Molecular docking studies investigating the interaction of a series of benzoquinone ansamycin Hsp90 inhibitors with NAD(P)H:quinone oxidoreductase 1 (NQO1)

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The active form of NAD(P)H:quinone oxidoreductase (NQO1) is a homodimer, composed of 273 amino acid residues and one flavin adenine dinucleotide (FAD) cofactor constituting one redox centre per monomer. NQO1 catalyzes the NAD(P)H-dependent two-electron reduction of quinones to hydroquinones and is therefore involved in the reductive activation of a number of antitumor quinone-based compounds. The benzoquinone ansamycin antibiotics are a class of anticancer agents that are capable of binding to and disrupting the function of Hsp90, leading to the depletion of multiple oncogenic client proteins. We have previously reported that NQO1 can reduce the benzoquinone ansamycin, 17-allylamino-17-demethoxy-geldanamycin (17AAG), to the corresponding hydroquinone ansamycin and that the hydroquinone form is a more potent Hsp90 inhibitor, when compared to the parent quinone. Here, we describe a computational-based molecular docking study of a series of benzoquinone ansamycins, into the FADH₂-site of the human NQO1 crystal structure (PDB: 1KBQ). The series of benzoquinone ansamycins examined in this study include GDM, 17AAG, 17AG, 17DMAG and 17AEP-GA. These benzoquinone ansamycins were docked into the binding site of NQO1 in the trans-isomer conformation, generated from the GDM cis-isomer structure co-crystallized in the human Hsp90 crystal structure (PDB: 1YET), by targeted molecular dynamics methods. Molecular docking simulations were performed using the Affinity module of Insight II (Accelrys Inc.), which rotates, translates and performs a conformational search of the benzoquinone ansamycin ligand of interest in the context of the binding site of NQO1, using a Monte Carlo algorithm. The Affinity run results in a set of structures that fall within specified energetic and geometric criteria. The resulting set of structures, for each benzoquinone ansamycin, were analyzed and scored by the total energy output by Affinity, the total interaction energy between the ligand and the protein evaluated using the Docking module, the Ludi Score3 of interaction, the number of hydrogen bonds between the protein and the ligand particularly between the amino acids Tyr126 and Tyr128 and the C21 carbonyl of the quinone and that the quinone moiety of the benzoquinone ansamycin is positioned parallel to the si-face of the isoalloxazine ring system of the FADH₂ cofactor. These docking studies support that NQO1 can accommodate the benzoquinone ansamycins as substrates for reduction to the corresponding hydroquinone ansamycin. In addition, the scoring of the series of benzoquinone ansamycins in this docking study correlated with their relative biochemical reduction rate data using purified recombinant human NQO1 (Supported by CA51210).