1
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Zhao Y, Zhao X, Duan L, Hou R, Gu Y, Liu Z, Chen J, Wu F, Yang L, Le XC, Wang Q, Yan X. Reinvent Aliphatic Arsenicals as Reversible Covalent Warheads toward Targeted Kinase Inhibition and Non-acute Promyelocytic Leukemia Cancer Treatment. J Med Chem 2024; 67:5458-5472. [PMID: 38556750 DOI: 10.1021/acs.jmedchem.3c02076] [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: 04/02/2024]
Abstract
The success of arsenic in acute promyelocytic leukemia (APL) treatment is hardly transferred to non-APL cancers, mainly due to the low selectivity and weak binding affinity of traditional arsenicals to oncoproteins critical for cancer survival. We present herein the reinvention of aliphatic trivalent arsenicals (As) as reversible covalent warheads of As-based targeting inhibitors toward Bruton's tyrosine kinase (BTK). The effects of As warheads' valency, thiol protection, methylation, spacer length, and size on inhibitors' activity were studied. We found that, in contrast to the bulky and rigid aromatic As warhead, the flexible aliphatic As warheads were well compatible with the well-optimized guiding group to achieve nanomolar inhibition against BTK. The optimized As inhibitors effectively blocked the BTK-mediated oncogenic signaling pathway, leading to elevated antiproliferative activities toward lymphoma cells and xenograft tumor. Our study provides a promising strategy enabling rational design of new aliphatic arsenic-based reversible covalent inhibitors toward non-APL cancer treatment.
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Affiliation(s)
- Yang Zhao
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xinyue Zhao
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Lewei Duan
- Laboratory of Epigenetics at Institutes of Biomedical Sciences and Intelligent Medicine Institute, Fudan University, Shanghai 200032, China
| | - Ruxue Hou
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yuxin Gu
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zhen Liu
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jianbin Chen
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Feizhen Wu
- Laboratory of Epigenetics at Institutes of Biomedical Sciences and Intelligent Medicine Institute, Fudan University, Shanghai 200032, China
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Limin Yang
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Qiuquan Wang
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xiaowen Yan
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
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2
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Karoń S, Drozd M, Malinowska E. A Careful Insight into DDI-Type Receptor Layers on the Way to Improvement of Click-Biology-Based Immunosensors. BIOSENSORS 2024; 14:136. [PMID: 38534243 DOI: 10.3390/bios14030136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/26/2024] [Accepted: 03/02/2024] [Indexed: 03/28/2024]
Abstract
Protein-based microarrays are important tools for high-throughput medical diagnostics, offering versatile platforms for multiplex immunodetection. However, challenges arise in protein microarrays due to the heterogeneous nature of proteins and, thus, differences in their immobilization conditions. This article advocates DNA-directed immobilization (DDI) as a solution, emphasizing its rapid and cost-effective fabrication of biosensing platforms. Thiolated single-stranded DNA and its analogues, such as ZNA® and PNA probes, were used to immobilize model proteins (anti-CRP antibodies and SARS-CoV nucleoprotein). The study explores factors influencing DDI-based immunosensor performance, including the purity of protein-DNA conjugates and the stability of their duplexes with DNA and analogues. It also provides insight into backfilling agent type and probe surface density. The research reveals that single-component monolayers lack protection against protein adsorption, while mixing the probes with long-chain ligands may hinder DNA-protein conjugate anchoring. Conventional DNA probes offer slightly higher surface density, while ZNA® probes exhibit better binding efficiency. Despite no enhanced stability in different ionic strength media, the cost-effectiveness of DNA probes led to their preference. The findings contribute to advancing microarray technology, paving the way for new generations of DDI-based multiplex platforms for rapid and robust diagnostics.
