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Comprehensive understanding of multiple binding of D-penicillamine with Cu2+-hexa aqua complex: a DFT approach

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Abstract

The multiple-ligand-binding of D-penicillamine with [Cu(H2O)6]2+ has been explored computationally using density functional theory (DFT). Because of the implementation of bulk aqueous medium and considering the pH at physiological level, both neutral as well as de-protonated analogues of D-penicillamine are taken into account to study the binding phenomena with Cu2+. In doing so, at first, we have studied the binding of both neutral and de-protonated analogues of two D-penicillamine with Cu2+ in bi-dentate mode by replacing four molecules of H2O (di-amino complex) and afterward, the binding of three D-penicillamine with Cu2+ has been investigated by substituting all six molecules of H2O (tri-amino complex). Apart from bi-dentate binding, the de-protonated form of D-penicillamine can also bind in tri-dentate mode and in that case, all six H2O molecules are substituted during di-amino complex formation. Based on the coordinating modes of the artificial amino acids, for each di- and tri-amino complex, more than one isomer has been detected and the isomers are designated accordingly. By analyzing the optimized geometries, it is noticed that most of the di- and tri-amino complexes are distorted hexa-coordinated in nature and in few cases, they adopt penta-coordinated geometry. To analyze the stability of the complexes, we have determined the binding energy (BE) in both DCM and CDCM mechanisms for each di- and tri-amino complex. Overall, the present study is arranged in such a way so that it can provide a complete understanding about the binding process of the aforementioned artificial amino acid with Cu2+-aqua complex.

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References

  1. Osredkar J, Sustar N (2011) Copper and zinc, biological role and significance of copper/zinc imbalance. J Clinic Toxicol S3:001

    Google Scholar 

  2. Bertini I, Gray HB, Lippard SJ (1994) Valentine, J. S. Bioinorganic Chemistry; University Science Books: Sausalito, CA, pp 1−36

  3. Desai V, Kaler SG (2008) Role of copper in human neurological disorders. Am J Clin Nutr 88:855S–858S

    CAS  PubMed  Google Scholar 

  4. Sarkar B (1999) Treatment of Wilson and Menkes diseases. Chem Rev 99:2535–2544

    CAS  PubMed  Google Scholar 

  5. Zhang H, Wang Y, Zhao M, Wu J, Zhang X, Gui L, Zheng M, Li L, Liu J, Peng S (2012) Synthesis and in vivo lead detoxification evaluation of poly-α,β-dl-aspartyl-l-methionine. Chem Res Toxicol 25:471–477

    PubMed  Google Scholar 

  6. Peisach J, Blumberg WE (1969) A mechanism for the action of penicillamine in the treatment of Wilson’s disease. Mol Pharmacol 5:200–209

    CAS  PubMed  Google Scholar 

  7. Kandanapitiye MS, Gunathilake C, Jaroniec M, Huang SD (2015) Biocompatible D-penicillamine conjugated au nanoparticles: targeting intracellular free copper ions for detoxification. J Mater Chem B 3:5553–5559

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Scheinberg IH, Sternlieb I, Schilsky M, Stockert RJ (1987) Penicillamine may detoxify copper in Wilson’s disease. Lancet 330:95

    Google Scholar 

  9. Jalilehvand F, Leung BO, Mah V (2009) Cadmium(II) complex formation with cysteine and penicillamine. Inorg Chem 48:5758–5771

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Baidya N, Olmstead MM, Mascharak PK (1991) Structure and properties of bis(D-penicillaminato-N,S)nickelate(II) tetrahydrate: a monomeric nickel complex of D-penicillamine, the antidote for nickel toxicity. Inorg Chem 30:3967–3969

    CAS  Google Scholar 

  11. Sangvanich T, Morry J, Fox C, Ngamcherdtrakul W, Goodyear S, Castro D, Fryxell GE, Addleman RS, Summers AO, Yantasee W (2014) Novel oral detoxification of mercury, cadmium, and lead with thiol-modified nanoporous silica. ACS Appl Mater Interfaces 6:5483–5493

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Belcastro M, Marino T, Russo N, Sicilia E (2204) Structure and coordination modes in the interaction between Cd2+ and 3-mercaptopropionic acid. J Phys Chem A 108:8407–8410

    Google Scholar 

  13. Bagchi S, Mandal D, Ghosh D, Das AK (2013) Interaction between group IIb divalent transition-metal cations and 3-mercaptopropionic acid: a computational and topological perspective. J Phys Chem A 117:1601–1613

    CAS  PubMed  Google Scholar 

  14. Shen H, Chen J, Dai H, Wang L, Hu M, Xia Q (2013) New insights into the sorption and detoxification of chromium(VI) by tetraethylenepentamine functionalized nanosized magnetic polymer adsorbents: mechanism and pH effect. Ind Eng Chem Res 52:12723–12732

