The development and characterization of protein-based stationary phases for studying drug-protein and protein-protein interactions

Proteomic applications in identifying protein-protein interactions

There are many things that can be used to characterize a protein. Size, isoelectric point, hydrophobicity, structure (primary to quaternary), and subcellular location are just a few parameters that are used. The most important feature of a protein, however, is its function. While there are many experiments that can indicate a protein's role, identifying the molecules it interacts with is probably the most definitive way of determining its function. Owing to technology limitations, protein interactions have historically been identified on a one molecule per experiment basis. The advent of high throughput multiplexed proteomic technologies in the 1990s, however, made identifying hundreds and thousands of proteins interactions within single experiments feasible. These proteomic technologies have dramatically increased the rate at which protein-protein interactions (PPIs) are discovered. While the improvement in mass spectrometry technology was an early driving force in the rapid pace of identifying PPIs, advances in sample preparation and chromatography have recently been propelling the field. In this chapter, we will discuss the importance of identifying PPIs and describe current state-of-the-art technologies that demonstrate what is currently possible in this important area of biological research.

Drug discovery from natural products - Old problems and novel solutions for the treatment of neurodegenerative diseases

The use of natural products has been shown to be a fruitful approach in the discovery of novel pharmaceuticals. In fact, many currently approved drugs originated from compounds that were first identified in nature. Chemical diversity of natural compounds cannot be matched by man-made libraries of chemically synthesized molecules. Many natural compounds interact with and modulate regulatory protein targets and can be considered evolutionarily-optimized drug-like molecules. Despite this, many pharmaceutical companies have reduced or eliminated their natural product discovery programs in the last two decades. Screening natural products for pharmacologically active compounds is a challenging task that requires high resource commitment. Novel approaches at the early stage of the drug discovery pipeline are needed to allow for rapid screening and identification of the most promising molecules. Here, we review the possible evolutionary roots for drug-like characteristics of numerous natural compounds. Since many of these compounds target evolutionarily conserved cellular signaling pathways, we propose novel, early-stage drug discovery approaches to identify drug candidates that can be used for the potential prevention and treatment of neurodegenerative diseases. Invertebrate in vivo animal models of neurodegenerative diseases and innovative tools used within these models are proposed here as a screening funnel to identify new drug candidates and to shuttle these hits into further stages of the drug discovery pipeline.

Development and characterization of a selective chromatographic approach to the rapid discovery of ligands binding to muscarinic-3 acetylcholine receptor

The pursuit of new ligands binding to muscarinic-3 acetylcholine receptor (M₃R) is viewed as challenging due to the lack of screening methods with high efficiency. To address such challenges, this work developed and characterized an approach to the rapid discovery of M₃R ligands using the immobilized receptor as the chromatographic stationary phase. We fused haloalkane dehalogenase (Halo) as a tag at the C-terminus of M₃R. The fusion M₃R was immobilized on 6-chlorocaproic acid-activated ammino-microspheres by the specific covalent reaction between the Halo-tag and the linker. Comprehensive characterizations of the immobilized M₃R were performed by scanning electron microscope, X-ray photoelectron spectroscopy, and the investigation on the binding of three specific ligands to the receptor. The feasibility of the immobilized M₃R in complex matrices was tested by screening the bioactive compounds in Zhisou oral liquid, assessing the interaction between the screened compounds and the receptor using zonal elution, and evaluating the in vivo activity of the targeted compounds. The results evidenced that the immobilized M₃R has high specificity, good stability, and the capacity to separate M₃R ligands from complex matrices. These allowed us to identify naringin, hesperidin, liquiritigenin, platycodin D, and glycyrrhizic acid as the potential ligands of M₃R. The association constants of the five compounds to M₃R were 4.44 × 10⁴, 1.11 × 10⁴, 7.20 × 10⁴, 4.15 × 10⁴, and 3.36 × 10⁴ M^-1. The synergistic application of the five compounds exhibited an equivalent expectorant activity to the original formula. We reasoned that the current method is possible to provide a highly efficient strategy for the discovery of receptor ligands.

