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Zhang Q, Ali T, Lin Z, Peng X. Development of 4,4'-dibromobinaphthalene analogues with potent photo-inducible DNA cross-linking capability and cytotoxicity towards breast MDA-MB 468 cancer cells. Bioorg Chem 2023; 140:106769. [PMID: 37633128 DOI: 10.1016/j.bioorg.2023.106769] [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: 04/12/2023] [Revised: 07/25/2023] [Accepted: 08/06/2023] [Indexed: 08/28/2023]
Abstract
Photoinduced DNA cross-linking process showed advantages of high spatio-temporal resolution and control. We have designed, synthesized, and characterized several 4,4'-dibromo binaphthalene analogues (1a-f) that can be activated by 350 nm irradiation to induce various DNA damage, including DNA interstrand cross-links (ICL) formation, strand cleavages, and alkaline labile DNA lesions. The degree and types of DNA damage induced by these compounds depend on the leaving groups of the substrates, pH value of the buffer solution, and DNA sequences. The DNA ICL products were produced from the carbocations formed via the oxidation of free radicals photo-generated from 1a-f. Most of these compounds alone exhibited minimum cytotoxicity towards cancer cells while 350 nm irradiation greatly improved their anticancer effects (up to 40-fold enhancement) because of photo-induced cellular DNA damage. This work provides guidance for further design of photo-inducible DNA cross-linking agents as potent photo-activated anticancer prodrugs with good control over toxicity and selectivity.
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Affiliation(s)
- Qi Zhang
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, WI 53211, United States
| | - Taufeeque Ali
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, WI 53211, United States
| | - Zechao Lin
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, WI 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, WI 53211, United States.
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2
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Zhang Q, Lin Z, Peng X. Photo-Reactivity of Binaphthalene Triphenylphosphonium Salts: DNA Interstrand Cross-Link Formation and Substituent Effects. Chem Res Toxicol 2022; 35:1334-1343. [PMID: 35857929 DOI: 10.1021/acs.chemrestox.1c00401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Five novel 1,1'-binaphthalene analogues 1a-1e with triphenylphosphonium (TPP+) salts as a leaving group have been synthesized and characterized as photo-activatable DNA alkylating agents. Phototriggered release of the TPP+ group from 1a-1e generated naphthalenylmethyl-free radicals that were spontaneously transformed to the corresponding cations directly producing DNA interstrand cross-link (ICL) formation via alkylation. The substituents at position 4 not only affect the efficiency of ICL formation but also influence the reaction rate for DNA cross-linking. Groups with small or medium size favor ICL formation, while a bulky substituent (e.g., phenyl group) prevents DNA interstrand cross-linking. DNA alkylation by the naphthalenylmethyl cations photo-generated from 1a-1e occurs at dG, dC, and dA, while interstrand cross-linking took place with dG/dC base pairs. The TPP+ salts (1a-1e) are cations with both lipophilic and hydrophilic properties, which have great potential for biological applications.
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Affiliation(s)
- Qi Zhang
- 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
| | - Zechao Lin
- 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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Fan H, Sun H, Zhang Q, Peng X. Photoinduced DNA Interstrand Cross-Linking by 1,1'-Biphenyl Analogues: Substituents and Leaving Groups Combine to Determine the Efficiency of Cross-Linker. Chemistry 2021; 27:5215-5224. [PMID: 33440025 DOI: 10.1002/chem.202005064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/05/2021] [Indexed: 11/11/2022]
Abstract
Two series of 1,1'-biphenyl analogues with various leaving groups (L=OAc, OCH3 , OCHCH=CH2 , OCH2 Ph, SPh, SePh, and Ph3 P+ ) were synthesized. Their reactivity towards DNA and the reaction mechanism were investigated by determining DNA interstrand cross-link (ICL) efficiency, radical and carbocation formation, and the cross-linking reaction sites. All compounds induced DNA ICL formation upon 350 nm irradiation via a carbocation that was generated from oxidation of the corresponding free radicals. The ICL efficiency and the reaction rate strongly depended on the combined effect of the leaving group and the substituent. Among all compounds tested, the high ICL efficiency (30-43 %) and fast reaction rate were observed with compounds carrying a nitrophenyl group and acetate (2 a), ether (2 b and 2 c), or triphenylphosphonium salt (2 g) as leaving groups. Most compounds with a 4-methoxybenzene group showed similar DNA ICL efficiency (≈30 %) with a slow DNA cross-linking reaction rate. Both cation trapping and free radical trapping adducts were detected in the photo activation process of these compounds, which provided direct evidence for the proposed mechanism. Heat stability study in combination with sequence study suggested that these photo-generated benzyl cations alkylate DNA at dG, dA, and dC sites.
