1
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Sammons RM, Cho EJ, Dalby KN. Identification and biochemical characterization of small molecule inhibitors of ERK2 that target the D-recruitment site. Methods Enzymol 2023; 690:445-499. [PMID: 37858538 PMCID: PMC10950554 DOI: 10.1016/bs.mie.2023.06.016] [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] [Indexed: 10/21/2023]
Abstract
Extracellular signal-regulated kinase (ERK) is the culmination of a mitogen-activated protein kinase cascade that regulates cellular processes like proliferation, migration, and survival. Consequently, abnormal ERK signaling often plays a role in the tumorigenesis and metastasis of numerous cancers. ERK inhibition is a sought-after treatment for cancers, especially since clinically approved drugs that target signaling upstream of ERK often induce acquired resistance. Furthermore, the ERK2 isoform may have a differential role in various cancers from the other canonical isoform, ERK1. We demonstrate that small molecules can inhibit ERK2 catalytic and noncatalytic functions by binding to the D-recruitment site (DRS), a protein-protein interaction site distal to the enzyme active site. Using a fluorescence anisotropy-based high-throughput screening, we identify compounds that bind to the DRS and exhibit dose-dependent inhibition of ERK2 activity and ERK2 phosphorylation. We characterize the dose-dependent potency of ERK2 inhibitors using fluorescence anisotropy-based binding assays, fluorescence-based ERK2 substrate phosphorylation assays, and in vitro ERK2 activation assays. In our example, the binding of a DRS inhibitor can be prevented by mutating the DRS residue Cys-159 to serine, indicating that this residue is essential for the interaction. Resulting inhibitors from this process can be assessed in cellular and in vivo experiments for inhibition of ERK signaling and can be evaluated as potential cancer drugs.
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Affiliation(s)
- R M Sammons
- Targeted Therapeutic Drug Discovery and Development Program, The University of Texas at Austin, Austin, TX, United States
| | - E J Cho
- Targeted Therapeutic Drug Discovery and Development Program, The University of Texas at Austin, Austin, TX, United States
| | - K N Dalby
- Targeted Therapeutic Drug Discovery and Development Program, The University of Texas at Austin, Austin, TX, United States; Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, United States.
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2
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Motiei L, Margulies D. Molecules that Generate Fingerprints: A New Class of Fluorescent Sensors for Chemical Biology, Medical Diagnosis, and Cryptography. Acc Chem Res 2023. [PMID: 37335975 DOI: 10.1021/acs.accounts.3c00162] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
ConspectusFluorescent molecular sensors, often referred to as "turn-on" or "turn-off" fluorescent probes, are synthetic agents that change their fluorescence signal in response to analyte binding. Although these sensors have become powerful analytical tools in a wide range of research fields, they are generally limited to detecting only one or a few analytes. Pattern-generating fluorescent probes, which can generate unique identification (ID) fingerprints for different analytes, have recently emerged as a new class of luminescent sensors that can address this limitation. A unique characteristic of these probes, termed ID-probes, is that they integrate the qualities of conventional small-molecule-based fluorescent sensors and cross-reactive sensor arrays (often referred to as chemical, optical, or electronic noses/tongues). On the one hand, ID-probes can discriminate between various analytes and their combinations, akin to array-based analytical devices. On the other hand, their minute size enables them to analyze small-volume samples, track dynamic changes in a single solution, and operate in the microscopic world, which the macroscopic arrays cannot access.Here, we describe the principles underlying the ID-probe technology, as well as provide an overview of different ID-probes that have been developed to date and the ways they can be applied to a wide range of research fields. We describe, for example, ID-probes that can identify combinations of protein biomarkers in biofluids and in living cells, screen for several protein inhibitors simultaneously, analyze the content of Aβ aggregates, as well as ensure the quality of small-molecule and biological drugs. These examples highlight the relevance of this technology to medical diagnosis, bioassay development, cell and chemical biology, and pharmaceutical quality assurance, among others. ID-probes that can authorize users and protect secret data are also presented and the mechanisms that enable them to hide (steganography), encrypt (cryptography), and prevent access to (password protection) information are discussed.The versatility of this technology is further demonstrated by describing two types of probes: unimolecular ID-probes and self-assembled ID-probes. Probes from the first type can operate inside living cells, be recycled, and their initial patterns can be more easily obtained in a reproducible manner. The second type of probes can be readily modified and optimized, allowing one to prepare various different probes from a much wider range of fluorescent reporters and supramolecular recognition elements. Taken together, these developments indicate that the ID-probe sensing methodology is generally applicable, and that such probes can better characterize analyte mixtures or process chemically encoded information than can the conventional fluorescent molecular sensors. We therefore hope that this review will inspire the development of new types of pattern-generating probes, which would extend the fluorescence molecular toolbox currently used in the analytical sciences.
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Affiliation(s)
- Leila Motiei
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - David Margulies
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
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3
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Prasad PK, Eizenshtadt N, Goliand I, Fellus-Alyagor L, Oren R, Golani O, Motiei L, Margulies D. Chemically programmable bacterial probes for the recognition of cell surface proteins. Mater Today Bio 2023; 20:100669. [PMID: 37334185 PMCID: PMC10275978 DOI: 10.1016/j.mtbio.2023.100669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 05/01/2023] [Accepted: 05/17/2023] [Indexed: 06/20/2023] Open
Abstract
Common methods to label cell surface proteins (CSPs) involve the use of fluorescently modified antibodies (Abs) or small-molecule-based ligands. However, optimizing the labeling efficiency of such systems, for example, by modifying them with additional fluorophores or recognition elements, is challenging. Herein we show that effective labeling of CSPs overexpressed in cancer cells and tissues can be obtained with fluorescent probes based on chemically modified bacteria. The bacterial probes (B-probes) are generated by non-covalently linking a bacterial membrane protein to DNA duplexes appended with fluorophores and small-molecule binders of CSPs overexpressed in cancer cells. We show that B-probes are exceptionally simple to prepare and modify because they are generated from self-assembled and easily synthesized components, such as self-replicating bacterial scaffolds and DNA constructs that can be readily appended, at well-defined positions, with various types of dyes and CSP binders. This structural programmability enabled us to create B-probes that can label different types of cancer cells with distinct colors, as well as generate very bright B-probes in which the multiple dyes are spatially separated along the DNA scaffold to avoid self-quenching. This enhancement in the emission signal enabled us to label the cancer cells with greater sensitivity and follow the internalization of the B-probes into these cells. The potential to apply the design principles underlying B-probes in therapy or inhibitor screening is also discussed here.
