Ligand Binding Strength Research Articles

Determination of the relative ligand‐binding strengths in heteroleptic IrIIIcomplexes by ESI‐Q‐TOF tandem mass spectrometry

An electrospray ionization quadrupole time-of-flight mass spectrometer has been utilized to investigate the relative ligand-binding strengths in a series of heteroleptic-charged iridium(III) complexes of the general formula [(C^N)(2) Ir(III) (S-tpy)](PF(6) ) by using variable collision energies. Collision-induced dissociation experiments were performed in order to study the stability of the Ir(III) complexes that are, for instance, suitable phosphors in light-emitting electrochemical cells. The ratio of signal intensities belonging to the fragment and the undissociated complex depends on the collision energy applied for the tandem mass spectra (MS/MS) analysis. By defining the threshold collision energy and the point of complete complex dissociation, it is possible to estimate the relative complex stabilities depending on the nature of the coordinated ligands [i.e. type of cyclometalating ligand (C^N), substituents on the S-shaped terpyridine (S-tpy)]. The collision energy values differed as a function of the coordination sphere of the Ir(III) centers.

Humic Ion-Binding Model VII: a revised parameterisation of cation-binding by humic substances

Environmental contextNatural organic matter exerts a powerful control on chemical conditions in waters and soils, affecting pH and influencing the biological availability, transport and retention of metals. To quantify the reactions, we collated a wealth of laboratory data covering 40 metals and acid–base reactions, and used them to parameterise the latest in a series of Humic Ion-Binding Models. Model VII is now available to interpret field data, and contribute to the prediction of environmental chemistry. AbstractHumic Ion-Binding Model VII aims to predict the competitive reactions of protons and metals with natural organic matter in soils and waters, based on laboratory results with isolated humic and fulvic acids (HA and FA). Model VII is simpler in its postulated multidentate metal binding sites than the previous Model VI. Three model parameters were eliminated by using a formal relationship between monodentate binding to strong- and weak-acid oxygen-containing ligands, and removing factors that provide ranges of ligand binding strengths. Thus Model VII uses a single adjustable parameter, the equilibrium constant for monodentate binding to strong-acid (carboxylate) groups (KMA), for each metallic cation. Proton-binding parameters, and mean values of log KMA were derived by fitting 248 published datasets (28 for protons, 220 for cationic metals). Default values of log KMA for FA were obtained by combining the fitted values for FA, results for HA, and the relationship for different metals between log KMA and equilibrium constants for simple oxygen-containing ligands. The equivalent approach was used for HA. The parameterised model improves on Model VI by incorporating more metals (40), providing better descriptions of metal binding at higher pH, and through more internally consistent parameter values.

High affinity soluble ILT2 receptor: a potent inhibitor of CD8+ T cell activation

Using directed mutagenesis and phage display on a soluble fragment of the human immunoglobulin super-family receptor ILT2 (synonyms: LIR1, MIR7, CD85j), we have selected a range of mutants with binding affinities enhanced by up to 168,000-fold towards the conserved region of major histocompatibility complex (MHC) class I molecules. Produced in a dimeric form, either by chemical cross-linking with bivalent polyethylene glycol (PEG) derivatives or as a genetic fusion with human IgG Fc-fragment, the mutants exhibited a further increase in ligand-binding strength due to the avidity effect, with resident half-times (t(1/2)) on the surface of MHC I-positive cells of many hours. The novel compounds antagonized the interaction of CD8 co-receptor with MHC I in vitro without affecting the peptide-specific binding of T-cell receptors (TCRs). In both cytokine-release assays and cell-killing experiments the engineered receptors inhibited the activation of CD8(+) cytotoxic T lymphocytes (CTLs) in the presence of their target cells, with subnanomolar potency and in a dose-dependent manner. As a selective inhibitor of CD8(+) CTL responses, the engineered high affinity ILT2 receptor presents a new tool for studying the activation mechanism of different subsets of CTLs and could have potential for the development of novel autoimmunity therapies.

