1
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Knutson SD, Buksh BF, Huth SW, Morgan DC, MacMillan DWC. Current advances in photocatalytic proximity labeling. Cell Chem Biol 2024; 31:1145-1161. [PMID: 38663396 PMCID: PMC11193652 DOI: 10.1016/j.chembiol.2024.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/31/2024] [Accepted: 03/29/2024] [Indexed: 06/23/2024]
Abstract
Understanding the intricate network of biomolecular interactions that govern cellular processes is a fundamental pursuit in biology. Over the past decade, photocatalytic proximity labeling has emerged as one of the most powerful and versatile techniques for studying these interactions as well as uncovering subcellular trafficking patterns, drug mechanisms of action, and basic cellular physiology. In this article, we review the basic principles, methodologies, and applications of photocatalytic proximity labeling as well as examine its modern development into currently available platforms. We also discuss recent key studies that have successfully leveraged these technologies and importantly highlight current challenges faced by the field. Together, this review seeks to underscore the potential of photocatalysis in proximity labeling for enhancing our understanding of cell biology while also providing perspective on technological advances needed for future discovery.
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Affiliation(s)
- Steve D Knutson
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Benito F Buksh
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Sean W Huth
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Danielle C Morgan
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - David W C MacMillan
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.
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2
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Huang C, Zhao C, Sun Y, Feng T, Ren J, Qu X. A Hydrogen-Bonded Organic Framework-Based Mitochondrion-Targeting Bioorthogonal Platform for the Modulation of Mitochondrial Epigenetics. NANO LETTERS 2024. [PMID: 38865330 DOI: 10.1021/acs.nanolett.4c01794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
Bioorthogonal chemistry represents a powerful tool in chemical biology, which shows great potential in epigenetic modulation. As a proof of concept, the epigenetic modulation model of mitochondrial DNA (mtDNA) is selected because mtDNA establishes a relative hypermethylation stage under oxidative stress, which impairs the mitochondrion-based therapeutic effect during cancer therapy. Herein, we design a new biocompatible hydrogen-bonded organic framework (HOF) for a HOF-based mitochondrion-targeting bioorthogonal platform TPP@P@PHOF-2. PHOF-2 can activate a prodrug (pro-procainamide) in situ, which can specifically inhibit DNA methyltransferase 1 (DNMT1) activity and remodel the epigenetic modification of mtDNA, making it more susceptible to ROS damage. In addition, PHOF-2 can also catalyze artemisinin to produce large amounts of ROS, effectively damaging mtDNA and achieving better chemodynamic therapy demonstrated by both in vitro and in vivo studies. This work provides new insights into developing advanced bioorthogonal therapy and expands the applications of HOF and bioorthogonal catalysis.
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Affiliation(s)
- Congcong Huang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Chuanqi Zhao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Yue Sun
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Tingting Feng
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
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3
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Zhang Y, Liu S, Guo F, Qin S, Zhou N, Liu Z, Fan X, Chen PR. Bioorthogonal Quinone Methide Decaging Enables Live-Cell Quantification of Tumor-Specific Immune Interactions. J Am Chem Soc 2024; 146:15186-15197. [PMID: 38789930 DOI: 10.1021/jacs.4c02052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Effective antitumor immunity hinges on the specific engagement between tumor and cytotoxic immune cells, especially cytotoxic T cells. Although investigating these intercellular interactions is crucial for characterizing immune responses and guiding immunotherapeutic applications, direct and quantitative detection of tumor-T cell interactions within a live-cell context remains challenging. We herein report a photocatalytic live-cell interaction labeling strategy (CAT-Cell) relying on the bioorthogonal decaging of quinone methide moieties for sensitive and selective investigation and quantification of tumor-T cell interactions. By developing quinone methide-derived probes optimized for capturing cell-cell interactions (CCIs), we demonstrated the capacity of CAT-Cell for detecting CCIs directed by various types of receptor-ligand pairs (e.g., CD40-CD40L, TCR-pMHC) and further quantified the strengths of tumor-T cell interactions that are crucial for evaluating the antitumor immune responses. We further applied CAT-Cell for ex vivo quantification of tumor-specific T cell interactions on splenocyte and solid tumor samples from mouse models. Finally, the broad compatibility and utility of CAT-Cell were demonstrated by integrating it with the antigen-specific targeting system as well as for tumor-natural killer cell interaction detection. By leveraging the bioorthogonal photocatalytic decaging chemistry on quinone methide, CAT-Cell provides a sensitive, tunable, universal, and noninvasive toolbox for unraveling and quantifying the crucial but delicate tumor-immune interactions under live-cell settings.
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Affiliation(s)
- Yan Zhang
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Shibo Liu
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Fuhu Guo
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Shan Qin
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Nan Zhou
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ziqi Liu
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xinyuan Fan
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Peng R Chen
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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4
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Wan C, Yang D, Song C, Liang M, An Y, Lian C, Dai C, Ye Y, Yin F, Wang R, Li Z. A pyridinium-based strategy for lysine-selective protein modification and chemoproteomic profiling in live cells. Chem Sci 2024; 15:5340-5348. [PMID: 38577373 PMCID: PMC10988577 DOI: 10.1039/d3sc05766f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/08/2024] [Indexed: 04/06/2024] Open
Abstract
Protein active states are dynamically regulated by various modifications; thus, endogenous protein modification is an important tool for understanding protein functions and networks in complicated biological systems. Here we developed a new pyridinium-based approach to label lysine residues under physiological conditions that is low-toxicity, efficient, and lysine-selective. Furthermore, we performed a large-scale analysis of the ∼70% lysine-selective proteome in MCF-7 cells using activity-based protein profiling (ABPP). We quantifically assessed 1216 lysine-labeled peptides in cell lysates and identified 386 modified lysine sites including 43 mitochondrial-localized proteins in live MCF-7 cells. Labeled proteins significantly preferred the mitochondria. This pyridinium-based methodology demonstrates the importance of analyzing endogenous proteins under native conditions and provides a robust chemical strategy utilizing either lysine-selective protein labeling or spatiotemporal profiling in a living system.
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Affiliation(s)
- Chuan Wan
- College of Health Science and Environmental Engineering, Shenzhen Technology University Shenzhen 518118 P. R. China
| | - Dongyan Yang
- College of Chemistry and Chemical Engineering, Zhongkai University of Agriculture and Engineering Guangzhou 510225 P. R. China
| | - Chunli Song
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory Shenzhen 518118 P. R. China
| | - Mingchan Liang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory Shenzhen 518118 P. R. China
| | - Yuhao An
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory Shenzhen 518118 P. R. China
| | - Chenshan Lian
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory Shenzhen 518118 P. R. China
| | - Chuan Dai
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory Shenzhen 518118 P. R. China
| | - Yuxin Ye
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory Shenzhen 518118 P. R. China
| | - Feng Yin
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory Shenzhen 518118 P. R. China
| | - Rui Wang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory Shenzhen 518118 P. R. China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen 518055 P. R. China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory Shenzhen 518118 P. R. China
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5
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Liu Z, Guo F, Zhu Y, Qin S, Hou Y, Guo H, Lin F, Chen PR, Fan X. Bioorthogonal photocatalytic proximity labeling in primary living samples. Nat Commun 2024; 15:2712. [PMID: 38548729 PMCID: PMC10978841 DOI: 10.1038/s41467-024-46985-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 03/14/2024] [Indexed: 04/01/2024] Open
Abstract
In situ profiling of subcellular proteomics in primary living systems, such as native tissues or clinic samples, is crucial for understanding life processes and diseases, yet challenging due to methodological obstacles. Here we report CAT-S, a bioorthogonal photocatalytic chemistry-enabled proximity labeling method, that expands proximity labeling to a wide range of primary living samples for in situ profiling of mitochondrial proteomes. Powered by our thioQM labeling warhead development and targeted bioorthogonal photocatalytic chemistry, CAT-S enables the labeling of mitochondrial proteins in living cells with high efficiency and specificity. We apply CAT-S to diverse cell cultures, dissociated mouse tissues as well as primary T cells from human blood, portraying the native-state mitochondrial proteomic characteristics, and unveiled hidden mitochondrial proteins (PTPN1, SLC35A4 uORF, and TRABD). Furthermore, CAT-S allows quantification of proteomic perturbations on dysfunctional tissues, exampled by diabetic mouse kidneys, revealing the alterations of lipid metabolism that may drive disease progression. Given the advantages of non-genetic operation, generality, and spatiotemporal resolution, CAT-S may open exciting avenues for subcellular proteomic investigations of primary samples that are otherwise inaccessible.
