New Insights on the Molecular Recognition of Imidacloprid with Aplysia californica AChBP: A Computational Study

• Published in: The journal of physical chemistry. B Vol. 117; no. 15; pp. 3944 - 3953
• Main Authors: Cerón-Carrasco, José P, Jacquemin, Denis, Graton, Jérôme, Thany, Steeve, Le Questel, Jean-Yves
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 18.04.2013
• Subjects: Amino acids; Animals; Aplysia; Binding; Binding Sites; Biological and medical sciences; Computer Simulation; Fundamental and applied biological sciences. Psychology; Hydroxyl groups; Imidacloprid; Imidazoles - chemistry; Insecticides; Life Sciences; Ligands; Mathematical models; Models, Biological; Models, Molecular; Molecular biophysics; Neonicotinoids; Nitro Compounds - chemistry; Receptors, Nicotinic - chemistry; Residues; Acetylcholine; Insecticide; Imidacloprid; Binding energy; Pesticides; nicotinic acetylcholine-receptor; noncovalent interaction regions; density functionals; docking programs; agonist binding; thermochemical kinetics; neonicotinoinsecticides; quantum-mechanics; diverse actions; hydrogen-bonds
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/jp310242n

The binding of imidacloprid (IMI), the forerunner of neonicotinoid insecticides, with the acetylcholine binding protein (AChBP) from Aplysia californica, the established model for the extracellular domain of insects nicotinic acetylcholine receptors, has been studied with a two-layer ONIOM partition approach (M06-2X/6-311G(d):PM6). Our calculations allow delineating the contributions of the key residues of AChBP for IMI binding. In particular, the importance of Trp147 and Cys190–191, through weak CH···π interactions and both van der Waals and hydrogen-bond (H-bond) interactions, respectively, are highlighted. Furthermore, H-bonds between hydroxyl groups of both Ser189 and Tyr55 and the IMI nitro group are pointed out. The participation of Ile118, whose main chain NH and carbonyl group are hydrogen-bonded with the IMI pyridinic nitrogen through a water molecule, is characterized. Our simulations also indicate the presence of a significant contribution of this residue through van der Waals interactions. The various trends obtained by the calculations of the pairwise interaction energies are confirmed through a complementary noncovalent interaction (NCI) analysis of selected IMI–AChBP amino acid pairs. Indeed, the contribution of a halogen-bond interaction between IMI and AChBP, recently proposed in the literature, is corroborated by our NCI analysis.