Implementing the “Best Template Searching” tool into Adenosiland platform

Background: Adenosine receptors (ARs) belong to the G protein-coupled receptors (GCPRs) family. The recent release of X-ray structures of the human A2A AR (h A2A AR ) in complex with agonists and antagonists has increased the application of structure-based drug design approaches to this class of receptors. Among them, homology modeling represents the method of choice to gather structural information on the other receptor subtypes, namely A1, A2B, and A3 ARs. With the aim of helping users in the selection of either a template to build its own models or ARs homology models publicly available on our platform, we implemented our web-resource dedicated to ARs, Adenosiland, with the “Best Template Searching” facility. This tool is freely accessible at the following web address: http://mms.dsfarm.unipd.it/Adenosiland/ligand.php. Findings: The template suggestions and homology models provided by the “Best Template Searching” tool are guided by the similarity of a query structure (putative or known ARs ligand) with all ligands co-crystallized with hA2A AR subtype. The tool computes several similarity indexes and sort the outcoming results according to the index selected by the user. Conclusions: We have implemented our web-resource dedicated to ARs Adenosiland with the “Best Template Searching” facility, a tool to guide template and models selection for hARs modelling. The underlying idea of our new facility, that is the selection of a template (or models built upon a template) whose co-crystallized ligand shares the highest similarity with the query structure, can be easily extended to other GPCRs

The Commons - Die Allmende

This research is in the fields of aesthetics, cartography and environmental change. A series of drone photographs, text, and a short film showing alternately on 4 separate screens around the exhibition space. Shot across continents over a year of the pandemic, this series of images, explores the contemporary notion of ‘die Allmende’, or the commons. Two vastly contrasting sites at the edge of their altitudinal and environmental extremes were chosen; the Aletsch Glacier in Switzerland and the southern shores of the Dead Sea in Israel and Jordan. Through the diverse media of text, cartography, (aerial) photography and film (6 minutes), an insight and context to their parallel and distinct evolution is documented and contrasted

Targeting Aquaporin Function:Potent Inhibition of Aquaglyceroporin-3 by a Gold-Based Compound

Aquaporins (AQPs) are membrane channels that conduct water and small solutes such as glycerol and are involved in many physiological functions. Aquaporin-based modulator drugs are predicted to be of broad potential utility in the treatment of several diseases. Until today few AQP inhibitors have been described as suitable candidates for clinical development. Here we report on the potent inhibition of AQP3 channels by gold(III) complexes screened on human red blood cells (hRBC) and AQP3-transfected PC12 cells by a stopped-flow method. Among the various metal compounds tested, Auphen is the most active on AQP3 (IC(50) = 0.8±0.08 µM in hRBC). Interestingly, the compound poorly affects the water permeability of AQP1. The mechanism of gold inhibition is related to the ability of Au(III) to interact with sulphydryls groups of proteins such as the thiolates of cysteine residues. Additional DFT and modeling studies on possible gold compound/AQP adducts provide a tentative description of the system at a molecular level. The mapping of the periplasmic surface of an homology model of human AQP3 evidenced the thiol group of Cys40 as a likely candidate for binding to gold(III) complexes. Moreover, the investigation of non-covalent binding of Au complexes by docking approaches revealed their preferential binding to AQP3 with respect to AQP1. The high selectivity and low concentration dependent inhibitory effect of Auphen (in the nanomolar range) together with its high water solubility makes the compound a suitable drug lead for future in vivo studies. These results may present novel metal-based scaffolds for AQP drug development

A3 adenosine receptor activation mechanisms: molecular dynamics analysis of inactive, active, and fully active states

We investigated the Gi-coupled A3 adenosine receptor (A3AR) activation mechanism by running 7.2 µs of molecular dynamics (MD) simulations. Based on homology to G protein-coupled receptor (GPCR) structures, three constitutively active mutant (CAM) and the wild-type (WT) A3ARs in the apo form were modeled. Conformational signatures associated with three different receptor states (inactive R, active R*, and bound to Gi protein mimic) were predicted by analyzing and comparing the CAMs with WT receptor and by considering site-directed mutagenesis data. Detected signatures that were correlated with receptor state included: Persistent salt-bridges involving key charged residues for activation (including a novel, putative ionic lock), rotameric state of conserved W6.48, and Na+ ions and water molecules present. Active-coupled state signatures similar to the X-ray structures of β2 adrenergic receptor-Gs protein and A2AAR-mini-Gs and the recently solved cryo-EM A1AR–Gi complexes were found. Our MD analysis suggests that constitutive activation might arise from the D1073.49–R1083.50 ionic lock destabilization in R and the D1073.49–R1113.53 ionic lock stabilization in R* that presumably lowers the energy barrier associated with an R to R* transition. This study provides new opportunities to understand the underlying interactions of different receptor states of other Gi protein-coupled GPCRs

