Combining de novo molecular design with semiempirical protein–ligand binding free energy calculation†

Abstract

Semi-empirical quantum chemistry methods estimate the binding free energies of protein–ligand complexes. We present an integrated approach combining the GFN2-xTB method with de novo design for the generation and evaluation of potential inhibitors of acetylcholinesterase (AChE). We employed chemical language model-based molecule generation to explore the synthetically accessible chemical space around the natural product Huperzine A, a potent AChE inhibitor. Four distinct molecular libraries were created using structure- and ligand-based molecular de novo design with SMILES and SELFIES representations, respectively. These libraries were computationally evaluated for synthesizability, novelty, and predicted biological activity. The candidate molecules were subjected to molecular docking to identify hypothetical binding poses, which were further refined using Gibbs free energy calculations. The structurally novel top-ranked molecule was chemically synthesized and biologically tested, demonstrating moderate micromolar activity against AChE. Our findings highlight the potential and certain limitations of integrating deep learning-based molecular generation with semi-empirical quantum chemistry-based activity prediction for structure-based drug design.