Disclosed are methods of inactivating a protein, such as cleaving a disulfide bond of a protein, that involve contacting the protein with a reducing agent, a denaturant, and a hydroxide ion, wherein the pH of the composition is about 10.0 to about 14.0. Also disclosed are methods of treating or preventing a disease in a subject, such as a toxin-related disease or a prion-related disease, that involve contacting a subject with a pharmaceutically effective amount of a reducing agent, a denaturant, and a hydroxide ion, wherein the pH of the composition is about 9.0 to about 14.0. Also disclosed are compositions that include a reducing agent, a denaturant, and a hydroxide ion, wherein the pH of the composition is about 9.0 to about 14.0.