Rich spectroscopic and molecular dynamic studies on the interaction of cytotoxic Pt(II) and Pd(II) complexes of glycine derivatives with calf thymus DNA

References

• Abu-Surrah, A. S., Al-Sa’doni, H. H., Abdalla, M. Y. (2008). Palladium-based chemotherapeutic agents: Routes toward complexes with good antitumor activity. Cancer Therapy, 6, 1–10.
   Google Scholar
• Abu-Surrah, A. S., & Kettunen, M. (2006). Platinum group Antitumor chemistry: Design and development of new anticancer drugs complementary to Cisplatin. Current Medicinal Chemistry, 13, 1337–1357.
   PubMed Web of Science ®Google Scholar
• Agostinelli, E., Marques, M. P. M., Calheiros, R., Gil, F. P. S. C., Tempera, G., Viceconte, N., … Toninello, A. (2010). Polyamines: Fundamental characters in chemistry and biology. Amino Acids, 38, 393–403.
   PubMed Web of Science ®Google Scholar
• Alverdi, V., Giovagnini, L., Marzano, C., Seraglia, R., Beltio, F., Sintran, S., … Fregona, D. (2004). Characterization studies and cytotoxicity assays of Pt(II) and Pd(II) dithiocarbamate complexes by means of FT-IR, NMR spectroscopy and mass spectrometry. Journal of Inorganic Biochemistry, 98, 1117–1128.
   PubMed Web of Science ®Google Scholar
• Anzellotti, A. I., Sabat, M., & Farrell, N. (2006). Covalent and noncovalent interactions for [metal(dien)nucleobase](2+) complexes with L-tryptophan derivatives: Formation of palladium-tryptophan species by nucleobase substitution under biologically relevant conditions. Inorganic Chemistry, 45, 1638–1645.
   PubMed Web of Science ®Google Scholar
• Åqvist, J., Medina, C., & Samuelsson, J. E. (1994). A new method for predicting binding affinity in computer-aided drug design. Protein Engineering, 7, 385–391.
   PubMedGoogle Scholar
• Barrow, G. M. (1988). Chapter. 7. In Physical Chemistry (5th ed.). New York, NY: MC Graw-Hill.
   Google Scholar
• Barton, J. K., Lipard, S. J. (1980). Heavy metal interactions with nucleic acids. In T. G. Spiro (Ed.), Metal ions in biology (Vol. 1, pp. 31–114). New York, NY: Wiley-Interscience.
   Google Scholar
• Bathaie, S. Z., Bolhasani, A., Hoshyar, R., Ranjbar, B., Sabouni, F., & Moosavi-Movahedi, A. A. (2007). Interaction of saffron carotenoids as anticancer compounds with ctDNA, oligo (dG.dC)15, and oligo (dA.dT)15. DNA and Cell Biology, 26, 533–540.
   PubMed Web of Science ®Google Scholar
• Bose, R. N., Ghosh, S. K., & Moghaddas, S. (1997). Kinetic analysis of the cis-diamminedichloroplatinum(II)--cysteine reaction: Implications to the extent of platinum--DNA binding. Journal of Inorganic Biochemistry, 65, 199–205.
   PubMed Web of Science ®Google Scholar
• Brandsdal, B. O., Aqvist, J., & Smalas, A. O. (2001). Computational analysis of binding of P1 variants to trypsin. Protein Science, 10, 1584–1595.
   PubMed Web of Science ®Google Scholar
• Bussi, G., Donadio, D., & Parrinello, M. (2007). Canonical sampling through velocity rescaling. The Journal of Chemical Physics, 126, 14101–14107.
   PubMed Web of Science ®Google Scholar
• Butour, J. L., & Macquet, J. P. (1977). Differentiation of DNA • Platinum complexes by fluorescence. European Journal of Biochemistry, 78, 455–463.
