Quantum Mechanical Study of some Intercalating and Groove Binding Anticancer Drugs with AT and GC Base Pair of DNA Nucleobase

Abstract

Anticancer drugs bind with DNA nucleobase pairs (AT and GC) through different binding modes such as intercalation, groove binding, covalent binding etc. Quantum mechanical DFT method is quite useful for computing the interaction energy value for anticancer drug-DNA nucleobase complexes. In our study, we have taken some of the anticancer drugs to investigate the interaction energy for drug-DNA complexes. Among the different binding modes of anticancer drugs; minor and major groove binding in DNA base pair is also an important aspect for anticancer drugs; therefore some anticancer drugs may be minor groove specific and some may be major groove specific. Since, such sequence-specific experimental studies for drug-DNA nucleobase complexes are very complicated and hence this may be investigated by using quantum mechanical theoretical studies, using M062X basis set. Our studies reveal that the stacked models of anticancer drugs-DNA nucleobase (AT and GC) complexes always show negative interaction energy values and among all such complexes the most negative interaction energy value results the most stable and favoured stacked systems. The stacking interaction energies for anticancer drugs-DNA nucleobase (AT and GC) complexes can easily be reflected in the interaction of energy plots.