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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
Figure 1 The catalytic site of BACE-1 (1TQF structure).
As depicted in Figure 2 A and B, both the 3-PC model (built from a single X-ray crystal structure) and 5-PC model (built from the actual complexes present in the PDB) behaved well for most of the compounds, However, the 1TQF ligand (inhibitor 2, co-crystallized ligand 32P [ 27 ]) was always determined to be an outlier in the COMBINE analysis, whether or not it was refined before being placed into the binding pocket of 1W51, or built from the actual complexes present in the PDB.
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 conformation (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.
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
Discovery of potent beta-secretase (bace-1) inhibitors by the synthesis of isophthalamide-containing hybrids.
(2009) Acta Pharmacol Sin 30
PubMed: 19169270 | PubMedCentral: PMC4002469 | DOI: 10.1038/aps.2008.26
The modeled structures of 10 and 16 bound to BACE-1 active sites were constructed (PDB entry 1TQF).
The 3-dimensional crystal structure of BACE-1 was retrieved from the PDB database (access PDB code 1TQF).
Publication Year: 2009
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