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Affiliation(s)
- Ziqi Liu
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Fuhu Guo
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Yufan Zhu
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Shengnan Qin
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Yuchen Hou
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Haotian Guo
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Feng Lin
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Peng R Chen
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
| | - Xinyuan Fan
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
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6
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D’Avino C, Gutiérrez S, Feldhaus MJ, Tomás-Gamasa M, Mascareñas JL. Intracellular Synthesis of Indoles Enabled by Visible-Light Photocatalysis. J Am Chem Soc 2024; 146:2895-2900. [PMID: 38277674 PMCID: PMC10859955 DOI: 10.1021/jacs.3c13647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/14/2024] [Accepted: 01/22/2024] [Indexed: 01/28/2024]
Abstract
Performing abiotic synthetic transformations in live cell environments represents a new, promising approach to interrogate and manipulate biology and to uncover new types of biomedical tools. We now found that photocatalytic bond-forming reactions can be added to the toolbox of bioorthogonal synthetic chemistry. Specifically, we demonstrate that exogenous styryl aryl azides can be converted into indoles inside living mammalian cells under photocatalytic conditions.
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Affiliation(s)
- Cinzia D’Avino
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS),
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Spain
| | - Sara Gutiérrez
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS),
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Spain
| | - Max J. Feldhaus
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS),
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Spain
| | - María Tomás-Gamasa
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS),
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Spain
| | - José Luis Mascareñas
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS),
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Spain
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7
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Kumar A, Lee IS. Designer Nanoreactors for Bioorthogonal Catalysis. Acc Chem Res 2024; 57:413-427. [PMID: 38243820 DOI: 10.1021/acs.accounts.3c00735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2024]
Abstract
The evolutionary complexity of compartmentalized biostructures (such as cells and organelles) endows life-sustaining multistep chemical cascades and intricate living functionalities. Relatively, within a very short time span, a synthetic paradigm has resulted in tremendous growth in controlling the materials at different length scales (molecular, nano, micro, and macro), improving mechanistic understanding and setting the design principals toward different compositions, configurations, and structures, and in turn fine-tuning their optoelectronic and catalytic properties for targeted applications. Bioorthogonal catalysis offers a highly versatile toolkit for biochemical modulation and the capability to perform new-to-nature reactions inside living systems, endowing augmented functions. However, conventional catalysts have limitations to control the reactions under physiological conditions due to the hostile bioenvironment. The present account details the development of bioapplicable multicomponent designer nanoreactors (NRs), where the compositions, morphologies, interfacial active sites, and microenvironments around different metal nanocatalysts can be precisely controlled by novel nanospace-confined chemistries. Different architectures of porous, hollow, and open-mouth silica-based nano-housings facilitate the accommodation, protection, and selective access of different nanoscale metal-based catalytic sites. The modular porosity/composition, optical transparency, thermal insulation, and nontoxicity of silica are highly useful. Moreover, large macropores or cavities can also be occupied by enzymes (for chemoenzymatic cascades) and selectivity enhancers (for stimuli-responsive gating) along with the metal nanocatalysts. Further, it is crucial to selectively activate and control catalytic reactions by a remotely operable biocompatible energy source. Integration of highly coupled plasmonic (Au) components having few-nanometer structural features (gaps, cavities, and junctions as electromagnetic hot-spots) endows an opportunity to efficiently harness low-power NIR light and selectively supply energy to the interfacial catalytic sites through localized photothermal and electronic effects. Different plasmonically integrated NRs with customizable plasmonic-catalytic components, cavities inside bilayer nanospaces, and metal-laminated nanocrystals inside hollow silica can perform NIR-/light-induced catalytic reactions in complex media including living cells. In addition, magnetothermia-induced NRs by selective growth of catalytic metals on a pre-installed superparamagnetic iron-oxide core inside a hollow-porous silica shell endowed the opportunity to apply AMF as a bioorthogonal stimulus to promote catalytic reactions. By combining "plasmonic-catalytic" and "magnetic-catalytic" components within a single NR, two distinct reaction steps can be desirably controlled by two energy sources (NIR light and AMF) of distinct energy regimes. The capability to perform multistep organic molecular transformations in harmony with the natural living system will reveal novel reaction schemes for in cellulo synthesis of active drug and bioimaging probes. Well-designed nanoscale discrete architectures of NRs can facilitate spatiotemporal control over abiotic chemical synthesis without adversely affecting the cell viability. However, in-depth understanding of heterogeneous surface catalytic reactions, rate induction mechanisms, selectivity control pathways, and targeted nanobio interactions is necessary. The broad field of biomedical engineering can hugely benefit from the aid of novel nanomaterials with chemistry-based designs and the synthesis of engineered NRs performing unique bioorthogonal chemistry functions.
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Affiliation(s)
- Amit Kumar
- Creative Research Initiative Center for Nanospace-Confined Chemical Reactions (NCCRs) and Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - In Su Lee
- Creative Research Initiative Center for Nanospace-Confined Chemical Reactions (NCCRs) and Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
- Institute for Convergence Research and Education in Advanced Technology (I-CREATE), Yonsei University, Seoul 03722, Korea
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8
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Guo F, Qin S, Liu Z, Chen PR, Fan X. Decaging-to-labeling: Development and investigation of quinone methide warhead for protein labeling. Bioorg Chem 2024; 143:107088. [PMID: 38194902 DOI: 10.1016/j.bioorg.2023.107088] [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: 10/31/2023] [Revised: 12/28/2023] [Accepted: 12/30/2023] [Indexed: 01/11/2024]
Abstract
Biomolecule labeling in living systems is crucial for understanding biological processes and discovering therapeutic targets. A variety of labeling warheads have been developed for multiple biological applications, including proteomics, bioimaging, sequencing, and drug development. Quinone methides (QMs), a class of highly reactive Michael receptors, have recently emerged as prominent warheads for on-demand biomolecule labeling. Their highly flexible functionality and tunability allow for diverse biological applications, but remain poorly explored at present. In this regard, we designed, synthesized, and evaluated a series of new QM probes with a trifluoromethyl group at the benzyl position and substituents on the aromatic ring to manipulate their chemical properties for biomolecule labeling. The engineered QM warhead efficiently labeled proteins both in vitro and under living cell conditions, with significantly enhanced activity compared to previous QM warheads. We further analyzed the labeling efficacy with the assistance of density functional theory (DFT) calculations, which revealed that the QM generation process, rather than the reactivity of QM, contributes more predominantly to the labeling efficacy. Noteworthy, twelve nucleophilic residues on the BSA were labeled by the probe, including Cys, Asp, Glu, His, Lys, Asn, Gln, Arg, Ser, Thr, Trp and Tyr. Given their high efficiency and tunability, these new QM warheads may hold great promise for a broad range of applications, especially spatiotemporal proteomic profiling for in-depth biological studies.
