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Tyagi S, Higerd-Rusli GP, Akin EJ, Baker CA, Liu S, Dib-Hajj FB, Waxman SG, Dib-Hajj SD. Real-time imaging of axonal membrane protein life cycles. Nat Protoc 2024:10.1038/s41596-024-00997-x. [PMID: 38831222 DOI: 10.1038/s41596-024-00997-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 02/12/2024] [Indexed: 06/05/2024]
Abstract
The construction of neuronal membranes is a dynamic process involving the biogenesis, vesicular packaging, transport, insertion and recycling of membrane proteins. Optical imaging is well suited for the study of protein spatial organization and transport. However, various shortcomings of existing imaging techniques have prevented the study of specific types of proteins and cellular processes. Here we describe strategies for protein tagging and labeling, cell culture and microscopy that enable the real-time imaging of axonal membrane protein trafficking and subcellular distribution as they progress through some stages of their life cycle. First, we describe a process for engineering membrane proteins with extracellular self-labeling tags (either HaloTag or SNAPTag), which can be labeled with fluorescent ligands of various colors and cell permeability, providing flexibility for investigating the trafficking and spatiotemporal regulation of multiple membrane proteins in neuronal compartments. Next, we detail the dissection, transfection and culture of dorsal root ganglion sensory neurons in microfluidic chambers, which physically compartmentalizes cell bodies and distal axons. Finally, we describe four labeling and imaging procedures that utilize these enzymatically tagged proteins, flexible fluorescent labels and compartmentalized neuronal cultures to study axonal membrane protein anterograde and retrograde transport, the cotransport of multiple proteins, protein subcellular localization, exocytosis and endocytosis. Additionally, we generated open-source software for analyzing the imaging data in a high throughput manner. The experimental and analysis workflows provide an approach for studying the dynamics of neuronal membrane protein homeostasis, addressing longstanding challenges in this area. The protocol requires 5-7 days and expertise in cell culture and microscopy.
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Affiliation(s)
- Sidharth Tyagi
- Medical Scientist Training Program, Yale School of Medicine, New Haven, CT, USA
- Center for Neuroscience and Regeneration Research, West Haven, CT, USA
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
- Center for Restoration of Nervous System Function, VA Connecticut Healthcare System, West Haven, CT, USA
| | - Grant P Higerd-Rusli
- Medical Scientist Training Program, Yale School of Medicine, New Haven, CT, USA
- Center for Neuroscience and Regeneration Research, West Haven, CT, USA
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
- Center for Restoration of Nervous System Function, VA Connecticut Healthcare System, West Haven, CT, USA
| | - Elizabeth J Akin
- Center for Neuroscience and Regeneration Research, West Haven, CT, USA
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
- Center for Restoration of Nervous System Function, VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Pharmacology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Christopher A Baker
- Center for Neuroscience and Regeneration Research, West Haven, CT, USA
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
- Center for Restoration of Nervous System Function, VA Connecticut Healthcare System, West Haven, CT, USA
| | - Shujun Liu
- Center for Neuroscience and Regeneration Research, West Haven, CT, USA
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
- Center for Restoration of Nervous System Function, VA Connecticut Healthcare System, West Haven, CT, USA
| | - Fadia B Dib-Hajj
- Center for Neuroscience and Regeneration Research, West Haven, CT, USA
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
- Center for Restoration of Nervous System Function, VA Connecticut Healthcare System, West Haven, CT, USA
| | - Stephen G Waxman
- Center for Neuroscience and Regeneration Research, West Haven, CT, USA.
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA.
- Center for Restoration of Nervous System Function, VA Connecticut Healthcare System, West Haven, CT, USA.
| | - Sulayman D Dib-Hajj
- Center for Neuroscience and Regeneration Research, West Haven, CT, USA.
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA.
- Center for Restoration of Nervous System Function, VA Connecticut Healthcare System, West Haven, CT, USA.
