On‐Bead Screens Sample Narrower Affinity Ranges of Protein–Ligand Interactions Compared to Equivalent Solution Assays

Conceptually, on‐bead screening is one of the most efficient high‐throughput screening (HTS) methods. One of its inherent advantages is that the solid support has a dual function: it serves as a synthesis platform and as a screening compartment. Compound purification, cleavage and storage and extensive liquid handling are not necessary in bead‐based HTS. Since the establishment of one‐bead one‐compound library synthesis, the properties of polymer beads in chemical reactions have been thoroughly investigated. However, the characterization of the kinetics and thermodynamics of protein–ligand interactions on the beads used for screening has received much less attention. Consequently, the majority of reported on‐bead screens are based on empirically derived procedures, independent of measured equilibrium constants and rate constants of protein binding to ligands on beads. More often than not, on‐bead screens reveal apparent high affinity binders through strong protein complexation on the matrix of the solid support. After decoding, resynthesis, and solution testing the primary hits turn out to be unexpectedly weak binders, or may even fall out of the detection limit of the solution assay. Only a quantitative comparison of on‐bead binding and solution binding events will allow systematically investigating affinity differences as function of protein and small molecule properties. This will open up routes for optimized bead materials, blocking conditions and other improved assay procedures. By making use of the unique features of our previously introduced confocal nanoscanning (CONA) method, we investigated the kinetic and thermodynamic properties of protein–ligand interactions on TentaGel beads, a popular solid support for on‐bead screening. The data obtained from these experiments allowed us to determine dissociation constants for the interaction of bead‐immobilized ligands with soluble proteins. Our results therefore provide, for the first time, a comparison of on‐bead versus solution binding thermodynamics. Our data indicate that affinity ranges found in on‐bead screening are indeed narrower compared to equivalent interactions in homogeneous solution. A thorough physico‐chemical understanding of the molecular recognition between proteins and surface bound ligands will further strengthen the role of on‐bead screening as an ultimately cost‐effective method in hit and lead finding.     

Combinatorial Synthesis and Multidimensional NMR Spectroscopy: An Approach to Understanding Protein–Ligand Interactions

Combinatorial chemistry is a laboratory emulation of natural recombination and selection processes. Strategies in this developing discipline involve the generation of diverse, molecular libraries through combinatorial synthesis and the selection of compounds that possess a desired property. Such approaches can facilitate the identification of ligands that bind to biological receptors, promoting our chemical understanding of cellular processes. This article illustrates that the coupling of combinatorial synthesis, multidimensional NMR spectroscopy, and biochemical methods has enhanced our understanding of a protein receptor used commonly in signal transduction, the Src Homology 3 (SH3) domain. This novel approach to studying molecular recognition has revealed a set of rules that govern SH3–ligand interactions, allowing models of receptor–ligand complexes to be constructed with only a knowledge of the polypeptide sequences. Combining combinatorial synthesis with structural methods provides a powerful new approach to understanding how proteins bind their ligands in general.     

Ligand–Receptor Binding Affinities from Saturation Transfer Difference (STD) NMR Spectroscopy: The Binding Isotherm of STD Initial Growth Rates

