Richard Ågren1,2, Hugo Zeberg2, Tomasz Maciej Stępniewski3,4,5, R Benjamin Free6, Sean W Reilly7, Robert R Luedtke8, Peter Århem1,2, Francisco Ciruela9,10, David R Sibley6, Robert H Mach7, Jana Selent3, Johanna Nilsson1, Kristoffer Sahlholm2,11,12. 1. Department of Clinical Neuroscience, Karolinska Institutet, Stockholm 171 77, Sweden. 2. Department of Neuroscience, Karolinska Institutet, Stockholm 171 77, Sweden. 3. Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences of Pompeu Fabra University (UPF)-Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain. 4. InterAx Biotech AG, PARK innovAARE, 5234 Villigen, Switzerland. 5. Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw 02-089, Poland. 6. Molecular Neuropharmacology Section, National Institute of Neurological Disorders and Stroke, Intramural Research Program, National Institutes of Health, Bethesda, Maryland 20892-3723, United States. 7. Department of Radiology, Division of Nuclear Medicine and Clinical Molecular Imaging, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States. 8. Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, Texas 76107, United States. 9. Pharmacology Unit, Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, L'Hospitalet de Llobregat 08907, Spain. 10. Neuropharmacology and Pain Group, Neuroscience Program, Institut d'Investigació Biomèdica de Bellvitge, IDIBELL, L'Hospitalet de Llobregat 08907, Spain. 11. Department of Integrative Medical Biology, Umeå University, Umeå 901 87, Sweden. 12. Wallenberg Centre for Molecular Medicine, Umeå University, Umeå 901 87, Sweden.
Abstract
A solid understanding of the mechanisms governing ligand binding is crucial for rational design of therapeutics targeting the dopamine D2 receptor (D2R). Here, we use G protein-coupled inward rectifier potassium (GIRK) channel activation in Xenopus oocytes to measure the kinetics of D2R antagonism by a series of aripiprazole analogues, as well as the recovery of dopamine (DA) responsivity upon washout. The aripiprazole analogues comprise an orthosteric and a secondary pharmacophore and differ by the length of the saturated carbon linker joining these two pharmacophores. Two compounds containing 3- and 5-carbon linkers allowed for a similar extent of recovery from antagonism in the presence of 1 or 100 μM DA (>25 and >90% of control, respectively), whereas recovery was less prominent (∼20%) upon washout of the 4-carbon linker compound, SV-III-130, both with 1 and 100 μM DA. Prolonging the coincubation time with SV-III-130 further diminished recovery. Curve-shift experiments were consistent with competition between SV-III-130 and DA. Two mutations in the secondary binding pocket (V91A and E95A) of D2R decreased antagonistic potency and increased recovery from SV-III-130 antagonism, whereas a third mutation (L94A) only increased recovery. Our results suggest that the secondary binding pocket influences recovery from inhibition by the studied aripiprazole analogues. We propose a mechanism, supported by in silico modeling, whereby SV-III-130 initially binds reversibly to the D2R, after which the drug-receptor complex undergoes a slow transition to a second ligand-bound state, which is dependent on secondary binding pocket integrity and irreversible during the time frame of our experiments.
A solid understanding of the mechanisms governing ligand binding is crucial for rational design of therapeutics targeting the dopamine D2 receptor (D2R). Here, we use G protein-coupled inward rectifier potassium (GIRK) channel activation in Xenopus oocytes to measure the kinetics of D2R antagonism by a series of aripiprazole analogues, as well as the recovery of dopamine (DA) responsivity upon washout. The aripiprazole analogues comprise an orthosteric and a secondary pharmacophore and differ by the length of the saturated carbon linker joining these two pharmacophores. Two compounds containing 3- and 5-carbon linkers allowed for a similar extent of recovery from antagonism in the presence of 1 or 100 μM DA (>25 and >90% of control, respectively), whereas recovery was less prominent (∼20%) upon washout of the 4-carbon linker compound, SV-III-130, both with 1 and 100 μM DA. Prolonging the coincubation time with SV-III-130 further diminished recovery. Curve-shift experiments were consistent with competition between SV-III-130 and DA. Two mutations in the secondary binding pocket (V91A and E95A) of D2R decreased antagonistic potency and increased recovery from SV-III-130 antagonism, whereas a third mutation (L94A) only increased recovery. Our results suggest that the secondary binding pocket influences recovery from inhibition by the studied aripiprazole analogues. We propose a mechanism, supported by in silico modeling, whereby SV-III-130 initially binds reversibly to the D2R, after which the drug-receptor complex undergoes a slow transition to a second ligand-bound state, which is dependent on secondary binding pocket integrity and irreversible during the time frame of our experiments.
Entities:
Keywords:
HEK cells; PET scan; Xenopus oocytes; antipsychotics; arrestin; competitive binding; drug kinetics; molecular dynamics simulation
The
dopamine D2 receptor (D2R) is a G protein-coupled
receptor (GPCR) and an important pharmaceutical target. D2R antagonism or weak partial agonism is the common denominator of
antipsychotic drugs, and D2R agonism is a mainstay of Parkinson’s
disease treatment.[1−4] The time course of receptor occupancy has been suggested to have
an important impact on the clinical properties of therapeutic ligands,
including antipsychotics, where transient rather than continuous D2R occupancy may be associated with a more favorable profile
in terms of extrapyramidal side effects.[5] Ligand binding kinetics is presumed to play an important role in
determining the time course of occupancy at the target receptor.[6,7] For example, the action of angiotensin-1 receptor antagonists is
prolonged by their long-lasting, induced-fit binding to their target
receptor, reflected by insurmountable antagonism in in vitro experiments.[8] Insurmountable antagonism
is characterized by a decrease in the maximal agonist-induced response,
which cannot be overcome by increasing the concentration of agonist.[8]Similarly, differences in dissociation[9] or association kinetics[10] between antipsychotics
have been linked to their differential side-effect profiles, although
this remains a matter of debate.[11] Receptor
binding kinetics has also been predicted to be an important determinant
of positron emission tomography (PET) tracer characteristics, such
as sensitivity to endogenous neurotransmitter release.[12]The recently reported D2R crystal
structure reveals
a deep orthosteric binding pocket, situated in the plane of the cell
membrane between transmembrane segments 3, 5, and 6, as well as a
secondary binding pocket, located more extracellularly and mainly
comprising residues from transmembrane segment 2 and extracellular
loop 1.[13] In search of GPCR ligands with
beneficial pharmacological properties and enhanced selectivity, attention
has been drawn to bivalent ligands, consisting of two distinct pharmacophores
targeting both the orthosteric and the secondary binding pocket.[14] To facilitate parallel engagement of both pockets,
the orthosteric- and secondary pharmacophores are covalently joined
by a linker, the length of which has been found to be critical.[15] At the D2R, ligand interactions with
the secondary binding pocket have been reported to confer selectivity
over the closely related D3R and, in some cases, to impart
signaling bias or allosteric properties.[16,17] In particular, a cluster of residues in transmembrane segment 2,
including V91, L94, and E95, has been found to mediate important contacts
between the ligand and the secondary binding pocket.[18−20]A series of candidate PET radiotracers, designed to selectively
target D2R, were derived from the scaffold of the clinically
used antipsychotic, aripiprazole. These compounds are composed of
an orthosteric 2-methoxyphenylpiperazine pharmacophore and a secondary
dihydroquinolinone pharmacophore, linked by alkyl chains of varying
length.[15] SWR-1-8, SV-III-130, and SWR-1-14
contain chains of 3, 4, and 5 carbon atoms, respectively (Figure A), resulting in
different distances and relative orientations between the two pharmacophores.
