Formation of chelate structure between His-Met dipeptide and diaqua-cisplatin complex; DFT/PCM computational study

  • Michal Maixner
  • Helio F. Dos Santos
  • Jaroslav V. Burda
Original Paper
  • 82 Downloads

Abstract

Interaction of cisplatin in activated diaqua-form with His-Met dipeptide is explored using DFT approach with PCM model. First the conformation space of the dipeptide is explored to find the most stable structure (labeled 0683). Several functionals with double-zeta basis set are used for optimization and obtained order of conformers is confirmed by the CCSD(T) single-point calculations. Supermolecular model is used to determine reaction coordinate for the replacement of aqua ligands consequently by N-site of histidine and S-site of methionine and reversely. Despite the monoadduct of Pt–S(Met) is thermodynamically less stable this reaction passes substantially faster (by several orders of magnitude) than coordination of cisplatin to histidine. The consequent chelate formation occurs relatively fast with energy release up to 12 kcal mol−1.

Keywords

Computational chemistry Density functional theory Thermodynamics Anticancer drug Heavy metal 

Notes

Acknowledgements

Authors (JVB and MM) are grateful for supporting this study to the Grant Agency of Czech Republic Project no 16-06240S. We would also like to acknowledge a generous access to computational facilities of the National Grid Infrastructure MetaCentrum, provided under the program ‘Projects of Large Infrastructure for Research, Development, and Innovations’ (LM2010005).

Supplementary material

775_2018_1536_MOESM1_ESM.pdf (97 kb)
Supplementary material 1 (PDF 97 kb)

