1
|
Schuster F, Grau BW, Xu HG, Mokhir A, Tsogoeva SB. Dipeptide-catalysed Michael reaction under physiological conditions: Examination of potential bioorthogonality. Bioorg Med Chem 2024; 103:117650. [PMID: 38492540 DOI: 10.1016/j.bmc.2024.117650] [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: 08/02/2023] [Revised: 02/13/2024] [Accepted: 02/19/2024] [Indexed: 03/18/2024]
Abstract
Reactions for drug synthesis under cell-like conditions or even inside living cells can potentially be used e.g., to minimize toxic side effects, to maximize bioactive compound efficacy and/or to address drug delivery problems. Those reactions should be bioorthogonal to enable the generation of drug-like compounds with sufficiently good yields. In the known bioorthogonal Michael reactions, using thiols and phosphines as nucleophiles (e.g., in CS and CP bond formation reactions) is very common. No bioorthogonal Michael addition with a carbon nucleophile is known yet. Therefore, the development of such a reaction might be interesting for future drug discovery research. In this work, the metal-free Michael addition between cyclohexanone and various trans-β-nitrostyrenes (CC bond formation reaction), catalysed by a dipeptide salt H-Pro-Phe-O-Na+, was investigated for the first time in the presence of glutathione (GSH) and in phosphate-buffered saline (PBS). We demonstrated that with electron-withdrawing substituents on the aromatic ring and in β-position of the trans-β-nitrostyrene yields up to 64% can be obtained under physiological conditions, indicating a potential bioorthogonality of the studied Michael reaction. In addition, the selected Michael products demonstrated activity against human ovarian cancer cells A2780. This study opens up a new vista for forming bioactive compounds via CC bond formation Michael reactions under physiological (cell-like) conditions.
Collapse
Affiliation(s)
- Florian Schuster
- Organic Chemistry Chair I, Friedrich-Alexander University of Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
| | - Benedikt W Grau
- Organic Chemistry Chair I, Friedrich-Alexander University of Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
| | - Hong-Gui Xu
- Organic Chemistry Chair II, Friedrich-Alexander University of Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
| | - Andriy Mokhir
- Organic Chemistry Chair II, Friedrich-Alexander University of Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
| | - Svetlana B Tsogoeva
- Organic Chemistry Chair I, Friedrich-Alexander University of Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany.
| |
Collapse
|
2
|
Kuzmina NS, Fedotova EA, Jankovic P, Gribova GP, Nyuchev AV, Fedorov AY, Otvagin VF. Enhancing Precision in Photodynamic Therapy: Innovations in Light-Driven and Bioorthogonal Activation. Pharmaceutics 2024; 16:479. [PMID: 38675140 PMCID: PMC11053670 DOI: 10.3390/pharmaceutics16040479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 03/29/2024] [Accepted: 03/29/2024] [Indexed: 04/28/2024] Open
Abstract
Over the past few decades, photodynamic therapy (PDT) has evolved as a minimally invasive treatment modality offering precise control over cancer and various other diseases. To address inherent challenges associated with PDT, researchers have been exploring two promising avenues: the development of intelligent photosensitizers activated through light-induced energy transfers, charges, or electron transfers, and the disruption of photosensitive bonds. Moreover, there is a growing emphasis on the bioorthogonal delivery or activation of photosensitizers within tumors, enabling targeted deployment and activation of these intelligent photosensitive systems in specific tissues, thus achieving highly precise PDT. This concise review highlights advancements made over the last decade in the realm of light-activated or bioorthogonal photosensitizers, comparing their efficacy and shaping future directions in the advancement of photodynamic therapy.
Collapse
Affiliation(s)
| | | | | | | | | | - Alexey Yu. Fedorov
- Department of Organic Chemistry, Lobachevsky State University of Nizhny Novgorod, Gagarina Av. 23, 603950 Nizhny Novgorod, Russia; (N.S.K.); (E.A.F.); (P.J.); (G.P.G.); (A.V.N.)
| | - Vasilii F. Otvagin
- Department of Organic Chemistry, Lobachevsky State University of Nizhny Novgorod, Gagarina Av. 23, 603950 Nizhny Novgorod, Russia; (N.S.K.); (E.A.F.); (P.J.); (G.P.G.); (A.V.N.)
| |
Collapse
|
3
|
Emanuelson C, Bardhan A, Deiters A. DNA Logic Gates for Small Molecule Activation Circuits in Cells. ACS Synth Biol 2024; 13:538-545. [PMID: 38306634 PMCID: PMC10877608 DOI: 10.1021/acssynbio.3c00474] [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: 08/02/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 02/04/2024]
Abstract
DNA-based devices such as DNA logic gates self-assemble into supramolecular structures, as dictated by the sequences of the constituent oligonucleotides and their predictable Watson-Crick base pairing interactions. The programmable nature of DNA-based devices permits the design and implementation of DNA circuits that interact in a dynamic and sequential manner capable of spatially arranging disparate DNA species. Here, we report the application of an activatable fluorescence reporter based on a proximity-driven inverse electron demand Diels-Alder (IEDDA) reaction and its robust integration with DNA strand displacement circuits. In response to specific DNA input patterns, sequential strand displacement reactions are initiated and culminate in the hybridization of two modified DNA strands carrying probes capable of undergoing an IEDDA reaction between a vinyl-ether-caged fluorophore and its reactive partner tetrazine, leading to the activation of fluorescence. This approach provides a major advantage for DNA computing in mammalian cells since circuit degradation does not induce fluorescence, in contrast to traditional fluorophore-quencher designs. We demonstrate the robustness and sensitivity of the reporter by testing its ability to serve as a readout for DNA logic circuits of varying complexity inside cells.
Collapse
Affiliation(s)
- Cole Emanuelson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Anirban Bardhan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| |
Collapse
|
4
|
Huang J, Yao Z, Li B, Ping Y. Targeted delivery of PROTAC-based prodrug activated by bond-cleavage bioorthogonal chemistry for microneedle-assisted cancer therapy. J Control Release 2023; 361:270-279. [PMID: 37541594 DOI: 10.1016/j.jconrel.2023.07.062] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/17/2023] [Accepted: 07/31/2023] [Indexed: 08/06/2023]
Abstract
Proteolysis-targeting chimera (PROTAC) is emerging as a new strategy to degrade target proteins in a precise way by taking advantage of the cellular ubiquitin-proteasome system. However, the potential cytotoxicity of PROTAC should be avoided to mitigate the off-target degradation of proteins in healthy tissues or cells. To address this issue, we herein present a strategy to cage a PROTAC with 4-(vinyloxy) benzyl carbonate (MZ1-O), which can be eliminated through a 3,6-dimethyl-1,2,4,5-tetrazine (Tz)-mediated inverse electron-demand Diels-Alder (iEDDA) reaction to generate a BRD4 (bromodomain-containing protein 4) degrader, MZ1. We further propose a dissolvable microneedle-assisted strategy for site-specific activation of MZ1-O that is delivered by a targeted delivery vector through systemic route in vivo, and demonstrate such a bioorthogonal strategy is efficient and precise for tumor treatment. Our study suggests that the bioorthogonal activation of PROTAC-based prodrug offers a highly specific and precise approach for cancer therapy.
Collapse
Affiliation(s)
- Jing Huang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
| | - Zhuo Yao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Department of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou 310003, China
| | - Bowen Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Yuan Ping
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China.
| |
Collapse
|
5
|
Gavriel K, van Doeselaar DCA, Geers DWT, Neumann K. Click'n lock: rapid exchange between unsymmetric tetrazines and thiols for reversible, chemoselective functionalisation of biomolecules with on-demand bioorthogonal locking. RSC Chem Biol 2023; 4:685-691. [PMID: 37654505 PMCID: PMC10467616 DOI: 10.1039/d3cb00062a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/19/2023] [Indexed: 09/02/2023] Open
Abstract
The late-stage functionalisation and diversification of complex structures including biomolecules is often achieved with the help of click chemistry. Besides employing irreversible click-like reactions, many synthetic applications benefit from reversible click reaction strategies, so called de-/trans-click approaches. Yet, the combination of both, reversible and irreversible click chemistry - while still respecting the stringent criteria of click transformations - remains so far elusive for modifications of biomolecular structures. Here, we report click'n lock as a concept that enables reversible click reactions and on-demand locking of chemical entities, thus switching from reversible to irreversible modifications of complex biomolecules. For this purpose, we employ the tetrazine-thiol exchange (TeTEx) reaction as a fully traceless click reaction with second order rate constants k2 higher than 2 M-1 s-1 within aqueous environments. Employing TeTEx as a reversible click reaction for the chemoselective modification of biomolecules is made possible by the use of 3,6-disubstituted 1,2,4,5-tetrazines bearing a single sulfide residue. The inherent reactivity of tetrazines towards inverse electron demand Diels-Alder (IEDDA) reactions allows to stabilize the clicked structure, switching from reversible to irreversible systems (click'n lock).
Collapse
Affiliation(s)
- Katerina Gavriel
- Systems Chemistry Department, Institute for Molecules and Materials, Radboud University Nijmegen Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Dustin C A van Doeselaar
- Systems Chemistry Department, Institute for Molecules and Materials, Radboud University Nijmegen Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Daniëlle W T Geers
- Systems Chemistry Department, Institute for Molecules and Materials, Radboud University Nijmegen Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Kevin Neumann
- Systems Chemistry Department, Institute for Molecules and Materials, Radboud University Nijmegen Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| |
Collapse
|
6
|
Yang J, Zhu B, Ran C. The Application of Bio-orthogonality for In Vivo Animal Imaging. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:434-447. [PMID: 37655167 PMCID: PMC10466453 DOI: 10.1021/cbmi.3c00033] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 09/02/2023]
Abstract
The application of bio-orthogonality has greatly facilitated numerous aspects of biological studies in recent years. In particular, bio-orthogonal chemistry has transformed biological research, including in vitro conjugate chemistry, target identification, and biomedical imaging. In this review, we highlighted examples of bio-orthogonal in vivo imaging published in recent years. We grouped the references into two major categories: bio-orthogonal chemistry-related imaging and in vivo imaging with bio-orthogonal nonconjugated pairing. Lastly, we discussed the challenges and opportunities of bio-orthogonality for in vivo imaging.