SV-III-130 was found to be ∼20-fold more potent at the D2R and ∼40-fold more selective for the D2R over D3R compared to SWR-1-8 and SWR-1-14, demonstrating
the crucial impact of linker length on D2R affinity. [11C]-SV-III-130 has subsequently been used as a D2R selective PET tracer in nonhuman primates.[21]
Figure 1
Structures,
potencies, recovery from antagonism, and binding kinetics
of SWR-1-8, SV-III-130, and SWR-1-14 at the D2R. A) Structures
of SWR-1-8, SV-III-130, and SWR-1-14. B) Concentration–response
relationship for DA-induced GIRK activation in oocytes coexpressing
D2R, RGS4, and GIRK1/4 channels (EC50 = 33 nM; n = 4). C) Concentration–response curves for the
inhibition of the GIRK response to 100 nM DA by SWR-1-8 (n = 3), SV-III-130 (n = 3), and SWR-1-14 (n = 3). D) Recovery of D2R-mediated GIRK activation
by DA after antagonism by SWR-1-8 (n = 8 for 1 μM
DA and n = 5 for 100 μM DA), SV-III-130 (n = 11 for 1 μM DA and n = 12 for
100 μM DA), and SWR-1-14 (n = 7 for 1 μM
DA and n = 4 for 100 μM DA). Graphs show mean
GIRK current traces normalized to the maximal response evoked by 1
μM DA (40 s), followed by 30 μM SWR-1-8 or SWR-1-14 or
1 μM SV-III-130 coapplied with 1 μM DA (125 s) and finally
reversed by 1 μM (thick dotted line) or 100 μM (thick
solid line) DA (400 s). Thin lines indicate SEM. E) Extent of recovery
from antagonism following application of 1 or 100 μM DA (data
from experiments shown in panel D). F) Rate of recovery from antagonism
following application of 1 or 100 μM DA (data from experiments
shown in panel D). G) Observed rates of GIRK response decay, kobs, upon application of varying concentrations
of antagonist in the presence of 100 nM DA during 125 s; n = 3–7. Data shown are means ± SEM *; p < 0.05, ***; p < 0.001, and ****; p < 0.0001, Student’s t test.
Structures,
potencies, recovery from antagonism, and binding kinetics
of SWR-1-8, SV-III-130, and SWR-1-14 at the D2R. A) Structures
of SWR-1-8, SV-III-130, and SWR-1-14. B) Concentration–response
relationship for DA-induced GIRK activation in oocytes coexpressing
D2R, RGS4, and GIRK1/4 channels (EC50 = 33 nM; n = 4). C) Concentration–response curves for the
inhibition of the GIRK response to 100 nM DA by SWR-1-8 (n = 3), SV-III-130 (n = 3), and SWR-1-14 (n = 3). D) Recovery of D2R-mediated GIRK activation
by DA after antagonism by SWR-1-8 (n = 8 for 1 μM
DA and n = 5 for 100 μM DA), SV-III-130 (n = 11 for 1 μM DA and n = 12 for
100 μM DA), and SWR-1-14 (n = 7 for 1 μM
DA and n = 4 for 100 μM DA). Graphs show mean
GIRK current traces normalized to the maximal response evoked by 1
μM DA (40 s), followed by 30 μM SWR-1-8 or SWR-1-14 or
1 μM SV-III-130 coapplied with 1 μM DA (125 s) and finally
reversed by 1 μM (thick dotted line) or 100 μM (thick
solid line) DA (400 s). Thin lines indicate SEM. E) Extent of recovery
from antagonism following application of 1 or 100 μM DA (data
from experiments shown in panel D). F) Rate of recovery from antagonism
following application of 1 or 100 μM DA (data from experiments
shown in panel D). G) Observed rates of GIRK response decay, kobs, upon application of varying concentrations
of antagonist in the presence of 100 nM DA during 125 s; n = 3–7. Data shown are means ± SEM *; p < 0.05, ***; p < 0.001, and ****; p < 0.0001, Student’s t test.While important roles of the D2R secondary
binding pocket
in mediating subtype selectivity and allosteric effects have been
described, the putative involvement of this pocket in the reversibility
of antagonism has not been examined. Here, we compared the binding
kinetics, reversibility, and surmountability of the three aripiprazole
analogues and examined the role of the secondary binding pocket in
determining these characteristics. To this end, we used a G protein-coupled
inward-rectifying potassium (GIRK) channel assay as a time-resolved
readout of D2R occupancy by dopamine (DA)[22,23] and developed a mechanistic model, supported by molecular dynamics
simulations, explaining our observations.
Results and Discussion
Role of
Linker Length in Determining Potency, Kinetics, and
Surmountability of Antagonism
To determine the influence
of linker length on the kinetics, reversibility, and surmountability
of D2R antagonism, we studied the properties of the three
aripiprazole analogues, SWR-1-8, SV-III-130, and SWR-1-14, in antagonizing
DA-evoked GIRK activation in Xenopus oocytes coexpressing
D2R with GIRK1/4 channels and RGS4 (Figure A, B). SV-III-130 was more potent compared
to SWR-1-8 and SWR-1-14 (Figure C; Table ). The Ki values derived from these experiments
were in relative agreement with previous Ki data from [125I]-IABN radioligand binding experiments
(SWR-1-8; 4.8 ± 0.9 nM, SV-III-130; 0.22 ± 0.01 nM, and
SWR-1-14; 7.3 ± 1.3 nM;[15]). Ligand-induced
GIRK channel block was observed to be <10% in all cases, as determined
by application of 30 μM SWR-1-8, SWR-1-14, and SV-III-130 to
oocytes expressing GIRK channels in the absence of D2R
(Supplementary Figure S1). Previous investigations
of SV-III-130 at the D2R reported partial agonism in an
adenylate cyclase inhibition assay but antagonism in GIRK activation
and ERK1/2 assays.[16] In our hands, weak
partial agonism at the D2R in the GIRK activation assay
was observed for SV-III-130 (6.6% of the response to 1 μM DA)
but not for SWR-1-8 and SWR-1-14, which behaved as antagonists/inverse
agonists (Supplementary Figure S2).
Table 1
Binding Kinetics and Affinity Estimates
of Ligands at the D2R WTa
receptor
ligand
koff (s–1)
kon (s–1 × M–1)
pKd
pKi
D2R WT
SWR-1-8
0.017 ± 0.002 (5)
3.4 ± 0.4 × 105 (3–6)
7.30 ± 0.04
8.01 ± 0.18 (3)
D2R WT
SV-III-130
0.007 ± 0.001 (11)
8.6 ± 0.5 × 105 (3–6)
8.09 ± 0.04
8.57 ± 0.05 (3)
D2R WT
SWR-1-14
0.021 ± 0.002 (4)
3.0 ± 0.4 × 105 (4–7)
7.15 ± 0.04
7.70 ± 0.13 (3)
koff values were calculated from response recovery t1/2 as koff = ln
(2)/t1/2. See the Methods
section for derivation of kon.
pKd was calculated from the koff and kon estimates as Kd = koff/kon, while pKi was
calculated
from the IC50 for GIRK channel inhibition using the Cheng–Prusoff
equation,[25] assuming a Kd of DA equaling its EC50 for GIRK activation
in our assay; i.e., 33 nM. The number of oocytes is shown in parentheses;
for kon, this corresponds to the number
of oocytes for each data point (see Figure G). Data shown are means ± SEM.
koff values were calculated from response recovery t1/2 as koff = ln
(2)/t1/2. See the Methods
section for derivation of kon.
pKd was calculated from the koff and kon estimates as Kd = koff/kon, while pKi was
calculated
from the IC50 for GIRK channel inhibition using the Cheng–Prusoff
equation,[25] assuming a Kd of DA equaling its EC50 for GIRK activation
in our assay; i.e., 33 nM. The number of oocytes is shown in parentheses;
for kon, this corresponds to the number
of oocytes for each data point (see Figure G). Data shown are means ± SEM.Reversibility of D2R
antagonism was evaluated using
a protocol consisting of three steps: (i) a baseline response evoked
by a maximally effective concentration (1 μM) of DA, (ii) antagonism
of this response by 30 μM of SWR-1-8/SWR-1-14 or 1 μM
SV-III-130, and (iii) recovery of the response upon washout of the
antagonist ligand in the presence of 1 or 100 μM DA. The GIRK
response is essentially saturated at 1 μM DA (Figure B). Therefore, any additional
increase in response recovery with 100 μM DA should be an effect
of increased competition with antagonist ligand which remains dissolved
in the membrane and/or interior of the cell following washout, as
has been reported to occur for some lipophilic compounds.[22−24] For SWR-1-8, SV-III-130, and SWR-1-14, a response recovery fraction
of 0.2 to 0.4 was observed when using 1 μM DA in the recovery
phase, while increasing the DA concentration during the recovery phase
to 100 μM significantly increased the response recovery following
SWR-1-8 and SWR-1-14 application to about 0.9 to 1.0 (Figure D, E). Conversely, recovery
from SV-III-130-induced antagonism was about 0.2 under both conditions
(Figure D, E), indicative
of insurmountable behavior. The response recovery kinetics in the
presence of 100 μM DA, which we previously used as a measure
of antagonist dissociation rate (koff[23]), was swift for SWR-1-8 and SWR-1-14 but slower
for SV-III-130 (Figure F; Table ). Response
recovery kinetics was similar at 1 μM and 100 μM DA for
SWR-1-8 and SV-III-130 but more rapid at 100 μM compared to
1 μM DA for SWR-1-14 (Figure F).To estimate compound association rate constants
(kons), we employed our previously published
strategy,[23] using the decay rate of the
DA-evoked GIRK current
at different concentrations of antagonist as a proxy measure of the
antagonist binding rate. Plotting the observed rates of inhibition
of the current response to DA against varying concentrations of competing
ligand suggested a more rapid kon of SV-III-130
at the D2R, compared to SWR-1-8 and SWR-1-14 which exhibited
similar kons (Figure G; Table ).
