Biology subjects

Katritch, V.

Publications and source records attributed to Katritch, V..

8 recordsLinked to original sources

bioRxiv2026

When DL-Based Prescreening Meets Synthon-Based Docking: Target-Adapting PharmacoNet via MEL-Steered Correction

As chemical libraries expand into the trillions of molecules, Virtual SYNthon Hierarchical Enumeration Screening (V-SYNTHES) has emerged as a leading strategy for making gigascale virtual screening computationally tractable. In V-SYNTHES, a Minimal Enumeration Library (MEL) of chemical fragments is docked against a target first, and only the top-scoring fragments are expanded into full ligands for large-scale docking. However, among the large number of comparably well-docked fragments, only a small fraction can be expanded under a fixed docking budget, leaving most similarly promising fragments unexplored. General-purpose prescreening tools can be adopted to address this constraint, reallocating the same docking budget across a larger pool of fragments' enumerated full ligands by their proxy score. However, such tools are applied without accounting for target-specific pocket environments. One such method, PharmacoNet, predicts interaction hotspots from a protein structure and ranks candidates via graph matching against a fixed set of interaction-type weights. We recognize that V-SYNTHES's initial fragment-docking step, ordinarily used only for selection of best fragments for expansion, already reveals which of these hotspots and interaction types a given pocket actually favors, and we can recover this signal to fine-tune PharmacoNet accordingly. We introduce MEL-Steered PharmacoNet, a parameter-efficient adaptation framework that specializes PharmacoNet to a given target through two composable mechanisms: (i) empirical density-map steering of predicted pharmacophore hotspots, and (ii) empirical fine-tuning of interaction-type scoring weights. Across three structurally distinct GPCR targets (CB2, GPR91, 5-HT2AR), MEL-Steered PharmacoNet achieves substantial enrichment factor (EF100) gains over a random baseline, and improves EF100 over PharmacoNet by 8.94x, 6.87x, and 1.69x, respectively. The fitted per-target weights further reveal distinct, chemically interpretable interaction profiles that PharmacoNet's generic fixed weights fail to capture. These results show that fragment-docking data already generated by the standard V-SYNTHES pipeline can adapt a general-purpose pharmacophore prescreening method to an individual target, significantly improving its performance while retaining its ultra-fast screening ability, with no additional experimental data or model retraining.

bioinformatics↗

bioRxiv2026

Structural basis of endogenous lipid recognition and G protein selectivity in GPR119

G protein-coupled receptors (GPCRs) often engage multiple intracellular transducers, yet the structural basis by which endogenous ligands influence G protein selectivity remains poorly understood. GPR119 is a lipid-activated receptor expressed in pancreatic {beta}-cells and enteroendocrine L-cells, where it regulates glucose-dependent insulin and incretin secretion, making it a promising therapeutic target for metabolic disease. Here, we present cryo-electron microscopy structures of GPR119 bound to its endogenous lipid agonist oleoylethanolamide (OEA) in complex with Gs and Gq proteins. These structures reveal that OEA occupies a deeply buried orthosteric pocket but adopts distinct conformations in the two signaling states. Structural and functional analyses further identify an extended TM5 helix that stabilizes the receptor-Gs interface and acts as a key determinant of G-protein subtype selectivity. Together, these findings provide mechanistic insights into endogenous lipid-driven multi-transducer signaling and establish a structural framework for the development of pathway-selective GPR119 therapeutics.

molecular biology↗

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↗

bioRxiv2025

Development of Potent, Selective cPLA2 Inhibitors for Targeting Neuroinflammation in Alzheimer's Disease and Other Neurodegenerative Disorders

Chronic neuroinflammation plays a key role in the progression of Alzheimers disease (AD), and the cytosolic calcium-dependent phospholipase A2 (cPLA2) enzyme is a critical mediator of inflammatory lipid signaling pathways. Here we investigate the therapeutic potential of novel cPLA2 inhibitors in modulating neuroinflammation in AD. By leveraging the giga-scale V-SYNTHES 2.0 virtual screening in on-demand chemical space and conducting two rounds of optimization for potency and selectivity, we have identified BRI-50460, achieving an IC50 of 0.88 nM in cellular assays of cPLA2 activity. In vivo studies revealed favorable brain-to-plasma ratios, highlighting the ability of BRI-50460 to penetrate the central nervous system, potentially modulating neuroinflammatory pathways and restoring lipid homeostasis. In cultured astrocytes and neurons derived from human induced pluripotent stem cells, BRI-50460 mitigates the effects of amyloid beta 42 oligomers on cPLA2 activation, tau hyperphosphorylation, and synaptic and dendritic reduction. Our results suggest that small molecule inhibitors of the cPLA2 enzyme can modulate the downstream inflammatory lipid signaling pathways, offering a promising therapeutic strategy for AD and other neurodegenerative diseases.