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Affiliation(s)
- Fuhu Guo
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Shengnan Qin
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ziqi Liu
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Peng R Chen
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
| | - Xinyuan Fan
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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9
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Sun H, Fu B, Qian X, Xu P, Qin W. Nuclear and cytoplasmic specific RNA binding proteome enrichment and its changes upon ferroptosis induction. Nat Commun 2024; 15:852. [PMID: 38286993 PMCID: PMC10825125 DOI: 10.1038/s41467-024-44987-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 01/11/2024] [Indexed: 01/31/2024] Open
Abstract
The key role of RNA-binding proteins (RBPs) in posttranscriptional regulation of gene expression is intimately tied to their subcellular localization. Here, we show a subcellular-specific RNA labeling method for efficient enrichment and deep profiling of nuclear and cytoplasmic RBPs. A total of 1221 nuclear RBPs and 1333 cytoplasmic RBPs were enriched and identified using nuclear/cytoplasm targeting enrichment probes, representing an increase of 54.4% and 85.7% compared with previous reports. The probes were further applied in the omics-level investigation of subcellular-specific RBP-RNA interactions upon ferroptosis induction. Interestingly, large-scale RBPs display enhanced interaction with RNAs in nucleus but reduced association with RNAs in cytoplasm during ferroptosis process. Furthermore, we discovered dozens of nucleoplasmic translocation candidate RBPs upon ferroptosis induction and validated representative ones by immunofluorescence imaging. The enrichment of Tricarboxylic acid cycle in the translocation candidate RBPs may provide insights for investigating their possible roles in ferroptosis induced metabolism dysregulation.
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Affiliation(s)
- Haofan Sun
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Bin Fu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Xiaohong Qian
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Ping Xu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Weijie Qin
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
- College of Chemistry and Materials Science, Hebei University, Baoding, 071002, China.
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10
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Liang X, Qian S, Lou Z, Hu R, Hou Y, Chen PR, Fan X. Near Infrared Light-Triggered Photocatalytic Decaging for Remote-Controlled Spatiotemporal Activation in Living Mice. Angew Chem Int Ed Engl 2023; 62:e202310920. [PMID: 37842955 DOI: 10.1002/anie.202310920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/30/2023] [Accepted: 10/11/2023] [Indexed: 10/17/2023]
Abstract
Spatiotemporal manipulation of biological processes in living animals using noninvasive, remote-controlled stimuli is a captivating but challenging endeavor. Herein, we present the development of a biocompatible photocatalytic technology termed CAT-NIR, which uses external near infrared light (NIR, 740 nm) to trigger decaging reactions in living mice. The Os(II) terpyridine complex was identified as an efficient NIR photocatalyst for promoting deboronative hydroxylation reactions via superoxide generation in the presence of NIR light, resulting in the deprotection of phenol groups and the release of bioactive molecules under living conditions. The validation of the CAT-NIR system was demonstrated through the NIR-triggered rescue of fluorophores, prodrugs as well as biomolecules ranging from amino acids, peptides to proteins. Furthermore, by combining genetic code expansion and computer-aided screening, CAT-NIR could regulate affibody binding to the cell surface receptor HER2, providing a selective cell tagging technology through external NIR light. In particular, the tissue-penetrating ability of NIR light allowed for facile prodrug activation in living mice, enabling noninvasive, remote-controlled rescue of drug molecules. Given its broad adaptability, this CAT-NIR system may open new opportunities for manipulating the functions of bioactive molecules in living animals using external NIR light with spatiotemporal resolution.
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Grants
- 22222701, 22077004, 92253301, 21937001, 22137001 National Natural Science Foundation of China
- 22222701, 22077004, 92253301, 22321005, 21937001, 22137001 National Natural Science Foundation of China
- 2019YFA0904201, 2022YFA1304700, 2022YFE0114900 Ministry of Science and Technology
- Z200010, Z221100007422046 Beijing Municipal Science and Technology Commission
- YGLX202338 Beijing Hospitals Authority Clinical Medicine Development Funding
- Li Ge-Zhao Ning Life Science Junior Research Fellowship
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Affiliation(s)
- Xuan Liang
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Shan Qian
- Department of Pharmaceutical Engineering, College of Food and Bioengineering, Xihua University, Chengdu, 610039, China
| | - Zhizheng Lou
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Renming Hu
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Yuchen Hou
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Peng R Chen
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Xinyuan Fan
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
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11
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Tang J, Liu J, Zheng Q, Yao R, Wang M. Neuroprotective Bioorthogonal Catalysis in Mitochondria Using Protein-Integrated Hydrogen-Bonded Organic Frameworks. Angew Chem Int Ed Engl 2023; 62:e202312784. [PMID: 37817650 DOI: 10.1002/anie.202312784] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 10/12/2023]
Abstract
Mitochondria-targeted bioorthogonal catalysis holds promise for controlling cell function precisely, yet achieving selective and efficient chemical reactions within organelles is challenging. In this study, we introduce a new strategy using protein-integrated hydrogen-bonded organic frameworks (HOFs) to enable synergistic bioorthogonal chemical catalysis and enzymatic catalysis within mitochondria. Utilizing catalytically active tris(4,4'-dicarboxylicacid-2,2'-bipyridyl) ruthenium(II) to self-assemble with [1,1'-biphenyl]-4,4'-biscarboximidamide, we synthesized nanoscale RuB-HOFs that exhibit high photocatalytic reduction activity. Notably, RuB-HOFs efficiently enter cells and preferentially localize to mitochondria, where they facilitate bioorthogonal photoreduction reactions. Moreover, we show that RuB-HOFs encapsulating catalase can produce hydrogen sulfide (H2 S) in mitochondria through photocatalytic reduction of pro-H2 S and degrade hydrogen peroxide through enzymatic catalysis simultaneously, offering a significant neuroprotective effect against oxidative stress. Our findings not only introduce a versatile chemical toolset for mitochondria-targeted bioorthogonal catalysis for prodrug activation but also pave the way for potential therapeutic applications in treating diseases related to cellular oxidative stress.
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Affiliation(s)
- Jiakang Tang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Ji Liu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Qizhen Zheng
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Rui Yao
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Ming Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
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12
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Fu Q, Shen S, Sun P, Gu Z, Bai Y, Wang X, Liu Z. Bioorthogonal chemistry for prodrug activation in vivo. Chem Soc Rev 2023; 52:7737-7772. [PMID: 37905601 DOI: 10.1039/d2cs00889k] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Prodrugs have emerged as a major strategy for addressing clinical challenges by improving drug pharmacokinetics, reducing toxicity, and enhancing treatment efficacy. The emergence of new bioorthogonal chemistry has greatly facilitated the development of prodrug strategies, enabling their activation through chemical and physical stimuli. This "on-demand" activation using bioorthogonal chemistry has revolutionized the research and development of prodrugs. Consequently, prodrug activation has garnered significant attention and emerged as an exciting field of translational research. This review summarizes the latest advancements in prodrug activation by utilizing bioorthogonal chemistry and mainly focuses on the activation of small-molecule prodrugs and antibody-drug conjugates. In addition, this review also discusses the opportunities and challenges of translating these advancements into clinical practice.