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2
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Perfilov MM, Zaitseva ER, Baleeva NS, Kublitski VS, Smirnov AY, Bogdanova YA, Krasnova SA, Myasnyanko IN, Mishin AS, Baranov MS. Meta-CF 3-Substituted Analogues of the GFP Chromophore with Remarkable Solvatochromism. Int J Mol Sci 2023; 24:9923. [PMID: 37373071 DOI: 10.3390/ijms24129923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
In this work, we have shown that the introduction of a trifluoromethyl group into the me-ta-position of arylidene imidazolones (GFP chromophore core) leads to a dramatic increase in their fluorescence in nonpolar and aprotic media. The presence of a pronounced solvent-dependent gradation of fluorescence intensity makes it possible to use these substances as fluorescent polarity sensors. In particular, we showed that one of the created compounds could be used for selective labeling of the endoplasmic reticulum of living cells.
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Affiliation(s)
- Maxim M Perfilov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Elvira R Zaitseva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
| | - Vadim S Kublitski
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Alexander Yu Smirnov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, Moscow 121205, Russia
| | - Yulia A Bogdanova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Svetlana A Krasnova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
| | - Alexander S Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
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3
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Punia K, Britton D, Hüll K, Yin L, Wang Y, Renfrew PD, Gilchrist ML, Bonneau R, Trauner D, Montclare JK. Fluorescent azobenzene-confined coiled-coil mesofibers. SOFT MATTER 2023; 19:497-501. [PMID: 36538008 DOI: 10.1039/d2sm01578a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Fluorescent protein biomaterials have important applications such as bioimaging in pharmacological studies. Self-assembly of proteins, especially into fibrils, is known to produce fluorescence in the blue band. Capable of self-assembly into nanofibers, we have shown we can modulate its aggregation into mesofibers by encapsulation of a small hydrophobic molecule. Conversely, azobenzenes are hydrophobic small molecules that are virtually non-fluorescent in solution due to their highly efficient photoisomerization. However, they demonstrate fluorogenic properties upon confinement in nanoscale assemblies by reducing the non-radiative photoisomerization. Here, we report the fluorescence of a hybrid protein-small molecule system in which azobenzene is confined in our protein assembly leading to fiber thickening and increased fluorescence. We show our engineered protein Q encapsulates AzoCholine, bearing a photoswitchable azobenzene moiety, in the hydrophobic pore to produce fluorescent mesofibers. This study further investigates the photocontrol of protein conformation as well as fluorescence of an azobenze-containing biomaterial.
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Affiliation(s)
- Kamia Punia
- Departments of Chemical and Biomolecular Engineering, Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, New York 11201, USA.
| | - Dustin Britton
- Departments of Chemical and Biomolecular Engineering, Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, New York 11201, USA.
| | - Katharina Hüll
- Department of Chemistry, New York University, New York, New York 10003, USA
- Department of Chemistry, Ludwig Maximilian University, München, Germany
| | - Liming Yin
- Departments of Chemical and Biomolecular Engineering, Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, New York 11201, USA.
| | - Yifei Wang
- Departments of Chemical and Biomolecular Engineering, Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, New York 11201, USA.
| | - P Douglas Renfrew
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
| | - M Lane Gilchrist
- Department of Chemical Engineering and Biomedical Engineering, The City College of the City University of New York, New York, New York 10031, USA
| | - Richard Bonneau
- Center for Genomics and Systems Biology, Department of Biology, New York University New York, New York 10003, USA
| | - Dirk Trauner
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jin K Montclare
- Departments of Chemical and Biomolecular Engineering, Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, New York 11201, USA.
- Department of Chemistry, New York University, New York, New York 10003, USA
- Department of Biomaterials, NYU College of Dentistry, New York, NY, 10010, USA
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4
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Khrulev AA, Baleeva NS, Kamzeeva PN, Baranov MS, Aralov AV. Cyanine Dyes as Fluorogens for FAST and NanoFAST Proteins. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1068162022040112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Zuo Z, Kang T, Hu S, Su W, Gan Y, Miao Z, Zhao H, Feng P, Ke B, Li M. A Bioluminescent Probe for Detecting Norepinephrine in Vivo. Anal Chem 2022; 94:6441-6445. [PMID: 35452217 DOI: 10.1021/acs.analchem.2c00460] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
As a neurotransmitter, norepinephrine (NE) is critical for psychiatric conditions, neurodegenerative diseases, and pheochromocytoma. A real-time and noninvasive method for the detection of NE as a tracer to investigate the NE-relevant disease treatment process is urgently desirable. Herein, we successfully developed a turn-on NE bioluminescent probe (NBP), which was grounded on p-toluenethiol deprotectrf by nucleophilic substitution. Compared with other analytes, the NBP exhibited high sensitivity and selectivity in vitro. More importantly, the NBP provides a promising strategy for in vivo imaging of NE in living animals with noninvasive visualization and real-time features.
