MOLECULAR-DYNAMICS SIMULATIONS OF CHLORAMBUCIL DNA-ADDUCTS - A STRUCTURAL BASIS FOR THE 5'-GNC INTERSTRAND DNA CROSS-LINK FORMED BY NITROGEN MUSTARDS

The alkylation of DNA by chlorambucil has been studied using a computa tional approach. Molecular dynamics simulations were performed on the fully solvated non-covalent complex two monoadducts and a crosslinked diadduct of chlorambucil with the d(CGG(3)G(2)CGC). d(GCG(1)CCCG) dupl ex, in which the N7 atoms of G(1), G(2) and G(3) are potential alkylat ion sites. The results provide a structural basis for the preference o f nitrogen mustards to crosslink DNA duplexes at a 5'-GNC site (a 1,3 crosslink G(1)-G(3)) rather than at a 5'-GC sites (a 1,2 crosslink, G( 1)-G(2)). In the non-covalent complex simulation the drug reoriented f rom a non-interstrand crosslinking location to a position favorable fo r G(1)-G(3) diadduct formation. It proved possible to construct a G(1) -G(3) diadduct from a structure from the non-covalent simulation, and continue the molecular dynamics calculation without further disruption of the DNA structure. A crosslinked diadduct developed with four B-II conformations on the 3' side of each alkylated guanine and of their r espective complementary cytosine. In the first monoadduct simulation t he starting point was the same DNA conformation used in the crosslinke d diadduct simulation with alkylation at G(1). In this simulation the DNA deformation was reduced, with the helix returning to a more canoni cal form. A second monoadduct simulation was started from a canonical DNA conformation alkylated at G(3). Here, no significant motion toward s a potential crosslinking conformation occurred. Collectively, the re sults suggest that crosslink formation is dependent upon the drug orie ntation prior to alkylation and the required deformation of the DNA to permit 1,3 crosslinking can largely be achieved in the non-covalent c omplex.