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Affiliation(s)
- Qunfeng Fu
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
- Changping Laboratory, Beijing 102206, China
| | - Siyong Shen
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Pengwei Sun
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Zhi Gu
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Yifei Bai
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Xianglin Wang
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Zhibo Liu
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
- Changping Laboratory, Beijing 102206, China
- Peking University-Tsinghua University Center for Life Sciences, Peking University, Beijing 100871, China
- Key Laboratory of Carcinogenesis and Translational Research of Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Radiopharmaceuticals, Department of Nuclear Medicine, Peking University Cancer Hospital & Institute, Beijing 100142, China
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13
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Lin Z, Schaefer K, Lui I, Yao Z, Fossati A, Swaney DL, Palar A, Sali A, Wells JA. Multi-scale photocatalytic proximity labeling reveals cell surface neighbors on and between cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.28.564055. [PMID: 37961561 PMCID: PMC10634877 DOI: 10.1101/2023.10.28.564055] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The cell membrane proteome is the primary biohub for cell communication, yet we are only beginning to understand the dynamic protein neighborhoods that form on the cell surface and between cells. Proximity labeling proteomics (PLP) strategies using chemically reactive probes are powerful approaches to yield snapshots of protein neighborhoods but are currently limited to one single resolution based on the probe labeling radius. Here, we describe a multi-scale PLP method with tunable resolution using a commercially available histological dye, Eosin Y, which upon visible light illumination, activates three different photo-probes with labeling radii ranging from ∼100 to 3000 Å. We applied this platform to profile neighborhoods of the oncogenic epidermal growth factor receptor (EGFR) and orthogonally validated >20 neighbors using immuno-assays and AlphaFold-Multimer prediction that generated plausible binary interaction models. We further profiled the protein neighborhoods of cell-cell synapses induced by bi-specific T-cell engagers (BiTEs) and chimeric antigen receptor (CAR)T cells at longer length scales. This integrated multi-scale PLP platform maps local and distal protein networks on cell surfaces and between cells. We believe this information will aid in the systematic construction of the cell surface interactome and reveal new opportunities for immunotherapeutics.
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14
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Ogorek AN, Zhou X, Martell JD. Switchable DNA Catalysts for Proximity Labeling at Sites of Protein-Protein Interactions. J Am Chem Soc 2023; 145:16913-16923. [PMID: 37463457 DOI: 10.1021/jacs.3c05578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Proximity labeling (PL) has emerged as a powerful approach to elucidate proteomes within a defined radius around a protein of interest (POI). In PL, a catalyst is attached to the POI and tags nearby endogenous proteins, which are then isolated by affinity purification and identified by mass spectrometry. Although existing PL methods have yielded numerous biological insights, proteomes with greater spatial resolution could be obtained if PL catalysts could be activated at more specific subcellular locations, such as sites where both the POI and a chemical stimulus are present or sites of protein-protein interactions (PPIs). Here, we report DNA-based switchable PL catalysts that are attached to a POI and become activated only when a secondary molecular trigger is present. The DNA catalysts consist of a photocatalyst and a spectral quencher tethered to a DNA oligomer. They are catalytically inactive by default but undergo a conformational change in response to a specific molecular trigger, thus activating PL. We designed a system in which the DNA catalyst becomes activated on living mammalian cells specifically at sites of Her2-Her3 heterodimers and c-Met homodimers, PPIs known to increase the invasion and growth of certain cancers. While this study employs a Ru(bpy)3-type complex for tagging proteins with biotin phenol, the switchable DNA catalyst design is compatible with diverse synthetic PL photocatalysts. Furthermore, the switchable DNA PL catalysts can be constructed from conformation-switching DNA aptamers that respond to small molecules, ions, and proteins, opening future opportunities for PL in highly specific subcellular locations.
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Affiliation(s)
- Ashley N Ogorek
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Xu Zhou
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Jeffrey D Martell
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53726, United States
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15
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Wang Y, Li W, Ye B, Bi X. Chemical and Biological Strategies for Profiling Protein-Protein Interactions in Living Cells. Chem Asian J 2023; 18:e202300226. [PMID: 37089007 PMCID: PMC10946512 DOI: 10.1002/asia.202300226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 04/25/2023]
Abstract
Protein-protein interactions (PPIs) play critical roles in almost all cellular signal transduction events. Characterization of PPIs without interfering with the functions of intact cells is very important for basic biology study and drug developments. However, the ability to profile PPIs especially those weak/transient interactions in their native states remains quite challenging. To this end, many endeavors are being made in developing new methods with high efficiency and strong operability. By coupling with advanced fluorescent microscopy and mass spectroscopy techniques, these strategies not only allow us to visualize the subcellular locations and monitor the functions of protein of interest (POI) in real time, but also enable the profiling and identification of potential unknown interacting partners in high-throughput manner, which greatly facilitates the elucidation of molecular mechanisms underlying numerous pathophysiological processes. In this review, we will summarize the typical methods for PPIs identification in living cells and their principles, advantages and limitations will also be discussed in detail.
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Affiliation(s)
- You‐Yu Wang
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals & College of Pharmaceutical SciencesZhejiang University of TechnologyHangzhou310014, Zhejiang ProvinceP. R. China
| | - Wenyi Li
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityVictoria3086Australia
| | - Bang‐Ce Ye
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals & College of Pharmaceutical SciencesZhejiang University of TechnologyHangzhou310014, Zhejiang ProvinceP. R. China
| | - Xiao‐Bao Bi
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals & College of Pharmaceutical SciencesZhejiang University of TechnologyHangzhou310014, Zhejiang ProvinceP. R. China
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16
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Liu J, Yang B, Wang L. Residue selective crosslinking of proteins through photoactivatable or proximity-enabled reactivity. Curr Opin Chem Biol 2023; 74:102285. [PMID: 36913752 PMCID: PMC10225350 DOI: 10.1016/j.cbpa.2023.102285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/08/2023] [Accepted: 02/12/2023] [Indexed: 03/13/2023]
Abstract
Photo- and chemical crosslinking of proteins have offered various avenues for studying protein structure and protein interactions with biomolecules. Conventional photoactivatable groups generally lack reaction selectivity toward amino acid residues. New photoactivatable groups reacting with selected residues have emerged recently, increasing crosslinking efficiency and facilitating crosslink identification. Traditional chemical crosslinking usually employs highly reactive functional groups, while recent advance has developed latent reactive groups with reactivity triggered by proximity, which reduce spurious crosslinks and improve biocompatibility. The employment of these residue selective chemical functional groups, activated by light or proximity, in small molecule crosslinkers and in genetically encoded unnatural amino acids is summarized. Together with new software development in identifying protein crosslinks, residue selective crosslinking has enhanced the research of elusive protein-protein interactions in vitro, in cell lysate, and in live cells. Residue selective crosslinking is expected to expand to other methods for the investigation of various protein-biomolecule interactions.
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Affiliation(s)
- Jun Liu
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Bing Yang
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Lei Wang
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, 94158, USA.
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17
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Zheng F, Yu C, Zhou X, Zou P. Genetically encoded photocatalytic protein labeling enables spatially-resolved profiling of intracellular proteome. Nat Commun 2023; 14:2978. [PMID: 37221179 PMCID: PMC10205723 DOI: 10.1038/s41467-023-38565-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 05/05/2023] [Indexed: 05/25/2023] Open
Abstract
Mapping the subcellular organization of proteins is crucial for understanding their biological functions. Herein, we report a reactive oxygen species induced protein labeling and identification (RinID) method for profiling subcellular proteome in the context of living cells. Our method capitalizes on a genetically encoded photocatalyst, miniSOG, to locally generate singlet oxygen that reacts with proximal proteins. Labeled proteins are conjugated in situ with an exogenously supplied nucleophilic probe, which serves as a functional handle for subsequent affinity enrichment and mass spectrometry-based protein identification. From a panel of nucleophilic compounds, we identify biotin-conjugated aniline and propargyl amine as highly reactive probes. As a demonstration of the spatial specificity and depth of coverage in mammalian cells, we apply RinID in the mitochondrial matrix, capturing 477 mitochondrial proteins with 94% specificity. We further demonstrate the broad applicability of RinID in various subcellular compartments, including the nucleus and the endoplasmic reticulum (ER). The temporal control of RinID enables pulse-chase labeling of ER proteome in HeLa cells, which reveals substantially higher clearance rate for secreted proteins than ER resident proteins.