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Affiliation(s)
- Zeping Zuo
- Laboratory of Anaesthesiology & Critical Care Medicine, Department of Anesthesiology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ting Kang
- Laboratory of Anaesthesiology & Critical Care Medicine, Department of Anesthesiology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Shilong Hu
- Laboratory of Anaesthesiology & Critical Care Medicine, Department of Anesthesiology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Wuyue Su
- Medical College, Tibet University, Lhasa 850000, China
| | - Yu Gan
- Laboratory of Anaesthesiology & Critical Care Medicine, Department of Anesthesiology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Zhuang Miao
- Laboratory of Anaesthesiology & Critical Care Medicine, Department of Anesthesiology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Hanqing Zhao
- Laboratory of Anaesthesiology & Critical Care Medicine, Department of Anesthesiology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ping Feng
- Institute of Clinical Trials, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Bowen Ke
- Laboratory of Anaesthesiology & Critical Care Medicine, Department of Anesthesiology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Minyong Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
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6
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Zhang Y, Zhou W, Xu N, Wang G, Li J, An K, Jiang W, Zhou X, Qiao Q, Jiang X, Xu Z. Aniline as a TICT rotor to derive methine fluorogens for biomolecules: A curcuminoid-BF2 compound for lighting up HSA/BSA. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.04.070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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7
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He J, Zhou Y, Liu Y, Guo R, Jiang J, Bruchez MP. Fluorogen-Activating-Protein-Loaded Tantalum Oxide Nanoshells for in Vivo On-Demand Fluorescence/Photoacoustic Imaging. ACS APPLIED BIO MATERIALS 2022; 5:1057-1063. [PMID: 35191667 DOI: 10.1021/acsabm.1c01113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Optical imaging of targeted compartments within living animals has been widely adopted in many research areas. In particular, various fluorescence-based probes and emerged photoacoustic molecules that enable sensitive and specific imaging through tissue have greatly advanced clinically relevant studies. However, delivery and signal penetration have placed requirements on the performance of conventional optical probes. Here, we use hallow tantalum oxide (TaOx) nanoparticles to enclose fluorogen-activating protein (FAP) for the in vivo fluorescence and photoacoustic imaging of cancer cells. We found that the TaOx shell can provide a natural cover for the enclosed fluorogen/FAP complexes, protecting them from photobleaching and common biodegradation. Moreover, we have developed a near-infrared excitable tetrafluorinated photoacoustic fluorogen for the specific and persistent photoacoustic imaging of tumors. We believe that this enclosing and delivery strategy of optical biomolecules will be an attractive alternative for bioimaging.
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Affiliation(s)
- Jianjun He
- College of Biology, Hunan University, Changsha 410082, China
| | - Yancen Zhou
- College of Biology, Hunan University, Changsha 410082, China
| | - Yinxia Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Rui Guo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jianhui Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Marcel P Bruchez
- Molecular Biosensor and Imaging Center, Department of Biological Sciences, Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15217, United States
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8
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Farrants H, Tebo AG. Fluorescent chemigenetic actuators and indicators for use in living animals. Curr Opin Pharmacol 2022; 62:159-167. [DOI: 10.1016/j.coph.2021.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/03/2021] [Accepted: 12/12/2021] [Indexed: 11/28/2022]
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9
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Recent Advancements in Tracking Bacterial Effector Protein Translocation. Microorganisms 2022; 10:microorganisms10020260. [PMID: 35208715 PMCID: PMC8876096 DOI: 10.3390/microorganisms10020260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 11/17/2022] Open
Abstract
Bacteria-host interactions are characterized by the delivery of bacterial virulence factors, i.e., effectors, into host cells where they counteract host immunity and exploit host responses allowing bacterial survival and spreading. These effectors are translocated into host cells by means of dedicated secretion systems such as the type 3 secretion system (T3SS). A comprehensive understanding of effector translocation in a spatio-temporal manner is of critical importance to gain insights into an effector’s mode of action. Various approaches have been developed to understand timing and order of effector translocation, quantities of translocated effectors and their subcellular localization upon translocation into host cells. Recently, the existing toolset has been expanded by newly developed state-of-the art methods to monitor bacterial effector translocation and dynamics. In this review, we elaborate on reported methods and discuss recent advances and shortcomings in this area of tracking bacterial effector translocation.
