Deciphering the Role of Noncovalent Interactions in the Conformations of Dibenzo-1,5-dichalcogenocines.

This work reports a combined experimental and theoretical study on the new dibenzo-1,5-ditellurocine 2-Te in order to get an overview on the parameters controlling conformational change and to explain the differences with sulfur and selenium analogues. The preference of the boat conformer over the chair one is revealed by DFT calculations. For 2-Te, a ΔG value of about 3 kJ/mol was calculated, close to the value measured by NMR (5 kJ/mol). However, DFT calculations with implicit solvation effects could not clearly establish the presence of an intramolecular Te…HC noncovalent interaction (NCI), as observed in the solid state. The Independent Gradient Model (IGM) methodology discloses an existent but probably not sufficiently discriminating Te…HC NCI. It also confirms that van der Waals interactions between phenyl rings is a source of stabilization of the boat conformer. Furthermore, electrostatic potential analysis suggests that chalcogen bonds between Te σ-holes and solvent might play an important role.

Addition of Vindoline to p-Benzoquinone: Regiochemistry, Stereochemistry and Symmetry Considerations.

Vindoline and catharanthine are the major alkaloids of Catharanthus roseus and are extracted in large quantities to prepare the pharmaceutically important Vinca type alkaloids vincaleukoblastine, vincristine and navelbine. The higher yield of vindoline relative to catharanthine makes it an attractive substrate for developing new chemistry and adding value to the plant. In this context, we have reacted vindoline with a selection of electrophiles among which benzoquinone. Conditions were developed to optimize the synthesis of a mono-adduct, of five bis-adducts, and of tri-adducts and tetra-adducts, several of these adducts being mixtures of conformational isomers. Copper(II) was added to the reactions to promote reoxidation of the intermediate hydroquinones and simplify the reaction products. The structures were solved by spectroscopic means and by symmetry considerations. Among the bis-isomers, the 2,3-diadduct consists of three unseparable species, two major ones with an axis of symmetry, thus giving a single set of signals and existing as two different species with indistinguishable NMR spectra. The third and minor isomer has no symmetry and therefore exhibits nonequivalence in the signals of the two vindoline moieties. These isomers are designated as syn (minor) and anti (major) and there exists a high energy barrier between them making their interconversion difficult. DFT calculations on simplified model compounds demonstrate that the syn-anti interconversion is not possible at room temperature on the NMR chemical shift time scale. These molecules are not rigid and calculations showed a back-and-forth conrotatory motion of the two vindolines. This "windshield wiper" effect is responsible for the observation of exchange correlations in the NOESY spectra. The same phenomenon is observed with the higher molecular weight adducts, which are also mixtures of rotational isomers. The same lack of rotations between syn and anti isomers is responsible for the formation of four tri-adducts and of seven tetra-adducts. On a biological standpoint, the mono adduct displayed anti-inflammatory properties at the 5 µM level while the di-adducts and tri-adducts showed moderate cytotoxicity against Au565, and HeLa cancer cell lines.

Pyridazinone derivatives as potential anti-inflammatory agents: synthesis and biological evaluation as PDE4 inhibitors.

Cyclic nucleotide phosphodiesterase type 4 (PDE4), which controls the intracellular level of cyclic adenosine monophosphate (cAMP), has aroused scientific attention as a suitable target for anti-inflammatory therapy of respiratory diseases. This work describes the development and characterization of pyridazinone derivatives bearing an indole moiety as potential PDE4 inhibitors and their evaluation as anti-inflammatory agents. Among these derivatives, 4-(5-methoxy-1H-indol-3-yl)-6-methylpyridazin-3(2H)-one possesses promising activity, and selectivity towards PDE4B isoenzymes and is able to regulate potent pro-inflammatory cytokine and chemokine production by human primary macrophages.

A Step toward the Quantification of Noncovalent Interactions in Large Biological Systems: The Independent Gradient Model-Extremely Localized Molecular Orbital Approach.

