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13C NMR spectrometry) measured on the synthetic sample were virtually indistinguishable from those reported for the natural product.
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13C NMR spectrometry) measured on the synthetic sample were virtually indistinguishable from those reported for the natural product.
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33947253712
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Since there is no X-ray structure of human HDAC1 available now, we have used the monomer form of the HDLP X-ray structure as receptor model. A sequence alignment shows a 35.2% sequence identity of HDLP and human HDAC1. The residues around the HDLP zinc-binding site are completely conservedjn human HDAC1 and all of the hydrophobic residues that make up the 11 Å channel in HDLP are identical in HDAC1. Most of the residues making up the 14 Å internal cavity are either identical or conservatively substituted in HDAC1 and, as can be expected from the high degree of sequence similarity, HDAC has the same structural features of HDLP described above.
-
Since there is no X-ray structure of human HDAC1 available now, we have used the monomer form of the HDLP X-ray structure as receptor model. A sequence alignment shows a 35.2% sequence identity of HDLP and human HDAC1. The residues around the HDLP zinc-binding site are completely conservedjn human HDAC1 and all of the hydrophobic residues that make up the 11 Å channel in HDLP are identical in HDAC1. Most of the residues making up the 14 Å internal cavity are either identical or conservatively substituted in HDAC1 and, as can be expected from the high degree of sequence similarity, HDAC has the same structural features of HDLP described above.
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36
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33947192740
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Both the β-amino acid stereogenic centers were inverted to retain the same relative configuration of the 3-amino-2-methyl-5-nonendioic acid
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Both the β-amino acid stereogenic centers were inverted to retain the same relative configuration of the 3-amino-2-methyl-5-nonendioic acid.
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39
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In a recently reported SAR study on cyclic hydroxamic acid containing cyclopeptides (designed as hybrid of trichostatin and trapoxin, see: Komatsu, Y, Tomizaki, K.-Y, Tsukamoto, M, Kato, T, Nishino, N, Sato, S, Yamori, T, Tsuruo, T, Furumai, R, Yoshida, M, Horinouchi, S, Hayashi, H. Cancer Res. 2001, 61, 4459-4466, the HDAC inhibitory potency of different amino acid D/L combinations was directly related to the hydrophobicity of the molecules (higher hydrophobicity meant higher membrane permeability, This assumption contrasted with the weak activity (2 orders of magnitude lower) observed for one of the synthesized derivatives showing HPLC retention time comparable with those of the cognate compounds, We believe that biological activity should be, more appropriately, attributable to the tetrapeptide- receptor interaction modes. Our studies clarify some aspects of the binding at molecular level
-
In a recently reported SAR study on cyclic hydroxamic acid containing cyclopeptides (designed as hybrid of trichostatin and trapoxin, see: Komatsu, Y.; Tomizaki, K.-Y.; Tsukamoto, M.; Kato, T.; Nishino, N.; Sato, S.; Yamori, T.; Tsuruo, T.; Furumai, R.; Yoshida, M.; Horinouchi, S.; Hayashi, H. Cancer Res. 2001, 61, 4459-4466), the HDAC inhibitory potency of different amino acid D/L combinations was directly related to the hydrophobicity of the molecules (higher hydrophobicity meant higher membrane permeability). This assumption contrasted with the weak activity (2 orders of magnitude lower) observed for one of the synthesized derivatives (showing HPLC retention time comparable with those of the cognate compounds). We believe that biological activity should be, more appropriately, attributable to the tetrapeptide- receptor interaction modes. Our studies clarify some aspects of the binding at molecular level.
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For the action of enantiomers of bioactive compounds on chiroselective target, see, for example: Bednarek, M. A.; Silva, M. V.; Arison, B.; MacNeil, T.; Kalyani, R. N.; Huang, R.-R. C.; Weinberg, D. H. Peptides 1999, 20, 401-409 (in which is described a significant drop of potency of the enantio-analog of the cyclic peptide MT-II).
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For the action of enantiomers of bioactive compounds on chiroselective target, see, for example: Bednarek, M. A.; Silva, M. V.; Arison, B.; MacNeil, T.; Kalyani, R. N.; Huang, R.-R. C.; Weinberg, D. H. Peptides 1999, 20, 401-409 (in which is described a significant drop of potency of the enantio-analog of the cyclic peptide MT-II).
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H131, H132, and Y297 are not shown in Figures 5-7 because they are too deep in the channel. They are reported (in the 3D models of the interaction between 5 and 8 with the HDLP binding site) in Figure S3 and S4 of the Supporting Information
-
H131, H132, and Y297 are not shown in Figures 5-7 because they are too deep in the channel. They are reported (in the 3D models of the interaction between 5 and 8 with the HDLP binding site) in Figure S3 and S4 of the Supporting Information.
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56
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For non-cyclopeptide compounds showing selective class I HDAC inhibitory activity, see
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For non-cyclopeptide compounds showing selective class I HDAC inhibitory activity, see: Jones, P.; Altamura, S.; Chakravarty, P. K.; Cecchetti, O.; De Francesco, R.; Gallinari, P.; Ingenito, R.; Meinke, P. T.; Petrocchi, A.; Rowley, M.; Scarpelli, R.; Serafini, S.; Steinkühler, C. Bioorg. Med. Chem. Lett. 2006, 16, 5948-5952.
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57
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0037142335
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50: 200 ± 100 nM) can be found in Woo, S. H.; Frechette, S.; Khalil, E. A.; Bouchain, G.; Vaisburg, A.; Bernstein, N.; Moradei, O.; Leit, S.; Allan, M.; Fournel, M.; Trachy-Bourget, M.-C.; Li, Z.; Besterman, J. M.; Delorme, D. J. Med. Chem. 2002, 45, 2877-2885.
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50: 200 ± 100 nM) can be found in Woo, S. H.; Frechette, S.; Khalil, E. A.; Bouchain, G.; Vaisburg, A.; Bernstein, N.; Moradei, O.; Leit, S.; Allan, M.; Fournel, M.; Trachy-Bourget, M.-C.; Li, Z.; Besterman, J. M.; Delorme, D. J. Med. Chem. 2002, 45, 2877-2885.
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