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Abstract
In a recent study, we described the enhanced double-strand cleavage of hairpin DNAs by Fe·bleomycin (Fe·BLM) that accompanies increasingly strong binding of this antitumor agent and suggested that this effect may be relevant to the mechanism by which BLM mediates its antitumor effects. Because the DNA in tumor cells is known to be hypomethylated on cytidine relative to that in normal cells, it seemed of interest to study the possible effects of methylation status on BLM-induced double-strand DNA cleavage. Three hairpin DNAs found to bind strongly to bleomycin, and their methylated counterparts, were used to study the effect of methylation on bleomycin-induced DNA degradation. Under conditions of limited DNA cleavage, there was a significant overall decrease in the cleavage of methylated hairpin DNAs. Cytidine methylation was found to result in decreased BLM-induced cleavage at the site of methylation and to result in enhanced cleavage at adjacent nonmethylated sites. For two of the three hairpin DNAs studied, methylation was accompanied by a dramatic decrease in the binding affinity for Fe·BLM, suggesting the likelihood of diminished double-strand cleavage. The source of the persistent binding of BLM by the third hairpin DNA was identified. Also identified was the probable molecular mechanism for diminished binding and cleavage of the methylated DNAs by BLM. The possible implications of these findings for the antitumor selectivity of bleomycin are discussed.
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52
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Alam MP, Khdour OM, Arce PM, Chen Y, Roy B, Johnson WG, Dey S, Hecht SM. Cytoprotective pyridinol antioxidants as potential therapeutic agents for neurodegenerative and mitochondrial diseases. Bioorg Med Chem 2014; 22:4935-47. [DOI: 10.1016/j.bmc.2014.06.040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 06/13/2014] [Accepted: 06/19/2014] [Indexed: 12/30/2022]
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53
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Bhattacharya C, Yu Z, Rishel MJ, Hecht SM. The carbamoylmannose moiety of bleomycin mediates selective tumor cell targeting. Biochemistry 2014; 53:3264-6. [PMID: 24811347 PMCID: PMC4038340 DOI: 10.1021/bi500482q] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Recently,
we reported that both bleomycin (BLM) and its disaccharide,
conjugated to the cyanine dye Cy5**, bound selectively to cancer cells.
Thus, the disaccharide moiety alone recapitulates the tumor cell targeting
properties of BLM. Here, we demonstrate that the conjugate of the
BLM carbamoylmannose moiety with Cy5** showed tumor cell selective
binding and also enhanced cellular uptake in most cancer cell lines.
The carbamoyl functionality was required for tumor cell targeting.
A dye conjugate prepared from a trivalent cluster of carbamoylmannose
exhibited levels of tumor cell binding and internalization significantly
greater than those of the simple carbamoylmannose–dye conjugate,
consistent with a possible multivalent receptor.
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54
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Roy B, Hecht SM. Hairpin DNA sequences bound strongly by bleomycin exhibit enhanced double-strand cleavage. J Am Chem Soc 2014; 136:4382-93. [PMID: 24548300 PMCID: PMC3988684 DOI: 10.1021/ja500414a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Clinically
used bleomycin A5 has been employed in a
study of double-strand cleavage of a library of 10 hairpin DNAs originally
selected on the basis of their strong binding to bleomycin. Each of
the DNAs underwent double-strand cleavage at more than one site, and
all of the cleavage sites were within, or in close proximity to, an
eight-base-pair region of the duplex that had been randomized to create
the original library. A total of 31 double-strand cleavage sites were
identified on the 10 DNAs, and 14 of these sites were found to represent
coupled cleavage sites, that is, events in which one of the two strands
was always cleaved first, followed by the associated site on the opposite
strand. Most of these coupled sites underwent cleavage by a mechanism
described previously by the Povirk laboratory and afforded cleavage
patterns entirely analogous to those reported. However, at least one
coupled cleavage event was noted that did not conform to the pattern
of those described previously. More surprisingly, 17 double-strand
cleavages were found not to result from coupled double-strand cleavage,
and we posit that these cleavages resulted from a new mechanism not
previously described. Enhanced double-strand cleavages at these sites
appear to be a consequence of the dynamic nature of the interaction
of Fe·BLM A5 with the strongly bound hairpin DNAs.
