1
|
Svatunek D. Computational Organic Chemistry: The Frontier for Understanding and Designing Bioorthogonal Cycloadditions. Top Curr Chem (Cham) 2024; 382:17. [PMID: 38727989 PMCID: PMC11087259 DOI: 10.1007/s41061-024-00461-0] [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: 11/08/2023] [Accepted: 04/06/2024] [Indexed: 05/13/2024]
Abstract
Computational organic chemistry has become a valuable tool in the field of bioorthogonal chemistry, offering insights and aiding in the progression of this branch of chemistry. In this review, I present an overview of computational work in this field, including an exploration of both the primary computational analysis methods used and their application in the main areas of bioorthogonal chemistry: (3 + 2) and [4 + 2] cycloadditions. In the context of (3 + 2) cycloadditions, detailed studies of electronic effects have informed the evolution of cycloalkyne/1,3-dipole cycloadditions. Through computational techniques, researchers have found ways to adjust the electronic structure via hyperconjugation to enhance reactions without compromising stability. For [4 + 2] cycloadditions, methods such as distortion/interaction analysis and energy decomposition analysis have been beneficial, leading to the development of bioorthogonal reactants with improved reactivity and the creation of orthogonal reaction pairs. To conclude, I touch upon the emerging fields of cheminformatics and machine learning, which promise to play a role in future reaction discovery and optimization.
Collapse
Affiliation(s)
- Dennis Svatunek
- Institute of Applied Synthetic Chemistry, Technische Universität Wien (TU Wien), Getreidemarkt 9, 1060, Vienna, Austria.
| |
Collapse
|
2
|
Fang Y, Hillman AS, Fox JM. Advances in the Synthesis of Bioorthogonal Reagents: s-Tetrazines, 1,2,4-Triazines, Cyclooctynes, Heterocycloheptynes, and trans-Cyclooctenes. Top Curr Chem (Cham) 2024; 382:15. [PMID: 38703255 DOI: 10.1007/s41061-024-00455-y] [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: 09/30/2023] [Accepted: 02/01/2024] [Indexed: 05/06/2024]
Abstract
Aligned with the increasing importance of bioorthogonal chemistry has been an increasing demand for more potent, affordable, multifunctional, and programmable bioorthogonal reagents. More advanced synthetic chemistry techniques, including transition-metal-catalyzed cross-coupling reactions, C-H activation, photoinduced chemistry, and continuous flow chemistry, have been employed in synthesizing novel bioorthogonal reagents for universal purposes. We discuss herein recent developments regarding the synthesis of popular bioorthogonal reagents, with a focus on s-tetrazines, 1,2,4-triazines, trans-cyclooctenes, cyclooctynes, hetero-cycloheptynes, and -trans-cycloheptenes. This review aims to summarize and discuss the most representative synthetic approaches of these reagents and their derivatives that are useful in bioorthogonal chemistry. The preparation of these molecules and their derivatives utilizes both classical approaches as well as the latest organic chemistry methodologies.
Collapse
Affiliation(s)
- Yinzhi Fang
- Department of Chemistry and Biochemistry, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA.
| | - Ashlyn S Hillman
- Department of Chemistry and Biochemistry, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA
| | - Joseph M Fox
- Department of Chemistry and Biochemistry, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA.
| |
Collapse
|
3
|
Hou W, Zhang Y, Huang F, Chen W, Gu Y, Wang Y, Pang J, Dong H, Pan K, Zhang S, Ma P, Xu H. Bioinspired Selenium-Nitrogen Exchange (SeNEx) Click Chemistry Suitable for Nanomole-Scale Medicinal Chemistry and Bioconjugation. Angew Chem Int Ed Engl 2024; 63:e202318534. [PMID: 38343199 DOI: 10.1002/anie.202318534] [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: 12/03/2023] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
Abstract
Click chemistry is a powerful molecular assembly strategy for rapid functional discovery. The development of click reactions with new connecting linkage is of great importance for expanding the click chemistry toolbox. We report the first selenium-nitrogen exchange (SeNEx) click reaction between benzoselenazolones and terminal alkynes (Se-N to Se-C), which is inspired by the biochemical SeNEx between Ebselen and cysteine (Cys) residue (Se-N to Se-S). The formed selenoalkyne connection is readily elaborated, thus endowing this chemistry with multidimensional molecular diversity. Besides, this reaction is modular, predictable, and high-yielding, features fast kinetics (k2≥14.43 M-1 s-1), excellent functional group compatibility, and works well at miniaturization (nanomole-scale), opening up many interesting opportunities for organo-Se synthesis and bioconjugation, as exemplified by sequential click chemistry (coupled with ruthenium-catalyzed azide-alkyne cycloaddition (RuAAC) and sulfur-fluoride exchange (SuFEx)), selenomacrocycle synthesis, nanomole-scale synthesis of Se-containing natural product library and DNA-encoded library (DEL), late-stage peptide modification and ligation, and multiple functionalization of proteins. These results indicated that SeNEx is a useful strategy for new click chemistry developments, and the established SeNEx chemistry will serve as a transformative platform in multidisciplinary fields such as synthetic chemistry, material science, chemical biology, medical chemistry, and drug discovery.
