A molecular basis for selective antagonist destabilization of dopamine D3 receptor quaternary organization

The dopamine D3 receptor (D3R) is a molecular target for both first-generation and several recently-developed antipsychotic agents. Following stable expression of this mEGFP-tagged receptor, Spatial Intensity Distribution Analysis indicated that a substantial proportion of the receptor was present within dimeric/oligomeric complexes and that increased expression levels of the receptor favored a greater dimer to monomer ratio. Addition of the antipsychotics, spiperone or haloperidol, resulted in re-organization of D3R quaternary structure to promote monomerization. This action was dependent on ligand concentration and reversed upon drug washout. By contrast, a number of other antagonists with high affinity at the D3R, did not alter the dimer/monomer ratio. Molecular dynamics simulations following docking of each of the ligands into a model of the D3R derived from the available atomic level structure, and comparisons to the receptor in the absence of ligand, were undertaken. They showed that, in contrast to the other antagonists, spiperone and haloperidol respectively increased the atomic distance between reference α carbon atoms of transmembrane domains IV and V and I and II, both of which provide key interfaces for D3R dimerization. These results offer a molecular explanation for the distinctive ability of spiperone and haloperidol to disrupt D3R dimerization

Human blue cone opsin regeneration involves secondary retinal binding with analog specificity

Human color vision is mediated by the red, green, and blue cone visual pigments. Cone opsins are G-protein-coupled receptors consisting of an opsin apoprotein covalently linked to the 11-cis-retinal chromophore. All visual pigments share a common evolutionary origin, and red and green cone opsins exhibit a higher homology, whereas blue cone opsin shows more resemblance to the dim light receptor rhodopsin. Here we show that chromophore regeneration in photoactivated blue cone opsin exhibits intermediate transient conformations and a secondary retinoid binding event with slower binding kinetics. We also detected a fine-tuning of the conformational change in the photoactivated blue cone opsin binding site that alters the retinal isomer binding specificity. Furthermore, the molecular models of active and inactive blue cone opsins show specific molecular interactions in the retinal binding site that are not present in other opsins. These findings highlight the differential conformational versatility of human cone opsin pigments in the chromophore regeneration process, particularly compared to rhodopsin, and point to relevant functional, unexpected roles other than spectral tuning for the cone visual pigmentsPeer ReviewedPostprint (author's final draft

Combined docking and machine learning identify key molecular determinants of ligand pharmacological activity on β2 adrenoceptor

G protein-coupled receptors (GPCRs) are valuable therapeutic targets for many diseases. A central question of GPCR drug discovery is to understand what determines the agonism or antagonism of ligands that bind them. Ligands exert their action via the interactions in the ligand binding pocket. We hypothesized that there is a common set of receptor interactions made by ligands of diverse structures that mediate their action and that among a large dataset of different ligands, the functionally important interactions will be over-represented. We computationally docked ~2700 known β2AR ligands to multiple β2AR structures, generating ca 75 000 docking poses and predicted all atomic interactions between the receptor and the ligand. We used machine learning (ML) techniques to identify specific interactions that correlate with the agonist or antagonist activity of these ligands. We demonstrate with the application of ML methods that it is possible to identify the key interactions associated with agonism or antagonism of ligands. The most representative interactions for agonist ligands involve K972.68×67 , F194ECL2 , S2035.42×43 , S2045.43×44 , S2075.46×641 , H2966.58×58 , and K3057.32×31 . Meanwhile, the antagonist ligands made interactions with W2866.48×48 and Y3167.43×42 , both residues considered to be important in GPCR activation. The interpretation of ML analysis in human understandable form allowed us to construct an exquisitely detailed structure-activity relationship that identifies small changes to the ligands that invert their pharmacological activity and thus helps to guide the drug discovery process. This approach can be readily applied to any drug target

Jardins per a la salut

Facultat de Farmàcia, Universitat de Barcelona. Ensenyament: Grau de Farmàcia. Assignatura: Botànica farmacèutica. Curs: 2014-2015. Coordinadors: Joan Simon, Cèsar Blanché i Maria Bosch.Els materials que aquí es presenten són el recull de les fitxes botàniques de 128 espècies presents en el Jardí Ferran Soldevila de l’Edifici Històric de la UB. Els treballs han estat realitzats manera individual per part dels estudiants dels grups M-3 i T-1 de l’assignatura Botànica Farmacèutica durant els mesos de febrer a maig del curs 2014-15 com a resultat final del Projecte d’Innovació Docent «Jardins per a la salut: aprenentatge servei a Botànica farmacèutica» (codi 2014PID-UB/054). Tots els treballs s’han dut a terme a través de la plataforma de GoogleDocs i han estat tutoritzats pels professors de l’assignatura. L’objectiu principal de l’activitat ha estat fomentar l’aprenentatge autònom i col·laboratiu en Botànica farmacèutica. També s’ha pretès motivar els estudiants a través del retorn de part del seu esforç a la societat a través d’una experiència d’Aprenentatge-Servei, deixant disponible finalment el treball dels estudiants per a poder ser consultable a través d’una Web pública amb la possibilitat de poder-ho fer in-situ en el propi jardí mitjançant codis QR amb un smartphone