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Affiliation(s)
- Fu Zheng
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Chenxin Yu
- Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Xinyue Zhou
- Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Peng Zou
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China.
- Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
- PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, 100871, China.
- Chinese Institute for Brain Research (CIBR), Beijing, 102206, China.
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18
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Xie X, Jiang Y, Chang CJ. LOV thy neighbor: Mapping protein interactomes by genetically encodable photoproximity labeling. Proc Natl Acad Sci U S A 2023; 120:e2305211120. [PMID: 37155840 PMCID: PMC10193944 DOI: 10.1073/pnas.2305211120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Affiliation(s)
- Xiao Xie
- Department of Chemistry, University of California, Berkeley, CA94720-1460
| | - Yishu Jiang
- Department of Chemistry, University of California, Berkeley, CA94720-1460
| | - Christopher J. Chang
- Department of Chemistry, University of California, Berkeley, CA94720-1460
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720-1460
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19
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Rosenberger JE, Xie Y, Fang Y, Lyu X, Trout WS, Dmitrenko O, Fox JM. Ligand-Directed Photocatalysts and Far-Red Light Enable Catalytic Bioorthogonal Uncaging inside Live Cells. J Am Chem Soc 2023; 145:6067-6078. [PMID: 36881718 PMCID: PMC10589873 DOI: 10.1021/jacs.2c10655] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Described are ligand-directed catalysts for live-cell, photocatalytic activation of bioorthogonal chemistry. Catalytic groups are localized via a tethered ligand either to DNA or to tubulin, and red light (660 nm) photocatalysis is used to initiate a cascade of DHTz oxidation, intramolecular Diels-Alder reaction, and elimination to release phenolic compounds. Silarhodamine (SiR) dyes, more conventionally used as biological fluorophores, serve as photocatalysts that have high cytocompatibility and produce minimal singlet oxygen. Commercially available conjugates of Hoechst dye (SiR-H) and docetaxel (SiR-T) are used to localize SiR to the nucleus and microtubules, respectively. Computation was used to assist the design of a new class of redox-activated photocage to release either phenol or n-CA4, a microtubule-destabilizing agent. In model studies, uncaging is complete within 5 min using only 2 μM SiR and 40 μM photocage. In situ spectroscopic studies support a mechanism involving rapid intramolecular Diels-Alder reaction and a rate-determining elimination step. In cellular studies, this uncaging process is successful at low concentrations of both the photocage (25 nM) and the SiR-H dye (500 nM). Uncaging n-CA4 causes microtubule depolymerization and an accompanying reduction in cell area. Control studies demonstrate that SiR-H catalyzes uncaging inside the cell, and not in the extracellular environment. With SiR-T, the same dye serves as a photocatalyst and the fluorescent reporter for microtubule depolymerization, and with confocal microscopy, it was possible to visualize microtubule depolymerization in real time as the result of photocatalytic uncaging in live cells.
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Affiliation(s)
- Julia E. Rosenberger
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Yixin Xie
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Yinzhi Fang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Xinyi Lyu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - William S. Trout
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Olga Dmitrenko
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Joseph M. Fox
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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20
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Zhang Y, Tan J, Chen Y. Visible-light-induced protein labeling in live cells with aryl azides. Chem Commun (Camb) 2023; 59:2413-2420. [PMID: 36744609 DOI: 10.1039/d2cc06987c] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Chemical labeling of proteins in live cells helps to probe their native functions in biological systems. Aryl azides are chemically inert under physiological conditions, but they are activated by certain external stimuli. Recently, photocatalytic live-cell applications of aryl azides by visible light irradiation have become a burgeoning new field in chemical biology. In this Feature Article, we focus on the recent progress of protein labeling in live cells with aryl azides induced by visible-light irradiation. Light irradiation activates aryl azides to generate highly reactive intermediates, which enables protein labeling for protein functionalization, crosslinking, and profiling. The activation mechanism of aryl azides by light irradiation is categorized as photolysis, energy-transfer, and electron-transfer. The extracellular and intracellular protein labeling applications in live cells with aryl azides induced by visible light are discussed, including recent advances in red-light-induced extracellular protein labeling.
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Affiliation(s)
- Yixin Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry Centre of Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China.
| | - Jiawei Tan
- State Key Laboratory of Bioorganic and Natural Products Chemistry Centre of Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China.
| | - Yiyun Chen
- State Key Laboratory of Bioorganic and Natural Products Chemistry Centre of Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China. .,School of Physical Science and Technology ShanghaiTech University, 100 Haike Road, Shanghai 201210, P. R. China.,School of Chemistry and Material Sciences, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou 310024, P. R. China
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21
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Ribéraud M, Porte K, Chevalier A, Madegard L, Rachet A, Delaunay-Moisan A, Vinchon F, Thuéry P, Chiappetta G, Champagne PA, Pieters G, Audisio D, Taran F. Fast and Bioorthogonal Release of Isocyanates in Living Cells from Iminosydnones and Cycloalkynes. J Am Chem Soc 2023; 145:2219-2229. [PMID: 36656821 DOI: 10.1021/jacs.2c09865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Bioorthogonal click-and-release reactions are powerful tools for chemical biology, allowing, for example, the selective release of drugs in biological media, including inside animals. Here, we developed two new families of iminosydnone mesoionic reactants that allow a bioorthogonal release of electrophilic species under physiological conditions. Their synthesis and reactivities as dipoles in cycloaddition reactions with strained alkynes have been studied in detail. Whereas the impact of the pH on the reaction kinetics was demonstrated experimentally, theoretical calculations suggest that the newly designed dipoles display reduced resonance stabilization energies compared to previously described iminosydnones, explaining their higher reactivity. These mesoionic compounds react smoothly with cycloalkynes under physiological, copper-free reaction conditions to form a click pyrazole product together with a released alkyl- or aryl-isocyanate. With rate constants up to 1000 M-1 s-1, this click-and-release reaction is among the fastest described to date and represents the first bioorthogonal process allowing the release of isocyanate electrophiles inside living cells, offering interesting perspectives in chemical biology.
