Prediction of the interaction of metallic moieties with proteins: An update for protein-ligand docking techniques

Journal of Computational Chemistry
Giuseppe SciortinoJean-Didier Maréchal

Abstract

In this article, we present a new approach to expand the range of application of protein-ligand docking methods in the prediction of the interaction of coordination complexes (i.e., metallodrugs, natural and artificial cofactors, etc.) with proteins. To do so, we assume that, from a pure computational point of view, hydrogen bond functions could be an adequate model for the coordination bonds as both share directionality and polarity aspects. In this model, docking of metalloligands can be performed without using any geometrical constraints or energy restraints. The hard work consists in generating the convenient atom types and scoring functions. To test this approach, we applied our model to 39 high-quality X-ray structures with transition and main group metal complexes bound via a unique coordination bond to a protein. This concept was implemented in the protein-ligand docking program GOLD. The results are in very good agreement with the experimental structures: the percentage for which the RMSD of the simulated pose is smaller than the X-ray spectra resolution is 92.3% and the mean value of RMSD is < 1.0 Å. Such results also show the viability of the method to predict metal complexes-proteins interactions when the X-ray stru...Continue Reading

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Citations

Feb 7, 2019·Metallomics : Integrated Biometal Science·Giuseppe SciortinoJean-Didier Maréchal
Apr 3, 2019·Future Medicinal Chemistry·Jacopo SgrignaniAlessandra Magistrato
Jun 13, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Chang WenJun Xu
May 22, 2020·Chemistry : a European Journal·Eugenio GarribbaJean-Didier Maréchal
Sep 15, 2020·Chemical Communications : Chem Comm·Giuseppe Sciortino, Eugenio Garribba
Jan 13, 2018·Dalton Transactions : an International Journal of Inorganic Chemistry·Daniele SannaEugenio Garribba
May 28, 2020·Frontiers in Chemistry·Giuseppe SciortinoEugenio Garribba
Dec 24, 2020·Expert Opinion on Drug Discovery·Julio Caballero
Jun 8, 2021·Physical Chemistry Chemical Physics : PCCP·Lorena Roldán-MartínJean-Didier Maréchal
Apr 3, 2020·Accounts of Chemical Research·Lur Alonso-CotchicoJean-Didier Maréchal
Dec 19, 2020·Journal of Chemical Information and Modeling·José-Emilio Sánchez-AparicioJean-Didier Maréchal
Apr 4, 2018·Inorganic Chemistry·Giuseppe SciortinoEugenio Garribba

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