An insight into the anticancer activities of Ru(II)-based metallocompounds using docking methods

Molecules

Volumn 18, Issue 9, 2013, Pages 10829-10856

  Adeniyi, Adebayo A ^a   Ajibade, Peter A ^a  

^a UNIVERSITY OF FORT HARE   (South Africa)

Author keywords

Anticancer; Docking methods; Receptors; Ruthenium complexes

Indexed keywords

ANTINEOPLASTIC AGENT; CELL SURFACE RECEPTOR; COORDINATION COMPOUND; PROTEIN BINDING; RUTHENIUM;

BINDING SITE; CHEMISTRY; HUMAN; HYDROGEN BOND; MOLECULAR DOCKING; ARTICLE; PROTEIN BINDING;

ANTINEOPLASTIC AGENTS; BINDING SITES; COORDINATION COMPLEXES; HUMANS; HYDROGEN BONDING; MOLECULAR DOCKING SIMULATION; PROTEIN BINDING; RECEPTORS, CELL SURFACE; RUTHENIUM;

EID: 84885132021     PISSN: None     EISSN: 14203049     Source Type: Journal    
DOI: 10.3390/molecules180910829     Document Type: Article

References (51)

1. Allardyce, C.S.; Dorcier, A.; Scolaro, C.; Dyson P.J. Development of organometallic (organo-transition metal) pharmaceuticals. Appl. Organometal. Chem. 2005, 19, 1-10. (Pubitemid 40173971)
2. Gasser, G.; Ott, I.; Metzler-Nolte, N. Organometallic anticancer compounds. J. Med. Chem. 2011, 54, 3-25.
3. Ang, W.H.; Daldini, E.; Scolaro, C.; Scopelliti, R.; Juillerat-Jeannerat, L.; Dyson, P.J. Development of organometallic ruthenium-arene anticancer drugs that resist hydrolysis. Inorg. Chem. 2006, 45, 9006-9013.
4. Dyson, P.J.; Sava, G. Metal-based antitumour drugs in the post genomic era. Dalton Trans. 2006, 23, 1929-1933. (Pubitemid 43797525)
5. Chatterjee, S.; Kundu, S.; Bhattacharyya, A.; Hartinger, C.G.; Dyson, P.J. The ruthenium(II)-arene compound RAPTA-C induces apoptosis in EAC cells through mitochondrial and p53-JNK pathways. J. Biol. Inorg. Chem. 2008, 13, 1149-1155.
6. Hartinger, C.G.; Jakupec, M.A.; Zorbas-Seifried, S.; Groessl, M.; Egger, A.; Berger, W.; Zorbas, H.; Dyson, P.J.; Keppler, B.K. KP1019, A new redox-active anticancer agent-preclinical development and results of a clinical phase I study in tumor patients. Chem. Biodivers. 2008, 5, 2140-2155.
7. Sava, G.; Bergamoa, A.; Dyson P.J. Metal-based antitumour drugs in the post-genomic era: What comes next? Dalton Trans. 2011, 40, 9069-9075.
8. Page, S. Ruthenium compounds as anticancer agents. Education in Chemistry January 2012.
9. Allardyce, C.S.; Dyson, P.J. Ruthenium in medicine: Current clinical uses and future prospects. Platin. Met. Rev. 2001, 45, 62-69. (Pubitemid 32535878)
10. Hu, X.; Shelver, W.H. Docking studies of matrix metalloproteinase inhibitors: Zinc parameter optimization to improve the binding free energy prediction. J Mol Graph Model. 2003, 22, 115-126. (Pubitemid 36976838)
11. Ciancetta, A.; Genheden, S.; Ryde, U. A QM/MM study of the binding of RAPTA ligands to cathepsin B. J. Comput. Aid. Molec. Design 2011, 25, 729-742.
12. Adeniyi, A.A.; Ajibade, P.A. Inhibitory activities and possible anticancer targets of Ru(II)-based complexes using computational docking method J. Mol. Graph. Model. 2012, 38, 60-69.
13. Adeniyi, A.A.; Ajibade, P.A. Comparing the suitability of autodock, gold and glide for the docking and predicting the possible targets of ru(ii)-based complexes as anticancer agents. Molecules 2013, 18, 3760-3778.
14. Casini, A.; Gabbiani, C.; Sorrentino, F.; Rigobello, M.P.; Bindoli, A.; Geldbach, T.J.; Marrone, A.; Re, N.; Hartinger, C.G.; Dyson, P.J.; et al. Emerging protein targets for anticancer metallodrugs: inhibition of thioredoxin reductase and cathepsin B by antitumor ruthenium(II)-arene compounds. J. Med. Chem. 2008, 51, 6773-6781.