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Affiliation(s)
- Maxime Ribéraud
- Département Médicaments et Technologies pour la Santé (DMTS), SCBM, Université Paris Saclay, CEA, INRAE, 91191 Gif-sur-Yvette, France
| | - Karine Porte
- Département Médicaments et Technologies pour la Santé (DMTS), SCBM, Université Paris Saclay, CEA, INRAE, 91191 Gif-sur-Yvette, France
| | - Arnaud Chevalier
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198 Gif-sur-Yvette, France
| | - Léa Madegard
- Département Médicaments et Technologies pour la Santé (DMTS), SCBM, Université Paris Saclay, CEA, INRAE, 91191 Gif-sur-Yvette, France
| | - Aurélie Rachet
- Université Paris Saclay, CEA, Institut de Biologie Intégrative de la Cellule (I2BC), 91191 Gif-sur-Yvette, France
| | - Agnès Delaunay-Moisan
- Université Paris Saclay, CEA, Institut de Biologie Intégrative de la Cellule (I2BC), 91191 Gif-sur-Yvette, France
| | - Florian Vinchon
- Département Médicaments et Technologies pour la Santé (DMTS), SCBM, Université Paris Saclay, CEA, INRAE, 91191 Gif-sur-Yvette, France
| | - Pierre Thuéry
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette, France
| | - Giovanni Chiappetta
- Biological Mass Spectrometry and Proteomics Group, SMBP, PDC CNRS UMR, 8249, ESPCI Paris, Université PSL, 10 rue Vauquelin, 75005 Paris, France
| | - Pier Alexandre Champagne
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Grégory Pieters
- Département Médicaments et Technologies pour la Santé (DMTS), SCBM, Université Paris Saclay, CEA, INRAE, 91191 Gif-sur-Yvette, France
| | - Davide Audisio
- Département Médicaments et Technologies pour la Santé (DMTS), SCBM, Université Paris Saclay, CEA, INRAE, 91191 Gif-sur-Yvette, France
| | - Frédéric Taran
- Département Médicaments et Technologies pour la Santé (DMTS), SCBM, Université Paris Saclay, CEA, INRAE, 91191 Gif-sur-Yvette, France
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22
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Wang R, Gan YF, Li YY, Chen XQ, Guo YY. Recent Advances in Quinone Methide Chemistry for Protein-Proximity Capturing. SYNTHESIS-STUTTGART 2023. [DOI: 10.1055/s-0042-1751402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
AbstractHere we summarize the most recent findings in the chemical-, photo-, or enzyme-triggered generation of nitrogen and oxygen anions leading to the formation of quinone methide intermediates (QMIs). This short review is divided into two categories: generation of nitrogen and oxygen anions. Based on quinone methide intermediates (QMIs), proximate capture of a wide range of proteins has been widely determined and studied. Generally, the triggers include, photoirradiation using 365/254 nm UV light, small molecules (ROS/TBAF/s-tetrazine), metal catalysis (iridium catalysis), and enzymes (NQO1/β-galactosidase). New directions including far-red light, heat, force, microwave, and more practical approaches are explored and illustrated.1 Introduction2 Generation of the Nitrogen Anion3 Generation of the Oxygen Anion4 Conclusion
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Affiliation(s)
- Rui Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology
- Shenzhen Huazhong University of Science and Technology Research Institute
| | - You F. Gan
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology
| | - Yuan Y. Li
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology
| | - Xiao Q. Chen
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology
| | - Yu Y. Guo
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology
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23
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Zhao H, Liu Z, Wei Y, Zhang L, Wang Z, Ren J, Qu X. NIR-II Light Leveraged Dual Drug Synthesis for Orthotopic Combination Therapy. ACS NANO 2022; 16:20353-20363. [PMID: 36398983 DOI: 10.1021/acsnano.2c06314] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Pd-catalyzed bioorthogonal bond cleavage reactions are widely used and frequently reported. It is circumscribed by low reaction efficiency, which may encumber the therapeutic outcome when applied to physiological environments. Herein, an NIR-II light promoted integrated catalyst (CuS@PDA/Pd) (PDA - polydopamine) is designed to accelerate the reaction efficiency and achieve a dual bioorthogonal reaction for combination therapy. As NIR-II light can penetrate deeply into tissue, the Pd-mediated cleavage reaction can be promoted both in vitro and in vivo by the photothermal properties of CuS, beneficial to orthotopic 4T1 tumor treatment. In addition, CuS also catalyzes the synthesis of active resveratrol analogs by the CuAAC reaction. These simultaneously produced anticancer agents result in enhanced antitumor cytotoxicity in comparison to the single treatments. This is a fascinating study to devise an integrated catalyst boosted by NIR-II light for dual bioorthogonal catalysis, which may provide the impetus for efficient bioorthogonal combination therapy in vivo.
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Affiliation(s)
- Huisi Zhao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- University of Science and Technology of China, Hefei, Anhui 230029, P. R. China
| | - Zhengwei Liu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- University of Chinese Academy of Sciences, Beijing 100039, PR China
| | - Yue Wei
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- University of Science and Technology of China, Hefei, Anhui 230029, P. R. China
| | - Lu Zhang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- University of Chinese Academy of Sciences, Beijing 100039, PR China
| | - Zhao Wang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- University of Science and Technology of China, Hefei, Anhui 230029, P. R. China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- University of Science and Technology of China, Hefei, Anhui 230029, P. R. China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- University of Science and Technology of China, Hefei, Anhui 230029, P. R. China
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24
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Fan X, Chen PR. Deciphering Life Sciences with “Live” Chemistry—The 2022 Nobel Prize in Chemistry. Sci China Chem 2022. [DOI: 10.1007/s11426-022-1430-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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25
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Wang H, Wang Z, Gao H, Liu J, Qiao Z, Zhao B, Liang Z, Jiang B, Zhang L, Zhang Y. A photo-oxidation driven proximity labeling strategy enables profiling of mitochondrial proteome dynamics in living cells. Chem Sci 2022; 13:11943-11950. [PMID: 36320915 PMCID: PMC9580500 DOI: 10.1039/d2sc04087e] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/27/2022] [Indexed: 07/21/2023] Open
Abstract
Mapping the proteomic landscape of mitochondria with spatiotemporal precision plays a pivotal role in elucidating the delicate biological functions and complex relationship with other organelles in a variety of dynamic physiological processes which necessitates efficient and controllable chemical tools. We herein report a photo-oxidation driven proximity labeling strategy to profile the mitochondrial proteome by light dependence in living cells with high spatiotemporal resolution. Taking advantage of organelle-localizable organic photoactivated probes generating reactive species and nucleophilic substrates for proximal protein oxidation and trapping, mitochondrial proteins were selectively labeled by spatially limited reactions in their native environment. Integration of photo-oxidation driven proximity labeling and quantitative proteomics facilitated the plotting of the mitochondrial proteome in which up to 310 mitochondrial proteins were identified with a specificity of 64% in HeLa cells. Furthermore, mitochondrial proteome dynamics was deciphered in drug resistant Huh7 and LPS stimulated HMC3 cells which were hard-to-transfect. A number of differential proteins were quantified which were intimately linked to critical processes and provided insights into the related molecular mechanisms of drug resistance and neuroinflammation in the perspective of mitochondria. The photo-oxidation driven proximity labeling strategy offers solid technical support to a highly precise proteomic platform in time and finer space for more knowledge of subcellular biology.
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Affiliation(s)
- He Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Zhiting Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Hang Gao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Jianhui Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Zichun Qiao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Baofeng Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Bo Jiang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
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Suzuki S, Geri JB, Knutson SD, Bell-Temin H, Tamura T, Fernández DF, Lovett GH, Till NA, Heller BL, Guo J, MacMillan DWC, Ploss A. Photochemical Identification of Auxiliary Severe Acute Respiratory Syndrome Coronavirus 2 Host Entry Factors Using μMap. J Am Chem Soc 2022; 144:16604-16611. [PMID: 36049228 PMCID: PMC9469761 DOI: 10.1021/jacs.2c06806] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Indexed: 12/20/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the infectious agent of the COVID-19 pandemic, remains a global medical problem. Angiotensin-converting enzyme 2 (ACE2) was identified as the primary viral entry receptor, and transmembrane serine protease 2 primes the spike protein for membrane fusion. However, ACE2 expression is generally low and variable across tissues, suggesting that auxiliary receptors facilitate viral entry. Identifying these factors is critical for understanding SARS-Cov-2 pathophysiology and developing new countermeasures. However, profiling host-virus interactomes involves extensive genetic screening or complex computational predictions. Here, we leverage the photocatalytic proximity labeling platform μMap to rapidly profile the spike interactome in human cells and identify eight novel candidate receptors. We systemically validate their functionality in SARS-CoV-2 pseudoviral uptake assays with both Wuhan and Delta spike variants and show that dual expression of ACE2 with either neuropilin-2, ephrin receptor A7, solute carrier family 6 member 15, or myelin and lymphocyte protein 2 significantly enhances viral uptake. Collectively, our data show that SARS-CoV-2 synergistically engages several host factors for cell entry and establishes μMap as a powerful tool for rapidly interrogating host-virus interactomes.