SV-III-130 Behaves Competitively When Coapplied
with Different
Concentrations of DA
The lack of increased response recovery
from SV-III-130-mediated antagonism in the face of increased concentrations
of DA could be indicative of a noncompetitive or possibly allosteric
binding mechanism. To further evaluate this mechanism, we performed
a curve-shift assay to test whether SV-III-130 and DA compete for
binding to the D2R when the two ligands are coapplied.
First, 1 μM DA was applied to each cell to elicit a full agonist
response which could then be compared to the pseudosteady-state response
elicited by 10 nM to 100 μM DA coapplied with varying concentrations
of SV-III-130, or vehicle, after 500 s coapplication (Figure A). The DA concentration–response
curve was progressively right-shifted with increasing concentrations
of SV-III-130 without any appreciable effect on the maximal response
(Figure B), consistent
with competition between DA and SV-III-130 for D2R binding.
Thus, SV-III-130 displayed differential behavior (i.e., insurmountable
vs competitive) after first being bound to D2R and then
washed out/competed with DA (Figure D, E), compared to when coapplied with DA without prior
D2R binding (Figure ). GIRK currents are known to demonstrate a time-dependent
decrease due to alterations of intracellular sodium levels during
prolonged recording protocols.[26] The effect
of this rundown is evident in Figure B, where the GIRK current response at the end of the
500 s coapplication period is ∼60% of the instantaneous response
to 1 μM DA.
Figure 2
Curve-shift GIRK activation assay of D2R antagonism
upon coapplication of SV-III-130 and DA. A) Assay principles; 1 μM
DA elicits a full agonist response (left, red arrow). The subsequent
response amplitude in the presence of variable concentrations of SV-III-130
and DA, following 500 s coapplication (right, green arrow), was normalized
to the control response elicited by 1 μM DA. In the example
shown, 1 μM SV-III-130 coapplied with 100 μM DA; n = 3 oocytes. Thick lines represent mean normalized currents,
whereas thin lines indicate SEM. B) Current amplitude at the end of
the 500 s coapplication period, normalized to the instantaneous maximum
response amplitude in the same oocyte and plotted against DA concentration,
for varying concentrations of SV-III-130 or control. n = 3–7 oocytes per data point. Data shown are means ±
SEM.
Curve-shift GIRK activation assay of D2R antagonism
upon coapplication of SV-III-130 and DA. A) Assay principles; 1 μM
DA elicits a full agonist response (left, red arrow). The subsequent
response amplitude in the presence of variable concentrations of SV-III-130
and DA, following 500 s coapplication (right, green arrow), was normalized
to the control response elicited by 1 μM DA. In the example
shown, 1 μM SV-III-130 coapplied with 100 μM DA; n = 3 oocytes. Thick lines represent mean normalized currents,
whereas thin lines indicate SEM. B) Current amplitude at the end of
the 500 s coapplication period, normalized to the instantaneous maximum
response amplitude in the same oocyte and plotted against DA concentration,
for varying concentrations of SV-III-130 or control. n = 3–7 oocytes per data point. Data shown are means ±
SEM.
Insurmountability of SV-III-130
Antagonism Depends on the D2R Secondary Binding Pocket
The high potency of SV-III-130
antagonism at the D2R and the insurmountability of this
antagonism, as observed during the recovery phase when washing out
the ligand in the presence of 1 or 100 μM DA (see Figure ), likely arise from interactions
between the secondary pharmacophore and the secondary binding pocket,
given the differential behavior of both SWR-1-8 and SWR-1-14. Previous
investigations suggested a crucial role for residues V91, L94, and
E95 in contacting the secondary pharmacophore of bivalent D2R ligands, including SV-III-130.[16,19] In addition,
W100A in extracellular loop 1 is located at the extracellular boundary
of the secondary binding pocket and has been shown to affect bivalent
ligand affinity and to adopt different conformations depending on
the nature of the bound ligand.[13,27] To investigate the
role of the secondary binding pocket in shaping SV-III-130 binding
kinetics and insurmountability, V91, L94, E95, and W100 were individually
mutated to alanine. First, we validated the expression of the D2R mutants by immunoblot experiments. Anti-D2R antibodies
detected a broad protein band at 80–100 kDa (Supplementary Figure S3), corresponding to the expected size
of fully glycosylated D2R, as previously reported.[28,29] Importantly, this immunoreactive band was absent in striatal membranes
from D2R–/– mice and in total
membranes from uninjected oocytes (Supplementary Figure S3), thus indicating the specificity of the antibody
used. Overall, these results indicated that WT D2R, V91A,
L94A, E95A, and W100A receptors were properly expressed in oocytes.Next, we assessed the surmountability of SV-III-130 at the D2R mutants in oocytes. In the GIRK activation assay, the DA
potencies were similar for the WT and L94A mutant D2R and
slightly higher for the V91A and E95A mutants (Figure A). In contrast to the other mutant receptors,
the potency of DA at W100A was markedly reduced by about 10-fold compared
to WT (Figure A).
This probably reflects a loss of DA affinity as the Western blot experiments
indicated relatively similar expression of W100A, WT D2R, and the other D2R mutants (Supplementary Figure S3). Further supporting a link between functional DA
potency in our GIRK assay and DA binding affinity, we have previously
shown that there is little or no receptor reserve under our assay
conditions.[23] Furthermore, the E95A and
L94A mutants were shown to express at similar levels as WT and showed
insignificant changes in DA potency in a previous study,[18] while alanine mutation of the interaction partner
of W100A, I184, significantly reduced DA potency despite similar expression.
In order to achieve similar receptor occupancies by DA, we used 1
μM instead of 100 nM DA for constructing concentration–response
curves for SV-III-130-mediated inhibition at the W100A mutant (Figure B) and 10 instead
of 1 μM DA to elicit the baseline response when studying the
W100A mutant in response recovery experiments (Figure C).
Figure 3
Potencies, recovery from antagonism, and binding
kinetics of SV-III-130
at the V91A, L94A, and E95A mutant D2R. A) DA potency at
V91A (EC50 = 21 nM, n = 3–4), L94A
(EC50 = 41 nM, n = 3–7), E95A (EC50 = 15 nM, n = 3–4), W100A (EC50 = 323 nM, n = 3), and WT (EC50 = 33 nM, n = 4) D2R. B) SV-III-130 potency
at the V91A (n = 4), L94A (n = 3),
E95A (n = 7), and W100A (n = 3)
D2R. C) Recovery of activation by DA at the V91A (n = 3 for 1 μM DA and n = 4 for 100
μM DA), L94A (n = 13 for 1 μM DA and n = 13 for 100 μM DA), E95A (n =
5 for 1 μM DA and n = 3 for 100 μM DA),
and W100A (n = 4 for 10 μM DA and n = 4 for 300 μM DA) mutant D2R following antagonism
by SV-III-130. GIRK current traces normalized to the maximal response
evoked by 1 μM (10 μM for W100A) DA. Thick lines represent
mean normalized currents, whereas thin lines indicate SEM. D) Extent
of recovery upon application of 1 or 100 μM (10 and 300 μM
for W100A) DA following antagonism by 30 μM (V91A and E95A),
3 μM (W100A), and 1 μM SV-III-130 (L94A; data from experiments
shown in panel C). E) Rate of recovery following application of 1
or 100 μM DA (10 and 300 μM for W100A; data from experiments
shown in panel C). F) Observed association rates, kobs, which allowed for calculation of association rates
for SV-III-130 at the V91A, L94A, and E95A D2R. n = 3–7. G) Clustering of kinetic Kd relative to Ki for SWR-1-8,
SWR-1-14, and SV-III-130 at the WT receptor and SV-III-130 at the
V91A, L94A, and E95A mutant receptors, as indicated. Data shown are
means ± SEM *; p < 0.05, **; p < 0.01, and ***; p < 0.001, Student’s t test.
