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Fan H, Peng X. Photoinduced DNA Interstrand Cross-Linking by Benzene Derivatives: Leaving Groups Determine the Efficiency of the Cross-Linker. J Org Chem 2021; 86:493-506. [PMID: 33253574 DOI: 10.1021/acs.joc.0c02234] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We have synthesized and characterized two small libraries of 2-OMe or 2-NO2-benzene analogues 2a-i and 3a-i containing a wide variety of leaving groups. Irradiation of these compounds at 350 nm generated benzyl radicals that were spontaneously oxidized to benzyl cations directly producing DNA interstrand cross-links (ICLs). Compounds with a 2-methoxy substituent showed a faster cross-linking reaction rate and higher ICL efficiency than the corresponding 2-nitro analogues. Apart from the aromatic substituent, the benzylic leaving groups greatly affected DNA cross-linking efficiency. Higher ICL yields were observed for compounds with OCH3 (3b), OCH2Ph (3d), or Ph3P+ (3i) as leaving groups than those containing OAc (3a), NMe2 (3e), morpholine (3f), OCH2CH═CH2 (3c), SPh (3g), or SePh (3h). The heat stability study of the isolated ICL products indicated that dGs were the preferred alkylation sites in DNA for the benzyl cations produced from 2a-i, 3c, and 3e-i while 3a (L = OAc), 3b (L = OMe), and 3d (L = OCH2Ph) showed a similar photoreactivity toward dGs and dAs. Although the photogenerated benzyl cations alkylated dG, dC, and dA, ICL assay with variation of DNA sequences showed that the ICL reaction occurred with opposing dG/dC but not with staggered dA/dA.
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Affiliation(s)
- Heli Fan
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin Milwaukee, 3210 N. Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Xiaohua Peng
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin Milwaukee, 3210 N. Cramer Street, Milwaukee, Wisconsin 53211, United States
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Li Y, Liang D, Li X, Huang W, Yuan L, Wang B, Cheng P. Br2- or HBr-catalyzed synthesis of asymmetric 3,3-di(indolyl)indolin-2-ones. HETEROCYCL COMMUN 2017. [DOI: 10.1515/hc-2016-0071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
AbstractUnder the catalysis of 1 mol% of Br
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George SRD, Elton TE, Harper JB. Electronic effects on the substitution reactions of benzhydrols and fluorenyl alcohols. Determination of mechanism and effects of antiaromaticity. Org Biomol Chem 2015; 13:10745-50. [DOI: 10.1039/c5ob01637a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fusion of benzhydrols to give fluorenols is found to not affect the electronic susceptibility of substitution reactions suggesting the antiaromaticity of the intermediate serves simply to slow the process.
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Affiliation(s)
| | - Timothy E. Elton
- School of Chemistry
- University of New South Wales
- UNSW Sydney
- Australia
| | - Jason B. Harper
- School of Chemistry
- University of New South Wales
- UNSW Sydney
- Australia
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4
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Ramos-Tomillero I, Mendive-Tapia L, Góngora-Benítez M, Nicolás E, Tulla-Puche J, Albericio F. Understanding acid lability of cysteine protecting groups. Molecules 2013; 18:5155-62. [PMID: 23648593 PMCID: PMC6270164 DOI: 10.3390/molecules18055155] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Revised: 04/26/2013] [Accepted: 05/02/2013] [Indexed: 02/02/2023] Open
Abstract
Cys-disulfide bonds contribute to the stabilization of peptide and protein structures. The synthesis of these molecules requires a proper protection of Cys residues, which is crucial to prevent side-reactions and also to achieve the correct Cys connectivity. Here we undertook a mechanistic study of a set of well-known acid-labile Cys protecting groups, as well other new promising groups, in order to better understand the nature of their acid-lability. The stability of the carbocation generated during the acid treatment was found to have a direct impact on the removal of the protective groups from the corresponding protected Cys-containing peptides. Hence a combination of steric and conjugative effects determines the stability of the carbocations generated. Here we propose diphenylmethyl (Dpm) as a promising protecting group on the basis of its intermediate relative carbocation stability. All the optimized geometries and energies presented in this study were determined using a B3LYP/6-31G(d,p) calculation. The results discussed herein may be of broader applicability for the development of new protecting groups.
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Affiliation(s)
- Iván Ramos-Tomillero
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028-Barcelona, Spain; E-Mails: (I.R.-T.); (L.M-T.); (M.G.-B.); (J.T.-P.)
