Intercalation of antitumor drug doxorubicin and its analogue by DNA duplex: Structural features and biological implications

• The important role of NH2 group in DOX was studied in drug–DNA interaction.
• Both DOX and FDOX intercalated into DNA duplex.
• DOX induced major DNA structural changes, while FDOX did not alter DNA conformation.
• The structural changes induced by DOX were related to its anticancer activity.
• NH2 group caused major differences between DOX– and FDOX–DNA interactions.

The intercalation of antitumor drug doxorubicin (DOX) and its analogue N-(trifluoroacetyl) doxorubicin (FDOX) with DNA duplex was investigated, using FTIR, CD, fluorescence spectroscopic methods and molecular modeling. Both DOX and FDOX were intercalated into DNA duplex with the free binding energy of −4.99 kcal for DOX–DNA and −4.92 kcal for FDOX–DNA adducts and the presence of H-bonding network between doxorubicin NH2 group and cytosine-19. Spectroscopic results showed FDOX forms more stable complexes than DOX with KDOX-DNA = 2.5(±0.5) × 104 M−1 and KFDOX-DNA = 3.4(±0.7) × 104 M−1. The number of drug molecules bound per DNA (n) was 1.2 for DOX and 0.6 for FDOX. Major alterations of DNA structure were observed by DOX intercalation with a partial B to A-DNA transition, while no DNA conformational changes occurred upon FDOX interaction. This study further confirms the importance of unmodified daunosamine amino group for optimal interactions with DNA. The results of in vitro MTT assay carried out on SKC01 colon carcinoma corroborate the observed DNA interactions. Such DNA structural changes can be related to doxorubicin antitumor activity, which prevents DNA duplication.

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