Biology subjects

Huang, X.-P.

Publications and source records attributed to Huang, X.-P..

16 recordsLinked to original sources

bioRxiv2026

Xylazine's k-opioid agonist activity is not shared with other FDA-approved alpha2-adrenergic agonists

Xylazine is a 2-adrenergic agonist typically used in as a sedative and analgesic in veterinary medicine. For some years, xylazine has been reported as an additive to fentanyl on the illicit drug market and has been associated with severe side-effects including severe ulcerations and potential amputations at the sites of injection along with an increased risk of respiratory depression and death. We recently reported that xylazine has modest {kappa} opioid agonist activity in vitro and in vivo and asked if other 2-adrenergic agonists had similar off-target activities. To test this hypothesis, we profiled US FDA-approved 2-adrenergic agonists at 320 G protein coupled receptors (GPCRs) to identify potentially deleterious and/or beneficial off-targets. Although all other tested 2-adrenergic agonists were devoid of {kappa} opioid agonist activity, each had a distinct pattern of activity at various GPCRs and differential patterns of signaling bias at 2-receptor subtypes. These findings suggest potential molecular targets for both side-effects and therapeutic activities among known 2-adrenergic agonists.

neuroscience↗

bioRxiv2026

The selectivity implications of docking libraries with greater and lesser similarities to bio-like molecules

As virtual libraries have expanded into the tens of billions via make-on-demand chemistry, their similarity to metabolites, natural products, and drugs ("bio-like" molecules) has rapidly diminished. Despite this divergence, molecular docking of these ultra-large libraries has yielded molecules at higher experimental hit-rates and with improved affinities. The structural divergence from bio-like space raises the possibility that molecules from these ultra-large libraries have improved selectivity. Just as plausibly, if hit-rates on-target are divorced from similarity to bio-like molecules, so too may be selectivity against off-targets. Here, we test whether docking hits for the 5-HT2A serotonin receptor from ultra-large libraries are more selective than those from smaller and more bio-like "in-stock" libraries. Chemoinformatic similarity predicts that docking actives from the in-stock library have more off-targets than the more chemically novel hits emerging from docking the ultra-large library. This may reflect the bias of the known, however, as when tested experimentally at scale against 318 GPCRs, both 16 agonists from the ultra-large library and 20 actives from the in-stock library had similar numbers of off-targets. While the ultra-large library hits are more sub-type selective for the 5-HT2A over the 5-HT2B and 5-HT2C receptors, overall these results may suggest that selectivity against off-targets, like affinity and hit-rates for on-targets, is divorced from library similarity to bio-like molecules.

biophysics↗

bioRxiv2025

The polypharmacological profiles of xanomeline and N-desmethylxanomeline

The muscarinic agonist xanomeline in combination with the peripherally restricted muscarinic antagonist trospium has recently been approved for treatment of schizophrenia. Xanomeline represents the first approved antipsychotic drug without apparent activity at D2-dopamine receptors. In humans, xanomeline is reported to be metabolized to N-desmethylxanomeline, which has a similar pharmacokinetic profile to xanomeline, although its pharmacology has not been reported. We discovered that xanomeline and N-desmethylxanomeline have potent agonist and antagonist actions at many biogenic amine G protein coupled receptors. These results suggest that at least some of the actions of xanomeline and N-desmethylxanomeline could be mediated by off-target actions at serotonergic, dopaminergic, histaminergic, adrenergic and other receptors. We discuss the potential implications of these findings.

neuroscience↗

bioRxiv2025

Differential effects of sodium on agonist-induced conformational transitions and signaling at μ and κ opioid receptors

Sodium ions are classically conceptualized as negative allosteric modulators for G protein coupled receptors (GPCRs), although there have been reports of either positive allosteric modulation or no effect of sodium on GPCR function. Here we identified opposing actions of sodium on the and {kappa} opioid receptors. We utilized a variety of methods including radioligand binding, real-time conformational monitoring of transitions using bioluminescence resonance energy transfer and signaling assays using the TRUPATH resource. At the receptors, sodium behaved as a negative allosteric modulator of binding, conformational transitions and signaling. Intriguingly, bitopic agonists were unaffected by sodium concentrations. By contrast, at the {kappa} opioid receptor sodium negatively modulated agonist binding and positively modulated conformational transitions and signaling. Taken together, these findings support the notion that the differential sensitivities to sodium concentrations will result in opposing effects on cell surface and intracellular signaling.

neuroscience↗

bioRxiv2024

An shRNA screen in primary human beta cells identifies the serotonin 1F receptor as a negative regulator of survival during transplant

