Development of CHARMM compatible force field parameters and molecular dynamics simulations for the pesticide flupyradifurone.

Flupyradifurone (FLU) is a novel butenolide insecticide with partial agonist activity for insect nicotinic acetylcholine receptors. Its safety for non-target organisms has been questioned in the literature, despite initial claims of its harmlessness. Detailed understanding of its toxicity and related molecular mechanisms remain under discussion. Thus, in this work, an optimized set of CHARMM compatible parameters for FLU is presented. CHARMM General Force Field program was used as a starting point while the non-bonded and bonded parameters were adjusted and optimized to reproduce MP2/6-31G(d) accuracy level results. For the validity assessment of these parameters, infrared spectrum, water-octanol partition coefficient, and normal modes were computed and compared to experimental values found in the literature. Several MD simulations of FLU in water and FLU in complex with an acetylcholine-binding protein were performed to estimate the ability of the optimized parameters to correctly describe its torsional space and reproduce observed crystallographic trends respectively.

Navigating the complexities of docking tools with nicotinic receptors and acetylcholine binding proteins in the realm of neonicotinoids.

Molecular docking, pivotal in predicting small-molecule ligand binding modes, struggles with accurately identifying binding conformations and affinities. This is particularly true for neonicotinoids, insecticides whose impacts on ecosystems require precise molecular interaction modeling. This study scrutinizes the effectiveness of prominent docking software (Ledock, ADFR, Autodock Vina, CDOCKER) in simulating interactions of environmental chemicals, especially neonicotinoid-like molecules with nicotinic acetylcholine receptors (nAChRs) and acetylcholine binding proteins (AChBPs). We aimed to assess the accuracy and reliability of these tools in reproducing crystallographic data, focusing on semi-flexible and flexible docking approaches. Our analysis identified Ledock as the most accurate in semi-flexible docking, while Autodock Vina with Vinardo scoring function proved most reliable. However, no software consistently excelled in both accuracy and reliability. Additionally, our evaluation revealed that none of the tools could establish a clear correlation between docking scores and experimental dissociation constants (Kd) for neonicotinoid-like compounds. In contrast, a strong correlation was found with drug-like compounds, bringing to light a bias in considered software towards pharmaceuticals, thus limiting their applicability to environmental chemicals. The comparison between semi-flexible and flexible docking revealed that the increased computational complexity of the latter did not result in enhanced accuracy. In fact, the higher computational cost of flexible docking with its lack of enhanced predictive accuracy, rendered this approach useless for this class of compounds. Conclusively, our findings emphasize the need for continued development of docking methodologies, particularly for environmental chemicals. This study not only illuminates current software capabilities but also underscores the urgency for advancements in computational molecular docking as it is a relevant tool to environmental sciences.

Identification of a Gain-of-Function LIPC Variant as a Novel Cause of Familial Combined Hypocholesterolemia.