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55
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Kendrick S, Kang HJ, Alam MP, Madathil MM, Agrawal P, Gokhale V, Yang D, Hecht SM, Hurley LH. The dynamic character of the BCL2 promoter i-motif provides a mechanism for modulation of gene expression by compounds that bind selectively to the alternative DNA hairpin structure. J Am Chem Soc 2014; 136:4161-71. [PMID: 24559410 PMCID: PMC3985915 DOI: 10.1021/ja410934b] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
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It
is generally accepted that DNA predominantly exists in duplex
form in cells. However, under torsional stress imposed by active transcription,
DNA can assume nonduplex structures. The BCL2 promoter
region forms two different secondary DNA structures on opposite strands
called the G-quadruplex and the i-motif. The i-motif is a highly dynamic
structure that exists in equilibrium with a flexible hairpin species.
Here we identify a pregnanol derivative and a class of piperidine
derivatives that differentially modulate gene expression by stabilizing
either the i-motif or the flexible hairpin species. Stabilization
of the i-motif structure results in significant upregulation of the BCL2 gene and associated protein expression; in contrast,
stabilization of the flexible hairpin species lowers BCL2 levels. The BCL2 levels reduced by the hairpin-binding
compound led to chemosensitization to etoposide in both in vitro and
in vivo models. Furthermore, we show antagonism between the two classes
of compounds in solution and in cells. For the first time, our results
demonstrate the principle of small molecule targeting of i-motif structures
in vitro and in vivo to modulate gene expression.
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56
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Kang HJ, Kendrick S, Hecht SM, Hurley LH. The transcriptional complex between the BCL2 i-motif and hnRNP LL is a molecular switch for control of gene expression that can be modulated by small molecules. J Am Chem Soc 2014; 136:4172-85. [PMID: 24559432 PMCID: PMC3985447 DOI: 10.1021/ja4109352] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
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In a companion paper (DOI: 10.021/ja410934b) we demonstrate that the C-rich
strand of the cis-regulatory element in the BCL2 promoter element
is highly dynamic in nature and can form either an i-motif or a flexible
hairpin. Under physiological conditions these two secondary DNA structures
are found in an equilibrium mixture, which can be shifted by the addition
of small molecules that trap out either the i-motif (IMC-48) or the
flexible hairpin (IMC-76). In cellular experiments we demonstrate
that the addition of these molecules has opposite effects on BCL2 gene expression and furthermore that these effects
are antagonistic. In this contribution we have identified a transcriptional
factor that recognizes and binds to the BCL2 i-motif
to activate transcription. The molecular basis for the recognition
of the i-motif by hnRNP LL is determined, and we demonstrate that
the protein unfolds the i-motif structure to form a stable single-stranded
complex. In subsequent experiments we show that IMC-48 and IMC-76
have opposite, antagonistic effects on the formation of the hnRNP
LL–i-motif complex as well as on the transcription factor occupancy
at the BCL2 promoter. For the first time we propose
that the i-motif acts as a molecular switch that controls gene expression
and that small molecules that target the dynamic equilibrium of the
i-motif and the flexible hairpin can differentially modulate gene
expression.
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57
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Talukder P, Chen S, Arce PM, Hecht SM. Efficient asymmetric synthesis of tryptophan analogues having useful photophysical properties. Org Lett 2014; 16:556-9. [PMID: 24392870 DOI: 10.1021/ol403429e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Two new fluorescent probes of protein structure and dynamics have been prepared by concise asymmetric syntheses using the Schöllkopf chiral auxiliary. The site-specific incorporation of one probe into dihydrofolate reductase is reported. The utility of these tryptophan derivatives lies in their absorption and emission maxima which differ from those of tryptophan, as well as in their large Stokes shifts and high molar absorptivities.