neuroscience↗

bioRxiv2024

An opioid efficacy switch for reversible optical control of peripheral analgesia

The mu-opioid receptor (MOR) is a major target for the treatment of pain. However, opioids are prone to side effects which limit their effectiveness as analgesics and can lead to opioid use disorders or, even, lethal overdose. The systemic administration of opioid agonists makes it both very difficult to decipher their underlying circuit mechanisms of action and to limit drug action to specific receptor subpopulations to isolate therapeutic effects from adverse side effects. Here we design, synthesize, and characterize a reversibly photoswitchable morphinan agonist termed "azo-morphine-3" (AM-3) which interconverts from low to high efficacy in response to different wavelengths of light to enable optical control of MOR signaling. Cryo-EM structures of the low efficacy "trans" and high efficacy "cis" states of AM-3 bound to the MOR reveal distinct binding modes of the photoswitchable azobenzene moiety, each inducing unique structural dynamics, providing insight into the molecular basis of agonist efficacy. In mice, AM-3 drives reversible and repeatable optical control of anti-nociception with a reduced side effect profile owing to its restriction to the periphery and its ability to be locally activated at the site of pain.

pharmacology and toxicology↗

bioRxiv2024

Angiotensin-(1-5) is a Potent Endogenous Angiotensin AT2-Receptor Agonist

BackgroundThe renin-angiotensin system involves many more enzymes, receptors and biologically active peptides than originally thought. With this study, we investigated whether angiotensin-(1-5) [Ang-(1-5)], a 5-amino acid fragment of angiotensin II, has biological activity, and through which receptor it elicits effects. MethodsThe effect of Ang-(1-5) (1{micro}M) on nitric oxide release was measured by DAF-FM staining in human aortic endothelial cells (HAEC), or Chinese Hamster Ovary (CHO) cells stably transfected with the angiotensin AT2-receptor (AT2R) or the receptor Mas. A potential vasodilatory effect of Ang-(1-5) was tested in mouse mesenteric and human renal arteries by wire myography; the effect on blood pressure was evaluated in normotensive C57BL/6 mice by Millar catheter. These experiments were performed in the presence or absence of a range of antagonists or inhibitors or in AT2R-knockout mice. Binding of Ang-(1-5) to the AT2R was confirmed and the preferred conformations determined by in silico docking simulations. The signaling network of Ang-(1-5) was mapped by quantitative phosphoproteomics. ResultsKey findings included: (1) Ang-(1-5) induced activation of eNOS by changes in phosphorylation at Ser1177eNOS and Tyr657eNOS and thereby (2) increased NO release from HAEC and AT2R-transfected CHO cells, but not from Mas-transfected or non-transfected CHO cells. (3) Ang-(1-5) induced relaxation of preconstricted mouse mesenteric and human renal arteries and (4) lowered blood pressure in normotensive mice - effects which were respectively absent in arteries from AT2R-KO or in PD123319-treated mice and which were more potent than effects of the established AT2R-agonist C21. (5) According to in silico modelling, Ang-(1-5) binds to the AT2R in two preferred conformations, one differing substantially from where the first five amino acids within angiotensin II bind to the AT2R. (6) Ang-(1-5) modifies signaling pathways in a protective RAS-typical way and with relevance for endothelial cell physiology and disease. ConclusionsAng-(1-5) is a potent, endogenous AT2R-agonist.

pharmacology and toxicology↗

bioRxiv2021

Novel Class of Psychedelic Iboga Alkaloids Disrupts Opioid Addiction States

Substance use and related mental health epidemics are causing increasing suffering and death in diverse communities.1,2 Despite extensive efforts focused on developing pharmacotherapies for treating substance use disorders, there is an urgent need for radically different therapeutic approaches.3,4 Ibogaine provides an important drug prototype in this direction, as a psychoactive iboga alkaloid suggested to have the ability to interrupt opioid use in drug-dependent humans.5 However, ibogaine and its major metabolite noribogaine present considerable safety risk associated with cardiac arrhythmias.6 We introduce a new class of iboga alkaloids - "oxa-iboga" - defined as benzofuran-containing iboga analogs and created via structural editing of the iboga skeleton. The oxa-iboga compounds act as potent kappa opioid receptor agonists in vitro and in vivo, but exhibit atypical behavioral features compared to standard kappa psychedelics. We show that oxa-noribogaine has greater therapeutic efficacy in rat models of opioid use, and no cardiac pro-arrhythmic potential, in contrast to noribogaine. Oxa-noribogaine induces long-lasting suppression of morphine and fentanyl intake after a single dose, persistent reduction of morphine intake and reinforcing efficacy after a short treatment regimen, and suppression of morphine and fentanyl drug seeking in relapse models. Oxa-noribogaine also induces a lasting elevation of neurotrophin proteins in the ventral tegmental area and medial prefrontal cortex, consistent with targeted neuroplasticity induction and alteration of addiction-like states. As such, oxa-iboga compounds represent candidates for a novel type of pharmacotherapy for treatment of opioid use disorder.

pharmacology and toxicology↗

bioRxiv2017

Intracellular Passage Of Na+ In An Active State G Protein Coupled Receptor

Playing a central role in cell signalling, GPCRs have evolved into the largest superfamily of membrane proteins and form the majority of drug targets in humans. How extracellular agonist binding triggers the activation of GPCRs and associated intracellular effector proteins remains, however, poorly understood. High resolution structural studies have recently revealed that inactive class-A GPCRs harbour a conserved binding site for Na+ ions in the centre of their transmembrane domain, accessible from the extracellular space. Here, we show that the opening of a conserved hydrated channel in the activated state receptors allows the Na+ ion to egress from its binding site into the cytosol. Coupled with protonation changes, this ion movement occurs without significant energy barriers, and can be driven by physiological transmembrane ion and voltage gradients. We propose that Na+ ion exchange with the cytosol is a key step in GPCR activation, which locks receptors in long-lived active-state conformations.

biophysics↗