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Peng Y, Wang Y, Wang X. Exploring the Thermodynamics of 7-Amino Actinomycin D-Induced Single-Stranded DNA Hairpin by Spectroscopic Techniques and Computational Simulations. J Phys Chem B 2020; 124:10007-10013. [PMID: 33136398 DOI: 10.1021/acs.jpcb.0c05593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
NMR studies have indicated that the anti-tumor therapeutic agent actinomycin D (ACTD) can induce seemingly single-stranded DNA (ssDNA) oligomer 5'-CCGTT3GTGG-3' to form a hairpin structure with tandem GT mismatches at the stem region next to a loop of three stacked thymine bases. In an effort to uncover the preference of binding sequence and to elucidate the thermodynamics properties of the binding, a combination of spectroscopic techniques and computational simulation studies was performed with d(CCGTTnGTGG) and d(CCGAAnGAGG) (denoted as GTTn and GAAn, respectively; n = 3, 5, and 7) sequences. In the presence of 7-amino actinomycin D (7AACTD), all the six oligomers formed stable hairpin structures. The GTT5-7AACTD/GAA5-7AACTD hairpin structure was more stable than the corresponding GTTn-7AACTD and GAAn-7AACTD (n = 3, 7). No significant ΔG difference was observed between GTTn-7AACTD and GAAn-7AACTD complexes with the same loop length. In agreement with the 7AACTD-induced hairpin stability results, the binding affinity of GTTn and GAAn with 7AACTD increased from n = 3 to n = 5 and then decreased when n is 7. Moreover, GTTn and GAAn with the same loop length showed comparable binding affinities to 7AACTD. Furthermore, molecular dynamics simulations found that van der Waals interactions between GTTn/GAAn and 7AACTD were the primary attractive forces for 7AACTD binding, and the electrostatic interactions between the carbonyl groups of 7AACTD and bases in the hairpin were the major unfavorable forces. These findings furthered our understanding that 7AACTD is sensitive to the loop size and sequence as well as tandem GT/GA mismatches of their deoxyribonucleic acid (DNA) targets. A deep understanding of the thermodynamics and the molecular recognition mechanism of 7AACTD with ssDNAs would further the development of ACTD-like antitumor agents.
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Affiliation(s)
- Yinghua Peng
- Key Laboratory of Special Animal Molecular Biology of Jilin Province, Specialty Research Institute of Chinese Academy of Agricultural Sciences, Changchun, Jilin 130022, China
| | - Yibo Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Xiaohui Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.,Department of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, China
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2
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Kang HJ, Park HJ. Novel molecular mechanism for actinomycin D activity as an oncogenic promoter G-quadruplex binder. Biochemistry 2009; 48:7392-8. [PMID: 19496619 DOI: 10.1021/bi9006836] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Actinomycin D (ActD) is a natural antibiotic that inhibits the transcription of genes by interacting with a GC-rich duplex, a single-stranded or hairpin form of DNA, and then interfering with the action of RNA polymerase. In this study, we identified a novel molecular mechanism of anticancer activity of ActD as an oncogenic c-Myc promoter G-quadruplex binder. ActD selectively inhibits the elongation of oligonucleotides containing c-Myc promoter G-quadruplex sequence in PCR-stop assays. UV-vis spectroscopic and circular dichroism studies suggest that ActD interacts with c-Myc promoter G-quadruplex via a surface end stacking interaction, inducing a mixed-type conformation of the G-quadruplex. ActD selectively inhibits the cellular growth and synthesis of c-Myc mRNA in Ramos cells having the NHEIII(1) region in the translocated c-Myc gene. In addition, the results of promoter assays using two kinds of NHEIII(1) region mutants and wild-type constructs strongly support the idea that binding of ActD with G-quadruplex formed in the promoter region results in the reporter gene being turned off. Our study reveals a novel mechanism underlying the anticancer activity of ActD, whereby ActD interacts with oncogenic promoter G-quadruplex DNA to repress gene expression.