BACKGROUND: Atherosclerotic cardiovascular disease is the main cause of mortality worldwide and is strongly influenced by circulating low-density lipoprotein (LDL) cholesterol levels. Only a few genes causally related to plasma LDL cholesterol levels have been identified so far, and only 1 gene, ANGPTL3, has been causally related to combined hypocholesterolemia. Here, our aim was to elucidate the genetic origin of an unexplained combined hypocholesterolemia inherited in 4 generations of a French family. METHODS: Using next-generation sequencing, we identified a novel dominant rare variant in the LIPC gene, encoding for hepatic lipase, which cosegregates with the phenotype. We characterized the impact of this LIPC-E97G variant on circulating lipid and lipoprotein levels in family members using nuclear magnetic resonance-based lipoprotein profiling and lipidomics. To uncover the mechanisms underlying the combined hypocholesterolemia, we used protein homology modeling, measured triglyceride lipase and phospholipase activities in cell culture, and studied the phenotype of APOE*3.Leiden.CETP mice after LIPC-E97G overexpression. RESULTS: Family members carrying the LIPC-E97G variant had very low circulating levels of LDL cholesterol and high-density lipoprotein cholesterol, LDL particle numbers, and phospholipids. The lysophospholipids/phospholipids ratio was increased in plasma of LIPC-E97G carriers, suggestive of an increased lipolytic activity on phospholipids. In vitro and in vivo studies confirmed that the LIPC-E97G variant specifically increases the phospholipase activity of hepatic lipase through modification of an evolutionarily conserved motif that determines substrate access to the hepatic lipase catalytic site. Mice overexpressing human LIPC-E97G recapitulated the combined hypocholesterolemic phenotype of the family and demonstrated that the increased phospholipase activity promotes catabolism of triglyceride-rich lipoproteins by different extrahepatic tissues but not the liver. CONCLUSIONS: We identified and characterized a novel rare variant in the LIPC gene in a family who presents with dominant familial combined hypocholesterolemia. This gain-of-function variant makes LIPC the second identified gene, after ANGPTL3, causally involved in familial combined hypocholesterolemia. Our mechanistic data highlight the critical role of hepatic lipase phospholipase activity in LDL cholesterol homeostasis and suggest a new LDL clearance mechanism.

Identification of sulfonamide compounds active on the insect nervous system: Molecular modeling, synthesis and biological evaluation.

Insect nicotinic acetylcholine receptors (nAChRs) are a recognized target for insecticide design. In this work, we have identified, from a structure-based approach using molecular modeling tools, ligands with potential selective activity for pests versus pollinators. A high-throughput virtual screening with the Openeye software was performed using a library from the ZINC database, thiacloprid being used as the target structure. The top sixteen molecules were then docked in α6 cockroach and honeybee homomeric nAChRs to check from a theoretical point of view relevant descriptors in favor of pest selectivity. Among the selected molecules, one original sulfonamide compound has afterward been synthesized, together with various analogs. Two compounds of this family have been shown to behave as activators of the cockroach cholinergic synaptic transmission.

Conformations and Physicochemical Properties of Biological Ligands in Various Environments.

An accurate description of the conformational behavior of drug-like molecules is often a prerequisite for a comprehensive understanding of their behavior, in particular in the targeted receptor surroundings [...].

The pKBHX Hydrogen-Bond Basicity Scale: From Molecules to Anions.

The pKBHX (logarithm of complexation constant K of 4-fluorophenol with bases) hydrogen-bond basicity scale of neutral hydrogen-bond acceptors (HBAs) is extended to anionic HBAs. The scale is constructed for 26 anions through (i) the infrared measurement of K on NBu4+X- ion pairs in CCl4, (ii) the estimation of K from linear free energy relationships between measured K values and literature K values for various phenols in polar solvents, and (iii) the computation of K at the density functional theory level in CCl4. The scale extends on a 9.4 pK unit range from fluoride to tetraphenylborate. Considering a number of anions as organic functions substituted with unipolar substituents, their pKBHX values can be related to the Hammett-Taft substituent constants σ. Unipolar substituents (O- and S-) obey the same pKBHX versus σ relationships as dipolar ionic (N-N+R3) and dipolar (OH, CF3, NR2, or OR) ones for the nitrile, carbonyl, nitroso, nitro, sulfonyl, and phosphoryl functions. Like dipolar substituents, unipolar substituents at carbon and nitrogen operate by field-inductive and resonance effects, whereas substituents at sulfur and phosphorus operate only by the field-inductive effect.

Relating Conformational Equilibria to Conformer-Specific Lipophilicities: New Opportunities in Drug Discovery.

Efficient drug discovery is based on a concerted effort in optimizing bioactivity and compound properties such as lipophilicity, and is guided by efficiency metrics that reflect both aspects. While conformation-activity relationships and ligand conformational control are known strategies to improve bioactivity, the use of conformer-specific lipophilicities (logp) is much less explored. Here we show how conformer-specific logp values can be obtained from knowledge of the macroscopic logP value, and of the equilibrium constants between the individual species in water and in octanol. This is illustrated with fluorinated amide rotamers, with integration of rotamer 19 F NMR signals as a facile, direct method to obtain logp values. The difference between logp and logP optimization is highlighted, giving rise to a novel avenue for lipophilicity control in drug discovery.

