J. Med. Chem., 1997, 40(14), 2113-2116, DOI:10.1021/jm970199z Terms & Conditions Electronic Supporting Information files are available without a subscription to ACS Web Editions. The American Chemical Society holds a copyright ownership interest in any copyrightable Supporting Information. Files available from the ACS website may be downloaded for personal use only. Users are not otherwise permitted to reproduce, republish, redistribute, or sell any Supporting Information from the ACS website, either in whole or in part, in either machinereadable form or any other form without permission from the American Chemical Society. For permission to reproduce, republish and redistribute this material, requesters must process their own requests via the RightsLink permission system. Information about how to use the RightsLink permission system can be found at http://pubs.acs.org/page/copyright/permissions.html Copyright 1997 American Chemical Society
vi I american onemicai zociety Journai ui ivieacinai knemistry vu rage zi Ii sm uppiemental rage I METHODS Molecular Modeling Molecular modeling protocols were evaluated to reproduce key structural features of the human telomere structure' and the parallel 5'-TGGGGT structure, 2 including G-tetrads and sodium ion positions. Intercalation sites of both structures were evaluated with the chromophore of compound 1 and a variety of substituents and were built from known intercalating structures [Nucleic Acid Database, entries DBBOO8, DDBOO9, and DDB034']. Macromodel v4.5 4 was used with the AMBER* force field and standard continuum solvation treatment (GB/SA model of water solvation, van der Waals cutoff of 8A, dielectric constant of 1) in conjunction with QUADRUN (an intercalator site search program; J. 0. Trent, to be published). QUADRUN translated the molecule in the intercalation site over an 8A square box (1A resolution) with rotation of ±900 (150 resolution) at each gridpoint, with the complex minimized at each position using AMBER*. Several stable intercalation models were found that were studied further with a variety of substituents using molecular mechanics (conformational searching for the position of the 2,6-diamidoanthraquinone substituents in the complex) and molecular dynamics (20 ps at 300 K equilibrium, 80 ps at 300 K production with time-averaging of 100 sampled structures) of the most stable conformations. Explicit solvation and counterion calculations and evaluation of substituents using AMBER 4.1' are continuing.
1 I; / -Vlllla l %-1111111L~dC13UULdL juuia UL il 11ilulumlal %'..lr111111 M1 V'-lu ragr, I-I IL 311 OL1tOUPIUMUIilLdi radgr z- Telomerase Assay Cell extracts from HeLa cells were prepared using CHAPS (0.5%), as described previously.' Reaction mixture contained 1 pm of 5'-biotinylated primers (5'-Bt- TTAGGGTTAGGGTTAGGG-3'), 1.2 pm [a- 32 P]-dGTP, 1 mm of datp and dttp, and 5 pl of cell extract in 20 pl of buffer containing 50 mm Tris-OAc (ph 8.5), 50 mm KOAc, 1 mm MgCl 2, 5 mm BME, and 1 mm spermidine. Reaction mixtures were incubated for 1 hr at 37 oc, and reaction was terminated by the addition of Dynabead- M280 Streptavidin solution. Biotinylated primers were immobilized with beads, which were washed to remove residual reaction mixture. After washing, the biotinylated products were separated from the beads by treatment with protein denaturants (guanine-hc1) and electrophoresed on an 8% denaturing polyacrylamide gel. Telomerase Kinetics By use of the standard telomerase assay and a 30-mer telomeric primer, compound 1 inhibition of telomerase-catalyzed elongation of primer was measured at various concentrations of inhibitor (0, 10, 20, and 50 MM) and substrate primer (0.1 to 4 pm) with fixed concentrations of the dntp substrates (TTP and datp, 1 mm; [a- 3 2 P]-dGTP, 4 MM). The kinetics of inhibition with respect to the substrate primer were evaluated by fitting the data to a model for a competitive inhibitor with noncompetitive substrate inhibition by use of the Grafit program (Erithacus Software): v = VmaxS/(Km(1 + I/I) + S)(1 + S/K.). Models for uncompetitive or noncompetitive inhibition did not fit the inhibition data as well as the competitive
I:;,:;, L-Vllll al %_1111111LIC11 3UULd LU uia11a ki virlum~lal %'.'111111L1 V'-lu ragr, I-I I LI 111 3tPIUMUIiLdi raglr J model. The model for a mixed noncompetitive inhibitor provided a nearly identical fit as the competitive model; however, there were not enough data to support the addition of another Ki term: v = VmaxS/(Km(1 + I/K) + S)(1 + S/Kii)(1 + S/Ks). REFERENCES (1) Wang, Y.; Patel, D. J. Solution Structure of the Human Telomeric Repeat d[ag(t 2 AG 3 ) 3 ] G-Tetraplex. Structure 1993, 1, 263-282. (2) Laughlan, G.; Murchie, A. I. H.; Norman, D. G.; Moore, M. H.; Moody, P. C. E.; Lilley, D. M. J.; Luisi, B. The High-Resolution Crystal Structure of a Parallel- Stranded Guanine Tetraplex. Science 1994, 265, 520-524. (3) Berman, H. M.; Olson, W. K.; Beveridge, D. L.; Westbrook, J.; Gelbin, A.; Demeny, T.; Hsieh, S.-H.; Srinivasan, A. R.; Schneider, B. The Nucleic Acid Database. A Comprehensive Relational Database of Three-Dimensional Structures of Nucleic Acids. Biophys. J. 1992, 63, 751-759. (4) (a) Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, S., Jr.; Weiner, P. A New Force-Field for Molecular Mechanical Simulation of Nucleic Acids and Proteins. J. Am. Chem. Soc. 1984, 106, 765-784. (b) Weiner, S. J.; Kollman, P. A.; Hguyen, D. T.; Case, D. A. An All-Atom Force-Field for the Simulation of Proteins and Nucleic Acids. J. Comput. Chem. 1986, 7, 230-252.
v i american onemicai zociety Journal ui ivieacicnai knemistry v u rage /I i 1iiun 3upplemental rage 4 (5) Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton, M.; Caufield, C.; Chang, G.; Hendrickson, T.; Still, W. C. MacroModel-An Integrated Software System for Modeling Organic and Bioorganic Molecules Using Molecular Mechanics. J. Comput. Chem. 1990, 11, 440-467. (6) Kim, N. W.; Piatyszek, M. A.; Prowse, K. R.; Harley, C. B.; West, M. D.; Ho, P. L. C.; Coviello, G. M.; Wright, W. E.; Weinrich, S. L.; Shay, J. W. Specific Association of Human Telomerase Activity with Immortal Cells and Cancer. Science 1994, 266, 2011-2015.