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Affiliation(s)
- Pragati K. Prasad
- Department of Chemical and Structural Biology, Weizmann Institute of Science Rehovot, 7610001, Israel
| | - Noa Eizenshtadt
- Department of Chemical and Structural Biology, Weizmann Institute of Science Rehovot, 7610001, Israel
| | - Inna Goliand
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Liat Fellus-Alyagor
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Roni Oren
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ofra Golani
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Leila Motiei
- Department of Chemical and Structural Biology, Weizmann Institute of Science Rehovot, 7610001, Israel
| | - David Margulies
- Department of Chemical and Structural Biology, Weizmann Institute of Science Rehovot, 7610001, Israel
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4
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Zeng L, Kaoud TS, Zamora-Olivares D, Bohanon AL, Li Y, Pridgen JR, Ekpo YE, Zhuang DL, Nye JR, Telles M, Winkler M, Rivera S, Marini F, Dalby KN, Anslyn EV. Multiplexing the Quantitation of MAP Kinase Activities Using Differential Sensing. J Am Chem Soc 2022; 144:4017-4025. [PMID: 35195411 DOI: 10.1021/jacs.1c12757] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein kinases are therapeutic targets for many human diseases, but the lack of user-friendly quantitative assays limits the ability to follow the activities of numerous kinases at once (multiplexing). To develop such an assay, we report an array of sulfonamido-oxine (SOX)-labeled peptides showing cross-reactivity to different mitogen-activated protein kinases (MAPKs) for use in a differential sensing scheme. We first verified using linear discriminant analysis that the array could differentiate MAPK isoforms. Then, using principal component analysis, the array was optimized based on the discrimination imparted by each SOX-peptide. Next, the activity of individual MAPK families in ternary mixtures was quantified by support vector machine regression. Finally, we multiplexed the quantification of three MAPK families using partial least squares regression in A549 cell lysates, which has possible interference from other kinase classes. Thus, our method simultaneously quantifies the activity of multiple kinases. The technique could be applied to other protein kinase families and the monitoring of diseases.
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Affiliation(s)
- Lingyu Zeng
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Tamer S Kaoud
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Diana Zamora-Olivares
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States.,Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Amanda L Bohanon
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Yiru Li
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jacey R Pridgen
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Yakndara E Ekpo
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Deborah L Zhuang
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jessica R Nye
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Mitchell Telles
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Michelle Winkler
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Sebastian Rivera
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Federico Marini
- Department of Chemistry, University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Eric V Anslyn
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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5
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Crook AA, Zamora-Olivares D, Bhinderwala F, Woods J, Winkler M, Rivera S, Shannon CE, Wagner HR, Zhuang DL, Lynch JE, Berryhill NR, Runnebaum RC, Anslyn EV, Powers R. Combination of two analytical techniques improves wine classification by Vineyard, Region, and vintage. Food Chem 2021; 354:129531. [PMID: 33756314 DOI: 10.1016/j.foodchem.2021.129531] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/29/2021] [Accepted: 03/02/2021] [Indexed: 12/13/2022]
Abstract
Three important wine parameters: vineyard, region, and vintage year, were evaluated using fifteen Vitis vinifera L. 'Pinot noir' wines derived from the same scion clone (Pinot noir 667). These wines were produced from two vintage years (2015 and 2016) and eight different regions along the Pacific Coast of the United States. We successfully improved the classification of the selected Pinot noir wines by combining an untargeted 1D 1H NMR analysis with a targeted peptide based differential sensing array. NMR spectroscopy was used to evaluate the chemical fingerprint of the wines, whereas the peptide-based sensing array is known to mimic the senses of taste, smell, and palate texture by characterizing the phenolic profile. Multivariate and univariate statistical analyses of the combined NMR and differential sensing array dataset classified the genetically identical Pinot noir wines on the basis of distinctive metabolic signatures associated with the region of growth, vineyard, and vintage year.
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Affiliation(s)
- Alexandra A Crook
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln NE 65888, United States
| | - Diana Zamora-Olivares
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States; Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, TX 78712, United States
| | - Fatema Bhinderwala
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln NE 65888, United States; Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln NE 68588, United States; Department of Structural Biology, University of Pittsburgh, School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15261, United States
| | - Jade Woods
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln NE 65888, United States
| | - Michelle Winkler
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, TX 78712, United States
| | - Sebastian Rivera
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, TX 78712, United States
| | - Cassandra E Shannon
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, TX 78712, United States
| | - Holden R Wagner
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, TX 78712, United States
| | - Deborah L Zhuang
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, TX 78712, United States
| | - Jessica E Lynch
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, TX 78712, United States
| | - Nathan R Berryhill
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, TX 78712, United States
| | - Ron C Runnebaum
- Department of Viticulture and Enology, and Department of Chemical Engineering, University of California-Davis, Davis, CA 95616, United States.
| | - Eric V Anslyn
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States.
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln NE 65888, United States; Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln NE 68588, United States.
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6
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Baker BR, Ives CM, Bray A, Caffrey M, Cochrane SA. Undecaprenol kinase: Function, mechanism and substrate specificity of a potential antibiotic target. Eur J Med Chem 2020; 210:113062. [PMID: 33310291 DOI: 10.1016/j.ejmech.2020.113062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 10/22/2022]
Abstract
The bifunctional undecaprenol kinase/phosphatase (UdpK) is a small, prokaryotic, integral membrane kinase, homologous with Escherichia coli diacylglycerol kinase and expressed by the dgkA gene. In Gram-positive bacteria, UdpK is involved in the homeostasis of the bacterial undecaprenoid pool, where it converts undecaprenol to undecaprenyl phosphate (C55P) and also catalyses the reverse process. C55P is the universal lipid carrier and critical to numerous glycopolymer and glycoprotein biosynthetic pathways in bacteria. DgkA gene expression has been linked to facilitating bacterial growth and survival in response to environmental stressors, as well being implicated as a resistance mechanism to the topical antibiotic bacitracin, by providing an additional route to C55P. Therefore, identification of UdpK inhibitors could lead to novel antibiotic treatments. A combination of homology modelling and mutagenesis experiments on UdpK have been used to identify residues that may be involved in kinase/phosphatase activity. In this review, we will summarise recent work on the mechanism and substrate specificity of UdpK.
