Sandbox Reserved 817: Difference between revisions

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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. <ref name="two">PMID:10887202</ref>

[[Image:APP cleavage at beta and alpha site.png|right|~~400px~~|thumb|'''Figure 1 :''' Cleavage of APP by the amyloidogenic and non amyloidogenic pathways '']]

[[Image:APP cleavage at beta and alpha site.png|right|300px|thumb|'''Figure 1 :''' Cleavage of APP by the amyloidogenic and non amyloidogenic pathways '']]

=== Biological functions ===

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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=~~name~~"un">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 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>

=== Inhibitors ===

[[Image:Inhibiteur4.jpg|right|300px|thumb|'''Figure 2 :''' Docking study on compound 4 bound to BACE1. The coordinates of BACE1 was taken from the crystal structure of 1FKN. The protein is shown in cartoon, while the important residues and ligand 4 are shown in stick model.'']]

Sandbox Reserved 817: Difference between revisions

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@@ Line 22: / Line 22: @@
 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. <ref name="two">PMID:10887202</ref>
-[[Image:APP cleavage at beta and alpha site.png|right|400px|thumb|'''Figure 1 :''' Cleavage of APP by the amyloidogenic and non amyloidogenic pathways '']]
+[[Image:APP cleavage at beta and alpha site.png|right|300px|thumb|'''Figure 1 :''' Cleavage of APP by the amyloidogenic and non amyloidogenic pathways '']]
 === Biological functions ===
@@ Line 52: / Line 52: @@
 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=name"un">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 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>
 === Inhibitors ===
 [[Image:Inhibiteur4.jpg|right|300px|thumb|'''Figure 2 :''' Docking study on compound 4 bound to BACE1. The coordinates of BACE1 was taken from the crystal structure of 1FKN. The protein is shown in cartoon, while the important residues and ligand 4 are shown in stick model.'']]