References

  1. 1.
    Eastman A (1999) In: Lippert B (ed) Cisplatin. Wiley-VCH, Weinheim, pp 111–134Google Scholar
  2. 2.
    Hindmarsh K, House DA, Turnbull MM (1997) Inorg Chim Acta 257:11–18Google Scholar
  3. 3.
    Miller SE, House DA (1991) Inorg Chim Acta 187:125–132Google Scholar
  4. 4.
    Miller SE, Gerard KJ, House DA (1991) Inorg Chim Acta 190:135–144Google Scholar
  5. 5.
    Zimmermann T, Leszczynski J, Burda JV (2011) J Mol Model 17:2385–2393PubMedGoogle Scholar
  6. 6.
    Burda JV, Zeizinger M, Leszczynski J (2005) J Comput Chem 26:907–914PubMedGoogle Scholar
  7. 7.
    Pascoe JM, Roberts JJ (1974) Biochem Pharmacol 23:1345–1357PubMedGoogle Scholar
  8. 8.
    Peleg-Shulman T, Najajreh Y, Gibson D (2002) J Inorg Biochem 91:306–311PubMedGoogle Scholar
  9. 9.
    Kartalou M, Essigmann JM (2001) Mutat Res Fundam Mol Mech Mutagen 478:1–21Google Scholar
  10. 10.
    Fojta M, Pivonkova H, Brazdova M, Kovarova L, Palecek E, Pospisilova S, Vojtesek B, Kasparkova J, Brabec V (2003) Biochem Pharmacol 65:1305–1316PubMedGoogle Scholar
  11. 11.
    Pivonkova H, Pecinka P, Ceskova P, Fojta M (2006) FEBS J 273:4693–4706PubMedGoogle Scholar
  12. 12.
    Donahue BA, Augot M, Bellon SF, Treiber DK, Toney JH, Lippard SJ, Essigmann JM (1990) Biochemistry 29:5872–5880PubMedGoogle Scholar
  13. 13.
    Andrews PA, Jones JA (1991) Cancer Commun 3:1–10Google Scholar
  14. 14.
    Burger AM, Double JA, Newell DR (1997) Eur J Cancer 33:638–644PubMedGoogle Scholar
  15. 15.
    Zamble DB, Lippard SJ (1999) In: Lippert B (ed) Cisplatin. Wiley-VCH, Weinheim, pp 73–110Google Scholar
  16. 16.
    Lippert B (1999) Cisplatin: chem. and biochemistry of a leading anticancer drug. Wiley-VCH, WienheimGoogle Scholar
  17. 17.
    Zimmermann T, Zeizinger M, Burda JV (2005) J Inorg Biochem 99:2184–2196PubMedGoogle Scholar
  18. 18.
    Zimmermann T, Chval Z, Burda JV (2009) J Phys Chem B 113:3139–3150.  https://doi.org/10.1021/jp807645x PubMedGoogle Scholar
  19. 19.
    Zimmermann T, Burda JV (2010) Dalton Trans 39:1295–1301PubMedGoogle Scholar
  20. 20.
    Norman RE, Ranford JD, Sadler PJ (1992) Inorg Chem 31:877–888Google Scholar
  21. 21.
    Williams KM, Rowan C, Mitchell J (2004) Inorg Chem 43:1190–1196PubMedGoogle Scholar
  22. 22.
    Appleton TG, Connor JW, Hall JR (1988) Inorg Chem 27:130–137Google Scholar
  23. 23.
    Wei HY, Liu Q, Lin J, Jiang PJ, Guo ZJ (2004) Inorg Chem Commun 7:792–794Google Scholar
  24. 24.
    Riley CM, Sternson LA, Repta AJ (1983) J Pharm Sci 72:351–355PubMedGoogle Scholar
  25. 25.
    Reedijk J (1999) Chem Rev 99:2499–2510PubMedGoogle Scholar
  26. 26.
    Vrana O, Brabec V (2002) Biochemistry 41:10994–10999PubMedGoogle Scholar
  27. 27.
    Manka S, Becker F, Hohage O, Sheldrick WS (2004) J Inorg Biochem 98:1947–1956PubMedGoogle Scholar
  28. 28.
    Hohage O, Sheldrick WS (2006) J Inorg Biochem 100:1506–1513PubMedGoogle Scholar
  29. 29.
    Appleton TG, Connor JW, Hall JR, Prenzler PD (1989) Inorg Chem 28:2030–2037Google Scholar
  30. 30.
    Bose RN, Ghosh SK, Moghaddas S (1997) J Inorg Biochem 65:199–205PubMedGoogle Scholar
  31. 31.
    Lau JKC, Deubel DV (2005) Chem Eur J 11:2849–2855PubMedGoogle Scholar
  32. 32.
    Hagrman D, Goodisman J, Souid A-K (2004) J. Pharmacol Exp Ther 308:658–666PubMedGoogle Scholar
  33. 33.
    Dabrowiak JC, Goodisman J, Souid A-K (2002) Drug Metab Dispos 30:1378–1384PubMedGoogle Scholar
  34. 34.
    Dedon PC, Borch RF (1987) Biochem Pharmacol 36:1955–1964PubMedGoogle Scholar
  35. 35.
    Bose RN, Moghaddas S, Weaver EL, Cox EH (1995) Inorg Chem 34:5878–5883Google Scholar
  36. 36.
    Zou J, Yang XD, An F, Wang K (1998) J Inorg Biochem 70:227–232PubMedGoogle Scholar
  37. 37.
    Da Silva VJ, Costa LAS, Dos Santos HF (2008) Int J Quantum Chem 108:401–414Google Scholar