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Affiliation(s)
- Sylwia Karoń
- Department of Medical Diagnostics, Centre for Advanced Materials and Technologies CEZAMAT, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Marcin Drozd
- Department of Medical Diagnostics, Centre for Advanced Materials and Technologies CEZAMAT, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Elżbieta Malinowska
- Department of Medical Diagnostics, Centre for Advanced Materials and Technologies CEZAMAT, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
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3
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Komiya E, Takamatsu S, Miura D, Tsukakoshi K, Tsugawa W, Sode K, Ikebukuro K, Asano R. Exploration and Application of DNA-Binding Proteins to Make a Versatile DNA-Protein Covalent-Linking Patch (D-Pclip): The Case of a Biosensing Element. J Am Chem Soc 2024; 146:4087-4097. [PMID: 38295327 PMCID: PMC10870700 DOI: 10.1021/jacs.3c12668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 02/02/2024]
Abstract
DNA-protein complexes are attractive components with broad applications in various research fields, such as DNA aptamer-enzyme complexes as biosensing elements. However, noncovalent DNA-protein complexes often decrease detection sensitivity because they are highly susceptible to environmental conditions. In this study, we developed a versatile DNA-protein covalent-linking patch (D-Pclip) for fabricating covalent and stoichiometric DNA-protein complexes. We comprehensively explored the database to determine the DNA-binding ability of the candidates and selected UdgX as the only uracil-DNA glycosylase known to form covalent bonds with DNA via uracil, with a binding efficiency >90%. We integrated a SpyTag/SpyCatcher protein-coupling system into UdgX to create a universal and convenient D-Pclip. The usability of D-Pclip was shown by preparing a stoichiometric model complex of a hemoglobin (Hb)-binding aptamer and glucose oxidase (GOx) by mixing at 4 °C. The prepared aptamer-GOx complexes detected Hb in a dose-dependent manner within the clinically required detection range in buffer and human serum without any washing procedures. D-Pclip covalently connects any uracil-inserted DNA sequence and any SpyCatcher-fused protein stoichiometrically; therefore, it has a high potential for various applications.
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Affiliation(s)
- Erika Komiya
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Shouhei Takamatsu
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Daimei Miura
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kaori Tsukakoshi
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Wakako Tsugawa
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Koji Sode
- Joint
Department of Biomedical Engineering, University
of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina 27599, United States
- Institute
of Global Innovation Research, Tokyo University
of Agriculture and Technology, 3-8-1 Harumi-cho, Fuchu, Tokyo 183-8509, Japan
| | - Kazunori Ikebukuro
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Ryutaro Asano
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
- Institute
of Global Innovation Research, Tokyo University
of Agriculture and Technology, 3-8-1 Harumi-cho, Fuchu, Tokyo 183-8509, Japan
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4
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Siciliano G, Alsadig A, Chiriacò MS, Turco A, Foscarini A, Ferrara F, Gigli G, Primiceri E. Beyond traditional biosensors: Recent advances in gold nanoparticles modified electrodes for biosensing applications. Talanta 2024; 268:125280. [PMID: 37862755 DOI: 10.1016/j.talanta.2023.125280] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/22/2023]
Abstract
Gold nanoparticles (AuNPs) have emerged as powerful tools in the construction of highly sensitive electrochemical biosensors. Their unique properties, such as the ability to serve as an effective platform for biomolecule immobilization and to facilitate electron transfer between the electrode surface and the immobilized molecules, make them a promising choice for biosensor applications. Utilizing AuNPs modified electrodes can lead to improved sensitivity and lower limits of detection compared to unmodified electrodes. This review provides a comprehensive overview of the recent advancements and applications of AuNPs-based electrochemical biosensors in the biomedical field. The synthesis methods of AuNPs, their key properties, and various strategies employed for electrode modification are discussed. Furthermore, this review highlights the remarkable applications of these nanostructure-integrated electrodes, including immunosensors, enzyme biosensors, and DNA biosensors.
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Affiliation(s)
- Giulia Siciliano
- CNR NANOTEC Institute of Nanotechnology, via Monteroni, 73100 Lecce, Italy
| | - Ahmed Alsadig
- CNR NANOTEC Institute of Nanotechnology, via Monteroni, 73100 Lecce, Italy
| | | | - Antonio Turco
- CNR NANOTEC Institute of Nanotechnology, via Monteroni, 73100 Lecce, Italy
| | - Alessia Foscarini
- CNR NANOTEC Institute of Nanotechnology, via Monteroni, 73100 Lecce, Italy
| | - Francesco Ferrara
- CNR NANOTEC Institute of Nanotechnology, via Monteroni, 73100 Lecce, Italy.
