Ion exchange chromatography of monoclonal antibodies: Effect of resin ligand density on dynamic binding capacity

Dynamic binding capacity (DBC) of a monoclonal antibody on agarose based strong cation exchange resins is determined as a function of resin ligand density, apparent pore size of the base matrix, and protein charge. The maximum DBC is found to be unaffected by resin ligand density, apparent pore size, or protein charge within the tested range. The critical conductivity (conductivity at maximum DBC) is seen to vary with ligand density. It is hypothesized that the maximum DBC is determined by the effective size of the proteins and the proximity to which they can approach one another. Once a certain minimum resin ligand density is supplied, additional ligand is not beneficial in terms of resin capacity. Additional ligand can provide flexibility in designing ion exchange resins for a particular application as the critical conductivity could be matched to the feedstock conductivity and it may also affect the selectivity.     

Spectra Library: An Assumption‐Free In Situ Method to Access the Kinetics of Catechols Binding to Colloidal ZnO Quantum Dots

Assumption‐free and in situ resolving of the kinetics of ligand binding to colloidal nanoparticles (NPs) with high time resolution is still a challenge in NP research. A unique concept of using spectra library and stopped‐flow together with a “search best‐match” Matlab algorithm to access the kinetics of ligand binding in colloidal systems is reported. Instead of deconvoluting superimposed spectra using assumptions, species absorbance contributions (ligand@ZnO NPs and ligand in solution) are obtained by offline experiments. Therefrom, a library of well‐defined targets with known ligand distribution between particle surface and solution is created. Finally, the evolution of bound ligand is derived by comparing in situ spectra recorded by stopped‐flow and the library spectra with the algorithm. Our concept is a widely applicable strategy for kinetic studies of ligand adsorption to colloidal NPs and a big step towards deep understanding of surface functionalization kinetics.     

Spatial localization of ligand binding sites from electron current density surfaces calculated from NMR chemical shift perturbations

Rapid, accurate structure determination of protein-ligand complexes is an essential component in structure-based drug design. We have developed a method that uses NMR protein chemical shift perturbations to spatially localize a ligand when it is complexed with a protein. Chemical shift perturbations on the protein arise primarily from the close proximity of electron current density from the ligand. In our approach the location of the center of the electron current density for a ligand aromatic ring was approximated by a point-dipole, and dot densities were used to represent ligand positions that are allowed by the experimental data. The dot density is increased in the region of space that is consistent for the most data. A surface can be formed in regions of the highest dot density that correlates to the center of the ligand aromatic ring. These surfaces allow for the rapid evaluation of ligand binding, which is demonstrated on a model system and on real data from HCV NS3 protease and HCV NS3 helicase, where the location of ligand binding can be compared to that obtained from difference electron density from X-ray crystallography.     

GalaxyDock3: Protein–ligand docking that considers the full ligand conformational flexibility

Predicting conformational changes of both the protein and the ligand is a major challenge when a protein–ligand complex structure is predicted from the unbound protein and ligand structures. Herein, we introduce a new protein–ligand docking program called GalaxyDock3 that considers the full ligand conformational flexibility by explicitly sampling the ligand ring conformation and allowing the relaxation of the full ligand degrees of freedom, including bond angles and lengths. This method is based on the previous version (GalaxyDock2) which performs the global optimization of a designed score function. Ligand ring conformation is sampled from a ring conformation library constructed from structure databases. The GalaxyDock3 score function was trained with an additional bonded energy term for the ligand on a large set of complex structures. The performance of GalaxyDock3 was improved compared to GalaxyDock2 when predicted ligand conformation was used as the input for docking, especially when the input ligand conformation differs significantly from the crystal conformation. GalaxyDock3 also compared favorably with other available docking programs on two benchmark tests that contained diverse ligand rings. The program is freely available at http://galaxy.seoklab.org/softwares/galaxydock.html . © 2019 Wiley Periodicals, Inc.     

Development of Rapid and Facile Solid-Phase Synthesis of PROTACs via a Variety of Binding Styles

Optimizing linker design is important for ensuring efficient degradation activity of proteolysis-targeting chimeras (PROTACs). Therefore, developing a straightforward synthetic approach that combines the protein-of-interest ligand (POI ligand) and the ligand for E3 ubiquitin ligase (E3 ligand) in various binding styles through a linker is essential for rapid PROTAC syntheses. Herein, a solid-phase approach for convenient PROTAC synthesis is presented. We designed azide intermediates with different linker lengths to which the E3 ligand, pomalidomide, is attached and performed facile PROTACs synthesis by forming triazole, amide, and urea bonds from the intermediates.     

