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Du L, Zhang X, Xue J, Tang W, Li MD, Lan X, Zhu J, Zhu R, Weng Y, Li YL, Phillips DL. Influence of Water in the Photogeneration and Properties of a Bifunctional Quinone Methide. J Phys Chem B 2016; 120:11132-11141. [PMID: 27723330 DOI: 10.1021/acs.jpcb.6b08705] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Quinone methides (QM) are crucial reactive species in molecular biology and organic chemistry, with little known regarding the mechanism(s) for the generation of short-lived reactive QM intermediates from relevant precursors in aqueous solutions. In this study, several time-resolved spectroscopy methods were used to directly examine the photophysics and photochemical pathways of 1,1'-(2,2'-dihydroxy-1,1'-binaphthyl-6,6'-diyl)bis(N,N,N-trimethylmethanaminium) bromide (BQMP-b) from initial photoexcitation to the generation of the key reactive binol QM intermediate (BQM) in aqueous solution. The fluorescence of BQMP-b is effectively quenched with a small amount of water, which suggests an excited state intramolecular proton transfer (ESIPT) occurs. The kinetics isotope effects observed in femtosecond and nanosecond time-resolved transient absorption experiments provide evidence for the participation of water molecules in the BQMP-b singlet excited state ESIPT process and in the subsequent -HNMe3+ group release and ground state intramolecular proton transfer that give rise to production of the reactive BQM intermediate. Nanosecond time-resolved resonance Raman (ns-TR3) measurements were also employed to investigate the structure and properties of several intermediates, including the key reactive BQM in aqueous solution. The ns-TR3 and density functional theory (DFT) computational results were compared, and this indicates the binol moiety and water molecules both have important roles in the characteristics and structure of the key reactive BQM intermediate produced from BQMP-b. The results presented here also provide new benchmark characterization of bifunctional quinone methide intermediates that can be utilized to guide direct time-resolved spectroscopic study of the alkylation and interstrand cross-linking reactions of quinone methides with DNA in the future.
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Affiliation(s)
- Lili Du
- Department of Chemistry, University of Hong Kong , Pokfulam Road, Hong Kong S.A.R., P. R. China
| | - Xiting Zhang
- Department of Chemistry, University of Hong Kong , Pokfulam Road, Hong Kong S.A.R., P. R. China
| | - Jiadan Xue
- Department of Chemistry, Zhejiang Sci-Tech University , Hangzhou 310018, P. R. China
| | - WenJian Tang
- School of Pharmacy, Anhui Medical University , Meishan Road 81, Hefei 230032, P.R. China
| | - Ming-De Li
- Department of Chemistry, University of Hong Kong , Pokfulam Road, Hong Kong S.A.R., P. R. China
| | - Xin Lan
- Department of Chemistry, University of Hong Kong , Pokfulam Road, Hong Kong S.A.R., P. R. China
| | - Jiangrui Zhu
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences , Beijing 100190, P. R. China
| | - Ruixue Zhu
- Department of Chemistry, University of Hong Kong , Pokfulam Road, Hong Kong S.A.R., P. R. China
| | - Yuxiang Weng
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences , Beijing 100190, P. R. China
| | - Yun-Liang Li
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences , Beijing 100190, P. R. China
| | - David Lee Phillips
- Department of Chemistry, University of Hong Kong , Pokfulam Road, Hong Kong S.A.R., P. R. China
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Verga D, Nadai M, Doria F, Percivalle C, Di Antonio M, Palumbo M, Richter SN, Freccero M. Photogeneration and reactivity of naphthoquinone methides as purine selective DNA alkylating agents. J Am Chem Soc 2011; 132:14625-37. [PMID: 20863115 DOI: 10.1021/ja1063857] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A one-step protecting-group-free synthesis of both 6-hydroxy-naphthalene-2-carbaldehyde and the bifunctional binaphthalenyl derivative afforded 6-hydroxymethylnaphthalen-2-ol, 6-methylaminomethyl-naphthalen-2-ol, [(2-hydroxy-3-naphthyl)methyl]trimethyl ammonium iodide, and a small library of bifunctional binol analogues in good yields. Irradiation of naphthol quaternary ammonium salt and binol-derivatives (X = OH, NHR, NMe(3)(+), OCOCH(3), and L-proline) at 310 and 360 nm resulted in the photogeneration of the 2,6-naphthoquinone-6-methide (NQM) and binol quinone methide analogues (BQMs) by a water-mediated excited-state proton transfer (ESPT). The hydration, the mono- and bis-alkylation reactions of morpholine and 2-ethanethiol, as N and S prototype nucleophiles, by the transient NQM (λ(max) 310, 330 nm) and BQMs (λ(max) 360 nm) were investigated in water by product distribution analysis and laser flash photolysis (LFP). Both the photogeneration and the reactivity of NQM and BQMs exhibited striking differences. BQMs were at least 2 orders of magnitude more reactive than NQM, and they were generated much more efficiently from a greater variety of photoprecursors including the hydroxymethyl, quaternary ammonium salt and several binol-amino acids. On the contrary, the only efficient precursor of NQM was the quaternary ammonium salt. All water-soluble BQM precursors were further investigated for their ability to alkylate and cross-link plasmid DNA and oligonucleotides by gel electrophoresis: the BQMs were more efficient than the isomeric o-BQM (binol quinone methide analogue of 2,3-naphthoquinone-3-methide). Sequence analysis by gel electrophoresis, HPLC, and MS showed that the alkylation occurred at purines, with a preference for guanine. In particular, a BQM was able to alkylate N7 of guanines resulting in depurination at the oligonucleotide level, and ribose loss at the nucleotide level. The photoreactivity of BQM precursors translated into photocytotoxic and cytotoxic effects on two human cancer cell lines: in particular, one compound showed promising selectivity index on both cell lines.
