1
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Li P, Kawade SK, Adak AK, Shen Y, Fan C, Hsieh Y, Angata T, Chen Y, Lin C. Ligand‐assisted imprinting‐probe‐labeling
strategy reveals Siglec‐7 ‐ glycoprotein interactions. J CHIN CHEM SOC-TAIP 2022. [DOI: 10.1002/jccs.202200127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Pei‐Jhen Li
- Department of Chemistry and Biochemistry National Chung Cheng University Chiayi Taiwan
| | | | - Avijit K. Adak
- Department of Chemistry National Tsing Hua University Hsinchu Taiwan
| | - Yu‐Ju Shen
- Department of Chemistry National Tsing Hua University Hsinchu Taiwan
| | - Chen‐Yo Fan
- Department of Chemistry National Tsing Hua University Hsinchu Taiwan
| | - Yu‐Heng Hsieh
- Institute of Chemistry, Academia Sinica Taipei Taiwan
| | - Takashi Angata
- Institute of Biological Chemistry, Academia Sinica Taipei Taiwan
| | - Yu‐Ju Chen
- Institute of Chemistry, Academia Sinica Taipei Taiwan
| | - Chun‐Cheng Lin
- Department of Chemistry National Tsing Hua University Hsinchu Taiwan
- Department of Medicinal and Applied Chemistry Kaohsiung Medical University Kaohsiung Taiwan
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2
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Abstract
A growing theme in chemistry is the joining of multiple organic molecular building blocks to create functional molecules. Diverse derivatizable structures—here termed “scaffolds” comprised of “hubs”—provide the foundation for systematic covalent organization of a rich variety of building blocks. This review encompasses 30 tri- or tetra-armed molecular hubs (e.g., triazine, lysine, arenes, dyes) that are used directly or in combination to give linear, cyclic, or branched scaffolds. Each scaffold is categorized by graph theory into one of 31 trees to express the molecular connectivity and overall architecture. Rational chemistry with exacting numbers of derivatizable sites is emphasized. The incorporation of water-solubilization motifs, robust or self-immolative linkers, enzymatically cleavable groups and functional appendages affords immense (and often late-stage) diversification of the scaffolds. Altogether, 107 target molecules are reviewed along with 19 syntheses to illustrate the distinctive chemistries for creating and derivatizing scaffolds. The review covers the history of the field up through 2020, briefly touching on statistically derivatized carriers employed in immunology as counterpoints to the rationally assembled and derivatized scaffolds here, although most citations are from the past two decades. The scaffolds are used widely in fields ranging from pure chemistry to artificial photosynthesis and biomedical sciences.
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3
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Fairbanks BD, Macdougall LJ, Mavila S, Sinha J, Kirkpatrick BE, Anseth KS, Bowman CN. Photoclick Chemistry: A Bright Idea. Chem Rev 2021; 121:6915-6990. [PMID: 33835796 PMCID: PMC9883840 DOI: 10.1021/acs.chemrev.0c01212] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
At its basic conceptualization, photoclick chemistry embodies a collection of click reactions that are performed via the application of light. The emergence of this concept has had diverse impact over a broad range of chemical and biological research due to the spatiotemporal control, high selectivity, and excellent product yields afforded by the combination of light and click chemistry. While the reactions designated as "photoclick" have many important features in common, each has its own particular combination of advantages and shortcomings. A more extensive realization of the potential of this chemistry requires a broader understanding of the physical and chemical characteristics of the specific reactions. This review discusses the features of the most frequently employed photoclick reactions reported in the literature: photomediated azide-alkyne cycloadditions, other 1,3-dipolarcycloadditions, Diels-Alder and inverse electron demand Diels-Alder additions, radical alternating addition chain transfer additions, and nucleophilic additions. Applications of these reactions in a variety of chemical syntheses, materials chemistry, and biological contexts are surveyed, with particular attention paid to the respective strengths and limitations of each reaction and how that reaction benefits from its combination with light. Finally, challenges to broader employment of these reactions are discussed, along with strategies and opportunities to mitigate such obstacles.