Collapse
Affiliation(s)
- Jun Yang
- Athinoula
A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Room 2301, Building 149, Charlestown, Boston, Massachusetts 02129, United States
| | - Biyue Zhu
- Athinoula
A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Room 2301, Building 149, Charlestown, Boston, Massachusetts 02129, United States
| | - Chongzhao Ran
- Athinoula
A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Room 2301, Building 149, Charlestown, Boston, Massachusetts 02129, United States
| |
Collapse
|
7
|
Kozma E, Bojtár M, Kele P. Bioorthogonally Assisted Phototherapy: Recent Advances and Prospects. Angew Chem Int Ed Engl 2023; 62:e202303198. [PMID: 37161824 DOI: 10.1002/anie.202303198] [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: 03/03/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/11/2023]
Abstract
Photoresponsive materials offer excellent spatiotemporal control over biological processes and the emerging phototherapeutic methods are expected to have significant effects on targeted cancer therapies. Recent examples show that combination of photoactivatable approaches with bioorthogonal chemistry enhances the precision of targeted phototherapies and profound implications are foreseen particularly in the treatment of disperse/diffuse tumors. The extra level of on-target selectivity and improved spatial/temporal control considerably intensified related bioorthogonally assisted phototherapy research. The anticipated growth of further developments in the field justifies the timeliness of a brief summary of the state of the art.
Collapse
Affiliation(s)
- Eszter Kozma
- Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - Márton Bojtár
- Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - Péter Kele
- Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| |
Collapse
|
8
|
Pham SL, Kim T, McDonald FE. Stereospecific Cu(I)-Catalyzed C-O Cross-Coupling Synthesis of Acyclic 1,2-Di- and Trisubstituted Vinylic Ethers from Alcohols and Vinylic Halides. Org Lett 2023. [PMID: 37437300 PMCID: PMC10367064 DOI: 10.1021/acs.orglett.3c01849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
CuI and trans-N,N'-dimethylcyclohexyldiamine catalyze the single-step C-O bond cross-coupling between 1,2-di- and trisubstituted vinylic halides with functionalized alcohols, producing acyclic vinylic ethers. This stereospecific transformation selectively gives each of the (E)- and (Z)-vinylic ether products from the corresponding vinyl halide precursors. This method is compatible with carbohydrate-derived primary and secondary alcohols and several other functional groups. The conditions are mild enough to reliably generate vinylic allylic ethers without promoting Claisen rearrangements.
Collapse
Affiliation(s)
- San L Pham
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| | - Taehee Kim
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| | - Frank E McDonald
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| |
Collapse
|
9
|
Devi G, Hedger AK, Whitby RJ, Watts JK. Double Click: Unexpected 1:2 Stoichiometry in a Norbornene-Tetrazine Reaction. J Org Chem 2023; 88:5341-5347. [PMID: 37058436 PMCID: PMC10167953 DOI: 10.1021/acs.joc.2c02861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Indexed: 04/15/2023]
Abstract
We report a new reactivity for the inverse electron demand Diels-Alder (iEDDA) reaction between norbornene and tetrazine. Instead of simple 1:1 condensation between norbornene- and tetrazine-conjugated biomolecules, we observed that dimeric products were preferentially formed. As such, an olefinic intermediate formed after the addition of the first tetrazine unit to norbornene rapidly undergoes a consecutive cycloaddition reaction with a second tetrazine unit to result in a conjugate with a 1:2 stoichiometric ratio. This unexpected dimer formation was consistently observed in the reactions of both small-molecule norbornenes and tetrazines, as well as oligonucleotide conjugates. When norbornene was replaced with bicyclononyne to bypass the formation of this olefinic reaction intermediate, the reactions resulted exclusively in rapid formation of the expected 1:1 stoichiometric conjugates.
Collapse
Affiliation(s)
- Gitali Devi
- RNA
Therapeutics Institute, UMass Chan Medical
School, Worcester, Massachusetts 01605, United States
| | - Adam K. Hedger
- RNA
Therapeutics Institute, UMass Chan Medical
School, Worcester, Massachusetts 01605, United States
- Department
of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Richard J. Whitby
- Department
of Chemistry, University of Southampton, SO17 1BJ Southampton, U.K.
| | - Jonathan K. Watts
- RNA
Therapeutics Institute, UMass Chan Medical
School, Worcester, Massachusetts 01605, United States
- Department
of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, Massachusetts 01605, United States
- Li Weibo
Rare Disease Institute, UMass Chan Medical
School, Worcester, Massachusetts 01605, United States
| |
Collapse
|
10
|
Shu Z, Sun S, Gu N, Yang Z, Shang Y, Yang Y, Xia M, Lin B, Yang P. An amphiphilic macrocyclic acylhydrazone dimer: Facile synthesis and dual channel detection and removal of phthalate anion. Anal Chim Acta 2023; 1253:341093. [PMID: 36965995 DOI: 10.1016/j.aca.2023.341093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023]
Abstract
Despite the large number of dicarboxylates' receptors, the dual channel ones capable of recognizing and removing of phthalate anion are rare and the task remains challenging. In this paper, a facilely synthesized amphiphilic macrocyclic acylhydrazone dimer (AMAD) can not only detect phthalate anion selectively, through both color changes and turn-on fluorescence in solution as well as in solid state, but is also able to remove it from either water or organic solvents. The current study paves the way for the search of more multiple functional receptors of dicarboxylates anions.
Collapse
Affiliation(s)
- Zhengning Shu
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Shitao Sun
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Ning Gu
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Zhichao Yang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Yongxin Shang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Yi Yang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Mingyu Xia
- School of Life Sciences and Biological Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, China.
| | - Bin Lin
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, 110016, China.
| | - Peng Yang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, 110016, China.
| |
Collapse
|
11
|
Niu L, Cao Q, Zhang T, Zhang Y, Liang T, Wang J. Simultaneous detection of mitochondrial viscosity and peroxynitrite in livers from subjects with drug-induced fatty liver disease using a novel fluorescent probe. Talanta 2023; 260:124591. [PMID: 37141820 DOI: 10.1016/j.talanta.2023.124591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/19/2023] [Accepted: 04/23/2023] [Indexed: 05/06/2023]
Abstract
Drug-induced fatty liver disease (DIFLD) is a basic clinicopathological example of drug-induced liver injury (DILI). Some drugs can inhibit β-oxidation in hepatocyte mitochondria, leading to steatosis in the liver. Additionally, drug-induced inhibition of β-oxidation and the electron transport chain (ETC) can lead to increased production of reactive oxygen species (ROS) such as peroxynitrite (ONOO-). Therefore, it is reasonable to suspect that compared to a healthy liver, viscosity and ONOO- levels are elevated in livers during DIFLD. A novel, smart, dual-response fluorescent probe-Mito-VO-was designed and synthesized for the simultaneous detection of viscosity and ONOO- content. This probe had a large emission shift of 293 nm and was capable of monitoring the viscosity of, and the ONOO- content in, cell and animal models alike, either individually or simultaneously. For the first time, Mito-VO was successfully used to demonstrate the elevated viscosity and the amount of ONOO- in livers from mice with DIFLD.
Collapse
Affiliation(s)
- Linqiang Niu
- Key Laboratory of Natural Medicine and Immuno-Engineering of Henan Province, Henan University, Kaifeng, 475004, PR China
| | - Qijuan Cao
- Key Laboratory of Natural Medicine and Immuno-Engineering of Henan Province, Henan University, Kaifeng, 475004, PR China
| | - Tian Zhang
- Key Laboratory of Natural Medicine and Immuno-Engineering of Henan Province, Henan University, Kaifeng, 475004, PR China
| | - Yahong Zhang
- Key Laboratory of Natural Medicine and Immuno-Engineering of Henan Province, Henan University, Kaifeng, 475004, PR China
| | - Tingting Liang
- Key Laboratory of Natural Medicine and Immuno-Engineering of Henan Province, Henan University, Kaifeng, 475004, PR China.
| | - Jianhong Wang
- Key Laboratory of Natural Medicine and Immuno-Engineering of Henan Province, Henan University, Kaifeng, 475004, PR China.
| |
Collapse
|
12
|
Rosenberger JE, Xie Y, Fang Y, Lyu X, Trout WS, Dmitrenko O, Fox JM. Ligand-Directed Photocatalysts and Far-Red Light Enable Catalytic Bioorthogonal Uncaging inside Live Cells. J Am Chem Soc 2023; 145:6067-6078. [PMID: 36881718 PMCID: PMC10589873 DOI: 10.1021/jacs.2c10655] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Described are ligand-directed catalysts for live-cell, photocatalytic activation of bioorthogonal chemistry. Catalytic groups are localized via a tethered ligand either to DNA or to tubulin, and red light (660 nm) photocatalysis is used to initiate a cascade of DHTz oxidation, intramolecular Diels-Alder reaction, and elimination to release phenolic compounds. Silarhodamine (SiR) dyes, more conventionally used as biological fluorophores, serve as photocatalysts that have high cytocompatibility and produce minimal singlet oxygen. Commercially available conjugates of Hoechst dye (SiR-H) and docetaxel (SiR-T) are used to localize SiR to the nucleus and microtubules, respectively. Computation was used to assist the design of a new class of redox-activated photocage to release either phenol or n-CA4, a microtubule-destabilizing agent. In model studies, uncaging is complete within 5 min using only 2 μM SiR and 40 μM photocage. In situ spectroscopic studies support a mechanism involving rapid intramolecular Diels-Alder reaction and a rate-determining elimination step. In cellular studies, this uncaging process is successful at low concentrations of both the photocage (25 nM) and the SiR-H dye (500 nM). Uncaging n-CA4 causes microtubule depolymerization and an accompanying reduction in cell area. Control studies demonstrate that SiR-H catalyzes uncaging inside the cell, and not in the extracellular environment. With SiR-T, the same dye serves as a photocatalyst and the fluorescent reporter for microtubule depolymerization, and with confocal microscopy, it was possible to visualize microtubule depolymerization in real time as the result of photocatalytic uncaging in live cells.