15. Wu, B.; Ong, M.S.; Groessl, M.; Adhireksan, Z.; Hartinger, C.G.; Dyson, P.J.; Davey, C.A. A Ruthenium antimetastasis agent forms specific histone protein adducts in the nucleosome core. Chem-Eur. J. 2011, 17, 3562-3566.
16. Xie, P.; Streu, C.; Qin, J.; Bregman, H.; Pagano, N.; Meggers, E.; Marmorstein, R. The crystal structure of BRAF in complex with an organoruthenium inhibitor reveals a mechanism for inhibition of an active form of BRAF kinase. Biochemistry 2009, 48, 5187-5198.
17. Stepanenko, I.N.; Casini, A.; Edafe, F.; Novak, M.S.; Arion, V.B.; Dyson, P.J.; Jakupec, M.A.; Keppler, B.K. Conjugation of organoruthenium(II) 3-(1H-Benzimidazol-2-yl)pyrazolo[3,4-b]pyridines and Indolo[3,2-d]benzazepines to recombinant human serum albumin: A strategy to enhance cytotoxicity in cancer cells. Inorg. Chem. 2011, 50, 12669-12679.
18. Hanif, M.; Henke, H.; Meier, S.M.; Martic, S.; Labib, M.; Kandioller, W.; Jakupec, M.A.; Arion, V.B.; Kraatz, H.; Keppler, B.K.; et al. Is the reactivity of M(II)-arene complexes of 3-hydroxy-2(1H)-pyridones to biomolecules the anticancer activity determining parameter? Inorg. Chem. 2010, 49, 7953-7963.
19. Zhuang, W.; Wu, X.; Zhou, Y.; Liu, G.; Wu, T.; Yao, X.; Du, L.; Wei, M. Polymorphisms of thymidylate synthase in the 5′- and 3′ -untranslated regions and gastric cancer. Dig. Dis. Sci. 2009, 54, 1379-1385.
20. Berg, J.M.; Tymoczko, J.L.; Stryer, L. Biochemistry, 5th ed.; W.H. Freeman: New York, NY, USA, 2002.
21. Gopal, Y.N.V.; Jayaraju, D.; Kondapi, A.K. Inhibition of topoisomerase II catalytic activity by two ruthenium compounds: A ligand-dependent mode of action. Biochemistry 1999, 38, 4382-4388.
22. Arpino, G.; Ciocca, D.R.; Weiss, H.; Allred, D.C.; Daguerre, P.; Vargas-Roig, L.; Leuzzi, M.; Gago, F.; Elledge, R.; and Mohsin, S.K. Predictive value of apoptosis, Proliferation, HER-2, and topoisomerase IIa for anthracycline chemotherapy in locally advanced breast cancer. Breast Cancer Res. Treat. 2005, 92, 69-75. (Pubitemid 40875080)
23. Holdgate, G.A.; Tunnicliffe, A.; Ward, W.H.J.; Weston, S.A.; Rosenbrock, G.; Barth, P.T.; Taylor, I.W.F.; Pauptit, R.A.; Timms, D. The entropic penalty of ordered water accounts for weaker binding of the antibiotic novobiocin to a resistant mutant of DNA gyrase: A thermodynamic and crystallographic study. Biochemistry 1997, 36, 9663-9673. (Pubitemid 27364677)
24. Ghaneya, S.; Hassan, G.S.; Nahla, A; Farag, N.A.; Gehan, H.; Hegazy, G.H.; Reem, K.; Arafa, R.K. Design and synthesis of novel benzopyran-2-one derivatives of expected antimicrobial activity through DNA gyrase-B inhibition. Arch. Pharm. 2008, 341, 725-733.
25. Caballero, N.A.; Meléndez, F.J.; Niño, A.; Muñoz-Caro, C. Molecular docking study of the binding of aminopyridines within the K+ channel. J. Mol. Model. 2007, 13, 579-586. (Pubitemid 46681656)
26. Morris, G.M.; Goodsell, D.S.; Halliday, R.S.; Huey, R.; Hart, W.E.; Belew, R.K.; Olson, A.J. Automated docking using a lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 1998, 19, 1639-1662. (Pubitemid 128590223)
27. Egger, A.E.; Hartinger, C.G.; Renfrew, A.K.; Dyson, P.J. Metabolization of [Ru(η6-C6H5CF3)(pta)Cl2]: A cytotoxic RAPTA-type complex with a strongly electron withdrawing arene ligand. J. Biol. Inorg. Chem. 2010, 15, 919-927.