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

Docking is one of the most commonly used techniques in drug design. It is used for both identifying correct poses of a ligand in the binding site of a protein as well as for the estimation of the strength of protein-ligand interaction. Because millions of compounds must be screened, before a suitable target for biological testing can be identified, all calculations should be done in a reasonable time frame. Thus, all programs currently in use exploit empirically based algorithms, avoiding systematic search of the conformational space. Similarly, the scoring is done using simple equations, which makes it possible to speed up the entire process. Therefore, docking results have to be verified by subsequent in vitro studies. The purpose of our work was to evaluate seven popular docking programs (Surflex, LigandFit, Glide, GOLD, FlexX, eHiTS, and AutoDock) on the extensive dataset composed of 1300 protein-ligands complexes from PDBbind 2007 database, where experimentally measured binding affinity values were also available. We compared independently the ability of proper posing [according to Root mean square deviation (or Root mean square distance) of predicted conformations versus the corresponding native one] and scoring (by calculating the correlation between docking score and ligand binding strength). To our knowledge, it is the first large-scale docking evaluation that covers both aspects of docking programs, that is, predicting ligand conformation and calculating the strength of its binding. More than 1000 protein-ligand pairs cover a wide range of different protein families and inhibitor classes. Our results clearly showed that the ligand binding conformation could be identified in most cases by using the existing software, yet we still observed the lack of universal scoring function for all types of molecules and protein families.

Postprocessing of Protein−Ligand Docking Poses Using Linear Response MM-PB/SA: Application to Wee1 Kinase Inhibitors

Prediction of the binding strength of untested ligands is a central issue in structure-based drug design. In order to rapidly screen large compound databases, simple scoring schemes are often used in target-based virtual screening. The resulting scores often correlate poorly with biological affinities. More rigorous scoring methods, such as MM-PB/SA, correlate better with biological data by considering solvation effects and protein flexibility in the calculation of the binding free energy of a ligand. Here we describe the performance of a modified MM-PB/SA method on 222 Wee1 kinase inhibitors (48 pyridopyrimidine and 174 pyrrolocarbazole derivatives). Docking of these inhibitors into the available Wee1 kinase crystal structure yielded a consistent binding mode, and the derived MM-PB/SA models showed a significant correlation between calculated and experimental data (r(2) values between 0.64 and 0.67). Further study of these models on external test sets of Wee1 kinase inhibitors and structurally related decoys showed that a model based on a single kinase-inhibitor conformation can discriminate the active inhibitors from decoys. We also tested whether the linear interaction energy method with continuum electrostatics (LIECE) yields comparable results to MM-PB/SA and whether the LIECE and MM-PB/SA models can be applied for virtual screening of compound libraries.

Solvent and temperature induced switching between structural isomers of Rh(I) phosphinoalkyl thioether (PS) complexes.

To develop functional systems based on the weak-link approach (WLA), it is important to understand how solvent and ligand binding strength alter the coordination geometry of complexes formed from this method. A series of phosphinoalkyl thioether (PS) hemilabile ligands with varying electron donating abilities were synthesized and incorporated into homoligated Rh(I)(PS)2Cl complexes to help understand the effects of solvent and ligand binding strength on the preferred coordination modes. The switching between closed and semiopen structural isomers of these Rh(I)(PS)2Cl complexes was studied by variable temperature 31P NMR spectroscopy in different solvent mixtures of CH2Cl2 and tetrahydrofuran (THF) to obtain thermodynamic parameters (DeltaG(o), DeltaH(o), TDeltaS(o), and K(eq)). The isomers differ in the position of the chloride counterion. In the closed isomer, the Cl- anion occupies the outer coordination sphere, while in the semiopen isomer, the Cl- has moved inner sphere and displaced one of the Rh-S bonds. The closed isomer is favored in CH2Cl2 and the semiopen isomer is favored in THF. The preference for either isomer at equilibrium depends on the solvent polarity, based upon the E(T)(N) solvent polarity scale, as was determined from 15 different solvents, with more polar solvents favoring the closed isomer. The isomer preference also depends on the electron donating ability of the group attached to the sulfur of the PS ligand, with electron donating groups favoring the closed isomers and electron withdrawing groups favoring the semiopen isomers. The formation of the semiopen isomer from the closed isomer is entropically favored but enthalpically disfavored under all conditions studied. Elucidation of the principles and environments that determine the equilibrium between the two isomers will aid in the design of functional complexes prepared by the WLA.