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.     

Boron–Ligand Cooperation: The Concept and Applications

The term boron–ligand cooperation was introduced to describe a specific mode of action by which certain metal-free systems activate chemical bonds. The main characteristic of this mode of action is that one covalently bound substituent at the boron is actively involved in the bond activation process and changes to a datively bound ligand in the course of the bond activation. Within this review, how the term boron–ligand cooperation evolved is reflected on and examples of bond activation by boron–ligand cooperation are discussed. It is furthermore shown that systems that operate via boron–ligand cooperation can complement the reactivity of classic intramolecular frustrated Lewis pairs and applications of this new concept for metal-free catalysis are summarized.     

In Situ FTIR and NMR Spectroscopic Investigations on Ruthenium‐Based Catalysts for Alkene Hydroformylation

Homogeneous ruthenium complexes modified by imidazole‐substituted monophosphines as catalysts for various highly efficient hydroformylation reactions were characterized by in situ IR spectroscopy under reaction conditions and NMR spectroscopy. A proper protocol for the preformation reaction from [Ru₃(CO)₁₂] is decisive to prevent the formation of inactive ligand‐modified polynuclear complexes. During catalysis, ligand‐modified mononuclear ruthenium(0) carbonyls were detected as resting states. Changes in the ligand structure have a crucial impact on the coordination behavior of the ligand and consequently on the catalytic performance. The substitution of CO by a nitrogen atom of the imidazolyl moiety in the ligand is not a general feature, but it takes place when structural prerequisites of the ligand are fulfilled.     

Synthesis, spectral characterization and crystal structure of N-2-hydroxy-4-methoxybenzaldehyde-N'-4-nitrobenzoyl hydrazone and its square planar Cu(II) complex

A new aroyl hydrazone, N-2-hydroxy-4-methoxybenzaldehyde-N'-4-nitrobenzoyl hydrazone (H2L) and its mixed ligand Cu(II) complex [CuLpy] [py, pyridine] have been prepared. The ligand is characterized by elemental analysis, electronic, infrared and NMR spectral studies and the complex by electronic, infrared, EPR spectral studies and the magnetic susceptibility data. The structures of the compounds were determined by single crystal X-ray diffraction studies. Both the ligand and the Cu complex crystallize into a triclinic lattice with a space group of PI. From the crystal studies, it is concluded that the ligand molecule exits in the keto form in the solid state, while at the time of complexation, it tautomerises into the enol form. The complex is formed by the double deprotonation of the ligand molecule--both the phenolic and the enolic protons.     

Immobilized metal ion affinity electrophoresis: a preliminary report.

The ligand "Sepharose-IDA-Cu(II)" was entrapped into an agarose gel used for affinity electrophoresis. The binding of three closely related proteins, namely alpha-chymotrypsinogen A, alpha-chymotrypsin, and alpha-chymotrypsin inactivated with diisopropyl fluorophosphate (DIFP) to the affinity gel, was investigated. When the protein having affinity for the ligand was run in the presence of small amounts of the ligand, the retention of the protein by the ligand caused "tailing" of the sample. This pattern was changed in the presence of increasing amounts of the ligand, leading to a "rocket" shape due to the stronger binding of the protein to the chelated metal ligand entrapped in the gel. The degree of retardation in the gel with the ligand is an expression of the affinity between the protein and the ligand. The migration distance of alpha-chymotrypsin and alpha-chymotrypsin treated with DIFP at a given concentration of the ligand is linearly related to the protein amount deposited on the gel. The dissociation constant for the tested proteins were calculated from the B?g-Hansen-Takeo plot. The difference in the affinity strength of these structurally related proteins towards the ligand suggests the involvement of the surface topography of histidine residues on their binding to the ligand.     

