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.     

σ-Accepting properties of a chlorobismuthine ligand

BiZness as usual? Not exactly! The bismuth atom of the tridentate diphosphinobismuthine (o-(Ph(2)P)C(6)H(4))(2) BiCl behaves as a Z rather than L ligand when in the coordination sphere of late transition metals such as gold. The σ-acceptor behavior of Bi is supported by its disphenoid coordination geometry and theoretical studies, which show a Au→Bi interaction.     

Platinum complexes bearing 2,2′-dipyridylamine ligand

The replacement of the iodide ligands in the complex [PtI₂(dpa)] (1) (dpa is 2,2′-dipyridylamine) by silver triflate in acetonitrile afforded the compound [Pt(dpa)(MeCN)₂](SO₃CF₃)₂ (2). Homoleptic complexes [Pt(dpa)₂](X)₂ (3·(X)₂) were synthesized by the treatment of [PtI₂(dpa)] (1) with 2,2′-dipyridylamine in the presence of silver salts AgX in methanol (X = NO₃) or acetonitrile (X = SO₃CF₃). The deprotonation of the complex [3](SO₃CF₃)₂ to give the homoleptic complex [Pt(dpa-H)₂] (4) was performed by two methods, e.g., by the treatment of [3](SO₃CF₃)₂ with 2 equiv. of NaOH in methanol or by the addition of excess Et₃N to a suspension of [3](SO₃CF₃)₂ in methanol. The structures of compounds 1–4 were established by elemental analyses, high resolution electrospray ionization mass spectrometry, IR and NMR spectroscopy; the crystal structure of complexes [2](SO₃CF₃)₂, [3](NO₃)₂·H₂O, [3](SO₃CF₃)₂·2H₂O, and 4 were determined by single-crystal X-ray diffraction.     

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.     

Derivation of ligand σ- and π-bonding parameters from density functional theoretical calculations and Bursten ligand additivity relationships

New ligand additivity equations, based on the Bursten model, describing dπ orbital energies in square-planar and square–pyramidal complexes are proposed and tested for hypothetical binary Cr(0) and Mn(I) complexes of CO and CNMe. Density functional theory calculations are used to calculate the energies of dπ orbitals of binary octahedral, square–planar, and square–pyramidal d⁶ complexes of Mn(I) and Cr(0). Combination of the modified equations for unsaturated species with Bursten’s original equations for octahedral species allows for calculation of individual ligand bonding parameters and the separation of σ- and π-bonding effects. The calculated parameters provide interesting insight into the nature of metal–ligand bonding in the species studied. The method of separating σ- and π-bonding effects, applied here to CO and CNMe, is proposed as general method for solution of the Bursten equations for low-spin d⁶ octahedral systems.     

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.     

9-Oxidophenalenone: a noninnocent β-diketonate ligand?

The redox systems [Ru(L)(bpy)(2)](k), [Ru(L)(2)(bpy)](m), and [Ru(L)(3)](n) containing the potentially redox-active ligand 9-oxidophenalenone = L(-) were investigated by spectroelectrochemistry (UV-vis-near-IR and electron paramagnetic resonance) in conjunction with density functional theory (DFT) calculations. Compounds [Ru(L(-))(bpy)(2)]ClO(4) ([1]ClO(4)) and [Ru(L(-))(2)(bpy)]ClO(4) ([2]ClO(4)) were structurally characterized. In addition to establishing electron-transfer processes involving the Ru(II)/Ru(III)/Ru(IV) and bpy(0)/bpy(?-) couples, evidence for the noninnocent behavior of L(-) was obtained from [Ru(IV)(L(?))(L(-))(bpy)](3+), which exhibits strong near-IR absorption due to ligand-to-ligand charge transfer. In contrast, the lability of the electrogenerated anion [Ru(L)(2)(bpy)](-) is attributed to a resonance situation [Ru(II)(L(?2-))(L(-))(bpy)](-)/[Ru(II)(L(-))(2) (bpy(?-))](-), as suggested by DFT calculations.     

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.     

Importance of inter-residue interactions in ligand—receptor binding

In the present study, the role of inter-residue interactions in ligand binding and the ligand—receptor interactions were examined. Computational chemistry methods of ligand docking and molecular dynamics simulations were used to study the binding of β-funaltrexamine (β-FNA) and N-methyl-β-funaltrexamine (N-methyl-β-FNA) to μ- and κ-opioid receptors and to the μ-receptor with Lys303^6.58Glu mutation. It was found that inter-residue interactions Lys233^5.39—Glu303^6.58 in the mutant receptor and Lys227^5.39—Asp223^5.35 in the κ-receptor are more likely to prevent covalent bond formation between β-FNA and the receptor than the ligand-receptor interactions. This emphasizes the importance of inter-residue interactions in ligand binding as well as the effects of point-mutations.     

