Zonal Affinity Chromatography Research Articles

Fragment screening for drug leads by weak affinity chromatography (WAC-MS).

Fragment-based drug discovery is an important tool for design of small molecule hit-to-lead compounds against various biological targets. Several approved drugs have been derived from an initial fragment screen and many such candidates are in various stages of clinical trials. Finding fragment hits, that are suitable for optimisation by medicinal chemists, is still a challenge as the binding between the small fragment and its target is weak in the range of mM to µM of Kd and irrelevant non-specific interactions are abundant in this area of transient interactions. Fortunately, there are methods that can study weak interactions quite efficiently of which NMR, surface plasmon resonance (SPR) and X-ray crystallography are the most prominent. Now, a new technology based on zonal affinity chromatography, weak affinity chromatography (WAC), has been introduced which has remedied many of the problems with other technologies. By combining WAC with mass spectrometry (WAC-MS), it is a powerful tool to identify binders quantitatively in terms of affinity and kinetics either from fragment libraries or from complex mixtures of biological extracts. As WAC-MS can be multiplexed by analysing mixtures of fragments (20-100 fragments) in one sample, this approach yields high throughput, where a whole library of e.g. >2000 fragments can be analysed quantitatively within a day. WAC-MS is easy to perform, where the robustness and quality of HPLC is fully utilized. This review will highlight the rationale behind the application of WAC-MS for fragment screening in drug discovery.

Cathepsin D immobilized capillary reactors for on-flow screening assays

The treatment of diseases using enzymes as targets has called for the development of new and reliable methods for screening. The protease cathepsin D is one such target involved in several diseases such as tumors, degenerative processes, and vital processes of parasites causing schistosomiasis. Herein, we describe the preparation of a fused silica capillary, cathepsin D (CatD)-immobilized enzyme reactor (IMER) using in a multidimensional High Performance Liquid Chromatography-based method (2D-HPLC) and zonal affinity chromatography as an alternative in the search for new ligands. The activity and kinetic parameters of CatD-IMER were evaluated by monitoring the product MOCAc-Gly-Lys-Pro-Ile-Leu-Phe (P-MOCAc) (KM = 81.9 ± 7.49 μmol/L) generated by cleavage of the fluorogenic substrate MOCAc-Gly-Lys-Pro-Ile-Leu-Phe-Phe-Arg-Leu-Lys(DNP)-d-Arg-NH2 (S-MOCAc). Stability studies have indicated that CatD-IMER retained 20% of activity after 5 months, a relevant result, because proteases are susceptible to autoproteolysis in solution assays with free enzyme. In the search for inhibitors, 12 crude natural product extracts were analyzed using CatD-IMER as the target, resulting in the isolation of different classes of natural products. In addition, 26 compounds obtained from different species of plants were also screened, demonstrating the efficiency and reproducibility of the herein reported assay even in the case of complex matrices such as plant crude extracts.

Direct analysis - no sample preparation - of bioavailable cortisol in human plasma by weak affinity chromatography (WAC).

Pre-analytical treatment of blood plasma is a time consuming and often rate limiting step in the workflow of LC/MS analysis. We present in this pilot study a new approach for quantitative LC/MS based on weak affinity chromatography (WAC) of crude plasma. The steroid hormone cortisol was selected as a clinically relevant biomarker, as it currently requires extensive pre-analytical preparation. A WAC unit with saturating, immobilized albumin as a prototypic weak binder was used in combination with an ion-funnel MS/MS detector to perform zonal affinity chromatography of cortisol directly from a plasma sample, followed by quantitative multiple reaction monitoring (MRM). This procedure also allowed us to determine the amount of bioavailable cortisol in the clinical plasma sample which is of significant therapeutic interest. This WAC-MS approach showed an excellent correlation (R2=0.86 (P<0.0001 (highly significant); n=60) with a state-of-the-art, clinical competitive immunoassay procedure for plasma cortisol analysis. With integration of WAC into LC/MS workflow, it may be possible to both accelerate and improve assay performance by eliminating the sample extraction step. Preliminary data with other steroid hormones indicate that WAC-MS can be applied to various biomolecules using a plasma transport protein such as albumin.

