Apo and inhibitor complex structures of BACE (beta-secretase)

Human BACE, also known as beta-secretase, shows promise as a potential therapeutic target for Alzheimer's disease. We determined the apo structure of BACE to 1.75 A, and a structure of a hydroxyethylamine inhibitor complex derived by soaking. These show significant active-site movements compared to previously described BACE structures. Additionally, the structures reveal two pockets that could be targeted by structure-based drug design.     

Green tea catechins as a BACE1 (beta-secretase) inhibitor

In the course of searching for BACE1 (beta-secretase) inhibitors from natural products, the ethyl acetate soluble fraction of green tea, which was suspected to be rich in catechin content, showed potent inhibitory activity. (-)-Epigallocatechin gallate, (-)-epicatechin gallate, and (-)-gallocatechin gallate were isolated with IC(50) values of 1.6 x 10(-6), 4.5 x 10(-6), and 1.8 x 10(-6) M, respectively. Seven additional authentic catechins were tested for a fundamental structure-activity relationship. (-)-Catechin gallate, (-)-gallocatechin, and (-)-epigallocatechin significantly inhibited BACE1 activity with IC(50) values of 6.0 x 10(-6), 2.5 x 10(-6), and 2.4 x 10(-6) M, respectively. However, (+)-catechin, (-)-catechin, (+)-epicatechin, and (-)-epicatechin exhibited about ten times less inhibitory activity. The stronger activity seemed to be related to the pyrogallol moiety on C-2 and/or C-3 of catechin skeleton, while the stereochemistry of C-2 and C-3 did not have an effect on the inhibitory activity. The active catechins inhibited BACE1 activity in a non-competitive manner with a substrate in Dixon plots.     

Synthesis and biological evaluation of phosphino dipeptide isostere inhibitor of human beta-secretase (BACE1)

Phosphino dipeptide (PDP) isosteres are known to be useful analogues of the transition state of metalloprotease substrates. Here we describe the use of this unit for the design of aspartic protease inhibitors. A PDP analogue of OM00-3, a potent BACE1 inhibitor, was synthesized and exhibited high biological activity (IC50 approximately 12 nM).     

人β-分泌酶 (BACE1) 在毕赤酵母中分泌表达及纯化

为了获得活性良好的重组人β-分泌酶 (β-secreatase, BACE1),用于研究其与抑制剂的作用模式,构建了携带β-分泌酶proBACE1和BACE1编码序列的重组表达质粒pPIC9K-MetBACE22和pPIC9K-MetBACE46,通过电击法转入毕赤酵母GS115中,分别得到重组子9k-B22和9k-B46。重组菌株在诱导表达培养基中诱导外源基因表达,结果显示9k-B22的上清活性明显高于9k-B46的上清活性。9k-B22表达上清浓缩后经HisTrap亲和柱纯化得到的蛋白具有良好的BACE1活性, SDS-PAGE/高碘酸-希夫试剂染色发现其为糖蛋白,并且其糖基侧链可以被Endo Hf完全切除,得到50 kDa左右的两条蛋白带。肽质量指纹图谱鉴定发现,这两个蛋白分别与proBACE1和BACE1匹配。活性检测发现糖基化BACE1和去糖基化BACE1的活性均低于HEK-293细胞表达的商品BACE1,这说明糖基化及其类型对BACE1的活性非常重要。然而已知的BACE1抑制剂对三者的抑制率无显著差异,这说明糖基化并不影响与抑制剂的相互作用。经过一系列培养条件优化BACE1纯化产量提高到1 mg/L,这为发现并优化BACE1新型抑制剂的相关研究奠定了物质基础。     

Measuring human beta-secretase (BACE1) activity using homogeneous time-resolved fluorescence

