1
|
Mischiati C, Finotti A, Sereni A, Boschetti S, Baraldi PG, Romagnoli R, Feriotto G, Jeang KT, Bianchi N, Borgatti M, Gambari R. Binding of hybrid molecules containing pyrrolo [2,1-c][1,4]benzodiazepine (PBD) and oligopyrrole carriers to the human immunodeficiency type 1 virus TAR-RNA. Biochem Pharmacol 2004; 67:401-10. [PMID: 15037192 DOI: 10.1016/j.bcp.2003.09.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2003] [Accepted: 09/03/2003] [Indexed: 11/27/2022]
Abstract
The binding properties of a set of four hybrids, prepared combining from one to four polypyrrole minor groove binders and pyrrolo [2,1-c][1,4]benzodiazepine (PBD), have been studied using as target molecule the HIV-1 TAR-RNA. We found that these hybrids bind to TAR-RNA and inhibit TAR/protein(s) interactions. The anti-proliferative activity of the hybrids has been tested in vitro on HL3T1 cells and compared to the anti-proliferative effects of the natural product distamycin A and PBD. The effects on HIV-1 LTR directed transcription were studied using the chloramphenicol-acetyltransferase gene reporter system, and structure-activity relationships are discussed. The results obtained demonstrate that the hybrids 22-25 exhibit different TAR-RNA binding activity with respect to both distamycin A and PBD. In addition, a direct relationship was found between number of pyrrole rings present in the hybrids 22-25 and anti-proliferative effects. It was found that increased length of the polypyrrole backbone leads to an increased in vitro anti-proliferative effect, i.e. the hybrid 25, containing the four pyrroles distamycin analogous, is more active than 22, 23 and 24 against cell proliferation. With respect to inhibition of HIV-1 LTR-driven transcription, it was found that the hybrids 23-25 containing two-four pyrroles are active. Therefore, when anti-proliferative effects are considered together with the inhibitory effects of HIV-1 LTR driven transcription, our results suggest that the hybrid 23 is the more interesting, since it exhibits low anti-proliferative activity and inhibits HIV-1 LTR driven transcription both in vitro and in ex vivo experiments.
Collapse
Affiliation(s)
- Carlo Mischiati
- Department of Biochemistry and Molecular Biology, University of Ferrara, Via Luigi Borsari 46, 44100 Ferrara, Italy
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
2
|
Boutorine AS, Arimondo PB. Sequence-Specific Cleavage of Double-Stranded DNA. In: Zenkova MA, editor. Artificial Nucleases. Berlin: Springer Berlin Heidelberg; 2004. pp. 243-68. [DOI: 10.1007/978-3-642-18510-6_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
3
|
Carrasco C, Helissey P, Haroun M, Baldeyrou B, Lansiaux A, Colson P, Houssier C, Giorgi-Renault S, Bailly C. Design of a composite ethidium-netropsin-anilinoacridine molecule for DNA recognition. Chembiochem 2003; 4:50-61. [PMID: 12512076 DOI: 10.1002/cbic.200390014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Control of gene expression is a cherished goal of cancer chemotherapy. Small ligand molecules able to bind tightly to DNA in a well-defined configuration are being actively searched for. With this goal in mind, we have designed and synthesized the trifunctional molecule R-132, which combines a bispyrrole skeleton for minor groove DNA recognition and two different chromophores, anilinoacridine and ethidium. The affinity and mode of binding of R-132 to DNA were studied by a combination of complementary biochemical and biophysical techniques, which included absorption and fluorescence spectroscopy and circular and linear dichroism. A surface plasmon resonance biosensor analysis was also performed to quantify the kinetic parameters of the drug-DNA interaction process. Altogether, the results demonstrate that the three moieties of the hybrid molecule are engaged in the interaction process, thus validating the rational design strategy. At the biological level, R-132 stabilizes topoisomerase-II-DNA covalent complexes and displays potent cytotoxic activities, which are attributable to its DNA-binding properties. R-132 easily enters and accumulates in cell nuclei, as evidenced by confocal microscopy. R-132 therefore provides a novel lead compound for the design of gene-targeted anticancer agents.
