Binding of Sulfoxaflor to Aplysia californica-AChBP: Computational Insights from Multiscale Approaches.

Structural features and binding properties of sulfoxaflor (SFX) with Ac-AChBP, the surrogate of the insect nAChR ligand binding domain (LBD), are reported herein using various complementary molecular modeling approaches (QM, molecular docking, molecular dynamics, and QM/QM'). The different SFX stereoisomers show distinct behaviors in terms of binding and interactions with Ac-AChBP. Molecular docking and Molecular Dynamics (MD) simulations highlight the specific intermolecular contacts involved in the binding of the different SFX isomers and the relative contribution of the SFX functional groups. QM/QM' calculations provide further insights and a significant refinement of the geometric and energetic contributions of the various residues leading to a preference for the SS and RR stereoisomers. Notable differences in terms of binding interactions are pointed out for the four stereoisomers. The results point out the induced fit of the Ac-AChBP binding site according to the SFX stereoisomer. In this process, the water molecules-mediated contacts play a key role, their energetic contribution being among the most important for the various stereoisomers. In all cases, the interaction with Trp147 is the major binding component, through CH···π and π···π interactions. This study provides a rationale for the binding of SFX to insect nAChR, in particular with respect to the new class of sulfoximine-based insect nAChR competitive modulators, and points out the requirements of various levels of theory for an accurate description of ligand-receptor interactions.

Conformations and Binding Properties of Thiametoxam and Clothianidin Neonicotinoid Insecticides to Nicotinic Acetylcholine Receptors: The Contribution of σ-Hole Interactions.

The structural features and molecular-interaction properties of thiamethoxam (THA) and clothianidin (CLO) - two neonicotinoids - have been investigated through a combined approach based on a wide range of molecular modeling methods and X-ray-structure observations. Despite their close chemical structures, significant differences are emphasized by QM (DFT), docking, molecular dynamics, and QM/QM' calculations. Thus, for the first time, their propensity to interact through chalcogen-bond interactions is highlighted. The influence of the surroundings on this behavior is pointed out: in CLO, an intramolecular S⋅⋅⋅N chalcogen bond is shown to stabilize the structure in the solid state whereas the interaction leads to the preferred conformations in the isolated and continuum solvent models for both compounds. Interestingly, this interaction potential appears to be used for their binding to Ac-AChBP through intermolecular S⋅⋅⋅O chalcogen bonds with the hydroxyl group of Tyr195. The use of a suitable level of theory to describe properly these interactions is underlined, the classical methods being unsuited to highlight these interactions. The contribution of halogen bonding through the chlorine atom of the chlorothiazole ring in the binding of the two compounds is also underlined, both in the solid state and in the Ac-AChBP surroundings. However, the accommodation of the two insecticides in the binding site leads to the fact that a halogen-bond contribution is pointed out only for CLO.

Molecular recognition of thiaclopride by Aplysia californica AChBP: new insights from a computational investigation.

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.

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

Structural features and selected physicochemical properties of four common pesticides: acetamiprid (neonicotinoid), chlorpyriphos (organophosphate insecticide), deltamethrin (pyrethroid) and fipronil (phenylpyrazole) have been investigated by Density Functional Theory quantum chemical calculations. The high flexible character of these insecticides is revealed by the numerous conformers obtained, located within a 20kJmol(-1) range in the gas phase. In line with this trend, a redistribution of the energetic minima is observed in water medium. Molecular electrostatic potential calculations provide a ranking of the potential interaction sites of the four insecticides. The theoretical studies reported in the present work are completed by comparative toxicological assays against three aphid strains. Thus, the same toxicity order for the two susceptible strains Myzus persicae 4106A and Acyrthosiphon pisum LSR1: acetamiprid>fipronil>deltamethrin>chlorpyriphos is revealed. In the resistant strain M. persicae 1300145, the toxicity order is modified: acetamiprid>fipronil>chlorpyriphos>deltamethrin. Interestingly, the strain 1300145 which is known to be resistant to neonicotinoids, is also less sensitive to deltamethrin, chlorpyriphos and fipronil.

Imidacloprid and thiacloprid neonicotinoids bind more favourably to cockroach than to honeybee α6 nicotinic acetylcholine receptor: insights from computational studies.

The binding interactions of two neonicotinoids, imidacloprid (IMI) and thiacloprid (THI) with the extracellular domains of cockroach and honeybee α6 nicotinic acetylcholine receptor (nAChR) subunits in an homomeric receptor have been studied through docking and molecular dynamics (MD) simulations. The binding mode predicted for the two neonicotinoids is validated through the good agreement observed between the theoretical results with the crystal structures of the corresponding complexes with Ac-AChBP, the recognized structural surrogate for insects nAChR extracellular ligand binding domain. The binding site of the two insect α6 receptors differs by only one residue of loop D, a serine residue (Ser83) in cockroach being replaced by a lysine residue (Lys108) in honeybee. The docking results show very close interactions for the two neonicotinoids with both α6 nAChR models, in correspondence to the trends observed in the experimental neonicotinoid-Ac-AChBP complexes. However, the docking parameters (scores and energies) are not significantly different between the two insect α6 nAChRs to draw clear conclusions. The MD results bring distinct trends. The analysis of the average interaction energies in the two insects α6 nAChRs shows indeed better affinity of neonicotinoids bound to α6 cockroach compared to honeybee nAChR. This preference is explained by tighter contacts with aromatic residues (Trp and Tyr) of the binding pocket. Interestingly, the non-conserved residue Lys108 of loop D of α6 honeybee nAChR interacts through van der Waals contacts with neonicotinoids, which appear more favourable than the direct or water mediated hydrogen-bond interaction between the OH group of Ser83 of α6 cockroach nAChR and the electronegative terminal group of the two neonicotinoids (nitro in IMI and cyano in THI). Finally, in both insects nAChRs, THI is consistently found to bind more favourably than IMI.

Hyperconjugation in Carbocations, a BLW Study with DFT approximation.

The geometry of ethyl cation is discussed, and the hyperconjugation effect in carbocations is evaluated at the B3LYP/6-311G(d) level. The Block Localized Wavefunction (BLW) method is used for all evaluations of the hyperconjugation, considered as the energy gained by the delocalization onto the C(+) atom. This energy is defined as the energy difference between the delocalized (standard) calculation, where the electrons are freely delocalized, and a localized form where the positive charge sits on the carbon center. It is evaluated for 18 carbocations, including conjugated systems. In these cases we were particularly interested in the additional stabilization brought by hyperconjugative effects. Among other effects, the ß-silicon effect is computed. Hyperconjugation amounts in several cases to an energy similar to conjugation effects.