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Affiliation(s)
- Saori Suzuki
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jacob B. Geri
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Steve D. Knutson
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | | | - Tomokazu Tamura
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | | | - Gabby H. Lovett
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Nicholas A. Till
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Brigitte L. Heller
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jinchao Guo
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - David W. C. MacMillan
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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27
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Kumar GS, Lin Q. Seeking Citius: Photochemical Access of Reactive Intermediates for Faster Bioorthogonal Reactions. Chembiochem 2022; 23:e202200175. [PMID: 35612501 PMCID: PMC9488641 DOI: 10.1002/cbic.202200175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/24/2022] [Indexed: 11/08/2022]
Abstract
Fast bioorthogonal reactions are sought after because of their superior performance in labeling low-abundance biomolecules in native cellular environments. An attractive strategy to increase reaction kinetics is to access the reactive intermediates through photochemical activation. To this end, significant progress was made in the last few years in harnessing two highly reactive intermediates-nitrile imine and tetrazine-generated through photoinduced ring rupture and catalytic photooxidation, respectively. The efficient capture of these reactive intermediates by their cognate reaction partners has enabled bioorthogonal fluorescent labeling of biomolecules in live cells.
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Affiliation(s)
- Gangam Srikanth Kumar
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, 14260-3000, USA
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, 14260-3000, USA
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28
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Reyes-Robles T, Olow AK, Bechtel TJ, Lesley SA, Fadeyi OO, Oslund RC. Nanoscale Mapping of EGFR and c-MET Protein Environments on Lung Cancer Cell Surfaces via Therapeutic Antibody Photocatalyst Conjugates. ACS Chem Biol 2022; 17:2304-2314. [PMID: 35939534 DOI: 10.1021/acschembio.2c00409] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Receptor tyrosine kinases are involved in essential signaling roles that impact cell growth, differentiation, and proliferation. The overexpression or mutation of these proteins can lead to aberrant signaling that has been directly linked to a number of diseases including cancer cell formation and progression. This has led to intense clinical focus on modulating RTK activity through direct targeting of signaling activity or cell types harboring aberrant RTK behavior. In particular, epidermal growth factor receptor (EGFR) has attracted intense clinical attention due to the impact of inhibiting this RTK on tumor growth. However, mutations incurred through targeting EGFR have led to therapeutic resistance that involves not only direct mutations to the EGFR protein but also the involvement of other RTKs, such as c-MET, that can overcome therapeutic-based EGFR inhibition effects. This has, not surprisingly, led to co-targeting strategies of RTKs such as EGFR and c-MET to overcome resistance mechanisms. While the ability to co-target these proteins has led to success in the clinic, a more comprehensive understanding of their proximal environments, particularly in the context of therapeutic modalities, could further enhance both our understanding of their signaling biology and provide additional avenues for targeting these surface proteins. Thus, to investigate EGFR and c-MET protein microenvironments, we utilized our recently developed iridium photocatalyst-based microenvironment mapping technology to catalog EGFR and c-MET surface environments on non-small cell lung cancer cell lines. Through this approach, we enriched EGFR and c-MET from the cell surface and identified known EGFR and c-MET associators as well as previously unidentified proximal proteins.
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Affiliation(s)
- Tamara Reyes-Robles
- Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Aleksandra K Olow
- Genetics and Pharmacogenomics, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Tyler J Bechtel
- Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Scott A Lesley
- Discovery Biologics, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Olugbeminiyi O Fadeyi
- Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Rob C Oslund
- Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
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29
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Zeng K, Han L, Chen Y. Endogenous Proteins Modulation in Live Cells with Small Molecules and Light. Chembiochem 2022; 23:e202200244. [PMID: 35822393 DOI: 10.1002/cbic.202200244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/23/2022] [Indexed: 11/05/2022]
Abstract
The protein modulation by light illumination enables the biological role investigation in high spatiotemporal precision. Compared to genetic methods, the small molecules approach is uniquely suited for modulating endogenous proteins. The endogenous protein modulation in live cells with small molecules and light has recently advanced on three distinctive frontiers: i) the infrared-light-induced or localized decaging of small molecules by photolysis, ii) the visible-light-induced photocatalytic releasing of small molecules, and iii) the small-molecule-ligand-directed caging for photo-modulation of proteins. Together, these methods provide powerful chemical biology tool kits for spatiotemporal modulation of endogenous proteins with potential therapeutic applications. This Concept aims to inspire organic chemists and chemical biologists to delve into this burgeoning endogenous protein modulation field for new biological discoveries.
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Affiliation(s)
- Kaixing Zeng
- Shanghai Institute Of Organic Chemistry State Key Laboratory of Bioorganic Chemistry, BNPC, CHINA
| | - Lili Han
- Shanghai Institute Of Organic Chemistry State Key Laboratory of Bioorganic Chemistry, BNPC, CHINA
| | - Yiyun Chen
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, BNPC, 345 Lingling Road, 200032, Shanghai, CHINA
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30
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Luo H, Tang W, Liu H, Zeng X, Ngai WSC, Gao R, Li H, Li R, Zheng H, Guo J, Qin F, Wang G, Li K, Fan X, Zou P, Chen PR. Photocatalytic Chemical Crosslinking for Profiling RNA–Protein Interactions in Living Cells. Angew Chem Int Ed Engl 2022; 61:e202202008. [DOI: 10.1002/anie.202202008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Huixin Luo
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines Institute of Materia Medica Chinese Academy of Medical Sciences and Peking UnionMedical College Beijing 100050 China
| | - Wei Tang
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
| | - Hongyu Liu
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Xiangmei Zeng
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - William Shu Ching Ngai
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Rui Gao
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
| | - Heyun Li
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Ran Li
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
| | - Huangtao Zheng
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Jianting Guo
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Fangfei Qin
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
| | - Gang Wang
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
| | - Kexin Li
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
| | - Xinyuan Fan
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Peng Zou
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
- PKU-IDG/McGovern Institute for Brain Research Beijing 100871 China
- Chinese Institute for Brain Research (CIBR) Beijing 102206 China
| | - Peng R. Chen
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
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31
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Wang S, Tan W, Lang W, Qian H, Guo S, Zhu L, Ge J. Fluorogenic and Mitochondria-Localizable Probe Enables Selective Labeling and Imaging of Nitroreductase. Anal Chem 2022; 94:7272-7277. [PMID: 35549110 DOI: 10.1021/acs.analchem.2c00512] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nitroreductase (NTR), one of the flavin-dependent enzymes and an upregulated enzyme under tumor hypoxia, has been studied for decades. Many fluorescent probes were developed to detect NTR activity; however, these probes tend to diffuse away from their reaction site (NTR) inevitably, leading to inappropriate sample fixation, lower accuracy of NTR localization, and weaker signal-to-noise ratio. Herein, we present the design, synthesis, in vitro evaluation, and biological applications of an NTR-activatable fluorogenic and labeling probe FY. By integrating with quinone methide (QM) proximity-based protein labeling, the additional fluoromethyl group on FY serves as a potential origin of QM. Compared with conventional fluorescent probes, this new NTR probe not only offers mitochondrial localizable and fluorogenic response but also achieves permanent retention on the site of activation with an enhanced spatial resolution to improve the detection sensitivity even after cell fixation. We believe our work could offer an expandable synthetic approach to develop these permanent labeling and imaging fluorescence probes for deciphering complex biological events.
