1
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Housh K, Gates KS. Synthesis of DNA Duplexes Containing Site-Specific Interstrand Cross-Links via Sequential Reductive Amination Reactions Involving Diamine Linkers and Abasic Sites on Complementary Oligodeoxynucleotides. Chem Res Toxicol 2021; 34:2384-2391. [PMID: 34694787 PMCID: PMC8650211 DOI: 10.1021/acs.chemrestox.1c00293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Interstrand DNA cross-links are important in biology, medicinal chemistry, and materials science. Accordingly, methods for the targeted installation of interstrand cross-links in DNA duplexes may be useful in diverse fields. Here, a simple procedure is reported for the preparation of DNA duplexes containing site-specific, chemically defined interstrand cross-links. The approach involves sequential reductive amination reactions between diamine linkers and two abasic (apurinic/apyrimidinic, AP) sites on complementary oligodeoxynucleotides. Use of the symmetrical triamine, tris(2-aminoethyl)amine, in this reaction sequence enabled the preparation of a cross-linked DNA duplex bearing a derivatizable aminoethyl group.
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Affiliation(s)
- Kurt Housh
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Kent S. Gates
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
- University of Missouri, Department of Biochemistry, 125 Chemistry Building, Columbia, MO 65211, United States
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2
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Zang C, Wang H, Li T, Zhang Y, Li J, Shang M, Du J, Xi Z, Zhou C. A light-responsive, self-immolative linker for controlled drug delivery via peptide- and protein-drug conjugates. Chem Sci 2019; 10:8973-8980. [PMID: 31762977 PMCID: PMC6857671 DOI: 10.1039/c9sc03016f] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 08/08/2019] [Indexed: 01/01/2023] Open
Abstract
Photoirradiation of the PC4AP linker generates an active intermediate that reacts intramolecularly with a primary amine on the carrier peptide/protein, leading to rapid release of the drug without generating any toxic side products.
When designing prodrugs, choosing an appropriate linker is the key to achieving efficient, controlled drug delivery. Herein, we report the use of a photocaged C4′-oxidized abasic site (PC4AP) as a light-responsive, self-immolative linker. Any amine- or hydroxyl-bearing drug can be loaded onto the linker via a carbamate or carbonate bond, and the linker is then conjugated to a carrier peptide or protein via an alkyl chain. The PC4AP linker is stable under physiologically relevant conditions. However, photodecaging of the linker generates an active intermediate that reacts intramolecularly with a primary amine (the ε-amine of a lysine residue and the N-terminal amine) on the carrier, leading to rapid and efficient release of the drug via an addition–elimination cascade, without generating any toxic side products. We demonstrated that the use of this self-immolative linker to conjugate the anticancer drug doxorubicin to a cell-penetrating peptide or an antibody enabled targeted, controlled delivery of the drug to cells. Our results suggest that the linker can be used with a broad range of carriers, such as cell-penetrating peptides, proteins, antibodies, and amine-functionalized polymers, and thus will find a wide range of practical applications.
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Affiliation(s)
- Chuanlong Zang
- State Key Laboratory of Elemento-Organic Chemistry , Department of Chemical Biology , College of Chemistry , Nankai University , Tianjin 300071 , China .
| | - Huawei Wang
- State Key Laboratory of Elemento-Organic Chemistry , Department of Chemical Biology , College of Chemistry , Nankai University , Tianjin 300071 , China .
| | - Tiantian Li
- School of Pharmaceutical Sciences , Tsinghua University , 30 Shuangqing Rd. , Beijing 100084 , China
| | - Yingqian Zhang
- State Key Laboratory of Elemento-Organic Chemistry , Department of Chemical Biology , College of Chemistry , Nankai University , Tianjin 300071 , China .
| | - Jiahui Li
- State Key Laboratory of Elemento-Organic Chemistry , Department of Chemical Biology , College of Chemistry , Nankai University , Tianjin 300071 , China .
| | - Mengdi Shang
- State Key Laboratory of Elemento-Organic Chemistry , Department of Chemical Biology , College of Chemistry , Nankai University , Tianjin 300071 , China .
| | - Juanjuan Du
- School of Pharmaceutical Sciences , Tsinghua University , 30 Shuangqing Rd. , Beijing 100084 , China
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry , Department of Chemical Biology , College of Chemistry , Nankai University , Tianjin 300071 , China .
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry , Department of Chemical Biology , College of Chemistry , Nankai University , Tianjin 300071 , China .