| | - Giuseppe Gigli
- CNR NANOTEC Institute of Nanotechnology, via Monteroni, 73100 Lecce, Italy
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5
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Gokulu IS, Banta S. Biotechnology applications of proteins functionalized with DNA oligonucleotides. Trends Biotechnol 2023; 41:575-585. [PMID: 36115723 DOI: 10.1016/j.tibtech.2022.08.004] [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: 07/11/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 10/14/2022]
Abstract
The functionalization of proteins with DNA through the formation of covalent bonds enables a wide range of biotechnology advancements. For example, single-molecule analytical methods rely on bioconjugated DNA as elastic biolinkers for protein immobilization. Labeling proteins with DNA enables facile protein identification, as well as spatial and temporal organization and control of protein within DNA-protein networks. Bioconjugation reactions can target native, engineered, and non-canonical amino acids (NCAAs) within proteins. In addition, further protein engineering via the incorporation of peptide tags and self-labeling proteins can also be used for conjugation reactions. The selection of techniques will depend on application requirements such as yield, selectivity, conjugation position, potential for steric hindrance, cost, commercial availability, and potential impact on protein function.
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Affiliation(s)
- Ipek Simay Gokulu
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, USA
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, USA.
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6
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Watson EE, Winssinger N. Synthesis of Protein-Oligonucleotide Conjugates. Biomolecules 2022; 12:biom12101523. [PMID: 36291732 PMCID: PMC9599799 DOI: 10.3390/biom12101523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
Nucleic acids and proteins form two of the key classes of functional biomolecules. Through the ability to access specific protein-oligonucleotide conjugates, a broader range of functional molecules becomes accessible which leverages both the programmability and recognition potential of nucleic acids and the structural, chemical and functional diversity of proteins. Herein, we summarize the available conjugation strategies to access such chimeric molecules and highlight some key case study examples within the field to showcase the power and utility of such technology.
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Affiliation(s)
- Emma E. Watson
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- Correspondence: (E.E.W.); (N.W.)
| | - Nicolas Winssinger
- Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, CH-1205 Geneva, Switzerland
- Correspondence: (E.E.W.); (N.W.)
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7
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Biomimetic synthesis of protein-DNA-CaHPO 4 hybrid nanosheets for biosensing: Detection of thrombin as an example. Anal Chim Acta 2022; 1225:340227. [PMID: 36038237 DOI: 10.1016/j.aca.2022.340227] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/27/2022] [Accepted: 08/01/2022] [Indexed: 11/27/2022]
Abstract
Traditional strategies for coupling of proteins with DNA involve the additional modifications on protein or DNA to construct protein-DNA conjugates, resulting in complex or time-consuming coupling process. This study presented a biomimetic synthesis strategy to elaborately synthesize a new type of biomolecule-inorganic hybrid nanosheets. Horseradish peroxidase (HRP) and DNA aptamer can be easily combined with CaHPO4 via coprecipitation simultaneously to form all-inclusive HRP-aptamer-CaHPO4 hybrid (HAC) nanosheets integrating bifunction of biorecognition and signal amplification, which was proceeded in the green environment at room temperature and required no additional modifications on CaHPO4, protein and DNA. Therefore, it avoided tedious linking and purification procedures. The HAC nanosheets were then employed as the signal labels and showed excellent performance for detecting thrombin. This bioinspired approach provides great possibilities to facile and efficient immobilization of protein, DNA or even other types of biomolecules (e.g., RNA and peptide) on inorganic nanomaterials and endows great potential in the preparation of a variety of multifunctional biomolecule-CaHPO4 two-dimensional (2D) nanobiohybrids for various applications extending from biosensing to energy, biomedicine, environmental science and catalysis.
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8
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Yang W, Nan H, Xu Z, Huang Z, Chen S, Li J, Li J, Yang H. DNA-Templated Glycan Labeling for Monitoring Receptor Spatial Distribution in Living Cells. Anal Chem 2021; 93:12265-12272. [PMID: 34474560 DOI: 10.1021/acs.analchem.1c01815] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Tracking the spatial distribution of receptor tyrosine kinases in their native environment contributes to understanding the homeostatic or pathological states at a molecular level. Conjugation of DNA tags to a specific receptor is a powerful tool for monitoring receptor spatial distribution. However, long-term stable trafficking in live cells without interfering with the intrinsic receptor function remains a challenge. Here, we report a general DNA-templated glycan labeling strategy to track spatial distribution of a specific receptor in living cells. Different from existing target-selective covalent methods, the DNA tags were incorporated in glycan of a specific receptor via aptamer-assisted metabolic glycan labeling, thus resulting in minimal perturbation to the receptor's biological function. As proof of concept, covalent tagging of MET, HER2, and EGFR was achieved, and then the spatial distribution was successfully monitored, including homo-/heterodimerization and internalization. Overall, the proposed strategy will greatly aid in investigating receptor dynamics and is conducive to understanding their biological function in the native environment.