IL-15Rα membrane anchorage in either cis or trans is required for stabilization of IL-15 and optimal signaling.

Interleukin (IL)-15 plays an important role in the communication between immune cells. It delivers its signal through different modes involving three receptor chains: IL-15Rα, IL-2Rß and IL-2Rγc. The combination of the different chains result in the formation of IL-15Rα/IL-2Rß/γc trimeric or IL-2Rß/γc dimeric receptors. In this study, we have investigated the role of the IL-15Rα chain in stabilizing the cytokine in the IL-2Rß/γc dimeric receptor. By analyzing the key amino acid residues of IL-15 facing IL-2Rß, we provide evidence of differential interfaces in the presence or in the absence of membrane-anchored IL-15Rα. Moreover, we found that the anchorage of IL-15Rα to the cell surface regardless its mode of presentation - i.e. cis or trans - is crucial for complete signaling. These observations show how the cells can finely modulate the intensity of cytokine signaling through the quality and the level of expression of the receptor chains.

Mode of Action of Neonicotinoid Insecticides Imidacloprid and Thiacloprid to the Cockroach Pameα7 Nicotinic Acetylcholine Receptor.

The functional expression of the cockroach Pameα7 nicotinic acetylcholine receptor subunit has been previously studied, and was found to be able to form a homomeric receptor when expressed in Xenopus laevis oocytes. In this study, we found that the neonicotinoid insecticide imidacloprid is unable to activate the cockroach Pameα7 receptor, although thiacloprid induces low inward currents, suggesting that it is a partial agonist. In addition, the co-application or 5 min pretreatment with 10 µM imidacloprid increased nicotine current amplitudes, while the co-application or 5 min pretreatment with 10 µM thiacloprid decreased nicotine-evoked current amplitudes by 54% and 28%, respectively. This suggesting that these two representatives of neonicotinoid insecticides bind differently to the cockroach Pameα7 receptor. Interestingly, the docking models demonstrate that the orientation and interactions of the two insecticides in the cockroach Pameα7 nAChR binding pocket are very similar. Electrophysiological results have provided evidence to suggest that imidacloprid and thiacloprid could act as modulators of the cockroach Pameα7 receptors.

Astatine Facing Janus: Halogen Bonding vs. Charge-Shift Bonding.

The nature of halogen-bond interactions was scrutinized from the perspective of astatine, potentially the strongest halogen-bond donor atom. In addition to its remarkable electronic properties (e.g., its higher aromaticity compared to benzene), C6At6 can be involved as a halogen-bond donor and acceptor. Two-component relativistic calculations and quantum chemical topology analyses were performed on C6At6 and its complexes as well as on their iodinated analogues for comparative purposes. The relativistic spin-orbit interaction was used as a tool to disclose the bonding patterns and the mechanisms that contribute to halogen-bond interactions. Despite the stronger polarizability of astatine, halogen bonds formed by C6At6 can be comparable or weaker than those of C6I6. This unexpected finding comes from the charge-shift bonding character of the C-At bonds. Because charge-shift bonding is connected to the Pauli repulsion between the bonding σ electrons and the σ lone-pair of astatine, it weakens the astatine electrophilicity at its σ-hole (reducing the charge transfer contribution to halogen bonding). These two antinomic characters, charge-shift bonding and halogen bonding, can result in weaker At-mediated interactions than their iodinated counterparts.

Characterization of Steroids through Collision Cross Sections: Contribution of Quantum Chemistry Calculations.