Islet transplantation can cure type 1 diabetes, but peri-transplant beta cell death limits this procedure to those with low insulin requirements. Improving human beta cell survival or proliferation may make islet transplantation a possibility for more type 1 patients. To identify novel regulators of beta cell survival and proliferation, we conducted a pooled small hairpin RNA (shRNA) screen in primary human beta cells transplanted into immunocompromised mice. shRNAs targeting several cyclin dependent kinase inhibitors were enriched after transplant. Here, we focused on the Gi/o-coupled GPCR, serotonin 1F receptor (HTR1F, 5-HT1F) which our screen identified as a negative regulator of beta cell numbers after transplant. In vitro, 5-HT1F knockdown induced human beta cell proliferation but only when combined with harmine and exendin-4. In vivo, knockdown of 5-HT1F reduced beta cell death during transplant. To demonstrate the feasibility of targeting 5-HT1F in islet transplant, we identified and validated a small molecule 5-HT1F antagonist. This antagonist increased glucose stimulated insulin secretion from primary human islets and cAMP accumulation in primary human beta cells. Finally, the 5-HT1F antagonist improved glycemia in marginal mass, human islet transplants into immunocompromised mice. We identify 5-HT1F as a novel druggable target to improve human beta cell survival in the setting of islet transplantation. One Sentence SummarySerotonin 1F receptor (5-HT1F) negatively regulates insulin secretion and beta cell survival during transplant.

cell biology↗

bioRxiv2024

Molecular basis of proton-sensing by G protein-coupled receptors

Three proton-sensing G protein-coupled receptors (GPCRs), GPR4, GPR65, and GPR68, respond to changes in extracellular pH to regulate diverse physiology and are implicated in a wide range of diseases. A central challenge in determining how protons activate these receptors is identifying the set of residues that bind protons. Here, we determine structures of each receptor to understand the spatial arrangement of putative proton sensing residues in the active state. With a newly developed deep mutational scanning approach, we determined the functional importance of every residue in proton activation for GPR68 by generating [~]9,500 mutants and measuring effects on signaling and surface expression. This unbiased screen revealed that, unlike other proton-sensitive cell surface channels and receptors, no single site is critical for proton recognition in GPR68. Instead, a network of titratable residues extend from the extracellular surface to the transmembrane region and converge on canonical class A GPCR activation motifs to activate proton-sensing GPCRs. More broadly, our approach integrating structure and unbiased functional interrogation defines a new framework for understanding the rich complexity of GPCR signaling. One-sentence summaryThe protonation networks governing activation of human pH-sensing GPCRs are uncovered by integrative cryo-EM and deep mutational scanning.

biochemistry↗

bioRxiv2023

Nonspecific membrane bilayer perturbations by ivermectin underlie SARS-CoV-2 in vitro activity

Since it was proposed as a potential host-directed antiviral agent for SARS-CoV-2, the antiparasitic drug ivermectin has been investigated thoroughly in clinical trials, which have provided insufficient support for its clinical efficacy. To examine the potential for ivermectin to be repurposed as an antiviral agent, we therefore undertook a series of preclinical studies. Consistent with early reports, ivermectin decreased SARS-CoV-2 viral burden in in vitro models at low micromolar concentrations, five-to ten-fold higher than the reported toxic clinical concentration. At similar concentrations, ivermectin also decreased cell viability and increased biomarkers of cytotoxicity and apoptosis. Further mechanistic and profiling studies revealed that ivermectin nonspecifically perturbs membrane bilayers at the same concentrations where it decreases the SARS-CoV-2 viral burden, resulting in nonspecific modulation of membrane-based targets such as G-protein coupled receptors and ion channels. These results suggest that a primary molecular mechanism for the in vitro antiviral activity of ivermectin may be nonspecific membrane perturbation, indicating that ivermectin is unlikely to be translatable into a safe and effective antiviral agent. These results and experimental workflow provide a useful paradigm for performing preclinical studies on (pandemic-related) drug repurposing candidates. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=61 SRC="FIGDIR/small/563088v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@a21f94org.highwire.dtl.DTLVardef@1c76751org.highwire.dtl.DTLVardef@500930org.highwire.dtl.DTLVardef@8b6c05_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

pharmacology and toxicology↗

bioRxiv2023

Xylazine is an agonist at kappa opioid receptors and exhibits sex-specific responses to naloxone administration

