc 2016; 138:13335-13343. [PMID: 27689866 DOI: 10.1021/jacs.6b07830] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Methylation is a fundamental mechanism used in Nature to modify the structure and function of biomolecules, including proteins, DNA, RNA, and metabolites. Methyl groups are predominantly installed into biomolecules by a large and diverse class of S-adenosyl methionine (SAM)-dependent methyltransferases (MTs), of which there are ∼200 known or putative members in the human proteome. Deregulated MT activity contributes to numerous diseases, including cancer, and several MT inhibitors are in clinical development. Nonetheless, a large fraction of the human MT family remains poorly characterized, underscoring the need for new technologies to characterize MTs and their inhibitors in native biological systems. Here, we describe a suite of S-adenosyl homocysteine (SAH) photoreactive probes and their application in chemical proteomic experiments to profile and enrich a large number of MTs (>50) from human cancer cell lysates with remarkable specificity over other classes of proteins. We further demonstrate that the SAH probes can enrich MT-associated proteins and be used to screen for and assess the selectivity of MT inhibitors, leading to the discovery of a covalent inhibitor of nicotinamide N-methyltransferase (NNMT), an enzyme implicated in cancer and metabolic disorders. The chemical proteomics probes and methods for their utilization reported herein should prove of value for the functional characterization of MTs, MT complexes, and MT inhibitors in mammalian biology and disease.
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Affiliation(s)
- Benjamin D Horning
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Radu M Suciu
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Darian A Ghadiri
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Olesya A Ulanovskaya
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Megan L Matthews
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Kenneth M Lum
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Keriann M Backus
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Steven J Brown
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Hugh Rosen
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Benjamin F Cravatt
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
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221
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Eleftheriadis N, Thee SA, Zwinderman MRH, Leus NGJ, Dekker FJ. Activity-Based Probes for 15-Lipoxygenase-1. Angew Chem Int Ed Engl 2016; 55:12300-5. [PMID: 27612308 PMCID: PMC5218545 DOI: 10.1002/anie.201606876] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Indexed: 12/12/2022]
Abstract
Human 15-lipoxygenase-1 (15-LOX-1) plays an important role in several inflammatory lung diseases, such as asthma, COPD, and chronic bronchitis, as well as various CNS diseases, such as Alzheimer's disease, Parkinson's disease, and stroke. Activity-based probes of 15-LOX-1 are required to explore the role of this enzyme further and to enable drug discovery. In this study, we developed a 15-LOX-1 activity-based probe for the efficient activity-based labeling of recombinant 15-LOX-1. 15-LOX-1-dependent labeling in cell lysates and tissue samples was also possible. To mimic the natural substrate of the enzyme, we designed activity-based probes that covalently bind to the active enzyme and include a terminal alkene as a chemical reporter for the bioorthogonal linkage of a detectable functionality through an oxidative Heck reaction. The activity-based labeling of 15-LOX-1 should enable the investigation and identification of this enzyme in complex biological samples, thus opening up completely new opportunities for drug discovery.
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Affiliation(s)
- Nikolaos Eleftheriadis
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Stephanie A Thee
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Martijn R H Zwinderman
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Niek G J Leus
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Frank J Dekker
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
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222
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Head SA, Liu JO. Identification of Small Molecule-binding Proteins in a Native Cellular Environment by Live-cell Photoaffinity Labeling. J Vis Exp 2016. [PMID: 27684515 DOI: 10.3791/54529] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Identifying the molecular target(s) of small molecules is a challenging but necessary step towards understanding their mechanism of action. While several target identification methods have been developed and used to successfully elucidate the binding proteins of a variety of small molecules, these techniques have drawbacks that make them unsuitable for detecting certain types of small molecule-target interactions. In particular, non-covalent interactions that depend on native cellular conditions, such as those of membrane proteins whose structures may be perturbed upon cell lysis, are often not amenable to affinity-based target identification methods. Here, we demonstrate a method wherein a probe containing a photolabile group is used to covalently crosslink to the small molecule binding protein within the environment of the live cell, allowing the detection and isolation of the target protein without the need for maintenance of the interaction after cell lysis. This technique is a valuable tool for studying biologically interesting small molecules with unknown mechanisms, both in the context of basic biology as well as drug discovery.
