Ligand Functional Groups Research Articles

NMR resonance assignments for the class II GTP binding RNA aptamer in complex with GTP

The structures of RNA-aptamer-ligand complexes solved in the last two decades were instrumental in realizing the amazing potential of RNA for forming complex tertiary structures and for molecular recognition of small molecules. For GTP as ligand the sequences and secondary structures for multiple families of aptamers were reported which differ widely in their structural complexity, ligand affinity and ligand functional groups involved in RNA-binding. However, for only one of these families the structure of the GTP-RNA complex was solved. In order to gain further insights into the variability of ligand recognition modes we are currently determining the structure of another GTP-aptamer--the so-called class II aptamer--bound to GTP using NMR-spectroscopy in solution. As a prerequisite for a full structure determination, we report here (1)H, (13)C, (15)N and partial (31)P-NMR resonance assignments for the class II GTP-aptamer bound to GTP.

Binding cooperativity between a ligand carbonyl group and a hydrophobic side chain can be enhanced by additional H-bonds in a distance dependent manner: A case study with thrombin inhibitors

One of the underappreciated non-covalent binding factors, which can significantly affect ligand-protein binding affinity, is the cooperativity between ligand functional groups. Using four different series of thrombin inhibitors, we reveal a strong positive cooperativity between an H-bond accepting carbonyl functionality and the adjacent P3 hydrophobic side chain. Adding an H-bond donating amine adjacent to the P3 hydrophobic side chain further increases this positive cooperativity thereby improving the Ki by as much as 546-fold. In contrast, adding an amidine multiple H-bond/salt bridge group in the distal S1 pocket does not affect this cooperativity. An analysis of the crystallographic B-factors of the ligand groups inside the binding site indicates that the strong cooperativity is mainly due to a significant mutual reduction in the residual mobility of the hydrophobic side chain and the H-bonding functionalities that is absent when the separation distance is large. This type of cooperativity is important to encode in binding affinity prediction software, and to consider in SAR studies.

Hydrogen‐Bond‐Assisted Activation of Allylic Alcohols for Palladium‐Catalyzed Coupling Reactions

We report direct activation of allylic alcohols using a hydrogen-bond-assisted palladium catalyst and use this for alkylation and amination reactions. The novel catalyst comprises a palladium complex based on a functionalized monodentate phosphoramidite ligand in combination with urea additives and affords linear alkylated and aminated allylic products selectively. Detailed kinetic analysis show that oxidative addition of the allyl alcohol is the rate-determining step, which is facilitated by hydrogen bonds between the alcohol, the ligand functional group, and the additional urea additive.

Aqueous Cu(II)–Organic Complexation Studied in Situ Using Soft X-ray and Vibrational Spectroscopies

In situ aqueous solutions containing copper-ligand mixtures were measured at the Cu L-edge using X-ray absorption near edge structure (XANES) and with attenuated total reflectance infrared (ATR-FTIR) spectroscopies. Copper complexation with environmentally relevant ligands such as EDTA, citrate, and malate provided a bridge between spectroscopic studies and general environmental behavior and will allow for future study of complex environmental samples. XANES results show that the lowest unoccupied molecular orbital (LUMO) energy is governed by the ligand field strength and is related to Lewis acid/base properties of the ligand functional groups. Complementary ATR-FTIR studies confirmed the importance of water molecules in the structure of these Cu-ligand complexes and provided in-depth structural analysis to support the XANES data. Copper-malate is shown to have a 5/6-O-ring structure, and Cu-ethylenediaminetetraacetate has pentadentate coordination. Cu L-edge XANES also revealed direct Cu-N coordination in these aqueous solutions with amide functional groups.