The human beta-secretase enzyme, BACE1, mediates a critical step in the production of A beta(40) and A beta(42) peptides which are responsible for the severe neuronal cell death and insoluble amyloid plaques of Alzheimer's disease (AD). Several lines of evidence suggest that potent BACE1 inhibitors represent an attractive A beta-lowering strategy for AD. We designed a simple homogeneous time-resolved fluorescence (HTRF) assay which utilizes the fluorescence resonance energy transfer (FRET) pair europium and allophycocyanin for measuring BACE1 enzymatic activity in a high-throughput manner. Robust FRET was observed when an 18-amino-acid APP Swedish-synthetic peptide that was N-terminally labeled with europium cryptate and C-terminally biotinylated was incubated with streptavidin-coupled cross-linked allophycocyanin (SA-XL665). Purified BACE1 enzyme caused a time- and concentration-dependent linear change in FRET at low nanomolar enzyme concentrations. This assay was used to compare the autoprocessed "mature" BACE1 enzyme (sautoBACe1) and the soluble proBACE1 for activity and inhibition by selected peptidic BACE inhibitors. sautoBACE1 displayed only a modest increase in activity compared to sproBACE1 and this activity was uninhibited by the BACE1 prodomain peptide. Interestingly, the BACE1 prodomain peptide was able to partially inhibit sproBACE1 activity. IC(50s) for a P10-P4' statine BACE1 inhibitor, OM99-2, and OM-003 determined using the HTRF assay were in good agreement with those reported in the literature. The primary advantages of the HTRF-formatted BACE1 protease assay include appropriate reflection of native BACE1 activity, high sensitivity, low variability, and intrinsic quench correction afforded by ratiometric measurements made between EuK and SA-XL665 fluorophores.     

Accessing the reproducibility and specificity of pepsin and other aspartic proteases

The aspartic protease pepsin is less specific than other endoproteinases. Because aspartic proteases like pepsin are active at low pH, they are utilized in hydrogen deuterium exchange mass spectrometry (HDX MS) experiments for digestion under hydrogen exchange quench conditions. We investigated the reproducibility, both qualitatively and quantitatively, of online and offline pepsin digestion to understand the compliment of reproducible pepsin fragments that can be expected during a typical pepsin digestion. The collection of reproducible peptides was identified from > 30 replicate digestions of the same protein and it was found that the number of reproducible peptides produced during pepsin digestion becomes constant above 5–6 replicate digestions. We also investigated a new aspartic protease from the stomach of the rice field eel (Monopterus albus Zuiew) and compared digestion efficiency and specificity to porcine pepsin and aspergillopepsin. Unique cleavage specificity was found for rice field eel pepsin at arginine, asparagine, and glycine. Different peptides produced by the various proteases can enhance protein sequence coverage and improve the spatial resolution of HDX MS data. This article is part of a Special Issue entitled: Mass spectrometry in structural biology.     

Precise and efficient cleavage of recombinant fusion proteins using mammalian aspartic proteases

Expression of recombinant proteins as translational fusions is commonly employed to enhance stability, increase solubility and facilitate purification of the desired protein. In general, such fusion proteins must be cleaved to release the mature protein in its native form. The usefulness of the procedure depends on the efficiency and precision of cleavage and its cost per unit activity. We report here the development of a general procedure for precise and highly efficient cleavage of recombinant fusion proteins using the protease chymosin. DNA encoding a modified pro-peptide from bovine chymosin was fused upstream of hirudin, carp growth hormone, thioredoxin and cystatin coding sequences and expressed in a bacterial Escherichia coli host. Each of the resulting fusion proteins was efficiently cleaved at the junction between the pro-peptide and the desired protein by the addition of chymosin, as determined by activity, N-terminal sequencing and mass spectrometry of the recovered protein. The system was tested further by cleavage of two fusion proteins, cystatin and thioredoxin, sequestered on oilbody particles obtained from transgenic Arabidopsis seeds. Even when the fusion protein was sequestered and immobilized on oilbodies, precise and efficient cleavage was obtained. The precision, efficiency and low cost of this procedure suggest that it could be used in larger scale manufacturing of recombinant proteins which benefit from expression as fusions in their host organism.     

