Carbocyclic Nucleoside Isosteres as Potential Antitumor and Antiviral Agents

Basic Sciences

Investigators

Linked publications & trials

Abstract

Nucleosides and nucleotides are inherently flexible molecules comprised of a sugar moiety and aheterocyclic base. The conformational flexibility of the sugar moiety can be described in terms ofthe pseudorotational phase angle (P), which takes into accoung the contribution of the five torsionangles of the sugar ring. The preferred ranges of P define two main domains centered around aNorth conformation (P = 0) and a South conformation (P = 180) which equilibrate rapidly in solution. 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 For the past several years we have designed a series of novel nucleosides where the flexible sugar moiety has been replaced by a rigid carbocyclic ring (i.e., bicyclo[3.1.0]hexane) that mimics either the North or South conformation of conventional nucleosides.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-DNAconformations associated with South and North conformations, respectively. Towards our firstobjective, we have demonstrated the clear preference of kinases (herpes thymidine kinase andcellular deoxycytidine kinase) for the South conformation. On the other hand, the polymerases(herpes DNA polymerase and HIV reverse transcriptase) show an almost exclusively preference for the North conformers. Relative to our second goal, we have synthesized a series of short (13 mers) and mid-size (27-mers) oligodeoxynucleotides (ODNs) containing rigid South and North abasic sites [unreadable]as well as a flexible (cyclopentane) reference[unreadable] to study the mechanism of base flipping of HhaI DNA (cytosine C5)-methyl transferase. In the process, we have discovered one of the most potent ODN inhibitors of this enzyme (IC50 = 14 nM) containing the abasic site locked in the South conformation. The syntheses of the requisite North and South phosphoramidites aswell as the syntheses of the corresponding ODNs were vastly improved. Novel 5-substituteduracil carbocyclic nucleosides built on a North bicyclo[3.1.0]hexane template were shown to haveextremely potent anti-herpes (e.g., the 5-bromo) and anti-varicela zoster (e.g., 5-bromovinyl)activity. These compounds, along with the thymidine analogue are being investigated for theirpotential use in the gene therapy of cancer. The increase demand for larger quantities of the Northbicyclo[3.1.0]hexane template has been met by a novel carbene insertion reaction where the entirebicyclic structure is constructed in one step. This carbene insertion reaction is also beinginvestigated to develop the antipodal South bicyclo[3.1.0]hexane template. AIDS title: Antiherpes activity for the adjuvant treatment of AIDS CANCER title: Gene therapy, DNA methyltransferase.