High-coordinated lanthanum(III) complexes with new mono- and bidentate phosphoryl donors; spectroscopic and structural aspects

Monodentate and bidentate ligands PhNHP(O)(NC 4H 8O) 2 ( 1) and PhC(O)NHP(O)(NH( tert-C 4H 9)) 2 ( 2) were used to prepare new 7, 9 and 10-coordinated lanthanum(III) complexes; La( 1) 2Cl 3(H 2O) 2 ( 3), La( 1) 2(NO 3) 3H 2O.La( 1) 2(NO 3) 3CH 3CN ( 4) and La( 2) 2(NO 3) 3 ( 5), respectively. Crystallization of compound 2 in CH 3OH:CH 3CN leads to one conformer in contrast to the crystallization result from CHCl 3: n-C 7H 16 (two conformers). Compound 4 contains two independent nine-coordinated La(III) complexes that are different in the solvated molecules (H 2O and CH 3CN). Some structural and electronic perturbations in coordinated ligand were occurred upon complexation, that are confirmed by increase of 2 J PH, 3 J PH and 6 J PH coupling constants from the free ligand 1 to complexes 3 and 4. The steric repulsions in the first coordination sphere of La 3+ ion, metal–ligand (M–L) binding strength and P O stretching frequency are very influenced by changing the counter ion from Cl − to NO 3 - . Comparing the X-ray crystallography data of free ligand 2 with bis-chelated complex 5, it is found that the phosphoryl group is more reactive than carbonyl counterpart. A blue shift of the ν(N–H) vibration is observed in line with the weakening of the hydrogen bond from N–H···O Phosphoryl in 1 to N–H···Cl in 3. Three dimensional butterfly-shape structures are seen in the unit cell of complex 3, which are produced by O Water–H···O Morpholine hydrogen bonds.

Modification and Characterization of Phytase for Animal Feed Production

Phytases catalyze the hydrolysis of inorganic phosphate from phytic acid and are able to improve the nutritional quality of phytate rich diet. Monogastric animal such as poultry and fish have lack of significant activity to hydrolyze phytate that contribute to elimination of beneficial nutrient for growth therefore contribute to land pollution, eutrophication of ground water and aquatic environment. Besides, it leads to the negative effect on vitamin utilization that lead to the emaciation, retarded growth and reproductive failure to animal. Due to the importance of, microbial sources for the commercial production of phytases, we have selected waste water bacterium phytase as the subject of interest in this study. In silico experiment is used to identify and examine the active site of waste water bacterium phytase. The factors influencing the ligand binding strength in the active site is analyzed and computational site directed mutagenesis experiments were carried out to evaluate the effects of mutations on the binding strength. Multiple mutations of M216R/E219R/H17A, M216R/E219R/F254E and some other multiple mutations showed improvement in the binding strength, primarily due to the addition of hydrogen bond with the adjacent residues. Automated docking based on genetic algorithm is used to dock the phytate in the active site and Partial Mean Force (PMF) scoring is used to calculate the strength of the binding before and after mutation.