    CAS  Google Scholar 

  15. Pathak RK, Hinge VK, Mondal M, Rao CP (2011) Triazole-linked-thiophene conjugate of calix[4]arene: its selective recog-nition of Zn2+ and as biomimetic model in supporting the events of the metal detoxification and oxidative stress involving metal-lothionein. J Org Chem 76:10039–10049

    CAS  PubMed  Google Scholar 

  16. Wang GF, Ren XL, Zhao M, Qiu XL, Qi AD (2011) Paraquat detoxification with p-sulfonatocalix-[4]arene by a pharma-cokinetic study. J Agric Food Chem 59:4294–4299

    CAS  PubMed  Google Scholar 

  17. Šponer J, Burda JV, Sabat M, Leszczynski J, Hobza P (1998) Interaction between the guanine−cytosine Watson−Crick DNA base pair and hydrated group IIa (Mg2+, Ca2+, Sr2+, Ba2+) and group IIb (Zn2+, Cd2+, Hg2+) metal cations. J Phys Chem A 102:5951–5957

    Google Scholar 

  18. Šponer J, Sabat M, Burda JV, Leszczynski J, Hobza P (1999) Interaction of the adenine−thymine Watson−Crick and adenine−adenine reverse-Hoogsteen DNA base pairs with hydrated group IIa (Mg2+, Ca2+, Sr2+, Ba2+) and IIb (Zn2+, Cd2+, Hg2+) metal cations: absence of the base pair stabilization by metal-induced polarization effects. J Phys Chem B 103:2528–2534

    Google Scholar 

  19. Rulíšek L, Šponer J (2003) Outer-shell and inner-shell coordination of phosphate group to hydrated metal ions (Mg2+, Cu2+, Zn2+, Cd2+) in the presence and absence of nucleobase. The role of nonelectrostatic effects. J Phys Chem B 107:1913–1923

    Google Scholar 

  20. Rulíšek L, Havlas Z (2003) Theoretical studies of metal ion selectivity. 1. DFT calculations of interaction energies of amino acid side chains with selected transition metal ions (Co2+, Ni2+, Cu2+, Zn2+, Cd2+ and Hg2+). J Am Chem Soc 122:10428–10439

    Google Scholar 

  21. Rulíšek L, Havlas Z (2002) Theoretical studies of metal ion selectivity.† 2. DFT calculations of complexation energies of selected transition metal ions (Co2+, Ni2+, Cu2+, Zn2+, Cd2+, and Hg2+) in metal-binding sites of metalloproteins. J Phys Chem A 106:3855–3866

    Google Scholar 

  22. Rulíšek L, Havlas Z (2003) Theoretical studies of metal ion selectivity. 3. A theoretical design of the most specific combinations of functional groups representing amino acid side chains for the selected metal ions (Co2+, Ni2+, Cu2+, Zn2+, Cd2+, and Hg2+)†. J Phys Chem B 107:2376–2385

    Google Scholar 

  23. Marino T, Toscano M, Russo N, Grand A (2006) Structural and electronic characterization of the complexes obtained by the interaction between bare and hydrated first-row transition-metal ions (Mn2+, Fe2+, Co2+, Ni2+, Cu2+, Zn2+) and glycine. J Phys Chem B 110:24666–24673

    CAS  PubMed  Google Scholar 

  24. Marino T, Russo N, Toscano M (2001) Potential energy surfaces for the gas-phase interaction between α-alanine and alkali metal ions (Li+, Na+, K+). a density functional study. Inorg Chem 40:6439–6443

    CAS  PubMed  Google Scholar 

  25. Hoyau S, Ohanessian G (1997) Absolute affinities of α-amino acids for cu+ in the gas phase. A theoretical study. J Am Chem Soc 119:2016–2024

    CAS  Google Scholar 

  26. Bertrán J, Rodríguez-Santiago L, Sodupe M (1999) The different nature of bonding in Cu+-glycine and Cu2+-glycine. J Phys Chem B 103:2310–2317

    Google Scholar 

  27. Spezia R, Tournois G, Cartailler T, Tortajada J, Jeanvoine Y (2006) Co2+ binding cysteine and selenocysteine: a DFT study. J Phys Chem A 110:9727–9735

    CAS  PubMed  Google Scholar 

  28. Leung BO, Jalilehvand F, Mah V, Parvez M, Wu Q (2013) Silver(I) complex formation with cysteine, penicillamine, and glutathione. Inorg Chem 52:4593–4602

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Ash T, Debnath T, Banu T, Das AK (2016) Exploration of binding interactions of Cu2+ with D-penicillamine and its O- and se- analogues in both gas and aqueous phases: a theoretical approach. J Phys Chem B 120:3467–3478