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Affiliation(s)
- Wen Yang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Hexin Nan
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Zhifei Xu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Zixiang Huang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Shan Chen
- Institute of Oceanography, Minjiang University, Fuzhou350108, Fujian, People's Republic of China
| | - Jingying Li
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China.,College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Juan Li
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Huanghao Yang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China
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9
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van der Zouwen AJ, Witte MD. Modular Approaches to Synthesize Activity- and Affinity-Based Chemical Probes. Front Chem 2021; 9:644811. [PMID: 33937194 PMCID: PMC8082414 DOI: 10.3389/fchem.2021.644811] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
Combinatorial and modular methods to synthesize small molecule modulators of protein activity have proven to be powerful tools in the development of new drug-like molecules. Over the past decade, these methodologies have been adapted toward utilization in the development of activity- and affinity-based chemical probes, as well as in chemoproteomic profiling. In this review, we will discuss how methods like multicomponent reactions, DNA-encoded libraries, phage displays, and others provide new ways to rapidly screen novel chemical probes against proteins of interest.
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Affiliation(s)
- Antonie J van der Zouwen
- Chemical Biology II, Stratingh Institute for Chemistry, University of Groningen, Groningen, Netherlands
| | - Martin D Witte
- Chemical Biology II, Stratingh Institute for Chemistry, University of Groningen, Groningen, Netherlands
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10
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Watson EE, Angerani S, Sabale PM, Winssinger N. Biosupramolecular Systems: Integrating Cues into Responses. J Am Chem Soc 2021; 143:4467-4482. [DOI: 10.1021/jacs.0c12970] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Emma E. Watson
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chem Biol, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Simona Angerani
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chem Biol, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Pramod M. Sabale
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chem Biol, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Nicolas Winssinger
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chem Biol, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
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11
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Flood D, Knouse KW, Vantourout JC, Kitamura S, Sanchez BB, Sturgell EJ, Chen JS, Wolan DW, Baran PS, Dawson PE. Synthetic Elaboration of Native DNA by RASS (SENDR). ACS CENTRAL SCIENCE 2020; 6:1789-1799. [PMID: 33145415 PMCID: PMC7596865 DOI: 10.1021/acscentsci.0c00680] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Indexed: 05/11/2023]
Abstract
Controlled site-specific bioconjugation through chemical methods to native DNA remains an unanswered challenge. Herein, we report a simple solution to achieve this conjugation through the tactical combination of two recently developed technologies: one for the manipulation of DNA in organic media and another for the chemoselective labeling of alcohols. Reversible adsorption of solid support (RASS) is employed to immobilize DNA and facilitate its transfer into dry acetonitrile. Subsequent reaction with P(V)-based Ψ reagents takes place in high yield with exquisite selectivity for the exposed 3' or 5' alcohols on DNA. This two-stage process, dubbed SENDR for Synthetic Elaboration of Native DNA by RASS, can be applied to a multitude of DNA conformations and sequences with a variety of functionalized Ψ reagents to generate useful constructs.
