1,721,057 research outputs found
Medicinal chemistry of the a(3) adenosine receptor: agonists, antagonists, and receptor engineering
No full textA(3) adenosine receptor (A(3)AR) ligands have been modified to optimize their interaction with the A(3)AR. Most of these modifications have been made to the N(6) and C2 positions of adenine as well as the ribose moiety, and using a combination of these substitutions leads to the most efficacious, selective, and potent ligands. A(3)AR agonists such as IB-MECA and Cl-IB-MECA are now advancing into Phase II clinical trials for treatments targeting diseases such as cancer, arthritis, and psoriasis. Also, a wide number of compounds exerting high potency and selectivity in antagonizing the human (h)A(3)AR have been discovered. These molecules are generally characterized by a notable structural diversity, taking into account that aromatic nitrogen-containing monocyclic (thiazoles and thiadiazoles), bicyclic (isoquinoline, quinozalines, (aza)adenines), tricyclic systems (pyrazoloquinolines, triazoloquinoxalines, pyrazolotriazolopyrimidines, triazolopurines, tricyclic xanthines) and nucleoside derivatives have been identified as potent and selective A(3)AR antagonists. Probably due to the "enigmatic" physiological role of A(3)AR, whose activation may produce opposite effects (for example, concerning tissue protection in inflammatory and cancer cells) and may produce effects that are species dependent, only a few molecules have reached preclinical investigation. Indeed, the most advanced A(3)AR antagonists remain in preclinical testing. Among the antagonists described above, compound OT-7999 is expected to enter clinical trials for the treatment of glaucoma, while several thiazole derivatives are in development as antiallergic, antiasthmatic and/or antiinflammatory drugs
Survey of ribose ring pucker of signaling nucleosides and nucleotides
Full text linkThe ribose of protein-bound nucleosides and nucleotides displays preferred conformations (usually either North or South), which can be exploited to design enhanced analogs having chemically fixed conformations. We introduce a computational protocol for assembling data from the protein database (PDB) on the ribose and ribose-like conformation of small molecule ligands when complexed with purinergic signaling proteins (including receptors, enzymes and transporters, and related intracellular pathways). Some targets prefer exclusively North (adenosine and P2Y1 receptors, CD73, adenosine kinase ATP/ADP-binding site, adenosine deaminase), others prefer South (P2Y12 receptor, E-NTPDase2) or East (adenosine kinase substrates), while others (P2XRs) allow various conformations
In Silico Drug Design for Purinergic GPCRs: Overview on Molecular Dynamics Applied to Adenosine and P2Y Receptors
Full text linkMolecular modeling has contributed to drug discovery for purinergic GPCRs, including adenosine receptors (ARs) and P2Y receptors (P2YRs). Experimental structures and homology modeling have proven to be useful in understanding and predicting structure activity relationships (SAR) of agonists and antagonists. This review provides an excursus on molecular dynamics (MD) simulations applied to ARs and P2YRs. The binding modes of newly synthesized A1AR- and A3AR-selective nucleoside derivatives, potentially of use against depression and inflammation, respectively, have been predicted to recapitulate their SAR and the species dependence of A3AR affinity. P2Y12R and P2Y1R crystallographic structures, respectively, have provided a detailed understanding of the recognition of anti-inflammatory P2Y14R antagonists and a large group of allosteric and orthosteric antagonists of P2Y1R, an antithrombotic and neuroprotective target. MD of A2AAR (an anticancer and neuroprotective target), A3AR, and P2Y1R has identified microswitches that are putatively involved in receptor activation. The approach pathways of different ligands toward A2AAR and P2Y1R binding sites have also been explored. A1AR, A2AAR, and A3AR were utilizes to study allosteric phenomena, but locating the binding site of structurally diverse allosteric modulators, such as an A3AR enhancer LUF6000, is challenging. Ligand residence time, a predictor of in vivo efficacy, and the structural role of water were investigated through A2AAR MD simulations. Thus, new MD and other modeling algorithms have contributed to purinergic GPCR drug discovery
Breakthrough in GPCR Crystallography and Its Impact on Computer-Aided Drug Design
