Synthesis of rhodium–carbonyl complexes bearing a novel P,N-chelating ligand of Schiff-base type

Schiff-base type N,P-chelating ligands, phosphorus analogues of imino–anilido ligands, were designed and synthesized as a new type of ligands toward transition metals, and the rhodium–carbonyl complexes bearing the novel imino–phosphido and phosphaalkenyl-anilido ligands were synthesized as stable crystalline compounds. Their structures were definitively revealed by X-ray crystallographic analysis, showing the unique electronic features of the ligands. In addition, the effective trans-influence of the phosphorus atom was suggested on the basis of the structural parameters and spectroscopic features of the isolated complexes.     

Analysis of Fas–ligand interactions using a molecular model of the receptor–ligand interface

A molecular model of the complex between Fas and its ligand was generated to better understand the location and putative effects of site-specific mutations, analyze interactions at the Fas–FasL interface, and identify contact residues. The modeling study was conservative in the sense that regions in Fas and its ligand which could not be predicted with confidence were omitted from the model to ensure accuracy of the analysis. Using the model, it was possible to map four of five N-linked glycosylation sites in Fas and FasL and to study 10 of 11 residues previously identified by mutagenesis as important for binding. Interactions involving six of these residues could be analyzed in detail and their importance for binding was rationalized based on the model. The predicted structure of the Fas–FasL interface was consistent with the experimentally established importance of these residues for binding. In addition, five previously not targeted residues were identified and predicted to contribute to binding via electrostatic interactions. Despite its limitations, the study provided a much improved basis to understand the role of Fas and FasL residues for binding compared to previous residue mapping studies using only a molecular model of Fas.     

NMR-based analysis of protein–ligand interactions

Physiological processes are mainly controlled by intermolecular recognition mechanisms involving protein–protein and protein–ligand (low molecular weight molecules) interactions. One of the most important tools for probing these interactions is high-field solution nuclear magnetic resonance (NMR) through protein-observed and ligand-observed experiments, where the protein receptor or the organic compounds are selectively detected. NMR binding experiments rely on comparison of NMR parameters of the free and bound states of the molecules. Ligand-observed methods are not limited by the protein molecular size and therefore have great applicability for analysing protein–ligand interactions. The use of these NMR techniques has considerably expanded in recent years, both in chemical biology and in drug discovery. We review here three major ligand-observed NMR methods that depend on the nuclear Overhauser effect—transferred nuclear Overhauser effect spectroscopy, saturation transfer difference spectroscopy and water–ligand interactions observed via gradient spectroscopy experiments—with the aim of reporting recent developments and applications for the characterization of protein–ligand complexes, including affinity measurements and structural determination.     

Self-assembly of metal–ligand coordinated charged vesicles

This review compiles recent research and developments on the metal–ligand coordinated charged vesicles, focusing on the phase behavior, properties, microstructures, and vesicle-phases of metal–ligand complexation as templating preparation of inorganic nanoparticles. Moreover, the other kind of salt-free vesicles, constructed by the electrostatic interaction with zero-charged ones were simply also compared with those constructed by the metal–ligand coordinated complexes with charged molecular membranes in the properties, the phase behaviors, and the microstructures.     

Dependence of the product on the P–P ligand in reactions of [RuCl3(NO)(P–P)] complexes (P–P = aromatic diphosphines) with 2-mercaptopyridine

This study presents the syntheses and characterization of 2-mercaptopyridine (pyS⁻) complexes containing ruthenium(II) with the following general formula [Ru(pyS)₂(P–P)], P–P = (c-dppen) = cis-1,2-bis(diphenylphosphino)ethylene) (1); (dppe) = 1,2-bis(diphenylphosphino)ethane (2); (dppp) = 1,3-bis(diphenylphosphino)propane (3) and (dppb) = 1,4-bis(diphenylphosphino)butane (4). The complexes were synthesized from the mer- or fac-[RuCl₃(NO)(P–P)] precursors in the presence of triethylamine in methanol solution with dependence of the product on the P–P ligand. The reaction of pyS⁻ with a ruthenium complex containing a bulky aromatic diphosphine dppb disclosed a major product with a dangling coordinated dppbO-P, the [Ru(pyS)₂(NO)(η¹-dppbO-P)]PF₆(5). In addition, this work also presents and discusses the spectroscopic and electrochemical behavior of 1–5, and report the X-ray structures for 1 and 5.     

