Provided are methods of designing a putative inhibitor of a 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase. The methods comprise designing a chemically stable compound that resembles the charge and geometry of the 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase transition state. Also provided are methods of inhibiting 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidases using the inhibitors found by the above methods.