Potencies, recovery from antagonism, and binding
kinetics of SV-III-130
at the V91A, L94A, and E95A mutant D2R. A) DA potency at
V91A (EC50 = 21 nM, n = 3–4), L94A
(EC50 = 41 nM, n = 3–7), E95A (EC50 = 15 nM, n = 3–4), W100A (EC50 = 323 nM, n = 3), and WT (EC50 = 33 nM, n = 4) D2R. B) SV-III-130 potency
at the V91A (n = 4), L94A (n = 3),
E95A (n = 7), and W100A (n = 3)
D2R. C) Recovery of activation by DA at the V91A (n = 3 for 1 μM DA and n = 4 for 100
μM DA), L94A (n = 13 for 1 μM DA and n = 13 for 100 μM DA), E95A (n =
5 for 1 μM DA and n = 3 for 100 μM DA),
and W100A (n = 4 for 10 μM DA and n = 4 for 300 μM DA) mutant D2R following antagonism
by SV-III-130. GIRK current traces normalized to the maximal response
evoked by 1 μM (10 μM for W100A) DA. Thick lines represent
mean normalized currents, whereas thin lines indicate SEM. D) Extent
of recovery upon application of 1 or 100 μM (10 and 300 μM
for W100A) DA following antagonism by 30 μM (V91A and E95A),
3 μM (W100A), and 1 μM SV-III-130 (L94A; data from experiments
shown in panel C). E) Rate of recovery following application of 1
or 100 μM DA (10 and 300 μM for W100A; data from experiments
shown in panel C). F) Observed association rates, kobs, which allowed for calculation of association rates
for SV-III-130 at the V91A, L94A, and E95AD2R. n = 3–7. G) Clustering of kinetic Kd relative to Ki for SWR-1-8,
SWR-1-14, and SV-III-130 at the WT receptor and SV-III-130 at the
V91A, L94A, and E95A mutant receptors, as indicated. Data shown are
means ± SEM *; p < 0.05, **; p < 0.01, and ***; p < 0.001, Student’s t test.The inhibitory potency
(corrected for differences in DA potency
and expressed as Ki) of SV-III-130 was
decreased 9-fold for V91A and W100A and 4-fold for E95A mutant D2R (Figure B and Table ). In
contrast, SV-III-130 was slightly more potent at the L94A mutant receptor
(about 2-fold) compared to WT D2R (Figure B and Table ). Partial agonist activity of SV-III-130 was lost
at the V91A mutant but retained at the L94A and E95A mutants (Supplementary Figure S4).
Table 2
Binding Kinetics and Affinity Estimates
of SV-III-130 at D2R Secondary Binding Pocket Mutantsa
receptor
ligand
koff (s–1)
kon (s–1 × M–1)
pKd
pKi
D2R V91A
SV-III-130
0.066 ± 0.005 (4)
4.9 ± 0.4 × 105 (4–5)
6.87 ± 0.05
7.63 ± 0.16 (4)
D2R L94A
SV-III-130
0.007 ± 0.001 (13)
8.9 ± 0.6 × 105 (3–7)
8.10 ± 0.05
8.95 ± 0.17 (3)
D2R E95A
SV-III-130
0.022 ± 0.005 (3)
3.3 ± 0.4 × 105 (3–4)
7.18 ± 0.05
7.97 ± 0.13 (7)
D2R W100A
SV-III-130
0.010 ± 0.001 (4)
n.d.
n.d.
7.63 ± 0.07 (3)
koff values were calculated
from response recovery t1/2 as koff = ln (2)/t1/2. See Methods section for derivation of kon. pKd was calculated
from the koff and kon estimates as Kd = koff/kon, while pKi was calculated
from the IC50 for GIRK channel inhibition using the Cheng–Prusoff
equation,[25] assuming the Kd of DA at the various mutants to equal the corresponding
EC50 for GIRK activation (see the legend of Figure A). Number of oocytes in parentheses;
for kon, this corresponds to the number
of oocytes for each data point (see Figure F). Data shown are means ± SEM. n.d.,
not determined.
koff values were calculated
from response recovery t1/2 as koff = ln (2)/t1/2. See Methods section for derivation of kon. pKd was calculated
from the koff and kon estimates as Kd = koff/kon, while pKi was calculated
from the IC50 for GIRK channel inhibition using the Cheng–Prusoff
equation,[25] assuming the Kd of DA at the various mutants to equal the corresponding
EC50 for GIRK activation (see the legend of Figure A). Number of oocytes in parentheses;
for kon, this corresponds to the number
of oocytes for each data point (see Figure F). Data shown are means ± SEM. n.d.,
not determined.Response
recovery experiments (employing the same protocol as in Figure D) with SV-III-130
using 1 μM (10 μM with W100A) DA in the recovery phase
demonstrated an increased recovery at V91A, L94A, E95A, and W100A
mutant D2R as compared to WT D2R (Figure C, D). When 100 μM (300
μM with W100A) DA was used in the recovery phase, the extent
of recovery at the four D2R mutants increased further,
suggesting surmountable antagonism by SV-III-130 at these mutants
(Figure C, D). Accelerated
SV-III-130 recovery kinetics was observed with 1 μM and 100
μM DA for the V91A and E95A mutant D2R and with 10
and 300 μM DA for the W100A mutant, whereas for the L94A mutant,
the time to half-maximal recovery was similar to that observed for
WT D2R (Figure E). kon and kinetic Kd estimates for SV-III-130 at the V91A and E95A mutants
were lower than at the WT receptor, while kon and kinetic Kd appeared similar at the
L94A mutant and WT D2R (Figure F, G; Table ). The preservation of SV-III-130 kon at the L94A mutant suggests that a high kon, which may affect ligand competition by causing rapid
rebinding to the receptor,[10] is not sufficient
to explain the insurmountable antagonism of SV-III-130 at the WT receptor.
Kinetic Binding Models Support an Induced-Fit Binding Mode of
SV-III-130 at the D2R
The distinct extents of
recovery from antagonism and differing association and dissociation
rate constants of SWR-1-8, SWR-1-14, and SV-III-130 at the D2R indicate differential binding modes. Based on the demonstrated
surmountability of SWR-1-8 and SWR-1-14 antagonism at the WT D2R in the response recovery experiments (Figure D, E), a three-state binding model including
unbound receptor (R), agonist-bound receptor (RA), and ligand-bound
receptor (RL) was constructed using the experimentally determined kon and koff rate
constants (Figure A; eq in the Methods section). To account for lipophilic accumulation
in the cell membrane,[24] a residual ligand
fraction of 2% was assumed throughout the response recovery phase.
Modeling of the low extent of recovery from and insurmountable nature
of SV-III-130 antagonism required the incorporation of an irreversible,
second ligand-bound state (RL*; Figure B; eq in the Methods section).
Figure 4
Simulations of three-
and four-state ligand binding at a receptor.
A) Scheme depicting a surmountable antagonist ligand (L) binding to
the receptor (R), in competition with the agonist (A; DA). B) Scheme
depicting induced-fit insurmountable antagonist ligand binding, where
RL* represents an irreversibly bound antagonist ligand. C, D, E) Simulation
of response recovery from antagonism by SWR-1-8 (C), SV-III-130 (D),
and SWR-1-14 (E) at WT D2R, with 1 or 100 μM DA during
the recovery phase. The response is assumed to be proportional to
the fraction of the agonist-bound state; RA. F) Simulated recovery
of WT D2R activation by DA after prolonged, 400-s antagonism
with SV-III-130. G) Experimental recovery of WT D2R activation
by DA after prolonged, 400-s antagonism with SV-III-130. H) Simulated
curve-shift assay with SV-III-130 at WT D2R, plotting the
RA fraction after 500 s simulation time for different concentrations
of DA and SV-III-130, as indicated. I) Simulated concentration–response
curves for SV-III-130 antagonism at WT and L94A mutant D2R. “Normalized response” corresponds to the RA fraction
after 100 s of simulation time, in the presence of 100 nM DA and varying
concentrations of SV-III-130, as indicated. The L94A mutant was simulated
by removing the fourth state, RL*, from the model. J) Simulation of
response recovery from antagonism by SV-III-130 at the L94A mutant
D2R. As in I), the three-state model is employed, using
kinetic data for SV-III-130 from the L94A mutant. Simulations of SWR-1-8
(C; kon(RL) = 340 M–1 s–1, koff(RL) = 0.017
s–1), SV-III-130 (D; kon(RL) = 860 M–1 s–1, koff(RL) = 0.007 s–1, kon(RL*) = 0.01 s–1), and SWR-1-14 (E; kon(RL) = 300 M–1 s–1, koff(RL) = 0.021 s–1) at WT D2R were conducted in the presence of 1 or 100
μM DA as agonist. kon(A) = 5 ×
106 M–1 s–1 and koff(A) = 0.17 s–1 for all
simulations at WT D2R. Parameters for the three-state model
of SV-III-130 interaction at D2R L94A; kon(RL) = 890 M–1 s–1, koff(RL) = 0.007/s, kon(A) = 5 × 106 M–1 s–1, and koff(A) = 0.21/s. koff(A) = was adjusted as necessary to yield
a Kd corresponding to the DA EC50 at D2R L94A.