The independent gradient model (IGM) is a recent electron density-based computational method that enables to detect and quantify covalent and noncovalent interactions. When applied to large systems, the original version of the technique still relies on promolecular electron densities given by the sum of spherically averaged atomic electron distributions, which leads to approximate evaluations of the inter- and intramolecular interactions occurring in systems of biological interest. To overcome this drawback and perform IGM analyses based on quantum mechanically rigorous electron densities also for macromolecular systems, we coupled the IGM approach with the recently constructed libraries of extremely localized molecular orbitals (ELMOs) that allow fast and reliable reconstructions of polypeptide and protein electron densities. The validation tests performed on small polypeptides and peptide dimers have shown that the novel IGM-ELMO strategy provides results that are systematically closer to the fully quantum mechanical ones and outperforms the IGM method based on the crude promolecular approximation, but still keeping a quite low computational cost. The results of the test calculations carried out on proteins have also confirmed the trends observed for the IGM analyses conducted on small systems. This makes us envisage the future application of the novel IGM-ELMO approach to unravel complicated noncovalent interaction networks (e.g., in protein-protein contacts) or to rationally design new drugs through molecular docking calculations and virtual high-throughput screenings.

Novel approach to accurately predict bond strength and ligand lability in platinum-based anticancer drugs.

Prompted by the antineoplastic properties of cisplatin, a plethora of platinum(ii)-based complexes have been synthesized in the past decades. At present, their rational design is based on a number of structure-activity relationships involving the nature of the ligands initially coordinated to platinum(ii): either non-labile (acting as a carrier) or labile (undergoing substitution). The coordinate bond strength of the labile ligand plays a key role in the first step of the drug mechanism of action, i.e., the hydrolysis process, which is associated to the retention time of the medicine in the body. Therefore, an accurate determination of the metal-ligand bond strength becomes highly relevant as it will help the rational design of novel chemotherapeutic agents. Herein, we challenge the recently developed intrinsic bond strength index (IBSI) as a rapid and practical tool to assess the ligand lability in Pt(ii) complexes. In a first stage, given the importance of the trans-effect in synthetic strategies of cisplatin-based drugs, the effect of eleven trans-directing ligands T is quantified in two sets of complexes [Pt(NH3)2(H2O)T]n+ and [PtCl2(NH3)T]m+ where T = H2O, F-, NH3, Cl-, Br-, I-, SO32-, CH3-, CN-, CO, and H-. An essential outcome of this work is a novel index IBSItrans = IBSIσ + IBSIπ able to rank the directing ligands by their trans-effect according to their σ-donation and π-backbonding electronic contributions. In a second stage, we apply the IBSI score to a panel of eleven case studies, comprising mostly antineoplastic agents, such as cisplatin, carboplatin, lobaplatin etc., in order to quantify the coordinate bond strength of the ligands, providing insights about the hydrolysis process. The obtained results, in good agreement with experimental data and reported theoretical studies, demonstrate that the IBSI score is able to deliver a rapid and reliable picture of the coordinate bond strength, representing a chemically intuitive tool helpful for the development of novel anticancer agents prior to synthetic efforts.

The Independent Gradient Model: A New Approach for Probing Strong and Weak Interactions in Molecules from Wave Function Calculations.

Extraction of the chemical interaction signature from local descriptors based on electron density (ED) is still a fruitful field of development in chemical interpretation. In a previous work that used promolecular ED (frozen ED), the new descriptor, δg , was defined. It represents the difference between a virtual upper limit of the ED gradient (∇ρIGM , IGM=independent gradient model) that represents a noninteracting system and the true ED gradient (∇ρ ). It can be seen as a measure of electron sharing brought by ED contragradience. A compelling feature of this model is to provide an automatic workflow that extracts the signature of interactions between selected groups of atoms. As with the noncovalent interaction (NCI) approach, it provides chemists with a visual understanding of the interactions present in chemical systems. ∇ρIGM is achieved simply by using absolute values upon summing the individual gradient contributions that make up the total ED gradient. Hereby, we extend this model to relaxed ED calculated from a wave function. To this end, we formulated gradient-based partitioning (GBP) to assess the contribution of each orbital to the total ED gradient. We highlight these new possibilities across two prototypical examples of organic chemistry: the unconventional hexamethylbenzene dication, with a hexa-coordinated carbon atom, and ß-thioaminoacrolein. It will be shown how a bond-by-bond picture can be obtained from a wave function, which opens the way to monitor specific interactions along reaction paths.

