Synthesis and insecticidal activity of N-(5-phenylpyrazin-2-yl)-benzamide derivatives: Elucidation of mode of action on chitin biosynthesis through symptomology and genetic studies.

Among the six-membered heterocycles, the pyrazine ring is poorly explored in crop protection and does not feature in any product listed in the current IRAC MoA classification. In an effort to identify new leads for internal research, we synthesized a series of N-(5-phenylpyrazin-2-yl)-benzamide derivatives and evaluated them for their insecticidal activity. N-(5-phenylpyrazin-2-yl)-benzamide derivatives 3 were prepared using an automated two-step synthesis protocol. These compounds were tested for their initial biological activity against a wide range of sucking and chewing insect pests and found to be active against lepidopterans only. More detailed experiments, including symptomology studies on the diamondback moth, Plutella xylostella (L.) and the Egyptian cotton leafworm, Spodoptera littoralis (Boisduval) showed that analog 3q causes severe abnormalities in the lepidopteran cuticle leading to larval mortality. Compound 3q shows strong potency against both P. xylostella and S. littoralis, whereas analog 3i shows better potency against S. littoralis causing also impaired cuticular structure and death of the larvae. Additionally, P. xylostella genetic studies showed that compound 3q resistance is linked to Chitin Synthase 1. Our studies show that N-(5-phenylpyrazin-2-yl)-benzamide derivatives 3, and in particular analogs 3i and 3q, act as insect growth modulator insecticides. Conformational similarities with lufenuron are discussed.

Structural Biology-Guided Design, Synthesis, and Biological Evaluation of Novel Insect Nicotinic Acetylcholine Receptor Orthosteric Modulators.

The development of novel and safe insecticides remains an important need for a growing world population to protect crops and animal and human health. New chemotypes modulating the insect nicotinic acetylcholine receptors have been recently brought to the agricultural market, yet with limited understanding of their molecular interactions at their target receptor. Herein, we disclose the first crystal structures of these insecticides, namely, sulfoxaflor, flupyradifurone, triflumezopyrim, flupyrimin, and the experimental compound, dicloromezotiaz, in a double-mutated acetylcholine-binding protein which mimics the insect-ion-channel orthosteric site. Enabled by these findings, we discovered novel pharmacophores with a related mode of action, and we describe herein their design, synthesis, and biological evaluation.

Molecular Dynamics Simulations of p97 Including Covalent, Allosteric and ATP-competitive Inhibitors.

Binary (nucleotide-protein dimer and hexamer complexes) and ternary (nucleotide-protein-inhibitor complexes) p97 complexes were subjected to molecular dynamics simulations in an attempt to further our understanding of the p97 protein oligomer domain stability and, more importantly, of the recently reported diverse molecular mechanisms of inhibition including allosteric, ATP-competitive and covalent inhibitors. Analysis of stable states following equilibration phases indicated a higher intrinsic stability of the homohexamer as opposed to the dimer, and of N-D1 domains as opposed to the D2 domain. The molecular dynamics of the proposed allosteric binding model reproduced important molecular interactions identified experimentally with high frequency throughout the trajectory. Observed conformational changes occurring in the D2 nucleotide binding site provided a novel bind-rearrange-react hypothesis of stepwise molecular events involved in the specific covalent inhibitor mode of action.

Strigolactone derivatives for potential crop enhancement applications.

New technologies able to mitigate the main abiotic stresses (i.e., drought, salinity, cold and heat) represent a substantial opportunity to contribute to a sustainable increase of agricultural production. In this context, the recently discovered phytohormone strigolactone is an important area of study which can underpin the quest for new anti-stress technologies. The pleiotropic roles played by strigolactones in plant growth/development and in plant adaptation to environmental changes can pave the way for new innovative crop enhancement applications. Although a significant scientific effort has been dedicated to the strigolactone subject, an updated review with emphasis on the crop protection perspective was missing. This paper aims to analyze the advancement in different areas of the strigolactone domain and the implications for agronomical applications.

Simplified strigolactams as potent analogues of strigolactones for the seed germination induction of Orobanche cumana Wallr.