   PubMedGoogle Scholar
• Divsalar, A., Saboury, A. A., Mansouri-Torshizi, H., & Mosavi-Movahedi, A. A. (2007). Binding properties of a new anti-tumor component (2,2'- bipyridin octylglycinato Pd(II) nitrate) with Bovine β-lactoglobulin –A and –B. Journal of Biomolecular Structure & Dynamics, 25, 173–181.
   PubMed Web of Science ®Google Scholar
• Divsalar, A., Saboury, A. A., Yousefi, R., Moosavi-Movahedi, A. A., & Mansouri-Torshizi, H. (2007). Spectroscopic and cytotoxic studies of the novel designed palladium(II) complexes: β-Lactoglobulin and K562 as the targets. International Journal of Biological Macromolecules, 40, 381–386.
   PubMed Web of Science ®Google Scholar
• Erkoc, S. (2001). Empirical potential energy functions used in the simulations of materials properties. In D. Stauffer (Ed.), Annual review of computational physics (Vol. IX, pp. 1–103). Singapore: World Scientific.
   Google Scholar
• Eslami Moghadam, M., Saidifar, M., Rostami-Charati, F., Ajloo, D., Ghadamgahi, M. (2014). Combinatorial Chemistry & High Throughput Screening, 17, 781–789.
   PubMed Web of Science ®Google Scholar
• Farrell, N. P. (1989). Transition metal complexes as drugs and chemotherapeutic agents. In R. Ugo & B. R. James (Eds.), Catalysis by metal complexes (Vol. 11, pp. 222–242). Dordrecht: Kluwer Academic.
   Google Scholar
• Fincham, D. (1992). Leapfrog rotational algorithms. Molecular Simulation, 8, 165–178.
   Web of Science ®Google Scholar
• Gao, H. (2003). Spontaneous insertion of DNA oligonucleotides into carbon nanotubes. Nano Letters, 3, 471–473.
   Web of Science ®Google Scholar
• Greene, R. F., & Pace, C. N. (1974). Urea and guanidine hydrochloride denaturation of ribonuclease, lysozyme, α chymotrypsin, and β lactoglobulin. Journal of Biological Chemistry, 249, 5388–5393.
   PubMed Web of Science ®Google Scholar
• Howe-Grant, M., Wu, K. C., Bauer, W. R., & Lippard, S. J. (1976). Binding of platinum and palladium metallointercalation reagents and antitumor drugs to closed and open DNAs. Biochemistry, 15, 4339–4346.
   PubMed Web of Science ®Google Scholar
• Islami-Moghaddam, M., Mansouri-Torshizi, H., Divsalar, A., & Saboury, A. A. (2009). Synthesis, characterization, cytotoxic and DNA binding studies of Diimine Platinum(II) and Palladium (II) complexes of short hydrocarbon chain ethyldithhiocarbamate ligand. Journal of the Iranian Chemical Society, 6, 552–569.
   Web of Science ®Google Scholar
• Jalili, S., Jaberi, A., Mahjani, M. G., & Jafarian, M. (2012). Molecular dynamics simulations of hydrogen adsorption/desorption by palladium decorated single-walled carbon nanotube bundle. Molecular Physics: An International Journal at the Interface between Chemistry and Physics, 110, 361–368.
   Web of Science ®Google Scholar
• Jin, V. X., & Ranford, J. D. (2000). Complexes of platinum(II) or palladium(II) with 1,10-phenanthroline and amino acids. Inorganica Chimica Acta, 304, 38–44.
   Web of Science ®Google Scholar
• Krishna, A. G., Kumar, D. V., Khan, B. M., Rawal, S. K., & Ganesh, K. N. (1998). Taxol-DNA interactions: Fluorescence and CD studies of DNA groove binding properties of taxol. Biochimica et Biophysica Acta (BBA) – General Subjects, 1381, 104–112.