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58
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Chen S, Fahmi NE, Bhattacharya C, Wang L, Jin Y, Benkovic SJ, Hecht SM. Fluorescent biphenyl derivatives of phenylalanine suitable for protein modification. Biochemistry 2013; 52:8580-9. [PMID: 24152169 PMCID: PMC3875372 DOI: 10.1021/bi401275v] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In a recent study, we demonstrated that structurally compact fluorophores incorporated into the side chains of amino acids could be introduced into dihydrofolate reductase from Escherichia coli (ecDHFR) with minimal disruption of protein structure or function, even when the site of incorporation was within a folded region of the protein. The modified proteins could be employed for FRET measurements, providing sensitive monitors of changes in protein conformation. The very favorable results achieved in that study encouraged us to prepare additional fluorescent amino acids of potential utility for studying protein dynamics. Presently, we describe the synthesis and photophysical characterization of four positional isomers of biphenyl-phenylalanine, all of which were found to exhibit potentially useful fluorescent properties. All four phenylalanine derivatives were used to activate suppressor tRNA transcripts and incorporated into multiple positions of ecDHFR. All phenylalanine derivatives were incorporated with good efficiency into position 16 of ecDHFR and afforded modified proteins that consumed NADPH at rates up to about twice the rate measured for wild type. This phenomenon has been noted on a number of occasions previously and shown to be due to an increase in the off-rate of tetrahydrofolate from the enzyme, altering a step that is normally rate limiting. When introduced into sterically accessible position 49, the four phenylalanine derivatives afforded DHFRs having catalytic function comparable to wild type. The four phenylalanine derivatives were also introduced into position 115 of ecDHFR, which is known to be a folded region of the protein less tolerant of structural alteration. As anticipated, significant differences were noted in the catalytic efficiencies of the derived proteins. The ability of two of the sizable biphenyl-phenylalanine derivatives to be accommodated at position 115 with minimal perturbation of DHFR function is attributed to rotational flexibility about the biphenyl bonds.
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59
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Madathil MM, Khdour OM, Jaruvangsanti J, Hecht SM. A structurally simplified analogue of geldanamycin exhibits neuroprotective activity. ACS Med Chem Lett 2013; 4:953-7. [PMID: 24900591 DOI: 10.1021/ml400207m] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 07/25/2013] [Indexed: 11/30/2022] Open
Abstract
The syntheses of a structurally simplified geldanamycin analogue 2 and two related compounds are described. Compound 2 conferred cytoprotection and quenched ROS and lipid peroxidation in a dose-dependent manner in Friedreich's ataxia (FRDA) lymphocytes at low micromolar concentrations. It also prevented ROS-induced damage of cellular lipid membranes and maintained the mitochondrial membrane potential of FRDA lymphocytes. In addition, 2 did not inhibit Hsp90 when tested at micromolar concentrations, exhibited no cytotoxicity, and afforded neuroprotection to differentiated SH-SY5Y cells under conditions of Aβ-induced cell toxicity.
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60
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Segerman ZJ, Roy B, Hecht SM. Correction to Characterization of Bleomycin-Mediated Cleavage of a Hairpin DNA Library. Biochemistry 2013. [DOI: 10.1021/bi401115d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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61
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Chen S, Fahmi NE, Wang L, Bhattacharya C, Benkovic SJ, Hecht SM. Detection of dihydrofolate reductase conformational change by FRET using two fluorescent amino acids. J Am Chem Soc 2013; 135:12924-7. [PMID: 23941571 PMCID: PMC3785542 DOI: 10.1021/ja403007r] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Two fluorescent amino acids, including the novel fluorescent species 4-biphenyl-l-phenylalanine (1), have been incorporated at positions 17 and 115 of dihydrofolate reductase (DHFR) to enable a study of conformational changes associated with inhibitor binding. Unlike most studies involving fluorescently labeled proteins, the fluorophores were incorporated into the amino acid side chains, and both probes [1 and L-(7-hydroxycoumarin-4-yl)ethylglycine (2)] were smaller than fluorophores typically used for such studies. The DHFR positions were chosen as potentially useful for Förster resonance energy transfer (FRET) measurements on the basis of their estimated separation (17-18 Å) and the expected change in distance along the reaction coordinate. Also of interest was the steric accessibility of the two sites: Glu17 is on the surface of DHFR, while Ile115 is within a folded region of the protein. Modified DHFR I (1 at position 17; 2 at position 115) and DHFR II (2 at position 17; 1 at position 115) were both catalytically competent. However, DHFR II containing the potentially rotatable biphenylphenylalanine moiety at sterically encumbered position 115 was significantly more active than DHFR I. Irradiation of the modified DHFRs at 280 nm effected excitation of 1, energy transfer to 2, and emission by 2 at 450 nm. However, the energy transfer was substantially more efficient in DHFR II. The effect of inhibitor binding was also measured. Trimethoprim mediated concentration-dependent diminution of the emission observed at 450 nm for DHFR II but not for DHFR I. These findings demonstrate that amino acids containing small fluorophores can be introduced into DHFR with minimal disruption of function and in a fashion that enables sensitive monitoring of changes in DHFR conformation.
