Sugar mimics and their probable binding sites: design and synthesis of thiazole linked coumarin-piperazine hybrids as galectin-1 inhibitors†

Abstract

Sugar mimics are valuable tools in medicinal chemistry, offering the potential to overcome the limitations of carbohydrate inhibitors, such as poor pharmacokinetics and non-selectivity. In our continued efforts to develop heterocyclic galectin-1 inhibitors, we report the synthesis and characterization of thiazole-linked coumarin piperazine hybrids (10a–10i) as Gal-1 inhibitors. The compounds were characterized using ¹H NMR, ¹³C NMR and HRMS. Among the synthesized molecules, four compounds demonstrated significant inhibitory activity, with more than 50% inhibition observed at a concentration of 20 μM in a Gal-1 enzyme assay. Fluorescence spectroscopy was further utilized to elucidate the binding constant for the synthesized compounds. 10g exhibited the highest affinity for Gal-1, with a binding constant (K_a) of 9.8 × 10⁴ M⁻¹. To elucidate the mode of binding, we performed extensive computational analyses with 10g, including 1.2 μs all-atom molecular dynamics simulations coupled with a robust machine learning tool. Our findings indicate that 10g binds to the carbohydrate binding site of Gal-1, with the coumarin moiety playing a key role in binding interactions. Additionally, our study underscores the limitations of relying solely on docking scores for conformational selection and highlights the critical importance of performing multiple MD replicas to gain accurate insights.