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47349105387
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note
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Optimal yield of the desired dipeptide alcohols 16-20 was obtained using 1.2 equiv of 15.
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47349094041
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note
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PBD file numbers: 1MDW, 1TL9, 1TLO, 1KXR, 2G8J, 2G8E, 2NQG, 2NQI, 2ARY, 1ZCM.
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31
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0037406469
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47349091937
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MacroModel, version 9.1, Schrödinger, LLC, New York, NY, 2005.
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MacroModel, version 9.1, Schrödinger, LLC, New York, NY, 2005.
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34
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47349130119
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Glide, version 4.0, Schrödinger, LLC, New York, NY, 2005.
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Glide, version 4.0, Schrödinger, LLC, New York, NY, 2005.
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35
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47349117588
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note
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271. Recent X-ray crystal structures, for example, SNJ1715 co-crystallised with r-CAPN1 construct (PDB code 2G8E), confirm the importance of these hydrogen bonds. These hydrogen bonds equate to the hydrogen bonds labelled A, B and C as reported in Table 2.
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36
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47349129543
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note
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The Leu amide in all of the docked compounds 4-13 is trans in all poses. We did not limit the programme to collecting only poses where the amide(s) is trans and for some poses the Val amine is in a cis configuration.
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37
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47349118130
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note
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Of the 84 poses generated for inhibitor 8 docked in the o-CAPN1 and o-CAPN2 models, 72 gave the carbonyl carbon of the aldehyde in proximity to the active site cysteine (<4.5 Å). Of these 72 poses 42 exhibited a β-strand arrangement of the inhibitor and 20 of these had the Val amide in a trans configuration.
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38
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47349118418
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note
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Of the 32 poses generated for inhibitor 9 docked in o-CAPN2 model only six gave the carbonyl carbon of the aldehyde in proximity to the active site cysteine (<4.5 Å). Of these six poses five including the lowest energy poses were in the shunted arrangement with only a single pose with the inhibitor in a more common binding mode as defined by hydrogen bonds A, B and C.
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39
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47349126247
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note
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The 5-formyl-pyrrole 9 possesses two aldehyde groups. Only two of the 72 poses collected in the docking studies with o-CANP1 and o-CANP2 show the pyrrole aldehyde in proximity to the active site cysteine sulfur (<4.5 Å). Thirty-three poses have the Leu aldehyde in proximity to the active site cysteine sulfur. Furthermore, the Leu aldehyde is the more reactive to nucleophilic attack since the nitrogen of the pyrrole aldehyde reduces the electrophilic character of the carbonyl. The dialdehyde 9 reacts with hydroxylamine only at the Leu aldehyde. This supports the Leu aldehyde as being responsible for the potency of 9.
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40
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47349089510
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note
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Glide Emodel combines the energy grid score, the binding affinity predicted by the GlideScore and the internal strain energy of the ligand for the model potential used to direct the conformational-search algorithm.
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41
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47349110743
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note
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Glide Einternal score is the internal strain energy of the ligand.
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42
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47349124951
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Abell, A. D.; Coxon, J. M.; Miyamoto, S.; Jones, M. A.; Neffe, A. T.; Aitken, S. G.; Stuart, B. G.; Nikkel, J. M.; Morton, J. D.; Bickerstaffe, R.; Robertson, L. J.; Lee, H. Y.; Muir. M. S. N.Z. Patent. 2007, 547303; U.S. Patent Appl., 2007, 20070293560.
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Abell, A. D.; Coxon, J. M.; Miyamoto, S.; Jones, M. A.; Neffe, A. T.; Aitken, S. G.; Stuart, B. G.; Nikkel, J. M.; Morton, J. D.; Bickerstaffe, R.; Robertson, L. J.; Lee, H. Y.; Muir. M. S. N.Z. Patent. 2007, 547303; U.S. Patent Appl., 2007, 20070293560.
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