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62
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Khdour OM, Arce PM, Roy B, Hecht SM. An optimized pyrimidinol multifunctional radical quencher. ACS Med Chem Lett 2013; 4:724-9. [PMID: 24900738 DOI: 10.1021/ml400130z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 05/28/2013] [Indexed: 01/23/2023] Open
Abstract
A series of aza analogues (4-9) of the experimental neuroprotective drug idebenone (1) have been prepared and evaluated for their ability to attenuate oxidative stress induced by glutathione depletion and to compensate for the decrease in oxidative phosphorylation efficiency in cultured Friedreich's ataxia (FRDA) fibroblasts and lymphocytes and also coenzyme Q10-deficient lymphocytes. Modification of the redox core of the previously reported 3 improved its antioxidant and cytoprotective properties. Compounds 4-9, having the same redox core, exhibited a range of antioxidant activities, reflecting side chain differences. Compounds having side chains extending 14-16 atoms from the pyrimidinol ring (6, 7, and 9) were potent antioxidants. They were superior to idebenone and more active than 3, 4, 5, and 8. Optimized analogue 7 and its acetate (7a) are of interest in defining potential therapeutic agents capable of blocking oxidative stress, maintaining mitochondrial membrane integrity, and augmenting ATP levels. Compounds with such properties may find utility in treating mitochondrial and neurodegenerative diseases such as FRDA and Alzheimer's disease.
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63
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Segerman ZJ, Roy B, Hecht SM. Characterization of bleomycin-mediated cleavage of a hairpin DNA library. Biochemistry 2013; 52:5315-27. [PMID: 23834496 DOI: 10.1021/bi400779r] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A study of BLM A5 was conducted using a previously isolated library of hairpin DNAs found to bind strongly to metal-free BLM. The ability of Fe(II)·BLM to affect cleavage on both the 3' and 5' arms of the hairpin DNAs was characterized. The strongly bound DNAs were found to be efficient substrates for Fe·BLM A5-mediated hairpin DNA cleavage. Surprisingly, the most prevalent site of BLM-mediated cleavage was found to be the 5'-AT-3' dinucleotide sequence. This dinucleotide sequence and other sequences generally not cleaved well by BLM when examined using arbitrarily chosen DNA substrates were apparent when examining the library of 10 hairpin DNAs. In total, 132 sites of DNA cleavage were produced by exposure of the hairpin DNA library to Fe·BLM A5. The existence of multiple sites of cleavage on both the 3' and 5' arms of the hairpin DNAs suggested that some of these might be double-strand cleavage events. Accordingly, an assay was developed to test the propensity of the hairpin DNAs to undergo double-strand DNA damage. One hairpin DNA was characterized using this method and gave results consistent with earlier reports of double-strand DNA cleavage but with a sequence selectivity that was different from those reported previously.