Structure and function of GPCRs

Los receptores acoplados a proteínas G (GPCRs) son la superfamilia más grande y diversa de proteínas transmembrana en Eucariotas. Estos receptores transducen una gran variedad de señales exógenas y endógenas como fotones, hormonas o neurotransmisores para iniciar la respuesta biológica en el interior de la célula. Son, por lo tanto, muy interesantes como dianas farmacológicas. Esta Tesis Doctoral se centra en la comprensión de la estructura y función de los GPCRs, mediante el uso de técnicas de la química computacional como son el modelado por homología, el anclaje molecular y las simulaciones de dinámica molecular. En concreto, la tesis aborda los determinantes estructurales asociados al mecanismo de activación, la regulación por moduladores alostéricos, la oligomerización con otro GPCR o proteínas adicionales, asícomo el acoplamiento de transductores (proteínas G o arrestinas).G protein-coupled receptors (GPCRs) are the largest and most diverse superfamily of transmembrane proteins in Eukaryotes. GPCRs transduce a huge variety of exogenous and endogenous signals such as photons, hormones or neurotransmitters to initiate biological responses in the cell interior. Therefore, they are very interesting therapeutic targets. This Doctoral Thesis focusses on the understanding of the structure and function of GPCRs, by applying computational chemistry techniques such as homology modelling, docking and molecular dynamics simulations. Particularly, the thesis addresses the structural determinants associated to the activation mechanism, the regulation by allosteric modulators, the oligomerization with other GPCR or additional proteins and the coupling to transducers (G proteins or arrestins)

Structure and function of GPCRs

Los receptores acoplados a proteínas G (GPCRs) son la superfamilia más grande y diversa de proteínas transmembrana en Eucariotas. Estos receptores transducen una gran variedad de señales exógenas y endógenas como fotones, hormonas o neurotransmisores para iniciar la respuesta biológica en el interior de la célula. Son, por lo tanto, muy interesantes como dianas farmacológicas. Esta Tesis Doctoral se centra en la comprensión de la estructura y función de los GPCRs, mediante el uso de técnicas de la química computacional como son el modelado por homología, el anclaje molecular y las simulaciones de dinámica molecular. En concreto, la tesis aborda los determinantes estructurales asociados al mecanismo de activación, la regulación por moduladores alostéricos, la oligomerización con otro GPCR o proteínas adicionales, asícomo el acoplamiento de transductores (proteínas G o arrestinas).G protein-coupled receptors (GPCRs) are the largest and most diverse superfamily of transmembrane proteins in Eukaryotes. GPCRs transduce a huge variety of exogenous and endogenous signals such as photons, hormones or neurotransmitters to initiate biological responses in the cell interior. Therefore, they are very interesting therapeutic targets. This Doctoral Thesis focusses on the understanding of the structure and function of GPCRs, by applying computational chemistry techniques such as homology modelling, docking and molecular dynamics simulations. Particularly, the thesis addresses the structural determinants associated to the activation mechanism, the regulation by allosteric modulators, the oligomerization with other GPCR or additional proteins and the coupling to transducers (G proteins or arrestins)

Structure and function of GPCRs /

Los receptores acoplados a proteínas G (GPCRs) son la superfamilia más grande y diversa de proteínas transmembrana en Eucariotas. Estos receptores transducen una gran variedad de señales exógenas y endógenas como fotones, hormonas o neurotransmisores para iniciar la respuesta biológica en el interior de la célula. Son, por lo tanto, muy interesantes como dianas farmacológicas. Esta Tesis Doctoral se centra en la comprensión de la estructura y función de los GPCRs, mediante el uso de técnicas de la química computacional como son el modelado por homología, el anclaje molecular y las simulaciones de dinámica molecular. En concreto, la tesis aborda los determinantes estructurales asociados al mecanismo de activación, la regulación por moduladores alostéricos, la oligomerización con otro GPCR o proteínas adicionales, asícomo el acoplamiento de transductores (proteínas G o arrestinas).G protein-coupled receptors (GPCRs) are the largest and most diverse superfamily of transmembrane proteins in Eukaryotes. GPCRs transduce a huge variety of exogenous and endogenous signals such as photons, hormones or neurotransmitters to initiate biological responses in the cell interior. Therefore, they are very interesting therapeutic targets. This Doctoral Thesis focusses on the understanding of the structure and function of GPCRs, by applying computational chemistry techniques such as homology modelling, docking and molecular dynamics simulations. Particularly, the thesis addresses the structural determinants associated to the activation mechanism, the regulation by allosteric modulators, the oligomerization with other GPCR or additional proteins and the coupling to transducers (G proteins or arrestins)

Human blue cone opsin regeneration involves secondary retinal binding with analog specificity

Human color vision is mediated by the red, green, and blue cone visual pigments. Cone opsins are G-protein-coupled receptors consisting of an opsin apoprotein covalently linked to the 11-cis-retinal chromophore. All visual pigments share a common evolutionary origin, and red and green cone opsins exhibit a higher homology, whereas blue cone opsin shows more resemblance to the dim light receptor rhodopsin. Here we show that chromophore regeneration in photoactivated blue cone opsin exhibits intermediate transient conformations and a secondary retinoid binding event with slower binding kinetics. We also detected a fine-tuning of the conformational change in the photoactivated blue cone opsin binding site that alters the retinal isomer binding specificity. Furthermore, the molecular models of active and inactive blue cone opsins show specific molecular interactions in the retinal binding site that are not present in other opsins. These findings highlight the differential conformational versatility of human cone opsin pigments in the chromophore regeneration process, particularly compared to rhodopsin, and point to relevant functional, unexpected roles other than spectral tuning for the cone visual pigmentsPeer Reviewe