Computational and Structure-Based Development of High Potent Cell-Active Covalent Inhibitor Targeting the Peptidyl-Prolyl Isomerase NIMA-Interacting‑1 (Pin1)
datasetposted on 2022-01-28, 15:09 authored by Liping Liu, Rui Zhu, Jiacheng Li, Yuan Pei, Shuangshuang Wang, Pan Xu, Mingyu Wang, Yu Wen, Hao Zhang, Daohai Du, Hong Ding, Hualiang Jiang, Kaixian Chen, Bing Zhou, Lifang Yu, Cheng Luo
The unique proline isomerase peptidyl-prolyl isomerase NIMA-interacting-1 (Pin1) is reported to activate numerous cancer-driving pathways simultaneously, and aberrant Pin1 activation is present in many human cancers. Here, we identified a novel hit compound, ZL-Pin01, that covalently modified Pin1 at Cys113 with an half-maximal inhibitory concentration (IC50) of 1.33 ± 0.07 μM through screening an in-house library. Crystallographic study drove the process of structure-guided optimization and led to the potent inhibitor ZL-Pin13 with an IC50 of 0.067 ± 0.03 μM. We obtained four co-crystal structures of Pin1 complexed with inhibitors that elucidated the detailed binding mode of the derivatives with Pin1. Interestingly, the co-crystal of Pin1 with ZL-Pin13 obtained by co-crystallization revealed the conformational change of Gln129 induced by the inhibitor. Furthermore, ZL-Pin13 effectively inhibited the proliferation and downregulated the Pin1 substrates in MDA-MB-231 cells. Collectively, we developed a potent covalent inhibitor of Pin1, ZL-Pin13, which could be an effective probe for studying the functional roles of Pin1.
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prolyl isomerase nimanovel hit compoundmaximal inhibitory concentrationmany human cancersdriving pathways simultaneouslydetailed binding modecrystallographic study droveactivate numerous cancerhigh potent cell33 ± 0067 ± 0covalently modified pin1aberrant pin1 activationpin13 </ b50 </ subpotent covalent inhibitorobtained four cointeracting ‑ 1potent inhibitorpin1 substratespin1 complexedhouse libraryguided optimizationgln129 inducedfunctional roleseffectively inhibitedeffective probecrystallization revealedconformational changebased development231 cells07 μm03 μm