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64
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Fash DM, Khdour OM, Sahdeo SJ, Goldschmidt R, Jaruvangsanti J, Dey S, Arce PM, Collin VC, Cortopassi GA, Hecht SM. Effects of alkyl side chain modification of coenzyme Q 10 on mitochondrial respiratory chain function and cytoprotection. Bioorg Med Chem 2013; 21:2346-2354. [DOI: 10.1016/j.bmc.2013.01.075] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 01/22/2013] [Accepted: 01/31/2013] [Indexed: 01/06/2023]
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65
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Yu Z, Schmaltz RM, Bozeman TC, Paul R, Rishel MJ, Tsosie KS, Hecht SM. Selective tumor cell targeting by the disaccharide moiety of bleomycin. J Am Chem Soc 2013; 135:2883-6. [PMID: 23379863 DOI: 10.1021/ja311090e] [Citation(s) in RCA: 224] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In a recent study, the well-documented tumor targeting properties of the antitumor agent bleomycin (BLM) were studied in cell culture using microbubbles that had been derivatized with multiple copies of BLM. It was shown that BLM selectively targeted MCF-7 human breast carcinoma cells but not the "normal" breast cell line MCF-10A. Furthermore, it was found that the BLM analogue deglycobleomycin, which lacks the disaccharide moiety of BLM, did not target either cell line, indicating that the BLM disaccharide moiety is necessary for tumor selectivity. Not resolved in the earlier study were the issues of whether the BLM disaccharide moiety alone is sufficient for tumor cell targeting and the possible cellular uptake of the disaccharide. In the present study, we conjugated BLM, deglycoBLM, and BLM disaccharide to the cyanine dye Cy5**. It was found that the BLM and BLM disaccharide conjugates, but not the deglycoBLM conjugate, bound selectively to MCF-7 cells and were internalized. The same was also true for the prostate cancer cell line DU-145 (but not for normal PZ-HPV-7 prostate cells) and for the pancreatic cancer cell line BxPC-3 (but not for normal SVR A221a pancreas cells). The targeting efficiency of the disaccharide was only slightly less than that of BLM in MCF-7 and DU-145 cells and comparable to that of BLM in BxPC-3 cells. These results establish that the BLM disaccharide is both necessary and sufficient for tumor cell targeting, a finding with obvious implications for the design of novel tumor imaging and therapeutic agents.
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66
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Maini R, Nguyen DT, Chen S, Dedkova LM, Chowdhury SR, Alcala-Torano R, Hecht SM. Incorporation of β-amino acids into dihydrofolate reductase by ribosomes having modifications in the peptidyltransferase center. Bioorg Med Chem 2013; 21:1088-96. [PMID: 23375097 DOI: 10.1016/j.bmc.2013.01.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 12/27/2012] [Accepted: 01/02/2013] [Indexed: 10/27/2022]
Abstract
Ribosomes containing modifications in three regions of 23S rRNA, all of which are in proximity to the ribosomal peptidyltransferase center (PTC), were utilized previously as a source of S-30 preparations for in vitro protein biosynthesis experiments. When utilized in the presence of mRNAs containing UAG codons at predetermined positions+β-alanyl-tRNA(CUA), the modified ribosomes produced enhanced levels of full length proteins via UAG codon suppression. In the present study, these earlier results have been extended by the use of substituted β-amino acids, and direct evidence for β-amino acid incorporation is provided. Presently, five of the clones having modified ribosomes are used in experiments employing four substituted β-amino acids, including α-methyl-β-alanine, β,β-dimethyl-β-alanine, β-phenylalanine, and β-(p-bromophenyl)alanine. The β-amino acids were incorporated into three different positions (10, 18 and 49) of Escherichia coli dihydrofolate reductase (DHFR) and their efficiencies of suppression of the UAG codons were compared with those of β-alanine and representative α-l-amino acids. The isolated proteins containing the modified β-amino acids were subjected to proteolytic digestion, and the derived fragments were characterized by mass spectrometry, establishing that the β-amino acids had been incorporated into DHFR, and that they were present exclusively in the anticipated peptide fragments. DHFR contains glutamic acid in position 17, and it has been shown previously that Glu-C endoproteinase can hydrolyze DHFR between amino acids residues 17 and 18. The incorporation of β,β-dimethyl-β-alanine into position 18 of DHFR prevented this cleavage, providing further evidence for the position of incorporation of the β-amino acid.
