Crystal structures of four morpholino-doxorubicin anticancer drugs complexed with d(Cgtacg) and d(cgatcg): Implications in drug-dna crosslink

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 A. 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 N³-morpholino-daunosamines in the minor groove. The morpholino moiety is flexible and may adopt different conformations dependent on the sequence context The O^1˝atoms of the two morpholino groups in the dmg-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.