NMR structural studies on the covalent DNA binding of a pyrrolobenzodiazepine-naphthalimide conjugate

The DNA binding of a naphthalimide drug conjugated through a piperazine containing linker with a pyrrolo[2,1-c][1,4]benzodiazepine (PBD) to d(AACAATTGTT)(2) was studied by a combination of high-resolution (1)H and (31)P 2D NMR spectroscopy and restrained molecular dynamics calculations in explicit solvent. The bifunctional hybrid binds with its PBD moiety covalently linked within the minor groove to a guanine with an S stereochemistry at its covalent linkage site at C11 and a 5'-orientation of its A-ring carrying the linker with the naphthalimide ligand. The latter inserts from the minor groove between an A-A.T-T base pair step resulting in an opposite buckling of the base pairs at the intercalation site and duplex unwinding at adjacent internucleotide steps. There is NMR spectroscopic evidence that the naphthalimide undergoes a ring-flip motion with exchange rates slow to intermediate on the chemical shift time scale at ambient temperatures.