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Viesser RV, Donald CP, May JA, Wu JI. Can Twisted Double Bonds Facilitate Stepwise [2 + 2] Cycloadditions? Org Lett 2024; 26:3778-3783. [PMID: 38684005 DOI: 10.1021/acs.orglett.4c00879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Computational studies for a series of low to high strain anti-Bredt alkenes suggest that those with highly twisted bridgehead double bonds and a small singlet-triplet energy gap may undergo facile stepwise [2 + 2] cycloadditions to furnish four membered rings. A selection of reaction substrates, including ethylene, acetylene, perfluoroethylene, and cyclooctyne are considered.
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Affiliation(s)
- Renan V Viesser
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Clayton P Donald
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Jeremy A May
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Judy I Wu
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
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2
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Tang F, Brune JE, Chang MY, Reeves SR, Altemeier WA, Frevert CW. Defining the versican interactome in lung health and disease. Am J Physiol Cell Physiol 2022; 323:C249-C276. [PMID: 35649251 PMCID: PMC9291419 DOI: 10.1152/ajpcell.00162.2022] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 05/17/2022] [Indexed: 11/22/2022]
Abstract
The extracellular matrix (ECM) imparts critical mechanical and biochemical information to cells in the lungs. Proteoglycans are essential constituents of the ECM and play a crucial role in controlling numerous biological processes, including regulating cellular phenotype and function. Versican, a chondroitin sulfate proteoglycan required for embryonic development, is almost absent from mature, healthy lungs and is reexpressed and accumulates in acute and chronic lung disease. Studies using genetically engineered mice show that the versican-enriched matrix can be pro- or anti-inflammatory depending on the cellular source or disease process studied. The mechanisms whereby versican develops a contextual ECM remain largely unknown. The primary goal of this review is to provide an overview of the interaction of versican with its many binding partners, the "versican interactome," and how through these interactions, versican is an integrator of complex extracellular information. Hopefully, the information provided in this review will be used to develop future studies to determine how versican and its binding partners can develop contextual ECMs that control select biological processes. Although this review focuses on versican and the lungs, what is described can be extended to other proteoglycans, tissues, and organs.
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Affiliation(s)
- Fengying Tang
- Center for Lung Biology, The University of Washington at South Lake Union, Seattle, Washington
- Department of Comparative Medicine, University of Washington, Seattle, Washington
| | - Jourdan E Brune
- Center for Lung Biology, The University of Washington at South Lake Union, Seattle, Washington
- Department of Comparative Medicine, University of Washington, Seattle, Washington
| | - Mary Y Chang
- Center for Lung Biology, The University of Washington at South Lake Union, Seattle, Washington
- Department of Comparative Medicine, University of Washington, Seattle, Washington
| | - Stephen R Reeves
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, University of Washington, Seattle, Washington
| | - William A Altemeier
- Center for Lung Biology, The University of Washington at South Lake Union, Seattle, Washington
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington
| | - Charles W Frevert
- Center for Lung Biology, The University of Washington at South Lake Union, Seattle, Washington
- Department of Comparative Medicine, University of Washington, Seattle, Washington
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington
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3
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Belen’kii LI, Gazieva GA, Evdokimenkova YB, Soboleva NO. The literature of heterocyclic chemistry, Part XX, 2020. ADVANCES IN HETEROCYCLIC CHEMISTRY 2022. [DOI: 10.1016/bs.aihch.2022.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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4