1H, 13C and 15N backbone resonance assignments of the monomeric human M-ficolin fibrinogen-like domain secreted by Brevibacillus choshinensis

M-ficolin, which forms trimer-based multimers, is a pathogen-recognition protein in the innate immune system, and it binds to ligands through its fibrinogen-like (FBG) domain. As the first step toward the elucidation of the molecular basis for pathogen-recognition by the M-ficolin multimers, we assigned the backbone resonances of the monomeric mutant of the M-ficolin FBG domain, recombinantly expressed by Brevibacillus choshinensis. Like the wild-type trimeric FBG domain, the monomeric FBG domain also requires His251, His284 and His297 for the ligand-binding activity, as judged by mutational analyses using zonal affinity chromatography. The secondary structure predicted by the backbone resonance assignments is similar to that of the trimeric FBG domain in the crystal, indicating that the monomeric FBG domain is folded correctly to perform its function.

Toward high‐throughput drug screening on a chip‐based parallel affinity separation platform

High-throughput screening of compound libraries, including the study of fragments, has become one of the cornerstones in modern drug discovery research. During this process hits are defined that may be developed into valuable leads and eventually into possible drug candidates. In this paper, we have demonstrated that parallel zonal weak affinity chromatography in microcolumns on a chip offers a possible screening format for weakly binding ligands toward a protein target. We used albumin as a model system because this transport protein is well established as a binder (both weak and strong) for drug substances. Bovine serum albumin was immobilized on microparticulate diolsilica particles and then packed into a 24-channel cartridge, which served as the separation platform. Analysis of the obtained chromatograms yielded information about affinity even in the millimolar range. Employing this approach, thousands of substances can be screened in just a day. We feel confident that zonal affinity chromatography will provide a useful technology in the future for performing high-throughput screening.

Binding site of C-reactive protein on M-ficolin

The binding abilities of human C-reactive protein (CRP) with the C-terminal fibrinogen-like (FBG) domain and the full-length form of human M-ficolin were investigated by pull-down and zonal affinity chromatography analyses. Pull-down assays using an N-acetyl-d-glucosamine (GlcNAc)-agarose column demonstrated that CRP binds to the trimeric FBG domains, and that the GlcNAc-binding ability of the FBG domain is unaffected by CRP binding. Interestingly, the full-length M-ficolin, comprising the N-terminal collagen-like (COL) and C-terminal FBG domains, displayed lower affinity for CRP, and the monomeric FBG domain showed virtually no binding to CRP, as qualitatively judged by zonal affinity chromatography using a GlcNAc column. These results indicated that CRP binding requires the trimeric form of the FBG domain, and that the presence of the COL domain reduces the interaction between CRP and M-ficolin. In addition, pull-down assays using a histidine-tag affinity column demonstrated that neither the full-length M-ficolin nor the trimeric FBG domains, immobilized through their C-terminal histidine tags, showed any affinity for CRP, indicating that the CRP binding site is located near Ala326 at the C-terminus of M-ficolin, spatially close to a neck region (around Pro115) between the FBG and COL domains. From these findings, we concluded that CRP binding is enhanced by conformational bending at the neck region of M-ficolin, to avoid steric hindrance by the COL domain. Such a situation may be generated by oligomeric M-ficolin binding to surfaces with widely distributed ligands, such as pathogens.

Interaction of lactate dehydrogenase with anthraquinone dyes: characterization of ligands for dye–ligand chromatography

Anthraquinone dyes (ADs), originally developed for the textile industry, are useful nucleotide-specific ligands for the purification of proteins by affinity techniques. Their specific feature is to mimic the adenine nucleotides ATP, ADP, NAD, NADH, which enables them to interact with the nucleotide-binding sites of enzymes such as dehydrogenases, kinases and ATPases. In the present study, the interactions and/or inhibitory effects of seven ADs, including Cibacron Blue F3G-A, Remazol Brilliant Blue R, on the activity of lactate dehydrogenase (LDH) were investigated. The ADs used in this paper could be divided into two groups: (i) AD1–AD3 which do not contain a triazine moiety; (ii) AD4–AD7 which contain the triazine moiety. Enzyme kinetics and zonal affinity chromatography were used for the characterization of the interaction affinity between the dye and LDH. Enzyme kinetic measurements were carried out at three different pH values: 6.5, 7.5 and 8.5. The relationship between physical and chemical properties of ADs (e.g., acid–basic properties, three dimensional structure of the respective dyes) and their interaction efficiency with LDH was studied. LDH activity was inhibited by all ADs, excluding AD1 (precursor of the blue dyes) and inhibition was always competitive. Similarity in the mutual position of the acidic and basic groups in NADH and the respective AD molecule was found to be a crucial factor for influencing the inhibitory action of the substance. The existence of ADs in the protonated form should be considered as another factor, important for the ADs inhibitory action on this enzyme.

