1
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Zhang P, Liu H, Xu S, He Y, He X, Sun B, Hu J. Direct Construction of 1,4-Dihydropyridazines and Pyrazoles via Annulation of Alkyl 2-Aroyl-1-chlorocyclopropanecarboxylates. J Org Chem 2024; 89:9853-9860. [PMID: 38822472 DOI: 10.1021/acs.joc.4c00520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2024]
Abstract
An efficient and chemodivergent synthesis of highly functionalized 1,4-dihydropyridazines and pyrazoles has been accomplished via base-promoted annulation between hydrazones and alkyl 2-aroyl-1-chlorocyclopropanecarboxylates, respectively. This transition-metal-free domino reaction proceeded rapidly under mild basic conditions, affording potentially bioactive 1,4-dihydropyridazine and pyrazole derivatives in moderate yields. The conversion of 1,4-dihydropyridazine to pyrazole was confirmed by adjusting the quantity of the base.
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Affiliation(s)
- Pengwei Zhang
- Key Laboratory of Functional Metal-Organic Compounds of Hunan Province, Key Laboratory of Functional Organometallic Materials, University of Hunan Province, Hengyang Normal University, Hengyang 421008, P. R. China
| | - Huili Liu
- Key Laboratory of Functional Metal-Organic Compounds of Hunan Province, Key Laboratory of Functional Organometallic Materials, University of Hunan Province, Hengyang Normal University, Hengyang 421008, P. R. China
| | - Shuo Xu
- Key Laboratory of Functional Metal-Organic Compounds of Hunan Province, Key Laboratory of Functional Organometallic Materials, University of Hunan Province, Hengyang Normal University, Hengyang 421008, P. R. China
| | - Yiqun He
- Key Laboratory of Functional Metal-Organic Compounds of Hunan Province, Key Laboratory of Functional Organometallic Materials, University of Hunan Province, Hengyang Normal University, Hengyang 421008, P. R. China
| | - Xinhao He
- Key Laboratory of Functional Metal-Organic Compounds of Hunan Province, Key Laboratory of Functional Organometallic Materials, University of Hunan Province, Hengyang Normal University, Hengyang 421008, P. R. China
| | - Bing Sun
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, P. R. China
| | - Junhao Hu
- Key Laboratory of Functional Metal-Organic Compounds of Hunan Province, Key Laboratory of Functional Organometallic Materials, University of Hunan Province, Hengyang Normal University, Hengyang 421008, P. R. China
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2
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Ma P, Svatunek D, Zhu Z, Boger DL, Duan XH, Houk KN. Computational Studies of Reactions of 1,2,4,5-Tetrazines with Enamines in MeOH and HFIP. J Am Chem Soc 2024; 146:18706-18713. [PMID: 38941192 DOI: 10.1021/jacs.4c06067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
The reaction between 1,2,4,5-tetrazines and alkenes in polar solvents proceeds through a Diels-Alder cycloaddition along the C-C axis (C3/C6 cycloaddition) of the tetrazine, followed by dinitrogen loss. By contrast, the reactions of 1,2,4,5-tetrazines with enamines in hexafluoroisopropanol (HFIP) give 1,2,4-triazine products stemming from a formal Diels-Alder addition across the N-N axis (N1/N4 cycloaddition). We explored the mechanism of this interesting solvent effect through DFT calculations in detail and revealed a novel reaction pathway characterized by C-N bond formation, deprotonation, and a 3,3-sigmatropic rearrangement. The participation of an HFIP molecule was found to be crucial to the N1/N4 selectivity over C3/C6 due to the more favored initial C-N bond formation than C-C bond formation.
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Affiliation(s)
- Pengchen Ma
- Department of Chemistry, School of Chemistry, Xi'an Key Laboratory of Sustainable Energy Material Chemistry and Engineering Research Center of Energy Storage Materials and Devices, Ministry of Education, Xi'an Jiaotong University, Xi'an 710049, China
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Dennis Svatunek
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- Institute of Applied Synthetic Chemistry, TU Wien, 1060 Vienna, Austria
| | - Zixi Zhu
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Dale L Boger
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Xin-Hua Duan
- Department of Chemistry, School of Chemistry, Xi'an Key Laboratory of Sustainable Energy Material Chemistry and Engineering Research Center of Energy Storage Materials and Devices, Ministry of Education, Xi'an Jiaotong University, Xi'an 710049, China
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
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3
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Azargoonjahromi A. The role of epigenetics in anxiety disorders. Mol Biol Rep 2023; 50:9625-9636. [PMID: 37804465 DOI: 10.1007/s11033-023-08787-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/30/2023] [Indexed: 10/09/2023]
Abstract
Anxiety disorders (ADs) are extremely common psychiatric conditions that frequently co-occur with other physical and mental disorders. The pathophysiology of ADs is multifaceted and involves intricate connections among biological elements, environmental stimuli, and psychological mechanisms. Recent discoveries have highlighted the significance of epigenetics in bridging the gap between multiple risk factors that contribute to ADs and expanding our understanding of the pathomechanisms underlying ADs. Epigenetics is the study of how changes in the environment and behavior can have an impact on gene function. Indeed, researchers have found that epigenetic mechanisms can affect how genes are activated or inactivated, as well as whether they are expressed. Such mechanisms may also affect how ADs form and are protected. That is, the bulk of pharmacological trials evaluating epigenetic treatments for the treatment of ADs have used histone deacetylase inhibitors (HDACi), yielding promising outcomes in both preclinical and clinical studies. This review will provide an outline of how epigenetic pathways can be used to treat ADs or lessen their risk. It will also present the findings from preclinical and clinical trials that are currently available on the use of epigenetic drugs to treat ADs.