Reactivity of the Ge–H,Sn–H,P–H,and Se–H Bonds in Radical Abstraction Reactions

The experimental data for the liquid- and gas-phase reactions of atoms and radicals with organoelement compounds R _{n – 1}E–H

Protein–ligand docking with multiple flexible side chains

In this work, we validate and analyze the results of previously published cross docking experiments and classify failed dockings based on the conformational changes observed in the receptors. We show that a majority of failed experiments (i.e. 25 out of 33, involving four different receptors: cAPK, CDK2, Ricin and HIVp) are due to conformational changes in side chains near the active site. For these cases, we identify the side chains to be made flexible during docking calculation by superimposing receptors and analyzing steric overlap between various ligands and receptor side chains. We demonstrate that allowing these side chains to assume rotameric conformations enables the successful cross docking of 19 complexes (ligand all atom RMSD < 2.0 A) using our docking software FLIPDock. The number of side receptor side chains interacting with a ligand can vary according to the ligand's size and shape. Hence, when starting from a complex with a particular ligand one might have to extend the region of potential interacting side chains beyond the ones interacting with the known ligand. We discuss distance-based methods for selecting additional side chains in the neighborhood of the known active site. We show that while using the molecular surface to grow the neighborhood is more efficient than Euclidian-distance selection, the number of side chains selected by these methods often remains too large and additional methods for reducing their count are needed. Despite these difficulties, using geometric constraints obtained from the network of bonded and non-bonded interactions to rank residues and allowing the top ranked side chains to be flexible during docking makes 22 out of 25 complexes successful.     

Recent developments in protein–ligand affinity mass spectrometry

This review provides an overview of direct and indirect technologies to screen protein–ligand interactions with mass spectrometry. These technologies have as a key feature the selection or affinity purification of ligands in mixtures prior to detection. Specific fields of interest for these technologies are metabolic profiling of bioactive metabolites, natural extract screening, and the screening of libraries for bioactives, such as parallel synthesis libraries and small combichem libraries. The review addresses the principles of each of the methods discussed, with a focus on developments in recent years, and the applicability of the methods to lead generation and development in drug discovery.     

Investigation of the importance of nitrogen substituents in a N–P chiral ligand for enantioselective allylic alkylation

The synthesis of three chiral chelate nitrogen–phosphorus (S)-valine derived ligands with the potential for stereogenic nitrogen donation is described. In palladium catalysed allylic substitution reactions the ligands induced varying enantioselectivities ranging from 92% e.e. of the (R)-enantiomer to 83% e.e. of the (S)-enantiomer. Structural and spectroscopic investigations into the origin of this effect were conducted, but were inconclusive. However, the importance of the consideration of N-substituents in such systems is highlighted.     

Palladium complexes of P,P and P,S type bidentate ligands: Implication in Suzuki–Miyaura cross-coupling reaction

New palladium complexes of the type [PdCl₂(η²–P∩P)] (1a,1b) and [PdCl₂(η²–P∩S)] (1c,1d) have been synthesised by the reaction of PdCl₂ with P,P and P,S type bidentate ligands in 1:1 mol ratio, where, P∩P = 9,9–dimethyl-4,5-bis(diphenylphosphanyl) xanthene {Xantphos}(a) or bis(2-diphenylphosphanylphenyl)ether{DPEphos}(b); P∩S = 9,9-dimethyl-4,5-bis(diphenyl -phosphanyl) xanthenemonosulfide {Xantphos(S)}(c) or bis(2-diphenylphosphanyl phenyl) ether monosulfide {DPEphos(S)}(d). The complexes are characterized by elemental analyses, mass spectrometry, ¹H, ¹³C and ³¹P NMR spectroscopy together with the single crystal X-ray structure determination of 1a and 1d. The palladium atom in all the complexes occupies the centre of a slightly distorted square planar environment formed by a P atom, a P/S atom and two Cl atoms. The catalytic activities of 1a–1d investigated for Suzuki–Miyaura cross-coupling reactions at room temperature exhibit higher yield of the coupling products than catalysed by PdCl₂ itself. Among 1a–1d, the palladium complexes of bidentate phosphine (1a, 1b) show higher efficacy than their monosulfide analogues (1c, 1d). However, the recycling experiments with the catalysts for a selected coupling reaction between 4-bromobenzonitrile and phenylboronic acid exhibit that 1c and 1d are more efficient than 1a and 1b, which may be due to the donor effect of the P,S ligands during catalytic reaction.     

