Mapping the Glycan Recognition Landscape of Galectin-3 through Enhanced Sampling Simulations

Abstract

Galectin-3 is a β-galactoside-binding protein involved in multiple biological processes, including cell proliferation, apoptosis, and inflammatory response. The pivotal role played by galectin-3 in diverse cellular processes makes it a therapeutic target of choice against cancers. However, the dynamic interplay of galectin-3 with diverse carbohydrate ligands is yet to be fully understood in detail. Elucidating molecular recognition mechanism(s) of ligand binding in a system such as galectin-3 is crucial for biological function and has promising implications in drug discovery. However, capturing these rare-event mechanisms using atomistic molecular dynamics simulations is a computationally expensive task. Our work aims to uncover the nuances of one such crucial mechanism using Gaussian accelerated molecular dynamics (GaMD) with galectin-3 as a prototypical system. The current work employs GaMD to explore the intricate binding mechanisms of galectin-3 with glycans of varying chain lengths. Our results show that pentasaccharides and ortho-fluoro derivatives as longer-chain glycans have interacted with galectin-3 strongly and stably, recapitulating the cocrystal pose. These ligands interact not only with the CRD of galectin-3 but also remain bound in the native pocket over longer time scales, in contrast to shorter-chain ligands such as beta-lactose and TF-antigen. However, due to inherent conformational flexibility, shorter-chain ligands were observed to sample allosteric pockets prior to reaching the native binding mode. This suggests that the length of the galectin-3 ligand plays a crucial role in determining its mode of interaction. This study advances the understanding of galectin-3 recognition and provides important considerations for designing effective galectin-3-targeting therapeutics. © 2026 American Chemical Society.