Can an ancillary ligand lead to a thermodynamically stable end-on 1 : 1 Cu-O2 adduct supported by a beta-diketiminate ligand?

The finding that dioxygen binds end-on to the Cu(B) site in the crystal structure of a precatalytic complex of peptidylglycine alpha-hydroxylating monooxygenase has spurred the search for biomimetic model complexes exhibiting the same dioxygen coordination. Recent work has not only indicated that sterically hindered beta-diketiminate ligands (L(1)) could support side-on 1 : 1 Cu-O(2) adducts, but also that an end-on L(1)Cu(THF)O(2) structure occurs as an unstable intermediate in the oxygenation mechanism of the Cu(I) complex. In this work, density functional theory and multireference methods are used to determine the potential of ancillary ligands, X, other than THF to yield thermodynamically stable end-on L(1)CuXO(2) species. A diverse set of ligands X, comprising phosphines, thiophene, cyclic ethers, acetonitrile, para-substituted pyridines, N-heterocyclic carbenes, and ligands bearing hydrogen bond donors, has been considered in order to identify ligand characteristics which energetically favor end-on L(1)CuXO(2) over: a) reversion to the Cu(I) complex and dioxygen, b) isomerization to side-on L(1)CuXO(2), and c) decay to L(1)CuO(2) and X. Ancillary ligands with judiciously chosen degrees and orientation of steric bulk and which bear potential hydrogen bond donors to an end-on bound dioxygen moiety most favor oxygenation of L(1)CuX to yield end-on L(1)CuXO(2). Conversion to the side-on isomer can be deterred through the use of a sufficiently bulky ligand X, such as one that is at least the size of a 5-membered ring. Loss of X to give L(1)CuO(2) can be made prohibitively endergonic by employing ligands X which are highly electron donating and which backbond strongly with and sigma-donate significantly to copper.     

Iron(Ⅱ) hydrides bearing a tetradentate PSNP ligand

Iron(II) hydrides bearing PSNP tetradentate ligand were synthesized and well characterized. The hydrido iron complex [2H(NCMe)](BF₄) is an extremely efficient catalyst for the hydroboration of aldehydes at room temperature.     

Metallomacrocycles incorporating a hemilabile Tröger's base derived ligand

Tr?ger's base, a chiral molecule with a rigid 90 degrees backbone, has been incorporated into a novel hemilabile phosphinoalkyl thioether ligand. Using the Weak Link Approach, this ligand has been reacted with Cu(CH3CN)4PF6 and [Rh(COE)2Cl]x (COE = cyclooctene) to form metallomacrocycles. Upon reaction of the ligand with Cu(I), which prefers a tetrahedral coordination geometry, a bimetallic macrocycle was formed. Alternatively, owing to the steric restrictions imposed by the 90 degrees backbone of the ligand and the square-planar geometry of Rh(I), when the ligand was reacted with [Rh(COE)2Cl]x, the formation of bimetallic closed macrocycles was not observed, and instead a mixture of tri- and tetrametallic closed macrocycles is formed. Introducing pyridine to the Cu(I) complex causes the weak thioether-Cu bonds to break, generating a large bimetallic open macrocycle. Upon reaction of the mixture of Rh(I) metallomacrocycles with CO and Cl-, the cyclic structure of these complexes becomes flexible enough that the dimeric bimetallic macrocycle forms, along with tri- and tetrameric open complexes. The mixture of differently sized Rh(I) macrocyclic complexes has been analyzed using gel permeation chromatography, and the tetramer has been characterized by a single-crystal X-ray diffraction study. These are the first examples of metallomacrocycles containing a Tr?ger's base derivative.     

Chemistry of nitrosyliron complexes supported by a β-diketiminate ligand

Several nitrosyl complexes of Fe and Co have been prepared using the sterically hindered Ar-nacnac ligand (Ar-nacnac = anion of [(2,6-diisopropylphenyl)NC(Me)](2)CH). The dinitrosyliron complexes [Fe(NO)(2)(Ar-nacnac)] (1) and (Bu(4)N)[Fe(NO)(2)(Ar-nacnac)] (2) react with [Fe(III)(TPP)Cl] (TPP = tetraphenylporphine dianion) to generate [Fe(II)(NO)(TPP)] and the corresponding mononitrosyliron complexes. The factors governing NO transfer with dinitrosyliron complexes (DNICs) 1 and 2 are evaluated, together with the chemistry of the related mononitrosyliron complex, [Fe(NO)Br(Ar-nacnac)] (4). The synthesis and properties of the related cobalt dinitrosyl [Co(NO)(2)(Ar-nacnac)] (3) is also discussed for comparison to DNICs 1 and 2. The solid-state structures of several of these compounds as determined by X-ray crystallography are reported.     

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.     

