Sub-PK/PD profiling provides a systems pharmacology framework to optimize intracellular combination therapies for bacterial infectionsNew Framework Aims to Improve Treatment for Internal Bacterial Infections

Intracellular bacterial pathogens represent one of the most formidable challenges in contemporary medicine. By exploiting host cellular niches, these organisms evade immune surveillance and withstand conventional antibiotic therapies, establishing persistent reservoirs that are difficult to eradicate. Although antibiotic combinations, host-directed interventions, and drug repurposing have shown promise, conventional discovery pipelines rarely capture the dynamic and compartmentalized nature of the intracellular environment. This review proposes a systems pharmacology framework centered on subcellular pharmacokinetic/pharmacodynamic (Sub-PK/PD) profiling to predict and optimize intracellular combination therapies. Mechanistic and translational studies of intracellular drug disposition, host–pathogen metabolism, computational combination design, and biomimetic infection models were synthesized in a targeted narrative review. Particular attention was given to spatially resolved measurements, dual ribonucleic acid (RNA) sequencing, metabolic flux analysis, machine learning, and organ-on-a-chip platforms. Pathogen-containing vacuoles, phagolysosomes, the host cytosol, lipid-rich macrophages, and tissue lesions impose distinct barriers to drug ionization, accumulation, stability, and target engagement. Persistent infection also produces reciprocal metabolic rewiring: host pathways supply carbon, nitrogen, lipids, metals, and reducing equivalents, while bacterial stress programs alter growth and antibiotic susceptibility. Integrating these processes can reveal shared metabolic bottlenecks suitable for combinations of pathogen-directed and host-directed agents. Computational models can prioritize combinations, but their predictions require validation under physiologically realistic concentration–time profiles. Linking systems biology to localized Sub-PK/PD provides a practical roadmap for designing niche-specific regimens. Such regimens could improve clearance of persistent intracellular reservoirs, reduce ineffective exposure, and limit the emergence of antimicrobial resistance.