Conformational analysis of brominated pA2′‐5′A2′‐5′A analogs

Abstract

NMR and model-building studies were carried out on pA2'-5'A2'-5'A and analogs in which one or more of the A residues were replaced by 8-bromoadenosine. Chemical shifts, coupling constants and NOE data were used to obtain structural information. The N/S equilibrium constant of the ribose rings as well as the phase angles and puckering amplitudes were determined from the experimental coupling constants with the aid of an improved version of the PSEUROT program. Chemical shifts in combination with NOE data were used to monitor basebase interactions and the orientation of the bases (syn or anti).The combined data suggest that different types of stacking interactions are present in the various compounds. Bromination of the first or second residue in the trimers results in a preference for N-type sugar and syn orientation of the base in these residues. When A(3) is brominated, an S-type sugar conformation together with a syn orientation of the base is favoured at the 2' terminus. Energy-minimized models of the different stacking interactions are presented which fit the present collection of data. The possible correlation between biological activity of these compounds and their conformation is briefly discussed.During the last decade it has become evident that pppA2'-5'A2'-5'A plays an important role in the antiviral action of interferon (reviewed in [l]) and possibly as a regulator of cell growth and/or differentiation [2 -51. This suggests the possibility to exploit the system to develop a novel chemotherapeutic approach to viral diseases. However, such applications are limited by two barriers : (a) pppA2'-5'A2'-5'A has a short biological half-life due to rapid degradation by a 2',5'-phosphodiesterase and (b) due to its highly negative charge, the molecule is unable to penetrate the cell membrane.A possible solution of these problems appears to lie in a search for modifications of the molecule in such a way that the binding to, and the activation of, the (2'-5')oligo(A)-dependent endonucleases (RNase L) remain comparable to the properties of the parent compound. Thus far, several modifications have been synthesized and tested upon binding and activity [6-91. For example, the 6-amino groups [6], the N7 atoms [6,9] and the 3'-OH functions [8] of the various residues were sequentially replaced in order to examine which of them are crucial for binding and/or activation. Another substitution was the replacement of adenosine by 8-bromoadenosine, not only in the case of the 5'-triphosphate parent Correspondence to C .