Chemistry Reference
In-Depth Information
Unfortunately, the crystal structure of the pure E64c compound is not available.
Hence, we used the known crystal structure of E64d [
135
] to compare the crystal
environment with the enzyme surrounding. In biological systems, E64d is the
precursor that is hydrolyzed by esterases to the active compound E64c [
127
,
128
]. Thus, for E64d X-ray scattering data of the enzyme-inhibitor complex are
not available.
As indicated in Fig.
12
the ring opening reaction can be induced by an attack of
the thiolate group of the Cys29 moiety at the
a
- or the
b
-carbon center of the
epoxide ring. In a polar solvent, the
-attack is preferred for epoxide carboxylates
reacting with phenylthiolate. Within the cathepsin B environment, E64c reacts only
via
b
a
-attack, i.e., the enzyme environment flips the regioselectivity of the reaction.
As already discussed previously [
131
], strong interactions between E64c and the
active site of cathepsin B result from the carboxylate group (C16-O17-O18) which
interacts with the oxy-anion hole (residue of Gln23 and backbone NH-group of
Cys29) and the protonated His199 residue. These interactions have a strong effect
on the kinetics of the inhibition reaction since they pull the inhibitor into the active
site toward the attacking thiolate group of the Cys29 residue. As can be seen from
the geometrical data summarized in Table
17
, the distance between the reacting
species becomes so small that the ring already starts to open in the reactant valley
(see the distance C2-O1 and the angle O1-C3-C2). In comparison to gas phase
or solvent data in the enzyme-inhibitor complex the C2-O1 bond is elongated and
the angle O1-C3-C2 is enlarged indicating a strong distortion of the reactant
structure toward the product arrangement. The single interactions connected with
the peptidomimetic side chain are considerably smaller but in sum lead to a more
pronounced regiospecificity [
131
] and determine the stereoselectivity [
132
] of the
inhibition process.
According to the AIM theory developed by Bader and co-workers [
9
], regions
with
2
0 represent domains with charge depletion. Upon chemical combi-
nation, the atomic region of VSCC, with
r
r
(
r
)
>
2
0, may be punctured and locally
destroyed, leading to the formation of regions of relative charge depletion within
the VSCC, often characterized by positive Laplacian values. The (3,+1)
r
r
(
r
)
<
2
r
(
r
) ring
r
critical points associated with the triangles formed by (3,
3) bonded or non-bonded
Table 17 Selected geometrical parameters of E64c in different environments
Parameter (E64c)
Gas phase
Solvent
Protein
C16-O18 (
˚
)
1.27
1.27
1.28
C16-O17 (
˚
)
1.26
1.27
1.25
C2-O1 (
˚
)
1.47
1.47
1.53
C3-O1 (
˚
)
1.43
1.45
1.45
O18-C16-C2 (
)
111.6
113.9
117.7
O17-C16-C2 (
)
116.9
118.3
119.1
O18-C16-C2-C3 (
)
128.7
128.7
166.8
O1-C2-C3 (
)
57.7
58.5
58.1
O1-C3-C2 (
)
60.0
59.8
64.0
C16-C2-C3-C4 (
)
141.9
147.5
156.3