A Measure for σ-Donor and π-Acceptor Properties of Diiminepyridine-Type Ligands

Relative metal−ligand binding strengths for the ZnCl2 and low-spin CoIMe fragments and a variety of diiminepyridine (DIP)-like ligands have been calculated at the DFT level. The assumption of a linear energy relation ΔEstab(F,L) = αFσL + βFπL for the relative binding energy of fragment F to ligand L was used to derive scales for ligand parameters σL and πL representing the σ-donor and π-acceptor qualities of these ligands. The results show that DIP ligands in general are only fair σ-donors but exceptionally good π-acceptors, being eclipsed only by their bis(diazo)pyridine analogues and bis(carbene)pyridine variations. Bis(phosphinimine)pyridines are much poorer π-acceptors than DIP, but are comparable in σ-donor capacity. Introduction of substituents at the pyridine or N-aryl rings of DIP results in changes that are much smaller than the above-mentioned replacement of the ligand side arms. The analysis method also puts metal fragments on a scale for Lewis acidity (αF) and π-basicity (βF). For the series o...

Ligand binding to nucleic acids and proteins: Does selectivity increase with strength?

The possible relation of strength and selectivity of ligand binding to biomacromolecules and its theoretical limitation is discussed and illustrated with some examples. It is shown that a linear correlation between selectivity and affinity may be expected on the basis of thermodynamic principles, which also imply that multivalency is as important for selectivity as for affinity enhancement. That strictly linear correlations are often not observed is, apart form statistical problems, mostly due to interactions which may remain constant only at some sites but can differ significantly at other sites, which, e.g., dominate the affinity. Nevertheless, some drugs exhibit in line with theory at the same time a peak affinity and selectivity, such as etonitazene with different opioid receptors. Double-stranded nucleic acids feature relative stable and uniform structures and therefore show relatively good correlations with simple polyamines as ligands and RNA or DNA model receptors. Metalloproteins possess strong binding centers with additional discrimination sites, and can exhibit linear correlations, at least with structurally related metalloproteinases and their inhibitors.

Travel Depth, a New Shape Descriptor for Macromolecules: Application to Ligand Binding

Depth is a term frequently applied to the shape and surface of macromolecules, describing for example the grooves in DNA, the shape of an enzyme active site, or the binding site for a small molecule in a protein. Yet depth is a difficult property to define rigorously in a macromolecule, and few computational tools exist to quantify this notion, to visualize it, or analyze the results. We present our notion of travel depth, simply put the physical distance a solvent molecule would have to travel from a surface point to a suitably defined reference surface. To define the reference surface, we use the limiting form of the molecular surface with increasing probe size: the convex hull. We then present a fast, robust approximation algorithm to compute travel depth to every surface point. The travel depth is useful because it works for pockets of any size and complexity. It also works for two interesting special cases. First, it works on the grooves in DNA, which are unbounded in one direction. Second, it works on the case of tunnels, that is pockets that have no “bottom”, but go through the entire macromolecule. Our algorithm makes it straightforward to quantify discussions of depth when analyzing structures. High-throughput analysis of macromolecule depth is also enabled by our algorithm. This is demonstrated by analyzing a database of protein-small molecule binding pockets, and the distribution of bound magnesium ions in RNA structures. These analyses show significant, but subtle effects of depth on ligand binding localization and strength.

