STRUCTURE AND DYNAMICS OF THE ANTITUMOR DRUGS NOGALAMYCIN AND DISNOGALAMYCIN COMPLEXED TO D(CGTACG)(2) - COMPARISON OF CRYSTAL AND SOLUTIONSTRUCTURES

The nuclear magnetic resonance (NMR) solution structures of the 2:1 co mplexes of nogalamycin-d(CGTACG)(2) (Ng-CGTACG) and disnogalamycin-d(C GTACG)(2) (DNg-CGTACG) have been determined by a quantitative treatmen t of two-dimensional nuclear Overhauser effect (2D-NOE) crosspeak inte nsities. The 1.3 Angstrom resolution crystal structure of the 2:1 comp lex of Ng-CGTACG was used as a starting model for refinement using the procedure, SPEDREF [Robinson and Wang, Biochemistry 31 (1992) 3524-35 33], which incorporates full matrix relaxation theory and simulated an nealing minimization. The refined solution structures have R-factors o f 16.1 and 19.6% between the observed and simulated NOEs for Ng-CGTACG and DNg-CGTACG, respectively. The refined NMR structures retain major features of the crystal structure in which the elongated aglycone chr omophore is intercalated between the CpG steps with its nogalose and a minoglucose lying in the minor and major grooves, respectively. The ro ot mean square deviation between the solution and crystal structure fo r the complexes is 1.01 Angstrom (Ng-CGTACG) and 1.20 Angstrom (DNg-CG TACG) for the drug, plus the three base pairs surrounding the drug, in dicating a very similar local structure at the intercalation site. In the NMR structure, the two G:C Watson-Crick base pairs (C-1:G(12) and G(2):C-11) that wrap around the aglycone have large buckles, as do tho se seen in the crystal structure. There is a 22 degrees bend at the T- 3-A(4) step in the refined solution structure. This rearrangement of t he solution conformation is likely due to the absence of crystal packi ng. Specific hydrogen bonds between the drug and G:C bases in both gro oves of the helix are preserved in the solution structure. A separate study of the 2:1 complex at low pH showed that the terminal G-C base p airing is destabilized.