Disclosed herein are protease transition state inhibitor/analogue prodrug compounds selected from the group consisting of esters, carbamates, ester phosphates, and pharmaceutically acceptable salts thereof. Compositions containing such prodrugs are also disclosed, along with methods of using such compounds therapeutically or prophylactically against calicivirus, picornavirus, and/or coronavirus infection, as well as other conditions, such as malaria, cancer, stroke, heart attack, neural degeneration, cataracts, and glaucoma through inhibition of the variety of proteases associated with progression of such conditions.