Biology subjects

Shiimura, Y.

Publications and source records attributed to Shiimura, Y..

4 recordsLinked to original sources

bioRxiv2026

Discovery and dynamic pharmacology of μ-opioid receptor positive allosteric modulators

Opioid agonists such as morphine and fentanyl exert analgesic effects by binding and activating the {micro}-opioid receptor ({micro}OR), yet agonism of the {micro}OR causes a slate of serious side effects. {micro}OR-mediated addiction and respiratory depression are the major causes of the current opioid overdose crisis, largely driven by the explosion in illicit use of fentanyl, a potent opioid receptor full agonist. Given these serious side effects (and high resulting societal cost), molecules that act as analgesics with distinct mechanisms of action are of great interest. Positive allosteric modulators (PAMs) of the {micro}OR have the potential to avoid many off-target side effects of conventional opioid orthosteric agonists by enhancing the signaling properties of natural opioid peptide systems. We used a DNA-encoded chemical library screening approach to selectively discover active-state-specific {micro}OR PAMs. Two out of 3 selected prospective PAMs displayed the anticipated enhancement in agonist activity. The most effective of these compounds enhanced the activity of all orthosteric opioid agonists tested, including the native opioid peptide met-enkephalin. Little is known about the underlying dynamic basis of allosteric modulation of Family A GPCRs like the {micro}OR. To that end, we used single-molecule fluorescence resonance energy transfer experiments to detail the impact that our novel {micro}OR PAM has on the dynamic activation behavior of a key region on the intracellular face of the receptor. Our results here provide both a new chemical scaffold that acts as a {micro}OR PAM and detailed pharmacological and dynamic insights into its mechanism of action.

biophysics↗

bioRxiv2025

Structural Insights into Biased Signaling at Chemokine Receptor CCR7

CC chemokine receptor 7 (CCR7), which orchestrates adaptive immunity, exhibits a phenomenon known as biased agonism. CCL19 induces robust G protein signaling and {beta}-arrestin recruitment, leading to transient signaling. In contrast, CCL21 preferentially activates G protein pathways with minimal arrestin engagement, resulting in sustained signaling and differential functional outcomes. Here, we present the cryo-EM structures of the human CCR7-Gi complex with either CCL19 or CCL21. The structures reveal that while both engage a conserved orthosteric pocket, they adopt markedly distinct binding poses. Notably, the compact 30s loop of CCL21 inserts deeply into the receptors extracellular vestibule, whereas the corresponding loop of CCL19 rests atop extracellular loop 2. Molecular dynamics simulations further reveal that these distinct binding modes induce differential intracellular dynamics, linked to the rotameric state of Y83 at the intracellular end of transmembrane helix 1. We demonstrate that CCL19 stabilizes a flexible conformational ensemble with a highly dynamic helix 8, creating a lateral opening favorable for GPCR kinase engagement. Conversely, CCL21 restricts this flexibility, locking the receptor in a state that precludes kinase interaction while maintaining G protein coupling. Corroborated by functional data, these findings provide key insights into the structural basis of biased agonism at CCR7 and establish a foundation for rational design of pathway-selective immunomodulators. Significance statementChemokine receptor CCR7 directs immune cell migration by activating distinct signaling pathways in response to CCL19 and CCL21, a phenomenon known as biased agonism. The structural basis for this divergence has remained unclear. By combining cryo-electron microscopy with molecular dynamics simulations, we reveal that although both ligands stabilize similar G protein-bound conformations, they drive distinct receptor dynamics. We demonstrate that CCL19 induces a flexible intracellular conformation necessary for recruiting regulatory kinases, whereas CCL21 locks the receptor in a state precluding this interaction. This "dynamic selection" model aligns with functional data and rationalizes a fundamental paradox in chemokine biology, highlighting the critical role of protein dynamics in signal transduction and providing a blueprint for designing precision immunotherapeutics.

biophysics↗

bioRxiv2023

Negative allosteric modulation of the μ-opioid receptor

The {micro}-opioid receptor ({micro}OR) is a well-established target for analgesia, yet conventional opioid receptor agonists cause serious adverse effects, notably addiction and respiratory depression, which have led to the present opioid overdose epidemic. {micro}OR negative allosteric modulators (NAMs) may serve as powerful tools in preventing opioid overdose deaths, but promising chemical scaffolds remain elusive. We screened a large DNA-encoded chemical library against inactive {micro}OR, counter-screening with active, G-protein and agonist bound receptor to "steer" selections toward functional negative allosteric modulators. We discovered a NAM compound with high and selective enrichment to inactive {micro}OR; the molecule potently blocks the activity of orthosteric agonists and enhances the affinity of the key opioid overdose reversal molecule, naloxone. It accomplishes this by binding to a site on the extracellular vestibule proximal to naloxone, stabilizing a unique inactive conformation of the extracellular portions of the second and seventh transmembrane helices. The NAM perturbs orthosteric ligand kinetics in therapeutically desirable ways and works cooperatively with low doses of naloxone in vivo to inhibit morphine-induced antinociception, respiratory depression and conditioned place preference while minimizing withdrawal behaviors. Our results provide detailed structural insights into the mechanism of a negative allosteric modulator for the {micro}OR and demonstrate how it can be exploited in vivo.

biochemistry↗

bioRxiv2023

Structure-based discovery of cannabinoid-1 receptor agonists with reduced side effects

Large library docking can reveal unexpected chemotypes that complement the structures of biological targets. Seeking new agonists for the cannabinoid-1 receptor (CB1R), we docked 74 million tangible molecules, prioritizing 46 high ranking ones for de novo synthesis and testing. Nine were active by radioligand competition, a 20% hit-rate. Structure-based optimization of one of the most potent of these (Ki = 0.7 {micro}M) led to 4042, a 1.9 nM ligand and a full CB1R agonist. A cryo-EM structure of the purified enantiomer of 4042 ( 1350) in complex with CB1R-Gi1 confirmed its docked pose. The new agonist was strongly analgesic, with generally a 5-10-fold therapeutic window over sedation and catalepsy and no observable conditioned place preference. These findings suggest that new cannabinoid chemotypes may disentangle characteristic cannabinoid side-effects from their analgesia, supporting the further development of cannabinoids as pain therapeutics.

pharmacology and toxicology↗