Palladium complexes of P,P and P,S type bidentate ligands: Implication in Suzuki–Miyaura cross-coupling reaction

New palladium complexes of the type [PdCl₂(η²–P∩P)] (1a,1b) and [PdCl₂(η²–P∩S)] (1c,1d) have been synthesised by the reaction of PdCl₂ with P,P and P,S type bidentate ligands in 1:1 mol ratio, where, P∩P = 9,9–dimethyl-4,5-bis(diphenylphosphanyl) xanthene {Xantphos}(a) or bis(2-diphenylphosphanylphenyl)ether{DPEphos}(b); P∩S = 9,9-dimethyl-4,5-bis(diphenyl -phosphanyl) xanthenemonosulfide {Xantphos(S)}(c) or bis(2-diphenylphosphanyl phenyl) ether monosulfide {DPEphos(S)}(d). The complexes are characterized by elemental analyses, mass spectrometry, ¹H, ¹³C and ³¹P NMR spectroscopy together with the single crystal X-ray structure determination of 1a and 1d. The palladium atom in all the complexes occupies the centre of a slightly distorted square planar environment formed by a P atom, a P/S atom and two Cl atoms. The catalytic activities of 1a–1d investigated for Suzuki–Miyaura cross-coupling reactions at room temperature exhibit higher yield of the coupling products than catalysed by PdCl₂ itself. Among 1a–1d, the palladium complexes of bidentate phosphine (1a, 1b) show higher efficacy than their monosulfide analogues (1c, 1d). However, the recycling experiments with the catalysts for a selected coupling reaction between 4-bromobenzonitrile and phenylboronic acid exhibit that 1c and 1d are more efficient than 1a and 1b, which may be due to the donor effect of the P,S ligands during catalytic reaction.     

An improved adaptive genetic algorithm for protein–ligand docking

A new optimization model of molecular docking is proposed, and a fast flexible docking method based on an improved adaptive genetic algorithm is developed in this paper. The algorithm takes some advanced techniques, such as multi-population genetic strategy, entropy-based searching technique with self-adaptation and the quasi-exact penalty. A new iteration scheme in conjunction with above techniques is employed to speed up the optimization process and to ensure very rapid and steady convergence. The docking accuracy and efficiency of the method are evaluated by docking results from GOLD test data set, which contains 134 protein-ligand complexes. In over 66.2% of the complexes, the docked pose was within 2.0 A root-mean-square deviation (RMSD) of the X-ray structure. Docking time is approximately in proportion to the number of the rotatable bonds of ligands.     

A new method for estimating the relative binding free energy,derived from a free energy variational principle for the Pim-1-kinase–ligand and FKBP–ligand systems

Journal of Computer-Aided Molecular Design - In this study, a new method is proposed for calculating the relative binding free energy between a ligand and a protein, derived from a free energy...     

Receptor–ligand interactions in a reconstituted bilayer lipid membrane

A simple method is described to reconstitute membrane receptors into bilayer lipid membranes (BLMs). After reconstitution, the receptor still retains its ligand activity. Furthermore, the relationship between receptor–ligand interactions and electrical properties of reconstituted BLMs such as membrane capacitance (C_m) and membrane resistance (R_m) was studied. When glycophorin in erythrocyte and asialoglycoprotein in hepatocyte were taken as examples, it was found that the resistance of reconstituted BLM decreased when adding blood type monoclonal antibody or the solutions of galactose, respectively, and the decrease is ligand-concentration dependent; however, the membrane capacitance was not influenced. This provides a simple, practical approach to determining the interactions between the receptor and its ligand.     

