1
|
Tong X, Chen J, Wang M, Liu J, Li J, Wang X, Zuo Y, Xu X, Wang Y, Wang B, Guo W, Zheng Y. Development of a Bioorthogonal Click-to-Release Reaction for Hydrogen Polysulfide (H 2S n) Detection. Anal Chem 2024. [PMID: 39287125 DOI: 10.1021/acs.analchem.4c02677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
In this study, we present an innovative "click-to-release" strategy for the design of highly specific H2Sn bioorthogonal probes that undergo a specific click reaction with H2Sn and release fluorophores by a following rearrangement. A library of cyclooctyne derivatives was established and successfully demonstrated the availability of the release strategy. Then, a model probe CM-CT was synthesized, which can achieve effective fluorophore release (>80%) in the presence of a H2Sn donor. To further validate the application of this class of probes, a new probe QN-RHO-CT based on Rhodamine 110 was developed. This probe showed good water solubility (>160 μM) and fast release kinetics and can achieve selective H2Sn detection in living cells. We used this probe to study the process of H2S-mediated protein S-persulfidation and demonstrated that excess H2S would directly react with protein persulfides to generate H2S2 and reduce the persulfides to thiols. Additionally, we elucidated the click-to-release mechanism in our design through a detailed mechanistic study, confirming the generation of the key intermediate α, β-unsaturated cyclooctanethione. This bioorthogonal click-to-release reaction provides a useful tool for investigating the function of H2Sn and paves the way for biological studies on H2Sn.
Collapse
Affiliation(s)
- Xidan Tong
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Jiaxuan Chen
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Maolin Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Jianru Liu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Jing Li
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Xin Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Yifei Zuo
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Xiaowei Xu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Yichen Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Binghe Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Weiwei Guo
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 211198, P. R. China
- Department of Chemistry, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Yueqin Zheng
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 211198, P. R. China
| |
Collapse
|
2
|
Bu YJ, Tijaro-Bulla S, Cui H, Nitz M. Oxidation-Controlled, Strain-Promoted Tellurophene-Alkyne Cycloaddition (OSTAC): A Bioorthogonal Tellurophene-Dependent Conjugation Reaction. J Am Chem Soc 2024. [PMID: 39259935 DOI: 10.1021/jacs.4c07275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Tellurophene-bearing small molecules have emerged as valuable tools for localizing cellular activities in vivo using mass cytometry. To broaden the utility of tellurophenes in chemical biology, we have developed a bioorthogonal reaction to facilitate tagging of tellurophene-bearing conjugates for downstream applications. Using TePhe, a tellurophene-based phenylalanine analogue, labeled recombinant proteins were generated for reaction development. Using these proteins, we demonstrate an oxidation-controlled, strain-promoted tellurophene-alkyne cycloaddition (OSTAC) reaction. Mild oxidation of the tellurophene ring with N-chlorosuccinimide produces a reactive Te(IV) species which undergoes rapid (k > 100 M-1 s-1) cycloaddition with bicyclo[6.1.0]nonyne (BCN) yielding a benzo-fused cyclooctane. Selective labeling of TePhe-containing proteins can be achieved in complex protein mixtures and on fixed cells. OSTAC reactions can be combined with strain-promoted azide alkyne cycloaddition (SPAAC) and copper-catalyzed azide alkyne click (CuAAC) reactions. Demonstrating the versatility of this approach, we observe the expected staining patterns for 5-ethynyl-2'-deoxyuridine (DNA synthesis-CuAAC) and immunohistochemistry targets in combination with TePhe (protein synthesis-OSTAC) in fixed cells. The favorable properties of the OSTAC reaction suggest its broad applicability in chemical biology.
Collapse
Affiliation(s)
- Yong Jia Bu
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | | | - Haissi Cui
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Mark Nitz
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| |
Collapse
|
3
|
Black MR, Bhattacharyya S, Argent SP, Pilgrim BS. Structural Transformations of Metal-Organic Cages through Tetrazine-Alkene Reactivity. J Am Chem Soc 2024. [PMID: 39236092 DOI: 10.1021/jacs.4c08591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2024]
Abstract
The assembly of metal-organic cages is governed by metal ion coordination preferences and the geometries of the typically rigid and planar precursor ligands. PdnL2n cages are among the most structurally diverse, with subtle differences in the metal-ligand coordination vectors resulting in drastically different assemblies, however almost all rely on rigid aromatic linkers to avoid the formation of intractable mixtures. Here we exploit the inverse electron-demand Diels-Alder (IEDDA) reaction between tetrazine linker groups and alkene reagents to trigger structural changes induced by post-assembly modification. The structure of the 1,4-dihydropyridazine produced by IEDDA (often an afterthought in click chemistry) is crucial; its two sp3 centers increase flexibility and nonplanarity, drastically changing the range of accessible coordination vectors. This triggers an initial Pd4L8 tetrahedral cage to transform into different Pd2L4 lantern cages, with both the transformation extent (thermodynamics) and rate (kinetics) dependent on the alkene dienophile selected. With cyclopentene, the unsymmetrical 1,4-dihydropyridazine ligands undergo integrative sorting in the solid state, with both head-to-tail orientation and enantiomer selection, leading to a single isomer from the 39 possible. This preference is rationalized through entropy, symmetry, and hydrogen bonding. Subsequent oxidation of the 1,4-dihydropyridazine to the aromatic pyridazine rigidifies the ligands, restoring planarity. The oxidized ligands no longer fit in the lantern structure, inducing further structural transformations into Pd4L8 tetrahedra and Pd3L6 double-walled triangles. The concept of controllable addition of limited additional flexibility and then its removal through well-defined reactivity we envisage being of great interest for structural transformations of any class of supramolecular architecture.
Collapse
Affiliation(s)
- Martin R Black
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | | | - Stephen P Argent
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Ben S Pilgrim
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| |
Collapse
|
4
|
Zhao R, Chen Y, Liang Y. Bioorthogonal Delivery of Carbon Disulfide in Living Cells. Angew Chem Int Ed Engl 2024; 63:e202400020. [PMID: 38752888 DOI: 10.1002/anie.202400020] [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: 01/01/2024] [Indexed: 06/27/2024]
Abstract
Carbon disulfide (CS2) is an environmental contaminant, which is deadly hazardous to the workers under chronic or acute exposure. However, the toxicity mechanisms of CS2 are still unclear due to the scarcity of biocompatible donors, which can release CS2 in cells. Here we developed the first bioorthogonal CS2 delivery system based on the "click-and-release" reactions between mesoionic 1,3-thiazolium-5-thiolates (TATs) and strained cyclooctyne exo-BCN-OH. We successfully realized intracellular CS2 release and investigated the causes of CS2-induced hepatotoxicity, including oxidative stress, proteotoxic stress and copper-dependent cell death. It is found that CS2 can be copper vehicles bypassing copper transporters after reacting with nucleophiles in cytoplasm, and extra copper supplementation will exacerbate the loss of homeostasis of cells and ultimately cell death. These findings inspired us to explore the anticancer activity of CS2 in combination with copper by introducing a copper chelating group in our CS2 delivery system.
Collapse
Affiliation(s)
- Ruohan Zhao
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yinghan Chen
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yong Liang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| |
Collapse
|
5
|
Wang Z, Wang S, Zhang Y, Ma M. Design, Synthesis, and Evaluation of Small Fluorescent Molecules with a 1,1-Dimethylnaphthalen-2-(1 H)-One Core. Molecules 2024; 29:3396. [PMID: 39064974 PMCID: PMC11280428 DOI: 10.3390/molecules29143396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/02/2024] [Accepted: 06/04/2024] [Indexed: 07/28/2024] Open
Abstract
A series of fluorescent molecules with 1,1-dimethylnaphthalene-2(1H)-one as the core were synthesized to overcome aggregation quenching and emit bright green fluorescence. The low molecular weight of these molecules led to them to smoothly pass through the cell membrane and penetrate deep into the nucleus to emit the corresponding fluorescence. Among them, NC-4-Br and NC-5-3O have good optical and in vitro properties and showed potential for use as fluorescent probes.
Collapse
Affiliation(s)
- Zhengyang Wang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Shuting Wang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Yuexing Zhang
- Shandong Provincial Key Laboratory of Monocrystalline Silicon Semiconductor Materials and Technology, Shandong Universities Engineering Research Center of Integrated Circuits Functional Materials and Expanded Applications, College of Chemistry and Chemical Engineering, Dezhou University, Dezhou 253023, China
| | - Mingliang Ma
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| |
Collapse
|
6
|
Vidyakina AA, Silonov SA, Govdi AI, Ivanov AY, Podolskaya EP, Balova IA, Bräse S, Danilkina NA. Key role of cycloalkyne nature in alkyne-dye reagents for enhanced specificity of intracellular imaging by bioorthogonal bioconjugation. Org Biomol Chem 2024. [PMID: 38973457 DOI: 10.1039/d4ob01032a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Conjugates of benzothiophene-fused azacyclononyne BT9N-NH2 with fluorescent dyes were developed to visualise azidoglycans intracellularly. The significance of the cycloalkyne core was demonstrated by comparing new reagents with DBCO- and BCN-dye conjugates. To reduce non-specificity during intracellular bioconjugation using SPAAC, less reactive BT9N-dye reagents are preferred over highly reactive DBCO- and BCN-dye conjugates.
Collapse
Affiliation(s)
- Alexandra A Vidyakina
- Institute of Chemistry, Saint Petersburg State University (SPbU), Saint Petersburg, 199034, Russia.
| | - Sergey A Silonov
- Institute of Chemistry, Saint Petersburg State University (SPbU), Saint Petersburg, 199034, Russia.
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 194064, Russia
| | - Anastasia I Govdi
- Institute of Chemistry, Saint Petersburg State University (SPbU), Saint Petersburg, 199034, Russia.
| | - Alexander Yu Ivanov
- Center for Magnetic Resonance, Research Park, Saint Petersburg State University (SPbU), Saint Petersburg, 199034, Russia
| | | | - Irina A Balova
- Institute of Chemistry, Saint Petersburg State University (SPbU), Saint Petersburg, 199034, Russia.
| | - Stefan Bräse
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany.