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Danilkina NA, Govdi AI, Khlebnikov AF, Tikhomirov AO, Sharoyko VV, Shtyrov AA, Ryazantsev MN, Bräse S, Balova IA. Heterocycloalkynes Fused to a Heterocyclic Core: Searching for an Island with Optimal Stability-Reactivity Balance. J Am Chem Soc 2021; 143:16519-16537. [PMID: 34582682 DOI: 10.1021/jacs.1c06041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In the search for fundamentally new, active, stable, and readily synthetically accessible cycloalkynes as strain-promoted azide-alkyne cycloaddition (SPAAC) reagents for bioorthogonal bioconjugation, we integrated two common approaches: the reagent destabilization by the increase of a ring strain and the transition state stabilization through electronic effects. As a result new SPAAC reagents, heterocyclononynes fused to a heterocyclic core, were created. These compounds can be obtained through a general synthetic route based on four crucial steps: the electrophile-promoted cyclization, Sonogashira coupling, Nicholas reaction, and final deprotection of Co-complexes of cycloalkynes from cobalt. Varying the natures of the heterocycle and heteroatom allows for reaching the optimal stability-reactivity balance for new strained systems. Computational and experimental studies revealed similar SPAAC reactivities for stable 9-membered isocoumarin- and benzothiophene-fused heterocycloalkynes and their unstable 8-membered homologues. We discovered that close reactivity is a result of the interplay of two electronic effects, which stabilize SPAAC transition states (πin* → σ* and π* → πin*) with structural effects such as conformational changes from eclipsed to staggered conformations in the cycloalkyne scaffold, that noticeably impact alkyne bending and reactivity. The concerted influence of a heterocycle and a heteroatom on the polarization of a triple bond in highly strained cycles along with a low HOMO-LUMO gap was assumed to be the reason for the unpredictable kinetic instability of all the cyclooctynes and the benzothiophene-fused oxacyclononyne. The applicability of stable isocoumarin-fused azacyclononyne IC9N-BDP-FL for in vitro bioconjugation was exemplified by labeling and visualization of HEK293 cells carrying azido-DNA and azido-glycans.
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Affiliation(s)
- Natalia A Danilkina
- Institute of Chemistry, Saint Petersburg State University (SPbU), Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia
| | - Anastasia I Govdi
- Institute of Chemistry, Saint Petersburg State University (SPbU), Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia
| | - Alexander F Khlebnikov
- Institute of Chemistry, Saint Petersburg State University (SPbU), Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia
| | - Alexander O Tikhomirov
- Institute of Chemistry, Saint Petersburg State University (SPbU), Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia
| | - Vladimir V Sharoyko
- Institute of Chemistry, Saint Petersburg State University (SPbU), Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia
| | - Andrey A Shtyrov
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, 8/3 Khlopina Street, 194021 Saint Petersburg, Russia
| | - Mikhail N Ryazantsev
- Institute of Chemistry, Saint Petersburg State University (SPbU), Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia
| | - Stefan Bräse
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Irina A Balova
- Institute of Chemistry, Saint Petersburg State University (SPbU), Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia
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Deb T, Tu J, Franzini RM. Mechanisms and Substituent Effects of Metal-Free Bioorthogonal Reactions. Chem Rev 2021; 121:6850-6914. [DOI: 10.1021/acs.chemrev.0c01013] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Titas Deb
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Julian Tu
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Raphael M. Franzini
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
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Escorihuela J, Looijen WJE, Wang X, Aquino AJA, Lischka H, Zuilhof H. Cycloaddition of Strained Cyclic Alkenes and Ortho-Quinones: A Distortion/Interaction Analysis. J Org Chem 2020; 85:13557-13566. [PMID: 33105075 PMCID: PMC7656516 DOI: 10.1021/acs.joc.0c01674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
The
chemistry of strained unsaturated cyclic compounds has experienced
remarkable growth in recent years via the development of metal–free
click reactions. Among these reactions, the cycloaddition of cyclopropenes
and their analogues to ortho-quinones has been established
as a highly promising click reaction. The present work investigates
the mechanism involved in the cycloaddition of strained dienes to ortho-quinones and structural factors that would influence
this reaction. For this purpose, we use B97D density functional theory
calculations throughout, and for relevant cases, we use spin component–scaled
MP2 calculations and single–point domain-based local pair natural
orbital coupled cluster (DLPNO-CCSD(T)) calculations. The outcomes
are analyzed in detail using the distortion/interaction model, and
suggestions for future experimental work are made.
