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.     

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.     

Analysis of humic acid fouling during microfiltration using a pore blockage–cake filtration model

Fouling by natural organic matter, such as humic substances, is a major factor limiting the use of microfiltration for water purification. The objective of this study was to develop a fundamental understanding of the underlying mechanisms governing humic acid fouling during microfiltration using a combined pore blockage–cake filtration model. Data were obtained over a range of humic acid concentrations, transmembrane pressures, and stirring speeds. The initial flux decline was due to pore blockage caused by the deposition of large humic acid aggregates on the membrane surface, with a humic acid deposit developing over those regions of the membrane that have first been blocked by an aggregate. The rate of cake growth approaches zero at a finite filtrate flux, similar to the critical flux concept developed for colloidal filtration. The data were in good agreement with model calculations, with the parameter values providing important insights into the mechanisms governing humic acid fouling during microfiltration. In addition, the basic approach provides a framework that can be used to analyze humic acid fouling under different conditions.     

Protein–emulsifier interactions at the air–water interface

The main interfacial physico-chemical characteristics and the kinetics of the formation of protein and emulsifier mixed films at the air–water interface are reviewed. Recent advances include the development of new molecular resolution and spectroscopic techniques coupled with surface rheological instruments and the incipient development of computer simulation of the displacement of proteins by emulsifiers.     

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.     

Prediction of ligand binding affinity using a multiple-conformations-multiple-protonation scheme: application to estrogen receptor α

A fast method that can predict the binding affinities of chemicals to a target protein with a high degree of accuracy will be very useful in drug design and regulatory science. We have been developing a scoring function for affinity prediction, which can be applied to extensive protein systems, and also trying to generate a prediction scheme that specializes in each target protein, with as high a predictive power as possible. In this study, we have constructed a prediction scheme with target-specific scores for estimating ligand-binding affinities to human estrogen receptor α (ERα), considering the major conformational change between agonist- and antagonist-bound forms and the change in protonation states of histidine at the ligand-binding site. The generated scheme calibrated with fewer training compounds (23 for the agonist-bound form, 17 for the antagonist-bound form) demonstrated good predictive power (a predictive r(2) of 0.83 for 154 validation compounds); this was also true for compounds with frameworks that were quite different from those of the training compounds. Our prediction scheme will be useful in drug development targeting ERα and in primary screening of endocrine disruptors, and provides a successful method of affinity prediction considering the major conformational changes in a protein.     

Accounting for non-optimal interactions in molecular recognition: a study of ion-π complexes using a QM/MM model with a dipole-polarisable MM region

For a quantitative understanding of molecular structure, interaction and dynamics, accurate modelling of the energetics of both near-equilibrium and less optimal contacts is important. In this work, we explore the potential energy surfaces of representative ion-π complexes. We examine the performance of a semi-empirical QM/MM approach and the corresponding QM/MMpol model, where inducible point dipoles are additionally employed in the MM region. The predicted potential energy surfaces of cation-benzene complexes are improved by inclusion of explicit MM polarisation of the π-molecule. For cation-formamide complexes, inducible dipoles appreciably improve energetic estimates at geometries forming non-optimal interactions. Energetic component analysis suggests that the implicit MM polarisation of the fixed charge QM/MM model mirrors the behaviour of the QM/MMpol dipole model for the energetics of near-equilibrium conformations. However, for complexes at less optimal orientations, the QM/MM model exhibits higher errors than the QM/MMpol approach, being unable to capture orientation-dependent variations in polarisation energy.     