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Natalia A Danilkina
- Institute of Chemistry, Saint Petersburg State University (SPbU), Saint Petersburg, 199034, Russia.
| |
Collapse
|
7
|
Venrooij KR, de Bondt L, Bonger KM. Mutually Orthogonal Bioorthogonal Reactions: Selective Chemistries for Labeling Multiple Biomolecules Simultaneously. Top Curr Chem (Cham) 2024; 382:24. [PMID: 38971884 PMCID: PMC11227474 DOI: 10.1007/s41061-024-00467-8] [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: 12/19/2023] [Accepted: 05/13/2024] [Indexed: 07/08/2024]
Abstract
Bioorthogonal click chemistry has played a transformative role in many research fields, including chemistry, biology, and medicine. Click reactions are crucial to produce increasingly complex bioconjugates, to visualize and manipulate biomolecules in living systems and for various applications in bioengineering and drug delivery. As biological (model) systems grow more complex, researchers have an increasing need for using multiple orthogonal click reactions simultaneously. In this review, we will introduce the most common bioorthogonal reactions and discuss their orthogonal use on the basis of their mechanism and electronic or steric tuning. We provide an overview of strategies to create reaction orthogonality and show recent examples of mutual orthogonal chemistry used for simultaneous biomolecule labeling. We end by discussing some considerations for the type of chemistry needed for labeling biomolecules in a system of choice.
Collapse
Affiliation(s)
- Kevin R Venrooij
- Chemical Biology Group, Department of Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Lucienne de Bondt
- Chemical Biology Group, Department of Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Kimberly M Bonger
- Chemical Biology Group, Department of Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
| |
Collapse
|
8
|
Liang P, Wei J, Wei Y, Wang X, Liu F, Wang T. Hetero Diels-Alder reactions of isolable N-borylenamines. Chem Commun (Camb) 2024; 60:5964-5967. [PMID: 38767204 DOI: 10.1039/d4cc01645a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
A new strategy for N-borylenamines by reaction of 2-alkynyl benzyl azides with B(C6F5)3 was developed. This novel 1,3-carboboration reaction proceeded via a 5-exo-dig cyclization/formal 1,1-carboboration/B(C6F5)2 shift reaction sequence. Additionally, N-borylenamines can undergo hetero Diels-Alder (HDA) reactions with a variety of dienophiles. Our results are an attractive complement to HDA reactions.
Collapse
Affiliation(s)
- Pei Liang
- School of Chemistry, Dalian University of Technology, Dalian 116024, P. R. China.
| | - Junhui Wei
- School of Chemistry, Dalian University of Technology, Dalian 116024, P. R. China.
| | - Yongliang Wei
- School of Chemistry, Dalian University of Technology, Dalian 116024, P. R. China.
| | - Xue Wang
- School of Chemistry, Dalian University of Technology, Dalian 116024, P. R. China.
| | - Fei Liu
- School of Chemistry, Dalian University of Technology, Dalian 116024, P. R. China.
| | - Tongdao Wang
- School of Chemistry, Dalian University of Technology, Dalian 116024, P. R. China.
| |
Collapse
|
9
|
Noël N, Martinez A, Massicot F, Vasse JL, Behr JB. Kinetics of Strain-Promoted Alkyne-Nitrone Cycloadditions (SPANC) with Unprotected Carbohydrate Scaffolded Nitrones. Org Lett 2024; 26:3917-3922. [PMID: 38690807 DOI: 10.1021/acs.orglett.4c01098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
The use of unprotected carbohydrate-derived nitrones as partners in strain-promoted alkyne-nitrone cycloadditions was investigated as a new tool for bioconjugation. The observed second-order reactions displayed rate constants of 3.4 × 10-4-5.8 × 10-2 M-1 s-1, which is the common order of magnitude of reaction kinetics with other simple aliphatic or aromatic nitrones. Applicability of this method to aqueous media was demonstrated by performing a one-pot protocol, which combines sequential formation of the nitrone and cycloaddition with cyclooctyne in water.
Collapse
Affiliation(s)
- Nathan Noël
- Université de Reims Champagne-Ardenne, CNRS UMR 7312, ICMR, 51687 Reims, France
| | - Agathe Martinez
- Université de Reims Champagne-Ardenne, CNRS UMR 7312, ICMR, 51687 Reims, France
| | - Fabien Massicot
- Université de Reims Champagne-Ardenne, CNRS UMR 7312, ICMR, 51687 Reims, France
| | - Jean-Luc Vasse
- Université de Reims Champagne-Ardenne, CNRS UMR 7312, ICMR, 51687 Reims, France
| | - Jean-Bernard Behr
- Université de Reims Champagne-Ardenne, CNRS UMR 7312, ICMR, 51687 Reims, France
| |
Collapse
|
10
|
Serhan M, Josephson JD, Masoud SS, Nakajima M, Pezacki JP. 3-Oxidopyridinium Ions Are Versatile Bioorthogonal Dipoles for Use in Cycloadditions with Cyclooctynes. Chemistry 2024; 30:e202303699. [PMID: 38367278 DOI: 10.1002/chem.202303699] [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: 12/06/2023] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 02/19/2024]
Abstract
3-oxidopyridinium ions are water stable and soluble heteroaromatic betaines that behave as latent dipoles and undergo a wide variety of cycloadditions. Research into the cycloaddition reactions of 3-oxidopyridiniums was spearheaded by Alan R. Katritzky and collaborators from the early 1970s until the late 1980s, but they have yet to be used for bioorthogonal applications. Herein we report that 3-oxidopyridiniums can readily react with 4-dibenzocyclooctynol (DIBO), a common bioorthogonal handle, in a [3+2] cycloaddition. The mechanism was investigated by altering the electronics of the reaction by changing the substituent on the 5 position of the pyridinium. Electron-donating 5-substituents have been shown to significantly increase the rate of the reaction, with bimolecular rate constants ranging from 3.3×10-4 s-1 with 5-trifluoromethyl-N-methyl-3-oxidopyridinium to 1.07 M-1 s-1 with 5-amino-N-methyl-3-oxidopyridinium. 3-oxidopyridiniums' appreciable cycloaddition rates and compatibility with bioorthogonally relevant environments give them the potential to be used in a variety of bioconjugation applications.
Collapse
Affiliation(s)
- Mariam Serhan
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, K1N 6N5, Canada
| | - Jason D Josephson
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, K1N 6N5, Canada
| | - Shadi Sedghi Masoud
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, K1N 6N5, Canada
| | - Masaya Nakajima
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, K1N 6N5, Canada
| |
Collapse
|
11
|
Xu Q, Hoye TR. A Cascade of Strain-Driven Events Converting Benzynes to Alkynylbenzocyclobutenes to 1,3-Dien-5-ynes to Cyclic Allenes to Benzocyclohexadienones. J Am Chem Soc 2024; 146:6438-6443. [PMID: 38437506 DOI: 10.1021/jacs.3c10225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
Here, we report a strain-promoted cascade reaction that proceeds via multiple strained intermediates, ultimately driven by the high potential energy inherent in alkyne triple bonds (C≡C). More specifically, four alkynes (three from an HDDA benzyne precursor and the fourth from a conjugated enyne reaction partner) are transformed into eight of the skeletal carbons in the benzocyclohexadienone products. The reaction pathway proceeds sequentially via strained benzyne, benzocyclobutene, and cyclic allene intermediates. DFT computations suggest that the slowest step following benzyne generation is the 4π-electrocyclic ring-opening of the alkynylbenzocyclobutene to a 1,3-dien-5-yne (an alkynylxylylene) intermediate. The activation energy for the subsequent 6π-electrocyclic ring-closure is lower than that for related acyclic dienynes because of the aromaticity that is being regained in the transition structure. Finally, the isolation of the benzocyclohexadienone products rather than their phenolic tautomers is notable.
Collapse
Affiliation(s)
- Qian Xu
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - Thomas R Hoye
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
12
|
Mehak, Singh G, Singh R, Singh G, Stanzin J, Singh H, Kaur G, Singh J. Clicking in harmony: exploring the bio-orthogonal overlap in click chemistry. RSC Adv 2024; 14:7383-7413. [PMID: 38433942 PMCID: PMC10906366 DOI: 10.1039/d4ra00494a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024] Open
Abstract
In the quest to scrutinize and modify biological systems, the global research community has continued to explore bio-orthogonal click reactions, a set of reactions exclusively targeting non-native molecules within biological systems. These methodologies have brought about a paradigm shift, demonstrating the feasibility of artificial chemical reactions occurring on cellular surfaces, in the cell cytosol, or within the body - an accomplishment challenging to achieve with the majority of conventional chemical reactions. This review delves into the principles of bio-orthogonal click chemistry, contrasting metal-catalyzed and metal-free reactions of bio-orthogonal nature. It comprehensively explores mechanistic details and applications, highlighting the versatility and potential of this methodology in diverse scientific contexts, from cell labelling to biosensing and polymer synthesis. Researchers globally continue to advance this powerful tool for precise and selective manipulation of biomolecules in complex biological systems.