Xylazine has been found in the unregulated drug supply at increasing rates, usually in combination with fentanyl. It has become critical to understand its basic pharmacology, how it impacts behavior, and how it interacts with fentanyl in rodent models of opioid administration. Despite commentary from scientists, politicians, and public health officials, it is not known if xylazine impacts the efficacy of naloxone, the opioid receptor antagonist used to reverse opioid induced respiratory depression. Furthermore, few studies have examined the effects of xylazine alone, without co-administration of ketamine. Here, we examine the impact of xylazine alone and in combination with fentanyl on several key behaviors in male and female mice. We demonstrate differential locomotor responses by dose and sex to xylazine. Surprisingly, our results further indicate that naloxone precipitates withdrawal from xylazine and a fentanyl/xylazine combination, in both sexes, with enhanced sensitivity in females. Further, we show that xylazine is a full agonist at the kappa opioid receptor, a potential mechanism for its naloxone sensitivity. One-Sentence SummaryWe present surprising new insights into xylazine and fentanyl pharmacology with immediate implications for clinical practice and frontline public health.

neuroscience↗

bioRxiv2023

De Novo Design of κ-Opioid Receptor Antagonists Using a Generative Deep Learning Framework

Likely effective pharmacological interventions for the treatment of opioid addiction include attempts to attenuate brain reward deficits during periods of abstinence. Pharmacological blockade of the {kappa}-opioid receptor (KOR) has been shown to abolish brain reward deficits in rodents during withdrawal, as well as to reduce the escalation of opioid use in rats with extended access to opioids. Although KOR antagonists represent promising candidates for the treatment of opioid addiction, very few potent selective KOR antagonists are known to date and most of them exhibit significant safety concerns. Here, we used a generative deep learning framework for the de novo design of chemotypes with putative KOR antagonistic activity. Molecules generated by models trained with this framework were prioritized for chemical synthesis based on their predicted optimal interactions with the receptor. Our models and proposed training protocol were experimentally validated by binding and functional assays.

bioinformatics↗

bioRxiv2022

Structural Genomics of the Human Dopamine Receptor System

The dopamine system, including five dopamine receptors (D1R to D5R), plays essential roles in the central nervous system (CNS) and ligands that activate dopamine receptors have been used to treat many neuropsychiatric disorders, including Parkinsons Disease (PD) and schizophrenia. Here, we report five cryo-EM structures of all subtypes of human dopamine receptors in complex with G-protein and bound to the pan agonist, Rotigotine, which is used to treat PD and restless legs syndrome. The structures reveal the basis of Rotigotine binding modes to different dopamine receptors. Structural analysis together with functional assays illuminate determinants of ligand polypharmacology and selectivity. The structures also uncover the mechanisms of the dopamine receptor activation, unique structural features among the five receptor subtypes, and the basis of G-protein coupling specificity. Our works provide a comprehensive set of structural templates for the rational design of specific ligands to treat CNS diseases targeting the dopaminergic system.

biochemistry↗

bioRxiv2022

Structure-based Discovery of Conformationally Selective Inhibitors of the Serotonin Transporter

The serotonin transporter (SERT) removes synaptic serotonin and is the target of anti-depressant drugs. SERT adopts three conformations: outward-open, occluded, and inward-open. All known inhibitors target the outward-open state except ibogaine, which has an unusual anti-depressant profile and stabilizes the inward-open conformation. Unfortunately, ibogaine is promiscuous and cardiotoxic, limiting understanding of inward-open state ligands. We computationally docked over 200 million small molecules against the ibogaine stabilized inward-open state of SERT. Thirty-six top-ranking compounds were synthesized and thirteen inhibited with potencies ranging from 29 to 5000 nM. Structure-based optimization led to two novel inhibitors with Ki values down to 3 nM. The new molecules stabilized an outward-closed state of the transporter and had little activity against off-targets. A cryo-EM structure of one of these bound to SERT confirmed the predicted geometry. In mouse behavioral assays, both had anxiolytic and anti-depressant activity, with potencies up to 200 better than fluoxetine.

biochemistry↗

bioRxiv2021

Crystal structures of the σ2 receptor template large-library docking for selective chemotypes active in vivo