Collapse
Affiliation(s)
- Carolina Carrasco
- INSERM U-524 et Laboratoire de Pharmacologie Antitumorale du Centre Oscar Lambret, IRCL, Place de Verdun, 59045 Lille, France
| | | | | | | | | | | | | | | | | |
Collapse
|
4
|
Rastogi K, Chang JY, Pan WY, Chen CH, Chou TC, Chen LT, Su TL. Antitumor AHMA linked to DNA minor groove binding agents: synthesis and biological evaluation. J Med Chem 2002; 45:4485-93. [PMID: 12238927 DOI: 10.1021/jm0200714] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA minor groove binder hybrid molecules, netropsin derivatives such as N-[2-(dimethylamino)ethyl]-1-methyl-4-aminopyrrolo-2-carboxamide (MePy) or its derivatives containing two units of N-methylpyrrolecarboxamide (diMePy) and bisbenzimidazole (Ho33258), were linked to the NH(2) function of AHMA or to the CH(2)OH group of AHMA-ethylcarbamate to form AHMA-N-netropsins (13-16) and AHMA-ethylcarbamate-O-netropsins (19-22), and AHMA-bisbenzimidazole (AHMA-Ho33258, 25), respectively. These conjugates' in vitro antitumor activity, inhibition of a variety of human tumor cell growth, revealed that AHMA-ethylcarbamate-O-netropsin derivatives were more cytotoxic than AHMA-N-netropsin compounds. In the same studies, all compounds bearing MePy were more potent than those compounds linked with diMePy. Moreover, AHMA-netropsin derivatives bearing a succinyl chain as the linking spacer were more potent than those compounds having a glutaryl bridge. Among these hybrid molecules, AHMA-ethylcarbamate-O-succinyl-MePy (19) was 2- to 6-fold more cytotoxic than the parent compound AHMA (5) in various cell lines, whereas compound 25 had very poor solubility and was inactive. Studies on the inhibitory effect against topoisomerase II (Topo II) and DNA interaction of these conjugates showed no correlation between the potency of DNA binding and inhibitory activity against Topo II.
Collapse
Affiliation(s)
- Kamesh Rastogi
- Laboratory of Bioorganic Chemistry, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | | | | | | | | | | | | |
Collapse
|
5
|
|
6
|
Helissey P, Giorgi-Renault S, Colson P, Houssier C, Bailly C. Sequence-recognition and cleavage of DNA by a netropsin-phenazine-di-N-oxide conjugate. Bioconjug Chem 2000; 11:219-27. [PMID: 10725099 DOI: 10.1021/bc990131t] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the synthesis, DNA-binding and cleaving properties, and cytotoxic activities of R-128, a hybrid molecule in which a bis-pyrrolecarboxamide-amidine element related to the antibiotic netropsin is covalently tethered to a phenazine-di-N-oxide chromophore. The affinity and mode of interaction of the conjugate with DNA were investigated by a combination of absorption spectroscopy, circular dichroism, and electric linear dichroism. This hybrid molecule binds to AT-rich sequences of DNA via a bimodal process involving minor groove binding of the netropsin moiety and intercalation of the phenazine moiety. The bidentate mode of binding was evidenced by linear dichroism using calf thymus DNA and poly(dA-dT).(dA-dT). In contrast, the drug fails to bind to poly(dG-dC).poly(dG-dC), because of the obstructive effect of the guanine 2-amino group exposed in the minor groove of this polynucleotide. DNase I footprinting studies indicated that the conjugate interacts preferentially with AT-rich sequences, but the cleavage of DNA in the presence of a reducing agent can occur at different sequences not restricted to the AT sites. The main cleavage sites were detected with a periodicity of about 10 base pairs corresponding to approximately one turn of the double helix. This suggests that the cleavage may be dictated by the structure of the double helix rather than the primary nucleotide sequence. The conjugate which is moderately toxic to cancer cells complements the tool box of reagents which can be utilized to produce DNA strand scission. The DNA cleaving properties of R-128 entreat further exploration into the use of phenazine-di-N-oxides as tools for investigating DNA structure.
