Structural studies of anti-HIV 3′-(α-fluorothymidine & 3′-(α-azidothymidine by 500 MHz 1H-NMR spectroscopy & molecular mechanics (MM2) calculations

Abstract

NMR studies of anti-HIV 3′-α-fluorothymidine (FLT) ( 1) and 3′-α-azidothymidine (AZT) ( 2) in aqueous solution gave insight into their conformational dynamics [pseudorotation of the furanose ring rotation around the C4′-C5′ bond (γ) and rotation around the glycosidic C1′-N1 bond (χ)]. The interpretation of scalar proton-proton coupling data for FLT ( 1) in solution showed a conformational bias towards a South-type (∼90%) puckered furanose conformation. Energy minimization by molecular mechanics calculations using the MM2 force field gave molecular structure which is in excellent agreement with the NMR data (P = 151° ν m = 34°). This solution structure is grossly similar to the available averaged crystal structures (P = 171° ν m= 34°). The phase angle P = 151° for FLT ( 1) in solution indicates that the preferred furanose geometry is an intermediate between the C2′-endo envelope and the C2′-endo/C1′-exo twist conformation while the averaged phase angle in the solid state (P = 171°) indicates an intermediate geometry between the C2′-endo envelope and the C2′-endo/C3′-exo twist structure. 1H-HMR studies indicated that the North- and South-type pseudorotamer population of the furanose ring in AZT ( 2) is approximately 1:1 but it failed to provide any definite estimation of P and ν m from the analysis of J-coupling constant because of identical chemical shifts of H2′ and H2″. Molecular mechanics calculations were used to model both the North and South form. MM2 calculations in the North region converge virtually to a structure with P = 21.6° (unsymmetrical twist with major C3′-endo and minor C4′-exo twist structure),ν m=40° χ = −160.8° and γ= 56.9° while the MM2 calculations in the South region show a predominant puckered geometry represented by P = 160.3° (envelope C2′-endo geometry) ν m = 35.5° χ = −157.8° and γ = 583°. Note that all six known X-ray structures for AZT belong to the South-type geometry. The MM2 calculated South geometry for AZT is grossly similar to one of the two independent molecules found in the asymmetric unit of X-ray crystal structures (P = 175° ν m = 32.3°). This discrepancy between solution and solid state structure may indicate the danger of only using crystal structural data for the formulation of structure-activity relationships for a candidate drug.