Simulations of three-
and four-state ligand binding at a receptor.
A) Scheme depicting a surmountable antagonist ligand (L) binding to
the receptor (R), in competition with the agonist (A; DA). B) Scheme
depicting induced-fit insurmountable antagonist ligand binding, where
RL* represents an irreversibly bound antagonist ligand. C, D, E) Simulation
of response recovery from antagonism by SWR-1-8 (C), SV-III-130 (D),
and SWR-1-14 (E) at WT D2R, with 1 or 100 μM DA during
the recovery phase. The response is assumed to be proportional to
the fraction of the agonist-bound state; RA. F) Simulated recovery
of WT D2R activation by DA after prolonged, 400-s antagonism
with SV-III-130. G) Experimental recovery of WT D2R activation
by DA after prolonged, 400-s antagonism with SV-III-130. H) Simulated
curve-shift assay with SV-III-130 at WT D2R, plotting the
RA fraction after 500 s simulation time for different concentrations
of DA and SV-III-130, as indicated. I) Simulated concentration–response
curves for SV-III-130 antagonism at WT and L94A mutant D2R. “Normalized response” corresponds to the RA fraction
after 100 s of simulation time, in the presence of 100 nM DA and varying
concentrations of SV-III-130, as indicated. The L94A mutant was simulated
by removing the fourth state, RL*, from the model. J) Simulation of
response recovery from antagonism by SV-III-130 at the L94A mutant
D2R. As in I), the three-state model is employed, using
kinetic data for SV-III-130 from the L94A mutant. Simulations of SWR-1-8
(C; kon(RL) = 340 M–1 s–1, koff(RL) = 0.017
s–1), SV-III-130 (D; kon(RL) = 860 M–1 s–1, koff(RL) = 0.007 s–1, kon(RL*) = 0.01 s–1), and SWR-1-14 (E; kon(RL) = 300 M–1 s–1, koff(RL) = 0.021 s–1) at WT D2R were conducted in the presence of 1 or 100
μM DA as agonist. kon(A) = 5 ×
106 M–1 s–1 and koff(A) = 0.17 s–1 for all
simulations at WT D2R. Parameters for the three-state model
of SV-III-130 interaction at D2RL94A; kon(RL) = 890 M–1 s–1, koff(RL) = 0.007/s, kon(A) = 5 × 106 M–1 s–1, and koff(A) = 0.21/s. koff(A) = was adjusted as necessary to yield
a Kd corresponding to the DA EC50 at D2RL94A.Assuming RA to be proportional to the experimentally observed GIRK
response, simulation of the experimental response recovery data presented
in Figure C for SWR-1-8
and SWR-1-14 using the three-state binding model recapitulated the
1 μM DA activation and blocking phases and demonstrated an increase
in the extent of response recovery with increasing DA concentration
(1 versus 100 μM DA; Figure C, E). For SV-III-130, the corresponding simulation
using the extended four-state binding model recapitulated the experimental
extent of recovery for both 1 and 100 μM of DA during the response
recovery phase (Figure D). The four-state model (Figure B) may be thought of as modeling induced-fit binding
and implies a time-dependence for SV-III-130 antagonism of the D2R, with a transition from RL to RL* defined by the fraction
1–1/(e*0.01), where t is time in seconds. The simulations predicted a RL-RL*
transition of ∼98% when SV-III-130 application was prolonged
from 125 to 400 s (Figure F). In agreement, in vitro experiments revealed
a virtual elimination of response recovery following application of
SV-III-130 during 400 s (Figure G). The four-state model also recapitulated the competitive
behavior of SV-III-130 when coapplied (without prior occupancy of
the receptor) with different concentrations of DA (Figure H), as was determined experimentally
in curve-shift experiments (Figure B).To simulate the L94A mutant receptor, at
which SV-III-130 did not
display insurmountable antagonism, the estimates of SV-III-130 kon and koff from
our experiments with L94AD2R were incorporated into a
three-state binding model. Simulated SV-III-130 inhibition curves
demonstrated similarities between the four-state (WT) and three-state
model with parameters from the L94A mutant D2R (Figure I). The simulated
curves support the notion that the irreversibly bound state contributes
very little to the Ki estimates derived
from inhibition curve experiments, which would be in agreement with
our experimental findings (see Figure G). The simulated response recovery from SV-III-130
antagonism in the three-state model (L94A mutant) was pronounced as
compared to the four-state model (WT), for both 1 and 100 μM
DA (Figure J).
L94A Mutation
Induces Conformational Changes in the Receptor
and Ligand Binding Mode of SV-III-130
To study the impact
of the L94A mutation on ligand binding and receptor dynamics at the
molecular level, we carried out all-atomistic molecular dynamics simulations
for the WT D2R and the L94A mutant receptor in complex
with SV-III-130 (Figure A). In the WT D2R, the orthosteric pharmacophore of SV-III-130
is buried deeply in the orthosteric binding pocket,[16,19] whereas the secondary pharmacophore is primarily stabilized by contacts
with I184 in extracellular loop 2 and W100 in extracellular loop 1
(shown as blue van der Waals radii; Figure A). Upon L94A mutation (orange van der Waals
radii; Figure A),
the ligand translates toward transmembrane segment 2 (yellow arrow
2; Figure A) while
maintaining similar contact ratios with I184 and W100 compared to
the WT (contact ratioW100/I184: 1.17 [mutant] vs 1.20 [WT]; Figure C, D). Interestingly,
the similar contact ratios correlate well with the similar estimated
affinities of SV-III-130 at the WT and L94A mutant receptors (Figure G).
Figure 5
Structural impact of
L94A mutation on SV-III-130. A) The most populated
SV-III-130 binding mode in the D2R WT (blue) and the L94A
(orange) receptors. Upon L94A mutation, the ligand translates toward
transmembrane segment 2 as indicated by the yellow arrows. Despite
translation in the L94A mutant, SV-III-130 is primarily sandwiched
by W100 and I184 similar to the WT complex. B) Comparison of the position
of W100 between the WT and L94A receptors in terms of distance between
Cα atoms of W100 and L/A94, as well as the position of the W100
side chain center of mass in the z-dimension (perpendicular
to the membrane). Both values are significantly different between
the WT and the L94A receptors. C) Representative ligand binding mode
in the WT receptor with W100 adopting a low z value
(putative RL complex). D) Representative ligand binding mode in the
L94A mutant receptor with W100 adopting a low z value
(putative RL complex). E, F) Ligand binding modes in the WT receptor
in which W100 adopts higher z values and stacks on
top of the ligand (potentially leading to RL* complexes). In C–F),
the position of the center of mass of the W100 side chain (red circle)
in the z-dimension (perpendicular to the membrane)
is highlighted. **; p < 0.01, Mann–Whitney
U test.
