Programmable Molecular Immune Operating System (PMIOS): A Computational Framework for Autonomous Disease Sensing and Precision Therapeutic Decision-Making

Pulmonary fibrosis remains a severe chronic lung disease with limited therapies that mainly slow progression rather than adapt to dynamic disease states. Here, we propose the Programmable Molecular Immune Operating System (PMIOS), a conceptual computational framework designed to emulate immune-like functions for precision therapeutic decision-making. PMIOS integrates four modules: molecular sensing of disease biomarkers (including ROS and cytokines), a programmable logic-based decision engine, an adaptive therapeutic execution system, and a feedback-control layer for maintaining tissue homeostasis. Using pulmonary fibrosis as a model, we present a computational strategy combining molecular modeling, docking, molecular dynamics, systems-level network analysis, and AI-assisted optimization to evaluate this framework. Rather than introducing a single therapeutic agent, PMIOS establishes a programmable molecular system capable of sensing, computing, responding, and self-regulating in evolving disease environments, offering a potential paradigm shift toward autonomous precision therapeutics.