Heparin activates beta-secretase (BACE1) of Alzheimer's disease and increases autocatalysis of the enzyme

BACE1 is an aspartic protease that generates the N-terminus of the beta-amyloid protein (Alphabeta) from the beta-amyloid precursor protein (APP). BACE1 is a key target for Alzheimer drug development. However, little is known about the physiological regulation of the enzyme. Heparin can promote beta-secretase cleavage of APP in neuroblastoma cells. However, heparin has also been reported to directly inhibit BACE1 activity in vitro. To clarify the role of heparin in regulating BACE1, we examined the effect of heparin on the activity of recombinant human BACE1 (rBACE1) in vitro. Low concentrations (1 microg/mL) of heparin were found to stimulate rBACE1, increasing enzyme V(max) and decreasing the K(M). In contrast, higher concentrations of heparin (10 or 100 microg/mL) were inhibitory. Heparin affinity chromatography demonstrated that heparin interacted strongly with the zymogen form of rBACE1 and bound to a peptide homologous to the N-terminal pro sequence of BACE1. Mature (pro sequence cleaved) enzyme lacked the capacity to be stimulated by heparin, indicating that the pro domain was necessary for the stimulation by heparin. Furthermore, in the presence of stimulatory concentrations of heparin, there was an increase in autocatalytic cleavage of the protease domain and a subsequent loss of enzyme activity in vitro. Our results strongly suggest that heparin stimulates the partially active BACE1 zymogen, and we propose that the activation is mediated by high-affinity binding of heparin to the pro domain. Our study provides evidence that heparan sulfate proteoglycans could regulate the rate of Alphabeta production in vivo.     

Design and synthesis of potent beta-secretase (BACE1) inhibitors with P1' carboxylic acid bioisosteres

Recently, we reported potent and small-sized beta-secretase (BACE1) inhibitors KMI-420 and KMI-429 in which we replaced the Glu residue at the P4 position of KMI-260 and KMI-360, respectively, with a 1H-tetrazole-5-carbonyl DAP (L-alpha,beta-diaminopropionic acid) residue. At the P1' position, these compounds contain one or two carboxylic acid groups, which are unfavorable for crossing the blood-brain barrier. Herein, we report BACE1 inhibitors with P1' carboxylic acid bioisosteres in order to develop practical anti-Alzheimer's disease drugs. Among them, tetrazole ring-containing compounds, KMI-570 (IC50=4.8 nM) and KMI-684 (IC50=1.2 nM), exhibited significantly potent BACE1 inhibitory activities.     

The low density lipoprotein receptor-related protein (LRP) is a novel beta-secretase (BACE1) substrate

BACE is a transmembrane protease with beta-secretase activity that cleaves the amyloid precursor protein (APP). After BACE cleavage, APP becomes a substrate for gamma-secretase, leading to release of amyloid-beta peptide (Abeta), which accumulates in senile plaques in Alzheimer disease. APP and BACE are co-internalized from the cell surface to early endosomes. APP is also known to interact at the cell surface and be internalized by the low density lipoprotein receptor-related protein (LRP), a multifunctional endocytic and signaling receptor. Using a new fluorescence resonance energy transfer (FRET)-based assay of protein proximity, fluorescence lifetime imaging (FLIM), and co-immunoprecipitation we demonstrate that the light chain of LRP interacts with BACE on the cell surface in association with lipid rafts. Surprisingly, the BACE-LRP interaction leads to an increase in LRP C-terminal fragment, release of secreted LRP in the media and subsequent release of the LRP intracellular domain from the membrane. Taken together, these data suggest that there is a close interaction between BACE and LRP on the cell surface, and that LRP is a novel BACE substrate.     