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Affiliation(s)
- Jorge Escorihuela
- Departament de Quı́mica Orgànica, Universitat de València, Av. Vicent Andrés Estellés s/n, 46100 Burjassot, Valencia, Spain
| | - Wilhelmus J E Looijen
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Xiao Wang
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, China
| | - Adelia J A Aquino
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, China.,Institute for Soil Research, University of Natural Resources and Life Sciences, Peter-Jordan-Strasse 82, A-1190 Vienna, Austria.,Department of Mechanical Engineering, Texas Tech University, Lubbock, Texas 79409, United States
| | - Hans Lischka
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, China.,Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A-1090 Vienna, Austria.,Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Han Zuilhof
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands.,School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, China.,Department of Chemical and Materials Engineering, Faculty of Engineering, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
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Longo B, Zanato C, Piras M, Dall'Angelo S, Windhorst AD, Vugts DJ, Baldassarre M, Zanda M. Design, Synthesis, Conjugation, and Reactivity of Novel trans,trans-1,5-Cyclooctadiene-Derived Bioorthogonal Linkers. Bioconjug Chem 2020; 31:2201-2210. [PMID: 32786505 DOI: 10.1021/acs.bioconjchem.0c00375] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The tetrazine/trans-cyclooctene (TCO) inverse electron-demand Diels-Alder (IEDDA) reaction is the fastest bioorthogonal "click" ligation process reported to date. In this context, TCO reagents have found widespread applications; however, their availability and structural diversity is still somewhat limited due to challenges connected with their synthesis and structural modification. To address this issue, we developed a novel strategy for the conjugation of TCO derivatives to a biomolecule, which allows for the creation of greater structural diversity from a single precursor molecule, i.e., trans,trans-1,5-cyclooctadiene [(E,E)-COD] 1, whose preparation requires standard laboratory equipment and readily available reagents. This two-step strategy relies on the use of new bifunctional TCO linkers (5a-11a) for IEDDA reactions, which can be synthesized via 1,3-dipolar cycloaddition of (E,E)-COD 1 with different azido spacers (5-11) carrying an electrophilic function (NHS-ester, N-succinimidyl carbonate, p-nitrophenyl-carbonate, maleimide) in the ω-position. Following bioconjugation of these electrophilic linkers to the nucleophilic residue (cysteine or lysine) of a protein (step 1), the resulting TCO-decorated constructs can be subjected to a IEDDA reaction with tetrazines functionalized with fluorescent or near-infrared (NIR) tags (step 2). We successfully used this strategy to label bovine serum albumin with the TCO linker 8a and subsequently reacted it in a cell lysate with the fluorescein-isothiocyanate (FITC)-derived tetrazine 12. The same strategy was then used to label the bacterial wall of Gram-positive Staphylococcus aureus, showing the potential of these linkers for live-cell imaging. Finally, we determined the impact of structural differences of the linkers upon the stability of the bioorthogonal constructs. The compounds for stability studies were prepared by conjugation of TCO linkers 6a, 8a, and 10a to mAbs, such as Rituximab and Obinutuzumab, and subsequent labeling with a reactive Cy3-functionalized tetrazine.
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Affiliation(s)
- Beatrice Longo
- Institute of Medical Sciences, Foresterhill, University of Aberdeen, AB252ZD Aberdeen, United Kingdom.,Centre for Sensing and Imaging Science, School of Science, Loughborough University, LB11 3TU Loughborough, United Kingdom
| | - Chiara Zanato
- Institute of Medical Sciences, Foresterhill, University of Aberdeen, AB252ZD Aberdeen, United Kingdom
| | - Monica Piras
- Institute of Medical Sciences, Foresterhill, University of Aberdeen, AB252ZD Aberdeen, United Kingdom
| | - Sergio Dall'Angelo
- Institute of Medical Sciences, Foresterhill, University of Aberdeen, AB252ZD Aberdeen, United Kingdom
| | - Albert D Windhorst
- Amsterdam UMC, Vrije Universiteit, dept. Radiology and Nuclear Medicine, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Danielle J Vugts
- Amsterdam UMC, Vrije Universiteit, dept. Radiology and Nuclear Medicine, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Massimiliano Baldassarre
- Institute of Medical Sciences, Foresterhill, University of Aberdeen, AB252ZD Aberdeen, United Kingdom
| | - Matteo Zanda
- Institute of Medical Sciences, Foresterhill, University of Aberdeen, AB252ZD Aberdeen, United Kingdom.,Centre for Sensing and Imaging Science, School of Science, Loughborough University, LB11 3TU Loughborough, United Kingdom.,CNR-SCITEC, via Mancinelli 7, 20131 Milan, Italy
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