Collapse
Affiliation(s)
- P Helissey
- Laboratoire de Chimie Thérapeutique, Faculté des Sciences Pharmaceutiques et Biologiques, UMR CNRS-Université René Descartes no. 8638, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France
| | | | | | | | | |
Collapse
|
7
|
Affiliation(s)
- C Bailly
- INSERM U-124 et Laboratoire de Pharmacologie Antitumorale Moléculaire du Centre Oscar Lambret, IRCL, Place de Verdun, 59045 Lille, France.
| | | |
Collapse
|
8
|
Affiliation(s)
- Bruce Armitage
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890
| |
Collapse
|
9
|
Bailly C. Sequence-specific recognition and modification of double-helical DNA by minor-groove binding conjugates structurally related to netropsin and distamycin. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s1067-568x(98)80007-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
|
10
|
Burgstaller P, Hermann T, Huber C, Westhof E, Famulok M. Isoalloxazine derivatives promote photocleavage of natural RNAs at G.U base pairs embedded within helices. Nucleic Acids Res 1997; 25:4018-27. [PMID: 9321652 PMCID: PMC146990 DOI: 10.1093/nar/25.20.4018] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We have recently shown that isoalloxazine derivatives are able to photocleave RNA specifically at G.U base pairs embedded within a helical stack. The reaction involves the selective molecular recognition of G.U base pairs by the isoalloxazine ring and the removal of one nucleoside downstream of the uracil residue. Divalent metal ions are absolutely required for cleavage. Here we extend our studies to complex natural RNA molecules with known secondary and tertiary structures, such as tRNAs and a group I intron (td). G.U pairs were cleaved in accordance with the phylogenetically and experimentally derived secondary and tertiary structures. Tandem G.U pairs or certain G.U pairs located at a helix extremity were not affected. These new cleavage data, together with the RNA crystal structure, allowed us to perform molecular dynamics simulations to provide a structural basis for the observed specificity. We present a stable structural model for the ternary complex of the G. U-containing helical stack, the isoalloxazine molecule and a metal ion. This model provides significant new insight into several aspects of the cleavage phenomenon, mechanism and specificity for G. U pairs. Our study shows that in large natural RNAs a secondary structure motif made of an unusual base pair can be recognized and cleaved with high specificity by a low molecular weight molecule. This photocleavage reaction thus opens up the possibility of probing the accessibility of G.U base pairs, which are endowed with specific structural and functional roles in numerous structured and catalytic RNAs and interactions of RNA with proteins, in folded RNAs.