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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, USA.,School of Pharmacy, Tianjin Medical University, 300070, Tianjin, P. R. China
| | - Huabing Sun
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, Wisconsin, 53211, USA.,School of Pharmacy, Tianjin Medical University, 300070, Tianjin, P. R. China
| | - Qi Zhang
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, Wisconsin, 53211, USA
| | - 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, USA
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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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Reeh K, Summers PA, Gould IR, Woscholski R, Vilar R. Design, synthesis and evaluation of a tripodal receptor for phosphatidylinositol phosphates. Sci Rep 2020; 10:18450. [PMID: 33116198 PMCID: PMC7595110 DOI: 10.1038/s41598-020-75484-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/15/2020] [Indexed: 11/30/2022] Open
Abstract
Phosphatidylinositol phosphates (PIPs) are membrane phospholipids that play crucial roles in a wide range of cellular processes. Their function is dictated by the number and positions of the phosphate groups in the inositol ring (with seven different PIPs being active in the cell). Therefore, there is significant interest in developing small-molecule receptors that can bind selectively to these species and in doing so affect their cellular function or be the basis for molecular probes. However, to date there are very few examples of such molecular receptors. Towards this aim, herein we report a novel tripodal molecule that acts as receptor for mono- and bis-phosphorylated PIPs in a cell free environment. To assess their affinity to PIPs we have developed a new cell free assay based on the ability of the receptor to prevent alkaline phosphatase from hydrolysing these substrates. The new receptor displays selectivity towards two out of the seven PIPs, namely PI(3)P and PI(3,4)P2. To rationalise these results, a DFT computational study was performed which corroborated the experimental results and provided insight into the host-guest binding mode.
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Affiliation(s)
- Katharina Reeh
- Department of Chemistry, Imperial College London, White City Campus, 84 Wood Lane, London, W12 0BZ, UK
- Institute of Chemical Biology, Imperial College London, White City Campus, 84 Wood Lane, London, W12 0BZ, UK
| | - Peter A Summers
- Department of Chemistry, Imperial College London, White City Campus, 84 Wood Lane, London, W12 0BZ, UK
| | - Ian R Gould
- Department of Chemistry, Imperial College London, White City Campus, 84 Wood Lane, London, W12 0BZ, UK
- Institute of Chemical Biology, Imperial College London, White City Campus, 84 Wood Lane, London, W12 0BZ, UK
| | - Rudiger Woscholski
- Department of Chemistry, Imperial College London, White City Campus, 84 Wood Lane, London, W12 0BZ, UK
- Institute of Chemical Biology, Imperial College London, White City Campus, 84 Wood Lane, London, W12 0BZ, UK
| | - Ramon Vilar
- Department of Chemistry, Imperial College London, White City Campus, 84 Wood Lane, London, W12 0BZ, UK.
- Institute of Chemical Biology, Imperial College London, White City Campus, 84 Wood Lane, London, W12 0BZ, UK.
