Abstract #4528: The effect of conformational dynamics of cisplatin- and oxaliplatin-DNA Adducts on binding of DNA damage recognition proteins such as HMGB1

Abstract

The DNA binding protein domain HMGB1a binds to cisplatin (CP)-GG DNA adducts with 20-fold greater affinity than to oxaliplatin (OX)-GG adducts when those adducts are in the TGGA sequence context. A thorough understanding of this differential binding affinity might lead to better understanding of the differences in efficacy, toxicity and mutagenesis of these platinum anticancer drugs. In this study, we performed 5, 10 ns MD simulations for CP- and OX- DNA adducts, both free in solution and bound to HMGB1a, in the 5'-d(CCTCTGGACTCC)-3' 5\#8217;-d(GGAGTCCAGAGG)-3\#8217; sequence context. CP- and OX-GG adducts in the TGGA sequence context differed in the pattern of hydrogen bond formation between platinum amine hydrogens and the surrounding DNA bases, with CP forming hydrogen bonds (H-bonds) with G7O6 and A8N7, while OX formed H-bonds with G7O6 and T17O4. The snapshots from each trajectory were clustered on the basis of the type of H-bond the drugs formed with surrounding DNA bases. No significant differences were observed between structures associated with the CP- and OX-G7O6 H-bonds. However, the differences in H-bond formation to A8N7 and T17O4 correlated with differences in DNA conformational dynamics that may be important for binding of HMGB1a. For example, structures associated with the CP-A8N7 H-bond differed significantly in twist, slide, shift and roll at the G7A8 base pair (bp) step compared with those associated with the OX-T1704 H-bond. In this case, the conformations associated with the OX-T17O4 H-bond were preferential for H-bond formation between Ser41 of HMGB1a and A8N3. In contrast, the CP-A8N7 H-bond cluster of structures explored a minor conformation for roll at G6G7 bp step that was more favorable for stacking of HMGB1a Phe37 with the 3\#8217;G (G7) than structures associated with the OX-T17O4 H-bond. Furthermore, these differences in roll at the G6G7 bp step were preserved in the simulations of the CP- and OX-DNA-HMGB1a complexes. Previous mutagenesis studies by He et al (Biochemistry, 39: 14426-14435, 2000) showed that the Phe37A mutation had a much stronger effect on DNA binding than the Ser41A mutation. Thus, the effects of CP- and OX-DNA adducts on DNA conformational dynamics are complex, but appear to favor HMGB1a binding to the CP-DNA adduct. In summary, we see significant differences in H-bond patterns between CP- and OX-GG adducts in the TGGA sequence context. These H-bond patterns strongly correlate with differences in DNA conformational dynamics which may influence the ability of damage recognition proteins such as HMGB1a to discriminate between CP- and OX-adducts. (Supported by NIH grant CA84480)

Citation Information: In: Proc Am Assoc Cancer Res; 2009 Apr 18-22; Denver, CO. Philadelphia (PA): AACR; 2009. Abstract nr 4528.