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Affiliation(s)
- Benjamin D Fairbanks
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - Laura J Macdougall
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - Sudheendran Mavila
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - Jasmine Sinha
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - Bruce E Kirkpatrick
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
- The BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
- Medical Scientist Training Program, School of Medicine, University of Colorado, Aurora, Coorado 80045, United States
| | - Kristi S Anseth
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
- The BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Christopher N Bowman
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
- Materials Science and Engineering Program, University of Colorado, Boulder, Colorado 80303, United States
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4
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Photoswitchable CAR-T Cell Function In Vitro and In Vivo via a Cleavable Mediator. Cell Chem Biol 2020; 28:60-69.e7. [PMID: 33113407 DOI: 10.1016/j.chembiol.2020.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/07/2020] [Accepted: 10/07/2020] [Indexed: 01/20/2023]
Abstract
Chimeric antigen receptor (CAR)-T-based therapeutics are a breakthrough in cancer treatment; however, they are hampered by constitutive activation, which leads to worrisome side effects. Engineering CAR-T cells to be as tightly controllable as possible remains a topic of ongoing investigation. Here, we report a photoswitchable approach that uses a mediator for the at-will regulation of CAR-T cells. This mediator carries dual folate and fluorescein isothiocyanate moieties tethered by an ortho-nitrobenzyl ester photocleavable linker. CAR-T cells were shown to be highly cytotoxic to targeted cells only in the presence of the mediator and acted in a dose-dependent manner. The toxicity of CAR-T cells can be rapidly terminated by cleavage of the mediator, and the effects of CAR-T cells can be activated again by resupplementation with the mediator without compromising tumor therapy. The approach described here provides a direction for enhancing the controllability of CAR-T cells and can likely be applied in other immunotherapies.
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5
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Jbara M, Eid E, Brik A. Gold(I)-Mediated Decaging or Cleavage of Propargylated Peptide Bond in Aqueous Conditions for Protein Synthesis and Manipulation. J Am Chem Soc 2020; 142:8203-8210. [PMID: 32290655 DOI: 10.1021/jacs.9b13216] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Chemists have been interested in the N-alkylation of a peptide bond because such a modification alters the conformation of the amide bond, interferes with hydrogen bond formation, and changes other properties of the peptide (e.g., solubility). This modification also opens the door for attaching functional groups for various applications. Nonetheless, the irreversibility of some of these modifications and the harsh conditions required for their removal currently limits the wide utility of this approach. Herein, we report applying a propargyl group for peptide bond modification at diverse junctions, which can be removed under mild and aqueous conditions via treatment with gold(I). Considering the straightforward conditions for both the installation and removal of this group, the propargyl group provides access to the benefits of backbone N-alkylation, while preserving the ability for on-demand depropargylation and full recovery of the native amide bond. This reversible modification was found to improve solid-phase peptide synthesis as demonstrated in the chemical synthesis of NEDD8 protein, without the use of special dipeptide analogues. Also, the reported approach was found to be useful in decaging a broad range of propargyl-based protecting groups used in chemical protein synthesis. Remarkably, reversing the order of the two residues in the propargylation site resulted in rapid amide bond cleavage, which extends the applicability of this approach beyond a removable backbone modification to a cleavable linker. The easy attach/detach of this functionality was also examined in loading and releasing of biotinylated peptides from streptavidin beads.
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Affiliation(s)
- Muhammad Jbara
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200008, Israel
| | - Emad Eid
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200008, Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200008, Israel
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6
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Li PJ, Anwar MT, Fan CY, Juang DS, Lin HY, Chang TC, Kawade SK, Chen HJ, Chen YJ, Tan KT, Lin CC. Fluorescence "Turn-on" Lectin Sensors Fabricated by Ligand-Assisted Labeling Probes for Detecting Protein-Glycoprotein Interactions. Biomacromolecules 2020; 21:815-824. [PMID: 31891486 DOI: 10.1021/acs.biomac.9b01495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Elucidation of protein-protein interactions (PPIs) is often very challenging and yields complex and unclear results. Lectin-glycoprotein interactions are especially difficult to study due to the noncovalent nature of the interactions and inherently low binding affinities of proteins to glycan ligands on glycoproteins. Here, we report a "ligand-directed labeling probe (LLP)"-based approach to fabricate protein probes for elucidating protein-glycoprotein interactions. LLP was designed with dual photoactivatable groups for the introduction of an alkyne handle proximal to the carbohydrate-binding pocket of lectins, Ricinus communis agglutinin 120 (RCA120) and recombinant human Siglec-2-Fc. In proof-of-principle studies, alkynylated lectins were conjugated with a photoreactive diazirine cross-linker and an environment-sensitive fluorophore, respectively, by the bioorthogonal click reaction. The modified RCA120 or Siglec-2-Fc was used for detecting the interaction with the target glycoprotein in the solution or endogenously expressed glycoproteins on live HeLa cells. We anticipate that the fabrication of these protein probes will accelerate the discovery of novel PPIs.
