1
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Sasmal M, Islam ASM, Moni D, Katarkar A, Ali M. A microenvironment-sensitive red emissive probe with a large Stokes shift for specific recognition and quantification of serum albumin in complex biofluids and live cells. J Mater Chem B 2024; 12:4478-4488. [PMID: 38629135 DOI: 10.1039/d3tb02985a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2024]
Abstract
Human serum albumin (HSA) is regarded as a useful biomarker for rapid medical diagnosis of various disorders mainly related to the kidneys and liver. Hence, it is crucial to identify and monitor the HSA level in complex biofluids (urine and blood samples) using a simple approach. Herein, we have designed and synthesized an intramolecular charge transfer (ICT) based environment-sensitive fluorescent molecular probe, (E)-2-(3-(2-(5-methoxy-1H-indol-3-yl)vinyl)-5,5-dimethylcyclohex-2-en-1-ylidene)malononitrile (DCI-MIN), that can selectively interact with HSA in PBS buffer solution and exhibit a ∼78-fold enhancement in fluorescence intensity with a significant Stokes shift (∼126 nm), which is important to avoid interference from the excitation light. The significant red fluorescence response can be attributed to the suppression of free intramolecular rotation of the DCI-MIN probe inside the hydrophobic binding cavity of HSA and the low polar microenvironment present within HSA. According to the 3σ/slope method, the detection limit was found to be 1.01 nM (0.0671 mg L-1) in aqueous solutions, which is significantly lower than the normal level of HSA in healthy urine and blood serum, indicating its high sensitivity. DCI-MIN has the ability to exhibit useful applications, including the detection and quantification of HSA concentration in complex biofluids (human urine and blood samples) as well as the imaging of serum albumin in living cells.
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Affiliation(s)
- Mihir Sasmal
- Department of Chemistry, Jadavpur University, Kolkata 700 032, India.
| | - Abu Saleh Musha Islam
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Kolkata 700032, India
| | - Dolan Moni
- Department of Chemistry, Jadavpur University, Kolkata 700 032, India.
| | - Atul Katarkar
- Department of Biochemistry, University of Lausanne, Ch. des Boveresses 155, 1066 Epalinges, Switzerland
| | - Mahammad Ali
- Department of Chemistry, Jadavpur University, Kolkata 700 032, India.
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2
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Clarke R, Zeng L, Atkinson BC, Kadodwala M, Thomson AR, Sutherland A. Fluorescent carbazole-derived α-amino acids: structural mimics of tryptophan. Chem Sci 2024; 15:5944-5949. [PMID: 38665535 PMCID: PMC11040653 DOI: 10.1039/d4sc01173b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024] Open
Abstract
Fluorescent tags are commonly used for imaging of proteins and peptides during biological events; however, the large size of dyes can disrupt protein structure and function, and typically require the use of a chemical spacer. Herein, we report the synthesis of a new class of fluorescent unnatural α-amino acid, containing carbazole side-chains designed to mimic l-tryptophan and thus, readily incorporated into peptides. The amino acids were constructed using a Negishi cross-coupling reaction as the key step and exhibited strong fluorescent emission, with high quantum yields in both organic solvents and water. Compatible with solid phase peptide synthesis, the carbazole amino acids were used to replace tryptophan in a β-hairpin model peptide and shown to be a close structural mimic with retention of conformation. They were also found to be effective fluorescent molecular reporters for biological events. Incorporation into a proline-rich ligand of the WW domain protein demonstrated that the fluorescent properties of a carbazole amino acid could be used to measure the protein-protein binding interaction of this important biological signalling process.
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Affiliation(s)
- Rebecca Clarke
- School of Chemistry, University of Glasgow Joseph Black Building, University Avenue Glasgow G12 8QQ UK
| | - Liyao Zeng
- School of Chemistry, University of Glasgow Joseph Black Building, University Avenue Glasgow G12 8QQ UK
| | - Bethany C Atkinson
- School of Chemistry, University of Glasgow Joseph Black Building, University Avenue Glasgow G12 8QQ UK
| | - Malcolm Kadodwala
- School of Chemistry, University of Glasgow Joseph Black Building, University Avenue Glasgow G12 8QQ UK
| | - Andrew R Thomson
- School of Chemistry, University of Glasgow Joseph Black Building, University Avenue Glasgow G12 8QQ UK
| | - Andrew Sutherland
- School of Chemistry, University of Glasgow Joseph Black Building, University Avenue Glasgow G12 8QQ UK
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3
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Suss O, Halfin O, Porat Z, Fridmann Sirkis Y, Motiei L, Margulies D. Artificial Protein Crosstalk with a Molecule that Exchanges Binding Partners. Angew Chem Int Ed Engl 2024; 63:e202312461. [PMID: 38010219 DOI: 10.1002/anie.202312461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 11/29/2023]
Abstract
Drawing inspiration from allosteric signaling enzymes, whose catalytic and regulatory units are non-covalently linked, we have devised a method to establish unnatural, effector-mediated enzyme activation within native cells. The feasibility of this approach is demonstrated by introducing a synthetic regulatory unit (sRU) onto glycogen synthase kinase 3 (GSK-3) through non-covalent means. Our study reveals that this synthetic regulator mediates an unnatural crosstalk between GSK-3 and lactate dehydrogenase A (LDHA), whose expression is regulated by cellular oxygen levels. Specifically, with this approach, the constitutively active GSK-3 is transformed into an activable enzyme, whereas LDHA is repurposed as an unnatural effector protein that controls the activity of the kinase, making it unnaturally dependent on the cell's hypoxic response. These findings demonstrate a step toward imitating the function of effector-regulated cell-signaling enzymes, which play a key biological role in mediating the response of cells to changes in their environment. In addition, at the proof-of-principle level, our results indicate the potential to develop a new class of protein inhibitors whose inhibitory effect in cells is dictated by the cell's environment and consequent protein expression profile.
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Affiliation(s)
- Ohad Suss
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Olga Halfin
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ziv Porat
- Flow Cytometry Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Yael Fridmann Sirkis
- Protein Analysis Unit, 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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Songsri S, Harkiss AH, Sutherland A. Synthesis and Photophysical Properties of Charge-Transfer-Based Pyrimidine-Derived α-Amino Acids. J Org Chem 2023; 88:13214-13224. [PMID: 37621156 PMCID: PMC10507667 DOI: 10.1021/acs.joc.3c01437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Indexed: 08/26/2023]
Abstract
The four-step synthesis of fluorescent pyrimidine-derived α-amino acids from an l-aspartic acid derivative is described. The key synthetic steps involved preparation of ynone intermediates via the reaction of alkynyl lithium salts with a Weinreb amide, followed by an ytterbium-catalyzed heterocyclization reaction with amidines. Variation of substituents at the C2- and C4-position of the pyrimidine ring allowed tuning of the photoluminescent properties of the α-amino acids. This revealed that a combination of highly conjugated or electron-rich aryl substituents with the π-deficient pyrimidine motif resulted in fluorophores with the highest quantum yields and overall brightness. Further analysis of the most fluorogenic α-amino acid demonstrated solvatochromism and sensitivity to pH.
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Affiliation(s)
- Sineenard Songsri
- School of Chemistry, The Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Alexander H. Harkiss
- School of Chemistry, The Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Andrew Sutherland
- School of Chemistry, The Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom
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5
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McGrory R, Clarke R, Marshall O, Sutherland A. Fluorescent α-amino acids via Heck-Matsuda reactions of phenylalanine-derived arenediazonium salts. Org Biomol Chem 2023; 21:6932-6939. [PMID: 37580965 DOI: 10.1039/d3ob01096a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
The Heck-Matsuda coupling reaction of arenediazonium salts derived from L-phenylalanine with various alkenes has been developed. A two-step process involving the preparation of a tetrafluoroborate diazonium salt from a 4-aminophenylalanine derivative, followed by a palladium(0)-catalysed Heck-Matsuda coupling reaction allowed access to a range of unnatural α-amino acids with cinnamate, vinylsulfone and stilbene side-chains. Analysis of the photophysical properties of these unnatural α-amino acids demonstrated that the (E)-stilbene analogues exhibited fluorescent properties with red-shifted absorption and emission spectra and larger quantum yields than L-phenylalanine.
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Affiliation(s)
- Rochelle McGrory
- School of Chemistry, University of Glasgow, The Joseph Black Building, Glasgow, G12 8QQ, UK.
| | - Rebecca Clarke
- School of Chemistry, University of Glasgow, The Joseph Black Building, Glasgow, G12 8QQ, UK.
| | - Olivia Marshall
- School of Chemistry, University of Glasgow, The Joseph Black Building, Glasgow, G12 8QQ, UK.
| | - Andrew Sutherland
- School of Chemistry, University of Glasgow, The Joseph Black Building, Glasgow, G12 8QQ, UK.
