Carbocyclic Nucleoside Isosteres as Potential Antitumor

Basic Sciences

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Abstract

The inherent flexibility of the sugar moiety of conventional nucleosides has been arrested by replacing the sugar moiety with a rigid carbocyclic ring (i.e. bicyclo[3.1.0]hexane) that mimics either the North (N) or South (S) conformations of conventional nucleosides in the pseudorotational cycle. Our main objective has been to systematically probe a series of nucleoside/nucleotide binding enzymes with sets of conformationally rigid N and S substrates to learn about the preferred mode of binding. A secondary objective has been to construct modified nucleic acids that incorporate some of these fixed units to either reinforce or disrupt the typical B- or A-DNA conformations associated with S and N conformations, respectively. The conformationally locked antipodes of thymidine, N and S methanocarba thymidines (N-MCT and S-MCT), provided a clear example of efficient conformational discrimination by two critical enzymes that control the outcome of biological activity. We have demonstrated that S-MCT is a much better substrate than N-MCT for the herpes (HSV-1) thymidine kinase (TK) in murine cancer cells (38MC) transfected with HSV-TK. Surprisingly, on the other hand, DNA incorporation was observed only for N-MCT, despite the higher levels of S-MCT triphosphate present in the cell. We believe that this finding represents the first clear demonstration that kinases and polymerases have different and opposing substrate conformational preferences. Since N-MCT and other 5-substituted uracil carbocyclic analogues are extremely potent anti-herpes (e.g. 5-bromo) and anti-varicela zoster (e.g. 5-bromovinyl) agents, and synthesis of the bicyclo[3.1.0]hexane template is rather difficult, we embarked on a project to develop a simplified approach for the synthesis of these compounds. The challenged was met by developing two novel intramolecular cyclopropanation approaches where the entire bicyclic structure is constructed in one step for both N and S series. To this chemistry, we added the inclusion of a lipase-catalyzed resolution step following the formation of the bicyclo[3.1.0]hexane system which will guarantee an ample supply of enatiomerically pure compounds required for further biological studies. Relative to our second goal, we have synthesized a series of short oligodeoxynucleotides (ODNs) corrresponding to the self-complementary EcoR1 recognition sequence [ds(5'-CGCGAATTCGCG-3')] where the middle A's have been replaced by locked adenosines. These sequences are the subject of current NMR and crystallographic studies to detect the formation of bends or kinks. The study on the use of short ODNs containing rigid S and N abasic sites as inhibitors of DNA methyltransferase was completed and published (Wang et al. J. Am. Chem. Soc. 2000, 122, 12422).