Methotrexate: Integrating molecular pharmacology, systems toxicology, and precision rescue strategies.

Methotrexate (MTX) remains a cornerstone therapy across oncology, rheumatology, dermatology, and reproductive medicine. Despite its long clinical history, MTX exhibits mechanistic complexity that extends far beyond classical antifolate activity, encompassing immunomodulation, metabolic reprogramming, and redox regulation. These diverse actions underpin both its therapeutic efficacy and its potential for toxicity. This review synthesizes contemporary insights into MTX pharmacology, systems toxicology, pharmacokinetics, clinical applications, and precision rescue strategies, integrating multi-omic evidence and real-world data to provide a modern, mechanistically informed framework for MTX therapy. MTX exerts dose-dependent effects on nucleotide synthesis, adenosine signaling, cytokine networks, mitochondrial function, and oxidative stress pathways. Toxicity arises from interconnected disturbances in metabolic, inflammatory, and transporter systems, with organ-specific manifestations in the liver, kidney, lung, and bone marrow. High-dose MTX requires meticulous pharmacokinetic monitoring and individualized rescue strategies, including leucovorin and glucarpidase. Real-world pharmacovigilance data highlight the influence of age, sex, comorbidities, and drug-drug interactions on MTX safety. Advances in pharmacogenomics, systems biology, and computational modeling are reshaping MTX dosing, toxicity prediction, and therapeutic optimization. MTX exemplifies how a legacy drug can be continually redefined through modern science. Integrating pharmacogenomic profiling, multi-omic biomarkers, and AI-driven prediction models promises to transform MTX therapy into a fully personalized, mechanism-guided approach. These innovations will expand MTX's therapeutic window, enhance safety, and ensure its continued relevance in precision pharmacotherapy.