Depletion of GGA3 stabilizes BACE and enhances beta-secretase activity

Beta-site APP-cleaving enzyme (BACE) is required for production of the Alzheimer's disease (AD)-associated Abeta protein. BACE levels are elevated in AD brain, and increasing evidence reveals BACE as a stress-related protease that is upregulated following cerebral ischemia. However, the molecular mechanism responsible is unknown. We show that increases in BACE and beta-secretase activity are due to posttranslational stabilization following caspase activation. We also found that during cerebral ischemia, levels of GGA3, an adaptor protein involved in BACE trafficking, are reduced, while BACE levels are increased. RNAi silencing of GGA3 also elevated levels of BACE and Abeta. Finally, in AD brain samples, GGA3 protein levels were significantly decreased and inversely correlated with increased levels of BACE. In summary, we have elucidated a GGA3-dependent mechanism regulating BACE levels and beta-secretase activity. This mechanism may explain increased cerebral levels of BACE and Abeta following cerebral ischemia and existing in AD.     

Analysis of binding interactions of pepsin inhibitor-3 to mammalian and malarial aspartic proteases

The nematode Ascaris suum primarily infects pigs, but also causes disease in humans. As part of its survival mechanism in the intestinal tract of the host, the worm produces a number of protease inhibitors, including pepsin inhibitor-3 (PI3), a 17 kDa protein. Recombinant PI3 expressed in E. coli has previously been shown to be a competitive inhibitor of a subgroup of aspartic proteinases: pepsin, gastricsin and cathepsin E. The previously determined crystal structure of the complex of PI3 with porcine pepsin (p. pepsin) showed that there are two regions of contact between PI3 and the enzyme. The first three N-terminal residues (QFL) bind into the prime side of the active site cleft and a polyproline helix (139-143) in the C-terminal domain of PI3 packs against residues 289-295 that form a loop in p. pepsin. Mutational analysis of both inhibitor regions was conducted to assess their contributions to the binding affinity for p. pepsin, human pepsin (h. pepsin) and several malarial aspartic proteases, the plasmepsins. Overall, the polyproline mutations have a limited influence on the Ki values for all the enzymes tested, with the values for p. pepsin remaining in the low-nanomolar range. The largest effect was seen with a Q1L mutant, with a 200-fold decrease in Ki for plasmepsin 2 from Plasmodium falciparum (PfPM2). Thermodynamic measurements of the binding of PI3 to p. pepsin and PfPM2 showed that inhibition of the enzymes is an entropy-driven reaction. Further analysis of the Q1L mutant showed that the increase in binding affinity to PfPM2 was due to improvements in both entropy and enthalpy.     

Design, synthesis, and evaluation of Leu*Ala hydroxyethylene-based non-peptide beta-secretase (BACE) inhibitors

With the aim of developing small molecular non-peptide beta-secretase (BACE) inhibitors, Leu*Ala hydroxyethylene (HE) was investigated as a scaffold to design and synthesize a series of compounds. Taking advantage of efficient combinatorial synthesis approaches and molecular modeling, extensive structure-activity relationship (SAR) studies were carried out on the N- and C-terminal residues of the Leu*Ala HE scaffold. Isobutyl amine was found to be an optimal C-cap, and suitable hydroxylalkylamines at the 3-position and nitro or methyl(methylsulfonyl)amine at the 5-position of isophthalamide as the N-terminus could form additional hydrogen bonds with BACE active sites and help improve potency. Many new potent non-peptide BACE inhibitors were identified in this study. Among them, compounds 37 and 44 exhibited excellent enzyme-inhibiting potency, comparable to that of OM99-2, and obvious inhibitory effects in cell-based assay with low molecular weights (<600).     

Macrocyclic peptidomimetic inhibitors of beta-secretase (BACE): first X-ray structure of a macrocyclic peptidomimetic-BACE complex

The synthesis of novel macrocyclic peptidomimetic inhibitors of the enzyme BACE1 is described. These macrocycles are derived from a hydroxyethylene core structure. Compound 7 was co-crystallized with BACE1 and the X-ray structure of the complex elucidated at 1.6 Angstrom resolution. This molecule inhibits the production of the Abeta peptide in HEK293 cells overexpressing APP751sw.     