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4
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Lei JH, Zhang L, Wang Z, Peltier R, Xie Y, Chen G, Lin S, Miao K, Deng CX, Sun H. FGFR2-BRD4 Axis Regulates Transcriptional Networks of Histone 3 Modification and Synergy Between Its Inhibitors and PD-1/PD-L1 in a TNBC Mouse Model. Front Immunol 2022; 13:861221. [PMID: 35547739 PMCID: PMC9084888 DOI: 10.3389/fimmu.2022.861221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
Epigenetic reprogramming is an independent mode of gene expression that often involves changes in the transcription and chromatin structure due to tumor initiation and development. In this study, we developed a specifically modified peptide array and searched for a recognized epigenetic reader. Our results demonstrated that BRD4 is not only an acetylation reader but of propionylation as well. We also studied the quantitative binding affinities between modified peptides and epigenetic regulators by isothermal titration calorimetry (ITC). Furthermore, we introduced the Fgfr2-S252W transgenic mouse model to confirm that this acetylation is associated with the activation of c-Myc and drives tumor formation. Targeted disruption of BRD4 in Fgfr2-S252W mouse tumor cells also confirmed that BRD4 is a key regulator of histone 3 acetylation. Finally, we developed a tumor slice culture system and demonstrated the synergy between immune checkpoint blockade and targeted therapy in triple-negative breast cancer (TNBC). These data extend our understanding of epigenetic reprogramming and epigenetics-based therapies.
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Affiliation(s)
- Josh Haipeng Lei
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, Macau SAR, China.,Ministry of Education (MOE) Frontier Science Centre for Precision Oncology, University of Macau, Taipa, Macau SAR, China.,Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Lei Zhang
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, Macau SAR, China.,Department of Vascular Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Zhenyi Wang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Heifei, China
| | - Raoul Peltier
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Yusheng Xie
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, China.,Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Ganchao Chen
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Shiqi Lin
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, Macau SAR, China.,Ministry of Education (MOE) Frontier Science Centre for Precision Oncology, University of Macau, Taipa, Macau SAR, China
| | - Kai Miao
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, Macau SAR, China.,Ministry of Education (MOE) Frontier Science Centre for Precision Oncology, University of Macau, Taipa, Macau SAR, China
| | - Chu-Xia Deng
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, Macau SAR, China.,Ministry of Education (MOE) Frontier Science Centre for Precision Oncology, University of Macau, Taipa, Macau SAR, China
| | - Hongyan Sun
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, China.,Key Laboratory of Biochip Technology, Biotech and Health Centre, City University of Hong Kong, Shenzhen Research Institute, Shenzhen, China
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5
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Catalyst-free photooxidation reaction from 1,4-dihydropyridazine to pyridazine under air. Tetrahedron 2021. [DOI: 10.1016/j.tet.2021.132411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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6
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Feng J, He T, Xie Y, Yu Y, Baell JB, Huang F. I 2-Promoted [4 + 2] cycloaddition of in situ generated azoalkenes with enaminones: facile and efficient synthesis of 1,4-dihydropyridazines and pyridazines. Org Biomol Chem 2020; 18:9483-9493. [PMID: 33179698 DOI: 10.1039/d0ob01958e] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A facile and efficient strategy for the synthesis of 1,4-dihydropyridazines and pyridazines through I2-promoted [4 + 2] cycloaddition of in situ generated azoalkenes with enaminones has been developed. The switch in selectivity is attributed to the judicious choice of different reaction temperatures. The key features of this work include controllable and selective synthesis, good functional group tolerance, good to excellent reaction yields, metal/base-free conditions, and also applicability to one-pot methodology.
