Stereochemistry of the α-carbon in the benzylic modifying moiety attached at the C-5 end of thymidine affects the potency of a newly identified anti-cancer lead nucleoside

Abstract The bioactivity of antimetabolites is connected to molecular recognition by the target proteins, which makes the stereochemical configuration of the chiral centers in these molecules, including those in the modifying moieties, of extreme importance. In an attempt to enhance the anti-cancer activity of a newly identified 5-[(R/S-α-tert-butyl-2-nitro-4-{2-phenyl}alkynyl)benzyloxy]methyl-2′-deoxyuridine, initially evaluated as a 1:1 mixture of diastereomers with respect to the modifying moiety, we first took the excision library approach, which revealed the importance of all the structural features of the moiety for bioactivity. We then proceeded with the synthesis of the secondary derivatives, varying the substitution pattern within the moiety. These attempts failed to improve bioactivity. However, examination of individually made stereoisomers revealed a 3-fold potency increase in the S-isomer compared with the diastereomeric mixture, without significantly affecting the toxicity against normal rapidly dividing cells.