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Affiliation(s)
- Pei-Jhen Li
- Department of Chemistry , National Tsing Hua University , 101 Section 2, Kuang Fu Road , Hsinchu 30013 , Taiwan
| | - Mohammad Tarigue Anwar
- Department of Chemistry , National Tsing Hua University , 101 Section 2, Kuang Fu Road , Hsinchu 30013 , Taiwan
| | - Chen-Yo Fan
- Department of Chemistry , National Tsing Hua University , 101 Section 2, Kuang Fu Road , Hsinchu 30013 , Taiwan
| | - Duane S Juang
- Department of Chemistry , National Tsing Hua University , 101 Section 2, Kuang Fu Road , Hsinchu 30013 , Taiwan
| | - Hsin-Yi Lin
- Institute of Chemistry , Academia Sinica , Taipei 11529 , Taiwan
| | - Tsung-Che Chang
- Department of Chemistry , National Tsing Hua University , 101 Section 2, Kuang Fu Road , Hsinchu 30013 , Taiwan
| | - Sachin Kisan Kawade
- Department of Chemistry , National Tsing Hua University , 101 Section 2, Kuang Fu Road , Hsinchu 30013 , Taiwan
| | - Hsiang-Jung Chen
- Department of Chemistry , National Tsing Hua University , 101 Section 2, Kuang Fu Road , Hsinchu 30013 , Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry , Academia Sinica , Taipei 11529 , Taiwan
| | - Kui-Thong Tan
- Department of Chemistry , National Tsing Hua University , 101 Section 2, Kuang Fu Road , Hsinchu 30013 , Taiwan
| | - Chun-Cheng Lin
- Department of Chemistry , National Tsing Hua University , 101 Section 2, Kuang Fu Road , Hsinchu 30013 , Taiwan.,Department of Medicinal and Applied Chemistry , Kaohsiung Medical University , Kaohsiung 80708 , Taiwan
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7
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Wu H, Kohler J. Photocrosslinking probes for capture of carbohydrate interactions. Curr Opin Chem Biol 2019; 53:173-182. [PMID: 31706134 DOI: 10.1016/j.cbpa.2019.09.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 09/13/2019] [Accepted: 09/17/2019] [Indexed: 01/03/2023]
Abstract
Glycan-mediated interactions are essential in many biological processes and regulate a wide variety of cellular functions. However, characterizing these interactions is difficult because glycan biosynthesis is not template driven and because carbohydrate recognition events are usually of low affinity and transient. Photocrosslinking carbohydrate probes can form a covalent bond with molecules in close proximity on UV irradiation and are capable of capturing interactions between glycans and glycan-binding proteins in situ. Because of these advantages, multiple photocrosslinking carbohydrate probes have been designed and applied to study the biological functions of glycans. This review will discuss recent advances in the development of novel photocrosslinking functional groups and the design of photocrosslinking probes to detect interactions mediated by glycolipids, peptidoglycan, and multivalent carbohydrate ligands. These probes have demonstrated the potential to address some of the major challenges in the study of glycan-mediated interactions in both model systems and in more complex biological settings.
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Affiliation(s)
- Han Wu
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jennifer Kohler
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA. http://
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8
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Zhang H, Li G, Liao C, Cai Y, Jiang G. Bio-related applications of porous organic frameworks (POFs). J Mater Chem B 2019; 7:2398-2420. [PMID: 32255118 DOI: 10.1039/c8tb03192d] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Porous organic frameworks (POFs) are promising candidates for bio-related applications. This review highlights the recent progress in POF-based bioapplications, including drug delivery, bioimaging, biosensing, therapeutics, and artificial shells. These encouraging performances suggest that POFs used for bioapplications deserve more attention in the future.
