Structure-Based Discovery of Novel and Selective 5‑Hydroxytryptamine 2B Receptor Antagonists for the Treatment of Irritable Bowel Syndrome

Here we employed structure-based ligand discovery techniques to explore a recently determined crystal structure of the 5-hydroxytryptamine 2B (5-HT_2B) receptor. Ten compounds containing a novel chemical scaffold were identified; among them, seven molecules were active in cellular function assays with the most potent one exhibiting an IC₅₀ value of 27.3 nM. We then systematically probed the binding characteristics of this scaffold by designing, synthesizing, and testing a series of structural modifications. The structure–activity relationship studies strongly support our predicted binding model. The binding profiling across a panel of 11 5-HT receptors indicated that these compounds are highly selective for the 5-HT_2B receptor. Oral administration of compound <b>15</b> (30 mg/kg) produced significant attenuation of visceral hypersensitivity in a rat model of irritable bowel syndrome (IBS). We expect this novel scaffold will serve as the foundation for the development of 5-HT_2B antagonists for the treatment of IBS

Heterotropic Cooperativity within and between Protomers of an Oligomeric M₂ Muscarinic Receptor

At least four allosteric sites have been found to mediate the dose-dependent effects of gallamine on the binding of [³H]­quinuclidinylbenzilate (QNB) and <i>N</i>-[³H]­methylscopolamine (NMS) to M₂ muscarinic receptors in membranes and solubilized preparations from porcine atria, CHO cells, and <i>Sf</i>9 cells. The rate of dissociation of [³H]­QNB was affected in a bell-shaped manner with at least one Hill coefficient (<i>n</i>_H) greater than 1, indicating that at least three allosteric sites are involved. The level of binding of [³H]­QNB was decreased in a biphasic manner, revealing at least two allosteric sites; binding of [³H]­NMS was affected in a triphasic, serpentine manner, revealing at least three sites, and values of <i>n</i>_H >1 pointed to at least four sites. Several lines of evidence indicate that all effects of gallamine were allosteric in nature and could be observed at equilibrium. The rates of equilibration and dissociation suggest that the receptor was predominately oligomeric, and the heterogeneity revealed by gallamine can be attributed to differences in its affinity for the constituent protomers of a tetramer. Those differences appear to arise from inter- and intramolecular cooperativity between gallamine and the radioligand

A Simple Representation of Three-Dimensional Molecular Structure

Statistical and machine learning approaches predict drug-to-target relationships from 2D small-molecule topology patterns. One might expect 3D information to improve these calculations. Here we apply the logic of the extended connectivity fingerprint (ECFP) to develop a rapid, alignment-invariant 3D representation of molecular conformers, the extended three-dimensional fingerprint (E3FP). By integrating E3FP with the similarity ensemble approach (SEA), we achieve higher precision-recall performance relative to SEA with ECFP on ChEMBL20 and equivalent receiver operating characteristic performance. We identify classes of molecules for which E3FP is a better predictor of similarity in bioactivity than is ECFP. Finally, we report novel drug-to-target binding predictions inaccessible by 2D fingerprints and confirm three of them experimentally with ligand efficiencies from 0.442–0.637 kcal/mol/heavy atom

Mesh plot summarizing pharmacology of 3 novel PCP analogues.

<p>Shown in three dimensional mesh plot format are the pKi values of the three novel PCP analogues (3-MeO-PCE, 3-MeO-phencyclidine and 4-MeO-phencyclidine; 1, 2 and 3 respectively) against a panel of 56 molecular targets.</p

Molecular Targets Profiled.

<p>Molecular Targets Profiled.</p

Chemical structures of ketamine, methoxetamine, phencyclidine and analogues.

<p>Chemical structures of ketamine, methoxetamine, phencyclidine and analogues.</p

Selectivity Challenges in Docking Screens for GPCR Targets and Antitargets

To investigate large library docking’s ability to find molecules with joint activity against on-targets and selectivity versus antitargets, the dopamine D₂ and serotonin 5-HT_2A receptors were targeted, seeking selectivity against the histamine H₁ receptor. In a second campaign, κ-opioid receptor ligands were sought with selectivity versus the μ-opioid receptor. While hit rates ranged from 40% to 63% against the on-targets, they were just as good against the antitargets, even though the molecules were selected for their putative lack of binding to the off-targets. Affinities, too, were often as good or better for the off-targets. Even though it was occasionally possible to find selective molecules, such as a mid-nanomolar D₂/5-HT_2A ligand with 21-fold selectivity versus the H₁ receptor, this was the exception. Whereas false-negatives are tolerable in docking screens against on-targets, they are intolerable against antitargets; addressing this problem may demand new strategies in the field

Selectivity Challenges in Docking Screens for GPCR Targets and Antitargets

To investigate large library docking’s ability to find molecules with joint activity against on-targets and selectivity versus antitargets, the dopamine D₂ and serotonin 5-HT_2A receptors were targeted, seeking selectivity against the histamine H₁ receptor. In a second campaign, κ-opioid receptor ligands were sought with selectivity versus the μ-opioid receptor. While hit rates ranged from 40% to 63% against the on-targets, they were just as good against the antitargets, even though the molecules were selected for their putative lack of binding to the off-targets. Affinities, too, were often as good or better for the off-targets. Even though it was occasionally possible to find selective molecules, such as a mid-nanomolar D₂/5-HT_2A ligand with 21-fold selectivity versus the H₁ receptor, this was the exception. Whereas false-negatives are tolerable in docking screens against on-targets, they are intolerable against antitargets; addressing this problem may demand new strategies in the field

Selectivity Challenges in Docking Screens for GPCR Targets and Antitargets

To investigate large library docking’s ability to find molecules with joint activity against on-targets and selectivity versus antitargets, the dopamine D₂ and serotonin 5-HT_2A receptors were targeted, seeking selectivity against the histamine H₁ receptor. In a second campaign, κ-opioid receptor ligands were sought with selectivity versus the μ-opioid receptor. While hit rates ranged from 40% to 63% against the on-targets, they were just as good against the antitargets, even though the molecules were selected for their putative lack of binding to the off-targets. Affinities, too, were often as good or better for the off-targets. Even though it was occasionally possible to find selective molecules, such as a mid-nanomolar D₂/5-HT_2A ligand with 21-fold selectivity versus the H₁ receptor, this was the exception. Whereas false-negatives are tolerable in docking screens against on-targets, they are intolerable against antitargets; addressing this problem may demand new strategies in the field

Selectivity Challenges in Docking Screens for GPCR Targets and Antitargets

To investigate large library docking’s ability to find molecules with joint activity against on-targets and selectivity versus antitargets, the dopamine D₂ and serotonin 5-HT_2A receptors were targeted, seeking selectivity against the histamine H₁ receptor. In a second campaign, κ-opioid receptor ligands were sought with selectivity versus the μ-opioid receptor. While hit rates ranged from 40% to 63% against the on-targets, they were just as good against the antitargets, even though the molecules were selected for their putative lack of binding to the off-targets. Affinities, too, were often as good or better for the off-targets. Even though it was occasionally possible to find selective molecules, such as a mid-nanomolar D₂/5-HT_2A ligand with 21-fold selectivity versus the H₁ receptor, this was the exception. Whereas false-negatives are tolerable in docking screens against on-targets, they are intolerable against antitargets; addressing this problem may demand new strategies in the field