  38. 38.
    Chang GR, Zhou LX, Chen D (2006) Chin J Struct Chem 25:533–542Google Scholar
  39. 39.
    Robertazzi A, Platts JA (2004) J Comput Chem 25:1060–1067PubMedGoogle Scholar
  40. 40.
    Robertazzi A, Platts JA (2005) Inorg Chem 44:267–274PubMedGoogle Scholar
  41. 41.
    Robertazzi A, Platts JA (2006) Chem Eur J 12:5747–5756PubMedGoogle Scholar
  42. 42.
    Wysokinski R, Hernik K, Szostak R, Michalska D (2007) Chem Phys 333:37–48Google Scholar
  43. 43.
    Yuan QH, Zhou LX (2007) Chin J Struct Chem 26:962–972Google Scholar
  44. 44.
    Erturk H, Hofmann A, Puchta R, van Eldik R (2007) Dalton Trans 22:2295–2301Google Scholar
  45. 45.
    Hao L, Zhang Y, Tan HW, Chen GJ (2007) Chem J Chin Univ Chin 28:1160–1164Google Scholar
  46. 46.
    Pavelka M, Lucas MFA, Russo N (2007) Chem Eur J 13:10108–10116PubMedGoogle Scholar
  47. 47.
    Pavelka M, Šimánek M, Šponer J, Burda JV (2006) J Phys Chem A 110:4795–4809PubMedGoogle Scholar
  48. 48.
    Hofmann A, Jaganyi D, Munro OQ, Liehr G, van Eldik R (2003) Inorg Chem 42:1688–1700PubMedGoogle Scholar
  49. 49.
    Zhu HJ, Ziegler T (2006) J Organomet Chem 691:4486–4497Google Scholar
  50. 50.
    Tsipis AC, Sigalas MP (2002) J Mol Struct (Theochem) 584:235–248Google Scholar
  51. 51.
    Zhu C, Raber J, Eriksson LA (2005) J Phys Chem B 109:12195–12205PubMedGoogle Scholar
  52. 52.
    Song T, Hu P (2006) J Chem Phys 125:091101PubMedGoogle Scholar
  53. 53.
    Jia M, Qu W, Yang Z, Chen G (2005) Int J Mod Phys B 19:2939–2949Google Scholar
  54. 54.
    Zhang Y, Guo Z, You X-Z (2001) J Am Chem Soc 123:9378–9387PubMedGoogle Scholar
  55. 55.
    Lau JKC, Deubel DV (2006) J Chem Theory Comput 2:103–106PubMedGoogle Scholar
  56. 56.
    Dos Santos HF, Marcial BL, De Miranda CF, Costa LAS, De Almeida WB (2006) J Inorg Biochem 100:1594–1605PubMedGoogle Scholar
  57. 57.
    Lopes JF, Menezes VSD, Duarte HA, Rocha WR, De Almeida WB, Dos Santos HF (2006) J Phys Chem B 110:12047–12054PubMedGoogle Scholar
  58. 58.
    Costa LA, Hambley TW, Rocha WR, Almeida WB, Dos Santos HF (2006) Int J Quantum Chem 106:2129–2144Google Scholar
  59. 59.
    Šebesta F, Burda JV (2017) J Inorg Biochem 172:100–109PubMedGoogle Scholar
  60. 60.
    Zimmermann T, Burda JV (2009) J Chem Phys 131:135101PubMedGoogle Scholar
  61. 61.
    Zeizinger M, Burda JV, Šponer J, Kapsa V, Leszczynski J (2001) J Phys Chem A 105:8086–8092Google Scholar
  62. 62.
    Burda JV, Zeizinger M, Leszczynski J (2004) J Chem Phys 120:1253–1262PubMedGoogle Scholar
  63. 63.
    Parr RG, Pearson RG (1983) J Am Chem Soc 105:7512Google Scholar
  64. 64.
    Miertus S, Scrocco E, Tomasi J (1981) Chem Phys 55:117–129Google Scholar
  65. 65.
    Miertus S, Tomasi J (1982) Chem Phys 65:239–245Google Scholar
  66. 66.
    Glendening ED, Badenhoop K, Ree AE, Carpenter JE, Bohmann JA, Morales M, Weinhold F (2001). University of Wisconsin, Madison, Wisconsin 53706, WisconsinGoogle Scholar
  67. 67.
    Barone V, Cossi M, Tomasi J (1997) J Chem Phys 107:3210–3221Google Scholar
  68. 68.
    Bader RFW (1990) Atoms in molecules: a quantum theory. Oxford University Press, OxfordGoogle Scholar
  69. 69.
    Keith TA (2014) http://aim.tkgristmill.com. Accessed 30 Sept 2014
  70. 70.
    Politzer P, Laurence PR, Jayasuriya K (1985) Environ Health Perspect 61:191–202PubMedPubMedCentralGoogle Scholar
  71. 71.
    Murray et al (2011) WIREs Comput Mol Sci 1:153Google Scholar
  72. 72.
    Sjoberg P, Murray JS, Brinck T, Politzer P (1990) Can J Chem 68:1440Google Scholar
  73. 73.
    Murray JS, Brinck T, Grice ME, Politzer P (1992) J Mol Struct Theor Chem 256:29–45Google Scholar
  74. 74.
    Politzer P, Murray JS, Bulat FA (2010) J Mol Model 16:1731PubMedGoogle Scholar
  75. 75.