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10
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Baleeva NS, Smirnov AY, Myasnyanko IN, Gavrikov AS, Baranov MS. A Thiophene Analog of the GFP Chromophore As Fluorogen for FAST Protein. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021050198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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11
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The Cutting Edge of Disease Modeling: Synergy of Induced Pluripotent Stem Cell Technology and Genetically Encoded Biosensors. Biomedicines 2021; 9:biomedicines9080960. [PMID: 34440164 PMCID: PMC8392144 DOI: 10.3390/biomedicines9080960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 08/02/2021] [Indexed: 11/17/2022] Open
Abstract
The development of cell models of human diseases based on induced pluripotent stem cells (iPSCs) and a cell therapy approach based on differentiated iPSC derivatives has provided a powerful stimulus in modern biomedical research development. Moreover, it led to the creation of personalized regenerative medicine. Due to this, in the last decade, the pathological mechanisms of many monogenic diseases at the cell level have been revealed, and clinical trials of various cell products derived from iPSCs have begun. However, it is necessary to reach a qualitatively new level of research with cell models of diseases based on iPSCs for more efficient searching and testing of drugs. Biosensor technology has a great application prospect together with iPSCs. Biosensors enable researchers to monitor ions, molecules, enzyme activities, and channel conformation in live cells and use them in live imaging and drug screening. These probes facilitate the measurement of steady-state concentrations or activity levels and the observation and quantification of in vivo flux and kinetics. Real-time monitoring of drug action in a specific cellular compartment, organ, or tissue type; the ability to screen at the single-cell resolution; and the elimination of the false-positive results caused by low drug bioavailability that is not detected by in vitro testing methods are a few of the benefits of using biosensors in drug screening. Here, we discuss the possibilities of using biosensor technology in combination with cell models based on human iPSCs and gene editing systems. Furthermore, we focus on the current achievements and problems of using these methods.
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12
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Wang X, Wang Q, Zhang Q, Han X, Xu S, Yin D, Hu HY. Developing fluoromodule-based probes for in vivo monitoring the bacterial infections and antibiotic responses. Talanta 2021; 233:122610. [PMID: 34215094 DOI: 10.1016/j.talanta.2021.122610] [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: 04/02/2021] [Revised: 05/26/2021] [Accepted: 06/09/2021] [Indexed: 10/21/2022]
Abstract
Recently, antibiotic resistant has become a serious public health concern, which warrants new generations of antibiotics to be developed. Pharmacodynamic evaluation is crucial in drug discovery processes. Despite numerous advanced imaging systems are available nowadays, technologies for the sensitive in vivo diagnosis of bacterial infections and direct visualization of drug efficacy are yet to be developed. In this study, we have developed novel near-infrared (NIR) fluorogenic probes. These probes are dark in solution but highly fluorescent when bound to the cognate reporter, fluorogen-activating protein (FAP). We established the in vivo bacterial infection model using FAP_dH6.2 recombinantly expressed E. coli and applied this NIR fluoromodule-based system for diagnosing bacterial infections and monitoring disease progressions and its responses to a type of antibiotics through classic mechanism of membrane lysis. This NIR fluoromodule-based system will discover new information on bacterial infections and identify newer antibacterial entities.