Structural impact of
L94A mutation on SV-III-130. A) The most populated
SV-III-130 binding mode in the D2R WT (blue) and the L94A
(orange) receptors. Upon L94A mutation, the ligand translates toward
transmembrane segment 2 as indicated by the yellow arrows. Despite
translation in the L94A mutant, SV-III-130 is primarily sandwiched
by W100 and I184 similar to the WT complex. B) Comparison of the position
of W100 between the WT and L94A receptors in terms of distance between
Cα atoms of W100 and L/A94, as well as the position of the W100
side chain center of mass in the z-dimension (perpendicular
to the membrane). Both values are significantly different between
the WT and the L94A receptors. C) Representative ligand binding mode
in the WT receptor with W100 adopting a low z value
(putative RL complex). D) Representative ligand binding mode in the
L94A mutant receptor with W100 adopting a low z value
(putative RL complex). E, F) Ligand binding modes in the WT receptor
in which W100 adopts higher z values and stacks on
top of the ligand (potentially leading to RL* complexes). In C–F),
the position of the center of mass of the W100 side chain (red circle)
in the z-dimension (perpendicular to the membrane)
is highlighted. **; p < 0.01, Mann–Whitney
U test.We found that L94A mutation creates
an empty space adjacent to
transmembrane segment 2 which becomes occupied by W100, enabling tight
packing of W100 against transmembrane segment 2 (Figure D). In contrast, the bulkier
L94 impedes such tight W100 packing in the WT receptor (Figure C). This finding was supported
by computing the distribution of the distances between the Cα
atoms of W100 and L/A94 in transmembrane segment 2 over the entire
simulation time (distanceW100 to TM2), which
revealed significantly shorter distances in the L94A mutant compared
to the WT D2R (Figure B, left panel). As a result of the tight W100 packing
(Figure A; yellow
arrow 1), SV-III-130 followed the movement of W100 (Figure A; yellow arrow 2) which in
turn led to an adaption of extracellular loop 2 (Figure A; yellow arrow 3).In
addition to this, the distance plot of W100 to transmembrane
segment 2 (Figure B, left panel) suggests that W100 in extracellular loop 1 is more
flexible in the WT D2R compared to the L94A mutant, as
reflected by its wider spatial distribution in the WT receptor. Among
these conformations, we observed receptor states with W100 buried
in the secondary binding pocket (Figure C) and conformations where W100 is exposed
to the solvent forming a “lid” on top of the ligand
(Figure E, F). The
location of W100 can be approximated by its position in the z dimension: a high z value (approximately
>22 Å) corresponds to the “lidlike” conformations
(Figure E, F), whereas
a low z value (approximately <22 Å) corresponds
to conformations where W100 is buried in the protein (Figure C). Interestingly, we found
that the “lidlike” conformations are only explored in
the WT receptor (Figure E, F) as highlighted by the box plot (Figure B, right panel). It is tempting to speculate
that such conformations obstruct the ligand exit gateway, leading
to a conformation of the D2R-SV-III-130 complex which has
a significantly slower koff than the conformation
presented in Figure C. Indeed, this hypothesis is supported by recent findings that L94
interacts with W100 and I184, forming a “lid” over the
secondary binding pocket in the risperidone-bound D2R crystal
structure, an interaction which influences ligand residence time in
radioligand binding experiments.[13] A recent
study by Lane et al.[30] likewise highlighted
the role of L94 in controlling the dynamics of W100 and also found
evidence for an important role of W100 in restricting ligand access
to and egress from the D2R orthosteric binding pocket.
Similar findings of ligand dissociation being restricted by a “lid”
formed by the extracellular loops have been reported for the serotonin
5-HT2A receptor as well.[31]As described above, we directly tested the role of W100 by mutagenesis,
creating a W100A D2R mutant. The loss of SV-III-130 affinity
observed at this mutant (Figure and Table ) is congruent with the molecular dynamics simulations presented
above, suggesting that W100 mediates important stabilizing contacts
between the secondary pharmacophore of SV-III-130 and the receptor
(Figure C, D). Notably,
the rates and extents of recovery from SV-III-130 inhibition were
increased at the W100A mutant, compared to WT D2R, both
when using 10 μM and 300 μM DA during the recovery phase
(Figure C–E).
These findings are in agreement with our hypothesis that W100 plays
a crucial role in trapping SV-III-130 in the WT D2R.
Surmountable and Insurmountable Behavior of Antagonist Ligands
in the GIRK Assay Is Recapitulated upon Ligand Preapplication in a
Beta-Arrestin Recruitment Assay
Using a BRET assay in transfected
HEK293 cells, full concentration–response curves for DA-induced
beta-arrestin2 recruitment to D2R were produced in the
presence of increasing concentrations of SWR-1-8, SV-III-130, and
SWR-1-14. Cells were preincubated with antagonist ligands for 5 min,
after which dopamine was added.Preincubation with SWR-1-8 or
SWR-1-14 induced a progressive right-shift of the concentration–response
curve for dopamine without affecting the maximum response amplitude
(Figure A, C), consistent
with competitive antagonism. On the other hand, the maximum effect
of dopamine was progressively diminished in the presence of increasing
concentrations of SV-III-130, while the EC50 of DA remained
virtually unchanged (Figure B), in agreement with an insurmountable mode of antagonism.
Figure 6
Curve-shift
beta-arrestin2 recruitment assay of D2R
antagonism resulting from preapplication of SWR-1-8, SV-III-130, and
SWR-1-14. Curve-shift experiments for DA-induced beta-arrestin2 recruitment
to D2R following 5 min preincubation with A) SWR-1-8, B)
SV-III-130, and C) SWR-1-14. The normalized data represent mean values
from three independent experiments (n = 3) performed
in triplicate. The curves represent the best fit to the data using
nonlinear regression analysis.
Curve-shift
beta-arrestin2 recruitment assay of D2R
antagonism resulting from preapplication of SWR-1-8, SV-III-130, and
SWR-1-14. Curve-shift experiments for DA-induced beta-arrestin2 recruitment
to D2R following 5 min preincubation with A) SWR-1-8, B)
SV-III-130, and C) SWR-1-14. The normalized data represent mean values
from three independent experiments (n = 3) performed
in triplicate. The curves represent the best fit to the data using
nonlinear regression analysis.Our study implies the existence of two distinct binding modes of
SV-III-130 at the D2R with the position of W100, relative
to the bound ligand, playing an important role in creating these two
states. The dynamics of W100 following ligand binding is apparently
slow enough to appreciate the existence of two separate binding states.
In agreement with the considerable flexibility of W100 suggested by
our molecular dynamics simulations, the position of this residue differs
markedly between the risperidone- and the haloperidol-bound D2R crystal structures.[13,27] Whereas W100 stacks
on top of risperidone, as noted above, the residue is rotated away
from the secondary binding pocket in the haloperidol-bound structure.[27] In future experiments, it will be interesting
to further study the role of W100 for the dissociation kinetics and
surmountabilities of risperidone and haloperidol. Moreover, the finding
that SV-III-130 behaves as an insurmountable antagonist when investigated
both in an assay of G protein-dependent signaling (GIRK activation)
and in an arrestin recruitment assay may imply that the conformation
of the secondary binding pocket, or at least of W100, does not differ
markedly between G protein- and arrestin-coupled states of D2R. This is particularly interesting given the suggested implication
of I184, which interacts with both SV-III-130 and W100, in mediating
agonist bias between G protein and arrestin signaling.[32]Our findings furthermore underscore how
measures of ligand potency
and kinetics can be heavily influenced by incubation time and order
of ligand addition: In the curve-shift GIRK experiments, SV-III-130
behaved as a classic competitive agonist when the ligand was added
simultaneously with DA, whereas in recovery experiments with WT D2R, there was a marked decrease in the ability of DA, even
at 100 μM, to activate the receptor following washout of SV-III-130
from the extracellular medium. Interestingly, this decrease became
even more pronounced with longer intervals of application of SV-III-130.
We interpret this phenomenon as an example of induced-fit binding.[8]The proposed induced-fit binding mechanism
of SV-III-130 may be
relevant for understanding the long-lasting receptor occupancy observed
with clinical dosing of the structurally similar weak partial agonist
antipsychotic, aripiprazole.[33] The information
beginning to be unraveled by the present study may also benefit PET
tracer development. Whereas [11C]-SV-III-130 binding is
displaced to some extent by amphetamine,[21] certain other D2R PET tracers, such as [11C]-(N-methyl)benperidol, show virtually no amphetamine-induced
displacement.[34] A radiotracer’s
receptor binding kinetics, as well as its tissue-to-plasma efflux
rate, has been suggested to affect sensitivity to endogenous transmitter
release,[12] and the reversibility of tracer
binding would also seem to be important for these characteristics.
Thus, better knowledge of the mechanisms responsible for induced-fit
insurmountable binding could potentially enable the rational design
of PET tracers suitable for measuring D2R density vs endogenous
DA release.As with all heterologous expression systems, the Xenopus oocyte system comes with several limitations. The
oocytes do not
express the full complement of D2R-interacting proteins
found in native cells, such as medium spiny neurons of the striatum.