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Affiliation(s)
- Sarah A Head
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine
| | - Jun O Liu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine; Department of Oncology, Johns Hopkins University School of Medicine;
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223
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Eleftheriadis N, Thee SA, Zwinderman MRH, Leus NGJ, Dekker FJ. Activity-Based Probes for 15-Lipoxygenase-1. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606876] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Nikolaos Eleftheriadis
- Department of Chemical and Pharmaceutical Biology; Groningen Research Institute of Pharmacy; University of Groningen; Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Stephanie A. Thee
- Department of Chemical and Pharmaceutical Biology; Groningen Research Institute of Pharmacy; University of Groningen; Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Martijn R. H. Zwinderman
- Department of Chemical and Pharmaceutical Biology; Groningen Research Institute of Pharmacy; University of Groningen; Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Niek G. J. Leus
- Department of Chemical and Pharmaceutical Biology; Groningen Research Institute of Pharmacy; University of Groningen; Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Frank J. Dekker
- Department of Chemical and Pharmaceutical Biology; Groningen Research Institute of Pharmacy; University of Groningen; Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
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224
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Fadeyi O, Parikh MD, Chen MZ, Kyne RE, Taylor AP, O'Doherty I, Kaiser SE, Barbas S, Niessen S, Shi M, Weinrich SL, Kath JC, Jones LH, Robinson RP. Chemoselective Preparation of Clickable Aryl Sulfonyl Fluoride Monomers: A Toolbox of Highly Functionalized Intermediates for Chemical Biology Probe Synthesis. Chembiochem 2016; 17:1925-1930. [PMID: 27504718 DOI: 10.1002/cbic.201600427] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Indexed: 11/08/2022]
Abstract
Sulfonyl fluoride (SF)-based activity probes have become important tools in chemical biology. Herein, exploiting the relative chemical stability of SF to carry out a number of unprecedented SF-sparing functional group manipulations, we report the chemoselective synthesis of a toolbox of highly functionalized aryl SF monomers that we used to quickly prepare SF chemical biology probes. In addition to SF, the monomers bear an embedded click handle (a terminal alkyne that can perform copper(I)-mediated azide-alkyne cycloaddition). The monomers can be used either as fragments to prepare clickable SF analogues of drugs (biologically active compounds) bearing an aryl ring or, alternatively, attached to drugs as minimalist clickable aryl SF substituents.
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Affiliation(s)
| | - Mihir D Parikh
- Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT, 06340, USA
| | - Ming Z Chen
- Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT, 06340, USA
| | - Robert E Kyne
- Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT, 06340, USA
| | | | - Inish O'Doherty
- Oncology RU Medicinal Chemistry, Pfizer Inc., 10770 Science Center Drive, San Diego, CA, 92121, USA
| | - Stephen E Kaiser
- Oncology RU Medicinal Chemistry, Pfizer Inc., 10770 Science Center Drive, San Diego, CA, 92121, USA
| | - Sabrina Barbas
- Oncology RU Medicinal Chemistry, Pfizer Inc., 10770 Science Center Drive, San Diego, CA, 92121, USA
| | - Sherry Niessen
- Oncology RU Medicinal Chemistry, Pfizer Inc., 10770 Science Center Drive, San Diego, CA, 92121, USA
| | - Manli Shi
- Oncology RU Medicinal Chemistry, Pfizer Inc., 10770 Science Center Drive, San Diego, CA, 92121, USA
| | - Scott L Weinrich
- Oncology RU Medicinal Chemistry, Pfizer Inc., 10770 Science Center Drive, San Diego, CA, 92121, USA
| | - John C Kath
- Oncology RU Medicinal Chemistry, Pfizer Inc., 10770 Science Center Drive, San Diego, CA, 92121, USA
| | - Lyn H Jones
- Medicine Design, Pfizer Inc., 610 Main Street, Cambridge, MA, 02139, USA
| | - Ralph P Robinson
- Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT, 06340, USA.
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225
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Crump CJ, Murrey HE, Ballard TE, am Ende CW, Wu X, Gertsik N, Johnson DS, Li YM. Development of Sulfonamide Photoaffinity Inhibitors for Probing Cellular γ-Secretase. ACS Chem Neurosci 2016; 7:1166-73. [PMID: 27253220 DOI: 10.1021/acschemneuro.6b00127] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
γ-Secretase is a multiprotein complex that catalyzes intramembrane proteolysis associated with Alzheimer's disease and cancer. Here, we have developed potent sulfonamide clickable photoaffinity probes that target γ-secretase in vitro and in cells by incorporating various photoreactive groups and walking the clickable alkyne handle to different positions around the molecule. We found that benzophenone is preferred over diazirine as a photoreactive group within the sulfonamide scaffold for labeling γ-secretase. Intriguingly, the placement of the alkyne at different positions has little effect on probe potency but has a significant impact on the efficiency of labeling of γ-secretase. Moreover, the optimized clickable photoprobe, 163-BP3, was utilized as a cellular probe to effectively assess the target engagement of inhibitors with γ-secretase in primary neuronal cells. In addition, biotinylated 163-BP3 probes were developed and used to capture the native γ-secretase complex in the 3-[(3-cholamidopropyl)dimethylammonio]-2-hydroxy-1-propanesulfonate (CHAPSO) solubilized state. Taken together, these next generation clickable and biotinylated sulfonamide probes offer new tools to study γ-secretase in biochemical and cellular systems. Finally, the data provide insights into structural features of the sulfonamide inhibitor binding site in relation to the active site and into the design of clickable photoaffinity probes.