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Affiliation(s)
- Jiajun Feng
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 211816, P. R. China.
| | - Tiantong He
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 211816, P. R. China.
| | - Yuxing Xie
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Yang Yu
- School of Environmental Science and Engineering, Nanjing Tech University, Nanjing 211816, P. R. China
| | - Jonathan B Baell
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 211816, P. R. China. and Medicinal Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Fei Huang
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 211816, P. R. China. and School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, P. R. China
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7
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Di Iorio D, Marti A, Koeman S, Huskens J. Clickable poly-l-lysine for the formation of biorecognition surfaces. RSC Adv 2019; 9:35608-35613. [PMID: 35528089 PMCID: PMC9074408 DOI: 10.1039/c9ra08714a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 10/24/2019] [Indexed: 11/24/2022] Open
Abstract
Biomolecules are immobilized onto surfaces employing the fast and stable adsorption of poly-l-lysine (PLL) polymers and the versatile copper-free click chemistry reactions. This method provides the combined advantages of versatile surface adsorption with density control using polyelectrolytes and of the covalent and orthogonal immobilization of biomolecules with higher reaction rates and improved yields of click chemistry. Using DNA attachment as a proof of concept, control over the DNA probe density and applicability in electrochemical detection are presented. The fast and stable adsorption of modified PLL on activated surfaces was combined with the versatile catalyst-free click chemistry for the fast and selective functionalization of substrates with DNA.![]()
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Affiliation(s)
- Daniele Di Iorio
- Molecular NanoFabrication Group
- MESA+ Institute for Nanotechnology
- University of Twente
- Enschede
- The Netherlands
| | - Almudena Marti
- Molecular NanoFabrication Group
- MESA+ Institute for Nanotechnology
- University of Twente
- Enschede
- The Netherlands
| | - Sander Koeman
- Molecular NanoFabrication Group
- MESA+ Institute for Nanotechnology
- University of Twente
- Enschede
- The Netherlands
| | - Jurriaan Huskens
- Molecular NanoFabrication Group
- MESA+ Institute for Nanotechnology
- University of Twente
- Enschede
- The Netherlands
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8
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Peng B, Yu C, Du S, Liew SS, Mao X, Yuan P, Na Z, Yao SQ. MSN-on-a-Chip: Cell-Based Screenings Made Possible on a Small-Molecule Microarray of Native Natural Products. Chembiochem 2018; 19:986-996. [PMID: 29465822 DOI: 10.1002/cbic.201800101] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Indexed: 12/17/2022]
Abstract
Standard small-molecule microarrays (SMMs) are not well-suited for cell-based screening assays. Of the few attempts made thus far to render SMMs cell-compatible, all encountered major limitations. Here we report the first mesoporous silica nanoparticle (MSN)-on-a-chip platform capable of allowing high-throughput cell-based screening to be conducted on SMMs. By making use of a glass surface on which hundreds of MSNs, each encapsulated with a different native natural product, were immobilized in spatially defined manner, followed by on-chip mammalian cell growth and on-demand compound release, high-content screening was successfully carried out with readily available phenotypic detection methods. By combining this new MSN-on-a-chip system with small interfering RNA technology for the first time, we discovered that (+)-usniacin possesses synergistic inhibitory properties similar to those of olaparib (an FDA-approved drug) in BRCA1-knockdown cancer cells.
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Affiliation(s)
- Bo Peng
- Department of Chemistry, National University of Singapore, 3 Science Drive, Singapore, 117543, Singapore
| | - Changmin Yu
- Institute of Advanced Materials (IAM), Nanjing Tech University, 30 South Puzhu Road, Nanjing, 21816, China
| | - Shubo Du
- Department of Chemistry, National University of Singapore, 3 Science Drive, Singapore, 117543, Singapore
| | - Si S Liew
- Department of Chemistry, National University of Singapore, 3 Science Drive, Singapore, 117543, Singapore
| | - Xin Mao
- Department of Chemistry, National University of Singapore, 3 Science Drive, Singapore, 117543, Singapore
| | - Peiyan Yuan
- Department of Chemistry, National University of Singapore, 3 Science Drive, Singapore, 117543, Singapore
| | - Zhenkun Na
- Department of Chemistry, National University of Singapore, 3 Science Drive, Singapore, 117543, Singapore
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive, Singapore, 117543, Singapore
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9
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Tyler DS, Vappiani J, Cañeque T, Lam EYN, Ward A, Gilan O, Chan YC, Hienzsch A, Rutkowska A, Werner T, Wagner AJ, Lugo D, Gregory R, Ramirez Molina C, Garton N, Wellaway CR, Jackson S, MacPherson L, Figueiredo M, Stolzenburg S, Bell CC, House C, Dawson SJ, Hawkins ED, Drewes G, Prinjha RK, Rodriguez R, Grandi P, Dawson MA. Click chemistry enables preclinical evaluation of targeted epigenetic therapies. Science 2017; 356:1397-1401. [PMID: 28619718 DOI: 10.1126/science.aal2066] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 06/01/2017] [Indexed: 12/12/2022]
Abstract
The success of new therapies hinges on our ability to understand their molecular and cellular mechanisms of action. We modified BET bromodomain inhibitors, an epigenetic-based therapy, to create functionally conserved compounds that are amenable to click chemistry and can be used as molecular probes in vitro and in vivo. We used click proteomics and click sequencing to explore the gene regulatory function of BRD4 (bromodomain containing protein 4) and the transcriptional changes induced by BET inhibitors. In our studies of mouse models of acute leukemia, we used high-resolution microscopy and flow cytometry to highlight the heterogeneity of drug activity within tumor cells located in different tissue compartments. We also demonstrate the differential distribution and effects of BET inhibitors in normal and malignant cells in vivo. This study provides a potential framework for the preclinical assessment of a wide range of drugs.
