The enzyme reaction mechanisms related to guanidino compounds that are uremic toxins were analyzed using a computational chemical method (in silico analysis). The target enzymes for analyzing guanidino compound metabolism were Glycineamidino transferase, Guanidinoacetate N-methyltransferase, and Creatine kinase. Visualizing these enzyme mechanisms clarifies the reaction processes target clinical tests, drug candidates, and supplements. Dosing cofactors like glycine, AdoMet, and ATP should accelerate the metabolism reactions; however, the medicine candidate is limited due to the complex handling. The details of enzyme reactions and the reaction mechanisms are visualized for clear explanations.