Collapse
Affiliation(s)
- Mehak
- School of Chemical Engineering and Physical Sciences, Lovely Professional University Phagwara-144411 Punjab India
| | - Gurleen Singh
- School of Chemical Engineering and Physical Sciences, Lovely Professional University Phagwara-144411 Punjab India
| | - Riddima Singh
- School of Chemical Engineering and Physical Sciences, Lovely Professional University Phagwara-144411 Punjab India
| | - Gurjaspreet Singh
- Department of Chemistry and Centre of Advanced Studies in Chemistry, Panjab University Chandigarh-160014 India
| | - Jigmat Stanzin
- Department of Chemistry and Centre of Advanced Studies in Chemistry, Panjab University Chandigarh-160014 India
| | - Harminder Singh
- School of Chemical Engineering and Physical Sciences, Lovely Professional University Phagwara-144411 Punjab India
| | - Gurpreet Kaur
- Department of Chemistry, Gujranwala Guru Nanak Khalsa College Civil Lines Ludhiana-141001 Punjab India
| | - Jandeep Singh
- School of Chemical Engineering and Physical Sciences, Lovely Professional University Phagwara-144411 Punjab India
| |
Collapse
|
13
|
Zuo Y, Liu M, Du J, Zhang T, Wang X, Wang C. Ir(iii)/Ag(i)-catalyzed directly C-H amidation of arenes with OH-free hydroxyamides as amidating agents. RSC Adv 2024; 14:5975-5980. [PMID: 38362076 PMCID: PMC10867557 DOI: 10.1039/d4ra00517a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 02/09/2024] [Indexed: 02/17/2024] Open
Abstract
A versatile Ir(iii)-catalyzed C-H amidation of arenes by employing readily available and stable OH-free hydroxyamides as a novel amidation source. The reaction occurred with high efficiency and tolerance of a range of functional groups. A wide scope of aryl OH-free hydroxyzamides, including conjugated and challenging non-conjugated OH-free hydroxyzamides, were capable of this transformation and no addition of an external oxidant is required. This protocol provided a simple, straightforward and economic method to a variety N-(2-(1H-pyrazol-1-yl)alkyl)amide derivates with good to excellent yield. Mechanistic study demonstrated that reversible C-H bond functionalisation might be involved in this reaction.
Collapse
Affiliation(s)
- Youpeng Zuo
- School of Chemistry and Chemical Engineering, Suzhou University Suzhou 234000 P. R. China
| | - Meijun Liu
- School of Chemistry and Chemical Engineering, Suzhou University Suzhou 234000 P. R. China
| | - Jun Du
- School of Chemistry and Chemical Engineering, Suzhou University Suzhou 234000 P. R. China
| | - Tianren Zhang
- School of Chemistry and Chemical Engineering, Suzhou University Suzhou 234000 P. R. China
| | - Xiaoqing Wang
- School of Chemistry and Chemical Engineering, Suzhou University Suzhou 234000 P. R. China
| | - Cong Wang
- School of Chemistry and Chemical Engineering, Suzhou University Suzhou 234000 P. R. China
| |
Collapse
|
14
|
Májek M, Trtúšek M. Discovery of new tetrazines for bioorthogonal reactions with strained alkenes via computational chemistry. RSC Adv 2024; 14:4345-4351. [PMID: 38304564 PMCID: PMC10828936 DOI: 10.1039/d3ra08712c] [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: 12/21/2023] [Accepted: 01/25/2024] [Indexed: 02/03/2024] Open
Abstract
Tetrazines are widely employed reagents in bioorthogonal chemistry, as they react readily with strained alkenes in inverse electron demand Diels-Alder reactions, allowing for selective labeling of biomacromolecules. For optimal performance, tetrazine reagents have to react readily with strained alkenes, while remaining inert against nucleophiles like thiols. Balancing these conditions is a challenge, as reactivity towards strained alkenes and nucleophiles is governed by the same factor - the energy of unoccupied orbitals of tetrazine. Herein, we utilize computational chemistry to screen a set of tetrazine derivatives, aiming to identify structural elements responsible for a better ratio of reactivity with strained alkenes vs. stability against nucleophiles. This advantageous trait is present in sulfone- and sulfoxide-substituted tetrazines. In the end, the distortion/interaction model helped us to identify that the reason behind this enhanced reactivity profile is a secondary orbital interaction between the strained alkene and sulfone-/sulfoxide-substituted tetrazine. This insight can be used to design new tetrazines for bioorthogonal chemistry with improved reactivity/stability profiles.
Collapse
Affiliation(s)
- Michal Májek
- Comenius University Bratislava, Faculty of Natural Sciences, Department of Organic Chemistry Mlynská Dolina, Ilkovičova 6 842 15 Bratislava Slovakia
| | - Matej Trtúšek
- Comenius University Bratislava, Faculty of Natural Sciences, Department of Organic Chemistry Mlynská Dolina, Ilkovičova 6 842 15 Bratislava Slovakia
| |
Collapse
|
15
|
Wang S, Wang H, Drabek A, Smith WS, Liang F, Huang ZR. Unleashing the Potential: Designing Antibody-Targeted Lipid Nanoparticles for Industrial Applications with CMC Considerations and Clinical Outlook. Mol Pharm 2024; 21:4-17. [PMID: 38117251 DOI: 10.1021/acs.molpharmaceut.3c00735] [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] [Indexed: 12/21/2023]
Abstract
Antibody-targeted lipid nanoparticles (Ab-LNPs) are rapidly gaining traction as multifaceted platforms in precision medicine, adept at delivering a diverse array of therapeutic agents, including nucleic acids and small molecules. This review provides an incisive overview of the latest developments in the field of Ab-LNP technology, with a special emphasis on pivotal design aspects such as antibody engineering, bioconjugation strategies, and advanced formulation techniques. Furthermore, it addresses critical chemistry, manufacturing, and controls (CMC) considerations and thoroughly examines the in vivo dynamics of Ab-LNPs, underscoring their promising potential for clinical application. By seamlessly blending scientific advancements with practical industrial perspectives, this review casts a spotlight on the burgeoning role of Ab-LNPs as an innovative and potent tool in the realm of targeted drug delivery.
Collapse
Affiliation(s)
- Sheryl Wang
- Sanofi, Genomic Medicine Unit, 225 Second Avenue, Waltham, Massachusetts 02451, United States
| | - Hong Wang
- Sanofi, Genomic Medicine Unit, 225 Second Avenue, Waltham, Massachusetts 02451, United States
| | - Andrew Drabek
- Sanofi, Genomic Medicine Unit, 225 Second Avenue, Waltham, Massachusetts 02451, United States
| | - Wenwen Sha Smith
- FUSION BioVenture, 15 Presidential Way, Woburn, Massachusetts 01801, United States
| | - Feng Liang
- Sanofi, Genomic Medicine Unit, 225 Second Avenue, Waltham, Massachusetts 02451, United States
| | - Zhaohua Richard Huang
- Sanofi, Genomic Medicine Unit, 225 Second Avenue, Waltham, Massachusetts 02451, United States
| |
Collapse
|
16
|
Min Q, Ji X. Bioorthogonal Bond Cleavage Chemistry for On-demand Prodrug Activation: Opportunities and Challenges. J Med Chem 2023; 66:16546-16567. [PMID: 38085596 DOI: 10.1021/acs.jmedchem.3c01459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Time- and space-resolved drug delivery is highly demanded for cancer treatment, which, however, can barely be achieved with a traditional prodrug strategy. In recent years, the prodrug strategy based on a bioorthogonal bond cleavage chemistry has emerged with the advantages of high temporospatial resolution over drug activation and homogeneous activation irrespective of individual heterogeneity. In the past five years, tremendous progress has been witnessed in this field with one such bioorthogonal prodrug entering Phase II clinical trials. This Perspective aims to highlight these new advances (2019-2023) and critically discuss their pros and cons. In addition, the remaining challenges and potential strategic directions for future progress will also be included.
Collapse
Affiliation(s)
- Qingqiang Min
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Science, Soochow University, Suzhou 215123, China
| | - Xingyue Ji
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Science, Soochow University, Suzhou 215123, China
| |
Collapse
|
17
|
Lee D, Latour S, Emblem M, Clark HJ, Santos JT, Jang J, McGuigan AP, Nitz M. Characterization of an N-Allylglyoxylamide-Based Bioorthogonal Nitrone Trap. Bioconjug Chem 2023; 34:2358-2365. [PMID: 38051144 DOI: 10.1021/acs.bioconjchem.3c00463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Aldehydes are attractive bioorthogonal coupling partners. The ease of manipulation of aldehydes and their orthogonality to other classes of bioorthogonal reactions have inspired the exploration of chemistries, which generate irreversible conjugates. Similarly, nitrones have been shown to be potent 1,3-dipoles in bioorthogonal reactions when paired with strained alkynes. Here, we combine the reactivity of nitrones with the simplicity of aldehydes using an N-allylglyoxylamide, in a cascade reaction with an N-alkylhydroxylamine to produce a bicyclic isoxazolidine. The reaction is found to be catalyzed by 5-methoxyanthranilic acid and proceeds at pH 7 with favorable kinetics. Using the HaloTag7 protein bearing an N-alkylhydroxylamine, we show the reaction to be bioorthogonal in a complex cell lysate and to proceed well at the surface of a HEK293 cell. Furthermore, the reaction is compatible with a typical strain-promoted alkyne-azide click reaction. The characteristics of this reaction suggest it will be a useful addition to the pallet of bioorthogonal reactions that have revolutionized chemical biology.
Collapse
Affiliation(s)
- Daniel Lee
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Simon Latour
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E6, Canada
| | - Michael Emblem
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Hunter J Clark
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Jobette T Santos
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Jaewan Jang
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Alison P McGuigan
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E6, Canada
| | - Mark Nitz
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| |
Collapse
|
18
|
Adrion DM, Karunaratne WV, Lopez SA. Multiconfigurational photodynamics simulations reveal the mechanism of photodecarbonylations of cyclopropenones in explicit aqueous environments. Chem Sci 2023; 14:13205-13218. [PMID: 38023495 PMCID: PMC10664470 DOI: 10.1039/d3sc03805j] [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: 07/21/2023] [Accepted: 11/02/2023] [Indexed: 12/01/2023] Open
Abstract
Gas-evolving photochemical reactions use light and mild conditions to access strained organic compounds irreversibly. Cyclopropenones are a class of light-responsive molecules used in bioorthogonal photoclick reactions; their excited-state decarbonylation reaction mechanisms are misunderstood due to their ultrafast (<100 femtosecond) lifetimes. We have combined multiconfigurational quantum mechanical (QM) calculations and non-adiabatic molecular dynamics (NAMD) simulations to uncover the excited-state mechanism of cyclopropenone and a photoprotected cyclooctyne-(COT)-precursor in gaseous and explicit aqueous environments. We explore the role of H-bonding with fully quantum mechanical explicitly solvated NAMD simulations for the decarbonylation reaction. The cyclopropenones pass through asynchronous conical intersections and have dynamically concerted photodecarbonylation mechanisms. The COT-precursor has a higher quantum yield of 55% than cyclopropenone (28%) because these trajectories prefer to break a σCC bond to avoid the strained trans-cyclooctene geometries. Our solvated simulations show an increased quantum yield (58%) for the systems studied here.