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 10, Barcelona 08028, Spain
- Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1-11, Barcelona 08028, Spain; E-Mail:
| | - Lorena Mendive-Tapia
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028-Barcelona, Spain; E-Mails: (I.R.-T.); (L.M-T.); (M.G.-B.); (J.T.-P.)
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 10, Barcelona 08028, Spain
- Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1-11, Barcelona 08028, Spain; E-Mail:
| | - Miriam Góngora-Benítez
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028-Barcelona, Spain; E-Mails: (I.R.-T.); (L.M-T.); (M.G.-B.); (J.T.-P.)
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 10, Barcelona 08028, Spain
- Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1-11, Barcelona 08028, Spain; E-Mail:
| | - Ernesto Nicolás
- Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1-11, Barcelona 08028, Spain; E-Mail:
| | - Judit Tulla-Puche
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028-Barcelona, Spain; E-Mails: (I.R.-T.); (L.M-T.); (M.G.-B.); (J.T.-P.)
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Fernando Albericio
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028-Barcelona, Spain; E-Mails: (I.R.-T.); (L.M-T.); (M.G.-B.); (J.T.-P.)
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 10, Barcelona 08028, Spain
- Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1-11, Barcelona 08028, Spain; E-Mail:
- School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa
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Pittelkow M, Nielsen CB, Brock-Nannestad T, Schau-Magnussen M, Christensen JB. A peri-Cyclised Naphthalene Dimer: Synthesis and Properties of an Unusual Vilsmeier-Haack Product of 1,3,6,8-Tetramethoxynaphthalene. European J Org Chem 2012. [DOI: 10.1002/ejoc.201200512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Djukic B, Perepichka DF. Unexpected formation of a cyclic vinylene sulfate in the synthesis of ethynyl-substituted acenes. Chem Commun (Camb) 2012; 48:6651-3. [DOI: 10.1039/c2cc32805d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Lutterman DA, Lazinski-Melanson LA, Asher Y, Johnston DH, Gallucci JC, Turro C. Effect of intraligand π-delocalization on the photophysical properties of two new Ru(II) complexes. J Photochem Photobiol A Chem 2011. [DOI: 10.1016/j.jphotochem.2010.09.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Affiliation(s)
- Ulrik Boas
- National Veterinary Institute, Technical University of Denmark, Bulowsvej 27, DK-1790 Copenhagen, Denmark
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Szaleniec M, Witko M, Heider J. Quantum chemical modelling of the C–H cleavage mechanism in oxidation of ethylbenzene and its derivates by ethylbenzene dehydrogenase. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.molcata.2008.02.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Pittelkow M, Boas U, Christensen JB. Carbocations in action. Design, synthesis, and evaluation of a highly acid-sensitive naphthalene-based backbone amide linker for solid-phase synthesis. Org Lett 2007; 8:5817-20. [PMID: 17134280 DOI: 10.1021/ol062410j] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The design, synthesis, and properties of an extremely acid-labile backbone amide linker based on a regiospecifically substituted tetraalkoxy naphthaldehyde core are presented. This handle enables cleavage of peptide backbone amides (secondary amides) off a solid support using as little as 0.5% TFA in CH2Cl2. This proceeds without cleavage of tert-butyl ethers and tert-butyl esters. The design is based on a DFT study that predicted the most stabile alkoxy-substituted methyl naphthyl carbocation. [structure: see text]
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Affiliation(s)
- Michael Pittelkow
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
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Hammershøj P, Jessing M, Madsen AØ, Jensen KJ, Christensen JB, Boas U. X-Ray Crystal Structure of a Highly Functionalized Thiophene as a New Backbone Amide Linker for Solid-phase Peptide Synthesis. Relationship between Crystal Structure and Reactivity. Int J Pept Res Ther 2007. [DOI: 10.1007/s10989-006-9068-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Norrby PO, Jensen KJ. Steric Effects in Release of Amides from Linkers in Solid-Phase Synthesis. Molecular Mechanics Modeling of Key Step in Peptide and Combinatorial Chemistry. Int J Pept Res Ther 2006. [DOI: 10.1007/s10989-006-9036-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Hammershøj P, Reenberg TK, Pittelkow M, Nielsen CB, Hammerich O, Christensen JB. Synthesis and Properties of 2,3-Dialkynyl-1,4-benzoquinones. European J Org Chem 2006. [DOI: 10.1002/ejoc.200600081] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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