Apo and Inhibitor Complex Structures of BACE (β-secretase)

Discovery of AZD3839, a Potent and Selective BACE1 Inhibitor Clinical Candidate for the Treatment of Alzheimer Disease

“…Protein Crystallography-Protein expression and purification for structural studies was done as previously described by Patel et al (36). Crystallization of compounds bound to BACE1 has been described by Swahn et al (37).…”

Crystal Structure of an Active Form of BACE1, an Enzyme Responsible for Amyloid β Protein Production

“…The protein solution was estimated to be Ͼ95% pure as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Crystallization for apo BACE1 was performed by the sitting-drop vapor diffusion method described previously (24). Equal volumes of protein solution and mother liquor, containing 15 to 22.5% (wt/vol) polyethylene glycol 5000 monomethyl ether (PEG 5000 MME), 200 mM ammonium iodide, 200 mM sodium citrate, pH 6.0 to 7.0, were mixed in a single droplet and equilibrated against 0.5 ml of mother liquor at 20°C.…”

“…These studies indicated that the active site of BACE1 is covered by a flexible antiparallel ␤-hairpin, called a flap, which is believed to control substrate access to the active site and set the substrate into the correct geometry for the catalytic process. It has been reported that the flap of the inhibitor-bound form is tightly packed in a closed conformation; however, the substrate-free (apo) structure of BACE1 showed that the flap was in an open conformation (14,24). These results indicate that a conformational change must take place upon binding of the inhibitor/ substrate to the active site and may participate kinetically in substrate binding in the closed conformation and product release in the open conformation.…”

“…BACE1 has become a major target in the development of drugs for AD, and X-ray crystallography has determined numerous structures of BACE1 complexes (12,13,24,34). These studies indicated that the active site of BACE1 is covered by a flexible antiparallel ␤-hairpin, called a flap, which is believed to control substrate access to the active site and set the substrate into the correct geometry for the catalytic process.…”

Loss of Cleavage at β′-Site Contributes to Apparent Increase in β-Amyloid Peptide (Aβ) Secretion by β-Secretase (BACE1)-Glycosylphosphatidylinositol (GPI) Processing of Amyloid Precursor Protein

“…In the x-ray structure of BACE1 (Protein Data Bank code 1W50) (41), the 10s loop is positioned between the third strand and insert F segments. The molecular dynamics simulation shows that the Gln 12 residue of the 10s loop mediates interactions between the third strand and insert F. In WTBACE1, the backbone and the side chain of Gln 12 (10s loop) form hydrogen bonds with the side chains of Ser 113 (third strand) and Glu…”