Crystal structure of the topoisomerase II poison 9-amino-[N-(2-dimethylamino)ethyl]acridine-4-carboxamide bound to the DNA hexanucleotide d(CGTACG)(2)

The structure of the complex formed between d(CGTACG)(2) and the antitumor agent 9-amino-[N- (2-dimethylamino)ethyl]acridine-4-carboxamide has been so lved to a resolution of 1.6 A using X-ray crystallography. The complex crys tallized in space group P6(4) with unit cell dimensions a = b = 30.2 Angstr om and c = 39.7 Angstrom, alpha = beta = 90 degrees, gamma = 120 degrees. T he asymmetric unit contains a single strand of DNA, 1.5 drug molecules, and 29 water molecules. The final structure has an overall R factor of 19.3%. A drug molecule intercalates between each of the CpG dinucleotide steps wit h its side chain lying in the major groove, and the protonated dimethylamin o group partially occupies positions close to (similar to 3.0 Angstrom) the N7 and O6 atoms of guanine G2. A water molecule forms bridging hydrogen bo nds between the 4-carboxamide NH and the phosphate group of the same guanin e, Sugar rings adopt the C2'-endo conformation except for cytosine C1 which moves to C3'-endo, thereby preventing steric collision between its C2' met hylene group and the intercalated acridine ring. The intercalation cavity i s opened by rotations of the main chain torsion angles alpha and gamma at g uanines G2 and G6. Intercalation perturbs helix winding throughout the hexa nucleotide compared to B-DNA, steps 1 and 2 being unwound by 8 degrees and 12 degrees, respectively, whereas the central TpA step is overwound by 17 d egrees. An additional drug molecule, lying with the 2-fold axis in the plan e of the acridine ring, is located at the end of each DNA helix, linking it to the next duplex to form a continuously stacked structure. The protonate d N,N-dimethylamino group of this "end-stacked" drug hydrogen bonds to the N7 atom of guanine G6, In both drug molecules, the 4-carboxamide group is i nternally hydrogen bonded to the protonated N-10 atom of the acridine ring. The structure of the intercalated complex enables a rationalization of the known structure-activity relationships for inhibition of topoisomerase II. activity, cytotoxicity, and DNA-binding kinetics for 9-amino acridine-4-ca rboxamides.