Inclusion of Multiple Fragment Types in the Site Identification by Ligand Competitive Saturation (SILCS) Approach

The site identification by ligand competitive saturation (SILCS) method identifies the location and approximate affinities of small molecular fragments on a target macromolecular surface by performing molecular dynamics (MD) simulations of the target in an aqueous solution of small molecules representative of different chemical functional groups. In this study, we introduce a set of small molecules to map potential interactions made by neutral hydrogen bond donors and acceptors and charged donor and acceptor fragments in addition to nonpolar fragments. The affinity pattern is obtained in the form of discretized probability or, equivalently, free energy maps, called FragMaps, which can be visualized with the target surface. We performed SILCS simulations for four proteins for which structural and thermodynamic data is available for multiple diverse ligands. Good overlap is shown between high affinity regions identified by the FragMaps and the crystallographic positions of ligand functional groups with similar chemical functionality, thus demonstrating the validity of the qualitative information obtained from the simulations. To test the ability of FragMaps in providing quantitative predictions, we calculate the previously introduced ligand grid free energy (LGFE) metric and observe its correspondence with experimentally measured binding affinity. LGFE is computed for different conformational ensembles and improvement in prediction is shown with increasing ligand conformational sampling. Ensemble generation includes a Monte Carlo sampling approach that uses the GFE FragMaps directly as the energy function. The results show that some but not all experimental trends are predicted and warrant improvements in the scoring methodology. In addition, the potential utility of atom-based free energy contributions to the LGFE scores and the use of multiple ligands in SILCS to identify displaceable water molecules during ligand design are discussed.

Potentiometry, Stability and Thermodynamics of Diethyltin(IV) Dichloride with Some Selected Biomolecules

The interaction of diethyltin(IV), DET, with selected bioligands having a variety of model functional groups was investigated at 25 °C and ionic strength 0.1 mol·dm−3 NaCl using the potentiometric technique. The hydrolysis constants of the DET cation and the formation constants of the complexes formed in solution were calculated using the MINIQUAD-75 program. The stoichiometry and stability constants for the complexes formed are reported. The results show the formation of 1:1 and 1:2 complexes with amino acids and DNA constituents. The dicarboxylic acids form 1:1 complexes. The peptides form both 110 complexes and the corresponding deprotonated amide species [Et2Sn(LH−1)] (11-1). The participation of different ligand functional groups in binding to organotin is discussed. The concentration distributions of the various complex species were evaluated as a function of pH. The standard thermodynamic parameters ΔH° and ΔS°, calculated from the temperature dependence of the equilibrium constants, were investigated for the interaction of DET with thymine as a representative example of DNA constituents. The effect of ionic strength and solvent on hydrolysis constants of DET, protonation equilibria of thymine and its complex formation with DET were investigated and discussed.

Comparative Sequence and Structure Analysis Reveals the Conservation and Diversity of Nucleotide Positions and Their Associated Tertiary Interactions in the Riboswitches

The tertiary motifs in complex RNA molecules play vital roles to either stabilize the formation of RNA 3D structure or to provide important biological functionality to the molecule. In order to better understand the roles of these tertiary motifs in riboswitches, we examined 11 representative riboswitch PDB structures for potential agreement of both motif occurrences and conservations. A total of 61 unique tertiary interactions were found in the reference structures. In addition to the expected common A-minor motifs and base-triples mainly involved in linking distant regions the riboswitch structures three highly conserved variants of A-minor interactions called G-minors were found in the SAM-I and FMN riboswitches where they appear to be involved in the recognition of the respective ligand’s functional groups. From our structural survey as well as corresponding structure and sequence alignments, the agreement between motif occurrences and conservations are very prominent across the representative riboswitches. Our analysis provide evidence that some of these tertiary interactions are essential components to form the structure where their sequence positions are conserved despite a high degree of diversity in other parts of the respective riboswitches sequences. This is indicative of a vital role for these tertiary interactions in determining the specific biological function of riboswitch.

