FOXDIE is a viral carrier cell destroying retrovirus, programmed to kill specific people by identifying the person's DNA and their nano machines, then inducing cardiac arrest. In Solid Snake and Liquid Snake's case, FOXDIE enhanced their DNA flaws as clones, causing them both to age at an extremely fast rate. The medicine necessary to suppress the "hyper aging" is contained in boxes of medical chocolates that are shipped to Snake and Liquid once a year, each costing $10,000 a box. Naomi Hunter spent time in South America trying to create a permanent cure for FOXDIE, but ultimately failed. A permanent cure was discovered somehow by Blaire, but only Liquid received it, presumably.
An annual shipment of FOXDIE chocolates to Solid Snake was stolen by Mario to give to Pauline. However, they had been poisoned by Blaire and ended up killing Pauline. As a result, Snake began aging rapidly throughout the season.
Snake's accelrated aging caught up with him at the beginning of the war against Ganondorf's forces, when he suffered from cardiac arrest and nearly died. He was revived by Dr. Naomi Hunter, who was able to reverse the FOXDIE and aging to an earlier state and restore Snake's youth. However, the FOXDIE still afflicted him, so Naomi gave Snake a bottle of pills to take to suppress the FOXDIE and aging whenever he experienced pain.