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Affiliation(s)
- Christina J. Crump
- Chemical
Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York
Avenue, New York, New York 10065, United States
| | - Heather E. Murrey
- Pfizer Worldwide Research and Development, Worldwide Medicinal Chemistry, Cambridge, Massachusetts 02139, United States
| | - T. Eric Ballard
- Pfizer Worldwide Research and Development, Worldwide
Medicinal Chemistry Groton, Connecticut 06340, United States
| | - Christopher W. am Ende
- Pfizer Worldwide Research and Development, Worldwide
Medicinal Chemistry Groton, Connecticut 06340, United States
| | - Xianzhong Wu
- Chemical
Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York
Avenue, New York, New York 10065, United States
| | - Natalya Gertsik
- Chemical
Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York
Avenue, New York, New York 10065, United States
| | - Douglas S. Johnson
- Pfizer Worldwide Research and Development, Worldwide Medicinal Chemistry, Cambridge, Massachusetts 02139, United States
| | - Yue-Ming Li
- Chemical
Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York
Avenue, New York, New York 10065, United States
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226
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Zhu B, Zhang H, Pan S, Wang C, Ge J, Lee JS, Yao SQ. In Situ Proteome Profiling and Bioimaging Applications of Small-Molecule Affinity-Based Probes Derived From DOT1L Inhibitors. Chemistry 2016; 22:7824-36. [PMID: 27115831 DOI: 10.1002/chem.201600259] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Indexed: 01/01/2023]
Abstract
DOT1L is the sole protein methyltransferase that methylates histone H3 on lysine 79 (H3K79), and is a promising drug target against cancers. Small-molecule inhibitors of DOT1L such as FED1 are potential anti-cancer agents and useful tools to investigate the biological roles of DOT1L in human diseases. FED1 showed excellent in vitro inhibitory activity against DOT1L, but its cellular effect was relatively poor. In this study, we designed and synthesized photo-reactive and "clickable" affinity-based probes (AfBPs), P1 and P2, which were cell-permeable and structural mimics of FED1. The binding and inhibitory effects of these two probes against DOT1L protein were extensively investigated in vitro and in live mammalian cells (in situ). The cellular uptake and sub-cellular localization properties of the probes were subsequently studied in live-cell imaging experiments, and our results revealed that, whereas both P1 and P2 readily entered mammalian cells, most of them were not able to reach the cell nucleus where functional DOT1L resides. This offers a plausible explanation for the poor cellular activity of FED1. Finally with P1/P2, large-scale cell-based proteome profiling, followed by quantitative LC-MS/MS, was carried out to identify potential cellular off-targets of FED1. Amongst the more than 100 candidate off-targets identified, NOP2 (a putative ribosomal RNA methyltransferase) was further confirmed to be likely a genuine off-target of FED1 by preliminary validation experiments including pull-down/Western blotting (PD/WB) and cellular thermal shift assay (CETSA).
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Affiliation(s)
- Biwei Zhu
- Department of Chemistry, National University of Singapore, 3 Science drive 3, Singapore, 117543, Singapore
| | - Hailong Zhang
- Department of Chemistry, National University of Singapore, 3 Science drive 3, Singapore, 117543, Singapore
| | - Sijun Pan
- Department of Chemistry, National University of Singapore, 3 Science drive 3, Singapore, 117543, Singapore
| | - Chenyu Wang
- Department of Chemistry, National University of Singapore, 3 Science drive 3, Singapore, 117543, Singapore
| | - Jingyan Ge
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, P.R. China
| | - Jun-Seok Lee
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST) and Department of Biological Chemistry, University of Science & Technology, Republic of Korea
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 3 Science drive 3, Singapore, 117543, Singapore.