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Affiliation(s)
- Xiang Wang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Qinghua Wang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Qingyang Zhang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Xiaowan Han
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Shengnan Xu
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Dali Yin
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
| | - Hai-Yu Hu
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
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13
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Sokolov AI, Myasnyanko IN, Baleeva NS, Baranov MS. Styrene Derivatives of Indole and Pyranone as Fluorogenic Substrates for FAST Protein. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021010234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Ding M, Baker D. Recent advances in high-throughput flow cytometry for drug discovery. Expert Opin Drug Discov 2020; 16:303-317. [PMID: 33054417 DOI: 10.1080/17460441.2021.1826433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION High-throughput flow cytometry (HTFC) has proven to be an important technology in drug discovery. The use of HTFC enables multi-parametric screening of suspension cells containing heterogenous cell populations and coated particles for screening proteins of interest. Novel targets, novel cell markers and compound clusters for drug development have been identified from HTFC screens. AREAS COVERED In this article, the authors focus on reviewing the recent HTFC applications reported during the last 5-6 years, including drug discovery screens and studies for immune, immune-oncology, infectious and inflammatory diseases. The main HTFC approaches, development of HTFC systems, and automated sample preparation systems for HTFC are also discussed. EXPERT OPINION The advance of HTFC technology coupled with automated sample acquisition and sample preparation has demonstrated its utility in screening large numbers of compounds using suspension cells, facilitated screening of disease-relevant human primary cells, and enabled deep understanding of mechanism of action by analyzing multiple parameters. The authors see HTFC as a very valuable tool in immune, immune-oncology, infectious and inflammatory diseases where immune cells play essential roles.
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Affiliation(s)
- Mei Ding
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - David Baker
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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Carpenter MA, Wang Y, Telmer CA, Schmidt BF, Yang Z, Bruchez MP. Protein Proximity Observed Using Fluorogen Activating Protein and Dye Activated by Proximal Anchoring (FAP-DAPA) System. ACS Chem Biol 2020; 15:2433-2443. [PMID: 32786268 DOI: 10.1021/acschembio.0c00419] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The development and function of tissues, blood, and the immune system is dependent upon proximity for cellular recognition and communication. However, the detection of cell-to-cell contacts is limited due to a lack of reversible, quantitative probes that can function at these dynamic sites of irregular geometry. Described here is a novel chemo-genetic tool developed for fluorescent detection of protein-protein proximity and cell apposition that utilizes the Fluorogen Activating Protein (FAP) in combination with a Dye Activated by Proximal Anchoring (DAPA). The FAP-DAPA system has two protein components, the HaloTag and FAP, expressed on separate protein targets or in separate cells. The proteins function to bind and activate a compound that has the hexyl chloride (HexCl) ligand connected to malachite green (MG), the FAP fluorogen, via a poly(ethylene glycol) spacer spanning up to 28 nm. The dehalogenase protein, HaloTag, covalently binds the HexCl ligand, locally concentrating the attached MG. If the FAP is within range of the anchored fluorogen, it will bind and activate MG specifically when the bath concentration is too low to saturate the FAP receptor. A new FAP variant was isolated with a 1000-fold reduced KD of ∼10-100 nM so that the fluorogen activation reports proximity without artificially enhancing it. The system was characterized using purified FRB and FKBP fusion proteins and showed a doubling of fluorescence upon rapamycin induced complex formation. In cocultured HEK293 cells (HaloTag and FAP-expressing) fluorescence increased at contact sites across a broad range of labeling conditions, more reliably providing contact-specific fluorescence activation with the lower-affinity FAP variant. When combined with suitable targeting and expression constructs, this labeling system may offer significant improvements in on-demand detection of intercellular contacts, potentially applicable in neurological and immunological synapse measurements and other transient, dynamic biological appositions that can be perturbed using other labeling methods that stabilize these interactions.