Synthesis of bisquinoline–pyrrole oligoamide as G-quadruplex binding ligand

A one-pot procedure using ammonium formate under palladium catalysis for the reductive dechlorination and reduction of nitro group of 4-chloro-8-nitro–quinoline derivatives has be successfully carried out. This has lead to the synthesis of bisquinoline–pyrrole oligoamide 1, which show significant G-quadruplex selectivity in preference to duplex DNA. The cooperativity between the bisquinoline and pyrrole oligoamide moieties for good binding affinity to G-quadruplex was proven by synthesizing 2 and 3 lacking a quinoline ring and pyrrole amide, respectively, and both show much reduce affinity to G-quadruplex. Altogether, the results demostrate that the appropriate combination of two chromophores to form the hybride can attenuate binding affinity and selectivity towards G-quadruplex, an important criteria for the rational drug design.     

Studying protein–protein affinity and immobilized ligand–protein affinity interactions using MS-based methods

This review discusses the most important current methods employing mass spectrometry (MS) analysis for the study of protein affinity interactions. The methods are discussed in depth with particular reference to MS-based approaches for analyzing protein–protein and protein–immobilized ligand interactions, analyzed either directly or indirectly. First, we introduce MS methods for the study of intact protein complexes in the gas phase. Next, pull-down methods for affinity-based analysis of protein–protein and protein–immobilized ligand interactions are discussed. Presently, this field of research is often called interactomics or interaction proteomics. A slightly different approach that will be discussed, chemical proteomics, allows one to analyze selectivity profiles of ligands for multiple drug targets and off-targets. Additionally, of particular interest is the use of surface plasmon resonance technologies coupled with MS for the study of protein interactions. The review addresses the principle of each of the methods with a focus on recent developments and the applicability to lead compound generation in drug discovery as well as the elucidation of protein interactions involved in cellular processes. The review focuses on the analysis of bioaffinity interactions of proteins with other proteins and with ligands, where the proteins are considered as the bioactives analyzed by MS.     

Molybdenum(VI)–oxodiperoxo complex containing an oxazine ligand: synthesis,X-ray studies,and catalytic activity

A new mononuclear molybdenum(VI)–oxodiperoxo complex [MoO(O₂)₂(phox)] with a simple bidentate ligand, 2-(2′-hydroxyphenyl)-5,6-dihydro-1,3-oxazine (Hphox), has been synthesized and characterized by X-ray structure analysis, elemental analysis, infrared, and ¹H NMR spectroscopy. A triclinic space group P-1 was determined by X-ray crystallography from single-crystal data of this complex. The resulting complex functioned as a facile sulfide oxidation catalyst with urea hydrogen peroxide as terminal oxidant at room temperature. The catalyst showed efficient reactivity in oxidation of sulfides giving high yield and selectivity.     

A novel N–O ligand for palladium-catalyzed Mizoroki–Heck reaction in neat water

1-(Morpholin-1-yl-pyridin-2-yl-methyl)-2-naphthol as a novel efficient N–O ligand has been developed for palladium-catalyzed Mizoroki–Heck reaction in neat water without the protection of an inert atmosphere. The reactions proceed smoothly and give the desired products in moderate to excellent yields. The catalyst system is reusable.     

Identification of target-specific bioisosteric fragments from ligand–protein crystallographic data

Bioisosteres are functional groups or atoms that are structurally different but that can form similar intermolecular interactions. Potential bioisosteres were identified here from analysing the X-ray crystallographic structures for sets of different ligands complexed with a fixed protein. The protein was used to align the ligands with each other, and then pairs of ligands compared to identify substructural features with high volume overlap that occurred in approximately the same region of geometric space. The resulting pairs of substructural features can suggest potential bioisosteric replacements for use in lead-optimisation studies. Experiments with 12 sets of ligand–protein complexes from the Protein Data Bank demonstrate the effectiveness of the procedure.