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Crystal structures of human NSDHL and development of its novel inhibitor with the potential to suppress EGFR activity

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Abstract

NAD(P)-dependent steroid dehydrogenase-like (NSDHL), an essential enzyme in human cholesterol synthesis and a regulator of epidermal growth factor receptor (EGFR) trafficking pathways, has attracted interest as a therapeutic target due to its crucial relevance to cholesterol-related diseases and carcinomas. However, the development of pharmacological agents for targeting NSDHL has been hindered by the absence of the atomic details of NSDHL. In this study, we reported two X-ray crystal structures of human NSDHL, which revealed a detailed description of the coenzyme-binding site and the unique conformational change upon the binding of a coenzyme. A structure-based virtual screening and biochemical evaluation were performed and identified a novel inhibitor for NSDHL harboring suppressive activity towards EGFR. In EGFR-driven human cancer cells, treatment with the potent NSDHL inhibitor enhanced the antitumor effect of an EGFR kinase inhibitor. Overall, these findings could serve as good platforms for the development of therapeutic agents against NSDHL-related diseases.

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Abbreviations

NAD:

Nicotinamide adenine dinucleotide

NADP:

Nicotinamide adenine dinucleotide phosphate

r.m.s.:

Root mean square

SEM:

Standard error of mean

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Acknowledgements

We thank the beamline (BL) staff members at the Pohang Light Source, Korea (BL-5C and BL-11C), and SPring-8, Japan [beamline BL44XU under the approval of the Japan Synchrotron Radiation Research Institute (proposal No. 2017B6773)], for assistance with the X-ray diffraction experiments. All chemical libraries used in this study were kindly provided by the Korean Chemical Bank at the Korean Research Institute of Chemical Technology. This work was funded by Korea Ministry of Science, Information, Communication, Technology, and Future Planning and the National Research Foundation (NRF) of Korea Grants (NRF-2018R1A2A1A19018526 and NRF-2018R1A5A2024425 to B.-J.L.; NRF-2016R1C1B2014609, NRF-2018R1A6B4023605 and NRF-2019R1H1A1102102 to S.J.L.; and NRF-2017R1C1B2012225 to H.S.K.). This work was also supported by the 2018 BK21 Plus Project for Medicine, Dentistry, and Pharmacy and the National Cancer Center Grant of Korea (NCC-1811040; NCC-1910032; and NCC-1910023).

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Authors and Affiliations

  1. Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea

    Dong-Gyun Kim, Sujin Cho, Kyu-Yeon Lee, Seung-Ho Cheon, Dongyoon Kim, Kwang-Soo Shin, Choong-Hyun Koh, Ji Sung Koo, Yu-Kyoung Oh, Yoo-Seong Jeong, Suk-Jae Chung & Bong-Jin Lee

  2. Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea

    Hye-Jin Yoon, Yuri Choi & Hyung Ho Lee

  3. Chemical Data-Driven Research Center, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea

    Joo-Youn Lee

  4. Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea

    Moonkyu Baek & Kwan-Young Jung

  5. Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, Daejeon, 34113, Republic of Korea

    Kwan-Young Jung

  6. Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do, 10408, Republic of Korea

    Hyo Jin Lim & Hyoun Sook Kim

  7. Gachon Institute of Pharmaceutical Sciences, College of Pharmacy, Gachon University, Incheon, 13120, Republic of Korea

    Sung Jean Park

  8. Department of Medicine, College of Medicine, Hanyang University, Seoul, 04763, Republic of Korea

    Jeong-Yeon Lee

  9. PAL-XFEL, Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk, 37673, Republic of Korea

    Sang Jae Lee

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  1. Dong-Gyun Kim
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Contributions

D-GK designed and performed most experiments, analyzed data, and wrote the paper. SC initiated the project and performed crystallization of NSDHLholo and mutation studies. K-YL and S-HC helped to perform in vitro competition assay and structural analysis. H-JY collected X-ray data of crystals and solved the structure of NSDHLholo. J-YL selected compounds for in vitro competition assay from chemical library and carried out molecular docking. DK and Y-KO offered facilities and reagents for cell experiments. K-SS and C-HK guided D-GK to perform and analyze the flow cytometry experiments. YC and HHL performed SEC-MALS. Y-SJ and S-JC performed and analyzed data on the kinetic solubility of compound 9. MB and K-YJ synthesize compound 9. HSK and HJL performed and analyzed TSA experiments. SJP and J-YL offered valuable scientific feedback in the paper. J-YL also supervised experiments in her fields. SJL and B-JL oversaw all aspects of this project.

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Correspondence to Sang Jae Lee or Bong-Jin Lee.

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Kim, DG., Cho, S., Lee, KY. et al. Crystal structures of human NSDHL and development of its novel inhibitor with the potential to suppress EGFR activity. Cell. Mol. Life Sci. 78, 207–225 (2021). https://doi.org/10.1007/s00018-020-03490-2

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