Molecular Evolution of the Transmembrane Domains of G Protein-Coupled Receptors

G protein-coupled receptors (GPCRs) are a superfamily of integral membrane proteins vital for signaling and are important targets for pharmaceutical intervention in humans. Previously, we identified a group of ten amino acid positions (called key positions), within the seven transmembrane domain (7TM) interhelical region, which had high mutual information with each other and many other positions in the 7TM. Here, we estimated the evolutionary selection pressure at those key positions. We found that the key positions of receptors for small molecule natural ligands were under strong negative selection. Receptors naturally activated by lipids had weaker negative selection in general when compared to small molecule-activated receptors. Selection pressure varied widely in peptide-activated receptors. We used this observation to predict that a subgroup of orphan GPCRs not under strong selection may not possess a natural small-molecule ligand. In the subgroup of MRGX1-type GPCRs, we identified a key position, along with two non-key positions, under statistically significant positive selection

Cosmological constraints from abundance, weak-lensing and clustering of galaxy clusters: application to the SDSS

The clustering of galaxy clusters is a powerful cosmological tool, which can help to break degeneracies between parameters when combined with other cosmological observables. We aim to demonstrate its potential in constraining cosmological parameters and scaling relations when combined with cluster counts and weak lensing mass information, using as a case study the redMaPPer cluster catalog derived from the Sloan Digital Sky Survey (SDSS). We extend the analysis of number counts and weak lensing signal performed by Costanzi et al. 2019a, with the addition of the real-space 2-point correlation function. We derive cosmological and scaling relation posteriors for all the possible combinations of the three observables to assess their constraining power, parameter degeneracies, and possible internal tensions. We find no evidence for tensions between the three data set analyzed. We demonstrate that the inclusion of the cluster clustering statistic can greatly enhance the constraining power of the sample thanks to its capability of breaking the $\Omega_{\rm m} - \sigma_8$ degeneracy characteristic of cluster abundance studies. In particular, for a flat $\Lambda$CDM model with massive neutrinos, we obtain $\Omega_{\rm m}=0.28 \pm 0.03$ and $\sigma_8 = 0.82 \pm 0.05$, a 33% and 50% improvement compared to the posteriors derived combining cluster abundance and weak lensing analyses. Our results are consistent with cosmological posteriors from other cluster surveys, as well as with Planck CMB results and DES-Y3 galaxy clustering and weak-lensing analysis.Comment: 15 pages, 10 figure

Low level exposure to cadmium increases the risk of chronic kidney disease: analysis of the NHANES 1999-2006

BACKGROUND: Environmental factors have been associated with the outbreak of chronic kidney disease (CKD). We evaluated the association of Cadmium (Cd) exposure with the risk of CKD in U.S. adults who participated in the 1999-2006 National Health and Nutrition Examination Surveys (NHANES). METHODS: 5426 subjects > or = 20 years were stratified for values of urinary and blood Cd and a multivariate logistic regression was performed to test the association between blood and urinary Cd, CKD and albuminuria (ALB) after adjustment for age, gender, race/ethnicity, body mass index and smoking habits. RESULTS: Subjects with urinary Cd > 1 mcg/g and subjects with blood Cd > 1 mcg/L showed a higher association with ALB (OR 1.63, 95% CI 1.23, 2.16; P = 0.001). Subjects with blood Cd > 1 mcg/L showed a higher association with both CKD (OR 1.48, 95% CI 1.01, 2.17; P = 0.046) and ALB (OR 1.41, 95% CI 1.10, 1.82; P = 0.007). An interaction effect on ALB was found for high levels of urinary and blood Cd (P = 0.014). CONCLUSIONS: Moderately high levels of urinary and blood Cd are associated with a higher proportion of CKD and ALB in the United States population

Terminal differentiation of adult hippocampal progenitor cells is a step functionally dissociable from proliferation and is controlled by Tis21, Id3 and NeuroD2

Cell proliferation and differentiation are interdependent processes. Here, we have asked to what extent the two processes of neural progenitor cell amplification and differentiation are functionally separated. Thus, we analyzed whether it is possible to rescue a defect of terminal differentiation in progenitor cells of the dentate gyrus, where new neurons are generated throughout life, by inducing their proliferation and/or their differentiation with different stimuli appropriately timed. As a model we used the Tis21 knockout mouse, whose dentate gyrus neurons, as demonstrated by us and others, have an intrinsic defect of terminal differentiation. We first tested the effect of two proliferative as well as differentiative neurogenic stimuli, one pharmacological (fluoxetine), the other cognitive (the Morris water maze (MWM) training). Both effectively enhanced the number of new dentate gyrus neurons produced, and fluoxetine also reduced the S-phase length of Tis21 knockout dentate gyrus progenitor cells and increased the rate of differentiation of control cells, but neither factor enhanced the defective rate of differentiation. In contrast, the defect of terminal differentiation was fully rescued by in vivo infection of proliferating dentate gyrus progenitor cells with retroviruses either silencing Id3, an inhibitor of neural differentiation, or expressing NeuroD2, a proneural gene expressed in terminally differentiated dentate gyrus neurons. This is the first demonstration that NeuroD2 or the silencing of Id3 can activate the differentiation of dentate gyrus neurons, complementing a defect of differentiation. It also highlights how the rate of differentiation of dentate gyrus neurons is regulated genetically at several levels and that a neurogenic stimulus for amplification of neural stem/progenitor cells may not be sufficient in itself to modify this rat