Collapse
Affiliation(s)
- Daniel M Adrion
- Department of Chemistry and Chemical Biology, Northeastern University Boston Massachusetts 02115 USA
| | - Waruni V Karunaratne
- Department of Chemistry and Chemical Biology, Northeastern University Boston Massachusetts 02115 USA
| | - Steven A Lopez
- Department of Chemistry and Chemical Biology, Northeastern University Boston Massachusetts 02115 USA
| |
Collapse
|
19
|
Zeng X, Ma X, Dong J, Li B, Hua Liu S, Yin J, Yang GF. A Protocol for Activated Bioorthogonal Fluorescence Labeling and Imaging of 4-Hydroxyphenylpyruvate Dioxygenase in Plants. Angew Chem Int Ed Engl 2023; 62:e202312618. [PMID: 37795547 DOI: 10.1002/anie.202312618] [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: 08/27/2023] [Revised: 09/25/2023] [Accepted: 10/04/2023] [Indexed: 10/06/2023]
Abstract
4-Hydroxyphenylpyruvate dioxygenase (HPPD) plays a crucial role in the synthesis of nutrients needed to maintain optimal plant growth. Its level is closely linked to the extent of abiotic stress experienced by plants. Moreover, it is also the target of commercial herbicides. Therefore, labeling of HPPD in plants not only enables visualization of its tissue distribution and cellular uptake, it also facilitates assessment of abiotic stress of plants and provides information needed for the development of effective environmentally friendly herbicides. In this study, we created a method for fluorescence labeling of HPPD that avoids interference with the normal growth of plants. In this strategy, a perylene-linked dibenzyl-cyclooctyne undergoes strain-promoted azide-alkyne cycloaddition with an azide-containing HPPD ligand. The activation-based labeling process results in a significant emission enhancement caused by the change in the fluorescent forms from an excimer to a monomer. Notably, this activated bioorthogonal strategy is applicable to visualizing HPPD in Arabidopsis thaliana, and assessing its response to multiple abiotic stresses. Also, it can be employed to monitor in vivo levels and locations of HPPD in crops. Consequently, the labeling strategy will be a significant tool in investigations of HPPD-related abiotic stress mechanisms, discovering novel herbicides, and uncovering unknown biological functions.
Collapse
Affiliation(s)
- Xiaoyan Zeng
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, College of chemistry, Central China Normal University, 430079, Wuhan, P. R. China
| | - Xiaoxie Ma
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, College of chemistry, Central China Normal University, 430079, Wuhan, P. R. China
| | - Jin Dong
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, College of chemistry, Central China Normal University, 430079, Wuhan, P. R. China
| | - Biao Li
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, College of chemistry, Central China Normal University, 430079, Wuhan, P. R. China
| | - Sheng Hua Liu
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, College of chemistry, Central China Normal University, 430079, Wuhan, P. R. China
| | - Jun Yin
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, College of chemistry, Central China Normal University, 430079, Wuhan, P. R. China
| | - Guang-Fu Yang
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, College of chemistry, Central China Normal University, 430079, Wuhan, P. R. China
| |
Collapse
|
20
|
Das E, Feliciano MAM, Yamanushkin P, Lin X, Gold B. Oxa-azabenzobenzocyclooctynes (O-ABCs): heterobiarylcyclooctynes bearing an endocyclic heteroatom. Org Biomol Chem 2023; 21:8857-8862. [PMID: 37881858 DOI: 10.1039/d3ob01559a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
We report the synthesis of heterobiarylcyclooctynes bearing an endocyclic heteroatom, oxa-azabenzobenzocyclooctynes (O-ABCs). The integration of design strategies for accelerating strain-promoted azide-alkyne cycloadditions results in reactivity with organic azides that surpasses all cyclooctyne reagents reported to date. O-ABCs and related compounds provide insights into the effects of structural modifications on reactivity that can aid in the design of new reagents for click and bioorthogonal chemistry.
Collapse
Affiliation(s)
- Eshani Das
- Department of Chemistry and Chemical Biology, University of New Mexico, New Mexico, 87131, USA
| | - Mark Aldren M Feliciano
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico, 88003, USA.
- Department of Chemistry and Chemical Biology, University of New Mexico, New Mexico, 87131, USA
| | - Pavel Yamanushkin
- Department of Chemistry and Chemical Biology, University of New Mexico, New Mexico, 87131, USA
| | - Xinsong Lin
- Department of Chemistry and Biochemistry Florida State University, Tallahassee, FL, 32306, USA
| | - Brian Gold
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico, 88003, USA.
- Department of Chemistry and Chemical Biology, University of New Mexico, New Mexico, 87131, USA
| |
Collapse
|
21
|
Yan Z, Pan Y, Jiao G, Xu M, Fan D, Hu Z, Wu J, Chen T, Liu M, Bao X, Ke H, Ji X. A Bioorthogonal Decaging Chemistry of N-Oxide and Silylborane for Prodrug Activation both In Vitro and In Vivo. J Am Chem Soc 2023; 145:24698-24706. [PMID: 37933858 DOI: 10.1021/jacs.3c08012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Bioorthogonal decaging chemistry with both fast kinetics and high efficiency is highly demanded for in vivo applications but remains very sporadic. Herein, we describe a new bioorthogonal decaging chemistry between N-oxide and silylborane. A simple replacement of "C" in boronic acid with "Si" was able to substantially accelerate the N-oxide decaging kinetics by 106 fold (k2: up to 103 M-1 s-1). Moreover, a new N-oxide-masked self-immolative spacer was developed for the traceless release of various payloads upon clicking with silylborane with fast kinetics and high efficiency (>90%). Impressively, one such N-oxide-based self-assembled bioorthogonal nano-prodrug in combination with silylborane led to significantly enhanced tumor suppression effects as compared to the parent drug in a 4T1 mouse breast tumor model. In aggregate, this new bioorthogonal click-and-release chemistry is featured with fast kinetics and high efficiency and is perceived to find widespread applications in chemical biology and drug delivery.
Collapse
Affiliation(s)
- Zhicheng Yan
- College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu 215021, China
| | - Yiyao Pan
- College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu 215021, China
| | - Guofeng Jiao
- College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu 215021, China
| | - Mengyu Xu
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, Jiangsu 215123, China
| | - Dongguang Fan
- College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu 215021, China
| | - Ziwei Hu
- College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu 215021, China
| | - Jiarui Wu
- College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu 215021, China
| | - Tao Chen
- College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu 215021, China
| | - Miao Liu
- College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu 215021, China
| | - Xiaoguang Bao
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, Jiangsu 215123, China
| | - Hengte Ke
- College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu 215021, China
| | - Xingyue Ji
- College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu 215021, China
| |
Collapse
|
22
|
Savastano M, López de la Torre MD, Pagliai M, Poggi G, Ridi F, Bazzicalupi C, Melguizo M, Bianchi A. Crystal engineering of high explosives through lone pair-π interactions: Insights for improving thermal safety. iScience 2023; 26:107330. [PMID: 37636051 PMCID: PMC10448033 DOI: 10.1016/j.isci.2023.107330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 06/27/2023] [Accepted: 07/05/2023] [Indexed: 08/29/2023] Open
Abstract
In this high-risk/high-reward study, we prepared complexes of a high explosive anion (picrate) with potentially explosive s-tetrazine-based ligands with the sole purpose of advancing the understanding of one of the weakest supramolecular forces: the lone pair-π interaction. This is a proof-of-concept study showing how lone pair-π contacts can be effectively used in crystal engineering, even of high explosives, and how the supramolecular architecture of the resulting crystalline phases influences their experimental thermokinetic properties. Herein we present XRD structures of 4 novel detonating compounds, all showcasing lone pair-π interactions, their thermal characterization (DSC, TGA), including the correlation of experimental thermokinetic parameters with crystal packing, and in silico explosion properties. This last aspect is relevant for improving the safety of high-energy materials.
Collapse
Affiliation(s)
- Matteo Savastano
- Department of Human Sciences and Quality of Life Promotion, University San Raffaele Roma, Via di Val Cannuta 247, 00166 Rome, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | | | - Marco Pagliai
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Giovanna Poggi
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- CSGI, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Francesca Ridi
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- CSGI, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Carla Bazzicalupi
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Manuel Melguizo
- Department of Inorganic and Organic Chemistry, University of Jaén, 23071 Jaén, Spain
| | - Antonio Bianchi
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| |
Collapse
|
23
|
Šlachtová V, Bellová S, La-Venia A, Galeta J, Dračínský M, Chalupský K, Dvořáková A, Mertlíková-Kaiserová H, Rukovanský P, Dzijak R, Vrabel M. Triazinium Ligation: Bioorthogonal Reaction of N1-Alkyl 1,2,4-Triazinium Salts. Angew Chem Int Ed Engl 2023; 62:e202306828. [PMID: 37436086 DOI: 10.1002/anie.202306828] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 07/13/2023]
Abstract
The development of reagents that can selectively react in complex biological media is an important challenge. Here we show that N1-alkylation of 1,2,4-triazines yields the corresponding triazinium salts, which are three orders of magnitude more reactive in reactions with strained alkynes than the parent 1,2,4-triazines. This powerful bioorthogonal ligation enables efficient modification of peptides and proteins. The positively charged N1-alkyl triazinium salts exhibit favorable cell permeability, which makes them superior for intracellular fluorescent labeling applications when compared to analogous 1,2,4,5-tetrazines. Due to their high reactivity, stability, synthetic accessibility and improved water solubility, the new ionic heterodienes represent a valuable addition to the repertoire of existing modern bioorthogonal reagents.