Mechanism of Redox‐Active Ligand‐Assisted Nitrene‐Group Transfer in a ZrIV Complex: Direct Ligand‐to‐Ligand Charge Transfer Preferred

The mechanism of the nitrene‐group transfer reaction from an organic azide to isonitrile catalyzed by a Zr^IV d⁰ complex carrying a redox‐active ligand was studied by using quantum chemical molecular‐modeling methods. The key step of the reaction involves the two‐electron reduction of the azide moiety to release dinitrogen and provide the nitrene fragment, which is subsequently transferred to the isonitrile substrate. The reducing equivalents are supplied by the redox‐active bis(2‐iso‐propylamido‐4‐methoxyphenyl)‐amide ligand. The main focus of this work is on the mechanism of this redox reaction, in particular, two plausible mechanistic scenarios are considered: 1) the metal center may actively participate in the electron‐transfer process by first recruiting the electrons from the redox‐active ligand and becoming formally reduced in the process, followed by a classical metal‐based reduction of the azide reactant. 2) Alternatively, a non‐classical, direct ligand‐to‐ligand charge‐transfer process can be envisioned, in which no appreciable amount of electron density is accumulated at the metal center during the course of the reaction. Our calculations indicate that the non‐classical ligand‐to‐ligand charge‐transfer mechanism is much more favorable energetically. Utilizing a series of carefully constructed putative intermediates, both mechanistic scenarios were compared and contrasted to rationalize the preference for ligand‐to‐ligand charge‐transfer mechanism.     

Energetics of the first and second coordination spheres of transition metal ions

For complexes of transition metals (manganese, iron, cobalt, nickel) with monodentate ligands, equilibrium metal-ligand distances and ligand bond energies in the first and second coordination spheres have been calculated by the CNDO method. Some effects of ligand bond energies in different coordination spheres are analyzed. These effects significantly differ between the first and second coordination spheres. In the first sphere, the ligand bond energy is mainly determined by the nature of the central ion and the type of donor atom of the ligand, but weakly depends on the structure of the ligand. Conversely, in the second coordination sphere, the ligand bond energy weakly depends on the nature of the central ion and the type of donor atom, but considerably depends on the structure of the ligands in the first coordination sphere. In the second coordination sphere, ligand binding is determined by ligand interactions with both the central ion and the ligands of the first sphere. In the general case, when strong specific interactions between ligands are absent, the energetics of the second sphere is determined by the size of the inner-spheric ligands, which may be considered to be a specific steric effect. V. I. Vernadskii Institute of Geochemistry and Analytical Chemistry. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 2, pp. 370–374, March–April, 1995. Translated from L. Smolina     

The role of the peripheral anionic site and cation-pi interactions in the ligand penetration of the human AChE gorge

We study the ligand (tetramethylammonium) recognition by the peripheral anionic site and its penetration of the human AChE gorge by using atomistic molecular dynamics simulations and our recently developed metadynamics method. The role of both the peripheral anionic site and the formation of cation-pi interactions in the ligand entrance are clearly shown. In particular, a simulation with the W286A mutant shows the fundamental role of this residue in anchoring the ligand at the peripheral anionic site of the enzyme and in positioning it prior to the gorge entrance. Once the ligand is properly oriented, the formation of specific and synchronized cation-pi interactions with W86, F295, and Y341 enables the gorge penetration. Eventually, the ligand is stabilized in a free energy basin by means of cation-pi interactions with W86.     

A Mesoionic Diselenolene Anion and the Corresponding Radical Dianion

Dichalcogenolenes are archetypal redox non-innocent ligands with numerous applications. Herein, a diselenolene ligand with fundamentally different electronic properties is described. A mesoionic diselenolene was prepared by selenation of a C2-protected imidazolium salt. This ligand is diamagnetic, which is in contrast to the paramagnetic nature of standard dichalcogenolene monoanions. The new ligand is also redox-active, as demonstrated by isolation of a stable diselenolene radical dianion. The unique electronic properties of the new ligand give rise to unusual coordination chemistry. Thus, preparation of a hexacoordinate aluminum tris(diselenolene) complex and a Lewis acidic aluminate complex with two ligand-centered unpaired electrons was achieved.     

Competition between coordination bonds and hydrogen bonds: the nitrile-silver(I) interaction using dicyanobithiophene as ligand

Reactions of the ligand 5,5′-dicyano-2,2′-bithiophene (T₂CN₂) with a variety of silver(I) salts are presented. In most cases, the ligand precipitates by itself without incorporating the silver(I) metal. However, when the counterion is triflate, in benzene or THF, a coordination compound is formed. The crystal structure of the species grown from benzene, a double-stranded one-dimensional polymer, is reported. In this structure, the bithiophene ligand is twisted into the uncommon syn orientation. The reasons for the lack of reactivity of the ligand are discussed by comparing the relative strengths of the interligand hydrogen bond with the ligand–metal bond.     