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Affiliation(s)
- Hyun-Jin Kang
- College of Pharmacy, Sungkyunkwan University, Suwon 440-746, Republic of Korea
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Biver T, Venturini M, Jares-Erijman EA, Jovin TM, Secco F. 7-Aminoactinomycin Binding to DNA Sequences Lacking GpC Sites: A Thermodynamic and Kinetic Study. Biochemistry 2008; 48:173-9. [DOI: 10.1021/bi801671c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tarita Biver
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy, Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria Pabellón II/3, 1428 Buenos Aires, Argentina, and Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, am Fassberg 11, 37077 Göttingen, Germany
| | - Marcella Venturini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy, Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria Pabellón II/3, 1428 Buenos Aires, Argentina, and Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, am Fassberg 11, 37077 Göttingen, Germany
| | - Elizabeth A. Jares-Erijman
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy, Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria Pabellón II/3, 1428 Buenos Aires, Argentina, and Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, am Fassberg 11, 37077 Göttingen, Germany
| | - Thomas M. Jovin
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy, Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria Pabellón II/3, 1428 Buenos Aires, Argentina, and Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, am Fassberg 11, 37077 Göttingen, Germany
| | - Fernando Secco
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy, Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria Pabellón II/3, 1428 Buenos Aires, Argentina, and Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, am Fassberg 11, 37077 Göttingen, Germany
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David-Cordonnier MH, Laine W, Lansiaux A, Rosu F, Colson P, de Pauw E, Michel S, Tillequin F, Koch M, Hickman JA, Pierré A, Bailly C. Covalent binding of antitumor benzoacronycines to double-stranded DNA induces helix opening and the formation of single-stranded DNA: Unique consequences of a novel DNA-bonding mechanism. Mol Cancer Ther 2005. [DOI: 10.1158/1535-7163.71.4.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The majority of DNA-binding small molecules known thus far stabilize duplex DNA against heat denaturation. A high, drug-induced increase in the melting temperature (Tm) of DNA is generally viewed as a good criterion to select DNA ligands and is a common feature of several anticancer drugs such as intercalators (e.g., anthracyclines) and alkylators (e.g., ecteinascidin 743). The reverse situation (destabilization of DNA to facilitate its denaturation) may be an attractive option for the identification of therapeutic agents acting on the DNA structure. We have identified the tumor-active benzoacronycine derivative S23906-1 [(±)-cis-1,2-diacetoxy-6-methoxy-3,3,14-trimethyl-1,2,3,14-tetrahydro-7H-benzo[b]pyrano[3,2]acridin-7-one] as a potent DNA alkylating agent endowed with a helicase-like activity. Using complementary molecular approaches, we show that covalent binding to DNA of the diacetate compound S23906-1 and its monoacetate analogue S28687-1 induces a marked destabilization of the double helix with the formation of alkylated ssDNA. The DNA-bonding properties and effects on DNA structure of a series of benzoacronycine derivatives, including the dicarbamate analogue S29385-1, were studied using complementary biochemical (electromobility shift assay, nuclease S1 mapping) and spectroscopic (fluorescence and Tm measurements) approaches. Alkylation of guanines in DNA by S28687-1 leads to a local denaturation of DNA, which becomes susceptible to cleavage by nuclease S1 and significantly decreases the Tm of DNA. The drug also directly alkylates single-strand DNA, but mass spectrometry experiments indicate that guanines in duplexes are largely preferred over single-stranded structures. This molecular study expands the repertoire of DNA-binding mechanisms and provides a new dimension for DNA recognition by small molecules.