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Affiliation(s)
- Brad R Baker
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, UK
| | - Callum M Ives
- School of Medicine and School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160, Pearse Street, Dublin 2, D02 R590, Ireland; Division of Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Ashley Bray
- School of Medicine and School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160, Pearse Street, Dublin 2, D02 R590, Ireland
| | - Martin Caffrey
- School of Medicine and School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160, Pearse Street, Dublin 2, D02 R590, Ireland.
| | - Stephen A Cochrane
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, UK.
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7
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A Multichannel Pattern-Recognition-Based Protein Sensor with a Fluorophore-Conjugated Single-Stranded DNA Set. SENSORS 2020; 20:s20185110. [PMID: 32911729 PMCID: PMC7570997 DOI: 10.3390/s20185110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/04/2020] [Accepted: 09/05/2020] [Indexed: 12/16/2022]
Abstract
Recently, pattern-recognition-based protein sensing has received considerable attention because it offers unique opportunities that complement more conventional antibody-based detection methods. Here, we report a multichannel pattern-recognition-based sensor using a set of fluorophore-conjugated single-stranded DNAs (ssDNAs), which can detect various proteins. Three different fluorophore-conjugated ssDNAs were placed into a single microplate well together with a target protein, and the generated optical response pattern that corresponds to each environment-sensitive fluorophore was read via multiple detection channels. Multivariate analysis of the resulting optical response patterns allowed an accurate detection of eight different proteases, indicating that fluorescence signal acquisition from a single compartment containing a mixture of ssDNAs is an effective strategy for the characterization of the target proteins. Additionally, the sensor could identify proteins, which are potential targets for disease diagnosis, in a protease and inhibitor mixture of different composition ratios. As our sensor benefits from simple construction and measurement procedures, and uses accessible materials, it offers a rapid and simple platform for the detection of proteins.
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8
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Martynko E, Kirsanov D. Application of Chemometrics in Biosensing: A Review. BIOSENSORS 2020; 10:E100. [PMID: 32824611 PMCID: PMC7460467 DOI: 10.3390/bios10080100] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/12/2020] [Accepted: 08/14/2020] [Indexed: 12/17/2022]
Abstract
The field of biosensing is rapidly developing, and the number of novel sensor architectures and different sensing elements is growing fast. One of the most important features of all biosensors is their very high selectivity stemming from the use of bioreceptor recognition elements. The typical calibration of a biosensor requires simple univariate regression to relate a response value with an analyte concentration. Nevertheless, dealing with complex real-world sample matrices may sometimes lead to undesired interference effects from various components. This is where chemometric tools can do a good job in extracting relevant information, improving selectivity, circumventing a non-linearity in a response. This brief review aims to discuss the motivation for the application of chemometric tools in biosensing and provide some examples of such applications from the recent literature.
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Affiliation(s)
| | - Dmitry Kirsanov
- Applied Chemometrics Laboratory, Institute of Chemistry, St. Petersburg State University, St. Petersburg, 198504 Peterhoff, Russia;
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9
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Liu Q, Xia Q, Xiong Y, Li BS, Tang BZ. Circularly Polarized Luminescence and Tunable Helical Assemblies of Aggregation-Induced Emission Amphiphilic Polytriazole Carrying Chiral l-Phenylalanine Pendants. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c01140] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Qiuming Liu
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
- Guangdong Innovative Research Team, State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, Guangzhou 510640, China
- Hong Kong University of Science & Technology (HKUST)-Shenzhen Research Institute, No. 9 Yuexing 1st RD, South Area, Hi-tech Park, Nanshan, Shenzhen 518057, China
| | - Qing Xia
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Yu Xiong
- Guangdong Innovative Research Team, State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, Guangzhou 510640, China
| | - Bing Shi Li
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Ben Zhong Tang
- Guangdong Innovative Research Team, State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, Guangzhou 510640, China
- Hong Kong University of Science & Technology (HKUST)-Shenzhen Research Institute, No. 9 Yuexing 1st RD, South Area, Hi-tech Park, Nanshan, Shenzhen 518057, China
- Department of Chemistry, Institute for Advanced Study, Institute of Molecular Functional Materials and State Key Laboratory of Molecular Neuroscience, HKUST, Clear Water Bay, Kowloon, Hong Kong China
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10
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Hewitt SH, Macey G, Mailhot R, Elsegood MRJ, Duarte F, Kenwright AM, Butler SJ. Tuning the anion binding properties of lanthanide receptors to discriminate nucleoside phosphates in a sensing array. Chem Sci 2020; 11:3619-3628. [PMID: 34094050 PMCID: PMC8152522 DOI: 10.1039/d0sc00343c] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 03/10/2020] [Indexed: 12/30/2022] Open
Abstract
The development of synthetic receptors for the selective binding and discrimination of anions in water requires an understanding of how anions interact with these synthetic receptors. Molecules designed to differentiate nucleoside phosphate anions (e.g. ATP, ADP, GTP, GDP, UDP) under physiological conditions could underpin exciting new sensing tools for biomedical research and drug discovery, but it is very challenging due to the similarities in anion structure, size and charge. We present a series of lanthanide-based anion receptors and establish key structural elements that impact on nucleoside phosphate anion binding and sensing. Structural evidence of anion binding using X-ray crystallographic and NMR data, supported by DFT calculations indicate the binding modes between the lanthanide complexes and certain phosphoanions, revealing a bidentate (α-, γ-) binding mode to ATP. We further use four of the receptors to allow discrimination of eight nucleoside phosphate anions in the first array-based assay using lanthanide complexes, taking advantage of the multiple emission bands and long emission lifetimes associated with luminescent lanthanide complexes.
