Insights into the Action of Inhibitor Enantiomers against Histone Lysine Demethylase 5A

Isomers of chiral drugs can exhibit marked differences in biological activities. We studied the binding and inhibitory activities of 12 compounds against KDM5A. Among them are two pairs of enantiomers representing two distinct inhibitor chemotypes, namely, (R)- and (S)-2-((2-chlorophenyl)­(2-(piperidin-1-yl)­ethoxy)­methyl)-1H-pyrrolo­[3,2-b]­pyridine-7-carboxylic acid (compounds N51 and N52) and (R)- and (S)-N-(1-(3-isopropyl-1H-pyrazole-5-carbonyl)­pyrrolidin-3-yl)­cyclopropane­carboxamide (compounds N54 and N55). In vitro, the S enantiomer of the N51/N52 pair (N52) and the R enantiomer of the N54/N55 pair (N54) exhibited about 4- to 5-fold greater binding affinity. The more potent enzyme inhibition of KDM5A by the R-isoform for the cell-permeable N54/N55 pair translated to differences in growth inhibitory activity. We determined structures of the KDM5A catalytic domain in complex with all 12 inhibitors, which revealed the interactions (or lack thereof) responsible for the differences in binding affinity. These results provide insights to guide improvements in binding potency and avenues for development of cell permeable inhibitors of the KDM5 family.手性药物的异构体往往表现出显著的生物学活性差异。本研究针对KDM5A系统评估了12种化合物的结合活性与抑制活性。其中包含两对分别代表两种不同抑制剂化学型的对映异构体，分别为(R)-和(S)-2-((2-氯苯基)(2-(1-哌啶基)乙氧基)甲基)-1H-吡咯并[3,2-b]吡啶-7-羧酸（化合物N51与N52），以及(R)-和(S)-N-(1-(3-异丙基-1H-吡唑-5-羰基)吡咯烷-3-基)环丙烷甲酰胺（化合物N54与N55）。体外实验结果显示，N51/N52对中的S型对映异构体（N52）与N54/N55对中的R型对映异构体（N54）的结合亲和力高出约4至5倍。针对可穿透细胞的N54/N55对，R型异构体对KDM5A的更强酶抑制活性，进而导致生长抑制活性出现显著差异。我们解析了KDM5A催化结构域与全部12种抑制剂形成复合物的三维结构，揭示了造成结合亲和力差异的相互作用（或缺乏相互作用）机制。本研究结果可为优化结合效力提供理论指导，同时为KDM5家族细胞可通透抑制剂的开发指明了可行方向。