Computational Drug Discovery and Design

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above 30% of marketed drugs [53]. Receptors belonging to this
class share a common topology of seven transmembrane helixes,
connected by three extracellular and intracellular loops, and an
amphipathic helix 8. They react to extracellular stimuli like light
or chemical molecules, and in response initiate diverse signaling
cascades through binding with intracellular signaling agents. Due
to their diversity and ubiquity in the human organism, these recep-
tors are involved in almost every aspect of human physiology and
various diseases [54].
The initial understanding of those proteins was that they elicit
their signaling response as a consequence of interacting with vari-
ous ligands in a 1:1 stoichiometry [55]. Currently, overwhelming
experimental data suggests that those proteins can form dimers and
higher order oligomers with other GPCRs. Intriguingly, those
complexes have a different signaling profile than a monomer
[56–58], and in fact in C-class receptor, dimer formation is obliga-
tory for canonical function [59]. Moreover, in A-class some signal-
ing pathways cannot be initiated by monomer proteins [60, 61]. It
also appears that there exists functional allosteric cross talk between
receptors in a dimer, thus activation of one of the receptors through
binding of a molecule can have effect on the other (i.e., change its
ligand affinity) [62, 63]. Although GPCR dimerization seems to be
an established concept, there is still a debate over prevalence of
oligomerization and to what extent it impacts signaling
[64, 65]. These doubts arise, because observed phenomena can
be artifacts derived from protein overexpression [66, 67], and also
current methods to study oligomerization describe protein–protein
proximity, but not stability of formed oligomers [65].
Alterations in the formation of dimers in GPCRs have been
suggested to be involved in many pathological conditions
[68, 69]. Since those conditions are related to the dimer, and not
one receptor alone, targeting oligomers shows promise for a tai-
lored and effective therapeutic intervention. Such ligands can uti-
lize two strategies (Fig.2):
l Act through both proteins forming the dimers, thus stabilizing
the dimer.
l Bind to the dimer binding site to prevent its formation.

Ligands from the first group (called multivalent or bivalent
ligands) consist of pharmacophores, which are able to bind specific
receptors forming the oligomer, a spacer connecting them, and two
linkers connecting the pharmacophores to the spacer [70]. Ligands
from the second group are primarily peptides [71–74].
Obtaining reliable GPCR multimer structures enables further
insight into the dynamics of dimer formation, stability, and rational
design of ligands targeting dimers (i.e., adjusting the length and
flexibility of the spacer in case of bivalent ligands). That being said,

294 Agnieszka A. Kaczor et al.

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