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Affiliation(s)
- Daniela Verga
- Dipartimento di Chimica Organica, Università di Pavia, V. le Taramelli 10, 27100 Pavia, Italy
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Majumder P, Pradhan SK, Devi PG, Pal S, Dasgupta D. Chromatin as a target for the DNA-binding anticancer drugs. Subcell Biochem 2007; 41:145-89. [PMID: 17484128 PMCID: PMC7121056 DOI: 10.1007/1-4020-5466-1_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Chemotherapy has been a major approach to treat cancer. Both constituents of chromatin, chromosomal DNA and the associated chromosomal histone proteins are the molecular targets of the anticancer drugs. Small DNA binding ligands, which inhibit enzymatic processes with DNA substrate, are well known in cancer chemotherapy. These drugs inhibit the polymerase and topoisomerase activity. With the advent in the knowledge of chromatin chemistry and biology, attempts have shifted from studies of the structural basis of the association of these drugs or small ligands (with the potential of drugs) with DNA to their association with chromatin and nucleosome. These drugs often inhibit the expression of specific genes leading to a series of biochemical events. An overview will be given about the latest understanding of the molecular basis of their action. We shall restrict to those drugs, synthetic or natural, whose prime cellular targets are so far known to be chromosomal DNA.
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Affiliation(s)
- Parijat Majumder
- Biophysics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-I, Bidhannagar, Kolkata-700 064, India
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Shi Y, Dodson GE, Shaikh S, Rundell K, Tibbetts RS. Ataxia-telangiectasia-mutated (ATM) is a T-antigen kinase that controls SV40 viral replication in vivo. J Biol Chem 2005; 280:40195-200. [PMID: 16221684 DOI: 10.1074/jbc.c500400200] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The structurally related ATM (ataxia-telangiectasia-mutated) and ATR (ATM-Rad3-related) protein kinases fulfill overlapping yet non-redundant functions as key regulators of cellular DNA damage responses. We recently showed that ATM phosphorylates the cyclic AMP response element-binding protein, CREB, following exposure to ionizing radiation (IR) and other DNA-damaging stimuli. Here, we show that a phospho-specific antibody recognizing the major ATM phosphorylation site in CREB cross-reacts with SV40 large tumor antigen (LTag), a multifunctional oncoprotein required for replication of the SV40 minichromosome. The relevant IR-induced phosphorylation site in LTag recognized by phospho-CREB antibody was mapped to Ser-120. IR strongly induced the phosphorylation of Ser-120 in an ATM-dependent manner in mouse embryo fibroblasts. Infection of African green monkey CV1 cells with SV40 resulted in the activation of ATM and phosphorylation of LTag and endogenous ATM substrates. Infection-induced LTag phosphorylation correlated with the onset of DNA replication, was ATM-dependent, and peaked when viral DNA levels reached their maximum. SV40 replication in CV1 cells required an intact LTag Ser-120 phosphorylation site and was inhibited following transfection with ATM small interfering RNA suggesting that ATM is required for optimal SV40 replication in primate cells. Our findings uncover a direct link between ATM and SV40 LTag that may have implications for understanding the replication cycle of oncogenic polyoma viruses.
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Affiliation(s)
- Yuling Shi
- Department of Pharmacology, University of Wisconsin Medical School, Madison, Wisconsin 53706, USA
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Nelson SM, Ferguson LR, Denny WA. DNA and the chromosome - varied targets for chemotherapy. CELL & CHROMOSOME 2004; 3:2. [PMID: 15157277 PMCID: PMC421739 DOI: 10.1186/1475-9268-3-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2004] [Accepted: 05/24/2004] [Indexed: 12/29/2022]
Abstract
The nucleus of the cell serves to maintain, regulate, and replicate the critical genetic information encoded by the genome. Genomic DNA is highly associated with proteins that enable simple nuclear structures such as nucleosomes to form higher-order organisation such as chromatin fibres. The temporal association of regulatory proteins with DNA creates a dynamic environment capable of quickly responding to cellular requirements and distress. The response is often mediated through alterations in the chromatin structure, resulting in changed accessibility of specific DNA sequences that are then recognized by specific proteins. Anti-cancer drugs that target cellular DNA have been used clinically for over four decades, but it is only recently that nuclease specific drugs have been developed to not only target the DNA but also other components of the nuclear structure and its regulation. In this review, we discuss some of the new drugs aimed at primary DNA sequences, DNA secondary structures, and associated proteins, keeping in mind that these agents are not only important from a clinical perspective but also as tools for understanding the nuclear environment in normal and cancer cells.