Structure-Guided Modification of Heterocyclic Antagonists of the P2Y 14 Receptor

The P2Y 14 receptor (P2Y 14 R) mediates inflammatory activity by activating neutrophil motility, but few classes of antagonists are known. We have explored the structure-activity relationship of a 3-(4-phenyl-1H-1,2,3-triazol-1-yl)-5-(aryl)benzoic acid antagonist scaffold, assisted by docking and molecular dynamics (MD) simulation at a P2Y 14 R homology model. A computational pipeline using the High Throughput MD Python environment guided the analogue design. Selection of candidates was based upon ligand-protein shape and complementarity and the persistence of ligand-protein interactions over time. Predictions of a favorable substitution of a 5-phenyl group with thiophene and an insertion of a three-methylene spacer between the 5-aromatic and alkyl amino moieties were largely consistent with empirical results. The substitution of a key carboxylate group on the core phenyl ring with tetrazole or truncation of the 5-aryl group reduced affinity. The most potent antagonists, using a fluorescent assay, were a primary 3-aminopropyl congener 20 (MRS4458) and phenyl p-carboxamide 30 (MRS4478)

Structural Probing and Molecular Modeling of the A3 Adenosine Receptor: A Focus on Agonist Binding

Adenosine is an endogenous modulator exerting its functions through the activation of four adenosine receptor (AR) subtypes, termed A1, A2A, A2B and A3, which belong to the G protein-coupled receptor (GPCR) superfamily. The human A3AR (hA3AR) subtype is implicated in several cytoprotective functions. Therefore, hA3AR modulators, and in particular agonists, are sought for their potential application as anti-inflammatory, anticancer, and cardioprotective agents. Structure-based molecular modeling techniques have been applied over the years to rationalize the structure–activity relationships (SARs) of newly emerged A3AR ligands, guide the subsequent lead optimization, and interpret site-directed mutagenesis (SDM) data from a molecular perspective. In this review, we showcase selected modeling-based and guided strategies that were applied to elucidate the binding of agonists to the A3AR and discuss the challenges associated with an accurate prediction of the receptor extracellular vestibule through homology modeling from the available X-ray templates

Structure-Based Scaffold Repurposing for G Protein-Coupled Receptors: Transformation of Adenosine Derivatives into 5HT2B/5HT2C Serotonin Receptor Antagonists

Adenosine derivatives developed to activate adenosine receptors (ARs) revealed micromolar activity at serotonin 5HT(2B) and 5HT(2C) receptors (5HTRs). We explored the structure activity relationship at 5HT(2)Rs and modeled receptor interactions in order to optimize affinity and simultaneously reduce AR affinity. Depending on N-6 substitution, small 5'-alkylamide modification maintained 5HT(2B)R affinity, which was enhanced upon ribose substitution with rigid bicyclo [3.1.0]-hexane (North (N)-methanocarba), e.g., N-6-dicydopropylmethyl 4'-CH2OH derivative 14 (K-i 11 nM). 5'-Methylamide 23 was 170-fold selective as antagonist for 5HT(2B)R vs 5HT(2C)R. 5'-Methyl 25 and ethyl 26 esters potently antagonized 5HT(2)Rs with moderate selectivity in comparison to ARs; related 6-N,N-dimethylamino analogue 30 was 5HT(2)R-selective. 5' position flexibility of substitution was indicated in 5HT(2B)R docking. Both 5'-ester and 5'-amide derivatives displayed in vivo t(1/2) of 3-4 h. Thus, we used G protein-coupled receptor modeling to repurpose nucleoside scaffolds in favor of binding at nonpurine receptors as novel 5HT(2)R antagonists, with potential for cardioprotection, liver protection, or central nervous system activity

Activation of Carboplatin by Carbonate

We carried out a theoretical study to investigate the thermodynamics and the kinetics of the activation of the anticancer drug carboplatin in a carbonate buffer, a process which has been suggested to play an important role in the uptake, antitumor activity and toxicity of this drug. The initial stages of this process have been investigated by considering both the carbonate and the bicarbonate ions, the main species in a carbonate buffer at physiological pH, as the attacking species and consist of an initial ring-opening step, involving the displacement of one arm of the chelating ring by the carbonate ion, followed by the protonation of the ring-opened carbonate to the corresponding bicarbonate species and its subsequent decarboxylation to give the final hydroxo product. The obtained results show that the overall process is exoergonic with relatively low activation free energy (below 120 kJ mol(-1)), suggesting that the reaction with carbonate might represent a viable pathway for the activation of carboplatin to give active intermediates which, in the biological environment, may easily further react to give thermodynamically more stable species