The direct evaluation of dissociation constants (K_D) from the variation of saturation transfer difference (STD) NMR spectroscopy values with the receptor–ligand ratio is not feasible due to the complex dependence of STD intensities on the spectral properties of the observed signals. Indirect evaluation, by competition experiments, allows the determination of K_D, as long as a ligand of known affinity is available for the protein under study. Herein, we present a novel protocol based on STD NMR spectroscopy for the direct measurements of receptor–ligand dissociation constants (K_D) from single‐ligand titration experiments. The influence of several experimental factors on STD values has been studied in detail, confirming the marked impact on standard determinations of protein–ligand affinities by STD NMR spectroscopy. These factors, namely, STD saturation time, ligand residence time in the complex, and the intensity of the signal, affect the accumulation of saturation in the free ligand by processes closely related to fast protein–ligand rebinding and longitudinal relaxation of the ligand signals. The proposed method avoids the dependence of the magnitudes of ligand STD signals at a given saturation time on spurious factors by constructing the binding isotherms using the initial growth rates of the STD amplification factors, in a similar way to the use of NOE growing rates to estimate cross relaxation rates for distance evaluations. Herein, it is demonstrated that the effects of these factors are cancelled out by analyzing the protein–ligand association curve using STD values at the limit of zero saturation time, when virtually no ligand rebinding or relaxation takes place. The approach is validated for two well‐studied protein–ligand systems: the binding of the saccharides GlcNAc and GlcNAcβ1,4GlcNAc (chitobiose) to the wheat germ agglutinin (WGA) lectin, and the interaction of the amino acid L ‐tryptophan to bovine serum albumin (BSA). In all cases, the experimental K_D measured under different experimental conditions converged to the thermodynamic values. The proposed protocol allows accurate determinations of protein–ligand dissociation constants, extending the applicability of the STD NMR spectroscopy for affinity measurements, which is of particular relevance for those proteins for which a ligand of known affinity is not available.     

Fullerene–Coumarin Dyad as a Selective Metal Receptor: Synthesis,Photophysical Properties,Electrochemistry and Ion Binding Studies

A coumarin derivative with a malonate unit has been synthesized and used for the preparation of a fullerene–coumarin dyad through the Bingel cyclopropanation method. The newly synthesized dyad is soluble in organic solvents and has been fully characterized with traditional spectroscopic techniques. Electronic interactions between the two components of the dyad were probed with the aid of UV/Vis spectroscopy, fluorescence emission, and electrochemistry measurements. Our studies clearly show the presence of electronic interactions between C₆₀ and modified coumarin in the ground state; efficient electron‐transfer quenching of the singlet excited state of the coumarin moiety by the appended fullerene sphere was also observed. Time‐resolved fluorescence measurements revealed lifetimes for the coumarin–C₆₀ dyad at a maximum of 50 ps, while the quantum yield was reaching unity. Additionally, the redox potentials of the C₆₀–coumarin dyad were determined and the energetics of the electron‐transfer processes were evaluated. Finally, after alkaline treatment of C₆₀–coumarin, which resulted in the deprotection of carboxylate units, the dyad was tested as a metal receptor for divalent metal cations; ion competition studies and fluorescence experiments showed binding selectivity for lead ions.     

Site‐Resolved Backbone and Side‐Chain Intermediate Dynamics in a Carbohydrate‐Binding Module Protein Studied by Magic‐Angle Spinning NMR Spectroscopy

Magic‐angle spinning solid‐state NMR spectroscopy has been applied to study the dynamics of CBM3b–Cbh9A from Clostridium thermocellum (ctCBM3b), a cellulose binding module protein. This 146‐residue protein has a nine‐stranded β‐sandwich fold, in which 35 % of the residues are in the β‐sheet and the remainder are composed of loops and turns. Dynamically averaged ¹H‐¹³C dipolar coupling order parameters were extracted in a site‐specific manner by using a pseudo‐three‐dimensional constant‐time recoupled separated‐local‐field experiment (dipolar‐chemical shift correlation experiment; DIPSHIFT). The backbone‐Cα and Cβ order parameters indicate that the majority of the protein, including turns, is rigid despite having a high content of loops; this suggests that restricted motions of the turns stabilize the loops and create a rigid structure. Water molecules, located in the crystalline interface between protein units, induce an increased dynamics of the interface residues thereby lubricating crystal water‐mediated contacts, whereas other crystal contacts remain rigid.     

