Poster Presentation RACI Biomolecular Division Conference 2013

Solution structures of the DNA complexes of cytotoxic bis(phenazine-1-carboxamides) (#87)

Andre Serobian 1 , Graham E Ball 2 , William A Denny 3 , Laurence P G Wakelin 1
  1. Department of Pharmacology, University of New South Wales, Randwick, New South Wales, Australia
  2. School of Chemistry, University of New South Wales, Randwick, New South Wales, Australia
  3. Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand

MLN 9441 is a bisintercalating experimental antitumour agent known to be a template inhibitor of transcription, and to inhibit the binding of transcription factors to DNA2,3. We have investigated the solution structures of three DNA complexes of MLN 944 and its Des-methyl MLN analogue with the self-complementary oligonucleotides d(ATGCAT)2, d(TATGCATA)2, and d(TACGCGTA)2 using a variety of 1D- and 2D-NMR methods and molecular dynamics simulations employing the AMBER 12 force field4,5. The dynamics simulations were conducted in explicit solvent with neutralising Na+ ions for a 10 ns calculation using particle-mesh Ewald electrostatics6. Simulations were performed with and without NOE-restraints, enabling an evaluation of the quality of the force field when used without experimental constraints. We find that for all three complexes MLN 944 binds as a dication, in which its phenazine-1-carboxamide chromophores are uncharged, in the DNA major groove spanning the central 2 GC base pairs in a manner that maintains the dyad symmetry of the DNA. The carboxamide group lies in the plane of the chromophore, its NH making hydrogen bonding interactions with the phenazine N10 nitrogen, and the protonated linkers form hydrogen bonds with the O6 atom of guanine. The NMR data for the Des-methyl MLN-DNA complexes yield analogous solution structures to those of MLN 944, indicating that possession of a 9-methyl group has little, if any, discernible effect on the structure of the DNA complexes of these two compounds. It does appear, however, that the Des-methyl MLN complexes are in somewhat faster exchange than those of MLN 944.

  1. Gamage, S. A., Spicer, J. A., Finlay, G. J., Stewart, A. J., Charlton, P., Baguley, B. C., et al., Dicationic bis(9-methylphenazine-1-carboxamides): relationships between biological activity and linker chain structure for a series of potent topoisomerase targeted anticancer drugs. Journal of Medicinal Chemistry, 2001. 44(9): p. 1407-15.
  2. Byers, S. A., Schafer, B., Sappal, D. S., Brown, J., and Price, D. H., The antiproliferative agent MLN944 preferentially inhibits transcription. Mol Cancer Ther, 2005. 4(8): p. 1260-7.
  3. Sappal, D. S., McClendon, A. K., Fleming, J. A., Thoroddsen, V., Connolly, K., Reimer, C., et al., Biological characterization of MLN944: a potent DNA binding agent. Mol Cancer Ther, 2004. 3(1): p. 47-58.
  4. D.A. Case, T.A. Darden, T.E. Cheatham, I., C.L. Simmerling, J. Wang, R.E. Duke, et al., AMBER 12. University of California, San Francisco., 2012.
  5. Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., and Case, D. A., Development and testing of a general amber force field. J Comput Chem, 2004. 25(9): p. 1157-74.
  6. Essmann, U., Perera, L., Berkowitz, M., Darden, T., Lee, H., and Pedersen, L., A smooth particle mesh Ewald method. The Journal of Chemical Physics, 1995. 103(19): p. 8577-8593.