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ACS Medicinal Chemistry Letters Nov 2010The structural and thermodynamic basis for the strength and selectivity of the interactions of minor groove binders (MGBs) with DNA is not fully understood. In 2003, we...
The structural and thermodynamic basis for the strength and selectivity of the interactions of minor groove binders (MGBs) with DNA is not fully understood. In 2003, we reported the first example of a thiazole-containing MGB that bound in a phase-shifted pattern that spanned six base pairs rather than the usual four (for tricyclic distamycin-like compounds). Since then, using DNA footprinting, NMR spectroscopy, isothermal titration calorimetry, and molecular dynamics, we have established that the flanking bases around the central four being read by the ligand have subtle effects on recognition. We have investigated the effect of these flanking sequences on binding and the reasons for the differences and established a computational method to rank ligand affinity against varying DNA sequences.
PubMed: 24900221
DOI: 10.1021/ml100047n -
Journal of Nucleic Acids May 2010Guanine-rich nucleic acid sequences can adopt G-quadruplex structures stabilized by layers of four Hoogsteen-paired guanine residues. Quadruplex-prone sequences are...
Guanine-rich nucleic acid sequences can adopt G-quadruplex structures stabilized by layers of four Hoogsteen-paired guanine residues. Quadruplex-prone sequences are found in many regions of human genome and in the telomeres of all eukaryotic organisms. Since small molecules that target G-quadruplexes have been found to be effective telomerase inhibitors, the identification of new specific ligands for G-quadruplexes is emerging as a promising approach to develop new anticancer drugs. Distamycin A is known to bind to AT-rich sequences of duplex DNA, but it has recently been shown to interact also with G-quadruplexes. Here, isothermal titration calorimetry (ITC) and NMR techniques have been employed to characterize the interaction between a dicationic derivative of distamycin A (compound 1) and the [d(TGGGGT)](4) quadruplex. Additionally, to compare the binding behaviour of netropsin and compound 1 to the same target, a calometric study of the interaction between netropsin and [d(TGGGGT)](4) has been performed. Experiments show that netropsin and compound 1 are able to bind to [d(TGGGGT)](4) with good affinity and comparable thermodynamic profiles. In both cases the interactions are entropically driven processes with a small favourable enthalpic contribution. Interestingly, the structural modifications of compound 1 decrease the affinity of the ligand toward the duplex, enhancing the selectivity.
PubMed: 20725616
DOI: 10.4061/2010/247137 -
Journal of Nucleic Acids 2010Pyrrolepolyamide-2'-deoxyguanosine hybrids (Hybrid 2 and Hybrid 3) incorporating the 3-aminopropionyl or 3-aminopropyl linker were designed and synthesized on the basis...
Pyrrolepolyamide-2'-deoxyguanosine hybrids (Hybrid 2 and Hybrid 3) incorporating the 3-aminopropionyl or 3-aminopropyl linker were designed and synthesized on the basis of previously reported results of a pyrrolepolyamide-adenosine hybrid (Hybrid 1). Evaluation of the DNA binding sequence selectivity of pyrrolepolyamide-2'-deoxyguanosine hybrids was performed by CD spectral and T(m) analyses. It was shown that Hybrid 3 possessed greater binding specificity than distamycin A, Hybrid 1 and Hybrid 2.
PubMed: 20700414
DOI: 10.4061/2010/235240 -
PloS One May 2010The architectural transcription factor High Mobility Group-A1 (HMGA1) binds to the minor groove of AT-rich DNA and forms transcription factor complexes ("enhanceosomes")...
BACKGROUND
The architectural transcription factor High Mobility Group-A1 (HMGA1) binds to the minor groove of AT-rich DNA and forms transcription factor complexes ("enhanceosomes") that upregulate expression of select genes within the inflammatory cascade during critical illness syndromes such as acute lung injury (ALI). AT-rich regions of DNA surround transcription factor binding sites in genes critical for the inflammatory response. Minor groove binding drugs (MGBs), such as Distamycin A (Dist A), interfere with AT-rich region DNA binding in a sequence and conformation-specific manner, and HMGA1 is one of the few transcription factors whose binding is inhibited by MGBs.
OBJECTIVES
To determine whether MGBs exert beneficial effects during endotoxemia through attenuating tissue inflammation via interfering with HMGA1-DNA binding and modulating expression of adhesion molecules.
METHODOLOGY/PRINCIPAL FINDINGS
Administration of Dist A significantly decreased lung and liver inflammation during murine endotoxemia. In intravital microscopy studies, Dist A attenuated neutrophil-endothelial interactions in vivo following an inflammatory stimulus. Endotoxin induction of P-selectin expression in lung and liver tissue and promoter activity in endothelial cells was significantly reduced by Dist A, while E-selectin induction was not significantly affected. Moreover, Dist A disrupted formation of an inducible complex containing NF-kappaB that binds an AT-rich region of the P-selectin promoter. Transfection studies demonstrated a critical role for HMGA1 in facilitating cytokine and NF-kappaB induction of P-selectin promoter activity, and Dist A inhibited binding of HMGA1 to this AT-rich region of the P-selectin promoter in vivo.