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Affiliation(s)
- Stephanie M Nelson
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Auckland 10000, New Zealand
| | - Lynnette R Ferguson
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Auckland 10000, New Zealand
| | - William A Denny
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Auckland 10000, New Zealand
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Wang YD, Dziegielewski J, Chang AY, Dervan PB, Beerman TA. Cell-free and cellular activities of a DNA sequence selective hairpin polyamide-CBI conjugate. J Biol Chem 2002; 277:42431-7. [PMID: 12196541 DOI: 10.1074/jbc.m207179200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Alkylating agents are generally highly reactive with DNA but demonstrate limited DNA sequence selectivity. In contrast, synthetic pyrrole-imidazole polyamides recognize specific DNA sequences with high affinity but are unable to permanently damage DNA. An eight-ring hairpin polyamide conjugated to the alkylating moiety cyclopropylpyrroloindole, related to the natural product CC-1065, affords a conjugate 1-CBI (polyamide 1-CBI (1-(chloromethyl)-5-hydroxyl-1,2-dihydro-3H-benz[e]indole) conjugate), which binds to specific sequences in the minor groove of DNA and alkylates a single adenine flanking the polyamide binding site. In this study, we show that 1-CBI alkylates DNA in both plasmid and intracellular minichromosomal form and inhibits DNA replication under both cell-free and cellular conditions. In addition, it inhibits cell growth and arrests cells in the G2/M phase of the cell cycle.
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Affiliation(s)
- Yong-Dong Wang
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
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Woynarowski JM. Targeting critical regions in genomic DNA with AT-specific anticancer drugs. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1587:300-8. [PMID: 12084472 DOI: 10.1016/s0925-4439(02)00093-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Cellular DNA is not a uniform target for DNA-reactive drugs. At the nucleotide level, drugs recognize and bind short motifs of a few base pairs. The location of drug adducts at the genomic level depends on how these short motifs are distributed in larger domains. This aspect, referred to as region specificity, may be critical for the biological outcome of drug action. Recent studies demonstrated that certain minor groove binding (MGB) drugs, such as bizelesin, produce region-specific lesions in cellular DNA. Bizelesin binds mainly T(A/T)(4)A sites, which are on average scarce, but occasionally cluster in distinct minisatellite regions (200-1000 bp of approximately 85-100% AT), herein referred to as AT islands. Bizelesin-targeted AT islands are likely to function as strong matrix attachment regions (MARs), domains that organize DNA loops on the nuclear matrix. Distortion of MAR-like AT islands may be a basis for the observed inhibition of new replicon initiation and the extreme lethality of bizelesin adducts (<10 adducts/cell for cell growth inhibition). Hence, long AT-islands represent a novel class of critical targets for anticancer drugs. The AT island paradigm illustrates the potential of the concept of regional targeting as an essential component of the rational design of new sequence-specific DNA-reactive drugs.
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Affiliation(s)
- Jan M Woynarowski
- Cancer Therapy and Research Center, Institute for Drug Development, University of Texas Health Science Center at San Antonio, 14960 Omicron Drive, San Antonio, TX 78245, USA.
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Preferential damage to defined regions of genomic DNA by AT-specific anticancer drugs. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s1067-568x(02)80003-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Liu JS, Kuo SR, McHugh MM, Beerman TA, Melendy T. Adozelesin triggers DNA damage response pathways and arrests SV40 DNA replication through replication protein A inactivation. J Biol Chem 2000; 275:1391-7. [PMID: 10625690 DOI: 10.1074/jbc.275.2.1391] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The cyclopropylpyrroloindole anti-cancer drug, adozelesin, binds to and alkylates DNA. Treatment of human cells with low levels of adozelesin results in potent inhibition of both cellular and simian virus 40 (SV40) DNA replication. Extracts were prepared from adozelesin-treated cells and shown to be deficient in their ability to support SV40 DNA replication in vitro. This effect on in vitro DNA replication was dependent on both the concentration of adozelesin used and the time of treatment but was not due to the presence of adozelesin in the in vitro assay. Adozelesin treatment of cells was shown to result in the following: induction of p53 protein levels, hyperphosphorylation of replication protein A (RPA), and disruption of the p53-RPA complex (but not disruption of the RPA-cdc2 complex), indicating that adozelesin treatment triggers cellular DNA damage response pathways. Interestingly, in vitro DNA replication could be rescued in extracts from adozelesin-treated cells by the addition of exogenous RPA. Therefore, whereas adozelesin and other anti-cancer therapeutics trigger common DNA damage response markers, adozelesin causes DNA replication arrest through a unique mechanism. The S phase checkpoint response triggered by adozelesin acts by inactivating RPA in some function essential for SV40 DNA replication.
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Affiliation(s)
- J S Liu
- Department of Microbiology and the Center for Microbial Pathogenesis, State University of New York School of Medicine and Biomedical Sciences, Buffalo, New York 14214, USA
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