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3
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Abstract
A facile, one-pot synthetic method for the synthesis of 5-methylene-2-pyrrolones (5MPs) from inexpensive furfuryl acetate is described. Bromine oxidation and trapping of the in situ generated 1,4-dicarbonyl compound by a primary amine provided the corresponding 5MPs in 50-69% yield.
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Affiliation(s)
- Marco Paolo Jacinto
- Department of Chemistry , Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
| | - Patricio Pichling
- Department of Chemistry , Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
| | - Marc M Greenberg
- Department of Chemistry , Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
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4
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Kasai Y, Sato K, Utsumi S, Ichikawa S. Improvement of S N Ar Reaction Rate by an Electron-Withdrawing Group in the Crosslinking of DNA Cytosine-5 Methyltransferase by a Covalent Oligodeoxyribonucleotide Inhibitor. Chembiochem 2018; 19:1866-1872. [PMID: 29900657 DOI: 10.1002/cbic.201800244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Indexed: 12/31/2022]
Abstract
DNA cytosine 5-methyltransferase (DNMT) catalyzes methylation at the C5 position of the cytosine residues in the CpG sequence. Aberrant DNA methylation patterns are found in cancer cells. Therefore, inhibition of human DNMT is an effective strategy for treating various cancers. The inhibitors of DNMT have an electron-deficient nucleobase because this group facilitates attack by the catalytic Cys residue in DNMTs. Recently, we reported the synthesis and properties of mechanism-based modified nucleosides, 2-amino-4-halopyridine-C-nucleosides (dX P), as inhibitors of DNMT. To develop a more efficient inhibitor of DNMT for oligonucleotide therapeutics, oligodeoxyribonucleotides (ODNs) containing other nucleoside analogues, which react more quickly with DNMT, are needed. Herein, we describe the design, synthesis, and evaluation of the properties of 2-amino-3-cyano-4-halopyridine-C-nucleosides (dX PCN ) and ODNs containing dX PCN , as more reactive inhibitors of DNMTs. Nucleophilic aromatic substitution (SN Ar) of the designed nucleosides, dX PCN , was faster than that of dX P, and the ODN containing dX PCN effectively formed a complex with DNMTs. This study suggests that the incorporation of an electron-withdrawing group would be an effective method to increase reactivity toward the nucleophile of the DNMTs, while maintaining high specificity.
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Affiliation(s)
- Yukiko Kasai
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Kousuke Sato
- Faculty of Pharmaceutical Sciences, Health Sciences, University of Hokkaido, 1757 Kanazawa, Tobetsu, Ishikari-gun, 061-0293, Japan
| | - Shohei Utsumi
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan.,Center for Research and Education on Drug Discovery, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
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5
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Zhang Y, Zhou X, Xie Y, Greenberg MM, Xi Z, Zhou C. Thiol Specific and Tracelessly Removable Bioconjugation via Michael Addition to 5-Methylene Pyrrolones. J Am Chem Soc 2017; 139:6146-6151. [PMID: 28407468 DOI: 10.1021/jacs.7b00670] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
5-Methylene pyrrolones (5MPs) are highly thiol-specific and tracelessly removable bioconjugation tools. 5MPs are readily prepared from primary amines in one step. 5MPs exhibit significantly improved stability under physiologically relevant conditions and cysteine specificity compared to commonly used analogues, maleimides. Michael addition of thiol to 5MPs occurs rapidly, cleanly, and does not generate a stereocenter. The conjugates efficiently release thiols via retro-Michael reaction in alkaline buffer (pH 9.5) or via thiol exchange at pH 7.5. This unique property makes 5MPs valuable for the controlled release of conjugated cargo and temporary thiol protection. The utilization of 5MPs for protein immobilization and pull-down of active complexes is illustrated using E. coli. acetohydroxyacid synthase isozyme I.
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Affiliation(s)
- Yingqian Zhang
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University , Tianjin 300071, China
| | - Xiaoping Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University , Tianjin 300071, China
| | - Yonghui Xie
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University , Tianjin 300071, China
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University , Tianjin 300071, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, China
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University , Tianjin 300071, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, China
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6
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Llamas EM, Tome JPC, Rodrigues JMM, Torres T, Madder A. Porphyrin-based photosensitizers and their DNA conjugates for singlet oxygen induced nucleic acid interstrand crosslinking. Org Biomol Chem 2017. [DOI: 10.1039/c7ob01269a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Porphyrin-based photosensitisers and their DNA conjugates have been evaluated for interstrand crosslink generation using furan containing oligonucleotides and red light.
