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Exploring the binding of BACE-1 inhibitors using comparative binding energy analysis (COMBINE).
(2012) BMC Struct Biol 12
PubMed: 22925713 | PubMedCentral: PMC3533579 | DOI: 10.1186/1472-6807-12-21
From the comparative analysis of the BACE-1 X-ray structures, it is clear that the 10S loop, a short loop located at the base of the S 3 sp, displays two primary low-energy conformations: an open conf... rmation (e.g., 1W51, 1TQF, 2F3E and 2B8V) and a closed conformation (e.g., 1FKN, 1M4H and 1XS7).
The 46 X-ray structures of BACE-1/inhibitor complexes used in this study are 1W51, 1TQF, 1YM2, 1YM4, 2B8V, 2F3E, 2F3F, 2IQG, 2IRZ, 2IS0, 2OAH, 2OHL, 2OHM, 2OHP, 2OHQ, I2OHR, 2OHS, 2OHT, 2OHU, 2P83, 2PH6, 2B8L, 2QZL, 2ZE1, 2QP8, 2VIE, 2VJ7, 2VJ9, 2VNM, 2VNN, 2WF0, 2WF1, 2ZDZ, 2FDP, 3CIB, 3CIC, 3CID, 3DUY, 3DV1, 2P4J, 3FKT, 2QK5, 1XS7, 1FKN and 1M4H.
Cartoon representation of the active site of the four BACE-1 X-ray structures used for the superposition study (1W51, 1FKN, 2OHL, and 2OHS are in green, cyan, magenta and yellow, respectively) with compound 1 shown as ball and sticks; hydrogen atoms are omitted for reasons of clarity.
Publication Year: 2012
Application of computational methods for the design of BACE-1 inhibitors: validation of in silico modelling.
(2014) Int J Mol Sci 15
PubMed: 24663084 | PubMedCentral: PMC3975444 | DOI: 10.3390/ijms15035128
The worst poses were predicted for peptidic inhibitors from 1FKN, 1M4H and 1TQF crystal structures.
Publication Year: 2014
Amino acid sequence and structural comparison of BACE1 and BACE2 using evolutionary trace method.
(2014) ScientificWorldJournal 2014
PubMed: 25254246 | PubMedCentral: PMC4164807 | DOI: 10.1155/2014/482463
Crystal structures of human BACE1 and BACE2 with the PDB codes 1FKN and 2EWY, respectively, were retrieved from Protein Data Bank (PDB) [ 16 ] and visualized by Python based Molecular Viewer software ... 17 ].
The amino acid numbering of BACE1 and BACE2 sequences is according to their 3D structures obtained from PDB file, 1FKN, and 2EWY, respectively.
Figure 4 Superimposition of chain A of crystal structures of BACE1 (1FKN) and BACE2 (2EWY), where BACE1 is coloured blue and BACE2 is coloured green.
Superimposition of the crystal structures of BACE1 (1FKN) and BACE2 (2EWY) gave a root-mean-square deviation (RMSD) of 1.46 over 373 C-alpha atoms indicating that the structures of BACE1 and BACE2 are very similar to each other ( Figure 4 ).
We mapped the ligand binding sites and their ET status onto the chain A of crystal structures of BACE1 (1FKN) and BACE2 (2EWY) ( Figure 5 ).
Coffee and caffeine potentiate the antiamyloidogenic activity of melatonin via inhibition of A? oligomerization and modulation of the Tau-mediated pathway in N2a/APP cells.
(2015) Drug Des Devel Ther 9
PubMed: 25565776 | PubMedCentral: PMC4284031 | DOI: 10.2147/DDDT.S71106
Materials and methods Molecular docking We employed the Discovery Studio program 3.1 designed by Accelrys Inc. (San Diego, CA, USA) to dock Caff and Mel into the active sites of ten human BACE1 struct... res (protein data bank [PDB] identification codes: 1FKN, 2OHU, 1W51, 2P4J, 2VKM, 4DH6, 3DV5, 2QU3, 3U6A, and 4FRS) as previously described by us.
Publication Year: 2015
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