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Affiliation(s)
- Sarah H Hewitt
- Department of Chemistry, Loughborough University Epinal Way Loughborough LE11 3TU UK
| | - Georgina Macey
- Department of Chemistry, Loughborough University Epinal Way Loughborough LE11 3TU UK
| | - Romain Mailhot
- Department of Chemistry, Loughborough University Epinal Way Loughborough LE11 3TU UK
| | - Mark R J Elsegood
- Department of Chemistry, Loughborough University Epinal Way Loughborough LE11 3TU UK
| | - Fernanda Duarte
- Chemistry Research Laboratory, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Alan M Kenwright
- Department of Chemistry, Durham University South Road Durham DH1 3LE UK
| | - Stephen J Butler
- Department of Chemistry, Loughborough University Epinal Way Loughborough LE11 3TU UK
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11
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Zamora-Olivares D, Kaoud TS, Zeng L, Pridgen JR, Zhuang DL, Ekpo YE, Nye JR, Telles M, Anslyn EV, Dalby KN. Quantification of ERK Kinase Activity in Biological Samples Using Differential Sensing. ACS Chem Biol 2020; 15:83-92. [PMID: 31775004 DOI: 10.1021/acschembio.9b00580] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The understanding of complex biological systems requires an ability to evaluate interacting networks of genes, proteins, and cellular reactions. Enabling technologies that support the rapid quantification of these networks will facilitate the development of biological models and help to identify treatment targets and to assess treatment plans. The biochemical process of protein phosphorylation, which underlies almost all aspects of cell signaling, is typically evaluated by immunoblotting procedures (Western blot) or more recently proteomics procedures, which provide qualitative estimates of the concentration of proteins and their modifications in cells. However, protein modifications are difficult to correlate with activity, and while immunoblotting and proteomics approaches have the potential to be quantitative, they require a complex series of steps that diminish reproducibility. Here, a complementary approach is presented that allows for the rapid quantification of a protein kinase activity in cell lysates and tumor samples. Using the activity of cellular ERK (extracellular signal-regulated kinase) as a test case, an array sensing approach that utilizes a library of differential peptide-based biosensors and chemometric tools was used to rapidly quantify nanograms of active ERK in micrograms of unfractionated cell lysates and tumor extracts. This approach has the potential both for high-throughput and for quantifying the activities of multiple protein kinases in a single biological sample. The critical advantages of this differential sensing approach over others are that it removes the need for the addition of exogenous inhibitors to suppress the activities of major off-target kinases and allows us to quantitate the amount of active kinase in tested samples rather than measuring the changes in its activity upon induction or inhibition.
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Affiliation(s)
- Diana Zamora-Olivares
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Tamer S. Kaoud
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
- Medicinal Chemistry Department, Faculty of Pharmacy, Minia University, Minia 61519, Egypt
| | - Lingyu Zeng
- College of Chemistry and Molecular Science, Wuhan University, Wuhan, Hubei 430072, China
| | - Jacey R. Pridgen
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Deborah L. Zhuang
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Yakndara E. Ekpo
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jessica R. Nye
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Mitchell Telles
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Eric V. Anslyn
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Kevin N. Dalby
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, Texas 78712, United States
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12
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Kaoud TS, Johnson WH, Ebelt ND, Piserchio A, Zamora-Olivares D, Van Ravenstein SX, Pridgen JR, Edupuganti R, Sammons R, Cano M, Warthaka M, Harger M, Tavares CDJ, Park J, Radwan MF, Ren P, Anslyn EV, Tsai KY, Ghose R, Dalby KN. Modulating multi-functional ERK complexes by covalent targeting of a recruitment site in vivo. Nat Commun 2019; 10:5232. [PMID: 31745079 PMCID: PMC6863825 DOI: 10.1038/s41467-019-12996-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 10/10/2019] [Indexed: 12/31/2022] Open
Abstract
Recently, the targeting of ERK with ATP-competitive inhibitors has emerged as a potential clinical strategy to overcome acquired resistance to BRAF and MEK inhibitor combination therapies. In this study, we investigate an alternative strategy of targeting the D-recruitment site (DRS) of ERK. The DRS is a conserved region that lies distal to the active site and mediates ERK-protein interactions. We demonstrate that the small molecule BI-78D3 binds to the DRS of ERK2 and forms a covalent adduct with a conserved cysteine residue (C159) within the pocket and disrupts signaling in vivo. BI-78D3 does not covalently modify p38MAPK, JNK or ERK5. BI-78D3 promotes apoptosis in BRAF inhibitor-naive and resistant melanoma cells containing a BRAF V600E mutation. These studies provide the basis for designing modulators of protein-protein interactions involving ERK, with the potential to impact ERK signaling dynamics and to induce cell cycle arrest and apoptosis in ERK-dependent cancers.
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Affiliation(s)
- Tamer S Kaoud
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA.,Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt
| | - William H Johnson
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Nancy D Ebelt
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Andrea Piserchio
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY, USA
| | | | - Sabrina X Van Ravenstein
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Jacey R Pridgen
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Ramakrishna Edupuganti
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Rachel Sammons
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Micael Cano
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Mangalika Warthaka
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Matthew Harger
- Biomedical Engineering Department, The University of Texas at Austin, Austin, TX, USA
| | - Clint D J Tavares
- Department of Cancer Biology, Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Jihyun Park
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mohamed F Radwan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Pengyu Ren
- Biomedical Engineering Department, The University of Texas at Austin, Austin, TX, USA
| | - Eric V Anslyn
- Department of Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | | | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY, USA.,Graduate Programs in Biochemistry, Chemistry and Physics, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA.
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13
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Sasaki Y, Leclerc É, Hamedpour V, Kubota R, Takizawa SY, Sakai Y, Minami T. Simplest Chemosensor Array for Phosphorylated Saccharides. Anal Chem 2019; 91:15570-15576. [DOI: 10.1021/acs.analchem.9b03578] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Yui Sasaki
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
| | - Éric Leclerc
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
- CNRS UMI 2820, Laboratory for Integrated Micro Mechatronic Systems, Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
| | - Vahid Hamedpour
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
| | - Riku Kubota
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
| | - Shin-ya Takizawa
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Yasuyuki Sakai
- CNRS UMI 2820, Laboratory for Integrated Micro Mechatronic Systems, Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
- Center for International Research on Integrative Biomedical Systems, Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
| | - Tsuyoshi Minami
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
- CNRS UMI 2820, Laboratory for Integrated Micro Mechatronic Systems, Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
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14
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Liu Y, Peng S, Angelova L, Nau WM, Hennig A. Label-Free Fluorescent Kinase and Phosphatase Enzyme Assays with Supramolecular Host-Dye Pairs. ChemistryOpen 2019; 8:1350-1354. [PMID: 31741820 PMCID: PMC6848908 DOI: 10.1002/open.201900299] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Indexed: 12/21/2022] Open
Abstract
The combination of the macrocyclic hosts p-sulfonatocalix[4]arene and cucurbit[7]uril with the fluorescent dyes lucigenin and berberine affords two label-free enzyme assays for the detection of kinase and phosphatase activity by fluorescence monitoring. In contrast to established assays, no substrate labeling is required. Since phosphorylation is one of the most important regulatory mechanisms in biological signal transduction, the assays should be useful for identification of inhibitors and activators in high-throughput screening (HTS) format for drug discovery.
