Biology Reference
In-Depth Information
30 years ago, have, however, crucial relevance for drug design. Targeting these com-
plexes selectively or designing small molecules that affect receptor-receptor inter-
actions might provide new opportunities for novel drug discovery. In order to study
the mechanisms and dynamics that rule GPCRs oligomerization, it is essential to
understand the dynamic process of receptor-receptor association and to identify
regions that are suitable for selective drug binding, which may be determined
with experimental methods such as F¨rster resonance energy transfer (FRET) or Bio-
luminescence resonance energy transfer (BRET) and computational sequence- and
structure-based approaches. The aim of this chapter is to provide a comprehensive
description of the structure-based molecular modeling methods for studying GPCR
dimerization, that is, protein-protein docking, molecular dynamics, normal mode
analysis, and electrostatics studies.
INTRODUCTION
Human membrane proteins, mainly metabotropic and ionotropic transmembrane re-
ceptors, constitute currently the largest group of targets for drugs on the market. This
includes G-protein-coupled receptors (GPCRs), which are drug targets for about 50%
of all marketed drugs. GPCRs are complex signaling molecules occurring at the cell
surface. They mediate signal transduction and convert extracellular stimuli, such as
hormones and neurotransmitters, into intracellular responses through the activation
of heterotrimeric G proteins (
Ding, Zhao, & Watts, 2013
). Some GPCRs are also in-
volved in the processes of vision, olfaction, and taste. The molecular architecture of
GPCRs is constituted by seven relatively conserved membrane-spanning
-helical seg-
ments connected with alternating intracellular and extracellular loop regions. GPCRs
are grouped into five families on the basis of their sequence and structural similarity:
rhodopsin (family A), secretin (family B), glutamate (family C), adhesion, and friz-
zled/taste. The rhodopsin family is the largest and most diverse of all families.
X-ray structures of some GPCRs have become available recently, including the
structures in the active state. Knowledge of a GPCR structure enables us to gain a
mechanistic insight into its function and dynamics and further aid rational drug de-
sign. The new structures make it also possible to design studies aimed to investigate
receptor dimerization and ligand-biased signaling (
Audet & Bouvier, 2012
). It may
lead to more selective and safer drugs as despite the advances in drug design; how-
ever, promiscuity between drug molecules and targets including GPCRs often leads
to undesired signaling effects, which result in unintended side effects (
McNeely,
Naranjo, & Robinson, 2012
).
Dimerization and oligomerization of GPCRs, proposed almost 30 years ago, have
been already accepted by the scientific community and have crucial relevance for
drug design. It is, however, still controversial how many receptors exist as mono-
mers, dimers, and oligomers in the cell membrane and if they are transient or rather
stable complexes. It should be emphasized that formation of GPCR oligomers may
a