A wide range of collision cross section (CCS) databases for different families of compounds have recently been established from ion mobility mass spectrometry (IM-MS) measurements. Nevertheless, the need to validate these new data sets to provide the necessary confidence about the use of this parameter is increasingly expressed by the scientific community. If such a validation requires that complementary mass spectrometry experiments are conducted, it also appears that alternative strategies can contribute to the validation of such empirical data. In particular, in silico approaches are relevant to compute theoretical CCS values, to be compared to experimental ones. A recently published CCS database for 300 steroids allowed one to observe experimentally significant deviations of the expected CCS versus m/z correlations for some compounds. The present work attempts to rationalize such deviations with Density Functional Theory (DFT) calculations. MN15/6-311++G(d,p) investigations have been carried out, starting with a conformational analysis of a sample of 20 selected steroids and the determination of their preferred gas-phase ionization site. CCS values were then computed and compared to the experimental data. This approach allowed one to rationalize the experimental trends, providing an accurate description of the key properties of the various steroids considered.

Synergic effect of a quinuclidine benzamide complexed with borane, the LMA10233, in combination with seven pesticides.

Some quinuclidine benzamide compounds have been found to modulate nicotinic acetylcholine receptors in both mammals and insects. In particular, the quaternarization of 3-amino quinuclidine benzamide derivatives with dichloromethane gave charged N-chloromethylated quinuclidine compounds, disclosing an antagonist profile on homomeric α7 nAChRs. Here, we synthesized and studied the toxicological effect of LMA10233, a quinuclidine-borane complex analogue, the LMA10233, on the pea aphid Acyrthosiphon pisum and found that LMA10233 only exhibit proper toxicity on A. pisum larvae when applied in concentrations of over 10 µg/ml. We assessed the ability of LMA10233 to enhance the toxicity of different insecticides. When a sublethal concentration of LMA10233 was combined with the LC10 of each compound, we found a strong increase in toxicity at 24 h and 48 h of exposure for clothianidin, fipronil and chlorpyrifos, and only at 24 h for imidacloprid, acetamiprid and deltamethrin. However, when the pesticide was used at the LC50, only acetamiprid showed a synergistic effect with LMA10233. When the concentration of LMA10233 was decreased, we found that up to 80-90% of mortality was obtained due to the synergism between acetamiprid and LMA10233. No similar effect was observed with other insecticides. We conclude that such quinuclidine-borane complex compounds could increase the toxic effect of insecticides at low concentrations.

Lipophilicity trends upon fluorination of isopropyl, cyclopropyl and 3-oxetanyl groups.

A systematic comparison of lipophilicity modulations upon fluorination of isopropyl, cyclopropyl and 3-oxetanyl substituents, at a single carbon atom, is provided using directly comparable, and easily accessible model compounds. In addition, comparison with relevant linear chain derivatives is provided, as well as lipophilicity changes occurring upon chain extension of acyclic precursors to give cyclopropyl containing compounds. For the compounds investigated, fluorination of the isopropyl substituent led to larger lipophilicity modulation compared to fluorination of the cyclopropyl substituent.

Synthesis of 2,3,4-Trideoxy-2,3,4-trifluoroglucose.

There is an increasing interest in investigating how polyfluorination of carbohydrates modifies their physical and biological properties. An example that has caught much attention is 2,3,4-trideoxy-2,3,4-trifluoroglucose. Four syntheses of this compound have been reported, which are either low yielding or long (13 or more steps). We report a 6-step synthesis of 2,3,4-trideoxy-2,3,4-trifluoroglucose starting from levoglucosan. The solution-phase structure of an intermediate, 1,6-anhydro-2,4-dideoxy-2,4-difluoroallose, features a rare example of a bifurcated F···H(O)···F hydrogen bond and is compared to its crystal structure.

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.

Di- and heptavalent nicotinic analogues to interfere with α7 nicotinic acetylcholine receptors.

