Molecular models of neocarzinostatin damage of DNA: analysis of sequence dependence in 5′GAGCG:5′CGCTC

Abstract

Model building and molecular mechanics and dynamics calculations have been performed on a number of complexes of the post-activated form of the neocarzinostatin chromophore (NCS) with the B-DNA oligomer 5'GAGCG:5'CGCTC. Stable structures with the naphthoic acid moiety intercalated at all base pairs can be constructed. The observed bistranded lesions consisting of an abasic site at the Cyt residue in AGC and a direct break at the Thy residue on the complementary strand can be explained by assuming that NCS in the (R,R) form intercalates between the Ade2-Thy9/Gua3-Cyt8 base step with its 'diradical' core oriented towards the 3'-end of the (+) strand. Sites at C5', C4' and C1' in the minor groove are within a short enough distance from the two radical centers on NCS to permit hydrogen atom abstraction and the formation of the bistranded lesions. Strand cleavage at Thy9 may occur as a single lesion if NCS is intercalated into the Gua3-Cyt8/Cyt4-Gua7 base step with its active core towards the 3'-end of the (-) strand. The results are analyzed, and the utility and limitations of this type of model building are discussed.

Selective abstraction of 2H from C-5' of thymidylate in an oligodeoxynucleotide by the radical center at C-6 of the diradical species of neocarzinostatin: chemical evidence for the structure of the activated drug-DNA complex.

“…Presumably the radical center at C-2 is responsible for abstraction of the C-1' hydrogen atom of the C residue on the complementary strand. These conclusions corroborate the prediction made by the molecular modeling studies and eliminate other energetically less favorable, but still possible, models involving sites of drug intercalation permitting C-2 of NCS* to attack at C-5' ofthe I residue (26). The experiments reported here do not, of course, distinguish which of the two prochiral hydrogen atoms at C-5' is abstracted by NCS*.…”

“…3 and ref. 15) raises the possibility that 2H abstraction from C-5' by the radical center at C-6 is in part due to a different mode of drug-DNA binding that leads only to direct single-strand breaks. Since every abasic site at the C residue is accompanied by a break at the I residue on the complementary strand (25), -44% of the latter could be due either to a different binding mechanism or to the same mechanism that leads to the bistranded lesion but, as discussed earlier (26), with abasic site formation being less efficient for either chemical or geometric reasons. On the other hand, it is also conceivable that relatively less damage is expressed at the C residue because it is repaired more readily by scavenging thiol.…”

“…The model depicted in Fig. 2 for the former lesion suggests that the GSH adduct at C-12 of the chromophore forces the diradical core deeper into the minor groove, where C-1' resides, to enable formation of the abasic lesion at the C residue (26). These results imply that it may be NCS* [or its proposed cumulene precursor (6,8)] that is the actual DNA-sequence-seeking species.…”

“…Molecular model building based on energy minimization and molecular dynamics simulations has led to a proposal for the NCS*-DNA complex responsible for the bistranded lesions at AGC-GCI in which the naphthoate moiety intercalates between the APT and G-C base pairs with its diradical core oriented toward the 3' end of the plus strand (26) (Fig. 2).…”

Neocarzinostatin naphthoate synthase: an unique iterative type I PKS from neocarzinostatin producer Streptomyces carzinostaticus

“…1(d)) may have a crucial role [14]. On the other hand, Goldberg and co-workers have proposed a model that involves the intercalation of naphthoate moiety between bases of DNA with simultaneous positioning of the warhead within the minor groove, which then abstracts C-5 0 hydrogen via a free-radical mechanism [15]. A 13 C labeled feeding experiment proved that naphthoate moiety is formed from six intact acetate units linked in head to tail fashion [16].…”