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Affiliation(s)
- Dean S Tyler
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Johanna Vappiani
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, Heidelberg, Germany
| | - Tatiana Cañeque
- Chemical Cell Biology Group, Institut Curie, Paris Sciences et Lettres Research University, 26 Rue d'Ulm, 75248 Paris Cedex 05, France.,CNRS UMR3666, 75005 Paris, France.,INSERM U1143, 75005 Paris, France
| | - Enid Y N Lam
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Aoife Ward
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, Heidelberg, Germany
| | - Omer Gilan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Yih-Chih Chan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Antje Hienzsch
- Chemical Cell Biology Group, Institut Curie, Paris Sciences et Lettres Research University, 26 Rue d'Ulm, 75248 Paris Cedex 05, France.,CNRS UMR3666, 75005 Paris, France.,INSERM U1143, 75005 Paris, France
| | - Anna Rutkowska
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, Heidelberg, Germany
| | - Thilo Werner
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, Heidelberg, Germany
| | - Anne J Wagner
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, Heidelberg, Germany
| | - Dave Lugo
- Epigenetics Discovery Performance Unit, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | - Richard Gregory
- Epigenetics Discovery Performance Unit, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | - Cesar Ramirez Molina
- Epigenetics Discovery Performance Unit, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | - Neil Garton
- Epigenetics Discovery Performance Unit, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | - Christopher R Wellaway
- Epigenetics Discovery Performance Unit, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | - Susan Jackson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Laura MacPherson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Margarida Figueiredo
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Sabine Stolzenburg
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Charles C Bell
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Colin House
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Sarah-Jane Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.,Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Edwin D Hawkins
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Gerard Drewes
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, Heidelberg, Germany
| | - Rab K Prinjha
- Epigenetics Discovery Performance Unit, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | - Raphaël Rodriguez
- Chemical Cell Biology Group, Institut Curie, Paris Sciences et Lettres Research University, 26 Rue d'Ulm, 75248 Paris Cedex 05, France.,CNRS UMR3666, 75005 Paris, France.,INSERM U1143, 75005 Paris, France
| | - Paola Grandi
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, Heidelberg, Germany.
| | - Mark A Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.,Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia.,Department of Haematology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
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10
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Abstract
Speed and throughput are vital ingredients for discovery driven, "-omics" research. The small molecule microarray (SMM) succeeds at delivering phenomenal screening throughput and versatility. The concept at the heart of the technology is elegant, yet simple: by presenting large collections of molecules in high density on a flat surface, one is able to interrogate all possible interactions with desired targets, in just a single step. SMMs have become established as the choice platform for screening, lead discovery, and molecular characterization. This introduction describes the principles governing microarray construction and use, focusing on practical challenges faced when conducting SMM experiments. It will explain the key design considerations and lay the foundation for the chapters that follow. (An earlier version of this chapter appeared in Small Molecule Microarrays: Methods and Protocols, published in 2010.).
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Affiliation(s)
- Mahesh Uttamchandani
- Defence Medical and Environmental Research Institute, DMERI, DSO National Laboratories, #09-01, 27 Medical Drive, Singapore, Singapore, 117510. .,Department of Chemistry, Faculty of Science, National University of Singapore, 3 Science Drive 3, Singapore, Singapore, 117543.
| | - Shao Q Yao
- Department of Chemistry, Faculty of Science, National University of Singapore, 3 Science Drive 3, Singapore, Singapore, 117543.
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11
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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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12
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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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13
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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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14
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Wang W, Fang Q, Hu Z. High-Throughput Peptide Screening on a Bimodal Imprinting Chip Through MS-SPRi Integration. Methods Mol Biol 2016; 1352:111-25. [PMID: 26490471 DOI: 10.1007/978-1-4939-3037-1_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Screening of high affinity and high specificity peptide probes towards various targets is important in the biomedical field while traditional peptide screening procedure is manual and tedious. Herein, a bimodal imprinting microarray system to embrace the whole peptide screening process is presented. Surface Plasmon Resonance imaging (SPRi) and matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) are combined for both quantitative and qualitative identification of the peptide. The method provides a solution for high efficiency peptide screening.
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Affiliation(s)
- Weizhi Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, No.11. Beiyitiao Zhongguancun, Beijing, 100190, China
| | - Qiaojun Fang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, No.11. Beiyitiao Zhongguancun, Beijing, 100190, China.
| | - Zhiyuan Hu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, No.11. Beiyitiao Zhongguancun, Beijing, 100190, China.