Furthermore, GIRK channel currents are an indirect readout of GPCR
occupancy by agonist. However, the GIRK assay does allow for the study
of dynamic processes with high temporal resolution and without the
need for receptor modification. Importantly, we have previously shown
that our affinity estimates, derived either from IC50 values
or from estimates of kinetic rate constants, are in good agreement
with published data from radioligand binding studies.[23] Finally, it should also be noted that SV-III-130 binding
could be almost completely displaced by the D2/3R antagonist, eticlopride, in a previous PET study,[21] seemingly at odds with the irreversible binding implied
by our model. However, this displacement took place over a longer
time course (∼40 min) than studied in our experiments, suggesting
that the induced-fit binding of SV-III-130 might be reversible on
a longer time scale. Moreover, the ability to compete with SV-III-130
bound in the putative RL* state may be ligand-specific.
Conclusions
Our experimental and in silico findings support
two distinct binding modes of SV-III-130 at D2R, where
the first binding mode is competitive and surmountable by DA, whereas
the second, induced-fit binding mode is irreversible and hence insurmountable.
In particular, L94A mutation preserved SV-III-130 potency but abolished
its insurmountability. Molecular dynamics simulations suggested that
the L94A mutation might perturb the positioning of W100 in extracellular
loop 1 over the ligand binding site, reducing the prevalence of “lidlike”
conformations where W100 stacks on top of the ligand, preventing its
egress. Thus, trapping by W100 may be the structural mechanism for
insurmountable antagonism by SV-III-130. The present insights into
the role of the secondary binding pocket for induced-fit, irreversible
binding at the D2R may provide information for the prospective
development of improved therapeutic and radiotracer ligands.
Methods
Molecular Biology
WT humandopamine D2L
receptor (D2R) cDNA was subcloned into pXOOM (provided
by Dr. Søren-Peter Olesen, University of Copenhagen, Denmark).
Mutagenesis was performed by Genscript Biotech (Piscataway, NJ). All
mutations were verified by sequencing. cDNA encoding humanGIRK1 (Kir3.1),
GIRK4 (Kir3.4) (provided by Dr. Terence Hebert, University of Montreal,
Canada), and regulator of G protein signaling 4 (RGS4) (from the Missouri
cDNA Resource Center; www.cdna.org) were in pCDNA3 (Invitrogen). Plasmids were linearized using the
appropriate restriction enzymes (D2R, RGS4; XhoI and GIRK1/GIRK4;
NotI), followed by in vitro transcription using the
T7 mMessage mMachine kit (Ambion, Austin, TX). cRNA concentration
and purity were determined by spectrophotometry.
Oocyte Preparation
Oocytes from the African clawed
toad, Xenopus laevis, were isolated surgically as
described previously.[35] The surgical procedures
were approved by the Swedish National Board for Laboratory Animals
and the Stockholm Ethical Committee. Following 24-h incubation at
12 °C, oocytes were injected (using a Nanoject microinjector;
Drummond Scientific) with 0.2 ng of D2L receptor cRNA,
40 ng of RGS4 cRNA, and 1 ng of each GIRK1 and GIRK4 cRNA in a volume
of 50 nL per oocyte. RGS4 is a GTPase activating protein and was included
in order to speed up the kinetics of G protein turnover, such that
GIRK channel opening more closely follows D2R occupancy
by DA.
D2R Ligands
DA was purchased from Sigma-Aldrich
(St. Louis, MO). SWR-1-8, SWR-1-14, and SV-III-130 were synthesized
as previously described,[15] dissolved in
DMSO, and diluted in the recording buffer to a maximum final DMSO
concentration of 0.3% v/v.
Electrophysiology Methods
Following
incubation of oocytes
for 5–7 days at 12 °C, two-electrode voltage-clamp (CA-1,
Dagan, Minneapolis, MN) recordings were conducted at room temperature
(22 °C), as previously described.[35] Data were acquired at a membrane potential of −80 mV and
134 Hz sampling frequency using pCLAMP8 (Molecular Devices, Sunnyvale,
CA). To increase the inward rectifier potassium channel current at
negative potentials, a high potassium concentration extracellular
perfusion buffer was used (in mM: 64 NaCl, 25 KCl, 0.8 MgCl2, 0.4 CaCl2, 15 HEPES, 1 ascorbic acid, adjusted to pH
7.4), yielding a K+ reversal potential of about −40
mV. Ascorbic acid was used to prevent the spontaneous oxidation of
DA. Oocytes were perfused with solutions at a rate of 1.5 mL/min using
the pressure-driven, computer-controlled SmartSquirt system (Automate
Scientific, Berkeley, CA).
Gel Electrophoresis and Immunoblotting
Striata from
WT and D2R knockout mice (tissue from an earlier study;
Taura et al., 2018[29]) or frozen injected
oocytes were homogenized in ice-cold 50 mM Tris HCl buffer (pH 7.4)
containing a protease inhibitor cocktail (Roche Molecular Systems,
Pleasanton, CA) using a Polytron for three periods of 10 s each. The
homogenate was centrifuged for 10 min at 1000g. The
resulting supernatant was centrifuged for 30 min at 12000g to pellet total membranes. The oocyte total membrane fractions were
solubilized in 1% Triton X-100 to eliminate a major contaminating
band of equivalent molecular mass that alters the normal migration
of D2R.[36]Sodium dodecyl
sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was performed
using 10% polyacrylamide gels. Proteins were transferred to a Hybond-LFP
polyvinylidene difluoride (PVDF) membrane (GE Healthcare, Chicago,
IL) using a Trans-Blot SD Semi-Dry Transfer Cell (Bio-Rad, Hercules,
CA). The PVDF membrane was blocked with 5% (w/v) dry nonfat milk in
phosphate-buffered saline containing 0.05% Tween-20 (PBS-T) for 45
min and immunoblotted using rabbit polyclonal anti-D2R
(1 μg/mL; Frontier Institute Co. Ltd., Ishikari City, Japan)
antibody in a blocking solution overnight at 4 °C. The PVDF membrane
was then washed with PBS-T three times (5 min each) before incubation
with horseradish peroxidase (HRP)-conjugated goat anti-rabbit IgG
(1/30,000; Pierce Biotechnology, Rockford, IL) in a blocking solution
at 20 °C during 2 h. After washing the PVDF membranes with PBS-T
three times (5 min each), the immunoreactive bands were developed
using a chemiluminescent detection kit (Thermo Fisher Scientific,
Waltham, MA) and detected with an Amersham Imager 600 (GE Healthcare
Europe GmbH, Barcelona, Spain). Subsequently, the PVDF membrane was
also immunoblotted with rabbit polyclonal anti-β-tubulin-HRP
(0.16 μg/mL; ab21058, Abcam, Cambridge, UK) for protein loading
control.
Cell Culture
Cell culture reagents and selection antibiotics
were purchased from LifeTechologies/Invitrogen (Grand Island, NY).
The D2 BRET cell line was constructed as indicated below.
All other buffers and compounds were purchased from Sigma-Aldrich
(St Louis, MO), unless specified otherwise. Stable D2-Rluc8
– Arrestin-Venus cells (D2-BRET-Arr) were created by doubly
transfecting Flp-In T-REx 293 HEK cells (Invitrogen, Carlsbad, CA)
with a beta-arrestin-2-mVenus acceptor vector expressed constitutively
and a D2 DAR-Rluc8 donor vector under control of a tetracycline
inducible promoter. In this way, the expression of the D2 DAR can be induced and thus the receptor-donor/arrestin expression
ratio controlled. D2-BRET-Arr cells were cultured in Dulbecco’s
modified Eagle’s Medium containing 10% FBS, 1000 units/mL penicillin,
1000 μg/mL streptomycin, 100 mM sodium pyruvate, 1 μg/mL
gentamicin, 2 μg/mL puromycin, and 100 μg/mL hygromycin.
Beta-Arrestin Recruitment Assay
Direct protein–protein
interaction between D2R and beta-arrestin2 was analyzed
using BRET assays where the interaction of the receptor (donor) with
beta-arrestin2 (acceptor) results in a shift of the emission spectra
of the Rluc8 tag (after incubation with coelenterazine-h) from 485
to 525 nm as previously described by our laboratory.[37] The resulting luminescence was read and quantified on a
Flexstation III multiplate reader (Molecular Devices, San Jose, CA).