Collapse
Affiliation(s)
- Julia E. Rosenberger
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Yixin Xie
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Yinzhi Fang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Xinyi Lyu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - William S. Trout
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Olga Dmitrenko
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Joseph M. Fox
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| |
Collapse
|
13
|
Dong R, Yang X, Wang B, Ji X. Mutual leveraging of proximity effects and click chemistry in chemical biology. Med Res Rev 2023; 43:319-342. [PMID: 36177531 DOI: 10.1002/med.21927] [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: 11/30/2021] [Revised: 08/14/2022] [Accepted: 09/11/2022] [Indexed: 02/05/2023]
Abstract
Nature has the remarkable ability to realize reactions under physiological conditions that normally would require high temperature and other forcing conditions. In doing so, often proximity effects such as simultaneous binding of two reactants in the same pocket and/or strategic positioning of catalytic functional groups are used as ways to achieve otherwise kinetically challenging reactions. Though true biomimicry is challenging, there have been many beautiful examples of how to leverage proximity effects in realizing reactions that otherwise would not readily happen under near-physiological conditions. Along this line, click chemistry is often used to endow proximity effects, and proximity effects are also used to further leverage the facile and bioorthogonal nature of click chemistry. This review brings otherwise seemingly unrelated topics in chemical biology and drug discovery under one unifying theme of mutual leveraging of proximity effects and click chemistry and aims to critically analyze the biomimicry use of such leveraging effects as powerful approaches in chemical biology and drug discovery. We hope that this review demonstrates the power of employing mutual leveraging proximity effects and click chemistry and inspires the development of new strategies that will address unmet needs in chemistry and biology.
Collapse
Affiliation(s)
- Ru Dong
- Department of Medicinal Chemistry, College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu, China
| | - Xiaoxiao Yang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Binghe Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Xingyue Ji
- Department of Medicinal Chemistry, College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu, China
| |
Collapse
|
14
|
Mitry MMA, Greco F, Osborn HMI. In Vivo Applications of Bioorthogonal Reactions: Chemistry and Targeting Mechanisms. Chemistry 2023; 29:e202203942. [PMID: 36656616 DOI: 10.1002/chem.202203942] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/20/2023]
Abstract
Bioorthogonal chemistry involves selective biocompatible reactions between functional groups that are not normally present in biology. It has been used to probe biomolecules in living systems, and has advanced biomedical strategies such as diagnostics and therapeutics. In this review, the challenges and opportunities encountered when translating in vitro bioorthogonal approaches to in vivo settings are presented, with a focus on methods to deliver the bioorthogonal reaction components. These methods include metabolic bioengineering, active targeting, passive targeting, and simultaneously used strategies. The suitability of bioorthogonal ligation reactions and bond cleavage reactions for in vivo applications is critically appraised, and practical considerations such as the optimum scheduling regimen in pretargeting approaches are discussed. Finally, we present our own perspectives for this area and identify what, in our view, are the key challenges that must be overcome to maximise the impact of these approaches.
Collapse
Affiliation(s)
- Madonna M A Mitry
- Reading School of Pharmacy, University of Reading Whiteknights, Reading, RG6 6AD, UK.,Department of Pharmaceutical Chemistry Faculty of Pharmacy, Ain Shams University, Cairo, 11566, Egypt
| | - Francesca Greco
- Reading School of Pharmacy, University of Reading Whiteknights, Reading, RG6 6AD, UK
| | - Helen M I Osborn
- Reading School of Pharmacy, University of Reading Whiteknights, Reading, RG6 6AD, UK
| |
Collapse
|
15
|
Dong F, Yan W, Dong W, Shang X, Xu Y, Liu W, Wu Y, Wei W, Zhao T. DNA-enabled fluorescent-based nanosensors monitoring tumor-related RNA toward advanced cancer diagnosis: A review. Front Bioeng Biotechnol 2022; 10:1059845. [DOI: 10.3389/fbioe.2022.1059845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 11/18/2022] [Indexed: 12/02/2022] Open
Abstract
As a burgeoning non-invasive indicator for reproducible cancer diagnosis, tumor-related biomarkers have a wide range of applications in early cancer screening, efficacy monitoring, and prognosis predicting. Accurate and efficient biomarker determination, therefore, is of great importance to prevent cancer progression at an early stage, thus reducing the disease burden on the entire population, and facilitating advanced therapies for cancer. During the last few years, various DNA structure-based fluorescent probes have established a versatile platform for biological measurements, due to their inherent biocompatibility, excellent capacity to recognize nucleic and non-nucleic acid targets, obvious accessibility to synthesis as well as chemical modification, and the ease of interfacing with signal amplification protocols. After decades of research, DNA fluorescent probe technology for detecting tumor-related mRNAs has gradually grown to maturity, especially the advent of fluorescent nanoprobes has taken the process to a new level. Here, a systematic introduction to recent trends and advances focusing on various nanomaterials-related DNA fluorescent probes and the physicochemical properties of various involved nanomaterials (such as AuNP, GO, MnO2, SiO2, AuNR, etc.) are also presented in detail. Further, the strengths and weaknesses of existing probes were described and their progress in the detection of tumor-related mRNAs was illustrated. Also, the salient challenges were discussed later, with a few potential solutions.
Collapse
|
16
|
Zhao G, Li Z, Zhang R, Zhou L, Zhao H, Jiang H. Tetrazine bioorthogonal chemistry derived in vivo imaging. Front Mol Biosci 2022; 9:1055823. [PMID: 36465558 PMCID: PMC9709424 DOI: 10.3389/fmolb.2022.1055823] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/26/2022] [Indexed: 09/02/2023] Open
Abstract
Bioorthogonal chemistry represents plenty of highly efficient and biocompatible reactions that proceed selectively and rapidly in biological situations without unexpected side reactions towards miscellaneous endogenous functional groups. Arise from the strict demands of physiological reactions, bioorthogonal chemical reactions are natively selective transformations that are rarely found in biological environments. Bioorthogonal chemistry has long been applied to tracking and real-time imaging of biomolecules in their physiological environments. Thereinto, tetrazine bioorthogonal reactions are particularly important and have increasing applications in these fields owing to their unique properties of easily controlled fluorescence or radiation off-on mechanism, which greatly facilitate the tracking of real signals without been disturbed by background. In this mini review, tetrazine bioorthogonal chemistry for in vivo imaging applications will be attentively appraised to raise some guidelines for prior tetrazine bioorthogonal chemical studies.
Collapse
Affiliation(s)
- Gaoxiang Zhao
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- Cancer Institute, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Zhutie Li
- China United Test and Evaluation (Qingdao) Co. Ltd., Qingdao, China
| | - Renshuai Zhang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- Cancer Institute, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Liman Zhou
- Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning, China
| | - Haibo Zhao
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- Department of Sports Medicine, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Hongfei Jiang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- Cancer Institute, Affiliated Hospital of Qingdao University, Qingdao, China
| |
Collapse
|
17
|
Chen Z, Wang WT, Wang W, Huang J, Liao JY, Zeng S, Qian L. Sensitive Imaging of Cellular RNA via Cascaded Proximity-Induced Fluorogenic Reactions. ACS APPLIED MATERIALS & INTERFACES 2022; 14:44054-44064. [PMID: 36153979 DOI: 10.1021/acsami.2c10355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Owing to its important biological functions, RNA has become a promising molecular biomarker of various diseases. With a dynamic change in its expression level and a relatively low amount within the complicated biological matrix, signal amplification detection based on DNA probes has been put forward, which is helpful for early diagnosis and prognostic prediction. However, conventional methods are confined to cell lysates or dead cells and are not only time-consuming in sample preparation but also inaccessible to the spatial-temporal information of target RNAs. To achieve live-cell imaging of specific RNAs, both the detection sensitivity and intracellular delivery issues should be addressed. Herein, a new cascaded fluorogenic system based on the combination of hybridization chain reactions (HCRs) and proximity-induced bioorthogonal chemistry is developed, in which a bioorthogonal reaction pair (a tetrazine-quenched dye and its complementary dienophile) is brought into spatial proximity upon target RNA triggering the HCR to turn on and amplify the fluorescence in one step, sensitively indicating the cellular distribution of RNA with minimal false positive results caused by unspecific degradation. Facilitated by a biodegradable carrier based on black phosphorus with high loading capacity and excellent biocompatibility, the resulting imaging platform allows wash-free tracking of target RNAs inside living cells.
Collapse
Affiliation(s)
- Zhiyan Chen
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Wen-Tao Wang
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Wenchao Wang
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Jinsong Huang
- Department of Liver Disease, Hangzhou Xixi Hospital, Hangzhou 310023, China
| | - Jia-Yu Liao
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou 310018, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Linghui Qian
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
18
|
Tang L, Bednar RM, Rozanov ND, Hemshorn ML, Mehl RA, Fang C. Rational Design for High Bioorthogonal Fluorogenicity of Tetrazine-Encoded Green Fluorescent Proteins. NATURAL SCIENCES (WEINHEIM, GERMANY) 2022; 2:e20220028. [PMID: 36440454 PMCID: PMC9699285 DOI: 10.1002/ntls.20220028] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The development of bioorthogonal fluorogenic probes constitutes a vital force to advance life sciences. Tetrazine-encoded green fluorescent proteins (GFPs) show high bioorthogonal reaction rate and genetic encodability, but suffer from low fluorogenicity. Here, we unveil the real-time fluorescence mechanisms by investigating two site-specific tetrazine-modified superfolder GFPs via ultrafast spectroscopy and theoretical calculations. Förster resonance energy transfer (FRET) is quantitatively modeled and revealed to govern the fluorescence quenching; for GFP150-Tet with a fluorescence turn-on ratio of ~9, it contains trimodal subpopulations with good (P1), random (P2), and poor (P3) alignments between the transition dipole moments of protein chromophore (donor) and tetrazine tag (Tet-v2.0, acceptor). By rationally designing a more free/tight environment, we created new mutants Y200A/S202Y to introduce more P2/P1 populations and improve the turn-on ratios to ~14/31, making the fluorogenicity of GFP150-Tet-S202Y the highest among all up-to-date tetrazine-encoded GFPs. In live eukaryotic cells, the GFP150-Tet-v3.0-S202Y mutant demonstrates notably increased fluorogenicity, substantiating our generalizable design strategy.