   PubMed Web of Science ®Google Scholar
• Kwon, Y. E., Whang, K. J., Park, Y. J., & Kim, K. H. (2003). Synthesis, characterization and antitumor activity of novel octahedral Pt(IV) complexes. Bioorganic & Medicinal Chemistry, 11, 1669–1676.
   PubMed Web of Science ®Google Scholar
• Manav, N., Mishra, A. K., & Kaushik, N. K. (2004). Triphenyl phosphine adducts of platinum(IV) and palladium(II) dithiocarbamates complexes: A spectral and in vitro study. Spectrochimica Acta Part A, 60, 3087–3092.
   PubMed Web of Science ®Google Scholar
• Mansouri-Torshizi, H., Eslami Moghaddam, M., Divsalar, A., & Saboury, A. A. (2011). DNA-binding studies of some potential Antitumor 2,2-bipyridine Pt(II)/Pd(II) complexes of piperidinedithiocarbamate. their synthesis, spectroscopy and cytotoxicity. Acta Chimica Slovenica, 58, 811–822.
   PubMed Web of Science ®Google Scholar
• Mansouri-Torshizi, H., I-Moghaddam, M., Divsalar, A., & Saboury, A. A. (2008). 2,2'- Bipyridinebutyldithiocarbamatoplatinum(II) and palladium(II) complsxes: Synthesis, characterization, cytotoxicity, and rich DNA-binding studies. Bioorganic & Medicinal Chemistry, 16, 9616–9625.
   PubMed Web of Science ®Google Scholar
• Mansouri-Torshizi, H., I-Moghaddam, M., Divsalar, A., & Saboury, A. A. (2009). Diimine platinum(II) and palladium(II) complexes of Dithiocarbamate derivative as potential antitumor agents: Synthesis, characterization, cytotoxicity, and detail DNA-binding studies. Journal of Biomolecular Structure & Dynamics, 26, 575–586.
   PubMed Web of Science ®Google Scholar
• Mansouri-Torshizi, H., Islami-Moghaddam, M., & Saboury, A. A. (2003). A microcalorimetry and spectroscopy study on the interaction of BSA with 2,2' Bipyridine Octylglycinato palladium (II) nitrate. Acta Biochimica et Biophysica Sinica, 35, 886–890.
   Web of Science ®Google Scholar
• Marques, M. P. M. (2013). Platinum and Palladium Polyamine complexes as anticancer agents: The structural factor. ISRN Spectroscopy, 2013, 1–29.
   Google Scholar
• Marzano, C., Trevisan, A., Giovagnini, L., & Fregona, D. (2002). Synthesis of a new platinum(II) complex: anticancer activity and nephrotoxicity in vitro. Toxicology in Vitro, 16, 413–419.
   PubMed Web of Science ®Google Scholar
• Mital, R., Jain, N., & Srivastava, T. S. (1989). Synthesis, characterization and cytotoxic studies of diamine and diimine palladium(II) complexes of diethyldithiocarbamate and binding of these and analogous platinum(II) complexes with DNA. Inorganica Chimica Acta, 166, 135–140.
   Web of Science ®Google Scholar
• Moradell, S., Lorenzo, J., Rovira, A., Zutphen, S. V., Aviles, F. X., Moreno, V., … Llobet, A. (2004). Water-soluble platinum(II) complexes of diamine chelating ligands bearing amino-acid type substituents: The effect of the linked amino acid and the diamine chelate ring size on antitumor activity, and interactions with 5'-GMP and DNA. Journal of Inorganic Biochemistry, 98, 1933–1946.
   PubMed Web of Science ®Google Scholar
• Mylonas, S., Valavanidis, A., & Voukouvalidis, V. (1981). Platinum(II) and Palladium(II) complexes with aminoacid derivatives. Synthesis, interpretation of IR and 1H-NMR spectra and conformational implications. Inorganica Chimica Acta, 55, 125–128.
   Web of Science ®Google Scholar
• Nome, R. A. (2010). Ultrafast dynamics of solvation: The story so far. Journal of the Brazilian Chemical Society, 21, 2189–2204.