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Affiliation(s)
- Marie-Hélène David-Cordonnier
- 1Institut National de la Santé et de la Recherche Médicale U-524 et Laboratoire de Pharmacologie Antitumorale du Centre Oscar Lambret, Institut de Recherches sur le Cancer de Lille, Lille, France
| | - William Laine
- 1Institut National de la Santé et de la Recherche Médicale U-524 et Laboratoire de Pharmacologie Antitumorale du Centre Oscar Lambret, Institut de Recherches sur le Cancer de Lille, Lille, France
| | - Amélie Lansiaux
- 1Institut National de la Santé et de la Recherche Médicale U-524 et Laboratoire de Pharmacologie Antitumorale du Centre Oscar Lambret, Institut de Recherches sur le Cancer de Lille, Lille, France
| | - Frédéric Rosu
- 2Biospectroscopy and Physical Chemistry Unit, University of Liege, Sart-Tilman, Liege, Belgium
| | - Pierre Colson
- 2Biospectroscopy and Physical Chemistry Unit, University of Liege, Sart-Tilman, Liege, Belgium
| | - Edwin de Pauw
- 2Biospectroscopy and Physical Chemistry Unit, University of Liege, Sart-Tilman, Liege, Belgium
| | - Sylvie Michel
- 3Laboratoire de Pharmacognosie, Université René Descartes (Paris 5), Centre National de la Recherche Scientifique UMR8638, Faculté des Sciences Pharmaceutiques et Biologiques, Paris, France; and
| | - Francois Tillequin
- 3Laboratoire de Pharmacognosie, Université René Descartes (Paris 5), Centre National de la Recherche Scientifique UMR8638, Faculté des Sciences Pharmaceutiques et Biologiques, Paris, France; and
| | - Michel Koch
- 3Laboratoire de Pharmacognosie, Université René Descartes (Paris 5), Centre National de la Recherche Scientifique UMR8638, Faculté des Sciences Pharmaceutiques et Biologiques, Paris, France; and
| | - John A. Hickman
- 4Division Recherche Cancérologie, Institut de Recherches Servier, Croissy sur Seine, France
| | - Alain Pierré
- 4Division Recherche Cancérologie, Institut de Recherches Servier, Croissy sur Seine, France
| | - Christian Bailly
- 1Institut National de la Santé et de la Recherche Médicale U-524 et Laboratoire de Pharmacologie Antitumorale du Centre Oscar Lambret, Institut de Recherches sur le Cancer de Lille, Lille, France
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Chen FM, Sha F, Chin KH, Chou SH. The nature of actinomycin D binding to d(AACCAXYG) sequence motifs. Nucleic Acids Res 2004; 32:271-7. [PMID: 14715925 PMCID: PMC373288 DOI: 10.1093/nar/gkh178] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Earlier studies by others had indicated that actinomycin D (ACTD) binds well to d(AACCATAG) and the end sequence TAG-3' is essential for its strong binding. In an effort to verify these assertions and to uncover other possible strong ACTD binding sequences as well as to elucidate the nature of their binding, systematic studies have been carried out with oligomers of d(AACCAXYG) sequence motifs, where X and Y can be any DNA base. The results indicate that in addition to TAG-3', oligomers ending with XAG-3' and XCG-3' all provide binding constants > or =1 x 10(7) M(-1) and even sequences ending with XTG-3' and XGG-3' exhibit binding affinities in the range 1-8 x 10(6) M(-1). The nature of the strong ACTD affinity of the sequences d(A1A2C3C4A5X6Y7G8) was delineated via comparative binding studies of d(AACCAAAG), d(AGCCAAAG) and their base substituted derivatives. Two binding modes are proposed to coexist, with the major component consisting of the 3'-terminus G base folding back to base pair with C4 and the ACTD inserting at A2C3C4 by looping out the C3 while both faces of the chromophore are stacked by A and G bases, respectively. The minor mode is for the G to base pair with C3 and to have the same A/chromophore/G stacking but without a looped out base. These assertions are supported by induced circular dichroic and fluorescence spectral measurements.
