Investigation of beta-adrenergic receptors
binding pocket based on selected beta-blockers
Paweł Książek, Karol Kaszuba, Krzysztof Bryl
University of Warmia and Mazury in Olsztyn, Chair of Physics and Biophysics
Introduction
β-adrenergic receptors are a member of G protein
coupled receptors family. At present, three β-adrener-
gic receptor subtypes have been identified in mam-
mals: β1, β2 and β3. Human cardiomiocytes express
all three β-adrenergic receptor subtypes. Importance
of β-adrenergic signaling in heart failure and cardiac
arrhythmia was reported. β-adrenergic antagonists (al-
so referred to as β-blockers) are important form of
management of heart diseases. New findings about β-
adrenergic signaling paths become basis for more effi-
cient therapies [1]. Detailed knowledge about β-adren-
ergic receptors binding pocket may help to construct
highly selective agents necessary to design new β-
adrenergic blocking strategies.
Binding pocket of β-adrenergic receptors (β2 as an example). Impor-
tant agonist binding residues shown with CPK drawing method. Dis-
tances between their α carbons indicated in angstroms (Å).
Objectives
The purpose of our work was to explore binding pocket
of β1 and β2-adrenergic receptor. With computational
techniques consisting of automated docking and ener-
gy minimization we expected to identify residues im-
portant to antagonists binding by both subtypes. We
also expected to identify binding pattern specific only
for β1-adrenergic receptor antagonists. Gained knowl-
edge should be helpful in constructing new highly spe-
cific β-blockers.
Materials & Methods
In our research we used structures of β1 and β2-
adrenergic receptor. Structure of β1-adrenergic recep-
tor was obtained with homology modeling technique
[2]. High-resolution crystal structure of β2-adrenergic
receptor was downloaded from Protein Data Bank
(PDBID: 2RH1) [3]. Two antagonists with different affin-
ity were used to determine β-adrenergic receptors
binding residues. Both, selective antagonist, esmolol
(binds only to β1-adrenergic receptor) [4], and non-se-
lective, sotalol (binds to both β1 and β2-adrenergic re-
ceptor) [5], are typical antyarrhythmia β-blockers.
We employed automated docking method implement-
ed in AutoDock 4.0 [6]. Energy of protein-ligand com-
plexes, that was obtained after docking, was minimized
with molecular dynamics simulation package NAMD
2.6 [7].First after docking, then after energy minimiza-
tion the complexes were visualized and analyzed with
molecular visualization program VMD [8]. During anal-
ysis we searched for typical non-bonded interactions,
that can be found in protein-ligand complexes: hydro-
gen bonds, ionic interactions and hydrophobic interac-
tions.
Structure of β1 (left) and β2-adrenergic receptor (right) shown with new
cartoon drawing method. Roman numerals indicate successive trans-
membrane regions.
Esmolol (top) and sotalol (bottom) structures shown with licorice
drawing method. Hydrogen atoms are omitted. Important atoms are
numerated. Lines indicate bounds: cyan — carbon, blue — nitrogen,
red — oxygen, yellow — sulphur.
Scheme of our research procedure. Protein-ligand complexes were
analyzed twice: after docking and after energy minimization.
Results
Research based on selected drugs (esmolol and so-
talol) shown that between receptor subtypes occur dif-
ferences in ligand binding pattern. Results obtained
from protein-ligand complexes analysis after automat-
ed docking revealed residues determining β1-selectivi-
ty: TYR367 (hydrogen bond), VAL142 (hydrophobic in-
teraction) and SER232 (hydrogen bond). Results ob-
tained from complexes analysis after energy minimiza-
tion revealed that THR220 residue (hydrogen bond) is
involved in β1-selectivity.
Results from automated docking differed from results
from energy minimization. Thus we decided to verify
our results with experimental data from induced muta-
genesis researches. Our results were successfully ver-
ified [9].
Residues of β1 and β2-adrenergic receptor involved in esmolol (se-
lective antagonist) and sotalol (non-selective antagonist) binding
marked in red. Residues shown with their homologues and region af-
filiation.
Conclusions
● Residues involved in ligand binding by both β-
adrenergic receptor subtypes are found in trans-
membrane regions III, V, VI, VII and extracellular
loop IV-V.
● Hydrophobic interactions play predominant role in
ligand binding by both β-adrenergic receptor sub-
types.
● Application of antagonists with different affinity re-
vealed differences in binding pattern.
● Selectivity of β1-adrenergic receptor is deter-
mined by hydrogen bonds.
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