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6
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McGrory R, Morgan DC, Jamieson AG, Sutherland A. Rotamer-Controlled Dual Emissive α-Amino Acids. Org Lett 2023; 25:5844-5849. [PMID: 37506290 PMCID: PMC10425982 DOI: 10.1021/acs.orglett.3c02112] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Indexed: 07/30/2023]
Abstract
The synthesis and photoluminescent properties of novel α-amino acids are described in which the biaryl benzotriazinone-containing chromophores were found to display dual emission fluorescence via locally excited (LE) and twisted intramolecular charge transfer (TICT) states. The intensity of each emission band could be controlled by the electronics and position of the substituents, and this led to the design of a 2-methoxyphenyl analogue that, due to twisting, displayed bright TICT fluorescence, solvatochromism, and pH sensitivity.
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Affiliation(s)
- Rochelle McGrory
- School
of Chemistry, The Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, United
Kingdom
| | - Danielle C. Morgan
- School
of Chemistry, Advanced Research Centre, University of Glasgow, Glasgow G11 6EW, United
Kingdom
| | - Andrew G. Jamieson
- School
of Chemistry, Advanced Research Centre, University of Glasgow, Glasgow G11 6EW, United
Kingdom
| | - Andrew Sutherland
- School
of Chemistry, The Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, United
Kingdom
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7
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Abuhasan OM, El-Barghouthi MI, Bodoor K, Rawashdeh AMM, Assaf KI. Molecular recognition of tripeptides containing tryptophan by cucurbit[8]uril: A computational study. ARAB J CHEM 2023. [DOI: 10.1016/j.arabjc.2023.104819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
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8
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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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9
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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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10
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Saibu OA, Hammed SO, Oladipo OO, Odunitan TT, Ajayi TM, Adejuyigbe AJ, Apanisile BT, Oyeneyin OE, Oluwafemi AT, Ayoola T, Olaoba OT, Alausa AO, Omoboyowa DA. Protein-protein interaction and interference of carcinogenesis by supramolecular modifications. Bioorg Med Chem 2023; 81:117211. [PMID: 36809721 DOI: 10.1016/j.bmc.2023.117211] [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: 10/25/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/18/2023]
Abstract
Protein-protein interactions (PPIs) are essential in normal biological processes, but they can become disrupted or imbalanced in cancer. Various technological advancements have led to an increase in the number of PPI inhibitors, which target hubs in cancer cell's protein networks. However, it remains difficult to develop PPI inhibitors with desired potency and specificity. Supramolecular chemistry has only lately become recognized as a promising method to modify protein activities. In this review, we highlight recent advances in the use of supramolecular modification approaches in cancer therapy. We make special note of efforts to apply supramolecular modifications, such as molecular tweezers, to targeting the nuclear export signal (NES), which can be used to attenuate signaling processes in carcinogenesis. Finally, we discuss the strengths and weaknesses of using supramolecular approaches to targeting PPIs.
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Affiliation(s)
- Oluwatosin A Saibu
- Department of Environmental Toxicology, Universitat Duisburg-Essen, NorthRhine-Westphalia, Germany
| | - Sodiq O Hammed
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria; Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Oladapo O Oladipo
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria.
| | - Tope T Odunitan
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria; Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Temitope M Ajayi
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Aderonke J Adejuyigbe
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Boluwatife T Apanisile
- Department of Nutrition and Dietetics, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Oluwatoba E Oyeneyin
- Theoretical and Computational Chemistry Unit, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
| | - Adenrele T Oluwafemi
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Tolulope Ayoola
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Olamide T Olaoba
- Department of Molecular Pathogenesis and Therapeutics, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Abdullahi O Alausa
- Department of Molecular Biology and Biotechnology, ITMO University, St Petersburg, Russia
| | - Damilola A Omoboyowa
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
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11
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Abstract
The genetically encoded fluorescent sensors convert chemical and physical signals into light. They are powerful tools for the visualisation of physiological processes in living cells and freely moving animals. The fluorescent protein is the reporter module of a genetically encoded biosensor. In this study, we first review the history of the fluorescent protein in full emission spectra on a structural basis. Then, we discuss the design of the genetically encoded biosensor. Finally, we briefly review several major types of genetically encoded biosensors that are currently widely used based on their design and molecular targets, which may be useful for the future design of fluorescent biosensors.
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Affiliation(s)
- Minji Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yifan Da
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
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12
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Zheng Z, Yuan L, Hu JJ, Xia F, Lou X. Modular Peptide Probe for Protein Analysis. Chemistry 2023; 29:e202203225. [PMID: 36333271 DOI: 10.1002/chem.202203225] [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: 10/15/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/07/2022]
Abstract
The analysis and regulation of proteins are of great significance for the development of disease diagnosis and treatment. However, complicated analytical environment and complex protein structure severely limit the accuracy of their analysis results. Nowadays, ascribing to the editability and bioactivity of peptides, peptide-based probes could meet the requirements of good selectivity and high affinity to overcome the challenges. In this review, we summarize the advances in the use of modular peptide probes for proteins analysis. It focuses on how to design and optimize the structure of probes, as well as their performance. Then, the strategies and application to improve the analysis result of modular peptide probes are introduced. Finally, we also discuss current challenge and provide some ideas for the future direction for modular peptide probes, hoping to accelerate their clinical transformation.
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Affiliation(s)
- Zhi Zheng
- State Key Laboratory of Biogeology and Environmental Geology Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Lizhen Yuan
- State Key Laboratory of Biogeology and Environmental Geology Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Jing-Jing Hu
- State Key Laboratory of Biogeology and Environmental Geology Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Xiaoding Lou
- State Key Laboratory of Biogeology and Environmental Geology Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
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13
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Riley L, Mclay TN, Sutherland A. Synthesis and Fluorescent Properties of Alkynyl- and Alkenyl-Fused Benzotriazole-Derived α-Amino Acids. J Org Chem 2023; 88:2453-2463. [PMID: 36749161 PMCID: PMC9942204 DOI: 10.1021/acs.joc.2c02886] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Fluorescent unnatural α-amino acids are widely used as probes in chemical biology and medicinal chemistry. While a variety of structural classes have been developed, there is still a requirement for new environmentally sensitive analogues that can closely mimic proteinogenic α-amino acids. Here, we report the synthesis and fluorescent properties of highly conjugated, benzotriazole-derived α-amino acids designed to mimic l-tryptophan. Alkynyl-substituted analogues were prepared using three key steps, nucleophilic aromatic substitution with a 3-aminoalanine derivative, benzotriazole formation via a one-pot diazotization and cyclization process, and a Sonogashira cross-coupling reaction. E-Alkenyl-substituted benzotriazoles were accessed by stereoselective partial hydrogenation of the alkynes using zinc iodide and palladium catalysis. The alkynyl analogues were found to possess higher quantum yields and stronger brightness and, a solvatochromic study with the most fluorogenic α-amino acids demonstrated sensitivity to polarity.
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14
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Sasmal M, Musha Islam AS, Moni D, Maiti D, Dutta A, Ali M. Serum Albumin Inspired Self-Assembly/Disassembly of a Fluorogenic Nanoprobe for Real-Time Monitoring and Quantification of Urinary Albumin with Live Cell Imaging Application. ACS APPLIED BIO MATERIALS 2022; 5:5854-5864. [PMID: 36441947 DOI: 10.1021/acsabm.2c00820] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Abnormal levels (high/low) of urinary human serum albumin (HSA) are associated with a number of diseases and thus act as an essential biomarker for quick therapeutic monitoring and biomedical diagnosis, entailing the urgent development of an effective chemosensor to quantify the albumin levels. Herein, we have rationally designed and developed a small fluorogenic molecular probe, (Z)-2-(5-((8-hydroxy-2,3,6,7-tetrahydro-1H,5H-pyrido[3,2,1-ij]quinolin-9-yl) methylene)-4-oxo-2-thioxothiazolidin-3-yl) acetic acid (HJRA) with a twisted intramolecular charge transfer (TICT) property, which can easily self-assemble into nonfluorescent nanoaggregates in aqueous solution. However, HJRA nanoaggregates can selectively bind with serum albumin proteins (HSA/BSA) in ∼100% PBS medium, thereby facilitating the disassembly of nanoaggregates into monomers, exhibiting a clear turn-on red fluorescent response toward HSA and BSA. Analysis of the specific binding mechanism between HJRA and HSA using a site-selective fluorescence displacement assay and molecular docking simulations indicates that a variety of noncovalent interactions are responsible for the disassembly of nanoaggregates with the concomitant trapping of the HJRA monomer at site I in HSA, yielding a substantial red emission caused by the inhibition of intramolecular rotation of HJRA probe inside the hydrophobic cavity of HSA. The limit of detection (LOD) determined by the 3σ/slope method was found to be 1.13 nM, which is substantially below the normal HSA concentration level in healthy urine, signifying the very high sensitivity of the probe toward HSA. The comparable results and quick response toward quantification of HSA in urine by HJRA with respect to the Bradford method clearly point toward the superiority of this method compared to the existing ones and may lead to biomedical applications for HSA quantification in urine. It may also find potential application in live-cell imaging of HSA.
