title: Development of Small-Molecule Cryptochrome Stabilizer Derivatives as Modulators of the Circadian Clock.
abstract: Small-molecule probes have been playing prominent roles in furthering our understanding of the molecular underpinnings of the circadian clock. We previously discovered a carbazole derivative, KL001 (N-(3-(9H-carbazol-9-yl)-2-hydroxypropyl)-N-(furan-2-ylmethyl)methanesulfonamide), as a stabilizer of the clock protein cryptochrome (CRY). Herein we describe an extensive structure-activity relationship analysis of KL001 derivatives leading to the development of a highly active derivative: 2-(9H-carbazol-9-yl)-N-(2-chloro-6-cyanophenyl)acetamide (KL044). Subsequent 3D-QSAR analysis identified critical features of KL001 derivatives and provided a molecular-level understanding of their interaction with CRY. The electron-rich carbazole, amide/hydroxy linker, sulfonyl group, and electron-withdrawing nitrile moieties contribute to greater biological activity. The hydrogen bonding interactions with Ser394 and His357 as well as stronger CH-π interactions with Trp290 make KL044 a better binder than KL001. KL044 lengthened the circadian period, repressed Per2 activity, and stabilized CRY in reporter assays with roughly tenfold higher potency than KL001. Altogether, KL044 is a powerful chemical tool to control the function of the circadian clock through its action on CRY.
authors.affiliation: Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037 (USA).|Natural Product Research Center, Korea Institute of Science and Technology, Department of Biological Chemistry, University of Science and Technology (Republic of Korea).
authors.forename: Jae Wook
authors.initials: JW
authors.lastname: Lee
authors.affiliation: Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601 (Japan). thirota@itbm.nagoya-u.ac.jp.|Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA, 90089 (USA). thirota@itbm.nagoya-u.ac.jp.|PRESTO, Japan Science and Technology Agency, Nagoya, 464-8601 (Japan). thirota@itbm.nagoya-u.ac.jp.
authors.forename: Tsuyoshi
authors.initials: T
authors.lastname: Hirota
authors.affiliation: Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601 (Japan). anupriya.veerman@gmail.com.|Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, 464-8602 (Japan). anupriya.veerman@gmail.com.
authors.forename: Anupriya
authors.initials: A
authors.lastname: Kumar
authors.affiliation: Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037 (USA).|Collage of Pharmacy, Kyung Hee University, Seoul, 130-701 (Republic of Korea).
authors.forename: Nam-Jung
authors.initials: NJ
authors.lastname: Kim
authors.affiliation: Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601 (Japan).|Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, 464-8602 (Japan).
authors.forename: Stephan
authors.initials: S
authors.lastname: Irle
authors.affiliation: Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601 (Japan). stevekay@usc.edu.|Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA, 90089 (USA). stevekay@usc.edu.
authors.forename: Steve A
authors.initials: SA
authors.lastname: Kay
mesh_terms: D000083:Acetanilides / Q000737:chemistry / Q000494:pharmacology; D002227:Carbazoles / Q000737:chemistry* / Q000494:pharmacology*; D057906:Circadian Clocks / Q000187:drug effects*; D056931:Cryptochromes / Q000235:genetics / Q000378:metabolism*; D057809:HEK293 Cells; D006639:Histidine / Q000737:chemistry; D006801:Humans; D006860:Hydrogen Bonding; D056950:Period Circadian Proteins / Q000235:genetics / Q000378:metabolism; D055550:Protein Stability; D021281:Quantitative Structure-Activity Relationship; D012694:Serine / Q000737:chemistry; D013449:Sulfonamides / Q000737:chemistry* / Q000494:pharmacology*
chemical_list: C000608411:2-(9H-carbazol-9-yl)-N-(2-chloro-6-cyanophenyl)acetamide; D000083:Acetanilides; C538963:CRY1 protein, human; D002227:Carbazoles; D056931:Cryptochromes; C574808:KL001; C421902:PER2 protein, human; D056950:Period Circadian Proteins; D013449:Sulfonamides; D012694:Serine; D006639:Histidine
keywords: 3D-QSAR; circadian clock; cryptochrome; protein degradation; small molecule