Molecular recognition of thiaclopride by Aplysia californica AChBP: new insights from a computational investigation | Journal of Computer-Aided Molecular Design
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Molecular recognition of thiaclopride by Aplysia californica AChBP: new insights from a computational investigation

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Abstract

The binding of thiaclopride (THI), a neonicotinoid insecticide, with Aplysia californica acetylcholine binding protein (Ac-AChBP), the surrogate of the extracellular domain of insects nicotinic acetylcholine receptors, has been studied with a QM/QM′ hybrid methodology using the ONIOM approach (M06-2X/6-311G(d):PM6). The contributions of Ac-AChBP key residues for THI binding are accurately quantified from a structural and energetic point of view. The importance of water mediated hydrogen-bond (H-bond) interactions involving two water molecules and Tyr55 and Ser189 residues in the vicinity of the THI nitrile group, is specially highlighted. A larger stabilization energy is obtained with the THI–Ac-AChBP complex compared to imidacloprid (IMI), the forerunner of neonicotinoid insecticides. Pairwise interaction energy calculations rationalize this result with, in particular, a significantly more important contribution of the pivotal aromatic residues Trp147 and Tyr188 with THI through CH···π/CH···O and π–π stacking interactions, respectively. These trends are confirmed through a complementary non-covalent interaction (NCI) analysis of selected THI–Ac-AChBP amino acid pairs.

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Acknowledgments

J.Y.L.Q. acknowledges the Région des Pays de la Loire for financial support in the framework of the ECRIN “Paris Scientifiques” Grant. This work was granted access to the HPC resources of [CCRT/CINES/IDRIS] under the allocation c2014085117 made by GENCI (Grand Equipement National de Calcul Intensif). The authors gratefully acknowledge the CCIPL (Centre de Calcul Intensif des Pays de la Loire) for grants of computer time.

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Author notes

  1. Balaji Selvam

    Present address: Roger Adams Laboratory, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL, 61801, USA

  2. José P. Cerón-Carrasco

    Present address: Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Science Department, Universidad Católica San Antonio de Murcia (UCAM), Campus de los Jerónimos, 30107, Murcia, Spain

Authors and Affiliations

  1. CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes, 2 rue de la Houssinière, BP 92208, Nantes, 44322, France

    Zakaria Alamiddine, Balaji Selvam, José P. Cerón-Carrasco, Monique Mathé-Allainmat, Jacques Lebreton, Adèle D. Laurent, Jérôme Graton & Jean-Yves Le Questel

  2. Laboratoire de Biologie des Ligneux et des Grandes Cultures, Université d’Orléans, UPRES EA 1207. Rue de Chartres, BP 6759, 45067, Orléans Cedex 2, France

    Steeve H. Thany

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  1. Zakaria Alamiddine
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Correspondence to Jean-Yves Le Questel.

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Alamiddine, Z., Selvam, B., Cerón-Carrasco, J.P. et al. Molecular recognition of thiaclopride by Aplysia californica AChBP: new insights from a computational investigation. J Comput Aided Mol Des 29, 1151–1167 (2015). https://doi.org/10.1007/s10822-015-9884-x

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