Collapse
Affiliation(s)
- Veronika Šlachtová
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 16000, Prague, Czech Republic
| | - Simona Bellová
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 16000, Prague, Czech Republic
| | - Agustina La-Venia
- Current address: Instituto de Química Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario-CONICET, Suipacha 531, S2002LRK, Rosario, Argentina
| | - Juraj Galeta
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 16000, Prague, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 16000, Prague, Czech Republic
| | - Karel Chalupský
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 16000, Prague, Czech Republic
| | - Alexandra Dvořáková
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 16000, Prague, Czech Republic
| | - Helena Mertlíková-Kaiserová
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 16000, Prague, Czech Republic
| | - Peter Rukovanský
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 16000, Prague, Czech Republic
| | - Rastislav Dzijak
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 16000, Prague, Czech Republic
| | - Milan Vrabel
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 16000, Prague, Czech Republic
| |
Collapse
|
24
|
Svatunek D, Chojnacki K, Deb T, Eckvahl H, Houk KN, Franzini RM. Orthogonal Inverse-Electron-Demand Cycloaddition Reactions Controlled by Frontier Molecular Orbital Interactions. Org Lett 2023; 25:6340-6345. [PMID: 37591496 PMCID: PMC10476241 DOI: 10.1021/acs.orglett.3c02265] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Indexed: 08/19/2023]
Abstract
Chemoselective pairs of bioorthogonal reactants enable the simultaneous labeling of several biomolecules. Here, we access orthogonal click reactions by exploiting differences in frontier molecular orbital interaction energies in transition states. We establish that five-membered cyclic dienes are inert to isonitriles but readily react with strained alkynes, while tetrazines with bulky substituents readily react with isonitriles. Strained alkynes show an opposite reactivity pattern. The approach was demonstrated by orthogonally labeling two proteins with different fluorophores.
Collapse
Affiliation(s)
- Dennis Svatunek
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095, United States
- Institute
of Applied Synthetic Chemistry, TU Wien, 1060 Vienna, Austria
| | - Konrad Chojnacki
- Department
of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Titas Deb
- Department
of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Hannah Eckvahl
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095, United States
| | - K. N. Houk
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095, United States
| | - Raphael M. Franzini
- Department
of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
- Huntsman
Cancer Institute, Salt Lake City, Utah 84112, United States
| |
Collapse
|
25
|
Vidyakina AA, Shtyrov AA, Ryazantsev MN, Khlebnikov AF, Kolesnikov IE, Sharoyko VV, Spiridonova DV, Balova IA, Bräse S, Danilkina NA. Development of Fluorescent Isocoumarin-Fused Oxacyclononyne - 1,2,3-Triazole Pairs. Chemistry 2023; 29:e202300540. [PMID: 37293937 DOI: 10.1002/chem.202300540] [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: 02/18/2023] [Revised: 06/02/2023] [Accepted: 06/09/2023] [Indexed: 06/10/2023]
Abstract
Fluorescent isocoumarin-fused cycloalkynes, which are reactive in SPAAC and give fluorescent triazoles regardless of the azide nature, have been developed. The key structural feature that converts the non-fluorescent cycloalkyne/triazole pair to its fluorescent counterpart is the pi-acceptor group (COOMe, CN) at the C6 position of the isocoumarin ring. The design of the fluorescent cycloalkyne/triazole pairs is based on the theoretical study of the S1 state deactivation mechanism of the non-fluorescent isocoumarin-fused cycloalkyne IC9O using multi-configurational ab initio and DFT methodologies. The calculations revealed that deactivation proceeds through the electrocyclic ring opening of the α-pyrone cycle and is accompanied by a redistribution of electron density in the fused benzene ring. We proposed that the S1 excited state deactivation barrier could be increased by introducing a pi-acceptor group into a position that is in direct conjugation with the formed C=O group and has a reduced electron density in the transition state. As a proof of concept, we designed and synthesized two fluorescent isocoumarin-fused cycloalkynes IC9O-COOMe and IC9O-CN bearing pi-acceptors at the C6 position. The importance of the nature of a pi-acceptor group was shown by the example of much less fluorescent CF3 -substituted cycloalkyne IC9O-CF3 .
Collapse
Affiliation(s)
- Aleksandra A Vidyakina
- Institute of Chemistry, Saint Petersburg State University (SPbU), Sankt-Peterburg, 199034 Saint Petersburg, Russia
| | - Andrey A Shtyrov
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, Sankt-Peterburg, 194021 Saint Petersburg, Russia
| | - Mikhail N Ryazantsev
- Institute of Chemistry, Saint Petersburg State University (SPbU), Sankt-Peterburg, 199034 Saint Petersburg, Russia
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, Sankt-Peterburg, 194021 Saint Petersburg, Russia
| | - Alexander F Khlebnikov
- Institute of Chemistry, Saint Petersburg State University (SPbU), Sankt-Peterburg, 199034 Saint Petersburg, Russia
| | - Ilya E Kolesnikov
- Institute of Chemistry, Saint Petersburg State University (SPbU), Sankt-Peterburg, 199034 Saint Petersburg, Russia
| | - Vladimir V Sharoyko
- Institute of Chemistry, Saint Petersburg State University (SPbU), Sankt-Peterburg, 199034 Saint Petersburg, Russia
| | - Dar'ya V Spiridonova
- Institute of Chemistry, Saint Petersburg State University (SPbU), Sankt-Peterburg, 199034 Saint Petersburg, Russia
| | - Irina A Balova
- Institute of Chemistry, Saint Petersburg State University (SPbU), Sankt-Peterburg, 199034 Saint Petersburg, Russia
| | - Stefan Bräse
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany
- Institute of Biological and Chemical Systems-, Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
| | - Natalia A Danilkina
- Institute of Chemistry, Saint Petersburg State University (SPbU), Sankt-Peterburg, 199034 Saint Petersburg, Russia
| |
Collapse
|
26
|
Abstract
As chemical biologists sought methods to modify and study biomolecules in their native environments, the need for bioorthogonal chemical reactions emerged. These fast and selective reactions between otherwise inert, abiotic functional groups have enabled exploration of some of the most intriguing and challenging questions in chemical biology. Further, the ability to perform organic reactions in cells and organisms has led to important applications in clinical spaces, and one reaction is now an integral part of a phase 2 trial for treating solid tumors. Given that bioorthogonal chemistry was a recipient of the 2022 Nobel Prize, we expect this field to be even more energized. Here, we highlight some of the most recent studies in this sphere and how these set the stage for where bioorthogonal chemistry is headed.
Collapse
Affiliation(s)
- Kaitlin M. Hartung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ellen M. Sletten
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| |
Collapse
|
27
|
Nan J, Huang G, Liu S, Wang J, Ma Y, Luan X. In(OTf) 3-catalyzed reorganization/cycloaddition of two imine units and subsequent modular assembly of acridinium photocatalysts. Chem Sci 2023; 14:5160-5166. [PMID: 37206409 PMCID: PMC10189902 DOI: 10.1039/d3sc00163f] [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: 01/11/2023] [Accepted: 04/15/2023] [Indexed: 05/21/2023] Open
Abstract
Herein, we disclose a novel reorganization/cycloaddition between two imine units catalyzed by In(OTf)3 Lewis acid that differs from the well-known [4 + 2] cycloaddition version via the Povarov reaction. By means of this unprecedented imine chemistry, a collection of synthetically useful dihydroacridines has been synthesized. Notably, the obtained products give rise to a series of structurally novel and fine-tuneable acridinium photocatalysts, offering a heuristic paradigm for synthesis and efficiently facilitating several encouraging dihydrogen coupling reactions.
Collapse
Affiliation(s)
- Jiang Nan
- The Youth Innovation Team of Shaanxi Universities, Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology Xi'an 710021 China
| | - Guanjie Huang
- The Youth Innovation Team of Shaanxi Universities, Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology Xi'an 710021 China
| | - Shilei Liu
- The Youth Innovation Team of Shaanxi Universities, Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology Xi'an 710021 China
| | - Jing Wang
- The Youth Innovation Team of Shaanxi Universities, Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology Xi'an 710021 China
| | - Yangmin Ma
- The Youth Innovation Team of Shaanxi Universities, Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology Xi'an 710021 China
| | - Xinjun Luan
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, Northwest University Xi'an 710021 China
| |
Collapse
|
28
|
Amankwah G, Ofori I, Atta-Kumi J, Kwawu CR, Tia R, Adei E. A quantum mechanistic insight into the chemo- and regio-selective [3 + 2]-cycloaddition reaction of aryl hetaryl thioketones with diazoalkanes and nitrile oxide derivatives. J Mol Graph Model 2023; 120:108418. [PMID: 36709702 DOI: 10.1016/j.jmgm.2023.108418] [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: 11/14/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 01/22/2023]
Abstract
In this quantum mechanistic study, density functional theory computations at the B3LYP hybrid level of theory, in addition to triple zeta basis set 6-311G (d, p), were utilized to investigate the chemoselectivities and regioselectivities of the [3 + 2] cycloaddition reaction of phenyl (2-thienyl) thioketone (B1) derivatives with nitrile oxide (B2) and diazopropane derivatives (B3). From the computations obtained, the reactions of nitrile oxide and diazopropane derivatives with phenyl (2-thienyl) thioketone proceed through an asynchronous one-step mechanism. The initial [3 + 2] cycloaddition reaction of B1 and B3 is followed by a nitrogen extrusion which is also highly asynchronous. Despite the steric and electronic effects of the substituent on the energetics, the reaction center is selectively observed at the thiocarbonyl site of B1. A study of the Parr functions at the different reaction sites in B1 indicates the addition of B2 and B3 via the atomic centers with the largest Mulliken atomic spin densities. These results show that the thiocarbonyl site is the most reactive center compared to the other ethylene groups on B1, irrespective of the three atom components used. The global electron density transfer results are in agreement with the selectivity and activation barriers observed in the reaction. Our results agree well with experimental observations.