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15
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Ding ZC, Yang Y, Cai SN, Wen JJ, Zhan ZP. Synthesis of 1,4-Dihydropyridazines from Propargylic Alcohols and Hydrazones via a Cs 2CO 3-mediated Process. CHEM LETT 2016. [DOI: 10.1246/cl.160397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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16
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Ding ZC, Ju LC, Yang Y, An XM, Zhou YB, Li RH, Tang HT, Ding CK, Zhan ZP. Silver(I)-Catalyzed Tandem Sigamatropic Rearrangement/1,3-H Shift/6π Aza-electrocyclization of N-Propargylic Hydrazones: A Mild Synthetic Route to 1,6-Dihydropyridazines. J Org Chem 2016; 81:3936-41. [DOI: 10.1021/acs.joc.6b00428] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zong-Cang Ding
- Department of Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, P. R. China
| | - Lu-Chuan Ju
- Department of Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, P. R. China
| | - Ying Yang
- Department of Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, P. R. China
| | - Xiao-Ming An
- Department of Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, P. R. China
| | - Yun-Bing Zhou
- Department of Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, P. R. China
| | - Ren-Hao Li
- Department of Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, P. R. China
| | - Hai-Tao Tang
- Department of Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, P. R. China
| | - Cheng-Ke Ding
- Department of Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, P. R. China
| | - Zhuang-Ping Zhan
- Department of Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, P. R. China
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17
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Yang YF, Liang Y, Liu F, Houk KN. Diels-Alder Reactivities of Benzene, Pyridine, and Di-, Tri-, and Tetrazines: The Roles of Geometrical Distortions and Orbital Interactions. J Am Chem Soc 2016; 138:1660-7. [PMID: 26804318 DOI: 10.1021/jacs.5b12054] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cycloadditions of benzene and ten different azabenzenes (pyridine, three diazines, three triazines, and three tetrazines) with the ethylene dienophile have been explored with density functional theory (M06-2X) and analyzed with the distortion/interaction model. Activation barriers correlate closely with both distortion energies and interaction energies over an activation energy range of 45 kcal/mol. The replacement of CH with N increases Diels-Alder reactivity due not only to the more favorable orbital interaction, but also to a decrease in distortion energy. The rates of reactions are greatly influenced by the nature of the bonds being formed: two C-C bonds > one C-C bond, and one C-N bond > two C-N bonds. The activation energy of Diels-Alder reactions correlates very well with reaction energies and with the NICS(0) values of the aromatic dienes. The distortion energy of the Diels-Alder reaction transition states mostly arises from the diene out-of-plane distortion energy.
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Affiliation(s)
- Yun-Fang Yang
- Department of Chemistry and Biochemistry, ‡Department of Chemical and Biomolecular Engineering, University of California , Los Angeles, California 90095, United States
| | - Yong Liang
- Department of Chemistry and Biochemistry, ‡Department of Chemical and Biomolecular Engineering, University of California , Los Angeles, California 90095, United States
| | - Fang Liu
- Department of Chemistry and Biochemistry, ‡Department of Chemical and Biomolecular Engineering, University of California , Los Angeles, California 90095, United States
| | - K N Houk
- Department of Chemistry and Biochemistry, ‡Department of Chemical and Biomolecular Engineering, University of California , Los Angeles, California 90095, United States
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18
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Wang Z, Wang W, Geng L, Hu Z. Distinguishing of tumor cell-targeting peptide ligands through a color-encoding microarray. LAB ON A CHIP 2015; 15:4512-4516. [PMID: 26530232 DOI: 10.1039/c5lc01010a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A silicon-based microarray system was constructed to discover the affinity peptides and to distinguish the specific peptides from a high throughput library. Using a color-encoding strategy, in situ peptide distinguishing between HER1 ligands and HER2 ligands was achieved. Novel affinity peptide sequences H1P (HER1 ligand) and H2P (HER2 ligand) were determined with nmol affinity.
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Affiliation(s)
- Zihua Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China.
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19
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Fu J, Yu C, Li L, Yao SQ. Intracellular Delivery of Functional Proteins and Native Drugs by Cell-Penetrating Poly(disulfide)s. J Am Chem Soc 2015; 137:12153-60. [DOI: 10.1021/jacs.5b08130] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Jiaqi Fu
- Department
of Chemistry, National University of Singapore, 117543 Singapore
| | - Changmin Yu
- Department
of Chemistry, National University of Singapore, 117543 Singapore
| | - Lin Li
- Department
of Chemistry, National University of Singapore, 117543 Singapore
- Key
Laboratory of Flexible Electronics and Institute of Advanced Materials,
National Jiangsu Synergistic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, P. R. China
| | - Shao Q. Yao
- Department
of Chemistry, National University of Singapore, 117543 Singapore
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20
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Zhu B, Jiang B, Na Z, Yao SQ. Controlled proliferation and screening of mammalian cells on a hydrogel-functionalized small molecule microarray. Chem Commun (Camb) 2015; 51:10431-4. [PMID: 26028192 DOI: 10.1039/c5cc03278d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A hydrogel-functionalized small molecule microarray has been developed, on which PC-3 cancer cells were selectively grown. Subsequent controlled release of immobilized bioactive compounds enabled cell-based screening to be directly carried out on this platform.
