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=== Mechanism of inhibition === | === Mechanism of inhibition === | ||
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 | 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, <scene name='56/568015/Arg235/1'>Arg235</scene> 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 <scene name='56/568015/Arg32/1'>Asp32</scene>Asp32 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 name="first">PMID:18005427</ref> | 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 <scene name='56/568015/Arg235/1'>Arg235</scene> 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 <scene name='56/568015/Arg235/1'>Arg235</scene> 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 name="first">PMID:18005427</ref> | ||
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In the past, major efforts in designing BACE1 inhibitors were focused on the transition state analogs such as hydroxyethylamines, hydroxyethylene, and tatine-based peptidomimetic inhibitors. Although a large number of potent peptidomimetic inhibitors have been discovered, their relatively large sizes and excessive number of hydrogen-bond donors and acceptors make it difficult for them to penetrate the blood brain barrier. Therefore many researchers in both academia and industry are trying to identify drug-like small molecules as BACE1 inhibitors, which hold great hopes to have good pharmacokinetic (PK) profiles and are suitable for drug development. | In the past, major efforts in designing BACE1 inhibitors were focused on the transition state analogs such as hydroxyethylamines, hydroxyethylene, and tatine-based peptidomimetic inhibitors. Although a large number of potent peptidomimetic inhibitors have been discovered, their relatively large sizes and excessive number of hydrogen-bond donors and acceptors make it difficult for them to penetrate the blood brain barrier. Therefore many researchers in both academia and industry are trying to identify drug-like small molecules as BACE1 inhibitors, which hold great hopes to have good pharmacokinetic (PK) profiles and are suitable for drug development. | ||
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). | 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 <scene name='56/568015/Asp228/1'>Asp228</scene>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. | 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. | ||