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67
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Goldschmidt R, Arce PM, Khdour OM, Collin VC, Dey S, Jaruvangsanti J, Fash DM, Hecht SM. Effects of cytoprotective antioxidants on lymphocytes from representative mitochondrial neurodegenerative diseases. Bioorg Med Chem 2012; 21:969-78. [PMID: 23313093 DOI: 10.1016/j.bmc.2012.11.051] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 11/27/2012] [Accepted: 11/30/2012] [Indexed: 01/03/2023]
Abstract
Two new aza analogues of the neuroprotective agent idebenone have been synthesized and characterized. Their antioxidant activity, and ability to augment ATP levels have been evaluated in several different cell lines having suboptimal mitochondrial function. Both compounds were found to be good ROS scavengers, and to protect the cells from oxidative stress induced by glutathione depletion. The compounds were more effective than idebenone in neurodegenerative disease cells. These novel pyrimidinol derivatives were also shown to augment ATP levels in coenzyme Q(10)-deficient human lymphocytes. The more lipophilic side chains attached to the pyrimidinol redox core in these compounds resulted in less inhibition of the electron transport chain and improved antioxidant activity.
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68
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Chen S, Wang L, Fahmi NE, Benkovic SJ, Hecht SM. Two pyrenylalanines in dihydrofolate reductase form an excimer enabling the study of protein dynamics. J Am Chem Soc 2012; 134:18883-5. [PMID: 23116258 DOI: 10.1021/ja307179q] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Because of the lack of sensitivity to small changes in distance by available FRET pairs (a constraint imposed by the dimensions of the enzyme), a DHFR containing two pyrene moieties was prepared to enable the observation of excimer formation. Pyren-1-ylalanine was introduced into DHFR positions 16 and 49 using an in vitro expression system in the presence of pyren-1-ylalanyl-tRNA(CUA). Excimer formation (λ(ex) 342 nm; λ(em) 481 nm) was observed in the modified DHFR, which retained its catalytic competence and was studied under multiple and single turnover conditions. The excimer appeared to follow a protein conformational change after the H transfer involving the relative position and orientation of the pyrene moieties and is likely associated with product dissociation.
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69
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Bozeman TC, Nanjunda R, Tang C, Liu Y, Segerman ZJ, Zaleski PA, Wilson WD, Hecht SM. Dynamics of bleomycin interaction with a strongly bound hairpin DNA substrate, and implications for cleavage of the bound DNA. J Am Chem Soc 2012; 134:17842-5. [PMID: 23072568 PMCID: PMC3840713 DOI: 10.1021/ja306233e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Recent studies involving DNAs bound strongly by bleomycins have documented that such DNAs are degraded by the antitumor antibiotic with characteristics different from those observed when studying the cleavage of randomly chosen DNAs in the presence of excess Fe·BLM. In the present study, surface plasmon resonance has been used to characterize the dynamics of BLM B(2) binding to a strongly bound hairpin DNA, to define the effects of Fe(3+), salt, and temperature on BLM-DNA interaction. One strong primary DNA binding site, and at least one much weaker site, were documented. In contrast, more than one strong cleavage site was found, an observation also made for two other hairpin DNAs. Evidence is presented for BLM equilibration between the stronger and weaker binding sites in a way that renders BLM unavailable to other, less strongly bound DNAs. Thus, enhanced binding to a given site does not necessarily result in increased DNA degradation at that site; i.e., for strongly bound DNAs, the facility of DNA cleavage must involve other parameters in addition to the intrinsic rate of C-4' H atom abstraction from DNA sugars.