Collapse
Affiliation(s)
- Gabriel Amankwah
- Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.
| | - Isaac Ofori
- Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.
| | - Joshua Atta-Kumi
- Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.
| | - Caroline R Kwawu
- Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.
| | - Richard Tia
- Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.
| | - Evans Adei
- Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.
| |
Collapse
|
29
|
Flemming A, Dutmer BC, Gilbert TM. Additivity of Diene Substituent Gibbs Free Energy Contributions for Diels-Alder Reactions between Me 2C=CMe 2 and Substituted Cyclopentadienes. ACS OMEGA 2023; 8:14160-14170. [PMID: 37091433 PMCID: PMC10116529 DOI: 10.1021/acsomega.3c00831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/28/2023] [Indexed: 05/03/2023]
Abstract
Systematic computational studies of pericyclic Diels-Alder reactions between (H3C)2C=C(CH3)2, 1, and all permutations of substituted cyclopentadienes c-C5R1R2R3R4R5aR5b (R = H, CH3, CF3, F) allowed isolation of substitutional effects on Gibbs free energy barrier heights and reaction Gibbs free energies. "Average Substitution Gibbs Free Energy Correction" ΔG ASC# ‡/ΔG ASC# values for each substituent in each position appeared to be additive. Substituent effects on barriers showed interesting contrasts. Methyl substitution at positions 5a and 5b increased barriers significantly, while substitution at all other positions had essentially no impact. In contrast, fluoro substitution at positions 5a and 5b lowered barriers more than substitution at other positions. Trifluoromethyl substitution mixed these effects, in that substitution at positions 5a and 5b increased barriers, but substitution at other positions lowered them. Despite the variances, ΔG ASC# ‡/ΔG ASC# values allowed reliable prediction of barriers and exergonicities for reactions between 1 and highly substituted cyclopentadienes, and between 1 and cyclopentadienes with random mixtures of CH3/CF3/F substituents. ΔG ASC# ‡/ΔG ASC# values were correlated with steric considerations and quantum theory of atoms in molecules (QTAIM) calculations. Overall, the ASC values provide a resource for predicting which Diels-Alder reactions of this type should occur at rapid rates and/or give stable bicyclic products.
Collapse
Affiliation(s)
- Austin
S. Flemming
- Department
of Chemistry, Highland Community College, Freeport, Illinois 61032, United States
| | - Brendan C. Dutmer
- Department
of Chemistry, Highland Community College, Freeport, Illinois 61032, United States
| | - Thomas M. Gilbert
- Department
of Chemistry and Biochemistry, Northern
Illinois University, DeKalb, Illinois 60115, United States
| |
Collapse
|
30
|
Schulz J, Clauss R, Kazimir A, Holzknecht S, Hey-Hawkins E. On the Edge of the Known: Extremely Electron-Rich (Di)Carboranyl Phosphines. Angew Chem Int Ed Engl 2023; 62:e202218648. [PMID: 36573025 DOI: 10.1002/anie.202218648] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Indexed: 12/28/2022]
Abstract
The syntheses of the first B9-connected carboranylphosphines (B9-Phos) featuring two carboranyl moieties as well as access to B9-Phos ligands with bulky electron-donating substituents, previously deemed unattainable, is reported. The electrochemical properties of the B9-Phos ligands were investigated, revealing the ability of the mesityl derivatives to form stabilized phosphoniumyl radical cations. The B9-Phos ligands display an extremely electron-releasing character surpassing that of alkyl phosphines and commonly used N-heterocyclic carbenes. This is demonstrated by their very small Tolman electronic parameters (TEPs) as well as extremely low P-Se coupling constants. Cone angles and buried volumes attest to the high steric demand exerted by the (di)carboranyl phosphines. The dicarboranyl phosphine AuI complexes show superior catalytic performance in the hydroamination of alkynes compared to the monocarboranyl phosphine analogs.
Collapse
Affiliation(s)
- Jan Schulz
- Leipzig University, Faculty of Chemistry and Mineralogy, Institute of Inorganic Chemistry, Johannisallee 29, 04103, Leipzig, Germany
| | - Reike Clauss
- Leipzig University, Faculty of Chemistry and Mineralogy, Institute of Inorganic Chemistry, Johannisallee 29, 04103, Leipzig, Germany
| | - Aleksandr Kazimir
- Leipzig University, Faculty of Chemistry and Mineralogy, Institute of Inorganic Chemistry, Johannisallee 29, 04103, Leipzig, Germany
| | - Sieglinde Holzknecht
- Leipzig University, Faculty of Chemistry and Mineralogy, Institute of Inorganic Chemistry, Johannisallee 29, 04103, Leipzig, Germany
| | - Evamarie Hey-Hawkins
- Leipzig University, Faculty of Chemistry and Mineralogy, Institute of Inorganic Chemistry, Johannisallee 29, 04103, Leipzig, Germany
| |
Collapse
|
31
|
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
|
32
|
Li Y, Zhou H, Liu H, Gan Y, Zheng Y, Sheng J, Wang R. Development of Nitroso-Based Probes for Labeling and Regulation of RAS Proteins in Cancer Cells via Sequential Ene-Ligation and Oxime Condensation. J Org Chem 2023; 88:1762-1771. [PMID: 36691112 DOI: 10.1021/acs.joc.2c02922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Prenyl functionalities have been widely discovered in natural products, nucleic acids, and proteins with significant biological roles in both healthy and diseased cells. In this work, we develop a series of new nitroso-based probes for the labeling, enrichment, and regulation of prenylated RAS protein, which is highly associated with ∼20% of human cancers and used to be regarded as an "undruggable" target via a sequential ene-ligation and oxime condensation (SELOC) process. We found that these nitroso species can rapidly react with prenyl-containing molecules through ene-ligation and install a molecular tag for functional applications under physiological conditions. We first investigated this ligation process on two peptide models and demonstrated its labeling efficiency on various proteins such as myoglobin, lysozyme, RNase A, BSA, and HSP40. We further coupled this reactive platform with proteolysis-targeting chimera technology targeting to increase its efficiency and accuracy, as well as to expand its application range. Using the prenylated RAS protein as the model, we demonstrated that RAS could be efficiently decorated with our nitroso probes, which further condensate with oxime and rapidly react with a pomalidomide-containing hydroxylamine probe for protein degradation. As a result, the RAS protein in both HeLa and A549 cell lines has been determined to be efficiently degraded both in vitro and in vivo. This is the first case targeting post-translational modification other than ligand-protein interaction to degrade and regulate RAS proteins. We envision that our SELOC strategy will have great potential in studying the fundamental structures and functions of prenylated biomolecules and developing new drugs based on these unique cellular pathways.
Collapse
Affiliation(s)
- Yuanyuan Li
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Hongling Zhou
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Huili Liu
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Youfang Gan
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Yaying Zheng
- Department of Chemistry, and The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Jia Sheng
- Department of Chemistry, and The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Rui Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China.,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, Guangdong 518063, China
| |
Collapse
|
33
|
Kufleitner M, Haiber LM, Wittmann V. Metabolic glycoengineering - exploring glycosylation with bioorthogonal chemistry. Chem Soc Rev 2023; 52:510-535. [PMID: 36537135 DOI: 10.1039/d2cs00764a] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Glycans are involved in numerous biological recognition events. Being secondary gene products, their labeling by genetic methods - comparable to GFP labeling of proteins - is not possible. To overcome this limitation, metabolic glycoengineering (MGE, also known as metabolic oligosaccharide engineering, MOE) has been developed. In this approach, cells or organisms are treated with synthetic carbohydrate derivatives that are modified with a chemical reporter group. In the cytosol, the compounds are metabolized and incorporated into newly synthesized glycoconjugates. Subsequently, the reporter groups can be further derivatized in a bioorthogonal ligation reaction. In this way, glycans can be visualized or isolated. Furthermore, diverse targeting strategies have been developed to direct drugs, nanoparticles, or whole cells to a desired location. This review summarizes research in the field of MGE carried out in recent years. After an introduction to the bioorthogonal ligation reactions that have been used in in connection with MGE, an overview on carbohydrate derivatives for MGE is given. The last part of the review focuses on the many applications of MGE starting from mammalian cells to experiments with animals and other organisms.
Collapse
Affiliation(s)
- Markus Kufleitner
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
| | - Lisa Maria Haiber
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
| | - Valentin Wittmann
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
| |
Collapse
|
34
|
Holzmann MJ, Khanal N, Yamanushkin P, Gold B. Remote Strain Activation in a Sulfate-Linked Dibenzocycloalkyne. Org Lett 2023; 25:309-313. [PMID: 36455206 DOI: 10.1021/acs.orglett.2c03397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Cycloalkynes and their utilization in cycloaddition reactions enable modular strategies spanning the molecular sciences. Strain─imparted by deviation from linearity─enables sufficient alkyne reactivity without the need for a catalyst (e.g., copper); however, the design and synthesis of stable reagents with suitable reactivity remains an ongoing challenge. We report the incorporation of an endocyclic sulfate within a dibenzocyclononyne scaffold to generate a cyclononyne displaying remarkable reactivity and stability. Through computational analyses, we revealed that the endocyclic sulfate group shares nearly half the total strain energy, providing an activation strategy that reduces alkyne bending. Rehybridization of alkyne carbons in the formation of the heterocyclic product relieves strain both at the reactive site and in the transannular sulfate group. This mode of remote activation enables rapid reactivity while minimizing distortion─and strain─at the reactive site (the alkyne). The result: a design strategy for a new class of cycloalkynes with increased stability and reactivity.