Collapse
Affiliation(s)
- Longteng Tang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331-4003, USA
| | - Riley M. Bednar
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences Building, Corvallis, Oregon 97331-7305, USA
| | - Nikita D. Rozanov
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331-4003, USA
| | - Marcus L. Hemshorn
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences Building, Corvallis, Oregon 97331-7305, USA
| | - Ryan A. Mehl
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences Building, Corvallis, Oregon 97331-7305, USA
| | - Chong Fang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331-4003, USA
| |
Collapse
|
19
|
Wang P, Li M, Zhou F, Yang Y, Yin X, Zhang XB, Song G. COF-based nanoreactors for click-activated prodrug delivery and precise anti-vascular therapy. Chem Commun (Camb) 2022; 58:11107-11110. [PMID: 36102676 DOI: 10.1039/d2cc03931a] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we report a new click-activated prodrug, CA4V, and a bioorthogonal nanoreactor, CA4V/ZIF-90@TzCOF@Apt, which consists of a ZIF-90 core, tetrazine-based covalent organic framework (COF) shells and an aptamer polymer coating. When targeting a tumor, the acid-causing collapse of ZIF-90 initiates a nanoconfined bioorthogonal reaction in defined COF cages, which boosts the click efficiency of CA4V activation and therapeutic effects in vivo.
Collapse
Affiliation(s)
- Peng Wang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China. .,The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Mili Li
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Fang Zhou
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China. .,The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yue Yang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Xia Yin
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Guosheng Song
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| |
Collapse
|
20
|
Kang D, Lee S, Kim J. Bioorthogonal Click and Release: A General, Rapid, Chemically Revertible Bioconjugation Strategy Employing Enamine N-oxides. Chem 2022; 8:2260-2277. [PMID: 36176744 PMCID: PMC9514142 DOI: 10.1016/j.chempr.2022.05.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A chemically revertible bioconjugation strategy featuring a new bioorthogonal dissociative reaction employing enamine N-oxides is described. The reaction is rapid, complete, directional, traceless, and displays a broad substrate scope. Reaction rates for cleavage of fluorophores from proteins are on the order of 82 M-1s-1, and the reaction is relatively insensitive to common aqueous buffers and pHs between 4 and 10. Diboron reagents with bidentate and tridentate ligands also effectively reduce the enamine N-oxide to induce dissociation and compound release. This reaction can be paired with the corresponding bioorthogonal hydroamination reaction to afford an integrated system of bioorthogonal click and release via an enamine N-oxide linchpin with a minimal footprint. The tandem associative and dissociative reactions are useful for the transient attachment of proteins and small molecules with access to a discrete, isolable intermediate. We demonstrate the effectiveness of this revertible transformation on cells using chemically cleavable antibody-drug conjugates.
Collapse
Affiliation(s)
- Dahye Kang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Sanghyeon Lee
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Justin Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Lead Contact
| |
Collapse
|
21
|
Schafzahl B, Knall AC, Slugovc C. The inverse-electron demand Diels–Alder reaction of tetrazines with cyclic enol ethers. MONATSHEFTE FUR CHEMIE 2022. [DOI: 10.1007/s00706-022-02957-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
AbstractInverse electron-demand Diels–Alder additions (iEDDA) between 1,2,4,5-tetrazines and suitable unsaturated dienophiles such as olefins, alkynes, or enol ethers provide facile access to pyridazines. Herein the use of cyclic enol ether derivatives for preparing pyridazines bearing 2-hydroxyethyl, 3-hyproxypropyl, and 3-oxopropyl substituents at the 4-position is disclosed and second order rate constants for the reactions with 2,3-dihydrofuran, 3,4-dihydro-2H-pyran, and 2-methoxy-3,4-dihydro-2H-pyran are presented.
Graphical abstract
Collapse
|
22
|
Wang Y, Shen G, Li J, Mao W, Sun H, Feng P, Wu H. Bioorthogonal Cleavage of Tetrazine-Caged Ethers and Esters Triggered by trans-Cyclooctene. Org Lett 2022; 24:5293-5297. [PMID: 35848542 DOI: 10.1021/acs.orglett.2c01873] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yayue Wang
- Huaxi MR Research Center, Department of Radiology, Functional and Molecular Imaging Key Laboratory of Sichuan Province, Frontiers Science Center for Disease Related Molecular Network, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Guohua Shen
- Department of Nuclear Medicine, Laboratory of Clinical Nuclear Medicine, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Jie Li
- Huaxi MR Research Center, Department of Radiology, Functional and Molecular Imaging Key Laboratory of Sichuan Province, Frontiers Science Center for Disease Related Molecular Network, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Wuyu Mao
- Huaxi MR Research Center, Department of Radiology, Functional and Molecular Imaging Key Laboratory of Sichuan Province, Frontiers Science Center for Disease Related Molecular Network, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Hongbao Sun
- Huaxi MR Research Center, Department of Radiology, Functional and Molecular Imaging Key Laboratory of Sichuan Province, Frontiers Science Center for Disease Related Molecular Network, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Ping Feng
- Clinical Trial Center, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Haoxing Wu
- Huaxi MR Research Center, Department of Radiology, Functional and Molecular Imaging Key Laboratory of Sichuan Province, Frontiers Science Center for Disease Related Molecular Network, West China Hospital of Sichuan University, Chengdu, 610041, China
| |
Collapse
|
23
|
Zhang X, Gao J, Tang Y, Yu J, Liew SS, Qiao C, Cao Y, Liu G, Fan H, Xia Y, Tian J, Pu K, Wang Z. Bioorthogonally activatable cyanine dye with torsion-induced disaggregation for in vivo tumor imaging. Nat Commun 2022; 13:3513. [PMID: 35717407 PMCID: PMC9206667 DOI: 10.1038/s41467-022-31136-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 05/27/2022] [Indexed: 11/17/2022] Open
Abstract
Advancement of bioorthogonal chemistry in molecular optical imaging lies in expanding the repertoire of fluorophores that can undergo fluorescence signal changes upon bioorthogonal ligation. However, most available bioorthogonally activatable fluorophores only emit shallow tissue-penetrating visible light via an intramolecular charge transfer mechanism. Herein, we report a serendipitous “torsion-induced disaggregation (TIDA)” phenomenon in the design of near-infrared (NIR) tetrazine (Tz)-based cyanine probe. The TIDA of the cyanine is triggered upon Tz-transcyclooctene ligation, converting its heptamethine chain from S-trans to S-cis conformation. Thus, after bioorthogonal reaction, the tendency of the resulting cyanine towards aggregation is reduced, leading to TIDA-induced fluorescence enhancement response. This Tz-cyanine probe sensitively delineates the tumor in living mice as early as 5 min post intravenous injection. As such, this work discovers a design mechanism for the construction of bioorthogonally activatable NIR fluorophores and opens up opportunities to further exploit bioorthogonal chemistry in in vivo imaging. Expanding the responsive dyes repertoire is currently a developing field in biorthogonal chemistry. In this article, the authors develop fluorophores that turn on their near-infrared fluorescence upon biorthogonal reaction based on a “torsion-induced disaggregation” approach, allowing for sensitive in vivo imaging of tumors.
Collapse
Affiliation(s)
- Xianghan Zhang
- Engineering Research Center of Molecular & Neuroimaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710126, China.,Academy of Advanced Interdisciplinary Research, Xidian University, Xi'an, Shaanxi, 710071, China
| | - Jingkai Gao
- Engineering Research Center of Molecular & Neuroimaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710126, China
| | - Yingdi Tang
- Engineering Research Center of Molecular & Neuroimaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710126, China
| | - Jie Yu
- Engineering Research Center of Molecular & Neuroimaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710126, China
| | - Si Si Liew
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
| | - Chaoqiang Qiao
- Engineering Research Center of Molecular & Neuroimaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710126, China
| | - Yutian Cao
- Engineering Research Center of Molecular & Neuroimaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710126, China
| | - Guohuan Liu
- Engineering Research Center of Molecular & Neuroimaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710126, China
| | - Hongyu Fan
- Engineering Research Center of Molecular & Neuroimaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710126, China
| | - Yuqiong Xia
- Engineering Research Center of Molecular & Neuroimaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710126, China
| | - Jie Tian
- Engineering Research Center of Molecular & Neuroimaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710126, China. .,Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Medicine, Beihang University, Beijing, 100191, China.
| | - Kanyi Pu
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore.
| | - Zhongliang Wang
- Engineering Research Center of Molecular & Neuroimaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710126, China. .,Academy of Advanced Interdisciplinary Research, Xidian University, Xi'an, Shaanxi, 710071, China.
| |
Collapse
|
24
|
Roy R, Khan A, Dutta T, Koner AL. Red to NIR-emissive anthracene-conjugated PMI dyes with dual functions: singlet-oxygen response and lipid-droplet imaging. J Mater Chem B 2022; 10:5352-5363. [PMID: 35583595 DOI: 10.1039/d2tb00349j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The rich chemistry of solution-processable red and near-infrared (NIR) organic emitters has emerged as an attractive and progressive research field because of their particular applications in organic optoelectronics and bioimaging. Also, one can see that the research area of perylene monoimide-based red and NIR-emissive fluorophores is underexplored, which prompted us to design and synthesize three anthracene-conjugated PMI dyes exhibiting strong emission in the red and NIR window in solution. Three PMI-based fluorophores were synthesized via conjoining anthracene and donor moieties (-Ph, -N,N-PhNMe2) with a PMI core via an acetylene linkage at the peri-position, which helped to attain extensive electronic conjugation, which was reflected in red and NIR-emission in solution. The key molecular features to be highlighted here are: all three dyes are strongly emissive in solution, as unveiled by the excellent absolute fluorescence QYs; and they possess tuneable emission properties, guided by the donor strength and a profound Stokes shift (100-200 nm). The three fluorescent dyes demonstrated appreciable singlet-oxygen (1O2) sensitivity when photoirradiated with methylene blue (MB) in solution, showing a substantial blue-shift in emission in a ratiometric manner. Further, the treatment of dye-MB solution with α-tocopherol (1O2 scavenger) validated the presence of 1O2 as the only oxidizing species generated by MB in solution. Computational investigations gave insight into the twisting of donor moieties in their ground-state optimized geometries, the modulation of the FMO energy gap, and the thermodynamic feasibility of the 1O2 reaction. Finally, via taking advantage of the red and NIR-emission, we successfully utilized one of the fluorophores as a lipid-droplet marker for bioimaging in HepG2 cells.