Development of Selective High Affinity Antagonists, Agonists, and Radioligands for the P2Y1 Receptor

The P2Y1 receptor is a member of the P2Y family of nucleotide-activated G protein-coupled receptors, and it is an important therapeutic target based on its broad tissue distribution and essential role in platelet aggregation. We have designed a set of highly selective and diverse pharmacological tools for studying the P2Y1 receptor using a rational approach to ligand design. Based on the discovery that bisphosphate analogues of the P2Y1 receptor agonist, ADP, are partial agonists/competitive antagonists of this receptor, an iterative approach was used to develop competitive antagonists with enhanced affinity and selectivity. Halogen substitutions of the 2-position of the adenine ring provided increased affinity while an N6 methyl substitution eliminated partial agonist activity. Furthermore, various replacements of the ribose ring with symmetrically branched, phosphorylated acyclic structures revealed that the ribose is not necessary for recognition at the P2Y1 receptor. Finally, replacement of the ribose ring with a five member methanocarba ring constrained in the Northern conformation conferred dramatic increases in affinity to both P2Y1 receptor antagonists as well as agonists. These combined structural modifications have resulted in a series of selective high affinity antagonists of the P2Y1 receptor, two broadly applicable radioligands, and a high affinity agonist capable of selectively activating the P2Y1 receptor in human platelets. Complementary receptor modeling and computational ligand docking have provided a putative structural framework for the drug-receptor interactions. A similar rational approach is being applied to develop selective ligands for other subtypes of P2Y receptors

Computational Drug Target Screening through Protein Interaction Profiles

The development of computational methods to discover novel drug-target interactions on a large scale is of great interest. We propose a new method for virtual screening based on protein interaction profile similarity to discover new targets for molecules, including existing drugs. We calculated Target Interaction Profile Fingerprints (TIPFs) based on ChEMBL database to evaluate drug similarity and generated new putative compound-target candidates from the non-intersecting targets in each pair of compounds. A set of drugs was further studied in monoamine oxidase B (MAO-B) and cyclooxygenase-1 (COX-1) enzyme through molecular docking and experimental assays. The drug ethoxzolamide and the natural compound piperlongumine, present in Piper longum L, showed hMAO-B activity with IC50 values of 25 and 65μM respectively. Five candidates, including lapatinib, SB-202190, RO-316233, GW786460X and indirubin-3′-monoxime were tested against human COX-1. Compounds SB-202190 and RO-316233 showed a IC50 in hCOX-1 of 24 and 25μM respectively (similar range as potent inhibitors such as diclofenac and indomethacin in the same experimental conditions). Lapatinib and indirubin3′-monoxime showed moderate hCOX-1 activity (19.5% and 28% of enzyme inhibition at 25μM respectively). Our modeling constitutes a multi-target predictor for large scale virtual screening with potential in lead discovery, repositioning and drug safetyThis study was supported by grant R01 LM006910 (GH) “Discovering and Applying Knowledge in Clinical Databases” from the U.S. National Library of Medicine, “Angeles Alvariño, Plan Galego de Investigación, Innovación e Crecemento 2011–2015 (I2C)” and European Social Fund (ESF)S

Adenosine receptor agonists: Synthesis and binding affinity of 2-(aryl)alkylthioadenosine derivatives

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Virtual screening leads to the discovery of novel non-nucleotide P2Y1 receptor antagonists

The P2Y1 receptor (P2Y1R) is a G protein-coupled receptor naturally activated by extracellular ADP. Its stimulation is an essential requirement of ADP-induced platelet aggregation, thus making antagonists highly sought compounds for the development of antithrombotic agents. Here, through a virtual screening campaign based on a pharmacophoric representation of the common characteristics of known P2Y1R ligands and the putative shape and size of the receptor binding pocket, we have identified novel antagonist hits of µM affinity derived from a N,N’-bis-arylurea chemotype. Unlike the vast majority of known P2Y1R antagonists, these drug-like compounds do not have a nucleotidic scaffold or highly negatively charged phosphate groups. Hence, our compounds may provide a direction for the development of receptor probes with altered physicochemical properties