Study of porous cellulose beads as an affinity adsorbent via quantitative measurements of interactions of lactate dehydrogenase with immobilized anthraquinone dyes

Dissociation constants and the character of interaction of immobilized anthraquinone dyes with lactate dehydrogenase (LDH) have been investigated with the aid of zonal affinity chromatography and batch adsorption. When processed by means of the time-concentration model, the data from adsorption experiments with LDH revealed that, contrary to adsorption onto Cibacron Blue (CB)-cellulose beads (found to be near to biospecific), the adsorption of enzyme onto Remazol Blue (RB)-cellulose beads could be characterized rather as a hydrophobic one. The missing biospecificity in the interaction of LDH with RB-cellulose beads was confirmed by the absence of any competition for the enzyme between the immobilized dye and NADH applied as a mobile ligand in conditions of zonal chromatography. On the other hand, in the case of CB-cellulose beads, NADH or CB-dextran conjugate applied separately as mobile ligands were found capable of competing for one binding site of tetrameric LDH. The strength of interaction of LDH with conjugate exceeded significantly the strength of interaction observed with NADH. This enables us to conclude that using CB-dextran conjugate the additional nonspecific binding interactions are considerably suppressed. It is reasonable to suppose that CB-dextran may represent a more powerful mobile ligand for dye-ligand chromatography than NADH, particularly in preparative scale.

Detection and isolation of oligosaccharides with Le a and Le b blood group activities by affinity chromatography using monoclonal antibodies

Affinity columns prepared by immobilizing monoclonal antibodies that specifically recognize the Le a or the Le b blood group antigens can be used for analytical or preparative isolation of oligosaccharides with the corresponding reactivities. The number of immobilized functional antibody combining sites on a column and the dissociation constants for standard oligosaccharides are determined by frontal analysis. By employing a simple approximation [K.-I. Kasai et al. (1986) J. Chromatogr. 376, 33–47]these parameters can be used to rationally design columns with properties appropriate for zonal affinity chromatography. The affinity for binding of the Le a-active oligosaccharide lacto- N-fucopentaose II (LNF II) by the anti-Le a antibody CO-514 doubles for each 8°C downward shift in temperature between 37 and 4°C. By zonal chromatography, Le a-or Le b-active oligosaccharides are recovered from a complex mixture of milk oligosaccharides containing more than a 20-fold molar excess of structurally similar but antigenically distinct oligosaccharides. The capacity for preparative isolation of an oligosaccharide increases in a linear fashion with the amount of antibody loaded on the solid support. The monoclonal antibodies used in these studies are products of hybridomas derived from mice immunized with human colorectal carcinoma cell lines [M. Blaszczyk et al. (1984) Arch. Biochem. Biophys. 233, 161–168]. The experiments establish that affinity chromatography applied to mixtures of oligosaccharides released by enzymatic or chemical cleavage of glycoconjugates may simplify the task of isolating and characterizing biologically interesting target antigens of monoclonal antibodies.

Evaluation of equilibrium constants for the interaction of lactate dehydrogenase isoenzymes with reduced nicotinamide-adenine dinucleotide by affinity chromatography

Rabbit muscle lactate dehydrogenase was subjected to frontal affinity chromatography on Sepharose-oxamate in the presence of various concentrations of NADH and sodium phosphate buffer (0.05 M, pH 6.8) containing 0.5 M-NaCl. Quantitative interpretation of the results yields an intrinsic association constant of 9.0 x 10 (4)M-1 for the interaction of enzyme with NADH at 5 degrees C, a value that is confirmed by equilibrium-binding measurements. In a second series of experiments, zonal affinity chromatography of a mouse tissue extract under the same conditions was used to evaluate assoication constants of the order 2 x 10(5)M-1, 3 x 10(5)M-1, 4 x 10(5)M-1, 7 x 10(5)M-1 and 2 x 10(6)M-1 for the interaction of NADH with the M4, M3H, M2H2, MH3 and H4 isoenzymes respectively of lactate dehydrogenase.