Collapse
MESH Headings
- Base Composition
- Binding Sites
- Cations, Divalent
- Flavin Mononucleotide/chemistry
- Flavin Mononucleotide/metabolism
- Flavins/metabolism
- Guanosine
- Introns
- Models, Molecular
- Molecular Structure
- Nucleic Acid Conformation
- Photolysis
- RNA/metabolism
- RNA, Transfer, Asp/chemistry
- RNA, Transfer, Asp/metabolism
- RNA, Transfer, Met/chemistry
- RNA, Transfer, Met/metabolism
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/metabolism
- RNA, Transfer, Val/chemistry
- RNA, Transfer, Val/metabolism
- Uracil
- Uridine
Collapse
Affiliation(s)
- P Burgstaller
- Institut für Biochemie der LMU München-Genzentrum, Würmtalstrasse 221, 81375 München, Germany
| | | | | | | | | |
Collapse
|
11
|
Frier C, Décout JL, Fontecave M. Method for Preparing New Flavin Derivatives: Synthesis of Flavin−Thymine Nucleotides and Flavin−Oligonucleotide Adducts. J Org Chem 1997. [DOI: 10.1021/jo962361w] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
12
|
Perrée-fauvet M, Verchère-béaur C, Tarnaud E, Anneheim-herbelin G, Bône N, Gaudemer A. New amino acid porphyrin derivatives. Part I: Synthesis. Tetrahedron 1996; 52:13569-88. [DOI: 10.1016/0040-4020(96)00832-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
13
|
Ketterlé C, Gabarro-Arpa J, Ouali M, Bouziane M, Auclair C, Helissey P, Giorgi-Renault S, Le Bret M. Binding of Net-Fla, a netropsin-flavin hybrid molecule, to DNA: molecular mechanics and dynamics studies in vacuo and in water solution. J Biomol Struct Dyn 1996; 13:963-77. [PMID: 8832379 DOI: 10.1080/07391102.1996.10508911] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We have studied the binding of the hybrid netropsin-flavin (Net-Fla) molecule onto four sequences containing four A. T base pairs. Molecular mechanics minimizations in vacuo show numerous minimal conformations separated by one base pair. 400 ps molecular dynamics simulations in vacuo have been performed using the lowest minima as the starting conformations. During these simulations, the flavin moiety of the drug makes two hydrogen bonds with an amino group of a neighboring guanine. A 200 ps molecular dynamics simulation in explicit water solution suggests that the binding of Net-Fla upon the DNA substrate is enhanced by water bridges. A water molecule bridging the amidinium of Net-Fla to the N3 atom of an adenine seems to be stuck in the drug-DNA complex during the whole simulation. The fluctuations of the DNA helical parameters and of the torsion angles of the sugar-phosphate backbone are very similar in the simulations in vacuo and in water. The time auto-correlation functions for the DNA helical parameters decrease rapidly in the picosecond range in vacuo. The same functions computed from the water solution molecular dynamics simulations seem to have two modes: the rapid mode is similar to the behavior in vacuo, and is followed by a slower mode in the 10 ps range.
Collapse
Affiliation(s)
- C Ketterlé
- Laboratoire de Physicochimie et Pharmacologie des Macromolécules Biologiques, CNRS URA 147, Villejuif, France
| | | | | | | | | | | | | | | |
Collapse
|
14
|
Perrée-Fauvet M, Gresh N. Molecular modelling and chemical synthesis of a bisarginyl derivative of a tricationic porphyrin designed to target the major groove of DNA. Tetrahedron Lett 1995. [DOI: 10.1016/0040-4039(95)00705-h] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
15
|
Huang L, Quada JC, Lown JW. Design, synthesis and sequence selective DNA cleavage of functional models of bleomycin--II. 1,2-trans-disubstituted cyclopropane units as novel linkers. Bioorg Med Chem 1995; 3:647-57. [PMID: 7582943 DOI: 10.1016/0968-0896(95)00058-o] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The design and syntheses of functional models for bleomycin in which AMPHIS, a simplified model of the metal-chelating subunit of bleomycin is connected to distamycin analogs with a series of linkers, are described. Kinetic studies and DNA cleavage assay show that 1,2-trans-disubstituted cyclopropane units are the best linkers within this series. Study of selective DNA cleavage on high resolution polyacrylamide sequencing gels indicates that the linker modified hybrids generally cleave selectively at the 5' end of poly T sites and at the 3' end of poly A sites. Cleavage activity is enhanced for most of the compounds related to those with shorter linkers, previously reported, (Huang, L.; Quada, Jr J. C.; Lown, J. W. Bioconjugate Chem. 1995, 6, 21, Ref. 1) probably as a result of the linker allowing the active complex to approach the target deoxyribose more closely and efficiently. Certain of the compounds, ones containing a (S)-methyl in the linker and the (S,S)-cyclopropyl linker, exhibit unique cleavage sites, indicating that these linkers allow the hybrids to locate novel, individual DNA binding sites.
Collapse
Affiliation(s)
- L Huang
- Department of Chemistry, University of Alberta, Edmonton, Canada
| | | | | |
Collapse
|