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Affiliation(s)
- Mihir Sasmal
- Department of Chemistry, Jadavpur University, 188, Raja S. C. Mullick Road, Kolkata700 032, India
| | - Abu Saleh Musha Islam
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Kolkata700032, India
| | - Dolan Moni
- Department of Chemistry, Jadavpur University, 188, Raja S. C. Mullick Road, Kolkata700 032, India
| | - Debjani Maiti
- Department of Chemistry, Jadavpur University, 188, Raja S. C. Mullick Road, Kolkata700 032, India
| | - Ananya Dutta
- Department of Chemistry, Jadavpur University, 188, Raja S. C. Mullick Road, Kolkata700 032, India
| | - Mahammad Ali
- Department of Chemistry, Jadavpur University, 188, Raja S. C. Mullick Road, Kolkata700 032, India
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15
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Höing A, Kirupakaran A, Beuck C, Pörschke M, Niemeyer FC, Seiler T, Hartmann L, Bayer P, Schrader T, Knauer SK. Recognition of a Flexible Protein Loop in Taspase 1 by Multivalent Supramolecular Tweezers. Biomacromolecules 2022; 23:4504-4518. [PMID: 36200481 DOI: 10.1021/acs.biomac.2c00652] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many natural proteins contain flexible loops utilizing well-defined complementary surface regions of their interacting partners and usually undergo major structural rearrangements to allow perfect binding. The molecular recognition of such flexible structures is still highly challenging due to the inherent conformational dynamics. Notably, protein-protein interactions are on the other hand characterized by a multivalent display of complementary binding partners to enhance molecular affinity and specificity. Imitating this natural concept, we here report the rational design of advanced multivalent supramolecular tweezers that allow addressing two lysine and arginine clusters on a flexible protein surface loop. The protease Taspase 1, which is involved in cancer development, carries a basic bipartite nuclear localization signal (NLS) and thus interacts with Importin α, a prerequisite for proteolytic activation. Newly established synthesis routes enabled us to covalently fuse several tweezer molecules into multivalent NLS ligands. The resulting bi- up to pentavalent constructs were then systematically compared in comprehensive biochemical assays. In this series, the stepwise increase in valency was robustly reflected by the ligands' gradually enhanced potency to disrupt the interaction of Taspase 1 with Importin α, correlated with both higher binding affinity and inhibition of proteolytic activity.
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Affiliation(s)
- Alexander Höing
- Molecular Biology II, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Abbna Kirupakaran
- Institute of Organic Chemistry I, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Christine Beuck
- Structural and Medicinal Biochemistry, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Marius Pörschke
- Structural and Medicinal Biochemistry, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Felix C Niemeyer
- Institute of Organic Chemistry I, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Theresa Seiler
- Organic Chemistry and Macromolecular Chemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Laura Hartmann
- Organic Chemistry and Macromolecular Chemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Peter Bayer
- Structural and Medicinal Biochemistry, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Thomas Schrader
- Institute of Organic Chemistry I, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Shirley K Knauer
- Molecular Biology II, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
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16
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Fabrication of self-healing magnetic nanoreceptors for glycoprotein via integrating boronate-affinity-oriented and sequential surface imprinting. Anal Chim Acta 2022; 1221:340108. [DOI: 10.1016/j.aca.2022.340108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/12/2022] [Accepted: 06/19/2022] [Indexed: 11/18/2022]
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17
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Yu XA, Zhang L, Zhang R, Bai X, Zhang Y, Hu Y, Wu Y, Li Z, Wang B, Tian J. Accurate identification of kidney injury progression via a fluorescent biosensor array. Mikrochim Acta 2022; 189:304. [PMID: 35915355 DOI: 10.1007/s00604-022-05380-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 06/26/2022] [Indexed: 11/25/2022]
Abstract
Identifying the progress of kidney injury may aid the effective treatment and intervention. Herein, we developed a fluorescent biosensor array for instantaneous and accurate identification of the kidney injury progression via "doubled" signals. The multichannel biosensor array consisted of polydopamine-polyethyleneimine (PDA-PEI) and multicolor-labelled different length of DNAs including AAAAA-Cyanine7 (5A-Cy7), AAAAAAAAAA-Texas Red (10A-Texas Red), and AAAAAAAAAAAAAAAAAAAA-VIC (20A-VIC). Facing to the variety of protein in urine with alterable charge accompanied with different progress of kidney injury, the composition of urine replaces the DNA signal molecules, forming their special fluorescence patterns. Taking the size of protein into consideration, the original three variables induced by the protein charge were extended to six variables induced by the two factors of protein particle size and charge difference, which could provide a more accurate strategy to identify the progress of kidney injury. Notably, this strategy not only opened up new perspective for identification the progress of kidney injury via the size and charge of urine protein, but also improved the resolving power of sensor array by increasing the number of sensor elements for extending their potential application to various diseases.
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Affiliation(s)
- Xie-An Yu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China
- NMPA Key Laboratory for Bioequivalence Research of Generic Drug Evaluation, Shenzhen Institute for Drug Control, Shenzhen, 518057, People's Republic of China
| | - Lei Zhang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China
| | - Ran Zhang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China
| | - Xuefei Bai
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China
| | - Ying Zhang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China
| | - Yiting Hu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China
| | - Yang Wu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China
| | - Ziyi Li
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China
| | - Bing Wang
- NMPA Key Laboratory for Bioequivalence Research of Generic Drug Evaluation, Shenzhen Institute for Drug Control, Shenzhen, 518057, People's Republic of China.
| | - Jiangwei Tian
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China.
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18
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Das Saha N, Pradhan S, Sasmal R, Sarkar A, Berač CM, Kölsch JC, Pahwa M, Show S, Rozenholc Y, Topçu Z, Alessandrini V, Guibourdenche J, Tsatsaris V, Gagey-Eilstein N, Agasti SS. Cucurbit[7]uril Macrocyclic Sensors for Optical Fingerprinting: Predicting Protein Structural Changes to Identifying Disease-Specific Amyloid Assemblies. J Am Chem Soc 2022; 144:14363-14379. [PMID: 35913703 DOI: 10.1021/jacs.2c05969] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In a three-dimensional (3D) representation, each protein molecule displays a specific pattern of chemical and topological features, which are altered during its misfolding and aggregation pathway. Generating a recognizable fingerprint from such features could provide an enticing approach not only to identify these biomolecules but also to gain clues regarding their folding state and the occurrence of pathologically lethal misfolded aggregates. We report here a universal strategy to generate a fluorescent fingerprint from biomolecules by employing the pan-selective molecular recognition feature of a cucurbit[7]uril (CB[7]) macrocyclic receptor. We implemented a direct sensing strategy by covalently tethering CB[7] with a library of fluorescent reporters. When CB[7] recognizes the chemical and geometrical features of a biomolecule, it brings the tethered fluorophore into the vicinity, concomitantly reporting the nature of its binding microenvironment through a change in their optical signature. The photophysical properties of the fluorophores allow a multitude of probing modes, while their structural features provide additional binding diversity, generating a distinct fluorescence fingerprint from the biomolecule. We first used this strategy to rapidly discriminate a diverse range of protein analytes. The macrocyclic sensor was then applied to probe conformational changes in the protein structure and identify the formation of oligomeric and fibrillar species from misfolded proteins. Notably, the sensor system allowed us to differentiate between different self-assembled forms of the disease-specific amyloid-β (Aβ) aggregates and segregated them from other generic amyloid structures with a 100% identification accuracy. Ultimately, this sensor system predicted clinically relevant changes by fingerprinting serum samples from a cohort of pregnant women.
