Nucleosides and nucleotides are inherently flexible molecules comprised of a sugar moiety and a heterocyclic ring. The conformational flexibility of the sugar moiety can be mathematically described as a trigonometric expression ?known as pseudorotational phase angle (P)? that encompasses the contribution of the five torsion angles of the sugar ring. The preferred ranges of P define two main domains centered around a North conformation (P = 0) and a South conformation (P = 180) which equilibrate rapidly in solution. In each of these domains the bond linking the sugar to the heterocyclic base (glycosyl torsion angle) adopts a preferred orientation (syn or anti) which is critical for recognition and binding to proteins. One of the main obstacles in interpreting structure-activity correlations in nucleosides and nucleotides is this high level of flexibility. For the past several years we have designed a series of novel nucleosides where the flexible sugar moiety has been replaced by a rigid carbocyclic ring (i.e., bicyclo[3.1.0]hexane) that mimics either the North or South conformation of conventional nucleosides. Our first objective is to systematically probe a series of nucleoside/nucleotide binding enzymes with sets of conformationally rigid North and South substrates to learn about the preferred mode of binding. Our second objective is to construct modified nucleic acids that incorporate some of these fixed units to either reinforce or disrupt the typical B- or A-DNA conformations that are associated, respectively, with South and North sugar templates. We have made significant progress towards both of these goals. In addition to the enzymes reported last year, HIV-reverse transcriptase, adenosine deaminase and S-adenosylhomocysteine hydrolase, we have added deoxycytidine kinase and several adenosine receptors like the P2Y1 receptor. In each of the cases studied, we find that there is a definitive preference to bind to a particular conformer. The results from these studies have been published or in press. Secondly, we have synthesized the first DNAs containing either conformationally rigid nucleosides or sugars (abasic sites) to probe the preference of DNA binding enzymes. For example, DNA methyltransferase is strongly inhibited by a 13-mer duplex containing a rigid South abasic site, whereas the 13-mer duplex containing the North abasic site was totally inactive. This result strongly suggests that an intact B-DNA structure of the GCGC binding domain is important for enzyme recognition. In view of the synthetic challenge presented by the bicyclo[3.1.0]hexane system, and the increasing demand for large quantities of these analogues, we have recently succeeded in assembling these molecules by a novel carbene insertion reaction where the entire bicyclic structure is generated in one step.AIDS title: Antiherpetic and Anti-HCMV Compounds for the Adjuvant Treatment of AIDS - carbocyclic nucleosides, chemotherapy, DNA binding, molecular models, nucleic acid chemistry,
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