Mapping Protein–Ligand Interactions in the Gas Phase Using a Functional Group Replacement Strategy. Comparison of CID and BIRD Activation Methods

Intermolecular interactions in the gaseous ions of two protein-ligand complexes, a single chain antibody (scFv) and its trisaccharide ligand (α-D-Galp-(1→2)-[α-D-Abep-(1→3)]-α-Manp-OCH3, L1) and streptavidin homotetramer (S4) and biotin (B), were investigated using a collision-induced dissociation (CID)-functional group replacement (FGR) strategy. CID was performed on protonated ions of a series of structurally related complexes based on the (scFv + L1) and (S4 + 4B) complexes, at the +10 and +13 charge states, respectively. Intermolecular interactions were identified from decreases in the collision energy required to dissociate 50% of the reactant ion (Ec50) upon modification of protein residues or ligand functional groups. For the (scFv + L1)(10+) ion, it was found that deoxygenation of L1 (at Gal C3 and C6 and Man C4 and C6) or mutation of His101 (to Ala) resulted in a decrease in Ec50 values. These results suggest that the four hydroxyl groups and His101 participate in intermolecular H-bonds. These findings agree with those obtained using the blackbody infrared radiative dissociation (BIRD)-FGR method. However, the CID-FGR method failed to reveal the relative strengths of the intermolecular interactions or establish Man C4 OH and His101 as an H-bond donor/acceptor pair. The CID-FGR method correctly identified Tyr43, but not Ser27, Trp79, and Trp120, as a stabilizing contact in the (S4 + 4B)(13+) ion. In fact, mutation of Trp79 and Trp120 led to an increase in the Ec50 value. Taken together, these results suggest that the CID-FGR method, as implemented here, does not represent a reliable approach for identifying interactions in the gaseous protein-ligand complexes.

Effects of the Protonation State of the Catalytic Residues and Ligands Upon Binding and Recognition in Targeted Proteins of HIV-1 and Influenza Viruses

The determination of the protonation state of the functional groups of ligands, and the amino acid residues with electrically charged side chains (His, Lys, Arg, Asp and Glu) or the nucleotide bases of the nucleic acids that they interact with, is important for ligand binding and recognition, the enzyme activity and reaction mechanism, and protein folding/unfolding and stability. Herein, the effects of different protonation state assignments of the small substrate and inhibitors and the critical residues on the reverse transcriptase and protease of human immunodeficiency virus type 1 (HIV-1) and the M2 proton channel of influenza A virus are reviewed. Theoretical studies on these topics are summarized and compared with the experimental data.

Investigation of palladium(II) detection and recovery using ligand modified conjugate adsorbent

This study aims to develop a highly selective ligand modified conjugate adsorbent to investigate the selective and sensitive detection and recovery of Pd(II) ions. The conjugate adsorbent was prepared by synthesized 3-(((5-ethoxybenzenethiol)imino)methyl)-salicylic acid ligand immobilization onto mesoporous silica monoliths carriers. The Pd(II) complexation with functional groups in ligand was enhanced the color formation and adsorption corresponding to formation of [Pd(II)-ligand]n+ complexes. Optimum conditions were evaluated as a function of pH, adsorbent dosage, contact time, selectivity and adsorption isotherms models. The data revealed that conjugate adsorbent offered simple and one-step ultra-trace detection procedure without using high tech instruments. This adsorbent was worked well in acidic media for selective take up of Pd(II). The isotherms data showed that the maximum uptake of Pd(II) was as high as 164.20mg/g. Different compositions of eluting solution were tested for the recovery of Pd(II) from conjugate adsorbent. It was found that 0.5MHCl was eluted all of the undesired trace metal ions, while HCl–thiourea was an effective eluent for Pd(II) from conjugate adsorbent. The regenerated adsorbent remained high selective to Pd(II) recovery and exhibited almost the same adsorption capacity as the fresh conjugate adsorbent. The adsorbent was stable without significant loss of adsorption and recovery efficiencies even after several cycles. Therefore, ligand modified conjugate adsorbent is a useful and cost-effective adsorbent for the recovery of precious Pd(II) metal from metal refining processes.