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Affiliation(s)
- He Zhang
- Research Center for Eco-Environmental Sciences
- Chinese Academy of Sciences
- Beijing 100085
- China
- University of the Chinese Academy of Sciences
| | - Guoliang Li
- Research Center for Eco-Environmental Sciences
- Chinese Academy of Sciences
- Beijing 100085
- China
| | - Chunyang Liao
- Research Center for Eco-Environmental Sciences
- Chinese Academy of Sciences
- Beijing 100085
- China
- University of the Chinese Academy of Sciences
| | - Yaqi Cai
- Research Center for Eco-Environmental Sciences
- Chinese Academy of Sciences
- Beijing 100085
- China
- University of the Chinese Academy of Sciences
| | - Guibin Jiang
- Research Center for Eco-Environmental Sciences
- Chinese Academy of Sciences
- Beijing 100085
- China
- University of the Chinese Academy of Sciences
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9
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Bruneau M, Bennici S, Brendle J, Dutournie P, Limousy L, Pluchon S. Systems for stimuli-controlled release: Materials and applications. J Control Release 2019; 294:355-371. [DOI: 10.1016/j.jconrel.2018.12.038] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/20/2018] [Accepted: 12/21/2018] [Indexed: 01/15/2023]
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10
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Zhou L, Qiu T, Lv F, Liu L, Ying J, Wang S. Self-Assembled Nanomedicines for Anticancer and Antibacterial Applications. Adv Healthc Mater 2018; 7:e1800670. [PMID: 30080319 DOI: 10.1002/adhm.201800670] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/03/2018] [Indexed: 01/28/2023]
Abstract
Self-assembly strategies have been widely applied in the nanomedicine field, which provide a convenient approach for building various structures for delivery carriers. When cooperating with biomolecules, self-assembly systems have significant influence on the cell activity and life process and could be used for regulating nanodrug activity. In this review, self-assembled nanomedicines are introduced, including materials, encapsulation, and releasing strategies, where self-assembly strategies are involved. Furthermore, as a promising and emerging area for nanomedicine, in situ self-assembly of anticancer drugs and supramolecular antibiotic switches is also discussed about how to regulate drug activity. Selective pericellular assembly can block mass transformation of cancer cells inducing cell apoptosis, and the intracellular assembly can either cause cell death or effectively avoid drug elimination from cytosol of cancer cells because of the assembly-induced retention (AIR) effect. Host-guest interactions of drug and competitive molecules offer reversible regulations of antibiotic activity, which can reduce drug-resistance and inhibit the generation of drug-resistant bacteria. Finally, the challenges and development trend in the field are discussed.
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Affiliation(s)
- Lingyun Zhou
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Organic Solids; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P. R. China
- College of Chemistry; University of Chinese Academy of Sciences; Beijing 100049 P. R. China
| | - Tian Qiu
- Department of Pathology; National Cancer Center/National Clinical Research Center for; Cancer/Cancer Hospital; Chinese Academy of Medical Sciences and Peking Union Medical College; Beijing 100021 P. R. China
| | - Fengting Lv
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Organic Solids; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P. R. China
| | - Libing Liu
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Organic Solids; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P. R. China
| | - Jianming Ying
- Department of Pathology; National Cancer Center/National Clinical Research Center for; Cancer/Cancer Hospital; Chinese Academy of Medical Sciences and Peking Union Medical College; Beijing 100021 P. R. China
| | - Shu Wang
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Organic Solids; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P. R. China
- College of Chemistry; University of Chinese Academy of Sciences; Beijing 100049 P. R. China
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11
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Wawro AM, Aoki Y, Muraoka T, Tsumoto K, Kinbara K. Enzymatically cleavable traceless biotin tags for protein PEGylation and purification. Chem Commun (Camb) 2018; 54:1913-1916. [DOI: 10.1039/c7cc05814d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Immobilized lipase was successfully employed for the rapid removal of a biotin tag from a protein–PEG conjugate under mild conditions.
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Affiliation(s)
- Adam M. Wawro
- School of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
- Department of Bioengineering
| | - Yusuke Aoki
- School of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Takahiro Muraoka
- School of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
- PRESTO
| | - Kouhei Tsumoto
- Department of Bioengineering
- School of Engineering
- The University of Tokyo
- Tokyo 108-8656
- Japan
| | - Kazushi Kinbara
- School of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
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12
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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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13
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Xie Z, Wan X, Zhong L, Yang H, Li P, Xu X. Carnosic acid alleviates hyperlipidemia and insulin resistance by promoting the degradation of SREBPs via the 26S proteasome. J Funct Foods 2017. [DOI: 10.1016/j.jff.2017.01.040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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