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Affiliation(s)
- Nilanjana Das Saha
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India.,Chemistry & Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
| | - Soumen Pradhan
- Chemistry & Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
| | - Ranjan Sasmal
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
| | - Aritra Sarkar
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
| | - Christian M Berač
- Department of Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, 55128 Mainz, Germany.,Graduate School of Materials Science in Mainz, Staudingerweg 9, 55128 Mainz, Germany
| | - Jonas C Kölsch
- Department of Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Meenakshi Pahwa
- Chemistry & Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
| | - Sushanta Show
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
| | - Yves Rozenholc
- UR 7537 BioSTM, Université Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France
| | - Zeki Topçu
- UR 7537 BioSTM, Université Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France
| | - Vivien Alessandrini
- INSERM UMR-S 1139, Université Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France.,Department of Obstetrics, Cochin Hospital, AP-HP, Université Paris Cité, FHU PREMA, 123 Bd Port-Royal, 75014 Paris, France
| | - Jean Guibourdenche
- INSERM UMR-S 1139, Université Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France.,Department of Obstetrics, Cochin Hospital, AP-HP, Université Paris Cité, FHU PREMA, 123 Bd Port-Royal, 75014 Paris, France
| | - Vassilis Tsatsaris
- INSERM UMR-S 1139, Université Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France.,Department of Obstetrics, Cochin Hospital, AP-HP, Université Paris Cité, FHU PREMA, 123 Bd Port-Royal, 75014 Paris, France
| | | | - Sarit S Agasti
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India.,Chemistry & Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
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19
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Hussain M, Lu Y, Tariq M, Jiang H, Shu Y, Luo S, Zhu Q, Zhang J, Liu J. A small-molecule Skp1 inhibitor elicits cell death by p53-dependent mechanism. iScience 2022; 25:104591. [PMID: 35789855 PMCID: PMC9249674 DOI: 10.1016/j.isci.2022.104591] [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: 08/13/2021] [Revised: 04/21/2022] [Accepted: 06/08/2022] [Indexed: 11/28/2022] Open
Abstract
Skp1 overexpression promotes tumor growth, whereas reduced Skp1 activity is also linked with genomic instability and neoplastic transformation. This highlights the need to gain better understanding of Skp1 biology in cancer settings. To this context, potent and cellularly active small-molecule Skp1 inhibitors may be of great value. Using a hypothesis-driven, structure-guided approach, we herein identify Z0933M as a potent Skp1 inhibitor with KD ∼0.054 μM. Z0933M occupies a hydrophobic hotspot (P1) – encompassing an aromatic cage of two phenylalanines (F101 and F139) – alongside C-terminal extension of Skp1 and, thus, hampers its ability to interact with F-box proteins, a prerequisite step to constitute intact and active SCF E3 ligase(s) complexes. In cellulo, Z0933M disrupted SCF E3 ligase(s) functioning, recapitulated previously reported effects of Skp1-reduced activity, and elicited cell death by a p53-dependent mechanism. We propose Z0933M as valuable tool for future efforts toward probing Skp1 cancer biology, with implications for cancer therapy. Z0933M manifests strong binding with Skp1 and inhibits Skp1-F-box PPIs Z0933M interacts with a P1 hotspot alongside C-terminal extension of Skp1 Z0933M alters SCF E3 ligase functioning, leading to substrate accumulation/modulation Z0933M causes cell-cycle arrest, and elicits cell death by p53-dependent mechanism
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Affiliation(s)
- Muzammal Hussain
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Guangdong Provincial Key Laboratory of Biocomputing, Institute of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yongzhi Lu
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Guangzhou 510530, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Muqddas Tariq
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Guangzhou 510530, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Hao Jiang
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Guangzhou 510530, China
| | - Yahai Shu
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Guangzhou 510530, China
| | - Shuang Luo
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Guangzhou 510530, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Qiang Zhu
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Guangzhou 510530, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Jiancun Zhang
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Guangdong Provincial Key Laboratory of Biocomputing, Institute of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jinsong Liu
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Biocomputing, Institute of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou 510530, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Corresponding author
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20
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Suzuki S, Homma A, Nishi R, Mizuno H, Kawauchi S, Fukuhara G. A Dynamically Responsive Chemosensor That Can be Modulated by an Effector: Amplification Sensing by Positive Heterotropic Allosterism. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20220088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Sho Suzuki
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Amane Homma
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Reiya Nishi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Hiroaki Mizuno
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Susumu Kawauchi
- Tokyo Tech Academy for Convergence of Materials and Informatics (TAC-MI), Tokyo Institute of Technology, S6-23, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Gaku Fukuhara
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
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21
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Hatai J, Altay Y, Sood A, Kiani A, Eleveld MJ, Motiei L, Margulies D, Otto S. An Optical Probe for Real-Time Monitoring of Self-Replicator Emergence and Distinguishing between Replicators. J Am Chem Soc 2022; 144:3074-3082. [PMID: 35139307 PMCID: PMC8874894 DOI: 10.1021/jacs.1c11594] [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] [Indexed: 11/30/2022]
Abstract
![]()
Self-replicating
systems play an important role in research on
the synthesis and origin of life. Monitoring of these systems has
mostly relied on techniques such as NMR or chromatography, which are
limited in throughput and demanding when monitoring replication in
real time. To circumvent these problems, we now developed a pattern-generating
fluorescent molecular probe (an ID-probe) capable of discriminating
replicators of different chemical composition and monitoring the process
of replicator formation in real time, giving distinct signatures for
starting materials, intermediates, and final products. Optical monitoring
of replicators dramatically reduces the analysis time and sample quantities
compared to most currently used methods and opens the door for future
high-throughput experimentation in protocell environments.
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Affiliation(s)
- Joydev Hatai
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Yigit Altay
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ankush Sood
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Armin Kiani
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marcel J Eleveld
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - 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
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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22
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Basuroy K, de J Velazquez-Garcia J, Storozhuk D, Gosztola DJ, Veedu ST, Techert S. Ultrafast sorting: Excimeric π-π stacking distinguishes pyrene-N-methylacetamide isomers on the ultrafast time scale. J Chem Phys 2021; 155:234304. [PMID: 34937351 DOI: 10.1063/5.0072785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Pyrene based molecules are inclined to form excimers through self-association upon photoexcitation. In this work, the pyrene core is functionalized with the N-methylacetamide group at the position 1 or 2 to develop pyren-1-methylacetamide (PyMA1) and pyren-2-methylacetamide (PyMA2), respectively. Upon photoexcitation with 345 nm, a portion of molecules in PyMA1 and PyMA2 solutions at ≥1.0 mM have formed static excimers. The steady state spectroscopic measurements suggest that, whether it is the dimerization of molecules in the ground state (GS) or in excimer formation, characteristic signs are more pronounced in PyMA1 than its isomeric counterpart, PyMA2. The shift of the excimer band in their respective emission spectra suggests that the extent of overlap in π-π stacking is greater for PyMA1 than for PyMA2 in the excited state. The optimized geometry of dimers in toluene shows that the overlapping area between the pyrene moieties in π-π stacking between the dimers is greater for PyMA1 than for PyMA2 in GS. The natural bond orbital analysis with the optimized GS geometries shows that the stabilization/interaction energy between the dimers in π-π stacking is higher in PyMA1 compared to PyMA2 in toluene. The transient absorption (TA) measurements in toluene over the fs-ps regime (fs-TA) showed that the formation of static excimers with pre-associated dimers in PyMA1 happens in ∼700 fs whereas the excimers for the pre-associated dimers in PyMA2 have formed in slightly slower time scale (∼1.95 ps). Contrary to what was observed in solution, the extent of overlap in π-π stacking is lower for PyMA1 dimers (∼17%) than for PyMA2 dimers (∼37%) in single crystals.
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Affiliation(s)
- Krishnayan Basuroy
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | - Darina Storozhuk
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - David J Gosztola
- Center for Nanoscale Materials, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | | | - Simone Techert
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
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23
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Singh R, Chen DG, Wang CH, Lan YC, Liu YH, Chou PT, Chen CT. Tailoring C-6-Substituted Coumarin Scaffolds for Novel Photophysical Properties and Stimuli-Responsive Chromism. J Phys Chem B 2021; 125:11557-11565. [PMID: 34633826 DOI: 10.1021/acs.jpcb.1c08133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A judicious strategy was utilized to envision the substantial regio-positional effects of substituents on the photophysical properties of the 2H-chromen-2-one-3-benzothiazole scaffold-based push-pull framework, named 6-X-CUMs. Among them, 6-NEt2-CUM reveals prominent excited-state intramolecular charge transfer with a large change of dipole moment (Δμ ∼ 18.23 D), hence displaying remarkable emission solvatochromism from the green (536 nm in cyclohexane) to far-red region (714 nm in dimethyl sulfoxide) and a high-temperature sensitivity (-0.23 nm °C-1). These, together with unique basicity and acido-/vaporchromism upon acidification elucidated by NMR and photospectroscopic studies, show stark contrast to the conventional 7-NEt2-CUM. The new series of these tailored 6-X-CUMs represents a new dimension in tailoring the photophysical properties for the development of a promising class of multistimuli-responsive materials.
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Affiliation(s)
- Ravinder Singh
- Department of Chemistry, National Taiwan University, Taipei, 10617 Taiwan, ROC
| | - Deng-Gao Chen
- Department of Chemistry, National Taiwan University, Taipei, 10617 Taiwan, ROC
| | - Chun-Hsiang Wang
- Department of Chemistry, National Taiwan University, Taipei, 10617 Taiwan, ROC
| | - Yi-Cheng Lan
- Department of Chemistry, National Taiwan University, Taipei, 10617 Taiwan, ROC
| | - Yi-Hung Liu
- Department of Chemistry, National Taiwan University, Taipei, 10617 Taiwan, ROC
| | - Pi-Tai Chou
- Department of Chemistry, National Taiwan University, Taipei, 10617 Taiwan, ROC
| | - Chao-Tsen Chen
- Department of Chemistry, National Taiwan University, Taipei, 10617 Taiwan, ROC
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24
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Morgan TF, Riley LM, Tavares AAS, Sutherland A. Automated Radiosynthesis of cis- and trans-4-[ 18F]Fluoro-l-proline Using [ 18F]Fluoride. J Org Chem 2021; 86:14054-14060. [PMID: 33913318 PMCID: PMC8524414 DOI: 10.1021/acs.joc.1c00755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Indexed: 01/21/2023]
Abstract
The positron emission tomography imaging agents cis- and trans-4-[18F]fluoro-l-proline are used for the detection of numerous diseases such as pulmonary fibrosis and various carcinomas. These imaging agents are typically prepared by nucleophilic fluorination of 4-hydroxy-l-proline derivatives, with [18F]fluoride, followed by deprotection. Although effective radiofluorination reactions have been developed, the overall radiosynthesis process is suboptimal due to deprotection methods that are performed manually, require multiple steps, or involve harsh conditions. Here we describe the development of two synthetic routes that allow access to precursors, which undergo highly selective radiofluorination reactions and rapid deprotection, under mild acidic conditions. These methods were found to be compatible with automation, avoiding manual handling of radioactive intermediates.