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227
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Yamada R, Hiraizumi M, Narita S, Sakurai K. Two-Step Synthesis of a Clickable Photoaffinity Probe from an Anticancer Saponin OSW-1 and its Photochemical Reactivity. ASIAN J ORG CHEM 2016. [DOI: 10.1002/ajoc.201500505] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- 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
| | - Masato Hiraizumi
- Department of Biotechnology and Life Science; Tokyo University of Agriculture and Technology; 2-24-16, Naka-cho Koganei-shi Tokyo 184-8588 Japan
| | - Sho Narita
- Department of Biotechnology and Life Science; Tokyo University of Agriculture and Technology; 2-24-16, Naka-cho Koganei-shi Tokyo 184-8588 Japan
| | - 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
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228
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Park J, Koh M, Koo JY, Lee S, Park SB. Investigation of Specific Binding Proteins to Photoaffinity Linkers for Efficient Deconvolution of Target Protein. ACS Chem Biol 2016; 11:44-52. [PMID: 26502221 DOI: 10.1021/acschembio.5b00671] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Photoaffinity-based target identification has received recent attention as an efficient research tool for chemical biology and drug discovery. The major obstacle of photoaffinity-based target identification is the nonspecific interaction between target identification probes and nontarget proteins. Consequently, the rational design of photoaffinity linkers has been spotlighted for successful target identification. These nonspecific interactions have been considered as random events, and therefore no systematic investigation has been conducted regarding nonspecific interactions between proteins and photoaffinity linkers. Herein, we report the protein-labeling analysis of photoaffinity linkers containing three photoactivatable moieties: benzophenone, diazirine, and arylazide. Each photoaffinity linker binds to a different set of proteins in a structure-dependent manner, in contrast to the previous conception. The list of proteins labeled by each photoaffinity linker was successfully used to eliminate the nonspecific binding proteins from target candidates, thereby increasing the success rate of target identification.
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Affiliation(s)
- Jongmin Park
- Department
of Biophysics and Chemical Biology/N-Bio Institute, Seoul National University, Seoul 151-747, Korea
| | - Minseob Koh
- Department
of Biophysics and Chemical Biology/N-Bio Institute, Seoul National University, Seoul 151-747, Korea
| | - Ja Young Koo
- Department
of Biophysics and Chemical Biology/N-Bio Institute, Seoul National University, Seoul 151-747, Korea
| | - Sanghee Lee
- Department
of Biophysics and Chemical Biology/N-Bio Institute, Seoul National University, Seoul 151-747, Korea
| | - Seung Bum Park
- Department
of Biophysics and Chemical Biology/N-Bio Institute, Seoul National University, Seoul 151-747, Korea
- Department
of Chemistry, Seoul National University, Seoul 151-747, Korea
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229
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Lehmann J, Wright MH, Sieber SA. Making a Long Journey Short: Alkyne Functionalization of Natural Product Scaffolds. Chemistry 2016; 22:4666-78. [PMID: 26752308 DOI: 10.1002/chem.201504419] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Indexed: 01/09/2023]
Abstract
Biological selection makes natural products promising scaffolds for drug development and the ever growing number of newly identified, structurally diverse molecules helps to fill the gaps in chemical space. Elucidating the function of a small molecule, such as identifying its protein binding partners, its on- and off-targets, is becoming increasingly important. Activity- and affinity-based protein profiling are modern strategies to acquire such molecular-level information. Introduction of a molecular handle (azide, alkyne, biotin) can shed light on the mode of action of small molecules. This Concept article covers central points on synthetic methodology for integrating a terminal alkyne into a molecule of interest.
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Affiliation(s)
- Johannes Lehmann
- Center for Integrated Protein Science, Munich (CIPSM), Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Megan H Wright
- Center for Integrated Protein Science, Munich (CIPSM), Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Stephan A Sieber
- Center for Integrated Protein Science, Munich (CIPSM), Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85747, Garching, Germany.
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230
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Park H, Koo JY, Srikanth YVV, Oh S, Lee J, Park J, Park SB. Nonspecific protein labeling of photoaffinity linkers correlates with their molecular shapes in living cells. Chem Commun (Camb) 2016; 52:5828-31. [DOI: 10.1039/c6cc01426g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The molecular shape of photoaffinity linkers significantly influences their nonspecific protein labeling of the cellular proteome.
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Affiliation(s)
- Hankum Park
- Department of Biophysics and Chemical Biology
- Seoul National University
- Seoul
- Korea
| | - Ja Young Koo
- Department of Chemistry
- Seoul National University
- Seoul
- Korea
| | | | - Sangmi Oh
- Department of Chemistry
- Seoul National University
- Seoul
- Korea
| | - Jiyoon Lee
- Mass Spectrometer Laboratory
- National Instrument Center for Environmental Management
- Seoul National University
- Seoul
- Korea
| | - Jongmin Park
- Department of Biophysics and Chemical Biology
- Seoul National University
- Seoul
- Korea
| | - Seung Bum Park
- Department of Biophysics and Chemical Biology
- Seoul National University
- Seoul
- Korea
- Department of Chemistry
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231
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Fu J, Na Z, Peng B, Uttamchandani M, Yao SQ. Accelerated cellular on- and off-target screening of bioactive compounds using microarrays. Org Biomol Chem 2016; 14:59-64. [DOI: 10.1039/c5ob02233a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In situ target screening of bioactive compounds using microarrays.