Hydride addition at μ-vinyliminium ligand obtained from disubstituted alkynes

New μ-vinylalkylidene complexes cis-[Fe₂{μ-η¹:η³-C_γ(R′)C_β(R″)C_αHN(Me)(R)}(μ-CO)(CO)(Cp)₂] (R = Me, R′ = R″ = Me, 3a; R = Me, R′ = R″ = Et, 3b; R = Me, R′ = R″ = Ph, 3c; R = CH₂Ph, R′ = R″ = Me, 3d; R = CH₂Ph, R′ = R″ = COOMe, 3e; R = CH₂ Ph, R′ = SiMe₃, R″ = Me, 3f) have been obtained b yreacting the corresponding vinyliminium complexes [Fe₂{μ-η¹:η³-C_γ(R′)C_β(R″)C_αN(Me)(R)}(μ-CO)(CO)(Cp)₂][SO₃CF₃] (2a-f) with NaBH₄. The formation of 3a-f occurs via selective hydride addition at the iminium carbon (C_α) of the precursors 2a-f. By contrast, the vinyliminium cis-[Fe₂{μ-η¹:η³-C_γ (R′) = C_β(R″)C_α = N(Me)(Xyl)}(μ-CO)(CO)(Cp)₂][SO₃CF₃] (R′ = R″ = COOMe, 4a; R′ = R″ = Me, 4b; R′ = Prⁿ, R″ = Me, 4c; Prⁿ = CH₂CH₂CH₃, Xyl = 2,6-Me₂C₆H₃) undergo H⁻ addition at the adjacent C_β, affording the bis-alkylidene complexes cis-[Fe₂{μ-η¹:η²-C(R′)C(H)(R″)CN(Me)(Xyl)}(μ-CO)(CO)(Cp)₂], (5a-c). The cis and trans isomers of [Fe₂{μ-η¹:η³-C_γ(Et)C_β(Et)C_αN(Me)(Xyl)}(μ-CO)(CO)(Cp)₂][SO₃CF₃] (4d) react differently with NaBH₄: the former reacts at C_α yielding cis-[Fe₂{μ-η¹:η³-C_γ(Et)C_β(Et)C_αHN(Me)(Xyl)}(μ-CO)(CO)(Cp)₂], 6a, whereas the hydride attack occurs at C_β of the latter, leading to the formation of the bis alkylidene trans-[Fe₂{μ-η¹:η²-C(Et)C(H)(Et)CN(Me)(Xyl)}(μ-CO)(CO)(Cp)₂] (5d). The structure of 5d has been determined by an X-ray diffraction study. Other μ-vinylalkylidene complexes cis-[Fe₂{μ-η¹:η³-C_γ(R′)C_β(R″)C_αHN(Me)(Xyl)}(μ-CO)(CO)(Cp)₂], (R′ = R″ = Ph, 6b; R′ = R″ = Me, 6c) have been prepared, and the structure of 6c has been determined by X-ray diffraction. Compound 6b results from treatment of cis-[Fe₂{μ-η¹:η³-C_γ(Ph)C_β(Ph)C_αN(Me)(Xyl)}(μ-CO)(CO)(Cp)₂][SO₃CF₃] (4e) with NaBH₄, whereas 6c has been obtained by reacting 4b with LiHBEt₃. Both cis-4d and trans-4d react with LiHBEt₃ affording cis-6a.     

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.     

Computational combinatorial ligand design: Application to human α-thrombin

Summary A new method is presented for computer-aided ligand design by combinatorial selection of fragments that bind favorably to a macromolecular target of known three-dimensional structure. Firstly, the multiple-copy simultaneous-search procedure (MCSS) is used to exhaustively search for optimal positions and orientations of functional groups on the surface of the macromolecule (enzyme or receptor fragment). The MCSS minima are then sorted according to an approximated binding free energy, whose solvation component is expressed as a sum of separate electrostatic and nonpolar contributions. The electrostatic solvation energy is calculated by the numerical solution of the linearized Poisson-Boltzmann equation, while the nonpolar contribution to the binding free energy is assumed to be proportional to the loss in solvent-accessible surface area. The program developed for computational combinatorial ligand design (CCLD) allows the fast and automatic generation of a multitude of highly diverse compounds, by connecting in a combinatorial fashion the functional groups in their minimized positions. The fragments are linked as two atoms may be either fused, or connected by a covalent bond or a small linker unit. To avoid the combinatorial explosion problem, pruning of the growing ligand is performed according to the average value of the approximated binding free energy of its fragments. The method is illustrated here by constructing candidate ligands for the active site of human -thrombin. The MCSS minima with favorable binding free energy reproduce the interaction patterns of known inhibitors. Starting from these fragments, CCLD generates a set of compounds that are closely related to high-affinity thrombin inhibitors. In addition, putative ligands with novel binding motifs are suggested. Probable implications of the MCSS-CCLD approach for the evolving scenario of drug discovery are discussed.     

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.