In the field of nicotinic acetylcholine receptors (nAChRs), recognized as important therapeutic targets, much effort has been dedicated to the development of nicotinic analogues to agonize or antagonize distinct homo- and heteropentamers nAChR subtypes, selectively. In this work we developed di- and heptavalent nicotinic derivatives based on ethylene glycol (EG) and cyclodextrin cores, respectively. The compounds showed a concentration dependent inhibition of acetylcholine-induced currents on α7 nAChR expressed by Xenopus oocytes. Interesting features were observed with the divalent nicotinic derivatives, acting as antagonists with varied inhibitory concentrations (IC50) in function of the spacer arm length. The best divalent compounds showed a 16-fold lowered IC50 compared to the monovalent reference (12 vs 195 µM). Docking investigations provide guidelines to rationalize these experimental findings.

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.

Spin-orbit coupling as a probe to decipher halogen bonding.

The nature of halogen-bond interactions is scrutinized from the perspective of astatine, the heaviest halogen element. Potentially the strongest halogen-bond donor, its ability is shown to be deeply affected by relativistic effects and especially by the spin-orbit coupling. Complexes between a series of XY dihalogens (X, Y = At, I, Br, Cl and F) and ammonia are studied with two-component relativistic quantum calculations, revealing that the spin-orbit interaction leads to a weaker halogen-bond donating ability of the diastatine species with respect to diiodine. In addition, the donating ability of the lighter halogen elements, iodine and bromine, in the AtI and AtBr species is more decreased by the spin-orbit coupling than that of astatine. This can only be rationalized from the evolution of a charge-transfer descriptor, the local electrophilicity ω+S,max, determined for the pre-reactive XY species. Finally, the investigation of the spin-orbit coupling effects by means of quantum chemical topology methods allows us to unveil the connection between the astatine propensity to form charge-shift bonds and the astatine ability to engage in halogen bonds.

Influence of Alcohol ß-Fluorination on Hydrogen-Bond Acidity of Conformationally Flexible Substrates.

Rational modulations of molecular interactions are of significant importance in compound properties optimization. We have previously shown that fluorination of conformationally rigid cyclohexanols leads to attenuation of their hydrogen-bond (H-bond) donating capacity (designated by pKAHY ) when OH⋅⋅⋅F intramolecular hydrogen-bond (IMHB) interactions occur, as opposed to an increase in pKAHY due to the fluorine electronegativity. This work has now been extended to a wider range of aliphatic ß-fluorohydrins with increasing degrees of conformational flexibility. We show that the observed differences in pKAHY between closely related diastereomers can be fully rationalized by subtle variations in populations of conformers able to engage in OH⋅⋅⋅F IMHB, as well as by the strength of these IMHBs. We also show that the Kenny theoretical Vα (r) descriptor of H-bond acidity accurately reflects the observed variations and a calibration equation extended to fluorohydrins is proposed. This work clearly underlines the importance of the weak OH⋅⋅⋅F IMHB in the modulation of alcohol H-bond donating capacity.

A Study of Intramolecular Hydrogen Bonding in Levoglucosan Derivatives.

Organofluorine is a weak hydrogen-bond (HB) acceptor. Bernet et al. have demonstrated its capability to perturb OH···O intramolecular hydrogen bonds (IMHBs), using conformationally rigid carbohydrate scaffolds including levoglucosan derivatives. These investigations are supplemented here by experimental and theoretical studies involving six new levoglucosan derivatives, and complement the findings of Bernet et al. However, it is shown that conformational analysis is instrumental in interpreting the experimental data, due to the occurrence of non-intramolecular hydrogen-bonded populations which, although minor, cannot be neglected and appears surprisingly significant. The DFT conformational analysis, together with the computation of NMR parameters (coupling constants and chemical shifts) and wavefunction analyses (AIM, NBO), provides a full picture. Thus, for all compounds, the most stabilized structures show the OH groups in a conformation allowing IMHB with O5 and O6, when possible. Furthermore, the combined approach points out the occurrence of various IMHBs and the effect of the chemical modulations on their features. Thus, two-center or three-center IMHB interactions are observed in these compounds, depending on the presence or absence of additional HB acceptors, such as methoxy or fluorine.