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Affiliation(s)
- Dillon
T. Flood
- Department
of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Kyle W. Knouse
- Department
of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Julien C. Vantourout
- Department
of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Seiya Kitamura
- Department
of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Brittany B. Sanchez
- Automated
Synthesis Facility, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Emily J. Sturgell
- Automated
Synthesis Facility, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jason S. Chen
- Automated
Synthesis Facility, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Dennis W. Wolan
- Department
of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Phil S. Baran
- Department
of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Philip E. Dawson
- Department
of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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12
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Lee J, Tatsumi A, Tsukakoshi K, Wilson ED, Abe K, Sode K, Ikebukuro K. Application of a Glucose Dehydrogenase-Fused with Zinc Finger Protein to Label DNA Aptamers for the Electrochemical Detection of VEGF. SENSORS 2020; 20:s20143878. [PMID: 32664558 PMCID: PMC7411789 DOI: 10.3390/s20143878] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/07/2020] [Accepted: 07/09/2020] [Indexed: 12/16/2022]
Abstract
Aptamer-based electrochemical sensors have gained attention in the context of developing a diagnostic biomarker detection method because of their rapid response, miniaturization ability, stability, and design flexibility. In such detection systems, enzymes are often used as labels to amplify the electrochemical signal. We have focused on glucose dehydrogenase (GDH) as a labeling enzyme for electrochemical detection owing to its high enzymatic activity, availability, and well-established electrochemical principle and platform. However, it is difficult and laborious to obtain one to one labeling of a GDH-aptamer complex with conventional chemical conjugation methods. In this study, we used GDH that was genetically fused to a DNA binding protein, i.e., zinc finger protein (ZF). Fused GDH can be attached to an aptamer spontaneously and site specifically in a buffer by exploiting the sequence-specific binding ability of ZF. Using such a fusion protein, we labeled a vascular endothelial growth factor (VEGF)-binding aptamer with GDH and detected the target electrochemically. As a result, upon the addition of glucose, the GDH labeled on the aptamer generated an amperometric signal, and the current response increased dependent on the VEGF concentration. Eventually, the developed electrochemical sensor proved to detect VEGF levels as low as 105 pM, thereby successfully demonstrating the concept of using ZF-fused GDH to enzymatically label aptamers.
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Affiliation(s)
- Jinhee Lee
- Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA; (J.L.); (E.D.W.); (K.S.)
| | - Atsuro Tatsumi
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan; (A.T.); (K.T.); (K.A.)
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan; (A.T.); (K.T.); (K.A.)
| | - Ellie D. Wilson
- Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA; (J.L.); (E.D.W.); (K.S.)
| | - Koichi Abe
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan; (A.T.); (K.T.); (K.A.)
| | - Koji Sode
- Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA; (J.L.); (E.D.W.); (K.S.)
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan; (A.T.); (K.T.); (K.A.)
- Correspondence: ; Tel.: +81-42-388-7030
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Mushtaq S, Park SH. Efficient 125I-radiolabeling of biomolecules using a strain-promoted oxidation-controlled cyclooctyne-1,2-quinone cycloaddition reaction. Chem Commun (Camb) 2020; 56:415-418. [PMID: 31821393 DOI: 10.1039/c9cc08982a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a novel 1,2-catechol based radioiodinated precursor for radioiodination of bicyclo[6.1.0]nonyne (BCN) installed biologically active molecules using a strain-promoted oxidation-controlled cyclooctyne-1,2-quinone cycloaddition reaction (SPOCQ) under ambient conditions. Compared to the reported methodologies, the new strategy demonstrates some clear advantages, including high in vitro and in vivo stability, high radiochemical yield, and exceptionally fast reaction kinetics at micro-molar concentration.
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Affiliation(s)
- Sajid Mushtaq
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeonbuk 56212, Republic of Korea.
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Dovgan I, Koniev O, Kolodych S, Wagner A. Antibody-Oligonucleotide Conjugates as Therapeutic, Imaging, and Detection Agents. Bioconjug Chem 2019; 30:2483-2501. [PMID: 31339691 DOI: 10.1021/acs.bioconjchem.9b00306] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Antibody-oligonucleotide conjugates (AOCs) are a novel class of synthetic chimeric biomolecules that has been continually gaining traction in different fields of modern biotechnology. This is mainly due to the unique combination of the properties of their two constituents, exceptional targeting abilities and antibody biodistribution profiles, in addition to an extensive scope of oligonucleotide functional and structural roles. Combining these two classes of biomolecules in one chimeric construct has therefore become an important milestone in the development of numerous biotechnological applications, including imaging (DNA-PAINT), detection (PLA, PEA), and therapeutics (targeted siRNA/antisense delivery). Numerous synthetic approaches have been developed to access AOCs ranging from stochastic chemical bioconjugation to site-specific conjugation with reactive handles, introduced into antibody sequences through protein engineering. This Review gives a general overview of the current status of AOC applications with a specific emphasis on the synthetic methods used for their preparation. The reported synthetic techniques are discussed in terms of their practical aspects and limitations. The importance of the development of novel methods for the facile generation of AOCs possessing a defined constitution is highlighted as a priority in AOC research to ensure the advance of their new applications.