Quantifying the Effect of Surface Ligands on Dendron–DNA Interactions: Insights into Multivalency through a Combined Experimental and Theoretical Approach

We report the synthesis, DNA binding ability and preliminary gene delivery profiles of dendrons with different amine surface groups, 1,3‐diaminopropane (DAP), N,N‐di‐(3‐aminopropyl)‐N‐(methyl)amine (DAPMA) and spermine (SPM). By using a combination of ethidium bromide displacement, gel electrophoresis and transfection assays, it is shown that the dendrons with SPM groups are the most effective DNA binders, while the DAPMA‐functionalised dendrons were the most effective systems for gene delivery (although the gene delivery profiles were still modest). In order to provide deeper insight into the experimental data, we performed a molecular dynamics simulation of the interactions between the dendrons and DNA. The results of these simulations demonstrated that, in general terms, the enthalpic contribution to binding was roughly proportional to the dendron surface charge, but that dendrons with DAP (and DAPMA) surface amines had significant entropic costs of binding to DNA. In the case of DAP, this is a consequence of the fact that the entire dendron structure has to be organised in order for each individual monoamine charge to make effective contact with DNA. For SPM, however, each surface ligand is already a multivalent triamine, therefore, each individual charge has a much lower entropic cost of binding. For DAPMA, we observed that strong binding of the hindered tertiary amine to the DNA double helix led to ligand back‐folding and significant geometric distortion of DNA. Although this weakens the overall binding, we suggest that this distortion might be an explanation for the experimentally observed enhanced gene delivery, in which DNA compaction is an important step. Overall, this paper demonstrates how structure–activity relationships can be developed for multivalent dendritic ligands and provides insights into the thermodynamics of multivalent interactions.     

Selective Binding Thermodynamics of Bile Acids by Oligo (ethylenediamino)-β-Cyclodextrins and Their Copper (II) Complexes

Complex stability constants (K _S), standard molar enthalpy changes (ΔH°) and entropy changes (TΔS°) for the inclusion complexation of native β-cyclodextrin (β-CD) (1) and some modified β-CDs, i.e., mono(6-ethylenediamino-6-deoxy)-β-CD (3), mono[6-diethylenetriamino-6-deoxy]-β-CD (4) and their corresponding copper complexes 5 and 6, with four representative bile acid guests, i.e., cholate (CA), deoxycholate (DCA), glycocholate (GCA) and taurocholate (TCA), were determined at 25 °C in aqueous phosphate buffer solution (pH 7.20) by means of isothermal titration microcalorimetry (ITC). The stoichiometry of resulting inclusion complexes between CDs and bile acids was demonstrated by UV and conductivity as well as ITC experiments, showing 1:1 binding model upon all inclusion complexation except for metal-mediated dimer 5. The complex stability constants for modified β-CD 2–4 are dramatically magnified with the extended length of amino tether. As compared with 3 and 4, copper(II) complexes 5 and 6 significantly enhance not only binding ability but also molecular selectivity toward bile guest molecule CA through multipoint recognition, but decreased complexes stability toward TCA could be attributed to the decreased hydrophobic microenvironment of CDs cavity due to the introduction of copper(II) coordination center. Thermodynamically, the resulting complexes between hosts and bile guests are driven absolutely by enthalpy, accompanied by entropy gain or loss. Using the present data and those previously reported for mono(6-amino-6-deoxy)-β-CD (2), thermodynamic behavior and enhanced molecular selectivity could be discussed from the viewpoint of hydrophobic interactions, electrostatic cooperation and van der Waals between the hosts and guests.     

Theoretical Consideration of the External Donor of Heterogeneous Ziegler–Natta Catalysts Using Molecular Mechanics,Molecular Dynamics,and QSAR Analysis

In the previous paper we calculated the most stable structure of the catalyst and cocatalyst of metallocene catalyst systems using molecular dynamics and molecular mechanics. In this paper we postulate the active site of the heterogeneous Ziegler–Natta catalyst, and analyze it by the same methods to clarify the main factors that control the activity and molecular weight distribution of the heterogeneous catalyst systems. The roles of the external donor were also considered, and we found that the interaction energy between an external donor and the active site of the catalyst, as well as the structural factors of the external donor itself, are strongly related to both activity and molecular weight distribution. These results reveal that molecular dynamics and molecular mechanics calculations are also effective methods to screen the heterogeneous catalyst systems.