Molecular Dynamics Identify Variances Between Galectin Carbohydrate‐Binding Sites That Impact the Binding Site Conformation and Ligand Binding

Galectins are a family of carbohydrate-binding proteins that aid in the progression of pathological conditions such as inflammation, bone disease, and cancers, making them attractive drug targets. Galectins share a conserved carbohydrate recognition domain providing a focus for inhibitor design incorporating modification of carbohydrate-based scaffolds that includes the addition of aromatic moieties. Some compounds exhibit nanomolar affinities but often show poor specificity toward particular galectins; thus cross-reactivity in the body is difficult to avoid and potentially detrimental for drug therapies. The low selectivity is due to the high conservation of amino acid residues among galectins that partake in ligand binding. Critically, although these amino acids are highly conserved, there are differences in the shape and physical characteristics of the binding site due to the slight variation in the surrounding amino acid residues of the more extended regions. Using molecular dynamic simulations, the effect of amino acids associated with the galectin binding site was explored. Besides the impact of large bulky side chain amino acids such as phenylalanine, tyrosine, and histidine, a series of salt-bridge interactions were identified within some galectins that influence the resulting shape of the binding site cavity, thus affecting ligand selectivity. In silico alanine point mutations disrupting these salt-bridge interactions or replacing the bulky side chain amino acid residues led to changes in the binding site conformation impacting ligand binding, as indicated by our cluster and energetic analyses. This investigation gives further insight into the galectin carbohydrate binding site that has relevance for ligand design as potential therapeutics.