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Affiliation(s)
- Biwei Zhu
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore117543.
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21
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Abstract
We have developed methods involving the use of alternate, safer reagents for the scalable syntheses of the potent BET bromodomain inhibitor JQ1. A one-pot three step method, involving the conversion of a benzodiazepine to a thioamde using Lawesson's reagent, followed by amidrazone formation and installation of the triazole moiety furnished JQ1. This method provides good yields and a facile purification process. For the synthesis of enantiomerically enriched (+)-JQ1, the highly toxic reagent diethyl chlorophosphate, used in a previous synthesis, was replaced with the safer reagent diphenyl chlorophosphate in the three-step one-pot triazole formation without effecting yields and enantiomeric purity of (+)-JQ1.
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Affiliation(s)
- Shameem Sultana Syeda
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, College of Pharmacy, University of Minnesota, Minneapolis, MN 55414, United States of America
| | - Sudhakar Jakkaraj
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, College of Pharmacy, University of Minnesota, Minneapolis, MN 55414, United States of America
| | - Gunda I Georg
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, College of Pharmacy, University of Minnesota, Minneapolis, MN 55414, United States of America
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22
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Daguer JP, Zambaldo C, Abegg D, Barluenga S, Tallant C, Müller S, Adibekian A, Winssinger N. Identifizierung von niedermolekularen kovalenten Bromodomäne-Bindern aus einer DNA-kodierten Bibliothek. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201412276] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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Daguer JP, Zambaldo C, Abegg D, Barluenga S, Tallant C, Müller S, Adibekian A, Winssinger N. Identification of Covalent Bromodomain Binders through DNA Display of Small Molecules. Angew Chem Int Ed Engl 2015; 54:6057-61. [DOI: 10.1002/anie.201412276] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Indexed: 01/08/2023]
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24
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25
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Na Z, Peng B, Ng S, Pan S, Lee JS, Shen HM, Yao SQ. A small-molecule protein-protein interaction inhibitor of PARP1 that targets its BRCT domain. Angew Chem Int Ed Engl 2015; 54:2515-9. [PMID: 25565365 DOI: 10.1002/anie.201410678] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 12/07/2014] [Indexed: 01/01/2023]
Abstract
Poly(ADP-ribose)polymerase-1 (PARP1) is a BRCT-containing enzyme (BRCT = BRCA1 C-terminus) mainly involved in DNA repair and damage response and a validated target for cancer treatment. Small-molecule inhibitors that target the PARP1 catalytic domain have been actively pursued as anticancer drugs, but are potentially problematic owing to a lack of selectivity. Compounds that are capable of disrupting protein-protein interactions of PARP1 provide an alternative by inhibiting its activities with improved selectivity profiles. Herein, by establishing a high-throughput microplate-based assay suitable for screening potential PPI inhibitors of the PARP1 BRCT domain, we have discovered that (±)-gossypol, a natural product with a number of known biological activities, possesses novel PARP1 inhibitory activity both in vitro and in cancer cells and presumably acts through disruption of protein-protein interactions. As the first known cell-permeable small-molecule PPI inhibitor of PAPR1, we further established that (-)-gossypol was likely the causative agent of PARP1 inhibition by promoting the formation of a 1:2 compound/PARP1 complex by reversible formation of a covalent imine linkage.
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Affiliation(s)
- Zhenkun Na
- 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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26
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Na Z, Peng B, Ng S, Pan S, Lee JS, Shen HM, Yao SQ. A Small-Molecule Protein-Protein Interaction Inhibitor of PARP1 That Targets Its BRCT Domain. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410678] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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27
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Wang W, Wei Z, Zhang D, Ma H, Wang Z, Bu X, Li M, Geng L, Lausted C, Hood L, Fang Q, Wang H, Hu Z. Rapid Screening of Peptide Probes through In Situ Single-Bead Sequencing Microarray. Anal Chem 2014; 86:11854-9. [DOI: 10.1021/ac503454z] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Weizhi Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Zewen Wei
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Di Zhang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Huailei Ma
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Zihua Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Xiangli Bu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Menglin Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Lingling Geng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Christopher Lausted
- Institute for Systems
Biology, 401 Terry Avenue N., Seattle, Washington 98109, United States
| | - Leroy Hood
- Institute for Systems
Biology, 401 Terry Avenue N., Seattle, Washington 98109, United States
| | - Qiaojun Fang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Hao Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Zhiyuan Hu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
- Beijing
Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
- Institute for Systems
Biology, 401 Terry Avenue N., Seattle, Washington 98109, United States
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28
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Späte AK, Schart VF, Schöllkopf S, Niederwieser A, Wittmann V. Terminal Alkenes as Versatile Chemical Reporter Groups for Metabolic Oligosaccharide Engineering. Chemistry 2014; 20:16502-8. [DOI: 10.1002/chem.201404716] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Indexed: 11/07/2022]
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29
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Liu F, Liang Y, Houk KN. Theoretical elucidation of the origins of substituent and strain effects on the rates of Diels-Alder reactions of 1,2,4,5-tetrazines. J Am Chem Soc 2014; 136:11483-93. [PMID: 25041719 DOI: 10.1021/ja505569a] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The Diels-Alder reactions of seven 1,2,4,5-tetrazines with unstrained and strained alkenes and alkynes were studied with quantum mechanical calculations (M06-2X density functional theory) and analyzed with the distortion/interaction model. The higher reactivities of alkenes compared to alkynes in the Diels-Alder reactions with tetrazines arise from the differences in both interaction and distortion energies. Alkenes have HOMO energies higher than those of alkynes and therefore stronger interaction energies in inverse-electron-demand Diels-Alder reactions with tetrazines. We have also found that the energies to distort alkenes into the Diels-Alder transition-state geometries are smaller than for alkynes in these reactions. The strained dienophiles, trans-cyclooctene and cyclooctyne, are much more reactive than unstrained trans-2-butene and 2-butyne, because they are predistorted toward the Diels-Alder transition structures. The reactivities of substituted tetrazines correlate with the electron-withdrawing abilities of the substituents. Electron-withdrawing groups lower the LUMO+1 of tetrazines, resulting in stronger interactions with the HOMO of dienophiles. Moreover, electron-withdrawing substituents destabilize the tetrazines, and this leads to smaller distortion energies in the Diels-Alder transition states.