BACKGROUND: Strigolactones play an important role in the rhizosphere as signalling molecules stimulating the seed germination of parasitic weed seeds and hyphal branching of arbuscular micorrhiza, and also act as hormones in plant roots and shoots. Strigolactone derivatives, e.g. strigolactams, could be used as suicidal germination inducers in the absence of a host crop for the decontamination of land infested with parasitic weed seeds. RESULTS: We report the stereoselective synthesis of novel strigolactams, together with some of their critical physicochemical properties, such as water solubility, hydrolytic stability, as well as their short soil persistence. In addition, we show that such strigolactams are potent germination stimulants of O. cumana parasitic weed seeds and do not affect the seed germination and the root growth of sunflower. CONCLUSIONS: The novel strigolactam derivatives described here compare favourably with the corresponding GR-28 strigolactones in terms of biological activity and physicochemical properties. However, we believe strigolactone and strigolactam derivatives require further structural optimisation to improve their soil persistence to demonstrate a potential for agronomical applications. © 2016 Society of Chemical Industry.

Target-site resistance to neonicotinoids.

Neonicotinoid insecticides selectively target the invertebrate nicotinic acetylcholine receptor and disrupt excitatory cholinergic neurotransmission. First launched over 20 years ago, their broad pest spectrum, variety of application methods and relatively low risk to nontarget organisms have resulted in this class dominating the insecticide market with global annual sales in excess of $3.5 bn. This remarkable commercial success brings with it conditions in the field that favour selection of resistant phenotypes. A number of important pest species have been identified with mutations at the nicotinic acetylcholine receptor associated with insensitivity to neonicotinoids. The detailed characterization of these mutations has facilitated a greater understanding of the invertebrate nicotinic acetylcholine receptor.

Efficient synthesis of fused bicyclic ethers and their application in herbicide chemistry.

A series of triketones 2 and 3 featuring novel fused bicyclic aryl ethers have been prepared. The syntheses utilized ring-closing olefin metathesis (compounds 2), or oxidative cyclization of allylphenols as the key steps. The herbicidal activity of the targeted triketones 2 and 3 on various grasses and broad-leaved weeds was determined and compared with compound 1. The strength of the novel compounds 2 and 3 is their good herbicidal activity on broad-leaved weeds in post-emergent applications, whereas activity on grasses was inferior compared to 1. In addition, computational methods have been applied to provide a deeper understanding of the SAR found for compounds 2 and 3.

Halogen bonds with benzene: an assessment of DFT functionals.

The performance of an extensive set of density functional theory functionals has been tested against CCSD(T) and MP2 results, extrapolated to the complete basis set (CBS) limit, for the interaction of either DCl or DBr (D = H, HCC, F, and NC) with the aromatic system of benzene. It was found that double hybrid functionals explicitly including dispersion, that is, B2PLYPD and mPW2PLYPD, provide the better agreement with the CCSD(T)/CBS results on both energies and equilibrium geometry, indicating the importance of dispersive contributions in determining this interaction. Among the less expensive functionals, the better performance is provided by the ωB97X and M062X functionals, while the ωB97XD and B97D functionals are shown to work very well for bromine complexes but not so well for chlorine complexes.

Computer aided design of FtsZ targeting oligopeptides†.

FtsZ is a protein involved in the bacterial division process and is thus an emerging target for antibacterial drugs. The network of interactions between FtsZ monomers necessary for exploitation of its biological function are studied here with molecular dynamics and free energy calculations. The results obtained led to the design of FtsZ targeting peptides which exhibited activity against the function of FtsZ in vitro.

Halogen-bonding interactions with π systems: CCSD(T), MP2, and DFT calculations.

Halogen bonding is a noncovalent interaction between a halogen atom and a nucleophilic site. Interactions involving the π electrons of aromatic rings have received, up to now, little attention, despite the large number of systems in which they are present. We report binding energies of the interaction between either NCX or PhX (X = F, Cl, Br, I) and the aromatic benzene system as determined with the coupled cluster with perturbative triple excitations method [CCSD(T)] extrapolated at the complete basis set limit. Results are compared with those obtained by Møller-Plesset perturbation theory to second order (MP2) and density functional theory (DFT) calculations by using some of the most common functionals. Results show the important role of DFT in studying this interaction.

Solvent effect on halogen bonding: the case of the I⋯O interaction.