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Affiliation(s)
- Igor Dovgan
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis , University of Strasbourg , 74 Route du Rhin , 67400 Illkirch-Graffenstaden , France
| | - Oleksandr Koniev
- Syndivia SAS , 650 Boulevard Gonthier d'Andernach , 67400 Illkirch-Graffenstaden , France
| | - Sergii Kolodych
- Syndivia SAS , 650 Boulevard Gonthier d'Andernach , 67400 Illkirch-Graffenstaden , France
| | - Alain Wagner
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis , University of Strasbourg , 74 Route du Rhin , 67400 Illkirch-Graffenstaden , France
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15
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Mortensen MR, Skovsgaard MB, Gothelf KV. Considerations on Probe Design for Affinity‐Guided Protein Conjugation. Chembiochem 2019; 20:2711-2728. [DOI: 10.1002/cbic.201900157] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Michael R. Mortensen
- Center for Multifunctional Biomolecular Drug DesignInterdisciplinary Nanoscience CenterAarhus University Gustav Wieds Vej 14 8000 Aarhus C Denmark
- Department of ChemistryAarhus University Langelandsgade 140 8000 Aarhus C Denmark
| | - Mikkel B. Skovsgaard
- Center for Multifunctional Biomolecular Drug DesignInterdisciplinary Nanoscience CenterAarhus University Gustav Wieds Vej 14 8000 Aarhus C Denmark
- Department of ChemistryAarhus University Langelandsgade 140 8000 Aarhus C Denmark
| | - Kurt V. Gothelf
- Center for Multifunctional Biomolecular Drug DesignInterdisciplinary Nanoscience CenterAarhus University Gustav Wieds Vej 14 8000 Aarhus C Denmark
- Department of ChemistryAarhus University Langelandsgade 140 8000 Aarhus C Denmark
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Abstract
The predictable nature of DNA interactions enables the programmable assembly of highly advanced 2D and 3D DNA structures of nanoscale dimensions. The access to ever larger and more complex structures has been achieved through decades of work on developing structural design principles. Concurrently, an increased focus has emerged on the applications of DNA nanostructures. In its nature, DNA is chemically inert and nanostructures based on unmodified DNA mostly lack function. However, functionality can be obtained through chemical modification of DNA nanostructures and the opportunities are endless. In this review, we discuss methodology for chemical functionalization of DNA nanostructures and provide examples of how this is being used to create functional nanodevices and make DNA nanostructures more applicable. We aim to encourage researchers to adopt chemical modifications as part of their work in DNA nanotechnology and inspire chemists to address current challenges and opportunities within the field.
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Affiliation(s)
- Mikael Madsen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
| | - Kurt V Gothelf
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
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17
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Burgahn T, Garrecht R, Rabe KS, Niemeyer CM. Solid-Phase Synthesis and Purification of Protein-DNA Origami Nanostructures. Chemistry 2019; 25:3483-3488. [PMID: 30609150 DOI: 10.1002/chem.201805506] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/07/2018] [Indexed: 12/13/2022]
Abstract
We present a facile method for the combined synthesis and purification of protein-decorated DNA origami nanostructures (DONs). DONs bearing reductively cleavable biotin groups in addition to ligands for ligation of recombinant proteins are bound to magnetic beads. Protein immobilization is conducted with a large protein excess to achieve high ligation yields. Subsequent to cleavage from the solid support, pure sample solutions are obtained which are suitable for direct AFM analysis of occupation patterns. We demonstrate the method's utility using three different orthogonal ligation methods, the "halo-based oligonucleotide binder" (HOB), a variant of Halo-tag, the "SpyTag/SpyCatcher" (ST/SC) system, and the enzymatic "ybbR tag" coupling. We find surprisingly low efficiency for ST/SC ligation, presumably due to electrostatic repulsion and steric hindrance, whereas the ybbR method, despite its ternary nature, shows good ligation yields. Our method is particularly useful for the development of novel ligation methods and the synthesis of mechanically fragile DONs that present protein patterns for surface-based cell assays.
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Affiliation(s)
- Teresa Burgahn
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Ruben Garrecht
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Kersten S Rabe
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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