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Affiliation(s)
- Yan‐Cen Liu
- Department of Life Sciences and ChemistryJacobs University Bremen gGmbHCampus Ring 128759BremenGermany
| | - Shu Peng
- Department of Life Sciences and ChemistryJacobs University Bremen gGmbHCampus Ring 128759BremenGermany
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials, Ministry of EducationNankai UniversityTianjin300071 TianjinChina
| | - Lora Angelova
- Department of Life Sciences and ChemistryJacobs University Bremen gGmbHCampus Ring 128759BremenGermany
| | - Werner M. Nau
- Department of Life Sciences and ChemistryJacobs University Bremen gGmbHCampus Ring 128759BremenGermany
| | - Andreas Hennig
- Department of Life Sciences and ChemistryJacobs University Bremen gGmbHCampus Ring 128759BremenGermany
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15
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Beck JR, Cabral F, Rasineni K, Casey CA, Harris EN, Stains CI. A Panel of Protein Kinase Chemosensors Distinguishes Different Types of Fatty Liver Disease. Biochemistry 2019; 58:3911-3917. [PMID: 31433166 DOI: 10.1021/acs.biochem.9b00547] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The worldwide incidence of fatty liver disease continues to rise, which may account for concurrent increases in the frequencies of more aggressive liver ailments. Given the existence of histologically identical fatty liver disease subtypes, there is a critical need for the identification of methods that can classify disease and potentially predict progression. Herein, we show that a panel of protein kinase chemosensors can distinguish fatty liver disease subtypes. These direct activity measurements highlight distinct differences between histologically identical fatty liver diseases arising from diets rich in fat versus alcohol and identify a previously unreported decrease in p38α activity associated with a high-fat diet. In addition, we have profiled kinase activities in both benign (diet-induced) and progressive (STAM) disease models. These experiments provide temporal insights into kinase activity during disease development and progression. Altogether, this work provides the basis for the future development of clinical diagnostics and potential treatment strategies.
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Affiliation(s)
- Jon R Beck
- Department of Chemistry , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , United States
| | - Fatima Cabral
- Department of Biochemistry , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , United States
| | - Karuna Rasineni
- Division of Gastroenterology-Hepatology , University of Nebraska Medical Center , Omaha , Nebraska 68198 , United States.,Research Service, Veterans' Affairs , Nebraska-Western Iowa Health Care System , Omaha , Nebraska 68105 , United States
| | - Carol A Casey
- Division of Gastroenterology-Hepatology , University of Nebraska Medical Center , Omaha , Nebraska 68198 , United States.,Research Service, Veterans' Affairs , Nebraska-Western Iowa Health Care System , Omaha , Nebraska 68105 , United States.,Nebraska Center for Integrated Biomolecular Communication , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , United States
| | - Edward N Harris
- Department of Biochemistry , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , United States.,Nebraska Center for Integrated Biomolecular Communication , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , United States.,Cancer Genes and Molecular Regulation Program, Fred & Pamela Buffet Cancer Center , University of Nebraska Medical Center , Omaha , Nebraska 68198 , United States
| | - Cliff I Stains
- Department of Chemistry , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , United States.,Nebraska Center for Integrated Biomolecular Communication , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , United States.,Cancer Genes and Molecular Regulation Program, Fred & Pamela Buffet Cancer Center , University of Nebraska Medical Center , Omaha , Nebraska 68198 , United States.,Department of Chemistry , University of Virginia , Charlottesville , Virginia 22904 , United States
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16
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17
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Geng Y, Peveler WJ, Rotello VM. Array-based "Chemical Nose" Sensing in Diagnostics and Drug Discovery. Angew Chem Int Ed Engl 2019; 58:5190-5200. [PMID: 30347522 PMCID: PMC6800156 DOI: 10.1002/anie.201809607] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Indexed: 12/29/2022]
Abstract
Array-based sensor "chemical nose/tongue" platforms are inspired by the mammalian olfactory system. Multiple sensor elements in these devices selectively interact with target analytes, producing a distinct pattern of response and enabling analyte identification. This approach offers unique opportunities relative to "traditional" highly specific sensor elements such as antibodies. Array-based sensors excel at distinguishing small changes in complex mixtures, and this capability is being leveraged for chemical biology studies and clinical pathology, enabled by a diverse toolkit of new molecular, bioconjugate and nanomaterial technologies. Innovation in the design and analysis of arrays provides a robust set of tools for advancing biomedical goals, including precision medicine.