Collapse
Affiliation(s)
- Rupam Roy
- Bionanotechnology Laboratory, Department of Chemistry Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, Madhya Pradesh, India.
| | - Aasif Khan
- Bionanotechnology Laboratory, Department of Chemistry Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, Madhya Pradesh, India.
| | - Tanoy Dutta
- Bionanotechnology Laboratory, Department of Chemistry Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, Madhya Pradesh, India.
| | - Apurba Lal Koner
- Bionanotechnology Laboratory, Department of Chemistry Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, Madhya Pradesh, India.
| |
Collapse
|
25
|
Heiss TK, Dorn RS, Ferreira AJ, Love AC, Prescher JA. Fluorogenic Cyclopropenones for Multicomponent, Real-Time Imaging. J Am Chem Soc 2022; 144:7871-7880. [PMID: 35442034 PMCID: PMC9377832 DOI: 10.1021/jacs.2c02058] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Fluorogenic bioorthogonal reactions enable biomolecule visualization in real time. These reactions comprise reporters that "light up" upon reaction with complementary partners. While the spectrum of fluorogenic chemistries is expanding, few transformations are compatible with live cells due to cross-reactivities or insufficient signal turn-on. To address the need for more suitable chemistries for cellular imaging, we developed a fluorogenic reaction featuring cyclopropenone reporters and phosphines. The transformation involves regioselective activation and cyclization of cyclopropenones to form coumarin products. With optimal probes, the reaction provides >1600-fold signal turn-on, one of the highest fluorescence enhancements reported to date. The bioorthogonal motifs were evaluated in vitro and in cells. The reaction was also found to be compatible with other common fluorogenic transformations, enabling multicomponent, real-time imaging. Collectively, these data suggest that the cyclopropenone-phosphine reaction will bolster efforts to track biomolecule targets in their native settings.
Collapse
Affiliation(s)
- Tyler K Heiss
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Robert S Dorn
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Andrew J Ferreira
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Anna C Love
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Jennifer A Prescher
- Department of Chemistry, University of California, Irvine, California 92697, United States.,Molecular Biology & Biochemistry, University of California, Irvine, California 92697, United States.,Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
| |
Collapse
|
26
|
Jiang L, Zheng T, Xu Z, Li J, Li H, Tang J, Liu S, Wang Y. New NIR spectroscopic probe with a large Stokes shift for Hg 2+ and Ag + detection and living cells imaging. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 271:120916. [PMID: 35085998 DOI: 10.1016/j.saa.2022.120916] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
A new near-infrared (NIR) probe based on a coumarinyl ligand (CL) was designed and synthesized. The probe CL can be used for simultaneous fluorescent turn-on and colorimetric detection of Hg2+ and Ag+ in ethanol/water medium. Colorless solution of probe CL changed to light yellow or dark yellow after addition of Hg2+ or Ag+ ions. Meanwhile the maximum absorption band shifted from 379 nm to 404 nm and the intensity increased enormously (for Hg2+) or moderately (for Ag+). Probe CL displayed an extraordinarily large Stokes shift of 316 nm and addition of Hg2+ or Ag+ to probe CL induced enhancement in the intensity of fluorescence emission at 695 nm by 15 or 8 fold. The detection limit of CL for Hg2+ and Ag+ ions is 0.83 and 8.8 μM, respectively. The applicable pH for sensing Hg2+ by probe CL is in a broad range of 2-12. Application of probe CL for in vitro U87MG cell imaging to detect Hg2+ ions was confirmed.
Collapse
Affiliation(s)
- Lin Jiang
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering & Biotechnology, Donghua University, Shanghai 201620, China
| | - Tao Zheng
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby 2800, Denmark.
| | - Zhenxiang Xu
- Penglai Xinguang Pigment Chemical Co, Ltd, Penglai 265601, China
| | - Jiayin Li
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering & Biotechnology, Donghua University, Shanghai 201620, China
| | - Hongqi Li
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering & Biotechnology, Donghua University, Shanghai 201620, China.
| | - Junjie Tang
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering & Biotechnology, Donghua University, Shanghai 201620, China
| | - Shicheng Liu
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering & Biotechnology, Donghua University, Shanghai 201620, China
| | - Yiyang Wang
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering & Biotechnology, Donghua University, Shanghai 201620, China
| |
Collapse
|
27
|
Sakamoto T, Yu Z, Otani Y. Dual-Color Fluorescence Switch-On Probe for Imaging G-Quadruplex and Double-Stranded DNA in Living Cells. Anal Chem 2022; 94:4269-4276. [PMID: 35234461 DOI: 10.1021/acs.analchem.1c04804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A tripodal quinone-cyanine dye having one donor and three acceptors, that is, one quinone and three N-methylbenzothiazolium moieties, QCy(MeBT)3, was synthesized by simple Knoevenagel condensation between 2-hydroxybenzene-1,3,5-tricarbaldehyde and N-methyl-2-methylbenzothiazolium iodide. The 700 nm (λex, 570 nm) and 600 nm (λex, 470 nm) fluorescence emission of QCy(MeBT)3 was significantly and individually enhanced with the addition of G-quadruplex (G4) DNA and double-stranded DNA (dsDNA), respectively. The results of docking simulations and the response against the viscosity change revealed that the dual-fluorescence response was caused by the difference in the binding mode of QCy(MeBT)3 depending on the DNA structure. The results of fluorescence microscopy imaging experiments using QCy(MeBT)3 suggested that G4 DNAs and dsDNAs in the cell nucleus can be imaged with near-infrared (NIR, 700 nm) and red (600 nm) fluorescence emissions. Furthermore, pyridostatin-induced G4 formation in the living cells can be imaged with NIR fluorescence. The results indicated that QCy(MeBT)3 has huge potential to be a NIR-fluorescent molecular probe for analyzing the structural dynamics of nucleic acids in living cells with a normal fluorescence microscope.
Collapse
Affiliation(s)
- Takashi Sakamoto
- Faculty of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan.,Graduate School of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Zehui Yu
- Faculty of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Yuto Otani
- Graduate School of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| |
Collapse
|
28
|
Schultz M, Müller R, Ermakova Y, Hoffmann JE, Schultz C. Membrane-Permeant, Bioactivatable Coumarin Derivatives for In-Cell Labelling. Chembiochem 2022; 23:e202100699. [PMID: 35199435 PMCID: PMC9305936 DOI: 10.1002/cbic.202100699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/21/2022] [Indexed: 11/29/2022]
Abstract
The delivery of small molecule fluorophores with minimal compartmentalization is currently one of the most critical technical problems in intracellular labelling. Here we introduce sulfonated and phosphonated coumarin dyes, demonstrate rapid cell entry via a prodrug approach, and show a lack of interaction with membranes, organelles, or other compartments. The dyes show no specific localization and are evenly distributed in the cells. Our fluorogenic, clickable phosphonate derivatives successfully tagged model targets in intact cells and the increase in brightness upon click reaction was around 60‐fold.
Collapse
Affiliation(s)
- Madeleine Schultz
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg, Germany
| | - Rainer Müller
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg, Germany
| | - Yulia Ermakova
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg, Germany
| | - Jan-Erik Hoffmann
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg, Germany
| | - Carsten Schultz
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg, Germany.,Dept. of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, USA
| |
Collapse
|
29
|
Dai Y, Teng X, Li J. Single‐Cell Visualization of Monogenic RNA G‐quadruplex and Occupied G‐quadruplex Ratio through a Module‐Assembled Multifunctional Probes Assay (MAMPA). Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yicong Dai
- Department of Chemistry Center for BioAnalytical Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 China
| | - Xucong Teng
- Department of Chemistry Center for BioAnalytical Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 China
| | - Jinghong Li
- Department of Chemistry Center for BioAnalytical Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 China
| |
Collapse
|
30
|
Zhao SJ, Zheng P, Wu Z, Jiang JH. DNA-Templated Bioorthogonal Reactions via Catalytic Hairpin Assembly for Precise RNA Imaging in Live Cells. Anal Chem 2022; 94:2693-2698. [PMID: 35119262 DOI: 10.1021/acs.analchem.1c05509] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There has been a significant interest in developing proximity-induced bioorthogonal reactions for nucleic acid detection and imaging, owing to their high specificity and tunable reaction kinetics. Herein, we reported the first design of a fluorogenic sensor by coupling a bioorthogonal reaction with a DNA cascade circuit for precise RNA imaging in live cells. Two DNA hairpin probes bearing tetrazines or vinyl ether caged fluorophores were designed and synthesized. Upon target mRNA triggering catalytic hairpin assembly, the chemical reaction partners were brought in a spatial proximity to yield high effective concentrations, which dramatically facilitated the bioorthogonal reaction efficiency to unmask the vinyl ether group to activate fluorescence. The proposed fluorogenic sensor was demonstrated to have a high signal-to-noise ratio up to ∼30 fold and enabled the sensitive detection of target mRNA with a detection limit of 4.6 pM. Importantly, the fluorogenic sensor presented low background signals in biological environments due to the unique "click to release" feature, avoiding false positive results caused by unspecific degradation. We also showed that the fluorogenic sensor could accurately image mRNA in live cells and distinguish the relative mRNA expression levels in both tumor and normal cells. Benefiting from these significant advantages, our method provides a useful tool for basic studies of bioorthogonal chemistry and early clinical diagnosis.
Collapse
Affiliation(s)
- Su-Jing Zhao
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Ping Zheng
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Zhenkun Wu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| |
Collapse
|
31
|
|
32
|
Sun H, Xue Q, Zhang C, Wu H, Feng P. Derivatization based on tetrazine scaffolds: synthesis of tetrazine derivatives and their biomedical applications. Org Chem Front 2022. [DOI: 10.1039/d1qo01324f] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The recent advances in tetrazine scaffold-based derivatizations have been summarized. The advantages and limitations of derivatization methods and applications of the developed tetrazine derivatives in bioorthogonal chemistry have been highlighted.