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Affiliation(s)
- Jiaqi Fu
- Department of Chemistry
- National University of Singapore
- Singapore 117543
- Singapore
| | - Zhenkun Na
- Department of Chemistry
- National University of Singapore
- Singapore 117543
- Singapore
| | - Bo Peng
- Department of Chemistry
- National University of Singapore
- Singapore 117543
- Singapore
| | - Mahesh Uttamchandani
- Department of Chemistry
- National University of Singapore
- Singapore 117543
- Singapore
- Defence Medical and Environmental Research Institute DSO National Laboratories
| | - Shao Q. Yao
- Department of Chemistry
- National University of Singapore
- Singapore 117543
- Singapore
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232
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Li Z, Qian L, Li L, Bernhammer JC, Huynh HV, Lee JS, Yao SQ. Tetrazole Photoclick Chemistry: Reinvestigating Its Suitability as a Bioorthogonal Reaction and Potential Applications. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508104] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Zhengqiu Li
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
- College of Pharmacy; Jinan University; Guangzhou 510632 China
| | - Linghui Qian
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
| | - Lin Li
- Key Laboratory of Flexible Electronics & Institute of Advanced Materials; Nanjing Tech University; Nanjing 211816 China
| | - Jan C. Bernhammer
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
| | - Han Vinh Huynh
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
| | - Jun-Seok Lee
- Molecular Recognition Research Center; Korea Institute of Science and Technology; Department of Biological Chemistry; University of Science & Technology; Republic of Korea
| | - Shao Q. Yao
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
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233
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Li Z, Qian L, Li L, Bernhammer JC, Huynh HV, Lee JS, Yao SQ. Tetrazole Photoclick Chemistry: Reinvestigating Its Suitability as a Bioorthogonal Reaction and Potential Applications. Angew Chem Int Ed Engl 2015; 55:2002-6. [DOI: 10.1002/anie.201508104] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Indexed: 12/19/2022]
Affiliation(s)
- Zhengqiu Li
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
- College of Pharmacy; Jinan University; Guangzhou 510632 China
| | - Linghui Qian
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
| | - Lin Li
- Key Laboratory of Flexible Electronics & Institute of Advanced Materials; Nanjing Tech University; Nanjing 211816 China
| | - Jan C. Bernhammer
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
| | - Han Vinh Huynh
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
| | - Jun-Seok Lee
- Molecular Recognition Research Center; Korea Institute of Science and Technology; Department of Biological Chemistry; University of Science & Technology; Republic of Korea
| | - Shao Q. Yao
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
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234
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Pahl A, Lakemeyer M, Vielberg M, Hackl MW, Vomacka J, Korotkov VS, Stein ML, Fetzer C, Lorenz‐Baath K, Richter K, Waldmann H, Groll M, Sieber SA. Reversible Inhibitors Arrest ClpP in a Defined Conformational State that Can Be Revoked by ClpX Association. Angew Chem Int Ed Engl 2015; 54:15892-6. [DOI: 10.1002/anie.201507266] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 09/15/2015] [Indexed: 01/29/2023]
Affiliation(s)
- Axel Pahl
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Markus Lakemeyer
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Marie‐Theres Vielberg
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Mathias W. Hackl
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Jan Vomacka
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Vadim S. Korotkov
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Martin L. Stein
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Christian Fetzer
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Katrin Lorenz‐Baath
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Klaus Richter
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Herbert Waldmann
- Department of Chemistry and Chemical Biology, Technische Universität Dortmund, Otto‐Hahn‐Strasse 6, 44221 Dortmund (Germany)
| | - Michael Groll
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Stephan A. Sieber
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
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235
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Pahl A, Lakemeyer M, Vielberg M, Hackl MW, Vomacka J, Korotkov VS, Stein ML, Fetzer C, Lorenz‐Baath K, Richter K, Waldmann H, Groll M, Sieber SA. Reversible Inhibitoren arretieren ClpP in einer definierten Konformation, die durch Bindung von ClpX aufgehoben wird. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507266] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Axel Pahl
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Markus Lakemeyer
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Marie‐Theres Vielberg
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Mathias W. Hackl
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Jan Vomacka
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Vadim S. Korotkov
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Martin L. Stein
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Christian Fetzer
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Katrin Lorenz‐Baath
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Klaus Richter
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Herbert Waldmann
- Department für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto‐Hahn‐Straße 6, 44221 Dortmund (Deutschland)
| | - Michael Groll
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Stephan A. Sieber
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
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236
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Wang T, Hong T, Huang Y, Su H, Wu F, Chen Y, Wei L, Huang W, Hua X, Xia Y, Xu J, Gan J, Yuan B, Feng Y, Zhang X, Yang CG, Zhou X. Fluorescein Derivatives as Bifunctional Molecules for the Simultaneous Inhibiting and Labeling of FTO Protein. J Am Chem Soc 2015; 137:13736-9. [PMID: 26457839 DOI: 10.1021/jacs.5b06690] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The FTO protein is unequivocally reported to play a critical role in human obesity and in the regulation of cellular levels of m(6)A modification, which makes FTO a significant and worthy subject of study. Here, we identified that fluorescein derivatives can selectively inhibit FTO demethylation, and the mechanisms behind these activities were elucidated after we determined the X-ray crystal structures of FTO/fluorescein and FTO/5-aminofluorescein. Furthermore, these inhibitors can also be applied to the direct labeling and enrichment of FTO protein combined with photoaffinity labeling assay.
