title: In silico discovery of small-molecule Ras inhibitors that display antitumor activity by blocking the Ras-effector interaction.
abstract: Mutational activation of the Ras oncogene products (H-Ras, K-Ras, and N-Ras) is frequently observed in human cancers, making them promising anticancer drug targets. Nonetheless, no effective strategy has been available for the development of Ras inhibitors, partly owing to the absence of well-defined surface pockets suitable for drug binding. Only recently, such pockets have been found in the crystal structures of a unique conformation of Ras⋅GTP. Here we report the successful development of small-molecule Ras inhibitors by an in silico screen targeting a pocket found in the crystal structure of M-Ras⋅GTP carrying an H-Ras-type substitution P40D. The selected compound Kobe0065 and its analog Kobe2602 exhibit inhibitory activity toward H-Ras⋅GTP-c-Raf-1 binding both in vivo and in vitro. They effectively inhibit both anchorage-dependent and -independent growth and induce apoptosis of H-ras(G12V)-transformed NIH 3T3 cells, which is accompanied by down-regulation of downstream molecules such as MEK/ERK, Akt, and RalA as well as an upstream molecule, Son of sevenless. Moreover, they exhibit antitumor activity on a xenograft of human colon carcinoma SW480 cells carrying the K-ras(G12V) gene by oral administration. The NMR structure of a complex of the compound with H-Ras⋅GTP(T35S), exclusively adopting the unique conformation, confirms its insertion into one of the surface pockets and provides a molecular basis for binding inhibition toward multiple Ras⋅GTP-interacting molecules. This study proves the effectiveness of our strategy for structure-based drug design to target Ras⋅GTP, and the resulting Kobe0065-family compounds may serve as a scaffold for the development of Ras inhibitors with higher potency and specificity.
authors: Division of Molecular Biology, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan. sfumi@med.kobe-u.ac.jp
authors: Fumi
authors: F
authors: Shima
authors: Yoko
authors: Y
authors: Yoshikawa
authors: Min
authors: M
authors: Ye
authors: Mitsugu
authors: M
authors: Araki
authors: Shigeyuki
authors: S
authors: Matsumoto
authors: Jingling
authors: J
authors: Liao
authors: Lizhi
authors: L
authors: Hu
authors: Takeshi
authors: T
authors: Sugimoto
authors: Yuichi
authors: Y
authors: Ijiri
authors: Azusa
authors: A
authors: Takeda
authors: Yuko
authors: Y
authors: Nishiyama
authors: Chie
authors: C
authors: Sato
authors: Shin
authors: S
authors: Muraoka
authors: Atsuo
authors: A
authors: Tamura
authors: Tsutomu
authors: T
authors: Osoda
authors: Ken-ichiro
authors: K
authors: Tsuda
authors: Tomoya
authors: T
authors: Miyakawa
authors: Hiroaki
authors: H
authors: Fukunishi
authors: Jiro
authors: J
authors: Shimada
authors: Takashi
authors: T
authors: Kumasaka
authors: Masaki
authors: M
authors: Yamamoto
authors: Tohru
authors: T
authors: Kataoka
mesh_terms: D000818:Animals; D000970:Antineoplastic Agents / Q000494:pharmacology*; D002461:Cell Line, Transformed; D045744:Cell Line, Tumor; D019295:Computational Biology / Q000379:methods; D015195:Drug Design; D005982:Glutathione Transferase / Q000378:metabolism; D006160:Guanosine Triphosphate / Q000737:chemistry; D006801:Humans; D051379:Mice; D008819:Mice, Nude; D008958:Models, Molecular; D008968:Molecular Conformation; D009154:Mutation; D041681:NIH 3T3 Cells; D009368:Neoplasm Transplantation; D011485:Protein Binding; D011487:Protein Conformation; D015398:Signal Transduction; D018631:ras Proteins / Q000037:antagonists & inhibitors* / Q000378:metabolism*
chemical_list: D000970:Antineoplastic Agents; D006160:Guanosine Triphosphate; D005982:Glutathione Transferase; D018631:ras Proteins
keywords: molecular targeted therapy; small-molecule inhibitor
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