Radiative and Nonradiative Lifetime Engineering of Quantum Dots in Multiple Solvents by Surface Atom Stoichiometry and Ligands

CdTe quantum dots have unique characteristics that are promising for applications in photoluminescence, photovoltaics or optoelectronics. However, wide variations of the reported quantum yields exist and the influence of ligand-surface interactions that are expected to control the excited state relaxation processes remains unknown. It is important to thoroughly understand the fundamental principles underlying these relaxation processes to tailor the QDs properties to their application. Here, we systematically investigate the roles of the surface atoms, ligand functional groups and solvent on the radiative and non-radiative relaxation rates. Combining a systematic synthetic approach with X-ray photoelectron, quantitative FT-IR and time-resolved visible spectroscopies, we find that CdTe QDs can be engineered with average radiative lifetimes ranging from nanoseconds up to microseconds. The non-radiative lifetimes are anticorrelated to the radiative lifetimes, although they show much less variation. The density, nature and orientation of the ligand functional groups and the dielectric constant of the solvent play major roles in determining charge carrier trapping and excitonic relaxation pathways. These results are used to propose a coupled dependence between hole-trapping on Te atoms and strong ligand coupling, primarily via Cd atoms, that can be used to engineer both the radiative and non-radiative lifetimes.

Crystal engineering of flexible metallorganic supramolecular networks

Flexibly porous crystalline materials have been obtained by engineering the structure of metal-containing molecules. In particular, the review deals with ‘wheel-and-axle’ compounds, molecules with two bulky and relatively rigid end groups (wheels) that are connected by a linear rigid link (axle). Owing to their irregular shape, ‘wheel-and-axle’ compounds do not pack efficiently, and for this reason they tend to form inclusion compounds. Here, we present the results obtained by using metal-containing ‘wheel-and-axle’ complexes, where metal ions are inserted in the axle or in the wheels. In particular, wheel-and-axle diols are obtained by inserting Pd(II) and Pt(II) ions into the axle, while metallorganic wheel-and-axle compounds are realized by using half-sandwich Ru(II) building units. A careful choice of metal coordination geometry and ligand functional groups leads to the isolation of crystalline materials with remarkable host–guest properties. Moreover, a close analysis of the crystal structures allows one to propose a model for guest uptake/release.

Water Mediated Ligand Functional Group Cooperativity: The Contribution of a Methyl Group to Binding Affinity is Enhanced by a COO– Group Through Changes in the Structure and Thermodynamics of the Hydration Waters of Ligand–Thermolysin Complexes

Ligand functional groups can modulate the contributions of one another to the ligand-protein binding thermodynamics, producing either positive or negative cooperativity. Data presented for four thermolysin phosphonamidate inhibitors demonstrate that the differential binding free energy and enthalpy caused by replacement of a H with a Me group, which binds in the well-hydrated S2' pocket, are more favorable in presence of a ligand carboxylate. The differential entropy is however less favorable. Dissection of these differential thermodynamic parameters, X-ray crystallography, and density-functional theory calculations suggest that these cooperativities are caused by variations in the thermodynamics of the complex hydration shell changes accompanying the H→Me replacement. Specifically, the COO(-) reduces both the enthalpic penalty and the entropic advantage of displacing water molecules from the S2' pocket and causes a subsequent acquisition of a more enthalpically, less entropically, favorable water network. This study contributes to understanding the important role water plays in ligand-protein binding.

Water Makes the Difference: Rearrangement of Water Solvation Layer Triggers Non‐additivity of Functional Group Contributions in Protein–Ligand Binding

The binding of four congeneric peptide-like thermolysin inhibitors has been studied by high-resolution crystal structure analysis and isothermal titration calorimetry. The ligands differ only by a terminal carboxylate and/or methyl group. A surprising non-additivity of functional group contributions for the carboxylate and/or methyl groups is detected. Adding the methyl first and then the carboxylate group results in a small Gibbs free energy increase and minor enthalpy/entropy partitioning for the first modification, whereas the second involves a strong affinity increase combined with large enthalpy/entropy changes. However, first adding the carboxylate and then the methyl group yields reverse effects: the acidic group attachment now causes minor effects, whereas the added methyl group provokes large changes. As all crystal structures show virtually identical binding modes, affinity changes are related to rearrangements of the first solvation layer next to the S(2)' pocket. About 20-25 water molecules are visible next to the studied complexes. The added COO(-) groups perturb the local water network in both carboxylated complexes, and the attached methyl groups provide favorable interaction sites for water molecules. Apart from one example, a contiguously connected water network between protein and ligand functional groups is observed in all complexes. In the complex with the carboxylated ligand, which still lacks the terminal methyl group, the water network is unfavorably ruptured. This results in a surprising thermodynamic signature showing only a minor affinity increase upon COO(-) group attachment. Because the further added methyl group provides a favorable interaction site for water, the network can be reestablished, and a strong affinity increase with a large enthalpy/entropy signature is then detected.

