2. Academic Validation
  3. Protein covariation networks for elucidating ferroptosis inducer mechanisms and potential synergistic drug targets

Protein covariation networks for elucidating ferroptosis inducer mechanisms and potential synergistic drug targets

  • Commun Biol. 2025 Mar 31;8(1):480. doi: 10.1038/s42003-025-07886-3.
Rina Kunishige 1 2,  Yoshiyuki Noguchi 2 3,  Naomi Okamoto 2,  Lei Li 2,  Akito Ono 4,  Masayuki Murata 1 2,  Fumi Kano 5 6 7
Affiliations

Affiliations

  • 1 Multimodal Cell Analysis Collaborative Research Cluster, Institute of Science Tokyo, Yokohama-shi, Kanagawa, Japan.
  • 2 Cellshoot Therapeutics, Inc., Koto-ku, Tokyo, Japan.
  • 3 International Research Center for Neurointelligence, Institutes for Advanced Study, The University of Tokyo, Tokyo, Japan.
  • 4 Axcelead Drug Discovery Partners, Inc., Fujisawa, Kanagawa, Japan.
  • 5 Multimodal Cell Analysis Collaborative Research Cluster, Institute of Science Tokyo, Yokohama-shi, Kanagawa, Japan. kanou.f.f7f1@m.isct.ac.jp.
  • 6 Cellshoot Therapeutics, Inc., Koto-ku, Tokyo, Japan. kanou.f.f7f1@m.isct.ac.jp.
  • 7 Cell Biology Center, Institute of Integrated Research, Institute of Science Tokyo, Yokohama-shi, Kanagawa, Japan. kanou.f.f7f1@m.isct.ac.jp.
PMID: 40164758 DOI: 10.1038/s42003-025-07886-3
Abstract

In drug development, systematically characterizing a compound's mechanism of action (MoA), including its direct targets and effector proteins, is crucial yet challenging. Network-based approaches, unlike those focused solely on direct targets, effectively detect a wide range of cellular responses elicited by compounds. This study applied protein covariation network analysis, leveraging quantitative, morphological, and localization features from immunostained microscopic images, to elucidate the MoA of AX-53802, a novel Ferroptosis inducer. From the candidate targets extracted through network analysis, GPX4 was verified as the direct target by validation experiments. Additionally, aggregates involving GPX4, TfR1, and F-actin were observed alongside iron reduction, suggesting a Ferroptosis defense mechanism. Furthermore, combination therapies targeting GPX4 and FAK/Src were found to enhance Cancer cell death, and MDM2, ezrin, and cortactin were identified as potential Ferroptosis inhibitor targets. These findings highlight the effectiveness of network-based approaches in uncovering a compound's MoA and developing combination therapies for Cancer.

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