Synthesis and Characterization of Hydrogen-Bonded Assemblies of W6S8L6 Clusters

Ligand-exchange reactions involving octahedral W6S8 clusters and a family of pyridine-based ligands (isonicotinic acid, isonicotinamide, 4-hydroxypyridine, 4-aminopyridine, 4-pyridineacetamide) have been explored with the goal of preparing compounds that crystallize in hydrogen-bonded arrays. Two new compounds, W6S8(4-pyridineacetamide)6.DMF.4-pyridineacetamide (1) and W6S8(4-aminopyridine)6.4DMF (2), were isolated and characterized by single-crystal X-ray diffraction. Both compounds crystallize in the P2(1)/c space group with a = 16.461(1), b = 33.08(2), c = 13.165(10) A, beta = 103.270(15) degrees for 1 and a = 13.8988(5), b = 13.2791(5), c = 15.6293(6) A, beta = 108.5410(10) degrees for 2. Each compound was further characterized by 1H NMR spectroscopy, elemental (CHN) analysis, and thermogravimetric analysis. Examination of the structures shows that 1 forms a three-dimensional hydrogen-bonded network in which each 4-pyridineacetamide ligand interacts with ligands on neighboring clusters or with the free ligand of crystallization. This is the first hydrogen-bonded network formed from W6S8 clusters. In 2, the amino groups act as hydrogen-bond donors toward DMF molecules of crystallization, but an extended array is not formed. In addition, the binding strengths of these pyridine-based ligands to the W6S8 cluster were studied through quantitative 1H NMR studies of ligand-exchange reactions. A qualitative relationship was found between ligand binding strengths and Hammett substituent constants for this group of ligands.

Studying protein–ligand interactions using protein crystallography

Protein X-ray crystallography is now a relatively high-throughput technique that plays a major role in structure-based drug design programs where the method of soaking small organic ligands into protein crystals is used to confirm or identify binding modes. In this review, we discuss some experimental approaches for ‘soaking-in’ ligands into protein crystals where the major problem is poor solubility of the ligand. We also provide examples showing how crystal soaking can be used as a technique for establishing ligand binding strength: K c (the apparent ligand–protein dissociation constant in the crystal), which for some proteins at least, is found to be very similar to the solution K d. Kinetic effects are also found to be important and the rate at which ligands soak into crystals is shown to vary by orders of magnitude from 10−1 to 107 s depending on the system.

The Effect of Organic Ligand Binding on the Growth of CdSe Nanoparticles Probed by Ab Initio Calculations

First principles electronic structure simulations are used to study the atomistic detail of the interaction between organic surfactant molecules and the surfaces of CdSe semiconductor nanoparticles. These calculations provide insights into the relaxed atomic geometry of organics bound to semiconductor surfaces at the nanoscale as well as the electronic charge transfer between surface atoms and the organics. We calculate the binding energy of phosphine oxide, phosphonic and carboxylic acids, and amine ligands to a range of CdSe nanoparticle facets. The dominant binding interaction is between oxygen atoms in the ligands and cadmium atoms on the nanoparticle surfaces. The most strongly bound ligands are phosphonic acid molecules, which bind preferentially to the facets forming the sides of CdSe nanorods. The calculated relative binding strengths of ligands to different facets support the hypothesis that these binding energies control the relative growth rates of different facets, and therefore the resulting ...

Predicting Protein‐Ligand Binding Affinities Using Novel Geometrical Descriptors and Machine‐Learning Methods.

Inspired by the concept of knowledge-based scoring functions, a new quantitative structure−activity relationship (QSAR) approach is introduced for scoring protein−ligand interactions. This approach considers that the strength of ligand binding is correlated with the nature of specific ligand/binding site atom pairs in a distance-dependent manner. In this technique, atom pair occurrence and distance-dependent atom pair features are used to generate an interaction score. Scoring and pattern recognition results obtained using Kernel PLS (partial least squares) modeling and a genetic algorithm-based feature selection method are discussed.

Predicting protein-ligand binding affinities using novel geometrical descriptors and machine-learning methods.

Inspired by the concept of knowledge-based scoring functions, a new quantitative structure-activity relationship (QSAR) approach is introduced for scoring protein-ligand interactions. This approach considers that the strength of ligand binding is correlated with the nature of specific ligand/binding site atom pairs in a distance-dependent manner. In this technique, atom pair occurrence and distance-dependent atom pair features are used to generate an interaction score. Scoring and pattern recognition results obtained using Kernel PLS (partial least squares) modeling and a genetic algorithm-based feature selection method are discussed.

