John Daly Lecture: Structure-guided Drug Design for Adenosine and P2Y Receptors

Abstract

We establish structure activity relationships of extracellular nucleosides and nucleotides at G protein-coupled receptors (GPCRs), e.g. adenosine receptors (ARs) and P2Y receptors (P2YRs), respectively. We synthesize selective agents for use as pharmacological probes and potential therapeutic agents (e.g. A3AR agonists for neuropathic pain). Detailed structural information derived from the X-ray crystallographic structures within these families enables the design of novel ligands, guides modification of known agonists and antagonists, and helps predict polypharmacology. Structures were recently reported for the P2Y12 receptor (P2Y12R), an anti-thrombotic target. Comparison of agonist-bound and antagonist-bound P2Y12R indicates unprecedented structural plasticity in the outer portions of the transmembrane (TM) domains and the extracellular loops. Nonphosphate-containing ligands of the P2YRs, such as the selective P2Y14R antagonist PPTN, are desired for bioavailability and increased stability. Also, A2AAR structures are effectively applied to homology modeling of closely related A1AR and A3AR, which are not yet crystallized. Conformational constraint of normally flexible ribose with bicyclic analogues increased the ligand selectivity. Comparison of rigid A3AR agonist congeners allows the exploration of interaction of specific regions of the nucleoside analogues with the target and off-target GPCRs, such as biogenic amine receptors. Molecular modeling predicts plasticity of the A3AR at TM2 to accommodate highly rigidified ligands. Novel fluorescent derivatives of high affinity GPCR ligands are useful tool compounds for characterization of receptors and their oligomeric assemblies. Fluorescent probes are useful for characterization of GPCRs in living cells by flow cytometry and other methods. Thus, 3D knowledge of receptor binding and activation facilitates drug discovery.

The Role of the Phosphorus Atom in Drug Design

“…The endogenous agonists are adenosine for the ARs and ATP for the P2XRs, whereas at the P2YRs a wide range of adenine and uracil nucleotides has been shown to be natural agonists such as ATP, ADP, UTP, UTP‐sugars and some dinucleoside polyphosphates . The extensive signaling system modulated by the production and degradation of nucleosides and nucleotides through these receptors, transporters, and enzymes is known as the purinome . In addition, P2YRs are found throughout the body and are involved in the regulation of nearly all systems: immune, digestive, nervous, endocrine, cardiovascular, pulmonary, renal, etc .…”

“…[164] The extensive signaling system modulated by the production and degradation of nucleosides and nucleotides throught hese receptors, transporters, and enzymes is knowna st he purinome. [169] In addition, P2YRs are found throughout the body and are involved in the regulation of nearly all systems:i mmune, digestive, nervous, endocrine, cardiovascular,p ulmonary,r enal, etc. [170] Eight P2YRs are known, and currently not all of the P2Y subtypes have selective agonists and antagonists at hand.…”

“…Structures of aristeromycin(166), and the conformationally rigid carbanucleosides N-methano-carba-adenosine (167), S-methano-carba-adenosine (168), the naturally occurring neplanocin C( 169), N-methano-carbathymidine(170), and S-methano-carba-thymidine(171).…”

Polypharmacology of conformationally locked methanocarba nucleosides

“…The concentrations of extracellular nucleosides and nucleotides, and consequently the levels of endogenous stimulation of these receptors, are controlled by enzymatic, transport and channel processes and by cell damage causing the release of these ligands from intracellular sources. The production and degradation of extracellular nucleosides and nucleotides along with their signaling functions through 19 receptors can be considered a ‘purinome’ [24]. Purinergic signaling through these receptors, transporters and enzymes has a role in most physiological processes and constitutes a major system for homeostatic control in the body.…”

“…This is a general modification of nucleosides and nucleotides that can enhance high-affinity interactions with a variety of protein targets. The methanocarba modification has been shown to increase the affinity or selectivity, or both parameters, compared with ribose at a target such as a GPCR by enforcing a specific conformation that approximates the target-preferred conformation, such as at a GPCR [24]. Thus, drug-like methanocarba AR ligands have been repurposed to satisfy the pharmacophoric requirements of various GPCRs and other protein targets.…”