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Affiliation(s)
| | | | - Yue Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, China
| | | | | | | | | | | | | | | | | | - Jianhua Gan
- School of Life Sciences, Fudan University , Shanghai 200433, China
| | | | | | | | - Cai-Guang Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, China
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237
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Recent developments and applications of clickable photoprobes in medicinal chemistry and chemical biology. Future Med Chem 2015; 7:2143-71. [DOI: 10.4155/fmc.15.136] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Photoaffinity labeling is a well-known biochemical technique that has grown significantly since the turn of the century, principally due to its combination with bioorthogonal/click chemistry reactions. This review highlights new developments and applications of clickable photoprobes in medicinal chemistry and chemical biology. In particular, recent examples of clickable photoprobes for target identification, activity- or affinity-based protein profiling (ABPP or AfBPP), characterization of sterol– or lipid–protein interactions and characterization of ligand-binding sites are presented.
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238
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A Global Map of Lipid-Binding Proteins and Their Ligandability in Cells. Cell 2015; 161:1668-80. [PMID: 26091042 DOI: 10.1016/j.cell.2015.05.045] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 02/24/2015] [Accepted: 05/04/2015] [Indexed: 01/17/2023]
Abstract
Lipids play central roles in physiology and disease, where their structural, metabolic, and signaling functions often arise from interactions with proteins. Here, we describe a set of lipid-based chemical proteomic probes and their global interaction map in mammalian cells. These interactions involve hundreds of proteins from diverse functional classes and frequently occur at sites of drug action. We determine the target profiles for several drugs across the lipid-interaction proteome, revealing that its ligandable content extends far beyond traditionally defined categories of druggable proteins. In further support of this finding, we describe a selective ligand for the lipid-binding protein nucleobindin-1 (NUCB1) and show that this compound perturbs the hydrolytic and oxidative metabolism of endocannabinoids in cells. The described chemical proteomic platform thus provides an integrated path to both discover and pharmacologically characterize a wide range of proteins that participate in lipid pathways in cells.
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239
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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]
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240
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Yu C, Qian L, Uttamchandani M, Li L, Yao SQ. Single-Vehicular Delivery of Antagomir and Small Molecules to Inhibit miR-122 Function in Hepatocellular Carcinoma Cells by using "Smart" Mesoporous Silica Nanoparticles. Angew Chem Int Ed Engl 2015; 54:10574-8. [PMID: 26179591 DOI: 10.1002/anie.201504913] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) regulate a variety of biological processes. The liver-specific, highly abundant miR-122 is implicated in many human diseases including cancer. Its inhibition has been found to result in a dramatic loss in the ability of Hepatitis C virus (HCV) to infect host cells. Both antisense technology and small molecules have been used to independently inhibit endogenous miR-122 function, but not in combination. Intracellular stability, efficient delivery, hydrophobicity, and controlled release are some of the current challenges associated with these novel therapeutic methods. Reported herein is the first single-vehicular system, based on mesoporous silica nanoparticles (MSNs), for simultaneous cellular delivery of miR-122 antagomir and small molecule inhibitors. The controlled release of both types of inhibitors depends on the expression levels of endogenous miR-122, thus enabling these drug-loaded MSNs to achieve combination inhibition of its targeted mRNAs in Huh7 cells.
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Affiliation(s)
- Changmin Yu
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543 (Singapore) http://staff.science.nus.edu.sg/∼syao
| | - Linghui Qian
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543 (Singapore) http://staff.science.nus.edu.sg/∼syao
| | - Mahesh Uttamchandani
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543 (Singapore) http://staff.science.nus.edu.sg/∼syao
| | - Lin Li
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543 (Singapore) http://staff.science.nus.edu.sg/∼syao
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543 (Singapore) http://staff.science.nus.edu.sg/∼syao.