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70
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Cai X, Khdour OM, Jaruvangsanti J, Hecht SM. Simplified bicyclic pyridinol analogues protect mitochondrial function. Bioorg Med Chem 2012; 20:3584-95. [DOI: 10.1016/j.bmc.2012.03.075] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2012] [Revised: 03/27/2012] [Accepted: 03/31/2012] [Indexed: 12/12/2022]
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71
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Zaleski PA, Maini R, Leiris SJ, Elban MA, Hecht SM. Synthesis and biological activities of topopyrones. JOURNAL OF NATURAL PRODUCTS 2012; 75:577-585. [PMID: 22462811 DOI: 10.1021/np200777z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Structure-activity studies were employed to investigate the stabilization of DNA-topoisomerases I and II covalent binary complexes by topopyrone analogues. The synthesis of five new topopyrone derivatives and study of their ability to stabilize DNA-topoisomerase I and DNA-topoisomerase II covalent binary complexes are described. The biochemical assays suggest that the orientation of the fused 1,4-pyrone ring and halogen substituents contribute importantly to the overall potency of the topopyrones as topoisomerase poisons.
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72
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Chen S, Fahmi NE, Nangreave RC, Mehellou Y, Hecht SM. Synthesis of pdCpAs and transfer RNAs activated with thiothreonine and derivatives. Bioorg Med Chem 2012; 20:2679-89. [PMID: 22405920 PMCID: PMC3575115 DOI: 10.1016/j.bmc.2012.02.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Revised: 02/05/2012] [Accepted: 02/08/2012] [Indexed: 11/29/2022]
Abstract
N,S-diprotected L-thiothreonine and L-allo-thiothreonine derivatives were synthesized using a novel chemical strategy, and used for esterification of the dinucleotide pdCpA. The aminoacylated dinucleotides were then employed for the preparation of activated suppressor tRNA(CUA) transcripts. Thiothreonine and allo-thiothreonine were incorporated into a predetermined position of a catalytically competent dihydrofolate reductase (DHFR) analogue lacking cysteine, and the elaborated proteins were derivatized site-specifically at the thiothreonine residue with a fluorophore.
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73
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Mrozowski RM, Vemula R, Wu B, Zhang Q, Schroeder BR, Hilinski MK, Clark DE, Hecht SM, O’Doherty GA, Lannigan DA. Improving the affinity of SL0101 for RSK using structure-based design. ACS Med Chem Lett 2012; 4:175-179. [PMID: 23519677 DOI: 10.1021/ml300298v] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Enhanced activity of the Ser/Thr protein kinase, RSK, is associated with transformation and metastasis, which suggests that RSK is an attractive drug target. The natural product, SL0101 (kaempferol 3-O-(3″,4″-di-O-acetyl-α-L-rhamnopyranoside), has been shown to be a RSK selective inhibitor. However, the Ki for SL0101 is 1 μM with a half-life of less than 30 min in vivo. To identify analogues with improved efficacy we designed a set of analogues based on the crystallographic model of SL0101 in complex with the RSK2 N-terminal kinase domain. We identified an analogue with a 5″-n-propyl group on the rhamnose that has > 40-fold improved affinity for RSK relative to SL0101 in an in vitro kinase assay. This analogue preferentially inhibited the proliferation of the human breast cancer line, MCF-7, versus the normal untransformed breast line, MCF-10A, which is consistent with results using SL0101. However, the efficacy of the 5″-n-propyl analogue to inhibit MCF-7 proliferation was only two-fold better than for SL0101, which we hypothesize is due to limited membrane permeability. The improved affinity of the 5″-n-propyl analogue for RSK will aid in the design of future compounds for in vivo use.
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Dedkova LM, Fahmi NE, Paul R, del Rosario M, Zhang L, Chen S, Feder G, Hecht SM. β-Puromycin Selection of Modified Ribosomes for in Vitro Incorporation of β-Amino Acids. Biochemistry 2011; 51:401-15. [DOI: 10.1021/bi2016124] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Rosso H, De Paolis M, Collin VC, Dey S, Hecht SM, Prandi C, Richard V, Maddaluno J. One-Pot Regio- and Stereoselective Synthesis of α′-Methoxy-γ-pyrones: Biological Evaluation as Mitochondrial Respiratory Complex Inhibitors. J Org Chem 2011; 76:9429-37. [DOI: 10.1021/jo201683u] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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