   Web of Science ®Google Scholar
• Palocsay, F. A., & Rund, J. V. (1969). Reaction between 1,10-phenanthroline and platinum(II) compounds. I. Reaction in aqueous solution. Inorganic Chemistry, 8, 524–528.
   Web of Science ®Google Scholar
• Peres-Flores, L., Ruiz-Chica, A. J., Delcros, J. G., Sanches, F. M., & Ramirez, F. J. (2008). Effect of spermine conjugation on the interaction of acridine with alternating purine–pyrimidine oligodeoxyribonucleotides studied by CD, fluorescence and absorption spectroscopies. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 69, 1089–1096.
   PubMed Web of Science ®Google Scholar
• Saboury, A. A. (2006). A review on the ligand binding studies by isothermal titration calorimetry. Journal of the Iranian Chemical Society, 3, 1–21.
   Web of Science ®Google Scholar
• Saboury, A. A., Shamsaei, A. A., Mosavi Movahedi, A. A., & Mansouri-Torshizi, H. (1999). Thermodynamics of binding 2,2¢-bipyridineglycinato palladium (II) chloride on human serum albumin. Journal of the Chinese Chemical Society, 46, 917–922.
   Web of Science ®Google Scholar
• Saeidifar, M., Mansouri-Torshizi, H., Palizdar, Y., Eslami-Moghadam, M., Divsalar, A., & Saboury, A. A. (2014). Synthesis, characterization, cytotoxicity and DNA binding studies of a novel anionic organopalladium(II) complex. Acta Chimica Slovenica, 61, 126–136.
   PubMed Web of Science ®Google Scholar
• Scatchard, G. (1949). The attractions of proteins for small molecules and ions. Annals of the New York Academy of Sciences, 51, 660–672.
   Web of Science ®Google Scholar
• Schuttelkopf, A. W., & van Aalten, D. M. F. (2004). PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica, 60, 1355–1363.
   PubMed Web of Science ®Google Scholar
• Shaikh, S. A., Ahmed, S. R., & Jayaram, B. (2004). A molecular thermodynamic view of DNA-drug interaction: A case study of 25 minor groove binders. Archives of Biochemistry and Biophysics, 429, 81–99.
   PubMed Web of Science ®Google Scholar
• Sigel, H. (1980). Metal ions in biological systems (Vol. 11, pp. 1–196). New York, NY: Marcel Dekker.
   Google Scholar
• Tan, J. J., Kong, R., Wang, C. X., & Chen, W. Z. (2004). Gp41 hydrophobic pocket entry inhibitor linear interaction energy MD simulation. Journal of Molecular Structure: THEOCHEM, 682, 9–15.
   Web of Science ®Google Scholar
• Van Der Spoel, D. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26, 1701–1718.
   PubMed Web of Science ®Google Scholar
• Wolf, M. G., & Groenhof, G. (2012). Evaluating nonpolarizable nucleic acid force fields: A systematic comparison of the nucleobases hydration free energies and chloroform-to-water partition coefficients. Journal of Computational Chemistry, 33, 2225–2232.
   PubMed Web of Science ®Google Scholar
• Xi, P. X., Xu, Z. H., Liu, X. H., Cheng, F. J., & Zeng, Z. Z. (2008). Synthesis, characterization and DNA-binding studies of 1-cyclohexyl-3-tosylurea and its Ni(II), and Cd(II) complexes. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 71, 523–528.
   PubMed Web of Science ®Google Scholar
• Xu, Z. H., Chen, F. J., Xi, P. X., Liu, X. H., & Zeng, Z. Z. (2008). Synthesis, characterization, and DNA-binding properties of the cobalt(II) and nickel(II) complexes with salicylaldehyde 2-phenylquinoline-4-carboylhydrazone. Journal of Photochemistry and Photobiology A: Chemistry, 196, 77–83.
   Web of Science ®Google Scholar