Chemistry Reference
In-Depth Information
variations in the ED. It is possible that such different conformers are found for the
structure of inhibitors in crystals of the pure compound and in enzyme environ-
ments. Thus, geometries were optimized in different surroundings to differentiate
between the direct influence of the environments on the EDs and these more
indirect structural effects. The computed data were used for a thorough discussion
of the influence of different environment on EDs, electrostatic potentials (ESPs),
and multipole moments. The EDs were analyzed with Bader's theory of Atoms in
Molecules [
9
].
The inhibition process of most reversible inhibitors does not involve a chemical
reaction, and the noncovalent interactions between inhibitor and enzyme may be
too weak for significant variations of the EDs. This is investigated using
trans
-4-
(aminomethyl)cyclohexane-1-carboxylic acid (AMCHA, Fig.
5
) as an example.
It forms a reversible inhibitor-enzyme complex with the recombinant kringle 1
domain of human plasminogen (K1
Pg
)[
101
]. The preparation of the enzyme-
inhibitor complex of AMCHA and K1
Pg
within the QM/MM framework was
obtained as follows: Starting from the 1CEB-crystal structure [
101
], the influence
of the surrounding solvent was incorporated by a water sphere with a radius of
50
˚
. Counterions were added to make the system neutral overall. Then a series of
consecutive constrained optimizations and further solvation steps were performed
until equilibrium structures were reached. The preparation of the system was done
by means of fully classical MD simulations using the CHARMM force field and
program package [
102
,
103
]. In the next step, the QM/MM approach was applied to
optimize the geometrical arrangement of the active site including the inhibitor at a
quantum mechanical level. Often a geometry optimization is necessary to obtain
reliable information about the ED at the BCP. The resulting structure is depicted in
Fig.
6a
which includes additionally the numbering of the centers in the AMCHA
molecule. The molecular structure of the environment is indicated by sticks, while
AMCHA is shown in ball and stick representation. Some important geometrical
parameters are collected in Table
7
. Finally, the ED of the inhibitor in this
reversible enzyme-inhibitor complex was computed. The QM/MM calculations
were performed with the ChemShell program [
105
] using the DL_POLY code
[
106
] for the MM and the TURBOMOLE program suite [
107
] for the QM part.
The EDs were obtained from single-point computations at the DFT/B3 [
108
]-LYP
[
109
,
110
]/TZVP [
111
] level using the geometries described above. This DFT level
is well known to describe many properties with an excellent cost-benefit ratio
[
112
-
116
], but in other cases fail to provide the right answers [
117
-
120
].
a
b
c
Fig. 5 (a) AMCHA, (b) Loxistatinic acid (E64c), (c) Loxistatin (E64d)