    Andrae D, Haussermann U, Dolg M, Stoll H, Preuss H (1990) Theor Chim Acta 77:123–141Google Scholar
  76. 76.
    Burda JV, Runenberg N, Pyykko P (1998) Chem Phys Lett 288:635–641Google Scholar
  77. 77.
    Burda JV, Zeizinger M, Sponer J, Leszczynski J (2000) J Chem Phys 113:2224–2232Google Scholar
  78. 78.
    Wertz DH (1980) J Am Chem Soc 102:5316–5322Google Scholar
  79. 79.
    Cheng M-J, Nielsen RJ, Goddard Iii WA (2014) Chem Commun 50:10994–10996.  https://doi.org/10.1039/C4CC03067B Google Scholar
  80. 80.
    Ramachandran GN, Ramakrishnan C, Sasisekharan V (1963) J Mol Biol 7:95–99PubMedGoogle Scholar
  81. 81.
    Chojnacki H, Kuduk-Jaworska J, Jaroszewicz I, Janski JJ (2009) Pol J Chem 83:1013–1024Google Scholar
  82. 82.
    Melchior A, Martínez JM, Pappalardo RR, Marcos ES (2013) J Chem Theory Comput 9:4562–4573PubMedGoogle Scholar
  83. 83.
    Burda JV, Sponer J, Leszczynski J (2000) J Biol Inorg Chem 5:178–188PubMedGoogle Scholar
  84. 84.
    Kozelka J, Chottard J-C (1990) Biophys Chem 35:165–178PubMedGoogle Scholar
  85. 85.
    Burda JV, Leszczynski J (2003) Inorg Chem 42:7162–7172PubMedGoogle Scholar
  86. 86.
    Spiegel K, Carloni P (2004) Abstr Pap Am Chem Soc 227:U1547–U1547Google Scholar
  87. 87.
    Zeizinger M, Burda JV, Leszczynski J (2004) Phys Chem Chem Phys 6:3585–3590Google Scholar
  88. 88.
    Deubel DV (2005) Abstr Pap Am Chem Soc 230:U2131–U2131Google Scholar
  89. 89.
    Raber J, Zhu C, Eriksson LA (2005) J Phys Chem B 109:11006–11015PubMedGoogle Scholar
  90. 90.
    Pavelka M, Burda JV (2007) J Mol Model 13:367–379PubMedGoogle Scholar
  91. 91.
    Gkionis K, Mutter ST, Platts JA (2013) RSC Adv 3:4066–4073.  https://doi.org/10.1039/C3RA23041D Google Scholar
  92. 92.
    Zhu M, Zhou L (2015) Comput Theor Chem 1051:24–34.  https://doi.org/10.1016/j.comptc.2014.10.036 Google Scholar
  93. 93.
    Ceron-Carrasco JP, Jacquemin D, Cauet E (2012) Phys Chem Chem Phys 14:12457–12464.  https://doi.org/10.1039/C2CP40515F PubMedGoogle Scholar
  94. 94.
    Deubel DV (2006) J Am Chem Soc 128:1654–1663PubMedGoogle Scholar
  95. 95.
    Froeling CDW, Sheldrick WS (1997) Chem Commun 1737–1738.  https://doi.org/10.1039/A702904G
  96. 96.
    Djuran MI, Dimitrijevic DP, Milinkovic SU, Bugarčic ŽD (2002) Transit Met Chem 27:151–158Google Scholar
  97. 97.
    Dos Santos HF, Paschoal D, Burda JV (2012) J Phys Chem A 116:11015–11024.  https://doi.org/10.1021/jp307977p PubMedGoogle Scholar
  98. 98.
    Dos Santos HF, Paschoal D, Burda JV (2012) Chem Phys Lett 548:64–70.  https://doi.org/10.1016/j.cplett.2012.07.080 Google Scholar
  99. 99.
    Bradáč O, Zimmermann T, Burda JV (2008) J Mol Model 14:705–716.  https://doi.org/10.1007/s00894-008-0285-0 PubMedGoogle Scholar
  100. 100.
    Futera Z, Platts JA, Burda JV (2012) J Comput Chem 33:2092–2101PubMedGoogle Scholar
  101. 101.
    Bancroft DP, Lepre CA, Lippard SJ (1990) J Am Chem Soc 112:6860–6871.  https://doi.org/10.1021/ja00175a020 Google Scholar
  102. 102.
    Kleine M, Wolters D, Sheldrick WS (2003) J Inorg Biochem 97:354–363PubMedGoogle Scholar
  103. 103.
    Barnham KJ, Djuran MJ, Murdoch PDS, Sadler PJ (1994) J Chem Soc Chem Commun.  https://doi.org/10.1039/C39940000721 Google Scholar
  104. 104.
    Djuran MI, Lempers ELM, Reedijk J (1991) Inorg Chem 30:2648–2652Google Scholar

Copyright information

© SBIC 2018

Authors and Affiliations

  • Michal Maixner
    • 1
  • Helio F. Dos Santos
    • 2
  • Jaroslav V. Burda
    • 1
  1. 1.Department of Chemical Physics and Optics, Faculty of Mathematics and PhysicsCharles UniversityPrague 2Czech Republic
  2. 2.NEQC: Núcleo de Estudos em Química Computacional, Departamento de Química-ICEUniversidade Federal e Juiz de ForaJuiz de ForaBrazil

Personalised recommendations