Collapse
Affiliation(s)
- Hongbao Sun
- Huaxi MR Research Center (HMRRC), Department of Radiology, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, Functional and Molecular Imaging Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qinghe Xue
- Huaxi MR Research Center (HMRRC), Department of Radiology, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, Functional and Molecular Imaging Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Chang Zhang
- Huaxi MR Research Center (HMRRC), Department of Radiology, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, Functional and Molecular Imaging Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Haoxing Wu
- Huaxi MR Research Center (HMRRC), Department of Radiology, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, Functional and Molecular Imaging Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ping Feng
- Clinical Trial Center, West China Hospital of Sichuan University, Chengdu 610041, China
| |
Collapse
|
33
|
Bujalska A, Basran K, Luedtke NW. [4+2] and [2+4] cycloaddition reactions on single- and double-stranded DNA: a dual-reactive nucleoside. RSC Chem Biol 2022; 3:698-701. [PMID: 35755194 PMCID: PMC9175100 DOI: 10.1039/d2cb00062h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/27/2022] [Indexed: 11/21/2022] Open
Abstract
Here we report dual reactivity of diene-modified duplex DNA containing 5-(1,3-butadienyl)-2'-deoxyuridine “BDdU”. Regular-electron demand [4+2] cycloaddition proceeded upon addition of a maleimide, whereas inversed-electron demand [2+4] cycloaddition occurred upon addition...
Collapse
Affiliation(s)
- Anna Bujalska
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Kaleena Basran
- Department of Chemistry, McGill University 801 Sherbrooke St. West Montréal Québec H3A 0B8 Canada
| | - Nathan W Luedtke
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190 8057 Zurich Switzerland
- Department of Chemistry, McGill University 801 Sherbrooke St. West Montréal Québec H3A 0B8 Canada
| |
Collapse
|
34
|
Zhang X, Xu H, Li J, Su D, Mao W, Shen G, Li L, Wu H. Isonitrile induced bioorthogonal activation of fluorophores and mutually orthogonal cleavage in live cells. Chem Commun (Camb) 2021; 58:573-576. [PMID: 34913446 DOI: 10.1039/d1cc05774j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Fluorophores with different emission wavelengths were efficiently quenched by a tert-butyl terminated tetrazylmethyl group and activated by an isonitrile-tetrazine click-to-release reaction. Nucleic acid templated chemistry significantly accelerated this bioorthogonal cleavage. Moreover, two mutually orthogonal fluorogenic cleavage reactions were simultaneously conducted in live cells for the first time.
Collapse
Affiliation(s)
- Xiaoyang Zhang
- Laboratory of Clinical Nuclear Medicine, Department of Nuclear Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hui Xu
- Huaxi MR Research Center, Department of Radiology, Functional and Molecular Imaging Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Jie Li
- Huaxi MR Research Center, Department of Radiology, Functional and Molecular Imaging Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Dunyan Su
- Huaxi MR Research Center, Department of Radiology, Functional and Molecular Imaging Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Wuyu Mao
- Huaxi MR Research Center, Department of Radiology, Functional and Molecular Imaging Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Guohua Shen
- Laboratory of Clinical Nuclear Medicine, Department of Nuclear Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lin Li
- Laboratory of Clinical Nuclear Medicine, Department of Nuclear Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Haoxing Wu
- Huaxi MR Research Center, Department of Radiology, Functional and Molecular Imaging Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China.
| |
Collapse
|
35
|
Abstract
Bioorthogonal chemistry is a set of methods using the chemistry of non-native functional groups to explore and understand biology in living organisms. In this review, we summarize the most common reactions used in bioorthogonal methods, their relative advantages and disadvantages, and their frequency of occurrence in the published literature. We also briefly discuss some of the less common but potentially useful methods. We then analyze the bioorthogonal-related publications in the CAS Content Collection to determine how often different types of biomolecules such as proteins, carbohydrates, glycans, and lipids have been studied using bioorthogonal chemistry. The most prevalent biological and chemical methods for attaching bioorthogonal functional groups to these biomolecules are elaborated. We also analyze the publication volume related to different types of bioorthogonal applications in the CAS Content Collection. The use of bioorthogonal chemistry for imaging, identifying, and characterizing biomolecules and for delivering drugs to treat disease is discussed at length. Bioorthogonal chemistry for the surface attachment of proteins and in the use of modified carbohydrates is briefly noted. Finally, we summarize the state of the art in bioorthogonal chemistry and its current limitations and promise for its future productive use in chemistry and biology.
Collapse
Affiliation(s)
- Robert E Bird
- CAS, a division of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43202, United States
| | - Steven A Lemmel
- CAS, a division of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43202, United States
| | - Xiang Yu
- CAS, a division of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43202, United States
| | - Qiongqiong Angela Zhou
- CAS, a division of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43202, United States
| |
Collapse
|
36
|
Dai Y, Teng X, Li J. Single-cell Visualization of Monogenic RNA G-quadruplex and Occupied G-quadruplex Ratio through Module Assembled Multifunctional Probes Assay (MAMPA). Angew Chem Int Ed Engl 2021; 61:e202111132. [PMID: 34773681 DOI: 10.1002/anie.202111132] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/24/2021] [Indexed: 11/12/2022]
Abstract
G-quadruplexes (G4s), non-canonical nucleic acid secondary structure, regulate many biological functions and are considered as potential molecular targets for therapeutics of cancers. However, due to the lack of analytical methods, the regulating mechanism of monogenic G4s is still unclear. Here, we developed a Module Assembled Multifunctional Probes Assay (MAMPA) for visualizing endogenous G4s in individual genes in single cells. Two modular probes separately recognize G4 structures and the adjacent RNA sequences, and the module assembly enables imaging of G4s in an individual RNA with high specificity. Through imaging G4s in several individual genes, we found that G4s were steadily occupied by G4 Binding Proteins (G4BPs) in various mRNAs in every cell line and defined "Occupied G4 Ratio". In all, we demonstrated MAMPA was suitable for most experiment situations and found that Occupied G4 Ratios had the potential to become a new parameter for the study of G4s in living cells.
Collapse
Affiliation(s)
- Yicong Dai
- Tsinghua University, Department of Chemistry, 100084, CHINA
| | - Xucong Teng
- Tsinghua University, Department of Chemistry, CHINA
| | - Jinghong Li
- Tsinghua University, Department of Chemistry, Haidian Street, Beijing, CHINA
| |
Collapse
|
37
|
Houska R, Stutz MB, Seitz O. Expanding the scope of native chemical ligation - templated small molecule drug synthesis via benzanilide formation. Chem Sci 2021; 12:13450-13457. [PMID: 34777764 PMCID: PMC8528049 DOI: 10.1039/d1sc00513h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 09/10/2021] [Indexed: 12/15/2022] Open
Abstract
We describe a reaction system that enables the synthesis of Bcr–Abl tyrosine kinase inhibitors (TKI) via benzanilide formation in water. The reaction is based on native chemical ligation (NCL). In contrast to previous applications, we used the NCL chemistry to establish aromatic rather than aliphatic amide bonds in coupling reactions between benzoyl and o-mercaptoaniline fragments. The method was applied for the synthesis of thiolated ponatinib and GZD824 derivatives. Acid treatment provided benzothiazole structures, which opens opportunities for diversification. Thiolation affected the affinity for Abl1 kinase only moderately. Of note, a ponatinib-derived benzothiazole also showed nanomolar affinity. NCL-enabled benzanilide formation may prove useful for fragment-based drug discovery. To show that benzanilide synthesis can be put under the control of a template, we connected the benzoyl and o-mercaptoaniline fragments to DNA and peptide nucleic acid (PNA) oligomers. Complementary RNA templates enabled adjacent binding of reactive conjugates triggering a rapid benzoyl transfer from a thioester-linked DNA conjugate to an o-mercaptoaniline-DNA or -PNA conjugate. We evaluated the influence of linker length and unpaired spacer nucleotides within the RNA template on the product yield. The data suggest that nucleic acid-templated benzanilide formation could find application in the establishment of DNA-encoded combinatorial libraries (DEL). The templated native chemical ligation between benzoyl thioesters and o-mercaptoaniline fragments proceeds in water and provides benzanilides that have nanomolar affinity for Abl1 kinase.![]()
Collapse
Affiliation(s)
- Richard Houska
- Department of Chemistry, Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 12489 Berlin Germany
| | - Marvin Björn Stutz
- Department of Chemistry, Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 12489 Berlin Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 12489 Berlin Germany
| |
Collapse
|
38
|
Roth M, Seitz O. A Self-immolative Molecular Beacon for Amplified Nucleic Acid Detection*. Chemistry 2021; 27:14189-14194. [PMID: 34516006 PMCID: PMC8597011 DOI: 10.1002/chem.202102600] [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: 07/18/2021] [Indexed: 01/18/2023]
Abstract
Fluorogenic hybridization probes allow the detection of RNA and DNA sequences in homogeneous solution. Typically, one target molecule activates the fluorescence of a single probe molecule. This limits the sensitivity of nucleic acid detection. Herein, we report a self‐immolative molecular beacon (iMB) that escapes the one‐target/one‐probe paradigm. The iMB probe includes a photoreductively cleavable N‐alkyl‐picolinium (NAP) linkage within the loop region. A fluorophore at the 5’‐end serves, on the one hand, as a reporter group and, on the other hand, as a photosensitizer of a NAP‐linker cleavage reaction. In the absence of target, the iMB adopts a hairpin shape. Quencher groups prevent photo‐induced cleavage. The iMB opens upon hybridization with a target, and both fluorescent emission as well as photo‐reductive cleavage of the NAP linker can occur. In contrast to previous chemical amplification reactions, iMBs are unimolecular probes that undergo cleavage leading to products that have lower target affinity than the probes before reaction. Aided by catalysis, the method allowed the detection of 5 pm RNA target within 100 min.