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241
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Yu C, Qian L, Uttamchandani M, Li L, Yao SQ. Single-Vehicular Delivery of Antagomir and Small Molecules to Inhibit miR-122 Function in Hepatocellular Carcinoma Cells by using “Smart” Mesoporous Silica Nanoparticles. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504913] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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242
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Li L, Wijaya H, Samanta S, Lam Y, Yao SQ. In situ imaging and proteome profiling indicate andrographolide is a highly promiscuous compound. Sci Rep 2015; 5:11522. [PMID: 26105662 PMCID: PMC4478469 DOI: 10.1038/srep11522] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/28/2015] [Indexed: 01/07/2023] Open
Abstract
Natural products represent an enormous source of pharmacologically useful compounds, and are often used as the starting point in modern drug discovery. Many biologically interesting natural products are however not being pursued as potential drug candidates, partly due to a lack of well-defined mechanism-of-action. Traditional in vitro methods for target identification of natural products based on affinity protein enrichment from crude cellular lysates cannot faithfully recapitulate protein-drug interactions in living cells. Reported herein are dual-purpose probes inspired by the natural product andrographolide, capable of both reaction-based, real-time bioimaging and in situ proteome profiling/target identification in live mammalian cells. Our results confirm that andrographolide is a highly promiscuous compound and engaged in covalent interactions with numerous previously unknown cellular targets in cell type-specific manner. We caution its potential therapeutic effects should be further investigated in detail.
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Affiliation(s)
- Lin Li
- 1] Department of Chemistry, National University of Singapore, Singapore 117543 [2] Key Laboratory of Flexible Electronics (KLOFE) &Institute of Advanced Materials (IAM), National Jiangsu Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (NanjingTech), Nanjing 211816, P. R. China
| | - Hadhi Wijaya
- Department of Chemistry, National University of Singapore, Singapore 117543
| | - Sanjay Samanta
- Department of Chemistry, National University of Singapore, Singapore 117543
| | - Yulin Lam
- Department of Chemistry, National University of Singapore, Singapore 117543
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore 117543
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243
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Yamaura K, Kuwata K, Tamura T, Kioi Y, Takaoka Y, Kiyonaka S, Hamachi I. Live cell off-target identification of lapatinib using ligand-directed tosyl chemistry. Chem Commun (Camb) 2015; 50:14097-100. [PMID: 25275302 DOI: 10.1039/c4cc05885b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We demonstrate that ligand-directed tosyl (LDT) chemistry is applicable to off-target identification in live cells. Lapatinib (Lap)-based LDT reagents not only labeled a receptor tyrosine kinase, HER2, target protein, but also the protein disulfide isomerase (PDI) that should be an off-target protein for Lap.
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Affiliation(s)
- Kei Yamaura
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
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244
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Zhu B, Ge J, Yao SQ. Developing new chemical tools for DNA methyltransferase 1 (DNMT 1): A small-molecule activity-based probe and novel tetrazole-containing inhibitors. Bioorg Med Chem 2015; 23:2917-27. [DOI: 10.1016/j.bmc.2015.03.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 02/25/2015] [Accepted: 03/02/2015] [Indexed: 12/31/2022]
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245
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Development of bioorthogonal reactions and their applications in bioconjugation. Molecules 2015; 20:3190-205. [PMID: 25690284 PMCID: PMC6290559 DOI: 10.3390/molecules20023190] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 01/19/2015] [Accepted: 02/02/2015] [Indexed: 12/12/2022] Open
Abstract
Biomolecule labeling using chemical probes with specific biological activities has played important roles for the elucidation of complicated biological processes. Selective bioconjugation strategies are highly-demanded in the construction of various small-molecule probes to explore complex biological systems. Bioorthogonal reactions that undergo fast and selective ligation under bio-compatible conditions have found diverse applications in the development of new bioconjugation strategies. The development of new bioorthogonal reactions in the past decade has been summarized with comments on their potentials as bioconjugation method in the construction of various biological probes for investigating their target biomolecules. For the applications of bioorthogonal reactions in the site-selective biomolecule conjugation, examples have been presented on the bioconjugation of protein, glycan, nucleic acids and lipids.
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246
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Yang P, Liu K. Activity-based protein profiling: recent advances in probe development and applications. Chembiochem 2015; 16:712-24. [PMID: 25652106 DOI: 10.1002/cbic.201402582] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Indexed: 11/08/2022]
Abstract
The completion of the human genome sequencing project has provided a wealth of new information regarding the genomic blueprint of the cell. Although, to date, there are roughly 20,000 genes in the human genome, the functions of only a handful of proteins are clear. The major challenge lies in translating genomic information into an understanding of their cellular functions. The recently developed activity-based protein profiling (ABPP) is an unconventional approach that is complementary for gene expression analysis and an ideal utensil in decoding this overflow of genomic information. This approach makes use of synthetic small molecules that covalently modify a set of related proteins and subsequently facilitates identification of the target protein, enabling rapid biochemical analysis and inhibitor discovery. This tutorial review introduces recent advances in the field of ABPP and its applications.