Results were expressed as a normalized ratio of emission observed
with control agonist alone. Since the BRET signal is dependent on
the donor/acceptor expression ratio, this must be optimized in order
to achieve the best response by varying the expression level of the
Rluc8-tagged receptor. D2-BRET-Arr cells were seeded at
3 × 106 cells/144 mm dish in culture media without
puromycin or hygromycin selection. Adherent cells were then incubated
with 40 nM tetracycline added directly to the culture media to induce
D2R expression. The cells were then incubated for 24 h
at 37 °C in 5% CO2 and 90% humidity. Following incubation,
cells were centrifuged at 1000g for 10 min and resuspended
(200,000 cells/mL) in Dulbecco’s Phosphate Buffered Saline
containing 0.01% sucrose. Cells were dispensed into solid-bottom white
96-well plates (Greiner Bio-one, Monroe, NC) at 100 μL/well
(20,000 cells/well) and incubated at room temperature for 45 min.
Following incubation, cells were incubated for 5 min with 5 μM
coelenterazine h (Nanolight Technology, Pinetop, AZ) in the dark.
Cells were then stimulated with the appropriately diluted agonist
for 5 min prior to reading. For antagonist assays, a test compound
was added to the cells and incubated for 5 min prior to agonist addition.
Concentration–Response Data Analysis
Electrophysiological
data were analyzed using Clampfit (Molecular Devices). Concentration–response
curves were calculated using the variable-slope sigmoidal functions
in GraphPad 5. For IC50 estimation, 100 nM DA was applied
to an oocyte to provide a baseline response, followed by increasing
concentrations of antagonist applied with 100-s intervals (for SWR-1-8
and SWR-1-14, 50-s intervals were used, as their relatively rapid
kinetics allowed for faster equilibration). For each cell, the response
amplitude at the end of each antagonist application interval was normalized
to the current elicited by 100 nM DA at the beginning of the protocol.
Data were fitted to the equationwhere Y is the response as
a fraction of 1, bottom is the maximal response inhibition evoked
by the antagonist, and X is the logarithm of ligand
concentration.For DA potency data, increasing concentrations
of DA were applied at 25-s intervals, and the response amplitudes
achieved with each concentration normalized to the response evoked
by 100 μM DA. The equation used for fitting agonist data wasIntrinsic efficacy of the ligands was evaluated
by a 100 s application and normalization to the response of 1 μM
DA in the same oocyte.[38] Data points were
represented as mean ± SEM.For curve-shift experiments,
a maximal response was first evoked
by application of 1 μM DA, which was subsequently washed out,
followed by the application of DA in the presence (or absence, to
generate the control curve for DA alone) of different concentrations
of SV-III-130. The current amplitude following 500 s of coapplication
of DA and SV-III-130 was normalized to the initial response elicited
by 1 μM DA.
Estimation of Rate Constants
Association
rate constants, kon, were calculated based
on the observed association
rate, kobs, in accordance with previous
descriptions[23]where
the antagonist concentration is known,
and the fraction of unoccupied receptors, R0, prior to antagonist application is derived from the concentration–response
curve of DA at D2R. Specifically, R0 for 100 nM DA at the WT D2R was estimated as 0.30
(Figure B). koff was estimated separately aswhere t1/2 is
the time for half-maximal response recovery.Ligand affinity
estimates based on binding kinetics were calculated as
Receptor
Binding Models
Recovery from D2R antagonism was
modeled as a three-state process, using experimental
values for kon and koff. The three states capturing competitive binding were unbound
receptor (R), agonist-bound receptor (RA), and ligand-bound receptor
(RL)where kon and koff are association and
dissociation rate constants for the competing ligand (L) and the agonist
DA (A). The induced-fit ligand binding was modeled aswhere RL*
denotes the ligand
bound to the induced-fit state of the receptor, and k2 is the association rate of the ligand to the RL* state.
Derivation of Kinetic Parameters
Based on the previously
described t1/2 for D2R-induced
GIRK response termination (in the presence of RGS4) upon DA washout,[39] the agonist dissociation rate koff(A) was approximated to 0.17/s. The association rate
constant kon(A) was calculated from the
experimental DA EC50: koff/EC50 = kon = 5 × 106 M–1 s–1. For the induced-fit
model (eq ), a constant,
irreversible flux kon(RL*) from RL to
RL* was selected with a time constant of 100 s to recapitulate the
features of the response recovery experiments.
Molecular
Dynamics Simulations
Molecular dynamics simulations
have been proven valuable for shedding light on molecular mechanisms
underlying ligand binding and GPCR functionality.[40−42] To generate
the D2R-SV-III-130 WT complex, we utilized the crystal
structure of the D2R (PDB code: 6CM4). The ligand was docked into the D2R structure using the standard docking protocol from MOE (www.chemcomp.com). The final
docking pose was selected based on scoring and visual inspection.
The generated WT complex was aligned to the membrane using the OPM
database,[43] placed in a POPC membrane,
and solvated with TIP3 waters, using the CHARMM-GUI server.[44] The ionic strength of the system was kept at
0.15 M using NaCl ions. The L94A system was generated by introducing
the mutation using the CHARMM-GUI pipeline.Simulations were
carried out similarly to previously published protocols[45−47] using the ACEMD simulation package.[48] Ligand parameters were assigned by ParamChem from the CGenFF force
field.[49,50] Parameters for other system components were
obtained from CHARMM36m[51] and CHARMM36
force fields.[52] In the simulation protocol,
we adhere to the guidelines of the GPCRmd consortium.[53]The systems were first relaxed during 200 ns of simulations
under
constant pressure and temperature (NPT) with a time step of 2 fs,
with gradually decreasing harmonic constraints applied to the protein
backbone. Temperature was maintained at 310 K using the Langevin thermostat,[54] and pressure was kept at 1 bar using the Berendsen
barostat.[55] The equilibration run was followed
by four 800 ns production runs under constant volume and temperature
(NVT) with a 4 fs time step. This allowed us to amass a complete simulation
time of 3.2 μs for the WT and L94A systems, respectively. The
temperature was maintained at 310 K using the Langevin thermostat.
No harmonic constraints are applied in the NVT phase. In all simulations,
we used van der Waals and short-range electrostatic interactions with
a cutoff of 9 Å and the particle mesh Ewald method[56] for long-range electrostatic interactions.Ligand–receptor contacts were quantified using the “get_contacts”
script.[57] The computed ratio of W100 and
I184 contacts was quantified by dividing the stability of W100 contacts
by I184 contacts.
Authors: Carmen Klein Herenbrink; Ravi Verma; Herman D Lim; Anitha Kopinathan; Alastair Keen; Jeremy Shonberg; Christopher J Draper-Joyce; Peter J Scammells; Arthur Christopoulos; Jonathan A Javitch; Ben Capuano; Lei Shi; J Robert Lane Journal: ACS Chem Biol Date: 2019-08-05 Impact factor: 5.100
Authors: Marta Sanchez-Soto; Ravi Kumar Verma; Blair K A Willette; Elizabeth C Gonye; Annah M Moore; Amy E Moritz; Comfort A Boateng; Hideaki Yano; R Benjamin Free; Lei Shi; David R Sibley Journal: Sci Signal Date: 2020-02-04 Impact factor: 8.192
Authors: Kristoffer Sahlholm; Hugo Zeberg; Johanna Nilsson; Sven Ove Ögren; Kjell Fuxe; Peter Århem Journal: Eur Neuropsychopharmacol Date: 2016-01-14 Impact factor: 4.600
Authors: J Robert Lane; Ara M Abramyan; Pramisha Adhikari; Alastair C Keen; Kuo-Hao Lee; Julie Sanchez; Ravi Kumar Verma; Herman D Lim; Hideaki Yano; Jonathan A Javitch; Lei Shi Journal: Elife Date: 2020-01-27 Impact factor: 8.140
Authors: Ravi Kumar Verma; Ara M Abramyan; Mayako Michino; R Benjamin Free; David R Sibley; Jonathan A Javitch; J Robert Lane; Lei Shi Journal: PLoS Comput Biol Date: 2018-01-16 Impact factor: 4.475
Authors: David A Sykes; Holly Moore; Lisa Stott; Nicholas Holliday; Jonathan A Javitch; J Robert Lane; Steven J Charlton Journal: Nat Commun Date: 2017-10-02 Impact factor: 14.919