Free energy calculations offer insights into the influence of receptor flexibility on ligand–receptor binding affinities

Docking algorithms for computer-aided drug discovery and design often ignore or restrain the flexibility of the receptor, which may lead to a loss of accuracy of the relative free enthalpies of binding. In order to evaluate the contribution of receptor flexibility to relative binding free enthalpies, two host–guest systems have been examined: inclusion complexes of α-cyclodextrin (αCD) with 1-chlorobenzene (ClBn), 1-bromobenzene (BrBn) and toluene (MeBn), and complexes of DNA with the minor-groove binding ligands netropsin (Net) and distamycin (Dist). Molecular dynamics simulations and free energy calculations reveal that restraining of the flexibility of the receptor can have a significant influence on the estimated relative ligand–receptor binding affinities as well as on the predicted structures of the biomolecular complexes. The influence is particularly pronounced in the case of flexible receptors such as DNA, where a 50% contribution of DNA flexibility towards the relative ligand–DNA binding affinities is observed. The differences in the free enthalpy of binding do not arise only from the changes in ligand–DNA interactions but also from changes in ligand–solvent interactions as well as from the loss of DNA configurational entropy upon restraining.     

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.     

FT-IR studies of molecular interactions in formamide–methanol mixtures

FT-IR spectra of formamide (FA)–methanol (MeOH) mixtures have been measured by ATR technique. Factor analysis applied to the spectra has shown two kinds of intermolecular complexes differing in a manner of polarization of component molecules. The composition of the complexes changes monotonically with the composition of the mixtures. The spectra in the CO stretching region have been analyzed separately using both: the factor analysis and the difference spectra method. Four different environments of carbonyl group of formamide has been revealed over the whole range of the mixture composition. The mean number of formamide molecules disturbed by one methanol molecule via carbonyl group in the formamide-rich region has been found as equal to 1.5. Presumable structures for the molecular complexes have been proposed to explain the results of the analyses.     

Discovery of a novel ligand that modulates the protein–protein interactions of the AAA+ superfamily oncoprotein reptin

Developing approaches to discover protein–protein interactions (PPIs) remains a fundamental challenge. A chemical biology platform is applied here to identify novel PPIs for the AAA+ superfamily oncoprotein reptin. An in silico screen coupled with chemical optimization provided Liddean, a nucleotide-mimetic which modulates reptin''s oligomerization status, protein-binding activity and global conformation. Combinatorial peptide phage library screening of Liddean-bound reptin with next generation sequencing identified interaction motifs including a novel reptin docking site on the p53 tumor suppressor protein. Proximity ligation assays demonstrated that endogenous reptin forms a predominantly cytoplasmic complex with its paralog pontin in cancer cells and Liddean promotes a shift of this complex to the nucleus. An emerging view of PPIs in higher eukaryotes is that they occur through a striking diversity of linear peptide motifs. The discovery of a compound that alters reptin''s protein interaction landscape potentially leads to novel avenues for therapeutic development.     

Examining the impact of ancillary ligand basicity on copper(I)–ethylene binding interactions: a DFT study

A theoretical investigation at the density functional theory level (B3LYP) has been conducted to elucidate the impact of ligand basicity on the binding interactions between ethylene and copper(I) ions in [Cu(?? ²-C₂H₄)]⁺ and a series of [Cu(L)(?? ²-C₂H₄)]⁺ complexes, where L?=?substituted 1,10-phenanthroline ligands. Molecular orbital analysis shows that binding in [Cu(?? ²-C₂H₄)]⁺ primarily involves interaction between the filled ethylene ??-bonding orbital and the empty Cu(4s) and Cu(4p) orbitals, with less interaction observed between the low energy Cu(3d) orbitals and the empty ethylene ??*-orbital. The presence of electron-donating ligands in the [Cu(L)(?? ²-C₂H₄)]⁺ complexes destabilizes the predominantly Cu(3d)-character filled frontier orbital of the [Cu(L)]⁺ fragment, promoting better overlap with the vacant ethylene ??*-orbital and increasing Cu????ethylene ??-backbonding. Moreover, the energy of the filled [Cu(L)]⁺ frontier orbital and mixing with the ethylene ??*-orbital increase with increasing pK _a of the 1,10-phenanthroline ligand. Natural bond orbital analysis reveals an increase in Cu????ethylene electron donation with addition of ligands to [Cu(?? ²-C₂H₄)]⁺ and an increase in backbonding with increasing ligand pK _a in the [Cu(L)(?? ²-C₂H₄)]⁺ complexes. Energy decomposition analysis (ALMO-EDA) calculations show that, while Cu????ethylene charge transfer (CT) increases with more basic ligands, ethylene????Cu CT and non-CT frozen density and polarization effects become less favorable, yielding little change in copper(I)?Cethylene binding energy with ligand pK _a. ALMO-EDA calculations on related [Cu(L)(NCCH₃)]⁺ complexes and calculated free energy changes for the displacement of acetonitrile by ethylene reveal a direct correlation between increasing ligand pK _a and the favorability of ethylene binding, consistent with experimental observations.     

