Protocol to infer off-target effects of drugs on cellular signaling using interactome-based deep learning.

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Meimetis N, Lauffenburger DA, Nilsson A

STAR Protoc 6 (1) 103573 [2025-01-16; online 2025-01-16]

Drugs that target specific proteins often have off-target effects. We present a protocol using artificial neural networks to model cellular transcriptional responses to drugs, aiming to understand their mechanisms of action. We detail steps for predicting transcriptional activities, inferring drug-target interactions, and explaining the off-target mechanism of action. As a case study, we analyze the off-target effects of lestaurtinib on FOXM1 in the A375 cell line. For complete details on the use and execution of this protocol, please refer to Meimetis et al.1.

Avlant Nilsson

DDLS Fellow

PubMed 39823233

DOI 10.1016/j.xpro.2024.103573

Crossref 10.1016/j.xpro.2024.103573

pmc: PMC11786766
pii: S2666-1667(24)00738-X