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Affiliation(s)
- Fu-Ming Chen
- Department of Chemistry, Tennessee State University, Nashville, TN 37209-1561, USA.
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Chen FM, Sha F, Chin KH, Chou SH. Unique actinomycin D binding to self-complementary d(CXYGGCCY'X'G) sequences: duplex disruption and binding to a nominally base-paired hairpin. Nucleic Acids Res 2003; 31:4238-46. [PMID: 12853642 PMCID: PMC167638 DOI: 10.1093/nar/gkg477] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Actinomycin D (ACTD) has been shown to bind weakly to the sequence -GGCC-, despite the presence of a GpC site. It was subsequently found, however, that d(CATGGCCATG) binds relatively well to ACTD but exhibits unusually slow association kinetics, contrary to the strong-binding -XGCY- sites. In an effort to elucidate the nature of such binding and to delineate the origin of its interesting kinetic behavior, studies have now been extended to include oligomers with the general sequence motifs of d(CXYGGCCY'X'G)(2). It was found that analogous binding characteristics are observed for these self-duplex decamers and comparative studies with progressively base-truncated oligomers from the 5'-end led to the finding that d(GGCCY'X'G) oligomers bind ACTD considerably stronger than their parent decamers and exhibit 1:1 drug/strand binding stoichiometry. Melting profiles monitored at the drug spectral region indicated additional drug binding prior to the onset of eventual complex disruptions with near identical melting temperatures for all the oligomers studied. These results are consistent with the notion that the related oligomers share a common strong binding mode of a hairpin-type, with the 3'-terminus G folding back to base-pair with the C base of GGC. A binding scheme is proposed in which the oligomers d(CXYGGCCY'X'G) exist predominantly in the duplex form and bind ACTD initially at the central GGCC weak site but subsequently disrupt to accommodate the stronger hairpin binding and thus the slow association kinetics. Such a mechanism is supported by the observation of distinct biphasic fluorescence kinetic traces in the binding of 7-amino-ACTD to these duplexes.
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Affiliation(s)
- Fu-Ming Chen
- Department of Chemistry, Tennessee State University, Nashville, TN 37209-1561, USA.
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Chin KH, Chen FM, Chou SH. Solution structure of the ActD-5'-CCGTT3GTGG-3' complex: drug interaction with tandem G.T mismatches and hairpin loop backbone. Nucleic Acids Res 2003; 31:2622-9. [PMID: 12736312 PMCID: PMC156035 DOI: 10.1093/nar/gkg353] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Binding of actinomycin D (ActD) to the seemingly single-stranded DNA (ssDNA) oligomer 5'-CCGTT3 GTGG-3' has been studied in solution using high-resolution nuclear magnetic resonance (NMR) techniques. A strong binding constant (8 x 10(6) M(-1)) and high quality NMR spectra have allowed us to determine the initial DNA structure using distance geometry as well as the final ActD-5'-CCGTT3 GTGG-3' complex structure using constrained molecular dynamics calculations. The DNA oligomer 5'-CCGTT3GTGG-3' in the complex forms a hairpin structure with tandem G.T mismatches at the stem region next to a loop of three stacked thymine bases pointing toward the major groove. Bipartite T2O-GH1 and T2O-G2NH2 hydrogen bonds were detected for the G.T mismatches that further stabilize this unusual DNA hairpin. The phenoxazone chromophore of ActD intercalates nicely between the tandem G.T mismatches in essentially one major orientation. Additional hydrophobic interactions between the ActD quinoid amino acid residues with the loop T5-T6-T7 backbone protons were also observed. The hydrophobic G-phenoxazone-G interaction in the ActD-5'-CCGTT3GTGG-3' complex is more robust than that of the classical ActD- 5'-CCGCT3GCGG-3' complex, consistent with the roughly 2-fold stronger binding of ActD to the 5'-CCGTT3GTGG-3' sequence than to its 5'-CCG CT3GCGG-3' counterpart. Stabilization by ActD of a hairpin containing non-canonical stem base pairs further strengthens the notion that ActD or other related compounds may serve as a sequence- specific ssDNA-binding agent that inhibits human immunodeficiency virus (HIV) and other retroviruses replicating through ssDNA intermediates.