Protein Pharmacophore Selection Using Hydration-Site Analysis

Virtual screening using pharmacophore models is an efficient method to identify potential lead compounds for target proteins. Pharmacophore models based on protein structures are advantageous because a priori knowledge of active ligands is not required and the models are not biased by the chemical space of previously identified actives. However, in order to capture most potential interactions between all potentially binding ligands and the protein, the size of the pharmacophore model, i.e. number of pharmacophore elements, is typically quite large and therefore reduces the efficiency of pharmacophore based screening. We have developed a new method to select important pharmacophore elements using hydration-site information. The basic premise is that ligand functional groups that replace water molecules in the apo protein contribute strongly to the overall binding affinity of the ligand, due to the additional free energy gained from releasing the water molecule into the bulk solvent. We computed the free energy of water released from the binding site for each hydration site using thermodynamic analysis of molecular dynamics (MD) simulations. Pharmacophores which are colocalized with hydration sites with estimated favorable contributions to the free energy of binding are selected to generate a reduced pharmacophore model. We constructed reduced pharmacophore models for three protein systems and demonstrated good enrichment quality combined with high efficiency. The reduction in pharmacophore model size reduces the required screening time by a factor of 200-500 compared to using all protein pharmacophore elements. We also describe a training process using a small set of known actives to reliably select the optimal set of criteria for pharmacophore selection for each protein system.

Comparative DFT study of inner-sphere As(iii) complexes on hydrated α-Fe2O3(0001) surface models

The long-recognized risk to human health arising from arsenic-contaminated waters is known to be linked to partitioning reactions between arsenic and natural solid phases. Currently, the ability to predict As surface complexation is limited by the lack of molecular-level understanding of As-solid interactions. In the present study, we use density functional theory (DFT) to model mono-, bi-, and tri-dentate As(III) surface complexes on different (previously proposed) structural models for hydrated hematite, modeled as α-Fe(2)O(3)(0001)-water interfaces. One of the modeled hematite-water interfaces is terminated entirely by hydroxyl surface functional groups, comprised of hematite lattice oxygen atoms. The other hematite-water interface is an iron-terminated model in which the outermost oxygen functional groups are water (and water dissociation product) ligands. We report the DFT trends in adsorption energies in terms of As-hematite coordination, hematite surface geometry/stoichiometry, and oxygen functional group identity. The DFT energetics predict that a monodentate As(III) surface complex is preferred on both hematite-water structures, suggesting that the two structural models here employed do not sufficiently represent the true surface structure to reproduce the experimental observation of As(III) bidentate coordination. However, the results do elucidate fundamental concepts of interface reactivity: A key result, supported by electronic structure analysis, is that ligand oxygen functional groups cannot be treated on equal ground with true surface oxygen functional groups. For the systems modeled here the distinction between surface and ligand functional groups supersedes the differences in oxygen coordination with surface Fe. We discuss the impact of this finding on the application of bond-valence-based predictions of mineral-water reactivity, and use the results of this study to pose questions and directions for ongoing modeling efforts aimed at linking macroscopic reactivity with molecular-level understanding.

