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Study of the chelating properties of Ge(OH)2 functionality as metal binding group for Zn2+ cation in simplified protease-like environments: a DFT analysis

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Abstract

The development of protease’s inhibitors is an active field of research in the pharmaceutical industry. As concerns the design of new inhibitors, the theoretical study of the binding patterns and energies of known metal binding groups (MBGs) toward Zn 2+ using quantum-chemical calculations may offer a better understanding of their interaction models and may be useful for the improvement and design of novel ZBGs. Here the properties of gem-Ge(OH)2-based compounds as ZBG were assessed theoretically using DFT calculations. [Zn(Imdz)2 R − OH 2]2+ complexes (Imdz =imidazole rings; R = imidazole ring, acetic acid molecule or acetate anion) were used to partially reproduce the coordination sphere in metalloproteases (ACE, amgiotensin converting enzyme, and TLN, thermolysine) being inhibited by related compounds (i.e., silanediols). The MBG- Zn 2+ interaction was analyzed through the energy of the reaction: [Zn(Imdz)2 R − OH 2]2+ + L → [Zn(Imdz)2 R − L]2+ + H 2 O using DFT (M06L/cc-pVDZ) in gas-phase and in solution (IEF-PCM). Although the functional used (M06L) has proven its efficiency to study systems containing transition metal governed by non-covalent interactions, dispersion effects were implemented by the correction of the computed energies using the DFT-D3 program. Accounting for dispersion effects produced a systematic increase of c.a. 13 kJ mol−1 on the energies, whereas the effect of solvent goes in the opposite direction (i.e., BE under the IEF-PCM model are on average 125 kJ mol−1 lower). The Ge(OH) 2 - Zn 2+ interaction seems to be similar (or even stronger) than the Si(OH)2 -Zn 2+. Their better performance as ZBG is explained by the combined NBO-AIM analysis. The results of this work may encourage the preparation, isolation, and experimental assay of the chelating properties of these compounds, which may propose a new family of protease’s inhibitors.

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Acknowledgments

The authors thank Andalussian government for funding (FQM173). P.G.R.O. thanks Spanish Ministerio de Educación for a FPU Ph.D. studentship (AP2009-3949) supporting this work.

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Authors and Affiliations

  1. Physical and Analytical Chemistry Department, University of Jaén, Campus “Las Lagunillas”, Ed. B3, Jaén, 23071, Spain

    Pilar Gema Rodríguez Ortega, Manuel Montejo & Juan Jesús López González

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  1. Pilar Gema Rodríguez Ortega
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  2. Manuel Montejo
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  3. Juan Jesús López González
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Correspondence to Juan Jesús López González.

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This paper belongs to Topical Collection QUITEL 2013

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Ortega, P.G.R., Montejo, M. & González, J.J.L. Study of the chelating properties of Ge(OH)2 functionality as metal binding group for Zn2+ cation in simplified protease-like environments: a DFT analysis. J Mol Model 20, 2430 (2014). https://doi.org/10.1007/s00894-014-2430-2

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