Bent metal carbene geometries in amido N-heterocyclic carbene complexes

Lithium(I) and uranium(VI) amido-tethered Bu(t)-substituted N-heterocyclic carbene (NHC) complexes exhibit very distorted metal-carbene bonds; the corresponding magnesium(II) and mesityl-substituted NHC uranium(VI) complexes are undistorted; the distortion does not affect the ligand binding strength, suggesting a dominance of electrostatic character in closed-shell electropositive metal-carbene bonds.

Mechanism of copper(I)-catalyzed cyclopropanation: a DFT study calibrated with copper(I) alkene complexes

The complete catalytic cycle of copper-catalyzed cyclopropanation is investigated by density functional model calculations. The study focuses on obtaining accurate relative stabilities of the ligand–metal cores of all catalytic intermediates and transition states. The copper iminophosphanamide [H 2P(NH 2) 2κ 2 N]Cu serves as model fragment, since three copper catalyst key intermediates with an iminophosphanamide ligand have been isolated or detected. The electronic structure of the active intermediates, copper(I) carbenes of the d 10-ML 3 type, and their reactivity towards ethene and vinyl alcohol is investigated. The reliability of the computed data is confirmed by their comparison with experimental data of [ t-Bu 2P(NSiMe 3) 2κ 2 N]Cu alkene and alkyne complexes, using relative ligand binding strengths and alkene ligand rotation barriers. The uncharged nature of the model complexes minimizes solvation artifacts and thus renders the evaluation of associative and dissociative ligand exchange pathways possible. The associative alkene ligand exchange with diazoalkane to a κ N,κ O-diazoalkane complex, subsequent intramolecular rearrangement to a κ C-complex and N 2 extrusion are identified on the most probable pathway to the electrophilic copper(I) carbene complexes of the Fischer type. They are predicted to react with alkenes to labile cupracyclobutanes with a planar N 2Cu IIIC 2 core, which undergo facile reductive elimination of a cyclopropane derivative.

KIR enrichment at the effector-target cell interface is more sensitive than signaling to the strength of ligand binding.

Target cell lysis by natural killer cells is inhibited by killer cell immunoglobulin-like receptors (KIR) that bind major histocompatibility complex class I molecules. Many lymphocyte receptors, including KIR, become enriched at the interface with ligand-bearing cells. The contribution of the enrichment to inhibitory signaling has not been determined. We now describe a KIR variant with enhanced green fluorescent protein (EGFP) at the N terminus that can mediate inhibitory signaling, but its enrichment is markedly reduced. This receptor is only slightly weaker at inhibiting lysis than the same KIR tagged with EGFP in the cytoplasmic tail, even though the latter enriched as extensively as wild-type KIR. A slight defect was also detected in the ability of the receptor to reduce adhesion to target cells and for binding of a soluble counterpart to cell surface HLA-C. Our findings suggest that the strength of the interaction required to readily detect receptor enrichment exceeds that required for signaling.

The structure of ligands and effects of the europium luminescence excitation

Results of studies of the luminescence excitation spectra of europium compounds: β-diketonates, aromatic carboxylates, nitrates with sulfoxides are presented. The processes of transfer and degradation of the excitation energy are discussed. Alteration of the relative contribution of two inequivalent ligands to the luminescence excitation of europium β-diketonates with 1,10-phenanthroline derivatives upon modification of ligand radicals and variation of relative binding strength of ligands by metal ion was investigated. The participation of the ligand–metal charge transfer states both in degradation of the excitation energy and in enhancement of Eu3+ luminescence excitation was analyzed. Increase of intraligand charge transfer upon introduction of a ligand's acceptor substituent such as nitro-group, decreasing the ligand–metal charge transfer, was demonstrated. Blocking effect of methylene or oxymethylene bridges on the energy transfer from ligand to Eu3+ ion was observed. This phenomenon witnesses about the electron exchange mechanism of the interaction between the disjuncted parts of the ligand.