Examining the impact of ancillary ligand basicity on copper(I)–ethylene binding interactions: a DFT study

A theoretical investigation at the density functional theory level (B3LYP) has been conducted to elucidate the impact of ligand basicity on the binding interactions between ethylene and copper(I) ions in [Cu(η ²-C₂H₄)]⁺ and a series of [Cu(L)(η ²-C₂H₄)]⁺ complexes, where L = substituted 1,10-phenanthroline ligands. Molecular orbital analysis shows that binding in [Cu(η ²-C₂H₄)]⁺ primarily involves interaction between the filled ethylene π-bonding orbital and the empty Cu(4s) and Cu(4p) orbitals, with less interaction observed between the low energy Cu(3d) orbitals and the empty ethylene π*-orbital. The presence of electron-donating ligands in the [Cu(L)(η ²-C₂H₄)]⁺ complexes destabilizes the predominantly Cu(3d)-character filled frontier orbital of the [Cu(L)]⁺ fragment, promoting better overlap with the vacant ethylene π*-orbital and increasing Cu → ethylene π-backbonding. Moreover, the energy of the filled [Cu(L)]⁺ frontier orbital and mixing with the ethylene π*-orbital increase with increasing pK _a of the 1,10-phenanthroline ligand. Natural bond orbital analysis reveals an increase in Cu → ethylene electron donation with addition of ligands to [Cu(η ²-C₂H₄)]⁺ and an increase in backbonding with increasing ligand pK _a in the [Cu(L)(η ²-C₂H₄)]⁺ complexes. Energy decomposition analysis (ALMO-EDA) calculations show that, while Cu → ethylene charge transfer (CT) increases with more basic ligands, ethylene → Cu CT and non-CT frozen density and polarization effects become less favorable, yielding little change in copper(I)–ethylene binding energy with ligand pK _a. ALMO-EDA calculations on related [Cu(L)(NCCH₃)]⁺ complexes and calculated free energy changes for the displacement of acetonitrile by ethylene reveal a direct correlation between increasing ligand pK _a and the favorability of ethylene binding, consistent with experimental observations.     

Consideration of dipole–quadrupole interactions in molecular based equations of state

The thermodynamic behaviour of a number of real substances is determined by dipolar as well as quadrupolar interactions of the molecules. In equations of state (EOS) like, e.g. BACKONE separate contributions to the Helmholtz energy for the dipolar and the quadrupolar interactions are considered but no cross contributions. Here, the concept of effective dipole and quadrupole contributions is suggested in which the effective dipole strength μ_e is influenced by the quadrupole cross interaction. Similarily, the effective quadrupole strength Q_e takes into account the dipole cross interaction. In order to arrive at these effective dipolar and quadrupolar strengths, molecular simulations are performed. From the simulation results correlation equations are derived which are used in combination with BACKONE for the calculation of vapour–liquid equilibria (VLE) of real mixtures. By using these effective moments, the only required binary mixing rule parameter k_ij tends to small values of about 0.01 and becomes temperature-independent. Moreover, the VLE pressures are predicted now considerably better than without consideration of the cross contributions.