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Affiliation(s)
- Pengyu Yang
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037 (USA)
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247
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Abstract
Eukaryotic and prokaryotic organisms possess huge numbers of uncharacterized enzymes. Selective inhibitors offer powerful probes for assigning functions to enzymes in native biological systems. Here, we discuss how the chemical proteomic platform activity-based protein profiling (ABPP) can be implemented to discover selective and in vivo-active inhibitors for enzymes. We further describe how these inhibitors have been used to delineate the biochemical and cellular functions of enzymes, leading to the discovery of metabolic and signaling pathways that make important contributions to human physiology and disease. These studies demonstrate the value of selective chemical probes as drivers of biological inquiry.
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Affiliation(s)
- Micah J Niphakis
- The Skaggs Institute for Chemical Biology and the Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037;
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248
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Su Y, Pan S, Li Z, Li L, Wu X, Hao P, Sze SK, Yao SQ. Multiplex imaging and cellular target identification of kinase inhibitors via an affinity-based proteome profiling approach. Sci Rep 2015; 5:7724. [PMID: 25579846 PMCID: PMC4290084 DOI: 10.1038/srep07724] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 12/09/2014] [Indexed: 12/14/2022] Open
Abstract
MLN8237 is a highly potent and presumably selective inhibitor of Aurora kinase A (AKA) and has shown promising antitumor activities. Like other kinase inhibitors which target the ATP-binding site of kinases, MLN8237 might be expected to have potential cellular off-targets. Herein, we report the first photoaffinity-based, small molecule AKA probe capable of both live-cell imaging of AKA activities and in situ proteome profiling of potential off-targets of MLN8237 (including AKA-associating proteins). By using two mutually compatible, bioorthogonal reactions (copper-catalyzed azide-alkyne cycloaddition chemistry and TCO-tetrazine ligation), we demostrate small molecule-based multiplex bioimaging for simultaneous in situ monitoring of two important cell-cycle regulating kinases (AKA and CDK1). A broad range of proteins, as potential off-targets of MLN8237 and AKA's-interacting partners, is subsequently identified by affinity-based proteome profiling coupled with large-scale LC-MS/MS analysis. From these studies, we discover novel AKA interactions which were further validated by cell-based immunoprecipitation (IP) experiments.
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Affiliation(s)
- Ying Su
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Sijun Pan
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Zhengqiu Li
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Lin Li
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Xiaoyuan Wu
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Piliang Hao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
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249
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Heydenreuter W, Kunold E, Sieber SA. Alkynol natural products target ALDH2 in cancer cells by irreversible binding to the active site. Chem Commun (Camb) 2015; 51:15784-7. [DOI: 10.1039/c5cc06424d] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Chemical proteomic studies reveal ALDH2 as a molecular target of falcarinol in cancer cells.
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Affiliation(s)
- Wolfgang Heydenreuter
- Department of Chemistry
- Center for Integrated Protein Science Munich (CIPSM)
- Technische Universität München
- Garching
- Germany
| | - Elena Kunold
- Department of Chemistry
- Center for Integrated Protein Science Munich (CIPSM)
- Technische Universität München
- Garching
- Germany
| | - Stephan A. Sieber
- Department of Chemistry
- Center for Integrated Protein Science Munich (CIPSM)
- Technische Universität München
- Garching
- Germany
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250
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Liu Y, Zheng W, Zhang W, Chen N, Liu Y, Chen L, Zhou X, Chen X, Zheng H, Li X. Photoaffinity labeling of transcription factors by DNA-templated crosslinking. Chem Sci 2015; 6:745-751. [PMID: 28706637 PMCID: PMC5494549 DOI: 10.1039/c4sc01953a] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 09/30/2014] [Indexed: 12/24/2022] Open
Abstract
Characterization of transcription factor-DNA interaction is of high importance in elucidating the molecular mechanisms of gene transcriptions. DNA-based affinity probes were developed to capture and identify transcription factors by covalent crosslinking; however, the requirement of a crosslinker on the affinity probe remains a disadvantage, as the crosslinker itself often interferes with the protein-DNA interactions. We report a dual-probe method able to capture DNA-binding transcription factors with unmodified protein-binding sites in scenarios where conventional probes have failed. We have also shown the method's converse application in selecting specific transcription factor-binding DNA sequences from a probe library and its extension to studying proteins recognizing epigenetic marks. This study may provide a new tool for exploring DNA-binding proteins in biology.
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Affiliation(s)
- Ying Liu
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Wenlu Zheng
- Key Laboratory of Chemical Genomics , School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen , China 518055
| | - Wan Zhang
- Key Laboratory of Chemical Genomics , School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen , China 518055
| | - Nan Chen
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Yang Liu
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Li Chen
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Xiaozhou Zhou
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Xingshuo Chen
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Haifeng Zheng
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Xiaoyu Li
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
- Key Laboratory of Chemical Genomics , School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen , China 518055
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