Collapse
Affiliation(s)
- Michael J Holzmann
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Namrata Khanal
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Pavel Yamanushkin
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Brian Gold
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| |
Collapse
|
35
|
Zhang R, Gao J, Zhao G, Zhou L, Kong F, Jiang T, Jiang H. Tetrazine bioorthogonal chemistry makes nanotechnology a powerful toolbox for biological applications. NANOSCALE 2023; 15:461-469. [PMID: 36533721 DOI: 10.1039/d2nr06056f] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Bioorthogonal chemistry enables researchers to manipulate bioactive molecules in living systems. These highly selective and biocompatible reactions can be carried out in various complex environments. Over the past two decades, a considerable number of strides have been made to expand the capacities of bioorthogonal chemistry coupled with the aim to fine-tune present reactions for specific applications. The good points of bioorthogonal chemistry have pushed material chemists to integrate bioorthogonal chemistry with nanotechnologies to broaden the biological applications of nanomaterials. Notably, bioorthogonal nanotechnologies fundamentally rely on, more than half, according to our investigation, tetrazine bioorthogonal chemistry (TBC) to function as bioorthogonal handles to react with target agents owing to the extremely rapid kinetics and high selectivities of TBC. Its utilization in combination with nanotechnologies has led to developments in various areas of biomedicine, such as in situ drug activation and targeted delivery, bioimaging and biosensing, and the understanding of cell-biomolecule interactions. Given the fantastic past achievements and the rapid developments in tetrazine bioorthogonal technologies, the future is certainly very bright.
Collapse
Affiliation(s)
- Renshuai Zhang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, China.
- Cancer Institute, Affiliated Hospital of Qingdao University, 266071, China
| | - Jiake Gao
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, China.
| | - Gaoxiang Zhao
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, China.
- Cancer Institute, Affiliated Hospital of Qingdao University, 266071, 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 530006, China.
| | - Fandong Kong
- 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 530006, China.
| | - Tao Jiang
- Key Laboratory of Marine Drugs Chinese Ministry of Education, Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.
| | - Hongfei Jiang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, China.
- Cancer Institute, Affiliated Hospital of Qingdao University, 266071, China
| |
Collapse
|
36
|
Bioorthogonal chemistry based on-demand drug delivery system in cancer therapy. Front Chem Sci Eng 2023. [DOI: 10.1007/s11705-022-2227-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
37
|
Tay NES, Ryu KA, Weber JL, Olow AK, Cabanero DC, Reichman DR, Oslund RC, Fadeyi OO, Rovis T. Targeted activation in localized protein environments via deep red photoredox catalysis. Nat Chem 2023; 15:101-109. [PMID: 36216892 PMCID: PMC9840673 DOI: 10.1038/s41557-022-01057-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 09/02/2022] [Indexed: 01/17/2023]
Abstract
State-of-the-art photoactivation strategies in chemical biology provide spatiotemporal control and visualization of biological processes. However, using high-energy light (λ < 500 nm) for substrate or photocatalyst sensitization can lead to background activation of photoactive small-molecule probes and reduce its efficacy in complex biological environments. Here we describe the development of targeted aryl azide activation via deep red-light (λ = 660 nm) photoredox catalysis and its use in photocatalysed proximity labelling. We demonstrate that aryl azides are converted to triplet nitrenes via a redox-centric mechanism and show that its spatially localized formation requires both red light and a photocatalyst-targeting modality. This technology was applied in different colon cancer cell systems for targeted protein environment labelling of epithelial cell adhesion molecule (EpCAM). We identified a small subset of proteins with previously known and unknown association to EpCAM, including CDH3, a clinically relevant protein that shares high tumour-selective expression with EpCAM.
Collapse
Affiliation(s)
| | - Keun Ah Ryu
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - John L Weber
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Aleksandra K Olow
- Genetics and Pharmacogenomics, Merck & Co., Inc., San Francisco, CA, USA
| | | | | | - Rob C Oslund
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA.
- InduPro, Cambridge, MA, USA.
| | - Olugbeminiyi O Fadeyi
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA.
- InduPro, Cambridge, MA, USA.
| | - Tomislav Rovis
- Department of Chemistry, Columbia University, New York, NY, USA.
| |
Collapse
|
38
|
Lu B, Shao X, Jiang X, Wang L, Xue J, Rauhut G, Tan G, Fang W, Zeng X. Diazophosphane HPN 2. J Am Chem Soc 2022; 144:21853-21857. [PMID: 36445205 DOI: 10.1021/jacs.2c10003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Diazophosphane HPN2, a heavy analogue of hydrazoic acid (HN3), has been synthesized at low temperature (10 K) through photolytic reactions of molecular nitrogen (N2) with phosphine (PH3) and phosphaketene (HPCO) under irradiations at 193 and 365 nm, respectively. The characterization of HPN2 and its isotopologues DPN2 and HP15N2 by matrix-isolation IR and UV-vis spectroscopy is supported by quantum chemical calculations at the CCSD(T)-F12a/cc-pVTZ-F12 level of theory. Upon irradiation at 266 nm, the P-N bond in HPN2 breaks, whereas its photolysis at 193 nm generates the elusive phosphinyl radical •PN2.
Collapse
Affiliation(s)
- Bo Lu
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysts and Innovative Materials, Fudan University, Shanghai 200433, China
| | - Xin Shao
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysts and Innovative Materials, Fudan University, Shanghai 200433, China
| | - Xin Jiang
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysts and Innovative Materials, Fudan University, Shanghai 200433, China
| | - Lina Wang
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysts and Innovative Materials, Fudan University, Shanghai 200433, China
| | - Junfei Xue
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysts and Innovative Materials, Fudan University, Shanghai 200433, China
| | - Guntram Rauhut
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Gengwen Tan
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Wei Fang
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysts and Innovative Materials, Fudan University, Shanghai 200433, China
| | - Xiaoqing Zeng
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysts and Innovative Materials, Fudan University, Shanghai 200433, China
| |
Collapse
|
39
|
Kang D, Wahl C, Kim J. Synthesis of push-pull-activated ynol ethers and their evaluation in the bioorthogonal hydroamination reaction. Org Biomol Chem 2022; 20:9217-9221. [PMID: 36367436 PMCID: PMC9769999 DOI: 10.1039/d2ob01917e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
A new class of push-pull-activated alkynes featuring di- and trifluorinated ynol ethers was synthesized. The difluorinated ynol ether exhibited an optimal balance of stability and reactivity, displaying a substantially improved half-life in the presence of aqueous thiols over the previously reported 1-haloalkyne analogs while reacting just as fast in the hydroamination reaction with N,N-diethylhydroxylamine. The trifluorinated ynol ether reacted significantly faster, exhibiting a second order rate constant of 0.56 M-1 s-1 in methanol, but it proved too unstable toward thiols. These fluorinated ynol ethers further demonstrate the importance of the hyperconjugation-rehybridization effect in activating alkynes and demonstrate how substituent effects can both activate and stabilize alkynes for bioorthogonal reactivity.
Collapse
Affiliation(s)
- Dahye Kang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Conrad Wahl
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.
| | - Justin Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| |
Collapse
|
40
|
Sakallioglu IT, Maroli AS, Leite ADL, Marshall DD, Evans BW, Zinniel DK, Dussault PH, Barletta RG, Powers R. Multi-omics Investigation into the Mechanism of Action of an Anti-tubercular Fatty Acid Analogue. J Am Chem Soc 2022; 144:21157-21173. [PMID: 36367461 PMCID: PMC10948109 DOI: 10.1021/jacs.2c08238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The mechanism of action (MoA) of a clickable fatty acid analogue 8-(2-cyclobuten-1-yl)octanoic acid (DA-CB) has been investigated for the first time. Proteomics, metabolomics, and lipidomics were combined with a network analysis to investigate the MoA of DA-CB against Mycobacterium smegmatis (Msm). The metabolomics results showed that DA-CB has a general MoA related to that of ethionamide (ETH), a mycolic acid inhibitor that targets enoyl-ACP reductase (InhA), but DA-CB likely inhibits a step downstream from InhA. Our combined multi-omics approach showed that DA-CB appears to disrupt the pathway leading to the biosynthesis of mycolic acids, an essential mycobacterial fatty acid for both Msm and Mycobacterium tuberculosis (Mtb). DA-CB decreased keto-meromycolic acid biosynthesis. This intermediate is essential in the formation of mature mycolic acid, which is a key component of the mycobacterial cell wall in a process that is catalyzed by the essential polyketide synthase Pks13 and the associated ligase FadD32. The multi-omics analysis revealed further collateral alterations in bacterial metabolism, including the overproduction of shorter carbon chain hydroxy fatty acids and branched chain fatty acids, alterations in pyrimidine metabolism, and a predominate downregulation of proteins involved in fatty acid biosynthesis. Overall, the results with DA-CB suggest the exploration of this and related compounds as a new class of tuberculosis (TB) therapeutics. Furthermore, the clickable nature of DA-CB may be leveraged to trace the cellular fate of the modified fatty acid or any derived metabolite or biosynthetic intermediate.
Collapse
Affiliation(s)
- Isin T. Sakallioglu
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
| | - Amith S. Maroli
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
| | - Aline De Lima Leite
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
| | - Darrell D. Marshall
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
- Total Analysis LLC, Detroit, MI 48204-3268, United States
| | - Boone W. Evans
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
| | - Denise K. Zinniel
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583-0905, United States
| | - Patrick H. Dussault
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
| | - Raúl G. Barletta
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583-0905, United States
- Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE 68588-0664, United States
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
- Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE 68588-0664, United States
| |
Collapse
|
41
|
Comprehensive Empirical Model of Substitution—Influence on Hydrogen Bonding in Aromatic Schiff Bases. Int J Mol Sci 2022; 23:ijms232012439. [DOI: 10.3390/ijms232012439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/07/2022] [Accepted: 10/12/2022] [Indexed: 11/16/2022] Open
Abstract
In this work, over 500 structures of tri-ring aromatic Schiff bases with different substitution patterns were investigated to develop a unified description of the substituent effect on the intramolecular hydrogen bridge. Both proximal and distal effects were examined using Density Functional Theory (DFT) in the gas phase and with solvent reaction field (Polarizable Continuum Model (PCM) and water as the solvent). In order to investigate and characterize the non-covalent interactions, a topological analysis was performed using the Quantum Theory of Atoms In Molecules (QTAIM) theory and Non-Covalent Interactions (NCI) index. The obtained results were summarized as the generalized, empirical model of the composite substituent effect, assessed using an additional group of simple ring-based Schiff bases. The composite substituent effect has been divided into separate increments describing the different interactions of the hydrogen bridge and the substituent: the classical substituent effect, involving resonance and induction mediated through the ring, steric increment based on substituent proximity to the bridge elements, and distal increment, derived from substitution on the distal ring.