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Affiliation(s)
- Yingying Geng
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, 710 N. Pleasant St., Amherst MA 01003, U.S.A
- Department of Chemistry, University of Massachusetts Amherst, 710 N. Pleasant St., Amherst MA 01003, U.S.A
| | - William J. Peveler
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow G12 8LT, U.K
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Vincent M. Rotello
- Department of Chemistry, University of Massachusetts Amherst, 710 N. Pleasant St., Amherst MA 01003, U.S.A
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18
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Geng Y, Peveler WJ, Rotello VM. Array‐basierte Sensorik mit der “chemischen Nase” in der Diagnostik und Wirkstoffentdeckung. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201809607] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Yingying Geng
- Molecular and Cellular Biology ProgramUniversity of Massachusetts Amherst 710 N. Pleasant St. Amherst MA 01003 USA
- Department of ChemistryUniversity of Massachusetts Amherst 710 N. Pleasant St. Amherst MA 01003 USA
| | - William J. Peveler
- Division of Biomedical EngineeringSchool of EngineeringUniversity of Glasgow Glasgow G12 8LT Großbritannien
- Department of ChemistryUniversity of British Columbia 2036 Main Mall Vancouver British Columbia V6T 1Z1 Kanada
| | - Vincent M. Rotello
- Department of ChemistryUniversity of Massachusetts Amherst 710 N. Pleasant St. Amherst MA 01003 USA
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19
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Peveler WJ, Algar WR. More Than a Light Switch: Engineering Unconventional Fluorescent Configurations for Biological Sensing. ACS Chem Biol 2018; 13:1752-1766. [PMID: 29461796 DOI: 10.1021/acschembio.7b01022] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorescence is a powerful and sensitive tool in biological detection, used widely for cellular imaging and in vitro molecular diagnostics. Over time, three prominent conventions have emerged in the design of fluorescent biosensors: a sensor is ideally specific for its target, only one fluorescence signal turns on or off in response to the target, and each target requires its own sensor and signal combination. These are conventions but not requirements, and sensors that break with one or more of these conventions can offer new capabilities and advantages. Here, we review "unconventional" fluorescent sensor configurations based on fluorescent dyes, proteins, and nanomaterials such as quantum dots and metal nanoclusters. These configurations include multifluorophore Förster resonance energy transfer (FRET) networks, temporal multiplexing, photonic logic, and cross-reactive arrays or "noses". The more complex but carefully engineered biorecognition and fluorescence signaling modalities in unconventional designs are richer in information, afford greater multiplexing capacity, and are potentially better suited to the analysis of complex biological samples, interactions, processes, and diseases. We conclude with a short perspective on the future of unconventional fluorescent sensors and encourage researchers to imagine sensing beyond the metaphorical light bulb and light switch combination.
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Affiliation(s)
- William J. Peveler
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow G12 8LT, U.K
| | - W. Russ Algar
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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20
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Sasaki Y, Minamiki T, Tokito S, Minami T. A molecular self-assembled colourimetric chemosensor array for simultaneous detection of metal ions in water. Chem Commun (Camb) 2018; 53:6561-6564. [PMID: 28574558 DOI: 10.1039/c7cc03218h] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We propose a novel strategy for a high-throughput sensing of metal ions using a molecular self-assembled colourimetric chemosensor array. The proposed colourimetric assay has been achieved by only using the combination of commercially available materials. Importantly, the easy-to-prepare assay can be utilised to quantitatively detect metal ions under competitive conditions.
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Affiliation(s)
- Yui Sasaki
- Institute of Industrial Science, the University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan.
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21
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Pode Z, Peri-Naor R, Georgeson JM, Ilani T, Kiss V, Unger T, Markus B, Barr HM, Motiei L, Margulies D. Protein recognition by a pattern-generating fluorescent molecular probe. NATURE NANOTECHNOLOGY 2017; 12:1161-1168. [PMID: 29035400 DOI: 10.1038/nnano.2017.175] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 07/25/2017] [Indexed: 06/07/2023]
Abstract
Fluorescent molecular probes have become valuable tools in protein research; however, the current methods for using these probes are less suitable for analysing specific populations of proteins in their native environment. In this study, we address this gap by developing a unimolecular fluorescent probe that combines the properties of small-molecule-based probes and cross-reactive sensor arrays (the so-called chemical 'noses/tongues'). On the one hand, the probe can detect different proteins by generating unique identification (ID) patterns, akin to cross-reactive arrays. On the other hand, its unimolecular scaffold and selective binding enable this ID-generating probe to identify combinations of specific protein families within complex mixtures and to discriminate among isoforms in living cells, where macroscopic arrays cannot access. The ability to recycle the molecular device and use it to track several binding interactions simultaneously further demonstrates how this approach could expand the fluorescent toolbox currently used to detect and image proteins.
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Affiliation(s)
- Zohar Pode
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ronny Peri-Naor
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Joseph M Georgeson
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tal Ilani
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Vladimir Kiss
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tamar Unger
- Israel Structural Proteomics Center, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Barak Markus
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Haim M Barr
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Leila Motiei
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - David Margulies
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
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22
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Hatai J, Motiei L, Margulies D. Analyzing Amyloid Beta Aggregates with a Combinatorial Fluorescent Molecular Sensor. J Am Chem Soc 2017; 139:2136-2139. [DOI: 10.1021/jacs.6b10809] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Joydev Hatai
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Leila Motiei
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - David Margulies
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
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23
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Shi L, Li X, Zhou M, Muhammad F, Ding Y, Wei H. An arylboronate locked fluorescent probe for hypochlorite. Analyst 2017; 142:2104-2108. [DOI: 10.1039/c7an00467b] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
An unusual arylboronate based fluorescent probeR1was synthesized for the selective and sensitive detection of ClO−.
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Affiliation(s)
- Leilei Shi
- Department of Biomedical Engineering
- College of Engineering and Applied Sciences
- Collaborative Innovation Center of Chemistry for Life Sciences
- Nanjing National Laboratory of Microstructures
- Nanjing University
| | - Xin Li
- Division of Theoretical Chemistry and Biology
- School of Biotechnology
- KTH Royal Institute of Technology
- SE-10691 Stockholm
- Sweden
| | - Min Zhou
- Department of Biomedical Engineering
- College of Engineering and Applied Sciences
- Collaborative Innovation Center of Chemistry for Life Sciences
- Nanjing National Laboratory of Microstructures
- Nanjing University
| | - Faheem Muhammad
- Department of Biomedical Engineering
- College of Engineering and Applied Sciences
- Collaborative Innovation Center of Chemistry for Life Sciences
- Nanjing National Laboratory of Microstructures
- Nanjing University
| | - Yubin Ding
- Department of Biomedical Engineering
- College of Engineering and Applied Sciences
- Collaborative Innovation Center of Chemistry for Life Sciences
- Nanjing National Laboratory of Microstructures
- Nanjing University
| | - Hui Wei
- Department of Biomedical Engineering
- College of Engineering and Applied Sciences
- Collaborative Innovation Center of Chemistry for Life Sciences
- Nanjing National Laboratory of Microstructures
- Nanjing University
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Abstract
Sensing using specific and selective receptors provides two very different but complementary strategies. This Sensor Issues article will discuss the merits and challenges of specific sensors, and selective sensors based on synthetic arrays. We will examine where each has been successfully applied to a sensing challenge, and then look at how a combined approach could take elements of both to provide new sensor platforms.