Accurately extracting the signature of intermolecular interactions present in the NCI plot of the reduced density gradient versus electron density.

An electron density (ED)-based methodology is developed for the automatic identification of intermolecular interactions using pro-molecular density. The expression of the ED gradient in terms of atomic components furnishes the basis for the Independent Gradient Model (IGM). This model leads to a density reference for non interacting atoms/fragments where the atomic densities are added whilst their interaction turns off. Founded on this ED reference function that features an exponential decay also in interference regions, IGM model provides a way to identify and quantify the net ED gradient attenuation due to interactions. Using an intra/inter uncoupling scheme, a descriptor (δginter) is then derived that uniquely defines intermolecular interaction regions. An attractive feature of the IGM methodology is to provide a workflow that automatically generates data composed solely of intermolecular interactions for drawing the corresponding 3D isosurface representations.

GPU accelerated implementation of NCI calculations using promolecular density.

The NCI approach is a modern tool to reveal chemical noncovalent interactions. It is particularly attractive to describe ligand-protein binding. A custom implementation for NCI using promolecular density is presented. It is designed to leverage the computational power of NVIDIA graphics processing unit (GPU) accelerators through the CUDA programming model. The code performances of three versions are examined on a test set of 144 systems. NCI calculations are particularly well suited to the GPU architecture, which reduces drastically the computational time. On a single compute node, the dual-GPU version leads to a 39-fold improvement for the biggest instance compared to the optimal OpenMP parallel run (C code, icc compiler) with 16 CPU cores. Energy consumption measurements carried out on both CPU and GPU NCI tests show that the GPU approach provides substantial energy savings. © 2017 Wiley Periodicals, Inc.

Molecular properties affecting the adsorption coefficient of pesticides from various chemical families.

Forty pesticides were selected in function of their chemical families and their physico-chemical properties to represent a wide range of pesticide properties. Adsorption of these pesticides was studied on two soils by batch experiments. The two soils differed largely in organic matter and calcite contents. Distribution coefficient Kd was determined for each pesticide on the two soils. Adsorption was higher for the soil having the highest organic matter content and the lowest calcite content. In order to identify pesticide properties governing retention, eight molecular descriptors were determined from three-dimensional (3D) structure of molecules. Class-specific quantitative structure properties relationship (QSPR) soil adsorption models using one and two parameters were developed from experimental Kd. Three properties seemed to influence most retention of pesticides: hydrophobicity, solubility, and polarisability. Models combining these properties were suggested and discussed.

Switching invariant natural killer T (iNKT) cell response from anticancerous to anti-inflammatory effect: molecular bases.

Since the discovery in 1995 of α-galactosylceramide 1 (α-GalCer), also known as KRN7000,1 hundreds of compounds have been synthesized in order to activate invariant natural killer T (iNKT) cells. Such keen interest for this lymphocyte cell type is due to its ability to produce different cytokines that bias the immune response toward a Th1 or Th2 profile. Thus, an understanding of the immune polarization mechanism via iNKT activation may pave the way toward new therapeutics in various domains including cancer and infectious and autoimmune diseases. In this review, we propose an up-to-date analysis of iNKT activators associated with a structure-activity relationship (SAR) study aimed at complementing available reviews by highlighting molecular bases for a selective immune response.

The stimulating adventure of KRN 7000.

Associated with the CD1d protein, KRN 7000, a potent synthetic α-galactosylceramide, is known to activate the invariant NKT immune cells. This stimulation then leads to the production of different cytokines modulating a T(H)1/T(H)2 immune response balance involved in protection against several pathologies such as autoimmune diseases and cancers. Various efforts have been made toward the synthesis of simple and more functionalized analogues in order to selectively induce T(H)1 or T(H)2-type cytokine production. Since the discovery of KRN 7000, structure-activity relationships, crystallographic and modelling studies have pointed to the potential of several GalCer analogues in term of selective bioactivity, and have highlighted interesting elements in order to better understand the recognition and activation mechanisms of immune iNKT cells. By presenting an up-to-date library of analogues, collecting recent breakthroughs done in crystallography and molecular modelling, and relating them to the available biological results, we hope that this review will highlight and help the scientific community in their KRN research.

