virtual screening studies in search of dopamine d1 receptor ligands as antipsychotic agents
TRANSCRIPT
Adam Bucki,1 Marcin Feder,2 Maciej Pawłowski,1 and Marcin Kołaczkowski 1,2
VIRTUAL SCREENING STUDIES IN SEARCH OF DOPAMINE D1 RECEPTOR LIGANDS AS ANTIPSYCHOTIC AGENTS
1Jagiellonian University Collegium Medicum, Cracow, Poland; 2Adamed Ltd., Pieńków, Poland
Glide, Induced Fit Docking and Phase were implemented in Schrödinger Suite 2010, licensed for Jagiellonian University Collegium Medicum.
1. Kołaczkowski M., Bucki A., Feder M., Pawłowski M. Ligand-optimized homology models of D1 and D2 dopamine receptors: Application for virtual screening. J. Chem. Inf. Model. 2013, 53, 638-48.
2. Goldman-Rakic P. S., Castner S. A., Svensson T. H., Siever L. J., Williams G. V. Targeting the Dopamine D1 Receptor in Schizophrenia: Insights for Cognitive Dysfunction. Psychopharmacology (Berl.) 2004, 174, 3–16.
3. Kolaczkowski M., Marcinkowska M., Bucki A., Pawlowski M., Krukowski A., Rusiecki R., Siwek A., Wolak M. Sulphonamide Derivatives of Alicyclic Amines for the Treatment of Central Nervous System Diseases. WO2013001505 (A2), January 3, 2013.
Virtual screening (VS) utilizing homology models of target receptors is a widely practised computational approach of structure-based drug design (SBDD). It allows for a rapid and increasingly efficacious assessment of biological activity of large libraries of chemical entities by high-throughput docking (HTD). We have developed method of building reliable ligand-optimized homology models of D1 and D2 dopamine receptors (D1R and D2R) and described several issues connected with their preparation and applicability in VS trials.1
Dopamine D1 receptors are involved in regulation of a variety of physiological processes affecting e.g. cognition, behavior and motor functions. Therefore compounds possessing D1R activity are supposed to be effective in therapy of cognition impairment and negative symptoms of schizophrenia.2
Dopamine D2 receptor ligands are well known to be effective in ameliorating positive symptoms of schizophrenia.
Rational design of novel D1R / D2R ligands is difficult because of distinct requirements for ligand spatial configuration, resulting from their binding sites. We therefore carried out VS study of our in house database of approximately 4200 compounds designed as monoaminergic receptors ligands in search of potential D1R affinity.
Homology model validation – retrospective virtual screening
Introduction Prospective virtual screening
Homology model preparation
References VS decoy database
The database was prepared based on ZINC’s usual CNS permeable subset which contains 344 596 chemical entities, characterized by properties, which favor blood−brain barrier permeability (PSA: 0 − 60, MW:150 − 400, and predicted xlogP: 1.5 − 2.7).
In order to exclude compounds considered to be unable to bind with monoaminergic receptors, the database was filtered with a simple pharmacophore model, representative for monoaminergic receptor ligands. To prepare this model, we selected several known antipsychotic drugs and found common pharmacophore features employing Phase. The two most important were taken into account: positively charged amine group and aromatic ring, situated in a distance of 6±1 Å from each other.
The designed database consisted of 17 196 compounds.
Active ligands library For virtual screening trials, the database was enriched with a set of 340 high-affinity ligands of D1R.
Ligands displaying the lowest Ki values for D1R (< 100nM) were acquired from ChEMBL database.
In vitro binding results
Conclusions
Homology models used in docking experiments performed well in VS studies. The obtained enrichments in test VS were significantly higher than random distribution, particularly when using combined results obtained from docking to 3 receptor models.
VS of 4200 compounds followed by in vitro binding assay of 411 selected compounds, resulted in 172 confirmed hits (hit rate 42%), verifying high capacity of VS tool in prediction of D1R affinity.
Amongst 5 distinct chemotypes, 4 may be considered as analogs of known antipsychotics displaying affinity for D1R (i.e. olanzapine, risperidone, ziprasidone) and therefore being somehow obvious.
One of them - arylsulfonamide derivative of aryloxyethylazetidine was recognized as a novel scaffold of D1R / D2R ligands. The representative compound (ADN-3772) displayed affinity for D1R equal 100%, while for D2R – 99% (inhibition of control specific binding in the concentration of 1μM).
3 Functional assays revealed its partial agonism efficacy in D2R (57% agonist effect and 97% antagonist effect in 1.0E-06 M concentration) and antagonism to D1R.
Negative symptoms Positive symptoms
Excessive stimulation of D2R in the limbic structures
Dopamine transmission
deficit in frontal cortex (D1R)
Optimization of binding site through induced-fit docking of active ligands
„RECONSTRUCTION OF A LOCK ON A KEY”
Single ligand‐optimized model EF1% = 17 BEDROC = 0.325
Combination of 3 best‐performing models EF1% = 19 BEDROC = 0.330 Random distribution
0
20
40
60
80
100
0 10 20 30 40 50 60 70 80 90 100
% of a
ctive compo
unds fo
und
% database
D1R/β2AR sequence alignment: GeneSilico Metaserver
Crude receptor models: Swiss-Model
Model selection: Glide XP VS criterion:
BEDROC
(1) EF1% = 17 BEDROC = 0.325 (2) EF1% = 17 BEDROC = 0.306
(3) EF1% = 19 BEDROC = 0.305
Library of 4190* original chemical entities:
compounds designed as monoaminergic receptors ligands,
potentially active in CNS disorders
*1213 structures published in 5 international patent applications
Automated docking to 3 homology models of D1R (Glide XP)
Affinity of best-scored (Glidescore) 411 compounds was determined by in vitro radioligand binding studies (Cerep, France)
172 compounds of substantial affinity for D1R identified (hit rate = 42%) >90% inhibition of control specific binding at 1.0E-06 M
5 (out of 9 in total) clusters representing distinct chemotypes:
*Test compound concentration: 1.0E-06 M Assay carried out in duplicate (n=2)
Hot ligand: SCH23390 (Ki = 1.3E-10 M)
Compound Structure GlideScore % inhibition of control
specific binding*
ADN-0958 -7.25 99.2
ADN-2039 -7.86 100
ADN-1300 -9.87 100
ADN-1435 -8.22 100
ADN-3772 -11.81 100
Olanzapine - - 94