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Affiliation(s)
- Timaeus
E. F. Morgan
- BHF-University
Centre for Cardiovascular Science, University
of Edinburgh, Edinburgh EH16 4TJ, United Kingdom
| | - Leanne M. Riley
- WestCHEM,
School of Chemistry, University of Glasgow, The Joseph Black Building, Glasgow G12 8QQ, United Kingdom
| | - Adriana A. S. Tavares
- BHF-University
Centre for Cardiovascular Science, University
of Edinburgh, Edinburgh EH16 4TJ, United Kingdom
| | - Andrew Sutherland
- WestCHEM,
School of Chemistry, University of Glasgow, The Joseph Black Building, Glasgow G12 8QQ, United Kingdom
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25
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Guillory X, Hadrović I, de Vink PJ, Sowislok A, Brunsveld L, Schrader T, Ottmann C. Supramolecular Enhancement of a Natural 14-3-3 Protein Ligand. J Am Chem Soc 2021; 143:13495-13500. [PMID: 34427424 DOI: 10.1021/jacs.1c07095] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rational design of protein-protein interaction (PPI) inhibitors is challenging. Connecting a general supramolecular protein binder with a specific peptidic ligand provides a novel conceptual approach. Thus, lysine-specific molecular tweezers were conjugated to a peptide-based 14-3-3 ligand and produced a strong PPI inhibitor with 100-fold elevated protein affinity. X-ray crystal structure elucidation of this supramolecular directed assembly provides unique molecular insight into the binding mode and fully aligns with Molecular Dynamics (MD) simulations. This new supramolecular chemical biology concept opens the path to novel chemical tools for studying PPIs.
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Affiliation(s)
- Xavier Guillory
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular System, Eindhoven University of Technology, (TU/e) Den Dolech 2, 5612 AZ Eindhoven, The Netherlands.,Department of Chemistry, University of Duisburg-Essen, Universitätsstraße 7, 45117 Essen, Germany
| | - Inesa Hadrović
- Department of Chemistry, University of Duisburg-Essen, Universitätsstraße 7, 45117 Essen, Germany
| | - Pim J de Vink
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular System, Eindhoven University of Technology, (TU/e) Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Andrea Sowislok
- University Clinics Essen, Experimental Orthopedics and Trauma Surgery, 45147 Essen, Germany
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular System, Eindhoven University of Technology, (TU/e) Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Thomas Schrader
- Department of Chemistry, University of Duisburg-Essen, Universitätsstraße 7, 45117 Essen, Germany
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular System, Eindhoven University of Technology, (TU/e) Den Dolech 2, 5612 AZ Eindhoven, The Netherlands.,Department of Chemistry, University of Duisburg-Essen, Universitätsstraße 7, 45117 Essen, Germany
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26
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Fernandes RJ, Remón P, Moro AJ, Seco A, Ferreira ASD, Pischel U, Basílio N. Toward Light-Controlled Supramolecular Peptide Dimerization. J Org Chem 2021; 86:8472-8478. [PMID: 34060851 PMCID: PMC9161448 DOI: 10.1021/acs.joc.1c00464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The selective photodeprotection of the NVoc-modified FGG tripeptide yields the transformation of its 1:1 receptor-ligand complex with cucurbit[8]uril into a homoternary FGG2@CB8 assembly. The resulting light-induced dimerization of the model peptide provides a tool for the implementation of stimuli-responsive supramolecular chemistry in biologically relevant contexts.
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Affiliation(s)
- Rita J Fernandes
- Laboratorio Associado para a Química Verde (LAQV), Rede de Química e Tecnologia (REQUIMTE), Departamento de Química, Faculdade de Ciências e Tecnología, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Patricia Remón
- CIQSO - Centre for Research in Sustainable Chemistry and Department of Chemistry, University of Huelva, Campus de El Carmen s/n, E-21071 Huelva, Spain
| | - Artur J Moro
- Laboratorio Associado para a Química Verde (LAQV), Rede de Química e Tecnologia (REQUIMTE), Departamento de Química, Faculdade de Ciências e Tecnología, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - André Seco
- Laboratorio Associado para a Química Verde (LAQV), Rede de Química e Tecnologia (REQUIMTE), Departamento de Química, Faculdade de Ciências e Tecnología, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Ana S D Ferreira
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Uwe Pischel
- CIQSO - Centre for Research in Sustainable Chemistry and Department of Chemistry, University of Huelva, Campus de El Carmen s/n, E-21071 Huelva, Spain
| | - Nuno Basílio
- Laboratorio Associado para a Química Verde (LAQV), Rede de Química e Tecnologia (REQUIMTE), Departamento de Química, Faculdade de Ciências e Tecnología, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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27
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Meiners A, Bäcker S, Hadrović I, Heid C, Beuck C, Ruiz-Blanco YB, Mieres-Perez J, Pörschke M, Grad JN, Vallet C, Hoffmann D, Bayer P, Sánchez-García E, Schrader T, Knauer SK. Specific inhibition of the Survivin-CRM1 interaction by peptide-modified molecular tweezers. Nat Commun 2021; 12:1505. [PMID: 33686072 PMCID: PMC7940618 DOI: 10.1038/s41467-021-21753-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 02/02/2021] [Indexed: 01/31/2023] Open
Abstract
Survivin's dual function as apoptosis inhibitor and regulator of cell proliferation is mediated via its interaction with the export receptor CRM1. This protein-protein interaction represents an attractive target in cancer research and therapy. Here, we report a sophisticated strategy addressing Survivin's nuclear export signal (NES), the binding site of CRM1, with advanced supramolecular tweezers for lysine and arginine. These were covalently connected to small peptides resembling the natural, self-complementary dimer interface which largely overlaps with the NES. Several biochemical methods demonstrated sequence-selective NES recognition and interference with the critical receptor interaction. These data were strongly supported by molecular dynamics simulations and multiscale computational studies. Rational design of lysine tweezers equipped with a peptidic recognition element thus allowed to address a previously unapproachable protein surface area. As an experimental proof-of-principle for specific transport signal interference, this concept should be transferable to any protein epitope with a flanking well-accessible lysine.
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Affiliation(s)
- Annika Meiners
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Sandra Bäcker
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Inesa Hadrović
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Christian Heid
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Christine Beuck
- Department of Structural and Medicinal Biology, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Yasser B Ruiz-Blanco
- Department of Computational Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Joel Mieres-Perez
- Department of Computational Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Marius Pörschke
- Department of Structural and Medicinal Biology, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Jean-Noël Grad
- Department of Bioinformatics and Computational Biophysics, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Cecilia Vallet
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Daniel Hoffmann
- Department of Bioinformatics and Computational Biophysics, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Peter Bayer
- Department of Structural and Medicinal Biology, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Elsa Sánchez-García
- Department of Computational Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany.
| | - Thomas Schrader
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany.
| | - Shirley K Knauer
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany.
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28
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Adler S, Motiei L, Mankovski N, Cohen H, Margulies D. Fluorescent Labelling of Cell Surface Proteins on a Solid Support. Isr J Chem 2021. [DOI: 10.1002/ijch.202100028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Sean Adler
- Department of Chemical and Structural Biology Weizmann Institute of Science Rehovot 7610001 Israel
| | - Leila Motiei
- Department of Chemical and Structural Biology Weizmann Institute of Science Rehovot 7610001 Israel
| | - Naama Mankovski
- Department of Chemical and Structural Biology Weizmann Institute of Science Rehovot 7610001 Israel
| | - Hagai Cohen
- Department of Chemical Research Support 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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29
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Chen SY, Li Z, Li K, Yu XQ. Small molecular fluorescent probes for the detection of lead, cadmium and mercury ions. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213691] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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30
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Tsuchiya T, Mizuno H, Fukuhara G. The factors that govern the allosteric chemical sensing of polythiophene chemosensors: scope and limitation toward signal-amplification sensing. RSC Adv 2021; 11:30472-30478. [PMID: 35493992 PMCID: PMC9041329 DOI: 10.1039/d1ra05795b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/01/2021] [Indexed: 12/15/2022] Open
Abstract
The newly designed polythiophene chemosensors (PT1 and PT2) were synthesized via the Suzuki–Miyaura polymerization with appropriate yields. The photophysical properties of PTs thus obtained were examined by means of UV/vis, fluorescence, excitation spectroscopy, and time-correlated single-photon-counting method. The π–π* transitions around 400–600 nm and the emissions in the range of 400–650 nm were observed. The binding behavior of PTs was also investigated upon the interaction of tetrabutylammonium or tetrabutylphosphonium isophthalate, affording the binding constants (K) of 5790–8310 M−1, which were quite smaller than those observed in the corresponding repeating unit. The comprehensive analyses of the UV/vis data and theoretical calculation supports revealed the origins of scope and limitation toward signal-amplification sensing. The present results obtained herein will guide the development of new amplification chemosensors. The allosteric sensing of target guest molecules was drastically inhibited by introducing thiophene spacers in the polythiophene backbone, which is caused by the conformational relaxation.![]()
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Affiliation(s)
- Tomoaki Tsuchiya
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Hiroaki Mizuno
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Gaku Fukuhara
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
- JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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31
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Selective Recognition of Amino Acids and Peptides by Small Supramolecular Receptors. Molecules 2020; 26:molecules26010106. [PMID: 33379401 PMCID: PMC7796322 DOI: 10.3390/molecules26010106] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/14/2020] [Accepted: 12/22/2020] [Indexed: 12/30/2022] Open
Abstract
To this day, the recognition and high affinity binding of biomolecules in water by synthetic receptors remains challenging, while the necessity for systems for their sensing, transport and modulation persists. This problematic is prevalent for the recognition of peptides, which not only have key roles in many biochemical pathways, as well as having pharmacological and biotechnological applications, but also frequently serve as models for the study of proteins. Taking inspiration in nature and on the interactions that occur between several receptors and peptide sequences, many researchers have developed and applied a variety of different synthetic receptors, as is the case of macrocyclic compounds, molecular imprinted polymers, organometallic cages, among others, to bind amino acids, small peptides and proteins. In this critical review, we present and discuss selected examples of synthetic receptors for amino acids and peptides, with a greater focus on supramolecular receptors, which show great promise for the selective recognition of these biomolecules in physiological conditions. We decided to focus preferentially on small synthetic receptors (leaving out of this review high molecular weight polymeric systems) for which more detailed and accurate molecular level information regarding the main structural and thermodynamic features of the receptor biomolecule assemblies is available.