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Affiliation(s)
- William J. Peveler
- Department
of Chemistry, University College London, London, WC1H 0AJ, United Kingdom
| | - Mahdieh Yazdani
- Department
of Chemistry, University of Massachusetts Amherst, 710 North Pleasant
Street, Amherst, Massachusetts 01003, United States
| | - Vincent M. Rotello
- Department
of Chemistry, University of Massachusetts Amherst, 710 North Pleasant
Street, Amherst, Massachusetts 01003, United States
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25
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Tomita S, Niwa O, Kurita R. Artificial Modification of an Enzyme for Construction of Cross-Reactive Polyion Complexes To Fingerprint Signatures of Proteins and Mammalian Cells. Anal Chem 2016; 88:9079-86. [DOI: 10.1021/acs.analchem.6b02010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Shunsuke Tomita
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, and DAILAB, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Osamu Niwa
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, and DAILAB, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
- Advanced
Science Research Laboratory, Saitama Institute of Technology, 1690 Fusaiji, Fukaya, Saitama 369-0293, Japan
| | - Ryoji Kurita
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, and DAILAB, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
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26
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Gu K, Xu Y, Li H, Guo Z, Zhu S, Zhu S, Shi P, James TD, Tian H, Zhu WH. Real-Time Tracking and In Vivo Visualization of β-Galactosidase Activity in Colorectal Tumor with a Ratiometric Near-Infrared Fluorescent Probe. J Am Chem Soc 2016; 138:5334-40. [DOI: 10.1021/jacs.6b01705] [Citation(s) in RCA: 357] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
| | | | - Hui Li
- Department
of Radiology, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai 200233, China
| | | | | | | | | | - Tony D. James
- Department
of Chemistry, University of Bath, Bath BA2 7AY, United Kingdom
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27
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Minami T, Minamiki T, Tokito S. Electric Detection of Phosphate Anions in Water by an Extended-gate-type Organic Field-effect Transistor Functionalized with a Zinc(II)–Dipicolylamine Derivative. CHEM LETT 2016. [DOI: 10.1246/cl.151193] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Tsuyoshi Minami
- Research Center for Organic Electronics, Graduate School of Science and Engineering, Yamagata University
| | - Tsukuru Minamiki
- Research Center for Organic Electronics, Graduate School of Science and Engineering, Yamagata University
| | - Shizuo Tokito
- Research Center for Organic Electronics, Graduate School of Science and Engineering, Yamagata University
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28
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Akdeniz A, Minami T, Watanabe S, Yokoyama M, Ema T, Anzenbacher P. Determination of enantiomeric excess of carboxylates by fluorescent macrocyclic sensors. Chem Sci 2016; 7:2016-2022. [PMID: 29899926 PMCID: PMC5968554 DOI: 10.1039/c5sc04235f] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 12/09/2015] [Indexed: 12/15/2022] Open
Abstract
Chiral fluorescent chemosensors featuring macrocycles comprising BINOL auxiliary and an array of hydrogen bond donors were synthesized. To enhance fluorescence of the chemosensors, conjugated moieties were attached to the 3,3'-positions of the BINOL auxiliary. The resulting chemosensors recognize a number of carboxylates, namely, enantiomers of ibuprofen, ketoprofen, 2-phenylpropanoate, mandelate, and phenylalanine in a stereoselective fashion. Depending on the structure of the chemosensor, the presence of carboxylate yields fluorescence quenching or amplification. This information-rich signal can be used to determine the identity of the analyte including the sense of chirality. Quantitative experiments were performed aimed at analysis of enantiomeric excess of chiral carboxylates. The quantitative analysis of enantiomeric composition of ibuprofen, ketoprofen, and phenylalanine shows that the sensors correctly identify mixtures with varying enantiomeric excess and correctly predict the enantiomeric excess of unknown samples with error of prediction <1.6%.
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Affiliation(s)
- Ali Akdeniz
- Department of Chemistry and Center for Photochemical Sciences , Bowling Green State University , Bowling Green , Ohio 43403 , USA .
| | - Tsuyoshi Minami
- Department of Chemistry and Center for Photochemical Sciences , Bowling Green State University , Bowling Green , Ohio 43403 , USA .
| | - Sagiri Watanabe
- Division of Applied Chemistry , Graduate School of Natural Science and Technology , Okayama University , Tsushima , Okayama 700-8530 , Japan .
| | - Maki Yokoyama
- Division of Applied Chemistry , Graduate School of Natural Science and Technology , Okayama University , Tsushima , Okayama 700-8530 , Japan .
| | - Tadashi Ema
- Division of Applied Chemistry , Graduate School of Natural Science and Technology , Okayama University , Tsushima , Okayama 700-8530 , Japan .
| | - Pavel Anzenbacher
- Department of Chemistry and Center for Photochemical Sciences , Bowling Green State University , Bowling Green , Ohio 43403 , USA .
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29
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Anslyn EV. Art, auto-mechanics, and supramolecular chemistry. A merging of hobbies and career. Beilstein J Org Chem 2016; 12:362-76. [PMID: 26977197 PMCID: PMC4778509 DOI: 10.3762/bjoc.12.40] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 02/12/2016] [Indexed: 12/24/2022] Open
Abstract
While the strict definition of supramolecular chemistry is "chemistry beyond the molecule", meaning having a focus on non-covalent interactions, the field is primarily associated with the creation of synthetic receptors and self-assembly. For synthetic ease, the receptors and assemblies routinely possess a high degree of symmetry, which lends them an aspect of aesthetic beauty. Pictures of electron orbitals similarly can be seen as akin to works of art. This similarity was an early draw for me to the fields of supramolecular chemistry and molecular orbital theory, because I grew up in a household filled with art. In addition to art, my childhood was filled with repairing and constructing mechanical entities, such as internal combustion motors, where many components work together to achieve a function. Analogously, the field of supramolecular chemistry creates systems of high complexity that achieve functions or perform tasks. Therefore, in retrospect a career in supramolecular chemistry appears to be simply an extension of childhood hobbies involving art and auto-mechanics.