    CAS  PubMed  Google Scholar 

  30. Pesonen H, Aksela R, Laasonen K (2010) Density functional complexation study of metal ions with cysteine. J Phys Chem A 114:466–473

    CAS  PubMed  Google Scholar 

  31. Sisombath NS, Jalilehvand F, Schell AC, Wu Q (2014) Lead(II) binding to the chelating agent D-penicillamine in aqueous solution. Inorg Chem 53:12459–12468

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Jalilehvand F, Sisombath NS, Schell AC, Facey GA (2015) Lead(II) complex formation with L-cysteine in aqueous solution. Inorg Chem 54:2160–2170

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Martínez A, Vargas R, Galano A (2018) How to identify promising metal scavengers? D-penicillamine with copper as a study case. Int J Quantum Chem 118:e25457

    Google Scholar 

  34. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery Jr JA, Peralta JE, Ogliaro F, Bearpark MJ, Heyd J, Brothers EN, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell AP, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam NJ, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas Ö, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2013) Gaussian 09, Revision D.01, Gaussian, Inc., Wallingford, CT, USA

  35. Zhao Y, Truhlar D (2008) The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, non-covalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other Functionals. Theor Chem Accounts 120:215

    CAS  Google Scholar 

  36. Zhao Y, Truhlar D (2006) A new local density functional for main-group thermochemistry, transition metal bonding, thermochemical kinetics, and noncovalent interactions. J Chem Phys 125:194101–194118

    PubMed  Google Scholar 

  37. Hay PJ, Wadt WR (1985) Ab initio effective core potentials for molecular calculations. Potentials for the transition metal atoms Sc to Hg. J Chem Phys 82:270–283

    CAS  Google Scholar 

  38. Hay PJ, Wadt WR (1985) Ab initio effective core potentials for molecular calculations. Potentials for K to Au including the outermost core orbitals. J Chem Phys 82:299–310

    CAS  Google Scholar 

  39. Hay PJ, Wadt WR (1985) Ab initio effective core potentials for molecular calculations. Potentials for main group elements Na to Bi. J Chem Phys 82:284–298

    Google Scholar 

  40. Klamt A, Schuurmann G (1993) COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. J Chem Soc Perkin Trans 2(2):799–805

    Google Scholar 

  41. Galano A (2016) Computational-aided design of melatonin analogues with outstanding multifunctional antioxidant capacity. RSC Adv 6:22951–22963

    CAS  Google Scholar 

  42. Francisco-Marquez M, Aguilar-Fernandez M, Galano A (2016) Anthranilic acid as a secondary antioxidant: Implications to the inhibition of .OH production and the associated oxidative stress Comput. Theor. Chem. 2016 1077:18–24

  43. Alvarez-Diduk R (2015) Galano a (2015) adrenaline and noradrenaline: protectors against oxidative stress or molecular targets? J Phys Chem B 119:3479–3491

    CAS  PubMed  Google Scholar 

  44. Leon-Carmona JR, Galano A (2012) Free radical scavenging activity of caffeine’s metabolites. Int J Quantum Chem 112:3472–3478

    CAS  Google Scholar 

  45. Galano A, Medina ME, Tan DX, Reiter RJ (2015) Melatonin and its metabolites as copper chelating agents and their role in inhibiting oxidative stress: a physicochemical analysis. J Pineal Res 58:107–116

    CAS  PubMed  Google Scholar 

  46. Alvarez-Diduk R, Galano A, Tan DX, Reiter RJ (2015) N-Acetylserotonin and 6-hydroxymelatonin against oxidative stress: implications for the overall protection exerted by melatonin. J Phys Chem B 119:8535–8543

    CAS  PubMed  Google Scholar 

  47. Camaioni M, Schwerdtfeger CA (2005) Comment on “accurate experimental values for the free energies of hydration of H+, OH−, and H3O+”. J Phys Chem A 109:10795–10797

    CAS  PubMed  Google Scholar 

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Acknowledgments

TA and TD are thankful to Indian Association for the Cultivation of Science and AG is thankful to UGC for providing them research fellowships.

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  1. School of Mathematical and Computational Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700032, India

    Tamalika Ash, Tanay Debnath, Avik Ghosh & Abhijit Kr. Das

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  1. Tamalika Ash
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Correspondence to Abhijit Kr. Das.

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Ash, T., Debnath, T., Ghosh, A. et al. Comprehensive understanding of multiple binding of D-penicillamine with Cu2+-hexa aqua complex: a DFT approach. Struct Chem 31, 155–169 (2020). https://doi.org/10.1007/s11224-019-01365-2

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