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32
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van der Meer SB, Hadrovic I, Meiners A, Loza K, Heggen M, Knauer SK, Bayer P, Schrader T, Beuck C, Epple M. New Tools to Probe the Protein Surface: Ultrasmall Gold Nanoparticles Carry Amino Acid Binders. J Phys Chem B 2020; 125:115-127. [DOI: 10.1021/acs.jpcb.0c09846] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Selina Beatrice van der Meer
- Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Universitätsstr. 5-7, 45117 Essen, Germany
| | - Inesa Hadrovic
- Organic Chemistry, University of Duisburg-Essen, Universitätsstr. 5-7, 45117 Essen, Germany
| | - Annika Meiners
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany
| | - Kateryna Loza
- Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Universitätsstr. 5-7, 45117 Essen, Germany
| | - Marc Heggen
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Shirley K. Knauer
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany
| | - Peter Bayer
- Department of Structural and Medicinal Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany
| | - Thomas Schrader
- Organic Chemistry, University of Duisburg-Essen, Universitätsstr. 5-7, 45117 Essen, Germany
| | - Christine Beuck
- Department of Structural and Medicinal Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany
| | - Matthias Epple
- Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Universitätsstr. 5-7, 45117 Essen, Germany
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33
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Dar TA, Sankar M. Fused Nickel(II) Porphyrins-Sensing of Toxic Anions and Selected Metal Ions Through Supramolecular Interactions. Front Chem 2020; 8:595177. [PMID: 33282838 PMCID: PMC7705245 DOI: 10.3389/fchem.2020.595177] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 10/12/2020] [Indexed: 11/13/2022] Open
Abstract
Ni(II) porphyrins having fused -NH group were synthesized and characterized by various spectroscopic techniques. The fused porphyrins 1 and 2 were used to detect species of opposite polarity. 1 was used to sense toxic anions viz. cyanide and fluoride ions whereas 2 was used for detecting some selective metal ions including toxic mercury(II) ions. 1 is having acidic -NH proton, which detects anions via hydrogen bonding interactions followed by anion-induced deprotonation. On the other hand, 2 senses the metal species via weak charge transfer interactions from oxygen atom of the formyl group to the added metal ions. The limit of detection was calculated in case of 1 as 2.13 and 3.15 ppm for cyanide and fluoride ions, respectively. Similarly, the detection limit was found to be 0.930, 2.231, and 0.718 ppm for Cu(II), Fe(III), and Hg(II) ions, respectively, for probe 2. The probes were recovered and reused for several cycles.
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Affiliation(s)
| | - Muniappan Sankar
- Department of Chemistry, Indian Institute of Technology, Roorkee, India
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34
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Tsuchiya T, Fukuhara G. Allosteric Signal Amplification Sensing Using a Bisthiourea-Binaphthyl-Polythiophene Conjugate: A Positive Homotropic Allosterim Case. J Org Chem 2020; 85:13239-13245. [PMID: 32880172 DOI: 10.1021/acs.joc.0c01326] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The development of signal amplification systems has attracted much attention and presents a highly challenging objective. Herein, we reveal the amplification processes using a newly synthesized bisthiourea-binaphthyl-polythiophene conjugate. The spectral data, behavior of supramolecular complexation, and thermodynamic parameters with calculation support comprehensively elucidated the factors that control the outcomes of the signal amplification. The present work provides a new perspective on functional chemosensors and an attractive alternative to conventional amplification systems.
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Affiliation(s)
- Tomoaki Tsuchiya
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Gaku Fukuhara
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan.,JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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35
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Dai SY, Yang D. A Visible and Near-Infrared Light Activatable Diazocoumarin Probe for Fluorogenic Protein Labeling in Living Cells. J Am Chem Soc 2020; 142:17156-17166. [PMID: 32870680 DOI: 10.1021/jacs.0c08068] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chemical modification of proteins in living cells permits valuable glimpses into the molecular interactions that underpin dynamic cellular events. While genetic engineering methods are often preferred, selective labeling of endogenous proteins in a complex intracellular milieu with chemical approaches represents a significant challenge. In this study, we report novel diazocoumarin compounds that can be photoactivated by visible (430-490 nm) and near-infrared light (800 nm) irradiation to photo-uncage reactive carbene intermediates, which could subsequently undergo an insertion reaction with concomitant fluorescence "turned on". With these new molecules in hand, we have developed a new approach for rapid, selective, and fluorogenic labeling of endogenous protein in living cells. By using CA-II and eDHFR as model proteins, we demonstrated that subcellular localization of proteins can be precisely visualized by live-cell imaging and protein levels can be reliably quantified in multiple cell types using flow cytometry. Dynamic protein regulations such as hypoxia-induced CA-IX accumulation can also be detected. In addition, by two-photon excitation with an 800 nm laser, cell-selective labeling can also be achieved with spatially controlled irradiation. Our method circumvents the cytotoxicity of UV light and obviates the need for introducing external reporters with "click chemistries". We believe that this approach of fluorescence labeling of endogenous protein by bioorthogonal photoirradiation opens up exciting opportunities for discoveries and mechanistic interrogation in chemical biology.
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Affiliation(s)
- Sheng-Yao Dai
- Morningside Laboratory for Chemical Biology, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Dan Yang
- Morningside Laboratory for Chemical Biology, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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36
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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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37
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Peri-Naor R, Pode Z, Lahav-Mankovski N, Rabinkov A, Motiei L, Margulies D. Glycoform Differentiation by a Targeted, Self-Assembled, Pattern-Generating Protein Surface Sensor. J Am Chem Soc 2020; 142:15790-15798. [PMID: 32786755 DOI: 10.1021/jacs.0c05644] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A method for generating targeted, pattern-generating, protein surface sensors via the self-assembly of modified oligodeoxynucleotides (ODNs) is described. The simplicity by which these systems can be created enabled the development of a sensor that can straightforwardly discriminate between distinct glycoform populations. By using this sensor to identify glycosylation states of a therapeutic protein, we demonstrate the diagnostic potential of this approach as well as the feasibility of integrating a wealth of supramolecular receptors and sensors into higher-order molecular analytical devices with advanced properties. For example, the facile device integration was used to attach the well-known anthracene-boronic acid (An-BA) probe to a biomimetic DNA scaffold and consequently, to use the unique photophysical properties of An-BA to improve glycoform differentiation. In addition, the noncovalent assembly enabled us to modify the sensor with a trinitrilotriacetic acid (tri-NTA)-Ni2+ complex, which endows it with selectivity toward a hexa-histidine tag (His-tag). The selective responses of the system to diverse His-tag-labeled proteins further demonstrate the potential applicability of such sensors and validate the mechanism underlying their function.
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Affiliation(s)
- Ronny Peri-Naor
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Zohar Pode
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Naama Lahav-Mankovski
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Aharon Rabinkov
- Life Sciences Core Facilities, 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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38
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Pérez RL, Cong M, Vaughan SR, Ayala CE, Galpothdeniya WIS, Mathaga JK, Warner IM. Protein Discrimination Using a Fluorescence-Based Sensor Array of Thiacarbocyanine-GUMBOS. ACS Sens 2020; 5:2422-2429. [PMID: 32686397 PMCID: PMC7460578 DOI: 10.1021/acssensors.0c00484] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
Sensitive and selective detection
of proteins from complex samples
has gained substantial interest within the scientific community. Early
and precise detection of key proteins plays an important role in potential
clinical diagnosis, treatment of different diseases, and proteomic
research. In the study reported here, six different compounds belonging
to a group of uniform materials based on organic salts (GUMBOS) have
been synthesized using three thiacarbocyanine (TC) dyes and employed
as fluorescent sensors. Fluorescence properties of micro- and nanoaggregates
of these TC-based GUMBOS formed in phosphate buffer solutions are
studied in the absence and presence of seven proteins. Fluorescence
response patterns of these TC-based GUMBOS were analyzed by linear
discriminant analysis (LDA). The constructed LDA model allowed discrimination
of these seven proteins at various concentrations with 100% accuracy.