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Affiliation(s)
- Eric V Anslyn
- Department of Chemistry, University of Texas, Austin, TX 78712, USA
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Han J, Bender M, Hahn S, Seehafer K, Bunz UHF. Polyelectrolyte Complexes Formed from Conjugated Polymers: Array-Based Sensing of Organic Acids. Chemistry 2016; 22:3230-3233. [DOI: 10.1002/chem.201504447] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Jinsong Han
- Organisch-Chemisches Institut; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Markus Bender
- Organisch-Chemisches Institut; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Sebastian Hahn
- Organisch-Chemisches Institut; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Kai Seehafer
- Organisch-Chemisches Institut; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Uwe H. F. Bunz
- Organisch-Chemisches Institut; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 270 69120 Heidelberg Germany
- Center of Advanced Materials; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 225 69120 Heidelberg Germany
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31
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Beck JR, Lawrence A, Tung AS, Harris EN, Stains CI. Interrogating Endogenous Protein Phosphatase Activity with Rationally Designed Chemosensors. ACS Chem Biol 2016; 11:284-90. [PMID: 26580981 DOI: 10.1021/acschembio.5b00506] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We introduce a versatile approach for repurposing protein kinase chemosensors, containing the phosphorylation-sensitive sulfonamido-oxine fluorophore termed Sox, for the specific determination of endogenous protein phosphatase activity from whole cell lysates and tissue homogenates. As a demonstration of this approach, we design and evaluate a direct chemosensor for protein tyrosine phosphatase-1B (PTP1B), an established signaling node in human disease. The optimal sensor design is capable of detecting as little as 6 pM (12 pg) full-length recombinant PTP1B and is remarkably selective for PTP1B among a panel of highly homologous tyrosine phosphatases. Coupling this robust activity probe with the specificity of antibodies allowed for the temporal analysis of endogenous PTP1B activity dynamics in lysates generated from HepG2 cells after stimulation with insulin. Lastly, we leveraged this assay format to profile PTP1B activity perturbations in a rat model of nonalcoholic fatty liver disease (NAFLD), providing direct evidence for elevated PTP1B catalytic activity in this disease state. Given the modular nature of this assay, we anticipate that this approach will have broad utility in monitoring phosphatase activity dynamics in human disease states.
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Affiliation(s)
- Jon R. Beck
- Department
of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Antoneal Lawrence
- Department
of Chemistry, Lincoln University, Lincoln University, Pennsylvania 19352, United States
| | - Amar S. Tung
- Department
of Chemistry, Lincoln University, Lincoln University, Pennsylvania 19352, United States
| | - Edward N. Harris
- Department
of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Cliff I. Stains
- Department
of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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Tomita S, Sakao M, Kurita R, Niwa O, Yoshimoto K. A polyion complex sensor array for markerless and noninvasive identification of differentiated mesenchymal stem cells from human adipose tissue. Chem Sci 2015; 6:5831-5836. [PMID: 28970874 PMCID: PMC5618151 DOI: 10.1039/c5sc01259g] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 06/29/2015] [Indexed: 12/12/2022] Open
Abstract
Currently available methods for stem cell evaluation require both prior knowledge of specific markers and invasive cell lysis or staining, hampering the development of stem cell products with assured safety and quality. Here, we present a strategy using optical cross-reactive sensor arrays for markerless and noninvasive identification of differentiated stem cell lineages with common laboratory equipment. The sensor array consists of a library of polyion complexes (PICs) between anionic enzymes and synthetic poly(ethylene glycol)-modified polyamines, which can recognize "secretomic signatures" in cell culture supernatants. Due to the reversible nature of PIC formation, the incubation of diluted culture supernatants with PICs caused enzyme release through competitive interactions between the secreted molecules and the PICs, generating unique patterns of recovery in enzyme activity for individual cell types or lineages. Linear discriminant analysis of the patterns allowed not only normal/cancer cell discrimination but also lineage identification of osteogenic and adipogenic differentiation of human mesenchymal stem cells, therefore providing an effective way to characterize cultured cells in the fields of regenerative medicine, tissue engineering and cell biology.
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Affiliation(s)
- Shunsuke Tomita
- Biomedical Research Institute , National Institute of Advanced Industrial Science and Technology , 1-1-1 Higashi , Tsukuba , Ibaraki 305-8566 , Japan .
| | - Miho Sakao
- College of Arts and Sciences , The University of Tokyo , 3-8-1 Komaba , Meguro , Tokyo 153-8902 , Japan .
| | - Ryoji Kurita
- Biomedical Research Institute , National Institute of Advanced Industrial Science and Technology , 1-1-1 Higashi , Tsukuba , Ibaraki 305-8566 , Japan .
| | - Osamu Niwa
- Biomedical Research Institute , National Institute of Advanced Industrial Science and Technology , 1-1-1 Higashi , Tsukuba , Ibaraki 305-8566 , Japan .
| | - Keitaro Yoshimoto
- College of Arts and Sciences , The University of Tokyo , 3-8-1 Komaba , Meguro , Tokyo 153-8902 , Japan .
- Department of Life Sciences , Graduate School of Arts and Sciences , The University of Tokyo , 3-8-1 Komaba , Meguro , Tokyo 153-8902 , Japan
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Xu Q, Zhang Y, Zhang CY. A triple-color fluorescent probe for multiple nuclease assays. Chem Commun (Camb) 2015; 51:9121-4. [DOI: 10.1039/c5cc02177d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We develop a triple-color fluorescent probe which may function as a lab-on-a-DNA-molecule for simultaneous detection of multiple nucleases.
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Affiliation(s)
- Qinfeng Xu
- Single-Molecule Detection and Imaging Laboratory
- Shenzhen Institutes of Advanced Technology
- Chinese Academy of Sciences
- Shenzhen 518055
- China
| | - Yihong Zhang
- Single-Molecule Detection and Imaging Laboratory
- Shenzhen Institutes of Advanced Technology
- Chinese Academy of Sciences
- Shenzhen 518055
- China
| | - Chun-yang Zhang
- Single-Molecule Detection and Imaging Laboratory
- Shenzhen Institutes of Advanced Technology
- Chinese Academy of Sciences
- Shenzhen 518055
- China
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