Collapse
Affiliation(s)
- Wei Hou
- College of Pharmaceutical Science and Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yiyuan Zhang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Fuchao Huang
- College of Pharmaceutical Science and Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Wanting Chen
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Yuang Gu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Yan Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Jiacheng Pang
- College of Pharmaceutical Science and Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Hewei Dong
- College of Pharmaceutical Science and Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Kangyin Pan
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Shuning Zhang
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, School of Medicine, 201210, Shanghai, China
| | - Peixiang Ma
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, School of Medicine, 201210, Shanghai, China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| |
Collapse
|
4
|
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
|
5
|
Šlachtová V, Bellová S, Vrabel M. Synthesis of C 3-Substituted N1- tert-Butyl 1,2,4-Triazinium Salts via the Liebeskind-Srogl Reaction for Fluorogenic Labeling of Live Cells. J Org Chem 2024. [PMID: 38224304 DOI: 10.1021/acs.joc.3c02454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
We recently described the development and application of a new bioorthogonal conjugation, the triazinium ligation. To explore the wider application of this reaction, in this work, we introduce a general method for synthesizing C3-substituted triazinium salts based on the Liebeskind-Srogl cross-coupling reaction and catalytic thioether reduction. These methods enabled the synthesis of triazinium derivatives for investigating the effect of different substituents on the ligation kinetics and stability of the compounds under biologically relevant conditions. Finally, we demonstrate that the combination of a coumarin fluorophore attached to position C3 with a C5-(4-methoxyphenyl) substituent yields a fluorogenic triazinium probe suitable for no-wash, live-cell labeling. The developed methodology represents a promising synthetic approach to the late-stage modification of triazinium salts, potentially widening their applications in bioorthogonal reactions.
Collapse
Affiliation(s)
- Veronika Šlachtová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16000 Prague, Czech Republic
| | - Simona Bellová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16000 Prague, Czech Republic
| | - Milan Vrabel
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16000 Prague, Czech Republic
| |
Collapse
|
6
|
Segawa S, He X, Tang BZ. Metal-free click and bioorthogonal reactions of aggregation-induced emission probes for lighting up living systems. LUMINESCENCE 2024; 39:e4619. [PMID: 37987236 DOI: 10.1002/bio.4619] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/10/2023] [Accepted: 10/16/2023] [Indexed: 11/22/2023]
Abstract
In 2002, two transformative research paradigms emerged: 'click chemistry' and 'aggregation-induced emission (AIE),' both leaving significant impacts on early 21st-century academia. Click chemistry, which describes the straightforward and reliable reactions for linking two building blocks, has simplified complex molecular syntheses and functionalization, propelling advancements in polymer, material, and life science. In particular, nontoxic, metal-free click reactions involving abiotic functional groups have matured into bioorthogonal reactions. These are organic ligations capable of selective and efficient operations even in congested living systems, therefore enabling in vitro to in vivo biomolecular labelling. Concurrently, AIE, a fluorogenic phenomenon of twisted π-conjugated compounds upon aggregation, has offered profound insight into solid-state photophysics and promoted the creation of aggregate materials. The inherent fluorogenicity and aggregate-emission properties of AIE luminogens have found extensive application in biological imaging, characterized by their high-contrast and photostable fluorescent signals. As such, the convergence of these two domains to yield efficient labelling with excellent fluorescence images is an anticipated progression in recent life science research. In this review, we intend to showcase the synergetic applications of AIE probes and metal-free click or bioorthogonal reactions, highlighting both the achievements and the unexplored avenues in this promising field.
Collapse
Affiliation(s)
- Shinsuke Segawa
- Department of Chemical and Biological Engineering, School of Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Xuewen He
- The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, Jiangsu, China
| | - Ben Zhong Tang
- School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced Study, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| |
Collapse
|
7
|
Zielke FM, Rutjes FPJT. Recent Advances in Bioorthogonal Ligation and Bioconjugation. Top Curr Chem (Cham) 2023; 381:35. [PMID: 37991570 PMCID: PMC10665463 DOI: 10.1007/s41061-023-00445-6] [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: 08/22/2023] [Accepted: 10/23/2023] [Indexed: 11/23/2023]
Abstract
The desire to create biomolecules modified with functionalities that go beyond nature's toolbox has resulted in the development of biocompatible and selective methodologies and reagents, each with different scope and limitations. In this overview, we highlight recent advances in the field of bioconjugation from 2016 to 2023. First, (metal-mediated) protein functionalization by exploiting the specific reactivity of amino acids will be discussed, followed by novel bioorthogonal reagents for bioconjugation of modified biomolecules.
Collapse
Affiliation(s)
- Florian M Zielke
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Floris P J T Rutjes
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
| |
Collapse
|