The sensing and discrimination abilities of these TC-based GUMBOS
were further evaluated in mixtures of two major proteins, i.e., human
serum albumin and hemoglobin. Fluorescence response patterns of these
mixtures were analyzed by LDA. This model allowed discrimination of
various mixtures with 100% accuracy. Moreover, spiked urine samples
were prepared and the responses of these sensors were collected and
analyzed by LDA. Remarkably, discrimination of these seven proteins
was also achieved with 100% accuracy.
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Affiliation(s)
- Rocío L. Pérez
- Chemistry Department, Louisiana State University, Baton Rouge, Lousiana 70803, United States
| | - Mingyan Cong
- Chemistry Department, Louisiana State University, Baton Rouge, Lousiana 70803, United States
| | - Stephanie R. Vaughan
- Chemistry Department, Louisiana State University, Baton Rouge, Lousiana 70803, United States
| | - Caitlan E. Ayala
- Chemistry Department, Louisiana State University, Baton Rouge, Lousiana 70803, United States
| | | | - John K. Mathaga
- Chemistry Department, Louisiana State University, Baton Rouge, Lousiana 70803, United States
| | - Isiah M. Warner
- Chemistry Department, Louisiana State University, Baton Rouge, Lousiana 70803, United States
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39
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Sugai H, Tomita S, Kurita R. Pattern-recognition-based Sensor Arrays for Cell Characterization: From Materials and Data Analyses to Biomedical Applications. ANAL SCI 2020; 36:923-934. [PMID: 32249248 DOI: 10.2116/analsci.20r002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
To capture a broader scope of complex biological phenomena, alternatives to conventional sensing based on specificity for cell detection and characterization are needed. Pattern-recognition-based sensing is an analytical method designed to mimic mammalian sensory systems for analyte identification based on the pattern recognition of multivariate data, which are generated using an array of multiple probes that cross-reactively interact with analytes. This sensing approach is significantly different from conventional specific cell sensing based on highly specific probes, including antibodies against biomarkers. Encouraged by the advantages of this technique, such as the simplicity, rapidity, and tunability of the systems without requiring a priori knowledge of biomarkers, numerous sensor arrays have been developed over the past decade and used in a variety of cell sensing applications; these include disease diagnosis, drug discovery, and fundamental research. This review summarizes recent progress in pattern-recognition-based cell sensing, with a particular focus on guidelines for designing materials and arrays, techniques for analyzing response patterns, and applications of sensor systems that are focused primarily for the biomedical field.
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Affiliation(s)
- Hiroka Sugai
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Shunsuke Tomita
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST).,DAILAB, DBT-AIST International Center for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science & Technology (AIST)
| | - Ryoji Kurita
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST).,DAILAB, DBT-AIST International Center for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science & Technology (AIST).,Faculty of Pure and Applied Sciences, University of Tsukuba
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40
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Zhao M, Huang S, Xie H, Wang J, Zhao X, Li M, Zhao M. Construction of Specific and Reversible Nanoreceptors for Proteins via Sequential Surface-Imprinting Strategy. Anal Chem 2020; 92:10540-10547. [DOI: 10.1021/acs.analchem.0c01366] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Muhua Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Shan Huang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Huaisyuan Xie
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Jiayu Wang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Xiaoli Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Mengyuan Li
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
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41
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Song Y, Xiong F, Peng J, Fung YME, Huang Y, Li X. Introducing aldehyde functionality to proteins using ligand-directed affinity labeling. Chem Commun (Camb) 2020; 56:6134-6137. [PMID: 32364188 DOI: 10.1039/d0cc01982h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Aldehyde is a versatile chemical handle for protein modification. Although many methods have been developed to label proteins with aldehyde, target-specific methods amenable to endogenous proteins are limited. Here, we report a simple affinity probe strategy to introduce aldehydes to native proteins. Notably, the probe contains a latent aldehyde functionality that is only exposed upon target binding, thereby enabling a one-pot labeling procedure.
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Affiliation(s)
- Yinan Song
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
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Well-Defined Conjugated Macromolecules Based on Oligo(Arylene Ethynylene)s in Sensing. Processes (Basel) 2020. [DOI: 10.3390/pr8050539] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Macromolecules with well-defined structures in terms of molar mass and monomer sequence became interesting building blocks for modern materials. The precision of the macromolecular structure makes fine-tuning of the properties of resulting materials possible. Conjugated macromolecules exhibit excellent optoelectronic properties that make them exceptional candidates for sensor construction. The importance of chain length and monomer sequence is particularly important in conjugated systems. The oligomer length, monomer sequence, and structural modification often influence the energy bang gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of the molecules that reflect in their properties. Moreover, the supramolecular aggregation that is often observed in oligo-conjugated systems is usually strongly affected by even minor structural changes that are used for sensor designs. This review discusses the examples of well-defined conjugated macromolecules based on oligo(arylene ethynylene) skeleton used for sensor applications. Here, exclusively examples of uniform macromolecules are summarized. The sensing mechanisms and importance of uniformity of structure are deliberated.
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Minamiki T, Kubota R, Sasaki Y, Asano K, Minami T. Protein Assays on Organic Electronics: Rational Device and Material Designs for Organic Transistor-Based Sensors. ChemistryOpen 2020; 9:573-581. [PMID: 32405448 PMCID: PMC7216454 DOI: 10.1002/open.202000025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/22/2020] [Indexed: 01/23/2023] Open
Abstract
Artificial receptor-based protein assays have various attractive features such as a long-term stability, a low-cost production process, and the ease of tuning the target specificity. However, such protein sensors are still immature compared with conventional immunoassays. To enhance the application potential of synthetic sensing materials, organic field-effect transistors (OFETs) are some of the suitable platforms for protein assays because of their solution processability, durability, and compact integration. Importantly, OFETs enable the electrical readout of the protein recognition phenomena of artificial receptors on sensing electrodes. Thus, we believe that OFETs functionalized with artificial protein receptors will be a powerful tool for the on-site analyses of target proteins. In this Minireview, we summarize the recent progress of the OFET-based protein assays including the rational design strategies for devices and sensing materials.
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Affiliation(s)
- Tsukuru Minamiki
- Institute of Industrial ScienceThe University of Tokyo4-6-1 Komaba, Meguro-kuTokyo153-8505Japan
| | - Riku Kubota
- Institute of Industrial ScienceThe University of Tokyo4-6-1 Komaba, Meguro-kuTokyo153-8505Japan
| | - Yui Sasaki
- Institute of Industrial ScienceThe University of Tokyo4-6-1 Komaba, Meguro-kuTokyo153-8505Japan
| | - Koichiro Asano
- Institute of Industrial ScienceThe University of Tokyo4-6-1 Komaba, Meguro-kuTokyo153-8505Japan
| | - Tsuyoshi Minami
- Institute of Industrial ScienceThe University of Tokyo4-6-1 Komaba, Meguro-kuTokyo153-8505Japan
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Minamiki T, Ichikawa Y, Kurita R. The Power of Assemblies at Interfaces: Nanosensor Platforms Based on Synthetic Receptor Membranes. SENSORS (BASEL, SWITZERLAND) 2020; 20:E2228. [PMID: 32326464 PMCID: PMC7218865 DOI: 10.3390/s20082228] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 11/17/2022]
Abstract
Synthetic sensing materials (artificial receptors) are some of the most attractive components of chemical/biosensors because of their long-term stability and low cost of production. However, the strategy for the practical design of these materials toward specific molecular recognition in water is not established yet. For the construction of artificial material-based chemical/biosensors, the bottom-up assembly of these materials is one of the effective methods. This is because the driving forces of molecular recognition on the receptors could be enhanced by the integration of such kinds of materials at the 'interfaces', such as the boundary portion between the liquid and solid phases. Additionally, the molecular assembly of such self-assembled monolayers (SAMs) can easily be installed in transducer devices. Thus, we believe that nanosensor platforms that consist of synthetic receptor membranes on the transducer surfaces can be applied to powerful tools for high-throughput analyses of the required targets. In this review, we briefly summarize a comprehensive overview that includes the preparation techniques for molecular assemblies, the characterization methods of the interfaces, and a few examples of receptor assembly-based chemical/biosensing platforms on each transduction mechanism.