CONCLUSIONS/SIGNIFICANCE
We describe a novel targeted approach in modulating lung and liver inflammation in vivo during murine endotoxemia through decreasing binding of HMGA1 to a distinct AT-rich region of the P-selectin promoter. These studies highlight the ability of MGBs to function as molecular tools for dissecting transcriptional mechanisms in vivo and suggest alternative treatment approaches for critical illness.
Topics: AT Rich Sequence; Animals; Cattle; Cell Communication; Cytokines; Distamycins; Endothelial Cells; Endotoxemia; Endotoxins; HMGA1a Protein; Humans; Inflammation; Liver; Lung; Male; Mice; Mice, Inbred C57BL; NF-kappa B; Neutrophils; P-Selectin; Promoter Regions, Genetic; Protein Binding
PubMed: 20498830
DOI: 10.1371/journal.pone.0010656 -
Yakugaku Zasshi : Journal of the... Mar 2010On the basis of reports that a minor groove binder pyrrolepolyamide can interfere with gene expression by the sequence-specific recognition of DNA, we expected that... (Review)
Review
On the basis of reports that a minor groove binder pyrrolepolyamide can interfere with gene expression by the sequence-specific recognition of DNA, we expected that nucleoside bearing a pyrrolepolyamide would be able to regulate gene expression. Therefore, we designed and synthesized the pyrrolepolyamide-adenosine (Hybrid 1) and -2'-deoxyguanosine hybrids (Hybrid 2 and Hybrid 3) as lead compounds for gene expression control compounds. The pyrrolepolyamide frame of Hybrid 2 and Hybrid 3 combines at the 2-exocyclic amino group of the 2'-deoxyguanosine by a linker and the 2-exocyclic amino group of guanine exists in the minor groove side of the duplex. Hybrid 2 is the 2'-deoxyguanosine-pyrrolepolyamide hybrid using the 3-aminopropionyl linker, while Hybrid 3 uses the 3-aminopropyl linker. An evaluation of the DNA binding sequence selectivity was performed by analysis of T(m) values and CD spectra, using distamycin A as a contrast. Hybrid 3 has provided more excellent sequence-distinguishable ability than other hybrids and Distamycin A. Moreover, on the basis of these results, we synthesized oligonucleotides conjugated to Hybrid 4, which is stable under conditions of DNA oligonucleotide solid phase synthesis, arranged from Hybrid 3. From T(m) values and CD spectral analysis, it was found that oligonucleotides conjugating Hybrid 4 possess high recognition ability and very high binding ability for the DNA that includes the pyrrolepolyamide binding sequence.
Topics: DNA; Drug Design; Gene Expression; Nucleosides; Nylons; Oligonucleotides
PubMed: 20190521
DOI: 10.1248/yakushi.130.355 -
Acta Poloniae Pharmaceutica 2009Six new aromatic oligopeptides were synthesized and evaluated for their activity in the standard cell line of the mammalian tumor MCF-7 as well as in a cell-free system...
Six new aromatic oligopeptides were synthesized and evaluated for their activity in the standard cell line of the mammalian tumor MCF-7 as well as in a cell-free system employing the topoisomerase I/II inhibition assay.
Topics: Antineoplastic Agents; Cell Line, Tumor; Distamycins; Humans; Topoisomerase Inhibitors
PubMed: 20050527
DOI: No ID Found -
Cytometry. Part a : the Journal of the... Nov 2009Drug resistant tumor "side-populations," enriched in cancer stem cells and identified by reduced accumulation of Hoechst 33342 under ABCG2-mediated efflux, may...
Drug resistant tumor "side-populations," enriched in cancer stem cells and identified by reduced accumulation of Hoechst 33342 under ABCG2-mediated efflux, may compromise therapeutic outcome. Side-population cells have predicted resistance to minor groove ligands, including the DNA topoisomerase I poison topotecan. We have used a stable Hoechst 33342-resistant murine L cell system (HoeR415) to study resistance patterns, removing the need for SP isolation before microarray analysis of gene expression and the tracking of cell cycle dynamics and cytotoxicity. The majority of HoeR415 cells displayed a side-population phenotype comparable with that of the side-population resident in the ABCG2 over-expressing A549 lung cancer cell line. Photo-crosslinking showed direct protection against minor groove ligand residence on DNA, driven by ABCG2-mediated efflux and not arising from any binding competition with endogenous polyamines. The covalent minor-groove binding properties of the drug FCE24517 (tallimustine) prevented resistance suggesting a mechanism for overcoming SP-related drug resistance. Hoechst 33342-resistant murine cells showed lower but significant crossresistance to topotecan, again attributable to enhanced ABCG2 expression, enabling cells to evade S-phase arrest. Hoechst 33342/TPT-resistant cells showed limited ancillary gene expression changes that could modify cellular capacity to cope with chronic stress including over-expression of Aldh1a1 and Mgst1, but under-expression of Plk2 and Nnt. There was no evidence to link the putative stem cell marker ALDH1A1 with any augmentation of the TPT resistance phenotype. The study has implications for the patterns of drug resistance arising during tumor repopulation and the basal resistance to minor groove-binding drugs of tumor side-populations.
