The new bisphenazine anticancer
drug MLN944 is a novel
cytotoxic agent with exceptional anti-
tumor activity against a range of human and murine
tumor models both in vitro and in vivo.
MLN944 has recently entered Phase I clinical trials. Despite the structural similarity with its parent monophenazine carboxamide and
acridine carboxamide anticancer compounds,
MLN944 appears to work by a distinct mechanism of inhibiting
DNA transcription rather than the expected mechanism of
topoisomerase I and II inhibition. Here we present the first NMR structure of
MLN944 complexed with
d(ATGCAT)(2)
DNA duplex, demonstrating a novel binding mode in which the two
phenazine rings bis-intercalate at the 5'-TpG site, with the carboxamide amino linker lying in the major groove of
DNA. The
MLN944 molecule adopts a significantly unexpected conformation and side chain orientation in the
DNA complex, with the N10 on the
phenazine ring protonated at pH 7. The
phenazine chromophore of
MLN944 is very well stacked with the flanking
DNA base pairs using the parallel base-stacking intercalation binding mode. The DNA sequence specificity and the groove recognition of
MLN944 binding is determined by several site-specific hydrogen bond interactions with the central G:C base pair as well as the favorable stacking interactions with the 5'-flanking
thymine. The specific binding site of
MLN944 is known to be recognized by a number of important
transcription factors. Our electrophoretic gel mobility shift assay results demonstrated that the c-Jun
DNA binding to the
AP-1 site is significantly inhibited by
MLN944 in a dose-dependent manner. Thus, the exceptional
biological activity of
MLN944 may be due to its novel
DNA binding mode leading to a unique mechanism of action.