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Affiliation(s)
- M. Alexandra Carpenter
- Carnegie Mellon University, Department of Chemistry, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Yi Wang
- Carnegie Mellon University, Department of Biological Sciences, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Cheryl A. Telmer
- Carnegie Mellon University, Department of Biological Sciences, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
- Carnegie Mellon University, Molecular Biosensor and Imaging Center, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Brigitte F. Schmidt
- Carnegie Mellon University, Molecular Biosensor and Imaging Center, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Zhipeng Yang
- Carnegie Mellon University, Department of Biological Sciences, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Marcel P. Bruchez
- Carnegie Mellon University, Department of Chemistry, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
- Carnegie Mellon University, Department of Biological Sciences, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
- Carnegie Mellon University, Molecular Biosensor and Imaging Center, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
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16
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Moeyaert B, Dedecker P. Genetically encoded biosensors based on innovative scaffolds. Int J Biochem Cell Biol 2020; 125:105761. [PMID: 32504671 DOI: 10.1016/j.biocel.2020.105761] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/27/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022]
Abstract
Genetically encoded biosensors are indispensable tools for visualizing the spatiotemporal dynamics of analytes or processes in living cells in vitro and in vivo. Their widespread adaptation has gone hand in hand with the development of sensors for new analytes or processes and improved functionality and robustness. In this review, we highlight some of the recent advances in genetically encoded biosensor development, with a special focus on novel and innovative scaffolds that will lead to new possibilities in the future.
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Affiliation(s)
- Benjamien Moeyaert
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Heverlee, Belgium
| | - Peter Dedecker
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Heverlee, Belgium.
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17
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Perkins LA, Bruchez MP. Fluorogen activating protein toolset for protein trafficking measurements. Traffic 2020; 21:333-348. [PMID: 32080949 PMCID: PMC7462100 DOI: 10.1111/tra.12722] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 12/11/2022]
Abstract
Throughout the past decade the use of fluorogen activating proteins (FAPs) has expanded with several unique reporter dyes that support a variety of methods to specifically quantify protein trafficking events. The platform's capabilities have been demonstrated in several systems and shared for widespread use. This review will highlight the current FAP labeling techniques for protein traffic measurements and focus on the use of the different designed fluorogenic dyes for selective and specific labeling applications.
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Affiliation(s)
- Lydia A. Perkins
- School of MedicineUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Marcel P. Bruchez
- The Department of Biological SciencesCarnegie MellonPittsburghPennsylvaniaUSA
- Department of ChemistryCarnegie MellonPittsburghPennsylvaniaUSA
- Molecular and Biosensor Imaging CenterCarnegie MellonPittsburghPennsylvaniaUSA
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18
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Song X, Deng X, Wang Q, Tian J, He FL, Hu HY, Tian W. Self-assembling morphology-tunable single-component supramolecular antibiotics for enhanced antibacterial manipulation. Polym Chem 2020. [DOI: 10.1039/c9py01440c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
This single-component supramolecular antibiotic can undergo reversible self-assembling morphology transitions under sequential ultrasonic and redox stimuli. The self-assemblies with different morphologies display effective antibacterial regulation.
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Affiliation(s)
- Xin Song
- MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions and Shaanxi Key Laboratory of Macromolecular Science and Technology
- School of Science
- Northwestern Polytechnical University
- Xi'an
- P. R. China
| | - Xudong Deng
- Key Laboratory for Space Bioscience and Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- Xi'an 710072
- P. R. China
| | - Qinghua Wang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine
- and Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation
- Institute of Materia Medica
- Peking Union Medical College and Chinese Academy of Medical Sciences
- Beijing 100050
| | - Jinjin Tian
- MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions and Shaanxi Key Laboratory of Macromolecular Science and Technology
- School of Science
- Northwestern Polytechnical University
- Xi'an
- P. R. China
| | - Feng-Li He
- Key Laboratory for Space Bioscience and Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- Xi'an 710072
- P. R. China
| | - Hai-Yu Hu
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine
- and Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation
- Institute of Materia Medica
- Peking Union Medical College and Chinese Academy of Medical Sciences
- Beijing 100050
| | - Wei Tian
- MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions and Shaanxi Key Laboratory of Macromolecular Science and Technology
- School of Science
- Northwestern Polytechnical University
- Xi'an
- P. R. China
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19
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Su Y, Bian S, Sawan M. Real-time in vivo detection techniques for neurotransmitters: a review. Analyst 2020; 145:6193-6210. [DOI: 10.1039/d0an01175d] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Functional synapses in the central nervous system depend on a chemical signal exchange process that involves neurotransmitter delivery between neurons and receptor cells in the neuro system.
