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BACE1, which stand for β-site of Amyloid precursor protein Cleaving Enzyme 1, is a β secretase also known as memapsin 2. It is an aspartyl protease that initiates the formation of β-amyloid which accumulation has a huge role in the Alzeimer disease. It had been brought to light that not only BACE1 levels rise in the brain of the patients suffering from this disease but that BACE1 knock out mices can’t produce β-amyloid, effectively preventing the formation of amyloid plaques and the development of the Alzheimer disease. This discovery makes the BACE1 a very interesting drug target for Alzheimer disease.The inhibition of this enzyme is a plausible course of action and several inhibitors like the ones that will be presented are considered. However, the total inhibition of BACE1 seems to leads to physiological and behavioural troubles. That would mean that BACE1 could also be involved in several other brain functions. So the regulation of BACE1 activity by partial inhibition seems to be a prefencial method. Anyway, a good understanding of the biological function, the structure and the mechanisms of inhibition of BACE1 is highly required for drug design.

BACE1 is synthetised in the endoplasmamic reticulum as an inactive precursor, pro-BACE1. This precursor is then maturated in the Golgi apparatus. It undergoes glycosylation of 4 residues : <scene name='56/568015/Asn/1'>Asn(153), Asn(172), Asn(223) and Asn(354) </scene>. This has  a role in the activity of BACE1. 3 cysteine residues of the cytosolic tail are also palmitoylated , it is has a role in the localization of the mature enzyme. The propeptide domain is then clived between Arg 45 and Glu 46 of pro-BACE1 by a proprotein convertase (protease). This clivage is known to increase the activity of the enzyme.

Structurally, the 501 amino acid sequence of BACE1 belongs to the eukaryotic aspartic proteases of the pepsin family and contains a bilobal structure constituted of by an N- and a C-terminal domains. Both N- and C-domains are formed by highly twisted <scene name='56/568015/Beta_sheet/2'> highly twisted β-sheet </scene> structures and each domain contributes with an aspartic acid to the catalytic module of the enzyme. The ligands containing a positive charged moiety might then be favorable to counteract the negative charged active site. BACE1 has two aspartic protease active site motifs, DTGS (<scene name='56/568015/93-96/1'>residues 93-96</scene>) and DSGT (<scene name='56/568015/289-292/1'>residues 289-292</scene>), and mutation of either aspartic acid renders the enzyme inactive. Like other aspartic proteases, BACE1 has an N-terminal signal sequence (residues 1–21) and a pro-peptide domain (residues 22–45) that are removed post-translationally, so the mature enzyme begins at residue Glu46. Importantly, BACE1 has a single transmembrane domain near its C-terminus (residues 455–480) and a palmitoylated cytoplasmic tail. Thus, BACE1 is a type I membrane  protein with a luminal active site, features predicted for β-secretase. The position of the BACE1 active site within the lumen of intracellular compartments provides the correct topological orientation for cleavage of APP at the β-secretase site. As observed with other aspartic proteases, BACE1 has <scene name='56/568015/Six_cysteines/1'>six luminal cysteine residues</scene> that form three intramolecular disulfide bonds ('''yellow''') and several N-linked glycosylation sites.<ref>PMID: 18005427</ref> <ref>PMID: 23681056</ref>

In mouse and human brain, native BACE1 occurs as a dimer. Dimerization is dependent on membrane attachment and increases BACE1 affinity and turnover rate toward APPSWE-like peptides when compared to the monomeric, soluble form. The different enzymatic properties of monomeric and dimeric BACE1 need to be considered in future drug screening and development processes. <ref> PMID:22363289 </ref>

