39: Targeting neuroplasticity in chronic neuropathic pain with novel small molecules

Topic: Basic Science
Subtopic: Pain category (ICD-11), Chronic neuropathic pain, , , , , , , , , , Pharmacological interventions

Background and Aims: Background and Aims
Neuropathic pain (NP) affects ~10% of the population; current standards of care provide adequate relief in fewer than half of patients and carry significant side-effect liabilities. No approved therapeutic targets the etiological CNS mechanisms underlying NP. Maladaptive dendritic spine remodeling in spinal dorsal horn neurons, driven by Rac GTPase signaling downstream of guanine nucleotide exchange factors (GEFs), is a central pathophysiological mechanism. Pharmacological Rac inhibition and Tiam1 GEF ablation produce long-lasting preclinical analgesia, validating this pathway. However, Rac’s ubiquitous expression necessitates tissue-selective upstream targeting. Kalirin is a CNS-enriched Rac-GEF concentrated at postsynaptic densities, upregulated in spinal neurons following nerve injury, and required for central sensitization — making it an ideal node for spatially restricted Rac inhibition. We aimed to identify first-in-class kalirin GEF inhibitors, characterize their neuronal activity and analgesic efficacy, and evaluate human genetic support for this pathway in chronic pain.​​​​​​​​​​​​​​​​

Methods: The crystal structure of the kalirin Rac-GEF domain (PDB:5O33) was used for SiteMap-guided binding site identification and virtual screening against 65 million synthetically accessible compounds using Glide docking. Hit compounds were validated in a fluorescence-based BODIPY-GDP GEF activity assay using recombinant kalirin and Rac1, and in a cellular active-Rac pulldown assay in kalirin-transfected HEK293T cells. Direct target engagement was assessed by fluorescence thermal shift. Neuronal effects were characterized by multi-electrode array (MEA) recording in cultured cortical neurons, and dendritic spine morphology was quantified by confocal imaging. In vivo pharmacokinetic analysis assessed oral bioavailability and CNS penetration. Analgesic efficacy was assessed in the formalin inflammatory pain model, the complete Freund’s adjuvant (CFA) model, and the spared nerve injury (SNI) model of NP. A comprehensive neurosafety behavioral battery assessed cognitive and motor function. Medicinal chemistry optimization generated structural analogues, screened by toxicity, MEA activity, and efficacy.

Results: In silico screening identified a small molecule series targeting kalirin. Lead compounds inhibited kalirin-dependent Rac activation in cellular assays and reduced spontaneous neuronal firing in cortical MEA cultures, with complete reversibility on washout. Acute systemic administration produced significant analgesia in formalin Phase II — consistent with kalirin knockout animals, which showed selective reduction of central sensitization-dependent Phase II responses — and in CFA-induced mechanical allodynia. In the SNI model, treatment produced robust analgesia that persisted for three weeks following cessation, suggesting disease-modifying activity rather than symptomatic relief. Critically, analgesia was fully replicated by a structurally unrelated direct Rac1 inhibitor, confirming on-pathway in vivo mechanism. Sub-chronic administration produced no impairment of locomotion, working memory, novel object recognition, or fear conditioning, and outperformed gabapentin on sedation endpoints. Medicinal chemistry optimization yielded analogues with up to 10-fold improved potency.

Conclusions: These findings establish kalirin as a viable molecular target for chronic neuropathic pain and provide a first-in-class small molecule series inhibiting kalirin-dependent Rac signaling with robust preclinical analgesic efficacy. The post-treatment persistence of analgesia in the SNI model is consistent with a disease-modifying mechanism — prevention of maladaptive synaptic remodeling underlying the acute-to-chronic pain transition — distinguishing this approach from all currently approved NP therapeutics. Mechanistic convergence between the lead scaffold and a direct Rac inhibitor validates on-pathway activity in vivo. Human GWAS analysis of chronic pain susceptibility loci reveals significant enrichment of kalirin-interacting proteins and excitatory synapse GO categories, providing translational genetic support for this pathway independent of rodent models. Ongoing lead optimization is directed toward increased potency, with a perioperative patient population — where an acute intervention window for preventing the chronic pain induction.

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Presenting Author: Peter Penzes
Submitting Author: Peter Penzes

Senior Author: Peter Penzes

IASP 2026 Global Year theme of Neuropathic Pain: Yes

• Euan Parnell - Northwestern University