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Affiliation(s)
- Yi Su
- Zhejiang university
- Hangzhou, 310058
- China
- CENBRAIN Lab
- School of Engineering
| | - Sumin Bian
- CENBRAIN Lab
- School of Engineering
- Westlake University
- Hangzhou
- China
| | - Mohamad Sawan
- CENBRAIN Lab
- School of Engineering
- Westlake University
- Hangzhou
- China
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20
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Gallo E. Fluorogen-Activating Proteins: Next-Generation Fluorescence Probes for Biological Research. Bioconjug Chem 2019; 31:16-27. [DOI: 10.1021/acs.bioconjchem.9b00710] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Eugenio Gallo
- Department of Molecular Genetics, University of Toronto, Charles Best Institute, 112 College Street, Toronto, Ontario M5G 1L6, Canada
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21
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Rapid Discovery of Illuminating Peptides for Instant Detection of Opioids in Blood and Body Fluids. Molecules 2019; 24:molecules24091813. [PMID: 31083395 PMCID: PMC6539258 DOI: 10.3390/molecules24091813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/03/2019] [Accepted: 05/05/2019] [Indexed: 01/03/2023] Open
Abstract
The United States is currently experiencing an opioid crisis, with more than 47,000 deaths in 2017 due to opioid overdoses. Current approaches for opioid identification and quantification in body fluids include immunoassays and chromatographic methods (e.g., LC-MS, GC-MS), which require expensive instrumentation and extensive sample preparation. Our aim was to develop a portable point-of-care device that can be used for the instant detection of opioids in body fluids. Here, we reported the development of a morphine-sensitive fluorescence-based sensor chip to sensitively detect morphine in the blood using a homogeneous immunoassay without any washing steps. Morphine-sensitive illuminating peptides were identified using a high throughput one-bead one-compound (OBOC) combinatorial peptide library approach. The OBOC libraries contain a large number of random peptides with a molecular rotor dye, malachite green (MG), that are coupled to the amino group on the side chain of lysine at different positions of the peptides. The OBOC libraries were then screened for fluorescent activation under a confocal microscope, using an anti-morphine monoclonal antibody as the screening probe, in the presence and absence of free morphine. Using this novel three-step fluorescent screening assay, we were able to identify the peptide-beads that fluoresce in the presence of an anti-morphine antibody, but lost fluorescence when the free morphine was present. After the positive beads were decoded using automatic Edman microsequencing, the morphine-sensitive illuminating peptides were then synthesized in soluble form, functionalized with an azido group, and immobilized onto microfabricated PEG-array spots on a glass slide. The sensor chip was then evaluated for the detection of morphine in plasma. We demonstrated that this proof-of-concept platform can be used to develop fluorescence-based sensors against morphine. More importantly, this technology can also be applied to the discovery of other novel illuminating peptidic sensors for the detection of illicit drugs and cancer biomarkers in body fluids.
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Abstract
Molecular conjugation refers to methods used in biomedicine, advanced materials and nanotechnology to link two partners - from small molecules to large and sometimes functionally complex biopolymers. The methods ideally have a broad structural scope, proceed under very mild conditions (including in H2O), occur at a rapid rate and in quantitative yield with no by-products, enable bioorthogonal reactivity and have zero toxicity. Over the past two decades, the field of click chemistry has emerged to afford us new and efficient methods of molecular conjugation. These methods are based on chemical reactions that produce permanently linked conjugates, and we refer to this field here as covalent click chemistry. Alternatively, if molecular conjugation is undertaken using a pair of complementary molecular recognition partners that associate strongly and selectively to form a thermodynamically stable non-covalent complex, then we refer to this strategy as non-covalent click chemistry. This Perspective is concerned with this latter approach and highlights two distinct applications of non-covalent click chemistry in molecular conjugation: the pre-assembly of molecular conjugates or surface-coated nanoparticles and the in situ capture of tagged biomolecular targets for imaging or analysis.