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Affiliation(s)
- Tsukuru Minamiki
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan;
- DAILAB, DBT-AIST International Center for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science and Technology (AIST), Central 5-41, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Yuki Ichikawa
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan;
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
| | - Ryoji Kurita
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan;
- DAILAB, DBT-AIST International Center for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science and Technology (AIST), Central 5-41, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
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Vallet C, Aschmann D, Beuck C, Killa M, Meiners A, Mertel M, Ehlers M, Bayer P, Schmuck C, Giese M, Knauer SK. Functional Disruption of the Cancer-Relevant Interaction between Survivin and Histone H3 with a Guanidiniocarbonyl Pyrrole Ligand. Angew Chem Int Ed Engl 2020; 59:5567-5571. [PMID: 31916356 PMCID: PMC7155087 DOI: 10.1002/anie.201915400] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Indexed: 12/21/2022]
Abstract
The protein Survivin is highly upregulated in most cancers and considered to be a key player in carcinogenesis. We explored a supramolecular approach to address Survivin as a drug target by inhibiting the protein-protein interaction of Survivin and its functionally relevant binding partner Histone H3. Ligand L1 is based on the guanidiniocarbonyl pyrrole cation and serves as a highly specific anion binder in order to target the interaction between Survivin and Histone H3. NMR titration confirmed binding of L1 to Survivin's Histone H3 binding site. The inhibition of the Survivin-Histone H3 interaction and consequently a reduction of cancer cell proliferation were demonstrated by microscopic and cellular assays.
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Affiliation(s)
- Cecilia Vallet
- Department of Molecular Biology IIUniversity of Duisburg-EssenUniversitätsstraße 545141EssenGermany
| | - Dennis Aschmann
- Institute for Organic ChemistryUniversity of Duisburg-EssenGermany
| | - Christine Beuck
- Department of Structural and Medicinal BiochemistryUniversity of Duisburg-EssenGermany
| | - Matthias Killa
- Institute for Organic ChemistryUniversity of Duisburg-EssenGermany
| | - Annika Meiners
- Department of Molecular Biology IIUniversity of Duisburg-EssenUniversitätsstraße 545141EssenGermany
| | - Marcel Mertel
- Institute for Organic ChemistryUniversity of Duisburg-EssenGermany
| | - Martin Ehlers
- Institute for Organic ChemistryUniversity of Duisburg-EssenGermany
| | - Peter Bayer
- Department of Structural and Medicinal BiochemistryUniversity of Duisburg-EssenGermany
| | - Carsten Schmuck
- Institute for Organic ChemistryUniversity of Duisburg-EssenGermany
| | - Michael Giese
- Institute for Organic ChemistryUniversity of Duisburg-EssenGermany
| | - Shirley K. Knauer
- Department of Molecular Biology IIUniversity of Duisburg-EssenUniversitätsstraße 545141EssenGermany
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Lahav-Mankovski N, Prasad PK, Oppenheimer-Low N, Raviv G, Dadosh T, Unger T, Salame TM, Motiei L, Margulies D. Decorating bacteria with self-assembled synthetic receptors. Nat Commun 2020; 11:1299. [PMID: 32157077 PMCID: PMC7064574 DOI: 10.1038/s41467-020-14336-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 12/16/2019] [Indexed: 02/07/2023] Open
Abstract
The responses of cells to their surroundings are mediated by the binding of cell surface proteins (CSPs) to extracellular signals. Such processes are regulated via dynamic changes in the structure, composition, and expression levels of CSPs. In this study, we demonstrate the possibility of decorating bacteria with artificial, self-assembled receptors that imitate the dynamic features of CSPs. We show that the local concentration of these receptors on the bacterial membrane and their structure can be reversibly controlled using suitable chemical signals, in a way that resembles changes that occur with CSP expression levels or posttranslational modifications (PTMs), respectively. We also show that these modifications can endow the bacteria with programmable properties, akin to the way CSP responses can induce cellular functions. By programming the bacteria to glow, adhere to surfaces, or interact with proteins or mammalian cells, we demonstrate the potential to tailor such biomimetic systems for specific applications. Cell surface proteins mediate the interactions between cells and their extracellular environment. Here the authors design synthetic biomemetic receptor-like sensors that facilitate programmable interactions between bacteria and their target.
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Affiliation(s)
- Naama Lahav-Mankovski
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Pragati Kishore Prasad
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Noa Oppenheimer-Low
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Gal Raviv
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Tali Dadosh
- Chemical Research Support, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Tamar Unger
- Life Sciences Core Facilities, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Tomer Meir Salame
- Life Sciences Core Facilities, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Leila Motiei
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel.
| | - David Margulies
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel.
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Fukuhara G. Analytical supramolecular chemistry: Colorimetric and fluorimetric chemosensors. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2020. [DOI: 10.1016/j.jphotochemrev.2020.100340] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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48
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Vallet C, Aschmann D, Beuck C, Killa M, Meiners A, Mertel M, Ehlers M, Bayer P, Schmuck C, Giese M, Knauer SK. Funktionelle Inhibition der krebsrelevanten Interaktion von Survivin und Histon H3 mit einem Guanidiniumcarbonylpyrrol‐Liganden. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Cecilia Vallet
- Lehrstuhl für Molekularbiologie II Universität Duisburg-Essen Universitätsstraße 5 45141 Essen Deutschland
| | - Dennis Aschmann
- Institut für organische Chemie Universität Duisburg-Essen Deutschland
| | - Christine Beuck
- Lehrstuhl für strukturelle und medizinische Biochemie Universität Duisburg-Essen Deutschland
| | - Matthias Killa
- Institut für organische Chemie Universität Duisburg-Essen Deutschland
| | - Annika Meiners
- Lehrstuhl für Molekularbiologie II Universität Duisburg-Essen Universitätsstraße 5 45141 Essen Deutschland
| | - Marcel Mertel
- Institut für organische Chemie Universität Duisburg-Essen Deutschland
| | - Martin Ehlers
- Institut für organische Chemie Universität Duisburg-Essen Deutschland
| | - Peter Bayer
- Lehrstuhl für strukturelle und medizinische Biochemie Universität Duisburg-Essen Deutschland
| | - Carsten Schmuck
- Institut für organische Chemie Universität Duisburg-Essen Deutschland
| | - Michael Giese
- Institut für organische Chemie Universität Duisburg-Essen Deutschland
| | - Shirley K. Knauer
- Lehrstuhl für Molekularbiologie II Universität Duisburg-Essen Universitätsstraße 5 45141 Essen Deutschland
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49
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Miyagawa A, Eng J, Okada T, Inoue Y, Penfold TJ, Fukuhara G. Hydrostatic Pressure-Induced Spectral Variation of Reichardt's Dye: A Polarity/Pressure Dual Indicator. ACS OMEGA 2020; 5:897-903. [PMID: 31956843 PMCID: PMC6964516 DOI: 10.1021/acsomega.9b03880] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 12/10/2019] [Indexed: 06/10/2023]
Abstract
The famous solvatochromic Reichardt's dye was applied to quantify hydrostatic pressure in media. The UV/vis spectra of the dye in various organic solvents are shifted bathochromically or hypsochromically at the shorter- or longer-wavelength band, respectively, upon hydrostatic pressurization. The E T value, determined by an absorption maximum, in ethyl acetate increases from 38.5 kcal mol-1 at 0.1 MPa to 39.2 kcal mol-1 at 300 MPa, which is mostly equal to the one in chloroform at 0.1 MPa. These spectroscopic origins were supported by the time-dependent density functional theory (TD-DFT) calculations. The concept and approach proposed in this paper, i.e., a dual indicator, should attract the attention of a broad spectrum in multidisciplinary science.
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Affiliation(s)
- Akihisa Miyagawa
- Department
of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Julien Eng
- Chemistry-
School of Natural and Environmental Sciences, Newcastle University, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Tetsuo Okada
- Department
of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Yoshihisa Inoue
- Department
of Applied Chemistry, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan
| | - Thomas James Penfold
- Chemistry-
School of Natural and Environmental Sciences, Newcastle University, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Gaku Fukuhara
- Department
of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
- JST,
PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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50
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Jana GC, Nayim S, Sahoo NK, Das S, Aktara MN, Patra A, Islam MM, Hossain M. Deciphering the positional impact of chlorine in a new series of berberine analogues towards the superb-selective “turn-on” hydrophobic signaling of bovine serum albumin at physiological pH. NEW J CHEM 2020. [DOI: 10.1039/c9nj05642d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We report a new 9-O-benzyl substituted berberine analogue for the selective detection of BSA with a limit of detection value of 3.30 nM.
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Affiliation(s)
- Gopal Chandra Jana
- Department of Chemistry and Chemical Technology
- Vidyasagar University
- Midnapore
- India
| | - Sk Nayim
- Department of Chemistry and Chemical Technology
- Vidyasagar University
- Midnapore
- India
| | - Nandan Kumar Sahoo
- Department of Chemistry and Chemical Technology
- Vidyasagar University
- Midnapore
- India
| | - Somnath Das
- Department of Chemistry and Chemical Technology
- Vidyasagar University
- Midnapore
- India
| | - Mt Nasima Aktara
- Department of Chemistry and Chemical Technology
- Vidyasagar University
- Midnapore
- India
| | - Anirudha Patra
- Department of Chemistry and Chemical Technology
- Vidyasagar University
- Midnapore
- India
| | | | - Maidul Hossain
- Department of Chemistry and Chemical Technology
- Vidyasagar University
- Midnapore
- India
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