Sequence-specific base pair mimics are efficient topoisomerase IB inhibitors

Self-assembled nanostructures of phosphomolybdate, nucleobase and metal ions synthesis and their in vitro cytotoxicity studies on cancer cell lines

The ability of the multidentate nucleobases, adenine and thymine, to coordinate polyoxometalate and metal ions leading to the formation of self-assembled nanostructures and their strong cytotoxicity toward cancer cell lines have been demonstrated. A unique synthetic approach is developed to make a series of functional nanoscale hybrid materials consisting of nucleobases (adenine and thymine) and phosphomolybdic acid (PMA) through solid state chemical reaction and self-assembly process. Adenine was protonated through its ring nitrogen, while the ketone group in thymine was protonated during the addition of PMA to these nucleobases. The self-assembled nanostructures formed as a result of the electrostatic interaction between the protonated nucleobases and polyanionic PMA. To promote the base pairing between the nucleobases, chloroaurate ions and silver ions were added to each PMA/adenine and PMA/thymine nanostructures. The complexation between the nucleobases and the added metal ions was found to drive the formation of subsequent self-assembled nanostructures. All the materials were screened for their anticancer activity against breast (MDAMB-231) and prostate (PC-3) cancer cells, and non-cancerous keratinocyte cells HaCaT. PMA/adenine/[AuCl4]- and PMA/thymine/Ag+ nanostructures were found to have strong anti-cancer activity, while PMA/adenine/Ag+, PMA/thymine/[AuCl4]-, and PMA/pdenine, PMA/thymine nanostructures did not exhibit such activity. The unique redox properties of these materials and the self-assembly of the PMA and metal ions were the major factors responsible for the cytotoxicity. This unique approach of making functional nanomaterials incorporate the nucleobase, PMA and metal ions using solid state self-assembly and their anti-cancer applications are considered to be an effective approach for the development of inorganic nucleoside analogue bio-pharmaceutical agents.

Sequence selectivity of the cleavage sites induced by topoisomerase I inhibitors: a molecular dynamics study

Topoisomerase IB (Top1) inhibitors, such as camptothecin (CPT), stabilize the Top1-DNA cleavage complex in a DNA sequence-dependent manner. The sequence selectivity of Top1 inhibitors is important for targeting specific genomic sequences of therapeutic value. However, the molecular mechanisms underlying this selectivity remain largely unknown. We performed molecular dynamics simulations to delineate structural, dynamic and energetic features that contribute to the differential sequence selectivity of the Top1 inhibitors. We found the sequence selectivity of CPT to be highly correlated with the drug binding energies, dynamic and structural properties of the linker domain. Chemical insights, gained by per-residue binding energy analysis revealed that the non-polar interaction between CPT and nucleotide at the +1 position of the cleavage site was the major (favorable) contributor to the total binding energy. Mechanistic insights gained by a potential of mean force analysis implicated that the drug dissociation step was associated with the sequence selectivity. Pharmaceutical insights gained by our molecular dynamics analyses explained why LMP-776, an indenoisoquinoline derivative under clinical development at the National Institutes of Health, displays different sequence selectivity when compared with camptothecin and its clinical derivatives.