Topics: ATP Binding Cassette Transporter, Subfamily G, Member 2; ATP-Binding Cassette Transporters; Animals; Benzimidazoles; Cell Line, Tumor; Cell Separation; Cross-Linking Reagents; Distamycins; Enzyme Inhibitors; Flow Cytometry; Fluorescent Dyes; Humans; Ligands; Mice; Nitrogen Mustard Compounds; Polyamines; Topotecan
PubMed: 19802874
DOI: 10.1002/cyto.a.20800 -
Rapid Communications in Mass... Sep 2009The study of the dissociation of the protonated molecular species [M+H](+) and selected fragment ions allowed proposals for the main fragmentation pathways of the title...
The study of the dissociation of the protonated molecular species [M+H](+) and selected fragment ions allowed proposals for the main fragmentation pathways of the title compounds. The main fragments are formed by expelling a molecule of thymine, thymidine (d4T) or isopropyl. The most striking feature of the tandem mass (MS/MS) spectra is the cleavage of C-CO bonds between N-methylpyrrole and carbonyl groups in the presence of the amidine. Electrospray ionization is proven to be a good method for the structural characterization and identification of these kinds of compounds.
Topics: Anti-HIV Agents; Distamycins; Molecular Structure; Organophosphonates; Spectrometry, Mass, Electrospray Ionization; Stavudine; Tandem Mass Spectrometry
PubMed: 19630033
DOI: 10.1002/rcm.4159 -
Nucleic Acids Research Oct 2008We have used metadynamics to investigate the mechanism of noncovalent dissociation from DNA by two representatives of alkylating and noncovalent minor groove (MG)...
We have used metadynamics to investigate the mechanism of noncovalent dissociation from DNA by two representatives of alkylating and noncovalent minor groove (MG) binders. The compounds are anthramycin in its anhydrous form (IMI) and distamycin A (DST), which differ in mode of binding, size, flexibility and net charge. This choice enables to evaluate the influence of such factors on the mechanism of dissociation. Dissociation of IMI requires an activation free energy of approximately 12 kcal/mol and occurs via local widening of the MG and loss of contacts between the drug and one DNA strand, along with the insertion of waters in between. The detachment of DST occurs at a larger free energy cost, approximately 16.5 or approximately 18 kcal/mol depending on the binding mode. These values compare well with that of 16.6 kcal/mol extracted from stopped-flow experiments. In contrast to IMI, an intermediate is found in which the ligand is anchored to the DNA through its amidinium tail. From this conformation, binding and unbinding occur almost at the same rate. Comparison between DST and with kinetic models for the dissociation of Hoechst 33258 from DNA uncovers common characteristics across different classes of noncovalent MG ligands.
Topics: Alkylating Agents; Anthramycin; Computational Biology; Computer Simulation; DNA; Distamycins; Models, Molecular; Nucleic Acid Conformation
PubMed: 18801848
DOI: 10.1093/nar/gkn561 -
Nucleic Acids Symposium Series (2004) 2008The binding properties of a series of known G-quadruplex ligands have been studied by ESI-MS experiments. The tetramolecular (TG(4)T)(4) quadruplex and its analogues I...
The binding properties of a series of known G-quadruplex ligands have been studied by ESI-MS experiments. The tetramolecular (TG(4)T)(4) quadruplex and its analogues I and II blocked, respectively, at the 3' or 5'-end by a tetra-end-linker (TEL) unit were chosen as the ligands targets. The stoichiometries of the obtained complexes as well as the ligand affinity and selectivity to the different quadruplexes were determined to deduce the ligand binding site. The TEL derivatives I and II allowed the probing of the grooves contribution to the binding of ligands to G-quadruplexes, demonstrating that the 3' and 5' quartets are not equivalent binding sites for ligand end-stacking.
Topics: Binding Sites; Distamycins; G-Quadruplexes; Ligands; Models, Molecular; Oligodeoxyribonucleotides; Perylene; Piperidines; Porphyrins; Spectrometry, Mass, Electrospray Ionization
PubMed: 18776305
DOI: 10.1093/nass/nrn084