-
Receptor preparation
The co-crystallized
structure of human FXR with GW4064 analogue (PDB
code:
3FXV,
resolution:
2.26
?)
was
selected
for
docking
study.
The
structures
were
prepared
using
the
“Protein
Preparation
Wizard”
module
in
Maestro
(
ref.1
).
The
protein
was
prepared
by
adding
missing
hydrogen
atoms,
assigning
ligand
bond
orders,
determining
ligand
protonation
state,
removing
waters,
optimizing
hydrogen
bond
network,
and
performing
a
restrained
minimization,
etc.
Docking
grid
files
were
then
generated
using
the
“Receptor
Grid
Generation”
module
at
their
default settings.
Ligand preparation
Compounds
were
prepared
with
LigPrep
(
ref.
2
)
to
generate
3D
structures
including
all
possible
stereoisomers
and
tautomers.
Epik
(
ref.
3
)
was
chosen
to
generate
all
possible
protonation
states
of
the
compounds
at
a
pH
from
5.0
to
9.0.
OPLS_2005
was adopted as force field. The remaining
parameters were used at their
default
values.
The
conformation
of
each
structure
was
sampled
using
macromodel
(
ref.
4
)
with
“
conformational
CSearch
”
protocol.
The
top
10
representative
conformations were obtained after a
clustering analysis by RMSD.
Precise docking by Glide
The Glide (
ref.
5
) software can perform high accuracy
docking. During the grid
generation,
six
hydrogen
bond
constraints
were
set
up
including
His451
(HBA),
Tyr365 (HBD), Tyr373 (HBD), Ser336
(HBA), Arg335 (HBD) and His298 (HBA).
At
least
one
hydrogen
bond
must
match
was
set
up
for
docking.
All
the
docking