Structural information about the interaction of substrate with the active site of BACE1 would greatly facilitate the rational design of small molecule BACE1 inhibitors. Towards this end, Sauder et al. used molecular modeling to simulate the BACE1 active site bound with wildtype or mutant APP substrates. The basic structure of most aspartic protease active sites is well conserved and the Xray structure of pepsin was used to model BACE1. The molecular modeling identified several residues in BACE1 that potentially contribute to substrate specificity. In particular, Arg235 forms a saltbridge with the P1' Asp+1 residue of the β-secretase cleavage site, thus explaining the unusual preference of BACE1 among aspartic proteases for substrates that are negatively charged at this position. In addition, several hydrophobic residues in BACE1 form a pocket for the hydrophobic P1 residue. The model also showed that the Swedish FAD mutation, LysMet→AsnLeu at P2-P1, interacts more favorably with Arg235 and the hydrophobic pocket of BACE1 than does wild-type substrate, providing an explanation for the enhanced cleavage of this mutation. Conversely, the substitution of Met→Val at P1 blocks the catalytic Asp93 residue, explaining the lack of cleavage of this mutation by BACE1.  

Shortly after the molecular modeling study, the X-ray structure of the BACE1 protease domain co-crystallized with a transition-state inhibitor was determined to 1.9 angstrom resolution. As expected, the BACE1 catalytic domain is similar in structure to pepsin and other aspartic proteases, despite the relatively low sequence similarity. Interestingly, the BACE1 active site is more open and less hydrophobic than that of other aspartic proteases. Four hydrogen bonds from the catalytic aspartic acid residues (Asp32 and Asp228) and ten additional hydrogen bonds from various residues in the active site are made with the inhibitor, most of which are conserved in other aspartic proteases. The X-ray structure indicates that Arg235 and the hydrophobic pocket of the active site play an important role in substrate binding, confirming the results of the molecular modelling study. In addition, the bound inhibitor has an unusual kinked conformation from P2' to P4'. The BACE1 X-ray structure suggests that small molecules targeting Arg235 and the hydrophobic pocket residues should inhibit β-secretase cleavage. Moreover, mimicking the unique P2'-P4' conformation of the bound inhibitor may increase the selectivity of inhibitors for BACE1 over BACE2 and the other aspartic proteases.<ref>PMID: 18005427</ref>

The compounds, 1-(2-(1H-indol-1-yl)ethyl)guanidine, showed weak inhibition activity towards BACE1, about 42% inhibition ratio at the ligand concentration of 100 μM in the fluorescence resonance energy transfer (FRET) assay system. These compound occupied the S1 pocket and the guanidine moiety formed key binding interactions with the two catalytic aspartic acids, <scene name='56/568015/32/1'>Asp32</scene> and Asp228 (Figure 2).

As exemplified in some known BACE1 inhibitors in which the guanidine group is usually acylated, a compound was designed by introducing a carbonyl group into the α-position of the guanidine moiety.  

To further improve the activity of this series of indole acylguanidines toward BACE1, the predicted conformation of inhibitors was scrutinized in the binding site of BACE1. There is a large hydrophobic sub-site at the top of the guanidine moiety. A benzyl group extending from the terminus of the guanidine moiety could fill this sub-pocket and thereby potentially increase the binding affinity. Analogs were synthesized based on indole and ethyl bromoacetate.

The acylguanidine formed crucial interactions with two catalytic aspartic acids (Asp228 and Asp32) through three hydrogen bonds. The carboxyl oxygen atoms of the acylguanidine formed water-bridged hydrogen bonds with the side chains of Gln73 and Thr72, and a direct hydrogen bond with Gln73 as well. The substituted benzyl group occupied the S1 subsite of the substrate binding pocket of BACE1. The carboxyl oxygen atom of acetamide also forms a water-bridged hydrogen bond with the nitrogen atom of the amide group of Gln73, while the acetamide nitrogen atom forms another hydrogen bond directly with the main chain carboxyl oxygen of Phe108. The two chlorine atoms may force the acetamide group adopting a perpendicular angle with respect to the benzyl group, which plays an important role in binding interactions between acetamide and BACE1. Besides, the hydrogen bonds of the inhibitor with residues Gln73 and Thr72 induce a semi-closed conformation. Such a conformation of the flap further strengthens the ligand binding to the enzyme. The indole group pointed toward the back of the S1’ pocket forming a cation-πinteraction with Arg235, which appears to contribute further interactions to improve the potency of the inhibitor.<ref>PMID: 23681056</ref>