The solvent effect on the I⋯O halogen bonding in complexes of iodobenzene derivatives with formaldehyde has been investigated by systematically varying the substituents on the iodobenzene ring. Calculations have been performed at MP2 and DFT levels of theory, using the aug-cc-pVDZ basis set and the pseudopotential for iodine. Within the DFT approach, a series of the most widely used exchange-correlation functionals have been considered, comprising PBE, PBE0, B3LYP, BH&HLYP, M06-2X and M06-HF. Results obtained in diethylether and in water using the conductor-like polarizable continuum model (CPCM) have been compared with in vacuo results. Though halogen bonding distances were found to systematically shorten when moving from vacuo to diethylether and then to water, the associated interaction energies showed a decrease in absolute value, indicating that solvent has a destabilizing effect on this interaction. By comparison with MP2 results, all the considered functionals, B3LYP excepted, have been found adequate to describe halogen bonding. As far as the interaction energies are concerned, the best performance was obtained with the M06-HF functional in vacuo and the PBE functional in solution. The geometrical parameters characterizing halogen bonds were better reproduced by the M06-2X functional.

Halogen bonding in ligand-receptor systems in the framework of classical force fields.

Halogen bond is an important non-covalent interaction which is receiving a growing attention in the study of protein-ligand complexes. Many drugs are halogenated molecules and it has been recently shown that many halogenated ligands establish halogen bonds with biomolecules. As the halogen bond nature is due to an anisotropy of the electrostatic potential around halogen atoms, it is not possible to use traditional force fields based on a set of atom-centred charges to study halogen bonds in biomolecules. We show that the introduction of pseudo-atoms on halogens permits us to correctly describe the anisotropy of the electrostatic potential and to perform molecular dynamics simulations on complexes of proteins with halogenated ligands that reproduce experimental values. The results are compared with crystallographic data and with hybrid quantum mechanics/molecular mechanics calculations.

Metadynamics study of a ß-hairpin stability in mixed solvents.

Understanding the molecular mechanisms that allow some organisms to survive in extremely harsh conditions is an important achievement that might disclose a wide range of applications and that is constantly drawing the attention of many research fields. The high adaptability of these living creatures is related to the presence in their tissues of a high concentration of osmoprotectants, small organic, highly soluble molecules. Despite osmoprotectants having been known for a long time, a full disclosure of the machinery behind their activity is still lacking. Here we describe a computational approach that, taking advantage of the recently developed metadynamics technique, allows one to fully describe the free energy surface of a small ß-hairpin peptide and how it is affected by an osmoprotectant, glycine betaine (GB) and for comparison by urea, a common denaturant. Simulations led to relevant thermodynamic information, including how the free energy difference of denaturation is affected by the two cosolvents; unlike urea, GB caused a considerable increase of the folded basin stability, which transposes into a higher melting temperature. NMR experiments confirmed the picture derived from the theoretical study. Further molecular dynamics simulations of selected conformations allowed investigation into deeper detail the role of GB in folded state protection. Simulations of the protein in GB solutions clearly showed an excess of osmoprotectant in the solvent bulk, rather than in the protein domain, confirming the exclusion from the protein surface, but also highlighted interesting features on its interactions, opening to new scenarios besides the classic "indirect mechanism" hypothesis.

Vinblastine perturbation of tubulin protofilament structure: a computational insight.

Tubulin is a heterodimeric protein whose self assembly leads to the formation of protofilaments and of more complex structures called microtubules, key components of the cytoskeleton which have a fundamental role in the cell division process. Due to its biological function, tubulin is the target of many antitumoral molecules that exert their action on proliferating tumoral cells. Among these drugs, vinblastine has been widely used in therapy for a long time, albeit its mechanism of interaction with tubulin has remained elusive until recently. Vinblastine acts as a microtubule destabilizing agent and induces the formation of curved or ring-shaped tubulin polymers instead of linear protofilaments in vitro. In this paper we compare, using molecular dynamics simulations and free energy calculations, the network of interactions that allow the assembly of model linear protofilaments with those present in curved tubulin polymers complexed with vinblastine. It is shown that vinblastine, wedging between tubulin heterodimers, actually mediates part of the interactions between them and acts by crosslinking the two proteins, leading to the observed curved polymers rather than to their disassembly.