Synthesis and biological evaluation of new penta- and heptacyclic indolo- and quinolinocarbazole ring systems obtained via Pd(0) catalysed reductive N-heteroannulation.

A short route, involving a tetramolecular condensation reaction and a Pd/C catalyst-H(2)-mediated reductive N-heteroannulation as the key-steps, has been found for the synthesis of some new penta- and heptacyclic indolo- (12), quinolino- (13) and indoloquinolinocarbazole (11) derivatives. HF-DFT (B3LYP) energy profiles and NMR calculations were carried out to help in the understanding of the experimental results. N-Alkylated indoloquinolinocarbazoles (16b, 17a, 17b and 18) were prepared and screened essentially toward some cancer-(G-quadruplex, DNA, topoisomerase I) and CNS-related (kinases) targets. Biological results evidenced 13 as a potent CDK-5 and GSK-3ß kinases inhibitor, while di- or triaminopropyl-substituted indoloquinolinocarbazoles 17b or 18 targeted rather DNA-duplex or telomeric G-quadruplex structures, respectively.

Synthesis of chiral ß-aminoalcohol palladium complexes exhibiting cytotoxic properties.

Original palladium complexes involving (-)-ephedrine, (-)-norephedrine, L-prolinol, L-valinol and L-isoleucinol have been rapidly prepared in neutral or basic medium and simply purified. They have been fully characterized by classical analytical methods and four of them were characterized by X-Ray analysis. In parallel with the experimental work, HF-DFT(B3LYP/PCM) computations were performed to obtain additional structural information. Their antiproliferative properties have been evaluated and some complexes showed small activities especially towards HT29 human cancer cells.

Compared behavior of 5-deoxy-5-iodo-D-xylo- and L-arabinofuranosides in the reductive elimination reaction: a strong dependence on structural parameters and on the presence of Zn2+. A combined experimental and theoretical investigation.

In the framework of a project devoted to the chemical transformation of monosaccharides from hemicelluloses into higher added value materials, the zinc-induced reductive elimination from 5-deoxy-5-iodo derivatives of D-xylose and L-arabinose was carried out. This study gave us the opportunity to observe surprising behaviors. In particular, the reaction strongly depends on structural parameters (protecting group pattern, configuration at C-4) and on the presence of Zn2+ ions. Collaterally with the experimental work, water solvent PCM HF-DFT (MPW1K/LANL2DZ) computations were performed to obtain insight into the mechanism for the reductive part of the reaction sequence. Without Zn2+, the zinc insertion reaction was found to proceed through a concerted but non-synchronous process involving a relatively large energy barrier (32 kcal mol-1) that directly leads to the presumed organozinc intermediate. In the presence of Zn2+, a three-step mechanism was identified in which the cation coordinates the anomeric and ring oxygen atoms and also the sugar iodine atom, causing an activating effect on the zinc insertion process by facilitating the homolytic rupture of the C-I bond. Complexes between zinc and Zn2+ bound carbohydrates were characterized with large stabilization energies, suggesting that Zn2+ might enhance the affinity of the organic compound with the zinc metal surface.

Novel seco-dibenzopyrrocoline alkaloid from Cryptocarya oubatchensis.

[structure: see text] A novel seco-dibenzopyrrocoline alkaloid, named oubatchensine 6, and five phenanthroindolizidines (1-5) were isolated from Cryptocarya oubatchensis, and their structures were elucidated. Displacement centrifugal partition chromatography was used to purify compounds 1 and 6. Structure determination of the latter was carried out by mass spectrometry, NMR spectroscopy, quantum chemistry, and computer-assisted structure determination. Cytotoxic activity against KB cells was then investigated.