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Kancherla S, Jørgensen KB. Synthesis of Phenacene-Helicene Hybrids by Directed Remote Metalation. J Org Chem 2020; 85:11140-11153. [PMID: 32786610 PMCID: PMC7498163 DOI: 10.1021/acs.joc.0c01097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) with six and seven rings were synthesized via directed metalation and cross-coupling of chrysenyl N,N-diethyl carboxamides with o-tolyl and methylnaphthalenyl derivatives. In the presence of competing ortho sites, the site selectivity in iodination of chrysenyl amides by directed ortho metalation (DoM) was influenced by the lithium base. The catalyst ligand bite angle was presumably important in the cross-coupling of sterically hindered bulky PAHs. Subsequent directed remote metalation of biaryls under standard conditions and at elevated temperatures afforded various fused six- and seven-ring PAHs, all in good yields and with fluorescent properties.
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Affiliation(s)
- Sindhu Kancherla
- Department of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, N-4036 Stavanger, Norway
| | - Kåre B Jørgensen
- Department of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, N-4036 Stavanger, Norway
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Xu Y, Wei H, Chen J, Gao K. A thiol-inducible and quick-response DNA cross-linking agent. Bioorg Med Chem Lett 2019; 29:281-283. [DOI: 10.1016/j.bmcl.2018.11.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/14/2018] [Accepted: 11/18/2018] [Indexed: 12/11/2022]
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Lin Z, Fan H, Zhang Q, Peng X. Design, Synthesis, and Characterization of Binaphthalene Precursors as Photoactivated DNA Interstrand Cross-Linkers. J Org Chem 2018; 83:8815-8826. [PMID: 29929368 DOI: 10.1021/acs.joc.8b00642] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Most recently, alkylation via photogenerated carbocations has been identified as a novel mechanism for photoinduced DNA interstrand cross-link (ICL) formation by bifunctional aryl compounds. However, most compounds showed a low efficiency for DNA cross-linking. Here, we have developed a series of new 1,1'-binaphthalene analogues that efficiently form DNA ICLs upon 350 nm irradiation via generated 2-naphthalenylmethyl cations. The DNA cross-linking efficiency depends on the substituents at position 4 of the naphthalene moiety as well as the leaving groups. Compounds with NO2, Ph, H, Br, or OMe substituents led to 2-4 times higher DNA ICL yields than those with a boronate ester group. Compounds with trimethylammonium salt as a leaving group showed slightly better cross-linking efficiency than those with bromo as a leaving group. Some of these compounds showed a better cross-linking efficiency than that of traditional alkylating agents, such as nitrogen mustard analogues or quinone methide precursors. These highly efficient photoactivated carbocation precursors allow determination and characterization of the adducts formed between the photogenerated naphthalenyl cations and four natural nucleosides, indicating that the alkylation sites for these naphthalene analogues are dG, dA, and dC.
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Affiliation(s)
- Zechao Lin
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery , University of Wisconsin-Milwaukee , 3210 North Cramer Street , Milwaukee , Wisconsin 53211 , United States
| | - Heli Fan
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery , University of Wisconsin-Milwaukee , 3210 North Cramer Street , Milwaukee , Wisconsin 53211 , United States
| | - Qi Zhang
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery , University of Wisconsin-Milwaukee , 3210 North 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 North Cramer Street , Milwaukee , Wisconsin 53211 , United States
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10
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Fan H, Sun H, Peng X. Substituents Have a Large Effect on Photochemical Generation of Benzyl Cations and DNA Cross-Linking. Chemistry 2018; 24:7671-7682. [DOI: 10.1002/chem.201705929] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Heli Fan
- Department of Chemistry and Biochemistry; University of Wisconsin-Milwaukee; 3210 N. Cramer Street Milwaukee Wisconsin 53211 USA
| | - Huabing Sun
- Department of Chemistry and Biochemistry; University of Wisconsin-Milwaukee; 3210 N. Cramer Street Milwaukee Wisconsin 53211 USA
| | - Xiaohua Peng
- Department of Chemistry and Biochemistry; University of Wisconsin-Milwaukee; 3210 N. Cramer Street Milwaukee Wisconsin 53211 USA
- Milwaukee Institute for Drug Discovery; University of Wisconsin-Milwaukee; 3210 N. Cramer Street Milwaukee Wisconsin 53211 USA
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