No full textRecent crystallographic structures of G protein-coupled receptors (GPCRs) have greatly advanced our understanding of the recognition of their diverse agonist and antagonist ligands. We illustrate here how this applies to A2A adenosine receptors (ARs) and to P2Y1 and P2Y12 receptors (P2YRs) for ADP. These X-ray structures have impacted the medicinal chemistry aimed at discovering new ligands for these two receptor families, including receptors that have not yet been crystallized but are closely related to the known structures. In this Chapter, we discuss recent structure-based drug design projects that led to the discovery of: (a) novel A3AR agonists based on a highly rigidified (N)-methanocarba scaffold for the treatment of chronic neuropathic pain and other conditions, (b) fluorescent probes of the ARs and P2Y14R, as chemical tools for structural probing of these GPCRs and for improving assay capabilities, and (c) new more drug-like antagonists of the inflammation-related P2Y14R. We also describe the computationally enabled molecular recognition of positive (for A3AR) and negative (P2Y1R) allosteric modulators that in some cases are shown to be consistent with structure-activity relationship (SAR) data. Thus, computational modeling has become an essential tool for the design of purine receptor ligands
Purinergic Signaling: Impact of GPCR Structures on Rational Drug Design
Full text linkThe purinergic signaling system includes membrane-bound receptors for extracellular purines and pyrimidines, and enzymes/transporters that regulate receptor activation by endogenous agonists. Receptors include: adenosine (A1, A2A, A2B, and A3) and P2Y (P2Y1, P2Y2, P2Y4, P2Y6, P2Y11, P2Y12, P2Y13, and P2Y14) receptors (all GPCRs), as well as P2X receptors (ion channels). Receptor activation, especially accompanying physiological stress or damage, creates a temporal sequence of signaling to counteract this stress and either mobilize (P2Rs) or suppress (ARs) immune responses. Thus, modulation of this large signaling family has broad potential for treating chronic diseases. Experimentally determined structures represent each of the three receptor families. We focus on selective purinergic agonists (A1, A3), antagonists (A3, P2Y14), and allosteric modulators (P2Y1, A3). Examples of applying structure-based design, including the rational modification of known ligands, are presented for antithrombotic P2Y1R antagonists and anti-inflammatory P2Y14R antagonists and A3AR agonists. A3AR agonists are a potential, nonaddictive treatment for chronic neuropathic pain
Structural Probing and Molecular Modeling of the A3 Adenosine Receptor: A Focus on Agonist Binding
No full textAdenosine 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
A3 adenosine receptor activation mechanisms: molecular dynamics analysis of inactive, active, and fully active states
No full textWe 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
Editorial: Geoffrey Burnstock - An Accidental Pharmacologist
No full textThis Special Issue of Biochemical Pharmacology is dedicated to the memory of Professor Geoffrey Burnstock, who died in Melbourne, Australia in June 2020, at the age of 91. Geoff left an indelible scientific legacy that included the conceptualization of the controversial, now well substantiated, purinergic hypothesis of neurotransmission [1] and the equally controversial concept of co-neurotransmission [2]. The origins of these hypotheses and their successful prosecution was a reflection of Geoff’s tenacious and unconventional “outside the box” approach to the scientific status quo where his intellectual curiosity, passion for good science and ability to motivate and mentor his colleagues and students resulted in a body of work of over 1500 papers that has been cited more than 125,000 times
P2Y14 Receptor
No full textHistorical Background
Extracellular purine and pyrimidine nucleotides act as signaling molecules through the activation of P2X ion channels and P2Y G protein-coupled receptors (GPCRs) (Abbracchio et al. 2006). Among the eight members of the P2Y receptor family, four respond to extracellular uracil nucleotides: P2Y2, P2Y4, P2Y6, and P2Y14 receptors. None of the P2X ion channels are substantially activated by uracil nucleotides.
P2Y2, P2Y4, and P2Y6 receptors belong to the P2Y1-like subgroup of Gq-coupled receptors, and the P2Y14 receptor belongs to the P2Y12-like subgroup that couples to G protein αi to inhibit adenylyl cyclase. The P2Y14 receptor is distributed in various tissues, that is, placenta, adipose, stomach, intestine, spleen, thymus, lung, heart, mast cells, and discrete brain regions (Freeman et al. 2001; Harden et al. 2010). It is activated by uridine-5′-diphosphoglucose (UDPG, 1, Fig. 1), other endogenous UDP-sugars, and uridine-5′-diphosphate..
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