Exploring human GABA transporter 3 binders for epilepsy through quantum reactivity analysis, molecular dynamics, machine learning prediction, and network pharmacology

Clinical Snapshot

Key Findings

• P Value: Not applicable for computational study

• Effect Size: Predicted pIC50 values: Comp_1 (7.95), Comp_2 (7.98), Comp_3 (7.63)

• Primary Outcome: Identification of three lead GAT3 inhibitor compounds with favorable binding properties

• Nnt Or Sensitivity: RMSD values 2.5-3.0 Å for most stable compound (Comp_2)

• Confidence Interval: Not reported

Clinical Application

Requires synthesis, preclinical testing, and clinical trials before therapeutic application Would need TGA approval pathway for novel antiepileptic drugs; potential relevance to Australian epilepsy patients if validated experimentally Patients with drug-resistant epilepsy, pending experimental validation

Abstract

CONTEXT: Drug-resistant epilepsy (DRE) remains a major therapeutic challenge, affecting millions of patients globally who do not respond to conventional antiepileptic medications. Recent evidence highlights GABA transporter 3 (GAT3), a glial subtype responsible for regulating extracellular GABA levels, as a promising molecular target for seizure control. Despite its therapeutic potential, selective and potent GAT3 inhibitors remain largely unexplored. This study aims to identify novel GAT3 inhibitors through an integrative computational strategy combining quantum chemical, molecular dynamics, and machine learning approaches to accelerate antiepileptic drug discovery. The cryo-EM-resolved human GAT3-SNAP-5114 complex structure was used for virtual screening, leading to the identification of three highest-ranking compounds, viz. Comp_1, Comp_2, and Comp_3, from the diverse chemically optimized screening library. Analysis of their quantum chemistry profiles indicated HOMO-LUMO energy gap values of 4.14 eV, 4.21 eV, and 3.26 eV, respectively, suggesting them to be maximally reactive with favorable electronic properties for interacting with biological molecules. Molecular dynamics simulations were performed in a fully hydrated POPC lipid bilayer using the AMBER force field, providing a physiologically relevant environment for assessing ligand binding and transporter dynamic, revealed stable binding modes, with the highest structural integrity or least deviations in the structure with Comp_2, having RMSD values ranging from 2.5 to 3.0 Å, with strong hydrogen bonding, while the binding mode was more flexible with strong anchorage for Comp_3, with its mode involving diverse interactions in the complex. Principal component and free energy landscape analyses identified energetically favorable, ligand-induced conformational states. Machine learning-based pIC₅₀ predictions using the AdaBoost regressor yielded values of 7.95 (Comp_1), 7.98 (Comp_2), and 7.63 (Comp_3), all comparable or superior to the reference inhibitor (7.89). A novel approach for network pharmacology integrating detailed drug-gene interaction profiling was additionally used to improve systems-level understanding of the discovered compound. These findings validate the potential of Comp_1-3 as lead GAT3-targeting antiepileptic agents. METHODS: A docking-based virtual screening of a structurally diverse compound library was performed against the cryo-EM structure of human GAT3 in complex with the reference inhibitor SNAP-5114. The top-scoring ligands were subjected to density functional theory (DFT) analysis to assess electronic properties such as HOMO-LUMO energy gaps, reflecting potential binding reactivity. Lead candidates were refined, docked, and evaluated through 500 ns molecular dynamics (MD) simulations, analyzing structural stability via RMSD, RMSF, hydrogen bonding, and interaction network profiles. Principal component analysis and free energy landscape evaluations were used to explore ligand-induced conformational dynamics. Furthermore, machine learning (ML) models-particularly the AdaBoost algorithm-were employed to predict pIC₅₀ values, confirming bioactivity trends. Finally, network pharmacology analysis was conducted to elucidate gene targets and pathway interconnections, revealing the multi-pathway involvement of top candidates in seizure regulation. This integrative computational framework underscores the potential of GAT3-focused modelling and ML-guided screening for rational antiepileptic drug design.

References

1. 1.Alam, P., Agrawal, G. P., Kirtipal, N., Akhtar, A., & Khurshid, F. (2026). Exploring human GABA transporter 3 binders for epilepsy through quantum reactivity analysis, molecular dynamics, machine learning prediction, and network pharmacology. Journal of Molecular Modeling. https://doi.org/10.3390/toxins15100608