Collapse
|
42
|
He L, Jiang C, Chen Z, Ma D, Yi L, Xi Z. A triple-diazonium reagent for virus crosslinking and the synthesis of an azo-linked molecular cage. Org Biomol Chem 2022; 20:7577-7581. [PMID: 36131636 DOI: 10.1039/d2ob01583h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first bench-stable triple-diazonium reagent (TDA-1) was rationally designed and synthesized for coupling and crosslinking. The three reactive sites of TDA-1 can react with phenol-containing molecules as well as plant viruses in aqueous buffers efficiently. In addition, a new-type azo-linked cage was constructed by the direct reaction of TDA-1 with a triple-phenol molecule and was characterized by X-ray crystallography.
Collapse
Affiliation(s)
- Lijun He
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Chenyang Jiang
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Zhuoyue Chen
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Dejun Ma
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, National Pesticide Engineering Research Center, Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China.
| | - Long Yi
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, National Pesticide Engineering Research Center, Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China.
| |
Collapse
|
43
|
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
|
44
|
Hernandez R RA, Burchell-Reyes K, Braga APCA, Lopez JK, Forgione P. Solvent-free synthesis of 3,5-isoxazoles via 1,3-dipolar cycloaddition of terminal alkynes and hydroxyimidoyl chlorides over Cu/Al 2O 3 surface under ball-milling conditions. RSC Adv 2022; 12:6396-6402. [PMID: 35424611 PMCID: PMC8981965 DOI: 10.1039/d1ra08443g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/10/2022] [Indexed: 01/20/2023] Open
Abstract
Scalable, solvent-free synthesis of 3,5-isoxazoles under ball-milling conditions has been developed. The proposed methodology allows the synthesis of 3,5-isoxazoles in moderate to excellent yields from terminal alkynes and hydroxyimidoyl chlorides, using a recyclable Cu/Al2O3 nanocomposite catalyst. Furthermore, the proposed conditions are reproducible to a 1.0-gram scale without further milling time variations. A practical and scalable mechanochemical 1,3-dipolar cycloaddition between hydroxyimidoyl chlorides and terminal alkynes catalyzed by Cu/Al2O3 allows a quick access to 3,5-isoxazole derivatives.![]()
Collapse
Affiliation(s)
- Rafael A Hernandez R
- Department of Chemistry and Biochemistry, Concordia University 7141 rue Sherbrooke O. Montréal QC Canada H4B 1R6
| | - Kelly Burchell-Reyes
- Department of Chemistry and Biochemistry, Concordia University 7141 rue Sherbrooke O. Montréal QC Canada H4B 1R6
| | - Arthur P C A Braga
- Department of Chemistry and Biochemistry, Concordia University 7141 rue Sherbrooke O. Montréal QC Canada H4B 1R6
| | - Jennifer Keough Lopez
- Department of Chemistry and Biochemistry, Concordia University 7141 rue Sherbrooke O. Montréal QC Canada H4B 1R6
| | - Pat Forgione
- Department of Chemistry and Biochemistry, Concordia University 7141 rue Sherbrooke O. Montréal QC Canada H4B 1R6 .,Centre for Green Chemistry and Catalysis, McGill University 801 rue Sherbrooke O. Montréal QC Canada H3A 0B8
| |
Collapse
|
45
|
Liu Z, Chen H, Gan X, Wang L, Lin P, Li J, Huang X, Tian R, Liu X, Gao W, Tang B. Consecutive 2-azidoallylation/click cycloaddition of active methylene for synthesis of functionalized hepta-1,6-dienes with a bis-1,2,3-triazole scaffold. Org Chem Front 2022. [DOI: 10.1039/d2qo01118b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A tandem 2-azidoallylation/click cycloaddition reaction to access novel hepta-1,6-diene skelecton can be successfully accomplished with methylene compounds, phenolic substituted vinyl azide and alkynes in one pot.
Collapse
Affiliation(s)
- Zhenhua Liu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, P. R. China
| | - Huimin Chen
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, P. R. China
| | - Xingxing Gan
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, P. R. China
| | - Lianxiao Wang
- No.1 Middle School of Qihe Shandong, Dezhou, 253000, P. R. China
| | - Ping Lin
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, P. R. China
| | - Jiayi Li
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, P. R. China
| | - Xiuxiu Huang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, P. R. China
| | - Rongbiao Tian
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, P. R. China
| | - Xuan Liu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, P. R. China
| | - Wen Gao
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, P. R. China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, P. R. China
| |
Collapse
|
46
|
Ishizawa S, Tumurkhuu M, Gross EJ, Ohata J. Site-specific DNA functionalization through the tetrazene-forming reaction in ionic liquids. Chem Sci 2022; 13:1780-1788. [PMID: 35282632 PMCID: PMC8826848 DOI: 10.1039/d1sc05204g] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 01/15/2022] [Indexed: 11/21/2022] Open
Abstract
Site-specific chemical modification of unprotected DNAs through a phosphine-mediated amine–azide coupling reaction in ionic liquid.
Collapse
Affiliation(s)
- Seiya Ishizawa
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Munkhtuya Tumurkhuu
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Elizabeth J. Gross
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Jun Ohata
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| |
Collapse
|
47
|
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
|
48
|
Xu J, Zhang Y, Han J, Su A, Qiao H, Zhang C, Tang J, Shen X, Sun B, Yu W, Zhai S, Wang X, Wu Y, Su W, Duan H. Providing direction for mechanistic inferences in radical cascade cyclization using Transformer model. Org Chem Front 2022. [DOI: 10.1039/d2qo00188h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Even in modern organic chemistry, predicting or proposing a reaction mechanism and speculating on reaction intermediates remains challenging. For example, it is challenging to predict the regioselectivity of radical attraction...
Collapse
|
49
|
Pocheć M, Kułacz K, Panek JJ, Jezierska A. How Substitution Combines with Non-Covalent Interactions to Modulate 1,4-Naphthoquinone and Its Derivatives Molecular Features-Multifactor Studies. Int J Mol Sci 2021; 22:ijms221910357. [PMID: 34638700 PMCID: PMC8508802 DOI: 10.3390/ijms221910357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022] Open
Abstract
Substitution is well-known to modulate the physico-chemical properties of molecules. In this study, a combined, multifactor approach was employed to determine a plethora of substitution patterns using –Br and –O-H in 1,4-naphthoquinone and its derivatives. On the basis of classical Density Functional Theory (DFT), 25 models divided into three groups were developed. The first group contains 1,4-naphthoquinone and its derivatives substituted only by –Br. The second group consists of compounds substituted by –Br and one –O-H group. As a result of the substitution, an intramolecular hydrogen bond was formed. The third group also contains –Br as a substituent, but two –O-H groups were introduced and two intramolecular hydrogen bonds were established. The simulations were performed at the ωB97XD/6-311++G(2d,2p) level of theory. The presence of substituents influenced the electronic structure of the parent compound and its derivatives by inductive effects, but it also affected the geometry of the 2 and 3 groups, due to the intramolecular hydrogen bonding and the formation of a quasi-ring/rings. The static DFT models were applied to investigate the aromaticity changes in the fused rings based on the Harmonic Oscillator Model of Aromaticity (HOMA). The OH stretching was detected for the compounds from groups 2 and 3 and further used to find correlations with energetic parameters. The evolution of the electronic structure was analyzed using Hirshfeld atomic charges and the Substituent Active Region (cSAR) parameter. The proton reaction path was investigated to provide information on the modulation of hydrogen bridge properties by diverse substitution positions on the donor and acceptor sides. Subsequently, Car–Parrinello Molecular Dynamics (CPMD) was carried out in the double-bridged systems (group 3) to assess the cooperative effects in double –O-H-substituted systems. It was determined that the –O-H influence on the core of the molecule is more significant than that of –Br, but the latter has a major impact on the bridge dynamics. The competitive or synergic effect of two –Br substituents was found to depend on the coupling between the intramolecular hydrogen bridges. Thus, the novel mechanism of a secondary (cooperative) substituent effect was established in the double-bridged systems via DFT and CPMD results comparison, consisting of a mediation of the bromine substitutions’ influence by the cooperative proton transfer events in the hydrogen bridges.
Collapse
Affiliation(s)
| | | | | | - Aneta Jezierska
- Correspondence: ; Tel.: +48-71-3757-224; Fax: +48-71-3282-348
| |
Collapse
|
50
|
Sakallioglu IT, Barletta RG, Dussault PH, Powers R. Deciphering the mechanism of action of antitubercular compounds with metabolomics. Comput Struct Biotechnol J 2021; 19:4284-4299. [PMID: 34429848 PMCID: PMC8358470 DOI: 10.1016/j.csbj.2021.07.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 01/08/2023] Open
Abstract
Tuberculosis (TB), one of the oldest and deadliest bacterial diseases, continues to cause serious global economic, health, and social problems. Current TB treatments are lengthy, expensive, and routinely ineffective against emerging drug resistant strains. Thus, there is an urgent need for the identification and development of novel TB drugs possessing comprehensive and specific mechanisms of action (MoAs). Metabolomics is a valuable approach to elucidating the MoA, toxicity, and potency of promising chemical leads, which is a critical step of the drug discovery process. Recent advances in metabolomics methodologies for deciphering MoAs include high-throughput screening techniques, the integration of multiple omics methods, mass spectrometry imaging, and software for automated analysis. This review describes recently introduced metabolomics methodologies and techniques for drug discovery, highlighting specific applications to the discovery of new antitubercular drugs and the elucidation of their MoAs.
Collapse
Affiliation(s)
- Isin T. Sakallioglu
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Raúl G. Barletta
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska Lincoln, Lincoln, NE 68583-0905, USA
| | - Patrick H. Dussault
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| |
Collapse
|