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Cited by 293Protein Kinase Regulation and GTPase SignalingComputational Drug Discovery MethodsProtein Tyrosine Phosphatases

In silico discovery of small-molecule Ras inhibitors that display antitumor activity by blocking the Ras–effector interaction

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Shima, Fumi, Yoshikawa, Yoko, Ye, Min, Araki, Mitsugu, Matsumoto, Shigeyuki, Liao, Jingling, Hu, Lizhi, Sugimoto, Takeshi +14 more·2013·Proceedings of the National Academy of Sciences
DOI 10.1073/pnas.1217730110PMC PMC3657810
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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.

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  • Recently, three studies used similar fragment-based small molecule screening to identify compounds that bind sites on the K-Ras surface and block its SOS-mediated activation.

    “Recently, three studies used similar fragment-based small molecule screening to identify compounds that bind sites on the K-Ras surface and block its SOS-mediated activation24–26 suggesting the approach has some promise.”

    From Discovery and characterization of small molecules that target the GTPase Ral (2014) · cites this paper as [26]

    The Discussion distinguishes this study from compounds that bind K-Ras and inhibit SOS-mediated nucleotide exchange: it says those were reported by Maurer et al., whereas this study's compounds primarily interfere with Ras–effector interactions. The Discovery section describes an in silico docking screen targeting an M-Ras structure, not fragment-based screening for inhibitors of SOS-mediated activation. (LLM, conf=0.91)

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Research works printed but not linked: 8

  1. [15]Nassar N, et al. (1995) The 2.2 A crystal structure of the Ras-binding domain of the serine/threonine kinase c-Raf1 in complex with Rap1A and a GTP analogue. Nature 375(6532):554 -560.
  2. [16]Pacold ME, et al. (2000) Crystal structure and functional analysis of Ras binding to its effector phosphoinositide 3-kinase gamma. Cell 103(6):931 -943.
  3. [17]Huang L, Hofer F, Martin GS, Kim SH (1998) Structural basis for the interaction of Ras with RalGDS. Nat Struct Biol 5(6):422 -426.
  4. [19]Maurer T, et al. (2012) Small-molecule ligands bind to a distinct pocket in Ras and inhibit SOS-mediated nucleotide exchange activity. Proc Natl Acad Sci USA 109(14): 5299 -5304.
  5. [20]Sun Q, et al. (2012) Discovery of small molecules that bind to K-Ras and inhibit Sosmediated activation. Angew Chem Int Ed Engl 51(25):6140 -6143.
  6. [21]Lim KH, Ancrile BB, Kashatus DF, Counter CM (2008) Tumour maintenance is mediated by eNOS. Nature 452(7187):646 -649.
  7. [24]Fukunishi Y, Mikami Y, Nakamura H (2005) Similarities among receptor pockets and among compounds: analysis and application to in silico ligand screening. J Mol Graph Model 24(1):34 -45.
  8. [27]Koradi R, Billeter M, Wuthrich K (1996) MOLMOL: A program for display and analysis of macromolecular structures. J Mol Graph 14(1):51 -55.

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Authors
Shima, F., Yoshikawa, Y., Ye, M., Araki, M., Matsumoto, S., Liao, J., Hu, L., Sugimoto, T., Ijiri, Y., Takeda, A., Nishiyama, Y., Sato, C., Muraoka, S., Tamura, A., Osoda, T., Tsuda, K.-I., Miyakawa, T., Fukunishi, H., Shimada, J., Kumasaka, T., Yamamoto, M., & Kataoka, T.
Affiliations
  • Kobe University (JP)
  • Business Innovation Center and
  • NEC (Japan) (JP)
  • Japan Synchrotron Radiation Research Institute (JP)
  • SPring-8 (JP)
ORCID
Venue
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences
Published
2013-04-29
Volume
110
Issue
20
Pages
8182-8187
ISSN
  • 0027-8424 (ISSN-L)
  • 1091-6490
DOI
10.1073/pnas.1217730110
PMC
PMC3657810
OpenAlex
W2012479646
Cited by
293
References
1
Citations by year
2026: 5 · 2025: 8 · 2024: 15 · 2023: 18 · 2022: 15 · 2021: 23 · 2020: 27 · 2019: 31 · 2018: 25 · 2017: 31 · 2016: 20 · 2015: 30 · 2014: 33 · 2013: 11
FWCI
11.93
Type
journal article
Language
en
Open access
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
Japan Society for the Promotion of Science (23390071)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Kinase Regulation and GTPase Signaling
  • Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Tyrosine Phosphatases
Keywords
RAS inhibitors, Ras-GTP, KRAS G12V, structure-based drug design, MEK/ERK signaling, Akt, RalA, Son of Sevenless, apoptosis, colon carcinoma xenografts, oncogenic Ras, small molecule inhibitors
MeSH terms
Animals, Antineoplastic Agents, Cell Line, Transformed, Glutathione Transferase, Guanosine Triphosphate, Humans, Mice, Nude, Models, Molecular, Molecular Conformation, Mutation, Neoplasm Transplantation, Protein Binding, Protein Conformation, Drug Design, Signal Transduction, ras Proteins, Computational Biology, NIH 3T3 Cells, Cell Line, Tumor, Mice

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