28. Wang, F.; Habtemariam, A.; van der Geer, E.P.L.; Fernandez, R.; Melchart, M.; Deeth, R.J.; Aird, R.; Guichard, S.; Fabbiani, F.P.A.; Lozano-Casal, P.; et al. Controlling ligand substitution reactions of organometallic complexes: Tuning cancer cell cytotoxicity. Proc. Natl. Acad. Sci. 2005, 102, 18269-18274. (Pubitemid 43011216)
29. Hu, W; Luo, Q; Ma, X; Wu, K; Liu, J; Chen, Y; Xiong, S; Wang, J; Sadler, P.J; Wang, F. Arene Control over thiolate to sulfinate oxidation in albumin by organometallic ruthenium anticancer complexes. Chem-Eur. J. 2009, 15, 6586-6594.
30. Caruso, F.; Rossi, M.; Benson, A.; Opazo, C.; Freedman, D.; Monti, E.; Gariboldi, M.B.; Shaulky, J.; Marchetti, F.; Pettinari, R.; et al. Ruthenium-arene complexes of curcumin: X-ray and density functional theory structure, Synthesis, and spectroscopic characterization, in vitro antitumor activity, and DNA docking studies of (p-cymene)Ru(curcuminato)chloro. J. Med. Chem. 2012, 55, 1072-1081.
31. Sugio, S.; Kashima, A.; Mochizuki, S.; Noda, M.; Kobayashi, K. Crystal structure of human serum albumin at 2.5 A resolution. Protein Eng. 1999, 12, 439-446. (Pubitemid 29322441)
32. Musil, D.; Zucic, D.; Turk, D.; Engh, R.A.; Mayr, I.; Huber, R.; Popovic, T.; Turk, V.; Towatari, T.; Katunuma, N.; et al. The refined 2.15 A X-ray crystal structure of human liver cathepsin B: The structural basis for its specificity. EMBO J. 1991, 10, 2321-2330. (Pubitemid 121000005)
33. Eriksson, M.; Uhlin, U.; Ramaswamy, S.; Ekberg, M.; Regnström, K.; Sjöberg, B.M.; Eklund, H. Binding of allosteric effectors to ribonucleotide reductase protein R1: Reduction of active-site cysteines promotes substrate binding. Structure 1997, 5, 1077-1092. (Pubitemid 27393092)
34. Sandalova, T.; Zhong, L.; Lindqvist, Y.; Holmgren, A.; Schneider, G. Three-dimensional structure of a mammalian thioredoxin reductase: implications for mechanism and evolution of a selenocysteine-dependent enzyme. Proc. Natl. Acad. Sci. 2001, 98, 9533-9538. (Pubitemid 32769338)
35. Newby, Z.; Lee, T.T.; Morse, R.J.; Liu, Y.; Liu, L.; Venkatraman, P.; Santi, D.V.; Finer-Moore, J.S.; Stroud, R.M. The role of protein dynamics in thymidylate synthase catalysis: variants of conserved 2′-deoxyuridine 5′-monophosphate (dUMP)-binding Tyr-261. Biochemistry 2006, 45, 7415-7428. (Pubitemid 43894935)
36. Schuetz, A.; Min, J.; Allali-Hassani, A.; Schapira, M.; Shuen, M.; Loppnau, P.; Mazitschek, R.; Kwiatkowski, N.P.; Lewis, T.A.; Maglathin, R.L.; et al. Human HDAC7 harbors a class IIa histone deacetylase-specific zinc binding motif and cryptic deacetylase activity. J. Biol. Chem. 2008, 283, 11355-11363.
37. Classen, S.; Olland, S.; Berger, J.M. Structure of the topoisomerase II ATPase region and its mechanism of inhibition by the chemotherapeutic agent ICRF-187. Proc. Natl. Acad. Sci. 2003, 100, 10629-10634. (Pubitemid 37140080)
38. Zhao, Y.; Biertümpfel, C.; Gregory, M.T.; Hua, Y.J.; Hanaoka, F.; Yang, W. Structural basis of human DNA polymerase η-mediated chemoresistance to cisplatin. Proc. Natl. Acad. Sci. 2012, 109, 7269-7274.
39. R Development Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing. Available online: http://www.R-project.org (accessed 1 May 2012).
40. Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Montgomery, J.A., Jr., Vreven, T., Kudin, K.N., Burant, J.C., Millam, J.M., Iyengar, S.S., Tomasi, J., Barone, V., Mennucci, B., Cossi, M., Scalmani, G., Rega, N., Petersson, G.A., Nakatsuji, H., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Klene, M., Li, X., Knox, J.E., Hratchian, H.P., Cross, J.B., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R.E., Yazyev, O., Austin, A.J., Cammi, R., Pomelli, C., Ochterski, J.W., Ayala, P.Y., Morokuma, K., Voth, G.A., Salvador, P., Dannenberg, J.J., Zakrzewski, V.G., Dapprich, S., Daniels, A.D., Strain, M.C., Farkas, O., Malick, D.K., Rabuck, A.D., Raghavachari, K., Foresman, J.B., Ortiz, J.V., Cui, Q., Baboul, A.G., Clifford, S., Cioslowski, J., Stefanov, B.B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Martin, R.L., Fox, D.J., Keith, T., Al-Laham, M.A., Peng, C.Y., Nanayakkara, A., Challacombe, M., Gill, P.M.W., Johnson, B., Chen, W., Wong, M.W., Gonzalez, C., Pople, J.A. Gaussian, Inc.: Pittsburgh, PA, USA, 2003.
41. Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G.A., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H.P., Izmaylov, A.F., Bloino, J., Zheng, G., Sonnenberg, J.L., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Vreven, T., Montgomery, J., J.A.;; Peralta, J.E., Ogliaro, F., Bearpark, M., Heyd, J.J., Brothers, E., Kudin, K.N., Staroverov, V.N., Kobayashi, R., Normand, J., Raghavachari, K., Rendell, A., Burant, J.C., Iyengar, S.S., Tomasi, J., Cossi, M., Rega, N., Millam, N.J., Klene, M., Knox, J.E., Cross, J.B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R.E., Yazyev, O., Austin, A.J., Cammi, R., Pomelli, C., Ochterski, J.W., Martin, R.L., Morokuma, K., Zakrzewski; V.G., Voth, G.A., Salvador, P., Dannenberg, J.J., Dapprich, S., Daniels, A.D., Farkas, Ö., Foresman, J.B., Ortiz, J.V., Cioslowski, J., Fox, D.J. Gaussian, Inc.: Wallingford, CT, USA, 2009.
42. Adamo, C.; Barone V. Toward reliable density functional methods without adjustable parameters: The PBE0 model. J. Chem. Phys. 1999, 110, 6158-6170.
43. Stevens, W.J.; Krauss, M.; Basch, H.; Jasien, P.G. Relativistic compact effective potentials and efficient, shared-exponent basis sets for the third-, fourth-, and fifth-row atoms Can. J. Chem. 1992, 70, 612-630.
44. Becke, A.D. Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 1993, 98, 5648-5652.
45. Dobbs, K.D., Hehre, W.J. Molecular orbital theory of the properties of inorganic and organometallic compounds 5. Extended basis sets for first-row transition metals. J. Comput. Chem. 1987, 6, 861-879.
46. Morris, G.M.; Huey, R.; Lindstrom, W.; Sanner, M.F.; Belew, R.K.; Goodsell, D.S.; Olson, A.J. Autodock4 and AutoDockTools4: Automated docking with selective receptor flexiblity. J. Comput. Chem. 2009, 30, 2785-2791.
47. Thomsen, R.; Christensen, M.H.; MolDock: A new technique for high-accuracy molecular docking. J. Med. Chem. 2006, 49, 3315-3321. (Pubitemid 43830529)
48. ADL: Parameters for docking with metal ions in receptor. Available online: http://autodock.1369657.n2.nabble.com/ADL-Parameters-for-docking-with- metal-ions-in-receptor-td2505649.html (accessed on 6 May 2012).
49. Sapre, N.S; Gupta, S.; Sapre, N. Assessing ligand efficiencies using template-based molecular docking and Tabu-clustering on tetrahydroimidazo-[4,5, 1-jk][1,4]-benzodiazepin-2(1H)-one and -thione (TIBO) derivatives as HIV-1RT inhibitors. J. Chem. Sci. 2008, 120, 395-404
50. Research collaboratory for structural bioinformatics (RCSB) online pdb database. Available online: http://www.rcsb.org (accessed 30 April 2013).
51. Pettersen, E.F.; Goddard, T.D.; Huang, C.C.; Couch, G.S.; Greenblatt, D.M.; Meng, E.C.; Ferrin, T.E. UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem. 2004, 25, 1605-1612.