Collapse
Affiliation(s)
- Magdalena Roth
- Institute of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Oliver Seitz
- Institute of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| |
Collapse
|
39
|
Yang H, Wang Y, Li X, Teng Y, Tian Y. A Dansyl Amide N-Oxide Fluorogenic Probe Based on a Bioorthogonal Decaging Reaction. ChemistryOpen 2021; 10:1013-1019. [PMID: 34637183 PMCID: PMC8507439 DOI: 10.1002/open.202100104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 09/10/2021] [Indexed: 11/24/2022] Open
Abstract
A smart fluorescence "turn-on" probe which contained a dansyl amide fluorophore and an N-oxide group was designed based on the bioorthogonal decaging reaction between N-oxide and the boron reagent. The reaction proceeds in a rapid kinetics (k2 =57.1±2.5 m-1 s-1 ), and the resulting reduction product showcases prominent fluorescence enhancement (up to 72-fold). Time dependent density functional theoretical (TD-DFT) calculation revealed that the process of photoinduced electron transfer (PET) from the N-oxide moiety to the dansyl amide fluorophore accounts for the quenching mechanism of N-oxide. This probe also showed high selectivity over various nucleophilic amino acids and good biocompatibility in physiological conditions. The successful application of the probe in HaloTag protein labeling and HepG2 live-cell imaging proves it a valuable tool for visualization of biomolecules.
Collapse
Affiliation(s)
- Hong Yang
- Key Laboratory of Bioactive Substances and Function of Natural MedicineBeijing Key Laboratory of Active Substances Discovery and Drugability EvaluationInstitute of Materia MedicaPeking Union Medical College and Chinese Academy of Medical Sciences1 Xian Nong Tan Street100050BeijingChina
| | - Yongcheng Wang
- Key Laboratory of Bioactive Substances and Function of Natural MedicineBeijing Key Laboratory of Active Substances Discovery and Drugability EvaluationInstitute of Materia MedicaPeking Union Medical College and Chinese Academy of Medical Sciences1 Xian Nong Tan Street100050BeijingChina
| | - Xiang Li
- Key Laboratory of Bioactive Substances and Function of Natural MedicineBeijing Key Laboratory of Active Substances Discovery and Drugability EvaluationInstitute of Materia MedicaPeking Union Medical College and Chinese Academy of Medical Sciences1 Xian Nong Tan Street100050BeijingChina
| | - Yu Teng
- Key Laboratory of Bioactive Substances and Function of Natural MedicineBeijing Key Laboratory of Active Substances Discovery and Drugability EvaluationInstitute of Materia MedicaPeking Union Medical College and Chinese Academy of Medical Sciences1 Xian Nong Tan Street100050BeijingChina
| | - Yulin Tian
- Key Laboratory of Bioactive Substances and Function of Natural MedicineBeijing Key Laboratory of Active Substances Discovery and Drugability EvaluationInstitute of Materia MedicaPeking Union Medical College and Chinese Academy of Medical Sciences1 Xian Nong Tan Street100050BeijingChina
| |
Collapse
|
40
|
Li Z, Chen Q, Wang J, Pan X, Lu W. Research Progress and Application of Bioorthogonal Reactions in Biomolecular Analysis and Disease Diagnosis. Top Curr Chem (Cham) 2021; 379:39. [PMID: 34590223 DOI: 10.1007/s41061-021-00352-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/14/2021] [Indexed: 12/14/2022]
Abstract
Bioorthogonal reactions are rapid, specific and high yield reactions that can be performed in in vivo microenvironments or simulated microenvironments. At present, the main biorthogonal reactions include Staudinger ligation, copper-catalyzed azide alkyne cycloaddition, strain-promoted [3 + 2] reaction, tetrazine ligation, metal-catalyzed coupling reaction and photo-induced biorthogonal reactions. To date, many reviews have reported that bioorthogonal reactions have been used widely as a powerful tool in the field of life sciences, such as in target recognition, drug discovery, drug activation, omics research, visualization of life processes or exogenous bacterial infection processes, signal transduction pathway research, chemical reaction dynamics analysis, disease diagnosis and treatment. In contrast, to date, few studies have investigated the application of bioorthogonal reactions in the analysis of biomacromolecules in vivo. Therefore, the application of bioorthogonal reactions in the analysis of proteins, nucleic acids, metabolites, enzyme activities and other endogenous molecules, and the determination of disease-related targets is reviewed. In addition, this review discusses the future development opportunities and challenges of biorthogonal reactions. This review presents an overview of recent advances for application in biomolecular analysis and disease diagnosis, with a focus on proteins, metabolites and RNA detection.
Collapse
Affiliation(s)
- Zilong Li
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Qinhua Chen
- Department of Pharmacy, Shenzhen Baoan Authentic TCM Therapy Hospital, Shenzhen, 518101, China
| | - Jin Wang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Xiaoyan Pan
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Wen Lu
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China.
| |
Collapse
|
41
|
Wickhorst PJ, Druzhinin SI, Ihmels H, Müller M, Sutera Sardo M, Schönherr H, Viola G. A Dimethylaminophenyl‐Substituted Naphtho[1,2‐
b
]quinolizinium as a Multicolor NIR Probe for the Fluorimetric Detection of Intracellular Nucleic Acids and Proteins. CHEMPHOTOCHEM 2021. [DOI: 10.1002/cptc.202100148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Peter Jonas Wickhorst
- Department of Chemistry – Biology University of Siegen, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ) Adolf-Reichwein-Str. 2 57068 Siegen Germany
| | - Sergey I. Druzhinin
- Department of Chemistry – Biology University of Siegen, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ) Adolf-Reichwein-Str. 2 57068 Siegen Germany
| | - Heiko Ihmels
- Department of Chemistry – Biology University of Siegen, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ) Adolf-Reichwein-Str. 2 57068 Siegen Germany
| | - Mareike Müller
- Department of Chemistry – Biology University of Siegen, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ) Adolf-Reichwein-Str. 2 57068 Siegen Germany
| | | | - Holger Schönherr
- Department of Chemistry – Biology University of Siegen, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ) Adolf-Reichwein-Str. 2 57068 Siegen Germany
| | - Giampietro Viola
- Department of Women's and Child's health Oncohematology laboratory University of Padova Via Giustiniani 2 I-35128 Padova Italy
| |
Collapse
|
42
|
Liu H, Zheng T, Zheng Y, Li B, Xie X, Shen X, Zhao X, Yu Z. Visible-light induced photo-click and release strategy between monoarylsydnone and phenoxylfumarate. Chem Commun (Camb) 2021; 57:8135-8138. [PMID: 34350920 DOI: 10.1039/d1cc02841c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We report a visible-light induced photo-click and release platform between monoarylsydnone (MASyd) and phenoxylfumarates. The pyrazoline produced by the cycloaddition undergoes a photo-aromatization to form a fluorescent pyrazole. Meanwhile, the photo-aromatization also serves as the driving force to release fluorophores that are quenched in the form of phenoxylfumarates.
Collapse
Affiliation(s)
- Hui Liu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, P. R. China.
| | | | | | | | | | | | | | | |
Collapse
|
43
|
Wang C, Zhang H, Zhang T, Zou X, Wang H, Rosenberger J, Vannam R, Trout WS, Grimm JB, Lavis LD, Thorpe C, Jia X, Li Z, Fox JM. Enabling In Vivo Photocatalytic Activation of Rapid Bioorthogonal Chemistry by Repurposing Silicon-Rhodamine Fluorophores as Cytocompatible Far-Red Photocatalysts. J Am Chem Soc 2021; 143:10793-10803. [PMID: 34250803 PMCID: PMC8765119 DOI: 10.1021/jacs.1c05547] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Chromophores that absorb in the tissue-penetrant far-red/near-infrared window have long served as photocatalysts to generate singlet oxygen for photodynamic therapy. However, the cytotoxicity and side reactions associated with singlet oxygen sensitization have posed a problem for using long-wavelength photocatalysis to initiate other types of chemical reactions in biological environments. Herein, silicon-Rhodamine compounds (SiRs) are described as photocatalysts for inducing rapid bioorthogonal chemistry using 660 nm light through the oxidation of a dihydrotetrazine to a tetrazine in the presence of trans-cyclooctene dienophiles. SiRs have been commonly used as fluorophores for bioimaging but have not been applied to catalyze chemical reactions. A series of SiR derivatives were evaluated, and the Janelia Fluor-SiR dyes were found to be especially effective in catalyzing photooxidation (typically 3%). A dihydrotetrazine/tetrazine pair is described that displays high stability in both oxidation states. A protein that was site-selectively modified by trans-cyclooctene was quantitatively conjugated upon exposure to 660 nm light and a dihydrotetrazine. By contrast, a previously described methylene blue catalyst was found to rapidly degrade the protein. SiR-red light photocatalysis was used to cross-link hyaluronic acid derivatives functionalized by dihydrotetrazine and trans-cyclooctenes, enabling 3D culture of human prostate cancer cells. Photoinducible hydrogel formation could also be carried out in live mice through subcutaneous injection of a Cy7-labeled hydrogel precursor solution, followed by brief irradiation to produce a stable hydrogel. This cytocompatible method for using red light photocatalysis to activate bioorthogonal chemistry is anticipated to find broad applications where spatiotemporal control is needed in biological environments.
Collapse
Affiliation(s)
- Chuanqi Wang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - He Zhang
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA
| | - Tao Zhang
- Department of Radiology and Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Xiaoyu Zou
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA
| | - Hui Wang
- Department of Radiology and Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Julia Rosenberger
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Raghu Vannam
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - William S. Trout
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Jonathan B. Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn Virginia, 20147, USA
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn Virginia, 20147, USA
| | - Colin Thorpe
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Xinqiao Jia
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA
- Delaware Biotechnology Institute, Newark, Delaware 19711, USA
| | - Zibo Li
- Department of Radiology and Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Joseph M. Fox
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA
| |
Collapse
|
44
|
Zhu MS, Zhang XQ, Wei-Ma, Sun R, Xu YJ, Ge JF. Design and synthesis of a series of OFF-ON near infrared fluorescent probes for nucleic acid in aqueous solution. Bioorg Med Chem Lett 2021; 48:128239. [PMID: 34229055 DOI: 10.1016/j.bmcl.2021.128239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/21/2021] [Accepted: 06/27/2021] [Indexed: 11/16/2022]
Abstract
Five cyanine dyes (6a-e) with aza units were prepared by the reaction of pyridinum or quinolinium with suitable aldehydes. They present several remarkable features including large Stokes shift (235-282 nm), long emission wavelength (640-698 nm) and excellent selectivity. Moreover, probes 6a-b display obvious and sensitive fluorescent response to DNA and RNA in aqueous solution, and the quantum yield of probe 6a response to RNA increases from 0 to 8.9%. More importantly, probes 6c and 6e can effectively avoid DNA interference and only respond to RNA in aqueous solution. In addition, laser confocal cell experiment has showed that probe 6b can image the nucleolus of nucleic acids in HeLa cells.