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Affiliation(s)
- Fang Liu
- Department of Chemistry and Biochemistry, University of California , Los Angeles, California 90095, United States
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30
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Lee JH, Domaille DW, Noh H, Oh T, Choi C, Jin S, Cha JN. High-yielding and photolabile approaches to the covalent attachment of biomolecules to surfaces via hydrazone chemistry. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:8452-8460. [PMID: 24972257 DOI: 10.1021/la500744s] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The development of strategies to couple biomolecules covalently to surfaces is necessary for constructing sensing arrays for biological and biomedical applications. One attractive conjugation reaction is hydrazone formation--the reaction of a hydrazine with an aldehyde or ketone--as both hydrazines and aldehydes/ketones are largely bioorthogonal, which makes this particular reaction suitable for conjugating biomolecules to a variety of substrates. We show that the mild reaction conditions afforded by hydrazone conjugation enable the conjugation of DNA and proteins to the substrate surface in significantly higher yields than can be achieved with traditional bioconjugation techniques, such as maleimide chemistry. Next, we designed and synthesized a photocaged aryl ketone that can be conjugated to a surface and photochemically activated to provide a suitable partner for subsequent hydrazone formation between the surface-anchored ketone and DNA- or protein-hydrazines. Finally, we exploit the latent functionality of the photocaged ketone and pattern multiple biomolecules on the same substrate, effectively demonstrating a strategy for designing substrates with well-defined domains of different biomolecules. We expect that this approach can be extended to the production of multiplexed assays by using an appropriate mask with sequential photoexposure and biomolecule conjugation steps.
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Affiliation(s)
- Ju Hun Lee
- Department of Chemical and Biological Engineering, University of Colorado, Boulder , 596 UCB, Boulder, Colorado 80303-1904, United States
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31
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Wang P, Na Z, Fu J, Tan CYJ, Zhang H, Yao SQ, Sun H. Microarray immobilization of biomolecules using a fast trans-cyclooctene (TCO)–tetrazine reaction. Chem Commun (Camb) 2014; 50:11818-21. [DOI: 10.1039/c4cc03838j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Li Z, Wang D, Li L, Pan S, Na Z, Tan CYJ, Yao SQ. "Minimalist" cyclopropene-containing photo-cross-linkers suitable for live-cell imaging and affinity-based protein labeling. J Am Chem Soc 2014; 136:9990-8. [PMID: 24972113 DOI: 10.1021/ja502780z] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Target identification of bioactive compounds within the native cellular environment is important in biomedical research and drug discovery, but it has traditionally been carried out in vitro. Information about how such molecules interact with their endogenous targets (on and off) is currently highly limited. An ideal strategy would be one that recapitulates protein-small molecule interactions in situ (e.g., in living cells) and at the same time enables enrichment of these complexes for subsequent proteome-wide target identification. Similarly, small molecule-based imaging approaches are becoming increasingly available for in situ monitoring of a variety of proteins including enzymes. Chemical proteomic strategies for simultaneous bioimaging and target identification of noncovalent bioactive compounds in live mammalian cells, however, are currently not available. This is due to a lack of photoaffinity labels that are minimally modified from their parental compounds, yet chemically tractable using copper-free bioorthogonal chemistry. We have herein developed novel minimalist linkers containing both an alkyl diazirine and a cyclopropene. We have shown chemical probes (e.g., BD-2) made from such linkers could be used for simultaneous in situ imaging and covalent labeling of endogenous BRD-4 (an important epigenetic protein) via a rapid, copper-free, tetrazine-cyclopropene ligation reaction (k2 > 5 M(-1) s(-1)). The key features of our cyclopropenes, with their unique C-1 linkage to BRD-4-targeting moiety, are their tunable reactivity and solubility, relative stability, and synthetic accessibility. BD-2, which is a linker-modified analogue of (+)-JQ1 (a recently discovered nanomolar protein-protein-interaction inhibitor of BRD-4), was subsequently used in a cell-based proteome profiling experiment for large-scale identification of potential off-targets of (+)-JQ1. Several newly identified targets were subsequently confirmed by preliminary validation experiments.