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Affiliation(s)
- Cynthia L Schreiber
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Bradley D Smith
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
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23
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Lin H, Yang WQ, Ye Z, Zhang CJ. Identification of Potent Caspase-8 Inhibitors from a Library of Fluorescent Natural Products Screened by an AIEgen-Based Light-Up Probe. Chembiochem 2019; 20:1292-1296. [PMID: 30648790 DOI: 10.1002/cbic.201800723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Indexed: 11/10/2022]
Abstract
Fluorescent natural products are a rich source of drugs and chemical probes, but their innate fluorescence can interfere with fluorescence-based screening assays. Caspase-8 is a key player in apoptosis, its inhibition having been found to be beneficial for treatment of inflammatory and neurodegenerative diseases. Small-molecular inhibitors of caspase-8 remain sparsely reported, however. In this study, we firstly developed a light-up probe based on an AIEgen and capable of targeting caspase-8. This fluorescent dye has a Stokes shift of 200 nm, which could allow the innate fluorescence signals of natural products to be avoided. On screening a library of 86 fluorescent natural products, we found for the first time that gossypol showed potent inhibition of caspase-8 in vitro and in situ. This unique light-up probe, coupled with colored natural products, could represent an efficient approach to hit discovery for druggable targets.
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Affiliation(s)
- Hao Lin
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences, and, Peking Union Medical College, 1 Xian Nong Tan Street, Beijing, 100050, China
| | - Wan-Qi Yang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences, and, Peking Union Medical College, 1 Xian Nong Tan Street, Beijing, 100050, China
| | - Zi Ye
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences, and, Peking Union Medical College, 1 Xian Nong Tan Street, Beijing, 100050, China
| | - Chong-Jing Zhang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences, and, Peking Union Medical College, 1 Xian Nong Tan Street, Beijing, 100050, China
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Chen S, Dong G, Wu S, Liu N, Zhang W, Sheng C. Novel fluorescent probes of 10-hydroxyevodiamine: autophagy and apoptosis-inducing anticancer mechanisms. Acta Pharm Sin B 2019; 9:144-156. [PMID: 30766786 PMCID: PMC6361730 DOI: 10.1016/j.apsb.2018.08.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/25/2018] [Accepted: 08/05/2018] [Indexed: 12/21/2022] Open
Abstract
Natural product evodiamine and its derivatives represent a promising class of multi-target antitumor agents. However, the clinical development of these compounds has been hampered by a poor understanding of their antitumor mechanisms. To tackle this obstacle, herein, novel fluorescent probes were designed to elucidate the antitumor mode of action of 10-hydroxyevodiamine. This compound was proven to be distributed in the mitochondria and lysosomes and to act by autophagy and apoptosis mechanisms.
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Key Words
- 10-Hydroxyevodiamine
- 3MA, 3-methyladenine
- Anticancer mechanisms
- Apoptosis
- Autophagy
- Boc, di-tert-butyl dicarbonate
- CCK8, cell counting kit-8
- DMAP, 4-dimethylaminopyridine
- DMSO, dimethylsulfoxide
- EDC, 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride
- Fluorescent probes
- HBTU, O-benzotriazole-N,N,N,N-tetramethyl-uronium-hexafluorophosphate
- MMP, mitochondrial membrane potential
- NPs, natural products
- TEA, trimethylamine
- TFA, trifluoroacetic acid
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Zeng G, Wang Y, Bruchez MP, Liang FS. Self-Reporting Chemically Induced Protein Proximity System Based on a Malachite Green Derivative and the L5** Fluorogen Activating Protein. Bioconjug Chem 2018; 29:3010-3015. [PMID: 30016083 DOI: 10.1021/acs.bioconjchem.8b00415] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A unique chemically induced proximity method is engineered based on mutant antibody VL domain using a fluorogenic malachite green derivative as the inducer, which gives fluorescent signals upon VL domain dimerization while simultaneously inducing downstream biological effects.
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Affiliation(s)
- Guihua Zeng
- Department of Chemistry and Chemical Biology , University of New Mexico , 300 Terrace Street NE , Albuquerque , New Mexico 87131 , United States
| | - Yi Wang
- Department of Chemistry, Department of Biological Sciences, and Molecular Biosensor and Imaging Center , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Marcel P Bruchez
- Department of Chemistry, Department of Biological Sciences, and Molecular Biosensor and Imaging Center , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Fu-Sen Liang
- Department of Chemistry and Chemical Biology , University of New Mexico , 300 Terrace Street NE , Albuquerque , New Mexico 87131 , United States
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