Crystal Structures of Four Morpholino-Doxorubicin Anticancer Drugs Complexed with d(CGTACG) and d(CGATCG): Implications in Drug-DNA Crosslink

Abstract

Among the new generations of anthracycline drugs, morpholino-doxorubicin (MDox) and its derivative have unusually potent activity when compared with the parent doxorubicin. 3″- Cyano-morpholino-doxorubicin (CN-MDox) has been suggested to form a covalent crosslink to DNA, although the exact mode of interactions remains unclear. To establish the structural basis of this crosslink, we carried out X-ray diffraction analyses of the complexes between four different morpholino-doxorubicins (i.e., MDox, CN-MDox, (R)- and (S)-2″-methoxy- morpholino-Dox (MMDox)) and two DNA hexamers CGTACG and CGATCG. Their crystal data are similar to other Dau/Dox complexes with space group P4₁2₁2,a=b ∼28 Å, c∼ 53 Å. The refined structures at ∼1.8 Å resolution revealed that two drug molecules bind to the duplex with the aglycons intercalated between the CpG steps with their N^3′ -morpholino- daunosamines in the minor groove. The morpholino moiety is flexible and may adopt different conformations dependent on the sequence context The O¹ atoms of the two morpholino groups in the drug-DNA complexes are in van der Waals contact The structural results suggest possible crosslinking mechanism of CN-MDox. It is worth pointing out that by linking two piperazinyl- or piperidinyl-doxorubicins at the 1″ positions a new type of bis-doxorubicin derivatives may be synthesized which may bind to a hexanucleotide sequence with some specificity.