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Affiliation(s)
- Zhengqiu Li
- Department of Chemistry, National University of Singapore , 3 Science Drive 3, Singapore 117543
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33
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Seo JS, Poulter CD. Sandwich antibody arrays using recombinant antibody-binding protein L. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:6629-6635. [PMID: 24841983 PMCID: PMC4059220 DOI: 10.1021/la500822w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/16/2014] [Indexed: 06/01/2023]
Abstract
Antibody arrays are a useful for detecting antigens and other antibodies. This technique typically requires a uniform and well-defined orientation of antibodies attached to a surface for optimal performance. A uniform orientation can be achieved by modification of antibodies to include a single site for attachment. Thus, uniformly oriented antibody arrays require a bioengineered modification for the antibodies directly immobilization on the solid surface. In this study, we describe a "sandwich-type" antibody array where unmodified antibodies are oriented through binding with regioselectively immobilized recombinant antibody-binding protein L. Recombinant proL-CVIA bearing C-terminal CVIA motif is post-translationally modified with an alkyne group by protein farnesyltransferase (PFTase) at the cysteine residue in the CVIA sequence to give proL-CVIApf, which is covalently attached to an azido-modified glass slide by a Huisgen [3 + 2] cycloaddition reaction. Slides bearing antibodies bound to slides coated with regioselectively immobilized proL-CVIApf gave stronger fluorescence outputs and those where the antibody-binding protein was immobilized in random orientations on an epoxy-modified slide. Properly selected capture and detection antibodies did not cross-react with immobilized proL-CVIApf in sandwich arrays, and the proL-CVIApf slides can be used for multiple cycles of detected over a period of several months.
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34
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Wang W, Li M, Wei Z, Wang Z, Bu X, Lai W, Yang S, Gong H, Zheng H, Wang Y, Liu Y, Li Q, Fang Q, Hu Z. Bimodal Imprint Chips for Peptide Screening: Integration of High-Throughput Sequencing by MS and Affinity Analyses by Surface Plasmon Resonance Imaging. Anal Chem 2014; 86:3703-7. [DOI: 10.1021/ac500465e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Weizhi Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Menglin Li
- Department
of Biomedical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Zewen Wei
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Zihua Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Xiangli Bu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Wenjia Lai
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Shu Yang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - He Gong
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Hui Zheng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Yuqiao Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Ying Liu
- Beijing
Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Qin Li
- Department
of Biomedical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Qiaojun Fang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Zhiyuan Hu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
- Beijing
Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
- Institute for Systems Biology, 401 Terry Avenue N, Seattle, Washington 98109, United States
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35
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Roling O, Mardyukov A, Lamping S, Vonhören B, Rinnen S, Arlinghaus HF, Studer A, Ravoo BJ. Surface patterning with natural and synthetic polymers via an inverse electron demand Diels–Alder reaction employing microcontact chemistry. Org Biomol Chem 2014; 12:7828-35. [DOI: 10.1039/c4ob01379d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Bioorthogonal ligation methods are the focus of current research due to their versatile applications in biotechnology and materials science for post-functionalization and immobilization of biomolecules.
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Affiliation(s)
- Oliver Roling
- Organisch-Chemisches Institut and Graduate School of Chemistry
- Westfälische Wilhelms-Universität Münster
- 48149 Münster, Germany
| | - Artur Mardyukov
- Organisch-Chemisches Institut and Graduate School of Chemistry
- Westfälische Wilhelms-Universität Münster
- 48149 Münster, Germany
| | - Sebastian Lamping
- Organisch-Chemisches Institut and Graduate School of Chemistry
- Westfälische Wilhelms-Universität Münster
- 48149 Münster, Germany
| | - Benjamin Vonhören
- Organisch-Chemisches Institut and Graduate School of Chemistry
- Westfälische Wilhelms-Universität Münster
- 48149 Münster, Germany
| | - Stefan Rinnen
- Physikalisches Institut
- Westfälische Wilhelms-Universität Münster
- 48149 Münster, Germany
| | | | - Armido Studer
- Organisch-Chemisches Institut and Graduate School of Chemistry
- Westfälische Wilhelms-Universität Münster
- 48149 Münster, Germany
| | - Bart Jan Ravoo
- Organisch-Chemisches Institut and Graduate School of Chemistry
- Westfälische Wilhelms-Universität Münster
- 48149 Münster, Germany
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