Metabolic modelling-based in silico drug target prediction identifies six novel repurposable drugs for melanoma

Research output: Contribution to journalResearch articleContributedpeer-review

Contributors

  • Tamara Bintener - , University of Luxembourg (Author)
  • Maria Pires Pacheco - , University of Luxembourg (Author)
  • Demetra Philippidou - , University of Luxembourg (Author)
  • Christiane Margue - , University of Luxembourg (Author)
  • Ali Kishk - , University of Luxembourg (Author)
  • Greta Del Mistro - , Department of Dermatology, National Center for Tumor Diseases Dresden (Author)
  • Luca Di Leo - , Danish Cancer Society (Author)
  • Maria Moscardó Garcia - , University of Luxembourg (Author)
  • Rashi Halder - , University of Luxembourg (Author)
  • Lasse Sinkkonen - , University of Luxembourg (Author)
  • Daniela De Zio - , Danish Cancer Society (Author)
  • Stephanie Kreis - , University of Luxembourg (Author)
  • Dagmar Kulms - , Department of Dermatology, National Center for Tumor Diseases Dresden (Author)
  • Thomas Sauter - , University of Luxembourg (Author)

Abstract

Despite high initial response rates to targeted kinase inhibitors, the majority of patients suffering from metastatic melanoma present with high relapse rates, demanding for alternative therapeutic options. We have previously developed a drug repurposing workflow to identify metabolic drug targets that, if depleted, inhibit the growth of cancer cells without harming healthy tissues. In the current study, we have applied a refined version of the workflow to specifically predict both, common essential genes across various cancer types, and melanoma-specific essential genes that could potentially be used as drug targets for melanoma treatment. The in silico single gene deletion step was adapted to simulate the knock-out of all targets of a drug on an objective function such as growth or energy balance. Based on publicly available, and in-house, large-scale transcriptomic data metabolic models for melanoma were reconstructed enabling the prediction of 28 candidate drugs and estimating their respective efficacy. Twelve highly efficacious drugs with low half-maximal inhibitory concentration values for the treatment of other cancers, which are not yet approved for melanoma treatment, were used for in vitro validation using melanoma cell lines. Combination of the top 4 out of 6 promising candidate drugs with BRAF or MEK inhibitors, partially showed synergistic growth inhibition compared to individual BRAF/MEK inhibition. Hence, the repurposing of drugs may enable an increase in therapeutic options e.g., for non-responders or upon acquired resistance to conventional melanoma treatments.

Details

Original languageEnglish
Article number468
JournalCell Death and Disease
Volume14
Issue number7
Publication statusPublished - 26 Jul 2023
Peer-reviewedYes

External IDs

PubMedCentral PMC10372000
Scopus 85165719664
ORCID /0000-0001-6874-0548/work/151980614

Keywords

Sustainable Development Goals

Keywords

  • Humans, Proto-Oncogene Proteins B-raf/metabolism, Neoplasm Recurrence, Local/drug therapy, Melanoma/drug therapy, Protein Kinase Inhibitors/pharmacology, Mitogen-Activated Protein Kinase Kinases, Drug Development, Drug Resistance, Neoplasm/genetics, Cell Line, Tumor