The 1,4-diphosphabuta-1,3-diene ligand for coordination of divalent group 13 and 14 elements: a density functional study

The 1,4-diphosphabuta-1,3-diene (DPB) ligand as a tool for stabilizing anionic group 13 (B, Al, Ga) and neutral group 14 (C, Si, Ge) cyclic Arduengo-type carbenes is studied by quantum chemical calculations at density functional level. Accordingly, for the former group this ligand is better suited than the corresponding 1,4-diazabuta-1,3-diene (DAB) ligand. It results in larger electron affinities for the corresponding doublet states. For the latter group the DPB ligand yields essentially smaller singlet-triplet separations than the DAB ligand. An exception is the anionic boron compound with relative low singlet stability for both the DAB and DPB ligands.     

Tuning the Dipolar Second‐Order Nonlinear Optical Properties of Cyclometalated Platinum(II) Complexes with Tridentate N^C^N Binding Ligands

Appropriate functionalization of the cyclometalated ligand, L , and the choice of the ancillary ligand, X, allows the dipolar second‐order nonlinear optical response of luminescent [Pt L X] complexes—in which L is an N^C^N‐coordinated 1,3‐di(2‐pyridyl)benzene ligand and X is a monodentate halide or acetylide ligand—to be controlled. The complementary use of electric‐field‐induced second‐harmonic (EFISH) generation and harmonic light scattering (HLS) measurements demonstrates how the quadratic hyperpolarizability of this appealing family of multifunctional chromophores, characterized by a good transparency throughout much of the visible region, is dominated by an octupolar contribution.     

Synthesis and crystal structure of (dibenzo-18-crown-6)(iodo)(trichlorometane)potassium

A new complex compound (dibenzo-18-crown-6)(iodo)(trichlorometane)potassium was obtained. Its crystal structure was studied by X-ray structural analysis. The complex molecule is built by the “guest-host” type: its K⁺ cation is in the crown ligand hollow and is coordinated via its all six O atoms, and also via the iodine ligand I and one Cl atom of the ligand CHCl₃ molecule. The coordination polyhedron of this K⁺ cation is a slightly distorted hexagonal bipyramid. In the crystal structure the complex molecules are connected in infinite chains by intercomplex hydrogen bonds Cl₃C-H?I ⁱ between the ligand molecule CHCl₃ and the iodine ligand of a neighboring complex molecule.     

A new thermodynamic model describes the effects of ligand density and type,salt concentration and protein species in hydrophobic interaction chromatography

A new thermodynamic model is derived that describes both loading and pulse-response behavior of proteins in hydrophobic interaction chromatography (HIC). The model describes adsorption in terms of protein and solvent activities, and water displacement from hydrophobic interfaces, and distinguishes contributions from ligand density, ligand type and protein species. Experimental isocratic response and loading data for a set of globular proteins on Sepharose™ resins of various ligand types and densities are described by the model with a limited number of parameters. The model is explicit in ligand density and may provide insight into the sensitivity of protein retention to ligand density in HIC as well as the limited reproducibility of HIC data.     

Metal- and ligation-dependent fragmentation of [M(1,10-Phenanthroline)(1,2,3)]2+ cations with M = Mn, Fe, Co, Ni, Cu, and Zn: Comparison between the gas phase and solution

The core ions [ML(n)]2+ with n = 1-3, where L = 1,10-phenanthroline and M is a first-row transition metal, have been successfully transferred from aqueous solution into the gas phase by electrospraying and then probed for their stabilities by collision-induced dissociation in a triple quadrupole mass spectrometer. The triply ligated metal dications [ML3]2+ were observed to dissociate by the extrusion of a neutral ligand, while ligand loss from both [ML2]2+ and [ML]2+ was accompanied by electron transfer. Comparisons are provided between gas-phase stabilities and stabilities for ligand loss measured in aqueous solution at 298 K. The measured onset for ligand loss from [ML3]2+ is quite insensitive to the metal, while a distinct stability order has been reported for aqueous solution. Low level density functional theory (DFT) calculations predict an intrinsic stability order for loss of ligand from [ML2]2+, but it differs from that in aqueous solution. Substantial agreement was obtained for the stability order for the loss of ligand from [ML]2+ deduced from onset energies measured for charge separation, computed with DFT, and reported for aqueous solution where hydration seems less decisive in influencing this stability order. A qualitative potential-energy diagram is presented that allows the energy for charge separation to be related to the energy for neutral ligand loss from [ML]2+ and shows that IE(M+) is decisive in determining the intrinsic stability order for loss of ligand from [ML]2+.