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Affiliation(s)
- Eva M. Llamas
- Department of Organic and Macromolecular Chemistry
- Ghent University
- 9000 Ghent
- Belgium
- Departamento de Química Orgánica
| | - João P. C. Tome
- Centro de Química Estrutural
- Departamento de Engenharia Química
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049-001 Lisboa
| | - João M. M. Rodrigues
- Centro de Química Estrutural
- Departamento de Engenharia Química
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049-001 Lisboa
| | - Tomás Torres
- Departamento de Química Orgánica
- Universidad Autónoma de Madrid
- 28049 Madrid
- Spain
- Imdea-Nanoscience
| | - Annemieke Madder
- Department of Organic and Macromolecular Chemistry
- Ghent University
- 9000 Ghent
- Belgium
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7
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Gatanaga C, Yang B, Inadomi Y, Usui K, Ota C, Katayama T, Suemune H, Aso M. Site-Specific Turn-On Fluorescent Labeling of DNA-Interacting Protein Using Oligodeoxynucleotides That Modify Lysines To Produce 5,6-Dimethoxy 3-Methyleneisoindolin-1-one. ACS Chem Biol 2016; 11:2216-21. [PMID: 27253874 DOI: 10.1021/acschembio.6b00090] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We have developed oligodeoxynucleotides (ODNs) that modify primary amines to produce 5,6-dimethoxy 3-methyleneisoindolin-1-one. Compared to the oxygen isosteric fluorophore, 4,5-dimethoxyphthalimide, this methyleneisoindolinone was more stable and exhibited an 85 nm blue-shifted fluorescent emission (λmax at 425 nm) with an intensity comparable to that of the phthalimide. Reaction of the DNA-binding domain of Escherichia coli DnaA protein with an ODN containing its binding sequence efficiently afforded a modified fluorescent protein at a specific lysine residue in the proximity of the ODN. A full-length DnaA protein was also successfully fluorescently labeled. These results demonstrate the potential utility of the ODNs developed in this study for the fluorescent labeling of DNA-interacting protein at the lysine residue of interest.
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Affiliation(s)
- Chiemi Gatanaga
- Graduate School of Pharmaceutical
Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Bo Yang
- Graduate School of Pharmaceutical
Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yuka Inadomi
- Graduate School of Pharmaceutical
Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kazuteru Usui
- Graduate School of Pharmaceutical
Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Chiyoe Ota
- Graduate School of Pharmaceutical
Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Tsutomu Katayama
- Graduate School of Pharmaceutical
Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Hiroshi Suemune
- Graduate School of Pharmaceutical
Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Mariko Aso
- Graduate School of Pharmaceutical
Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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8
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Olszewska A, Pohl R, Brázdová M, Fojta M, Hocek M. Chloroacetamide-Linked Nucleotides and DNA for Cross-Linking with Peptides and Proteins. Bioconjug Chem 2016; 27:2089-94. [PMID: 27479485 DOI: 10.1021/acs.bioconjchem.6b00342] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nucleotides, 2'-deoxyribonucleoside triphosphates (dNTPs), and DNA probes bearing reactive chloroacetamido group linked to nucleobase (cytosine or 7-deazadaenine) through a propargyl tether were prepared and tested in cross-linking with cysteine- or histidine-containing peptides and proteins. The chloroacetamide-modifed dNTPs proved to be good substrates for DNA polymerases in the enzymatic synthesis of modified DNA probes. Modified nucleotides and DNA reacted efficiently with cysteine and cysteine-containing peptides, whereas the reaction with histidine was sluggish and low yielding. The modified DNA efficiently cross-linked with p53 protein through alkylation of cysteine and showed potential for cross-linking with histidine (in C277H mutant of p53).
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Affiliation(s)
- Agata Olszewska
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Gilead Sciences & IOCB Research Center , Flemingovo namesti 2, 166 10 Prague 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Gilead Sciences & IOCB Research Center , Flemingovo namesti 2, 166 10 Prague 6, Czech Republic
| | - Marie Brázdová
- Institute of Biophysics, Czech Academy of Sciences , Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics, Czech Academy of Sciences , Kralovopolska 135, 612 65 Brno, Czech Republic.,Central European Institute of Technology, Masaryk University , Kamenice 753/5, CZ-625 00 Brno, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Gilead Sciences & IOCB Research Center , Flemingovo namesti 2, 166 10 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague , Hlavova 8, 12843 Prague 2, Czech Republic
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