MLAC: MicroED-assisted ligand structure analysis in complexes and its application to hERG-ligand complexes

作者：Tanaka Keita, Miyashita Yasuomi, Kenji Iwasaki, Saito Tetsuichiro, Yamada Yusuke, Murata Takeshi, Naruhiko Adachi · 发表于：Institutional Repositories DataBase (IRDB) · 年份：2026 · 研究领域：Enzyme Structure and Function、Advanced Electron Microscopy Techniques and Applications、Protein Structure and Dynamics

Accurate determination of ligand structures in protein-ligand complexes is essential for elucidating molecular recognition mechanisms and advancing structure-based drug discovery. Cryogenic electron microscopy (cryo-EM) has emerged as a powerful technique for determining macromolecular structures; however, reliable identification of small-molecule ligands from cryo-EM maps remains challenging, particularly in the absence of accurate initial ligand models. Here, we present MLAC (MicroED-assisted Ligand structure Analysis in Complexes), an integrative framework that combines microcrystal electron diffraction (MicroED) with cryo-EM single-particle analysis (SPA). In MLAC, high-resolution ligand structures determined by MicroED from submicrometer-sized crystals are used as initial models for fitting into cryo-EM maps of protein-ligand complexes. As a proof of concept, previously reported hERG-ligand complexes were reanalyzed. MicroED structures of representative hERG ligands-astemizole, pimozide, and E-4031-were determined at resolutions of 0.66-0.92 & Aring; and then used for model fitting and refinement. Several quantitative metrics, including Q-score, atom inclusion, model-to-map correlation coefficients, clash analysis, and Mogul analysis, together with visual inspection, indicated that MicroED-derived ligand structures can facilitate ligand modeling for astemizole and, to a lesser extent, pimozide, whereas no clear advantage was observed for E-4031. Notably, MicroED frequent...