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Affiliation(s)
- Shuyi Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wei Tan
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wenjie Lang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Huijuan Qian
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Shuhong Guo
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Liquan Zhu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
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32
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Wang F, Kong H, Meng X, Tian X, Wang C, Xu L, Zhang X, Wang L, Xie R. A light-initiated chemical reporter strategy for spatiotemporal labeling of biomolecules. RSC Chem Biol 2022; 3:539-545. [PMID: 35656482 PMCID: PMC9092362 DOI: 10.1039/d2cb00072e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 03/28/2022] [Indexed: 11/21/2022] Open
Abstract
The emergence of optochemical approaches has had a diverse impact over a broad range of biological research due to spatiotemporal regulation. Herein, we integrate this feature into the bioorthogonal chemical reporter strategy, which enables visible light-controlled spatiotemporal labeling of cell-surface glycans, lipids, and proteins. The metabolic precursors were first incorporated into live cells, and next the bioorthogonal reaction converted the azide/alkyne into a photo-active functional group, which allowed for subsequent photo-click reaction. We demonstrated this strategy by specifically labeling sialome, mucin-type O-glycome, phospholipids and newly-synthesized membrane proteins, respectively. The sequential photoirradiation-orthogonal reporter tagging (SPORT) should facilitate the probing of biomolecules in complex biological systems with high spatiotemporal precision.
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Affiliation(s)
- Feifei Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Hao Kong
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Xiangfeng Meng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Xiao Tian
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Changjiang Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Lei Xu
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated, Hospital of Nanjing University Medical School Nanjing 210008 China
- Department of Gastroenterology, Nanjing Drum Tower Hospital, Drum Tower, Clinical Medical College of Nanjing Medical University Nanjing 210008 China
| | - Xiang Zhang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated, Hospital of Nanjing University Medical School Nanjing 210008 China
- Department of Gastroenterology, Nanjing Drum Tower Hospital, Drum Tower, Clinical Medical College of Nanjing Medical University Nanjing 210008 China
| | - Lei Wang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated, Hospital of Nanjing University Medical School Nanjing 210008 China
- Department of Gastroenterology, Nanjing Drum Tower Hospital, Drum Tower, Clinical Medical College of Nanjing Medical University Nanjing 210008 China
| | - Ran Xie
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University Nanjing 210023 China
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33
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Liu Z, Xie X, Huang Z, Lin F, Liu S, Chen Z, Qin S, Fan X, Chen PR. Spatially resolved cell tagging and surfaceome labeling via targeted photocatalytic decaging. Chem 2022. [DOI: 10.1016/j.chempr.2022.04.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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34
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Luo H, Tang W, Liu H, Zeng X, Ngai WSC, Gao R, Li H, Li R, Zheng H, Guo J, Qin F, Wang G, Li K, Fan X, Zou P, Chen P. Photocatalytic Chemical Crosslinking for Profiling RNA‐Protein Interactions in Living Cells. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202202008] [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)
- Huixin Luo
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | - Wei Tang
- PKU: Peking University Peking-Tsinghua Center for Life Sciences CHINA
| | - Hongyu Liu
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | - Xiangmei Zeng
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | | | - Rui Gao
- PKU: Peking University Peking-Tsinghua Center for Life Sciences CHINA
| | - Heyun Li
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | - Ran Li
- PKU: Peking University Peking-Tsinghua Center for Life Sciences CHINA
| | - Huangtao Zheng
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | - Jianting Guo
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | - Fangfei Qin
- PKU: Peking University Peking-Tsinghua Center for Life Sciences CHINA
| | - Gang Wang
- PKU: Peking University Peking-Tsinghua Center for Life Sciences CHINA
| | - Kexin Li
- PKU: Peking University Peking-Tsinghua Center for Life Sciences CHINA
| | - Xinyuan Fan
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | - Peng Zou
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | - Peng Chen
- Peking University tional Laboratory for Molecular Sciences College of Chemistry and Molecular Engineering 100871 Beijing CHINA
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35
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Liu H, Luo H, Xue Q, Qin S, Qiu S, Liu S, Lin J, Li JP, Chen PR. Antigen-Specific T Cell Detection via Photocatalytic Proximity Cell Labeling (PhoXCELL). J Am Chem Soc 2022; 144:5517-5526. [PMID: 35312320 DOI: 10.1021/jacs.2c00159] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Quantitative detection and characterization of antigen-specific T cells are crucial to our understanding of immune responses as well as the development of new immunotherapies. Herein, we report a spatiotemporally resolved method for the detection and quantification of cell-cell interactions via Photocatalytic proXimity CELl Labeling (PhoXCELL). The biocompatible photosensitizer dibromofluorescein (DBF) was leveraged and optimized as a nongenetic alternative of enzymatic approaches for efficient generation of singlet oxygen upon photoirradiation (520 nm) on the cell surface, which allowed the subsequent labeling of nearby oxidized proteins with primary aliphatic amine-based probes. We demonstrated that DBF-functionalized dendritic cells (DCs) could spatiotemporally label interacting T cells in immune synapses via rapid photoirradiation with quantitatively discriminated interaction strength, which revealed distinct gene signatures for T cells that strongly interact with antigen-pulsed DCs. Furthermore, we employed PhoXCELL to simultaneously detect tumor antigen-specific CD8+ as well as CD4+ T cells from tumor-infiltrating lymphocytes and draining lymph nodes in murine tumor models, enabling PhoXCELL as a powerful platform to identify antigen-specific T cells in T cell receptor (TCR)-relevant personal immunotherapy.
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Affiliation(s)
- Hongyu Liu
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Huixin Luo
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Qi Xue
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shan Qin
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shuang Qiu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shibo Liu
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jian Lin
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jie P Li
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Peng R Chen
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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36
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Guo S, Yuan C, Lang W, Hong D, Liu J, Huang J, Dong J, Ge J. Photocontrollable Probes for Mitochondrial Protein Profiling. Chembiochem 2022; 23:e202200066. [PMID: 35344259 DOI: 10.1002/cbic.202200066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/21/2022] [Indexed: 11/10/2022]
Abstract
Mitochondrion is the core site of cell signaling, energy metabolism and biosynthesis. Here, taking advantage of activitybased probes, we synthesized two photocontrollable probes ( YGH-1 and YGH-2 ), composed of a mitochondrial localization moiety "triphenylphosphonium", a photo triggered group to achieve spatial and temporal controlled protein capture and an alkyne group to enrich the labeled protein. Proteomic validation was further carried out to facilitate identifications of mitochondrial proteomes in HeLa cells. The results showed that half of identified protein hits (~300) labeled by probes YGH-1 and YGH-2 belong to mitochondria, mostly localizing in mitochondrial matrix and inner mitochondrial membrane. Our research results provide a new tool for spatial and temporal analysis of subcellular proteome.
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Affiliation(s)
- Shuhong Guo
- Zhejiang University of Technology Chaohui Campus: Zhejiang University of Technology, College of Biotechnology and Bioengineering, CHINA
| | - Chaonan Yuan
- Zhejiang University of Technology, College of Biotechnology and Bioengineering, CHINA
| | - Wenjie Lang
- Zhejiang University of Technology Chaohui Campus: Zhejiang University of Technology, College of Biotechnology and Bioengineering, CHINA
| | - Danqi Hong
- Zhejiang University of Technology Chaohui Campus: Zhejiang University of Technology, College of Biotechnology and Bioengineering, CHINA
| | - Jian Liu
- Zhejiang University of Technology Chaohui Campus: Zhejiang University of Technology, College of Biotechnology and Bioengineering, CHINA
| | - Jintao Huang
- Zhejiang University of Technology Chaohui Campus: Zhejiang University of Technology, College of Biotechnology and Bioengineering, CHINA
| | - Jia Dong
- Zhejiang University of Technology Chaohui Campus: Zhejiang University of Technology, College of Biotechnology and Bioengineering, CHINA
| | - Jingyan Ge
- Zhejiang University of Technology, College of Biotechnology and Bioengineering, Chaowang Road 18, Hangzhou, China, 310014, Hangzhou, CHINA
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