Altered beta-secretase enzyme kinetics and levels of both BACE1 and BACE2 in the Alzheimer's disease brain

beta-Secretase is the rate limiting enzymatic activity in the production of amyloid-beta peptide, the primary component of senile plaque pathology in Alzheimer's disease (AD). This study performed the first comparative analysis of beta-secretase enzyme kinetics in AD and control brain tissue. Results found V(max) values for beta-secretase to be significantly increased, and K(m) values unchanged in AD temporal cortex compared to matched control temporal cortex. The increased V(max) in AD cases, did not correlate with levels of BACE1, and decreased BACE1 and BACE2 levels correlated with the severity of neurofibrillary pathology (I-VI), and synaptic loss in AD. These results indicate that increased V(max) for beta-secretase is a feature of AD pathogenesis and this increase does not correlate directly with levels of BACE1, the principal beta-secretase in brain.     

Collagenolytic activity of crustacean midgut serine proteases: comparison with the bacterial and mammalian enzymes.

1. We have investigated the collagenolytic activity of the following serine proteases: proteinase K, subtilisin Novo, Staphylococcal endoproteinase Glu-C, Streptomyces pronases, the trypsins and chymotrypsins from shrimp midgut and bovine pancreas. 2. By assays on both the insoluble 3H-collagen fibrils and the soluble type I collagen, it was demonstrated that the shrimp midgut serine proteases, and less efficiently, the pronases from Streptomyces griseus, could hydrolyze collagen while the other serine proteases tested could not. 3. Our data indicate that the trypsins and chymotrypsins of shrimp (Penaeus monodon) directly and indirectly digest native collagen, and that the indirect pathway probably involves activation of procollagenase in the native collagen by these serine proteases.     

Mechanism of action of aspartic proteases. IV.Conformational characteristics of a substrate and an inhibitor of rhizopuspepsin ]

On the basis of theoretical conformational analysis of separate peptide fragments, the conformational characteristics of two substrates and a substrate-like inhibitor of aspartic protease rhizopuspepsin were studied. It was shown that the spatial structure of these molecules is described by several families of conformations, the transition between which does not require the overcoming of high energy barriers. It was assumed that the stabilization of beta-structural conformations experimentally observed in inhibitor complexes is due to the greater predisposition of extended structures to the formation of effective intermolecular contacts with amino acid residues of the active site of the enzyme.     

Inhibition of beta-secretase in vivo via antibody binding to unique loops (D and F) of BACE1

β-Secretase (BACE1) is an attractive drug target for Alzheimer disease. However, the design of clinical useful inhibitors targeting its active site has been extremely challenging. To identify alternative drug targeting sites we have generated a panel of BACE1 monoclonal antibodies (mAbs) that interfere with BACE1 activity in various assays and determined their binding epitopes. mAb 1A11 inhibited BACE1 in vitro using a large APP sequence based substrate (IC(50) ～0.76 nm), in primary neurons (EC(50) ～1.8 nm), and in mouse brain after stereotactic injection. Paradoxically, mAb 1A11 increased BACE1 activity in vitro when a short synthetic peptide was used as substrate, indicating that mAb 1A11 does not occupy the active-site. Epitope mapping revealed that mAb 1A11 binds to adjacent loops D and F, which together with nearby helix A, distinguishes BACE1 from other aspartyl proteases. Interestingly, mutagenesis of loop F and helix A decreased or increased BACE1 activity, identifying them as enzymatic regulatory elements and as potential alternative sites for inhibitor design. In contrast, mAb 5G7 was a potent BACE1 inhibitor in cell-free enzymatic assays (IC(50) ～0.47 nm) but displayed no inhibitory effect in primary neurons. Its epitope, a surface helix 299-312, is inaccessible in membrane-anchored BACE1. Remarkably, mutagenesis of helix 299-312 strongly reduced BACE1 ectodomain shedding, suggesting that this helix plays a role in BACE1 cellular biology. In conclusion, this study generated highly selective and potent BACE1 inhibitory mAbs, which recognize unique structural and functional elements in BACE1, and uncovered interesting alternative sites on BACE1 that could become targets for drug development.