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

Abstract

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.

Molecular features and toxicological properties of four common pesticides, acetamiprid, deltamethrin, chlorpyriphos and fipronil

“…This behaviour has indeed been suggested by recent theoretical studies in the case of neonicotinoids 11,54 and reviewed in protein-halocarbon complexes through careful surveys of PDB crystallographic data. 55,56 Much more than for the minimum electrostatic potential, it appears that the conformational effect is very important in ACE on the maximum electrostatic potential (almost 50%), and presumably, on the halogen-bond ability of the chlorine atom.…”

“…9 In this context, quantum chemical studies, structural bioinformatics and molecular modelling methodologies (docking, 3D-QSAR, molecular dynamic simulations) have appeared as promising and complementary tools. The first allows quantifying accurately relevant properties of insecticides, [10][11][12][13] the second gives the possibility of building the protein targets through homology modelling and the last provides detailed (static or dynamic) pictures of the insecticides-receptor interactions. [14][15][16] In this paper, we investigate, through Density Functional Theory calculations, the structural features and some physicochemical properties of four common pesticides belonging to different chemical classes, namely acetamiprid (ACE, neonicotinoid), chlorpyriphos (CHL, organophosphate), deltamethrin (DEL, pyrethroid) and fipronil (FIP, phenylpyrazole) ( Figure 1).…”

Fmoc–RGDS based fibrils: atomistic details of their hierarchical assembly

“…Within this context, first principle theoretical studies through sophisticated quantum mechanical (QM) calculations are known to be useful tools for quantifying both intramolecular and intermolecular interactions that govern sensor···analyte binding. [20][21][22][23][24][25][26][27][28][29] Indeed, such methods provide accurate molecular geometries, give access to the conformational energetic and are able to delineate the sensor···analyte interactions pattern. Indeed, our QM investigations on complexes formed by model EPs and different types of analytes (e.g.…”

Conformation preference and related intramolecular noncovalent interaction of selected short chain chlorinated paraffins

“…Dessent et al [39] have successfully used M06-2X for calculating the conformationally flexible anionic clusters with dispersion and ionic hydrogen-bonding interactions. Moreover, M06-2X was even utilized to explore the molecular recognition of imidacloprid with Aplysia californica AChBP as well as the NCIs in the system [40]. (∆E 0 ) corrected with the zero-point vibrational energy at 0 K, relative enthalpy (∆H), relative Gibbs free energy (∆G) at 298.15 K and the dihedral angles ( 1 ,  2 ,  3 and  4 ) of the distinct conformers of the two model molecules.…”