Biology Reference
In-Depth Information
5.2.1
Recent milestones in simulating GPCRs
The “insuperable” barrier that impeded the obtention of further structural insights
into GPCRs after the release of the first X-ray crystal structure of bovine rhodopsin
in 2000 is linked to the inherent flexibility of GPCRs. A tremendous work in protein
engineering was undertaken to stabilize these flexible receptors preluding eventually
a new era of novel high-resolution structures for different receptor types. These new
receptor structures give an extraordinary glimpse into one possible conformational
state in the life cycle of GPCRs. However, the latest paradigm assumes the existence
of a vast amount of conformational receptor states (
Park, 2012
), which underlies their
ability to respond to diverse extracellular signals in a distinct manner. In this sce-
nario, MD simulations have been exploited to elucidate the dynamic nature of
GPCRs taking into account interaction with chemically diverse ligands, solvent ef-
fects, allosteric modulation of ions, membrane effects, and last but not least forma-
tion of higher-order complexes.
One of the most important question in GPCR drug discovery is how do drugs bind
to GPCRs: from initial association, followed by drug entry and adoption of the final
binding pose. Recently, this pharmaceutically critical process has been captured
using the first unbiased MD simulations for several beta-blockers for the
b
1
and
b
2
in atomic detail (
Dror, Pan, et al., 2011
). A surprising finding is that the first drug
association with the receptor at the extracellular part (15
˚
distant from the binding
pocket) constitutes the largest energetic barrier to ligand binding. This high barrier
seems to be a cause of drug dehydration that happens during the course of first drug
association to the extracellular receptor part. In a subsequent step, drug entrance re-
quires a receptor deformation and squeezing of the ligand through a narrow opening.
The final binding pose occurs after microseconds—in case of alprenolol after
3.5
s—which is still, using modern simulation techniques, a challenging timescale
for a complex GPCR-membrane system. This first atomic description of the pathway
and mechanism of drug binding to GPCRs provides suggestions for optimization of
drug binding as well as ideas for allosteric receptor modulation (
Dror, Pan, et al.,
2011
). In this context, also the allosteric binding of cations at the dopaminergic
D
2
receptor was computationally observed via microsecond simulation (
Selent,
Sanz, Pastor, & De Fabritiis, 2010
). Similar to the aforementioned beta-blockers, so-
dium ions enter the receptor from the extracellular receptor side. Once inside the re-
ceptor, sodium ions bind first to the orthosteric site D3.32 before penetrating even
deeper into the receptor occupying the well-known allosteric site D2.50. Remark-
ably, the final observed cation binding pose at D2.50 was later confirmed by an ex-
perimentally obtained X-ray structure (
Liu et al., 2012
), stressing the predictive
value of their structural model.
Another milestone in simulating GPCRs is a first molecular insight into GPCR
activation. Soon after the release of the activated
m
b
2
-adrenergic receptor in complex
with a G-protein-mimetic nanobody, Dror, Arlow, et al. tried to elucidated the dy-
namic steps that lead to receptor activation (
Dror, Arlow, et al., 2011
). For this pur-
pose, they started from the activated conformation observing its inactivation by