The {sigma}2 receptor is a poorly understood transmembrane receptor that has attracted intense interest in many areas of biology including cancer imaging, Alzheimers disease, schizophrenia, and neuropathic pain. However, little is known regarding the molecular details of the receptor, and few highly selective ligands are available. Here, we report the crystal structure of the {sigma}2 receptor in complex with the clinical drug candidate roluperidone and the probe compound PB28. These structures, in turn, templated a large-scale docking screen of 490 million make-on-demand molecules. Of these, 484 compounds were synthesized and tested, prioritizing not only high-ranking docked molecules, but also those with mediocre and poor scores. Overall, 127 compounds with binding affinities superior to 1 M were identified, all in new chemotypes, 31 of which had affinities superior to 50 nM. Intriguingly, hit rate fell smoothly and monotonically with docking score. Seeking to develop selective and biologically active probe molecules, we optimized three of the original docking hits for potency and for selectivity, achieving affinities in the 3 to 48 nM range and to up to 250-fold selectivity vs. the {sigma}1 receptor. Crystal structures of the newly discovered ligands bound to the {sigma}2 receptor were subsequently determined, confirming the docked poses. To investigate the contribution of the {sigma}2 receptor in pain processing, and to distinguish it from the contribution of the {sigma}1 receptor, two potent {sigma}2-selective and one potent {sigma}1/{sigma}2 non-selective ligand were tested for efficacy in a mouse model of neuropathic pain. All three ligands demonstrated timedependent decreases in mechanical hypersensitivity in the spared nerve injury model, supporting a role for the {sigma}2 receptor in nociception, and a possible role for {sigma}1/{sigma}2 polypharmacology. This study illustrates the opportunities for rapid discovery of in vivo active and selective probes to study under-explored areas of biology using structurebased screens of diverse, ultra-large libraries following the elucidation of protein structures.

pharmacology and toxicology↗

bioRxiv2021

Mechanism of dopamine binding and allosteric modulation of the human D1 dopamine receptor

Dopamine is an essential neurotransmitter, which functions are mediated by five G protein-coupled receptors, dopamine D1 to D5 receptors (D1R-D5R) in mammals. Among them, D1R is the most abundantly expressed dopamine receptor in the CNS and is the central receptor mediating excitatory dopamine signaling in multiple dopaminergic pathways. Dysregulation of D1R signaling has been directly linked to Parkinsons disease (PD), schizophrenia, and drug abuse. Due to its fundamental functions in human diseases, D1R has long been the subject of intensive drug development effort toward the treatment of neuropsychiatric diseases. Here, we report the structures of D1R-Gs complex bound to endogenous agonist dopamine and synthetic agonist SKF81297, both with positive allosteric modulator LY3154207. These structures reveal the basis of dopamine recognition, the binding and potential allosteric regulation of DRD1 PAM LY3154207, and provide structural templates for design of subtype-selective D1R ligand for drug discovery targeting DRD1 for treating various CNS diseases.

molecular biology↗

bioRxiv2019

A novel G protein-biased and subtype selective agonist for a G protein-coupled receptor discovered from screening herbal extracts

Subtype selectivity and functional bias are vital in current drug discovery for G protein-coupled receptors (GPCRs) as selective and biased ligands are expected to yield drug leads with optimal on-target benefits and minimal side-effects. However, structure-based design and medicinal chemistry exploration remain challenging in part because of highly conserved binding pockets within subfamilies. Herein, we present an affinity mass spectrometry approach for screening herbal extracts to identify active ligands of a GPCR, the 5-HT2C receptor. Using this method, we discovered a naturally occurring aporphine 1857 that displayed strong selectivity for activating 5-HT2C without activating the 5-HT2A or 5-HT2B receptors. Remarkably, this novel ligand exhibited exclusive bias towards G protein signaling for which key residues were identified, and it showed comparable in vivo efficacy for food intake suppression and weight loss as the anti-obesity drug, lorcaserin. Our study establishes an efficient approach to discovering novel GPCR ligands by exploring the largely untapped chemical space of natural products.

biochemistry↗

bioRxiv2019

Deschloroclozapine: a potent and selective chemogenetic actuator enables rapid neuronal and behavioral modulations in mice and monkeys

The chemogenetic technology Designer Receptors Exclusively Activated by Designer Drugs (DREADDs) affords remotely reversible control of cellular signaling, neuronal activity and behavior. Although the combination of muscarinic-based DREADDs with clozapine-N-oxide (CNO) has been widely used, sluggish kinetics, metabolic liabilities, and potential off-target effects of CNO represent areas for improvement. Here we provide a new high affinity and selective agonist deschloroclozapine (DCZ) for muscarinic-based DREADDs. Positron emission tomography revealed that DCZ selectively bound to and occupied DREADDs in both mice and monkeys. Systemic delivery of low doses of DCZ (1 or 3 g/kg) enhanced neuronal activity via hM3Dq within minutes in mice and monkeys. Intramuscular injections of DCZ (100 g/kg) reversibly induced spatial working memory deficits in monkeys expressing hM4Di in the prefrontal cortex. DCZ represents the most potent, selective, metabolically stable and fast-acting DREADD agonist reported with utility in both mice and non-human primates for a variety of applications.

neuroscience↗

bioRxiv2017

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.

bioinformatics↗