Variable ligand- and receptor-binding hot spots in key strains of influenza neuraminidase

Influenza A continues to be a major public health concern due to its ability to cause epidemic and pandemic disease outbreaks in humans. Computational investigations of structural dynamics of the major influenza glycoproteins, especially the neuraminidase (NA) enzyme, are able to provide key insights beyond what is currently accessible with standard experimental techniques. In particular, all-atom molecular dynamics simulations reveal the varying degrees of flexibility for such enzymes. Here we present an analysis of the relative flexibility of the ligand- and receptor-binding area of three key strains of influenza A: highly pathogenic H5N1, the 2009 pandemic H1N1, and a human N2 strain. Through computational solvent mapping, we investigate the various ligand- and receptor-binding "hot spots" that exist on the surface of NA which interacts with both sialic acid receptors on the host cells and antiviral drugs. This analysis suggests that the variable cavities found in the different strains and their corresponding capacities to bind ligand functional groups may play an important role in the ability of NA to form competent reaction encounter complexes with other species of interest, including antiviral drugs, sialic acid receptors on the host cell surface, and the hemagglutinin protein. Such considerations may be especially useful for the prediction of how such complexes form and with what binding capacity.

Facile Preparation of Highly Blue Fluorescent Metal Nanoclusters in Organic Media

A multifunctional polymer ligand, containing thiol, thioether, and ester functional groups, is designed and used to prepare intense blue fluorescent gold nanoclusters (AuNCs) with a diameter of ∼1.2 nm and high quantum yield (QY) of 24.3% in organic media without using additional phase-transfer reagents. The size and QY of AuNCs can be fairly controlled by adjusting the molecular weight (Mn) and concentration of multifunctional polymer ligand. The AuNCs retain their fluorescence in various organic solvents and are fairly stable for several months. The same polymer can also be used to prepare silver and platinum nanoclusters (AgNCs and PtNCs), which are not very fluorescent. All of these metal nanoclusters (MNCs) have been characterized thoroughly using TEM, XPS, MALDI-TOF, and other common optical techniques. Apart from the diverse applications of silver and platinum NCs, the highly fluorescent AuNCs may have potential applications in thermal gradient optical imaging, single molecule optoelectronics, sensors and optical components of the detectors.

Reproducing crystal binding modes of ligand functional groups using Site-Identification by Ligand Competitive Saturation (SILCS) simulations.

The applicability of a computational method, Site Identification by Ligand Competitive Saturation (SILCS), to identify regions on a protein surface with which different types of functional groups on low-molecular weight inhibitors interact is demonstrated. The method involves molecular dynamics (MD) simulations of a protein in an aqueous solution of chemically diverse small molecules from which probability distributions of fragments types, termed FragMaps, are obtained. In the present application, SILCS simulations are performed with an aqueous solution of 1 M benzene and propane to map the affinity pattern of the protein for aromatic and aliphatic functional groups. In addition, water hydrogen and oxygen atoms serve as probes for hydrogen-bond donor and acceptor affinity, respectively. The method is tested using a set of 7 proteins for which crystal structures of complexes with several high affinity inhibitors are known. Good agreement is obtained between FragMaps and the positions of chemically similar functional groups in inhibitors as observed in the X-ray crystallographic structures. Quantitative capabilities of the SILCS approach are demonstrated by converting FragMaps to free energies, termed Grid Free Energies (GFE), and showing correlation between the GFE values and experimental binding affinities. For proteins for which ligand decoy sets are available, GFE values are shown to typically score the crystal conformation and conformations similar to it more favorable than decoys. Additionally, SILCS is tested for its ability to capture the subtle differences in ligand affinity across homologous proteins, information which may be of utility toward specificity-guided drug design. Taken together, our results show that SILCS can recapitulate the known location of functional groups of bound inhibitors for a number of proteins, suggesting that the method may be of utility for rational drug design.

Wide Control of Proton Conductivity in Porous Coordination Polymers

The proton conductivities of the porous coordination polymers M(OH)(bdc-R) [H(2)bdc = 1,4-benzenedicarboxylic acid; M = Al, Fe; R = H, NH(2), OH, (COOH)(2)] were investigated under humid conditions. Good correlations among pK(a), proton conductivity, and activation energy were observed. Fe(OH)(bdc-(COOH)(2)), having carboxy group and the lowest pK(a), showed the highest proton conductivity and the lowest activation energy in this system. This is the first example in which proton conductivity has been widely controlled by substitution of ligand functional groups in an isostructural series.