AI-enhanced virtual screening identifies a potent small-molecule modulator of ClC-3 for cervical cancer drug discovery.

Abstract

ClC-3 chloride channels play essential roles in cervical cancer progression by regulating lysosomal acidification, cell volume homeostasis, and chemoresistance. However, no highly selective small-molecule modulators of ClC-3 have been reported to date. Motivated by the urgent clinical need to reverse ClC-3-mediated chemoresistance and the challenge of processing massive chemical libraries under limited computational hardware resources, we propose a novel AI-driven Drug Discovery (AIDD) pipeline. Here, we present an integrated virtual drug discovery framework that transitions from traditional Computer-Aided Drug Design (CADD) by combining large-scale molecular docking, deep-learning-based rescoring, pharmacokinetic filtering, and atomistic molecular dynamics (MD) simulations. The primary advantage of this proposed scheme lies in the integration of GNINA 3D-convolutional neural network (CNN) rescoring, which significantly reduces the false-positive rates inherent in empirical scoring functions for membrane proteins. A library of ∼180,000 ZINC15 compounds was initially screened using AutoDock Vina, followed by GNINA convolutional neural network rescoring to refine predicted binding affinity and pose confidence. ADMET profiling further narrowed the candidates, providing computational proof of drug-likeness and toxicity criteria rather than experimental validation. Ultimately, only ZINC000001556308 (Lig8) satisfied all in silico criteria. To validate binding stability, we performed 100-ns all-atom MD simulations of the ClC-3-Lig8 complex embedded in a lipid bilayer. Lig8 induced reduced RMSD fluctuations, lower RMSF values across key transmembrane helices, and a more compact radius of gyration, indicating enhanced structural stabilization of ClC-3. MM/PBSA calculations confirmed favorable binding energetics dominated by van der Waals interactions, while per-residue decomposition identified PHE527, GLY283, and GLY584 as major contributors to ligand recognition. These results reveal a previously uncharacterized binding pocket within the ClC-3 transmembrane domain and highlight Lig8 as a promising lead compound for targeting ClC-3-mediated oncogenic signaling. Overall, this study establishes the first comprehensive computational framework for ClC-3 modulator discovery and provides a validated chemical scaffold for future therapeutic development against cervical cancer.