Collapse
Affiliation(s)
- Ming-Sen Zhu
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, 199 Ren'Ai Road, Suzhou 215123, China
| | - Xiao-Qing Zhang
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Wei-Ma
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, 199 Ren'Ai Road, Suzhou 215123, China
| | - Ru Sun
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, 199 Ren'Ai Road, Suzhou 215123, China
| | - Yu-Jie Xu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China.
| | - Jian-Feng Ge
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, 199 Ren'Ai Road, Suzhou 215123, China.
| |
Collapse
|
45
|
Wang J, Wang X, Fan X, Chen PR. Unleashing the Power of Bond Cleavage Chemistry in Living Systems. ACS CENTRAL SCIENCE 2021; 7:929-943. [PMID: 34235254 PMCID: PMC8227596 DOI: 10.1021/acscentsci.1c00124] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Indexed: 05/02/2023]
Abstract
Bioorthogonal cleavage chemistry has been rapidly emerging as a powerful tool for manipulation and gain-of-function studies of biomolecules in living systems. While the initial bond formation-centered bioorthogonal reactions have been widely adopted for labeling, tracing, and capturing biomolecules, the newly developed bond cleavage-enabled bioorthogonal reactions have opened new possibilities for rescuing small molecules as well as biomacromolecules in living systems, allowing multidimensional controls over biological processes in vitro and in vivo. In this Outlook, we first summarized the development and applications of bioorthogonal cleavage reactions (BCRs) that restore the functions of chemical structures as well as more complex networks, including the liberation of prodrugs, release of bioconjugates, and in situ reactivation of intracellular proteins. As we embarked on this fruitful progress, we outlined the unmet scientific needs and future directions along this exciting avenue. We believe that the potential of BCRs will be further unleashed when combined with other frontier technologies, such as genetic code expansion and proximity-enabled chemical labeling.
Collapse
Affiliation(s)
- Jie Wang
- Beijing
National Laboratory for Molecular Sciences, Synthetic and Functional
Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of Ministry of Education, College of Chemistry and Molecular
Engineering, Peking University, Beijing 100871, China
- Department
of Chemistry, Southern University of Science
and Technology, Shenzhen 518055, China
| | - Xin Wang
- Beijing
National Laboratory for Molecular Sciences, Synthetic and Functional
Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of Ministry of Education, College of Chemistry and Molecular
Engineering, Peking University, Beijing 100871, China
| | - Xinyuan Fan
- Beijing
National Laboratory for Molecular Sciences, Synthetic and Functional
Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of Ministry of Education, College of Chemistry and Molecular
Engineering, Peking University, Beijing 100871, China
| | - Peng R. Chen
- Beijing
National Laboratory for Molecular Sciences, Synthetic and Functional
Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of Ministry of Education, College of Chemistry and Molecular
Engineering, Peking University, Beijing 100871, China
- Peking−Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, China
| |
Collapse
|
46
|
Shieh P, Hill MR, Zhang W, Kristufek SL, Johnson JA. Clip Chemistry: Diverse (Bio)(macro)molecular and Material Function through Breaking Covalent Bonds. Chem Rev 2021; 121:7059-7121. [PMID: 33823111 DOI: 10.1021/acs.chemrev.0c01282] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In the two decades since the introduction of the "click chemistry" concept, the toolbox of "click reactions" has continually expanded, enabling chemists, materials scientists, and biologists to rapidly and selectively build complexity for their applications of interest. Similarly, selective and efficient covalent bond breaking reactions have provided and will continue to provide transformative advances. Here, we review key examples and applications of efficient, selective covalent bond cleavage reactions, which we refer to herein as "clip reactions." The strategic application of clip reactions offers opportunities to tailor the compositions and structures of complex (bio)(macro)molecular systems with exquisite control. Working in concert, click chemistry and clip chemistry offer scientists and engineers powerful methods to address next-generation challenges across the chemical sciences.
Collapse
Affiliation(s)
- Peyton Shieh
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Megan R Hill
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Wenxu Zhang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Samantha L Kristufek
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jeremiah A Johnson
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
47
|
Mancuso F, Rahm M, Dzijak R, Mertlíková-Kaiserová H, Vrabel M. Transition-Metal-Mediated versus Tetrazine-Triggered Bioorthogonal Release Reactions: Direct Comparison and Combinations Thereof. Chempluschem 2021; 85:1669-1675. [PMID: 32757364 DOI: 10.1002/cplu.202000477] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/16/2020] [Indexed: 01/14/2023]
Abstract
Bioorthogonal cleavage reactions are gaining popularity in chemically inducible prodrug activation and in the control of biomolecular functions. Despite similar applications, these reactions were developed and optimized on different substrates and under different experimental conditions. Reported herein is a side-by-side comparison of palladium-, ruthenium- and tetrazine-triggered release reactions, which aims at comparing the reaction kinetics, efficiency and overall advantages and limitations of the methods. In addition, we disclose the possibility of mutual combination of the cleavage reactions. Finally, we compare the efficiency of the bioorthogonal deprotections in cellular experiments, which revealed that among the three methods investigated, the palladium- and the tetrazine-promoted reaction can be used for efficient prodrug activation, but only the tetrazine-triggered reactions proceed efficiently inside cells.
Collapse
Affiliation(s)
- Francesca Mancuso
- University of Messina, Department of Chemical, Biological Pharmaceutical and Environmental Sciences (CHIBIOFARAM), Viale Palatucci 13, I-98168, Messina, Italy
| | - Michal Rahm
- Institute of Organic Chemistry, and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10, Prague, Czech Republic
| | - Rastislav Dzijak
- Institute of Organic Chemistry, and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10, Prague, Czech Republic
| | - Helena Mertlíková-Kaiserová
- Institute of Organic Chemistry, and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10, Prague, Czech Republic
| | - Milan Vrabel
- Institute of Organic Chemistry, and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10, Prague, Czech Republic
| |
Collapse
|
48
|
Ganguly S, Murugan NA, Ghosh D, Narayanaswamy N, Govindaraju T, Basu G. DNA Minor Groove-Induced cis- trans Isomerization of a Near-Infrared Fluorescent Probe. Biochemistry 2021; 60:2084-2097. [PMID: 34142803 DOI: 10.1021/acs.biochem.1c00281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The discovery of small molecules that exhibit turn-on far-red or near-infrared (NIR) fluorescence upon DNA binding and understanding how they bind DNA are important for imaging and bioanalytical applications. Here we report the DNA-bound structure and the DNA binding mechanism of quinone cyanine dithiazole (QCy-DT), a recently reported AT-specific turn-on NIR fluorescent probe for double-stranded DNA. The nuclear magnetic resonance (NMR)-derived structure showed minor groove binding but no specific ligand-DNA interactions, consistent with an endothermic and entropy-driven binding mechanism deduced from isothermal titration calorimetry. Minor groove binding is typically fast because it minimally perturbs the DNA structure. However, QCy-DT exhibited unusually slow DNA binding. The cyanine-based probe is capable of cis-trans isomerization due to overlapping methine bridges, with 16 possible slowly interconverting cis/trans isomers. Using NMR, density functional theory, and free energy calculations, we show that the DNA-free and DNA-bound environments of QCy-DT prefer distinctly different isomers, indicating that the origin of the slow kinetics is a cis-trans isomerization and that the minor groove preferentially selects an otherwise unstable cis/trans isomer of QCy-DT. Flux analysis showed the conformational selection pathway to be the dominating DNA binding mechanism at low DNA concentrations, which switches to the induced fit pathway at high DNA concentrations. This report of cis/trans isomerization of a ligand, upon binding the DNA minor groove, expands the prevailing understanding of unique discriminatory powers of the minor groove and has an important bearing on using polymethine cyanine dyes to probe the kinetics of molecular interactions.
Collapse
Affiliation(s)
- Sudakshina Ganguly
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, West Bengal, India
| | - N Arul Murugan
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Debasis Ghosh
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - Nagarjun Narayanaswamy
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - Gautam Basu
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, West Bengal, India
| |
Collapse
|
49
|
Biocompatible and noncytotoxic nucleoside-based AIEgens sensor for lighting-up nucleic acids. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.02.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
50
|
Ashokkumar P, Collot M, Klymchenko AS. Fluorogenic Squaraine Dendrimers for Background-Free Imaging of Integrin Receptors in Cancer Cells. Chemistry 2021; 27:6795-6803. [PMID: 33567148 DOI: 10.1002/chem.202100480] [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: 02/07/2021] [Indexed: 11/06/2022]
Abstract
To overcome the limited brightness of existing fluorogenic molecular probes for biomolecular targets, we introduce a concept of fluorogenic dendrimer probe, which undergoes polarity-dependent switching due to intramolecular aggregation-caused quenching of its fluorophores. Based on a rational design of dendrimers with four and eight squaraine dyes, we found that octamer bearing dyes through a sufficiently long PEG(8) linker displays >400-fold fluorescence enhancement from water to non-polar dioxane. High extinction coefficient (≈2,300,000 m-1 cm-1 ) resulted from eight squaraine dyes and quantum yield (≈25 %) make this octamer the brightest environment-sensitive fluorogenic molecule reported to date. Its conjugate with cyclic RGD used at low concentration (3 nm) enables integrin-specific fluorescence imaging of cancer cells with high signal-to-background ratio. The developed dendrimer probe is a "golden middle" between molecular probes and nanoparticles, combining small size, turn-on response and high brightness, important for bioimaging.
Collapse
Affiliation(s)
- Pichandi Ashokkumar
- Laboratoire de Biophotonique et Pharmacologie, CNRS UMR 7213, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401, Illkirch, France.,Department of Bioelectronics and Biosensors, Alagappa University, Karaikudi, 630 004, Tamil Nadu, India
| | - Mayeul Collot
- Laboratoire de Biophotonique et Pharmacologie, CNRS UMR 7213, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401, Illkirch, France
| | - Andrey S Klymchenko
- Laboratoire de Biophotonique et Pharmacologie, CNRS UMR 7213, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401, Illkirch, France
| |
Collapse
|