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Affiliation(s)
- Ko-Hsin Chin
- Institute of Biochemistry, National Chung-Hsing University, Taichung, 40227, Taiwan
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Chen FM, Sha F, Chin KH, Chou SH. Binding of actinomycin D to single-stranded DNA of sequence motifs d(TGTCT(n)G) and d(TGT(n)GTCT). Biophys J 2003; 84:432-9. [PMID: 12524296 PMCID: PMC1302624 DOI: 10.1016/s0006-3495(03)74863-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Our recent binding studies with oligomers derived from base replacements on d(CGTCGTCG) had led to the finding that actinomycin D (ACTD) binds strongly to d(TGTCATTG) of apparent single-stranded conformation without GpC sequence. A fold-back binding model was speculated in which the planar phenoxazone inserts at the GTC site with a loop-out T base whereas the G base at the 3'-terminus folds back to form a basepair with the internal C and stacks on the opposite face of the chromophore. To provide a more concrete support for such a model, ACTD equilibrium binding studies were carried out and the results are reported herein on oligomers of sequence motifs d(TGTCT(n)G) and d(TGT(n)GTC). These oligomers are not expected to form dimeric duplexes and contain no canonical GpC sequences. It was found that ACTD binds strongly to d(TGTCTTTTG), d(TGTTTTGTC), and d(TGTTTTTGTC), all exhibiting 1:1 drug/strand binding stoichiometry. The fold-back binding model with displaced T base is further supported by the finding that appending TC and TCA at the 3'-terminus of d(TGTCTTTTG) results in oligomers that exhibit enhanced ACTD affinities, consequence of the added basepairing to facilitate the hairpin formation of d(TGTCTTTTGTC) and d(TGTCTTTTGTCA) in stabilizing the GTC/GTC binding site for juxtaposing the two G bases for easy stacking on both faces of the phenoxazone chromophore. Further support comes from the observation of considerable reduction in ACTD affinity when GTC is replaced by GTTC in an oligomer, in line with the reasoning that displacing two T bases to form a bulge for ACTD binding is more difficult than displacing a single base. Based on the elucidated binding principle of phenoxazone ring requiring its opposite faces to be stacked by the 3'-sides of two G bases for tight ACTD binding, several oligonucleotide sequences have been designed and found to bind well.
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Affiliation(s)
- Fu-Ming Chen
- Department of Chemistry, Tennessee State University, Nashville 37209, USA.
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Chou SH, Chin KH, Chen FM. Looped out and perpendicular: deformation of Watson-Crick base pair associated with actinomycin D binding. Proc Natl Acad Sci U S A 2002; 99:6625-30. [PMID: 12011426 PMCID: PMC124453 DOI: 10.1073/pnas.102580399] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many anticancer drugs interact directly with DNA to exert their biological functions. To date, all noncovalent, intercalating drugs interact with DNA exclusively by inserting their chromophores into base steps to form elongated and unwound duplex structures without disrupting the flanking base pairs. By using actinomycin D (ActD)-5'-GXC/CYG-5' complexes as examples, we have found a rather unusual interaction mode for the intercalated drug; the central Watson-Crick X/Y base pairs are looped out and displaced by the ActD chromophore. The looped-out bases are not disordered but interact perpendicularly with the base/chromophore and form specific H bonds with DNA. Such a complex structure provides intriguing insights into how ligand interacts with DNA and enlarges the repertoires for sequence-specific DNA recognition.
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Affiliation(s)
- Shan-Ho Chou
- Institute of Biochemistry, National Chung-Hsing University, Taichung, Taiwan 40227, Republic of China.
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