Repositioning of histamine H1 receptor antagonist: Doxepin inhibits viropexis of SARS-CoV-2 Spike pseudovirus by blocking ACE2

The spread of the corona virus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been intensifying in the past year, posing a huge threat to global health. There is an urgent need for effective drugs and vaccines to fight the COVID-19, but their advent may not be quite fast. Drug repurposing is a feasible strategy in the current situation, which could greatly shorten drug development time and help to response quickly to the novel virus outbreak. It has been reported that histamine H₁ receptor antagonists have broad-spectrum antiviral effects. Therefore, in this study, we aim to screen potential drugs among histamine H₁ receptor antagonists that may inhibit SARS-CoV-2 infection. Based on the model of angiotensin-converting enzyme 2 (ACE2) overexpressing HEK293T cell membrane chromatography (CMC), five FDA-approved histamine H₁ receptor antagonists were found to have bioaffinity to ACE2. Then we determined the interaction between these drugs and ACE2 by frontal analysis and surface plasmon resonance (SPR), which consistently demonstrated that these hits bind to ACE2 at micromolar levels of affinity. Through the pseudovirus assay, we finally identified that doxepin could inhibit SARS-CoV-2 spike pseudovirus from entering the ACE2-expressing cell, reducing the infection rate to 25.82%. These preliminary results indicate that the histamine H₁ receptor antagonist, doxepin, is a viable drug candidate for clinical trials. Therefore, we hope the work timely provides rational help for developing anti-SARS-CoV-2 drugs to control the rapid spread of SARS-CoV-2.

Advances in cell membrane chromatography

Cell membrane chromatography (CMC) is a biomimetic chromatographic method based on the ability of membrane receptors to selectively interact with their ligands in vivo. Using membrane receptors as a stationary phase, the CMC method helps in determining the binding characteristics between ligands and membrane receptors and in efficiently identifying specific target components in a complex sample that produce the cellular biological effects of ligands (drugs, antibodies, enzymes, cytokines, etc.). CMC is an analytical tool for revealing characteristics of ligand-receptor interactions, screening and discovering target substances, and accurately controlling the quality of drugs. Since establishment of CMC in the early 1990s, with the rapid development of cell biology, significant progress has been made in the development of high-expression receptors, engineered cell cultures, and standardized preparations, which allowed in vitro immobilization of cell membrane receptors and miniaturization of binding assays. A variety of CMC models have been established using different membrane receptors as a stationary phase, and many new methods have been developed by combining CMC with high-performance liquid chromatography (HPLC)/mass spectrometry or HPLC-IT-TOF technologies. CMC methods have been widely used to study drug-receptor interactions and to screen complex samples for effective or harmful components.

Analysis of solute-protein interactions and solute-solute competition by zonal elution affinity chromatography

Many biological processes involve solute-protein interactions and solute-solute competition for protein binding. One method that has been developed to examine these interactions is zonal elution affinity chromatography. This review discusses the theory and principles of zonal elution affinity chromatography, along with its general applications. Examples of applications that are examined include the use of this method to estimate the relative extent of solute-protein binding, to examine solute-solute competition and displacement from proteins, and to measure the strength of these interactions. It is also shown how zonal elution affinity chromatography can be used in solvent and temperature studies and to characterize the binding sites for solutes on proteins. In addition, several alternative applications of zonal elution affinity chromatography are discussed, which include the analysis of binding by a solute with a soluble binding agent and studies of allosteric effects. Other recent applications that are considered are the combined use of immunoextraction and zonal elution for drug-protein binding studies, and binding studies that are based on immobilized receptors or small targets.

Overview of the detection methods for equilibrium dissociation constant KD of drug-receptor interaction

Drug-receptor interaction plays an important role in a series of biological effects, such as cell proliferation, immune response, tumor metastasis, and drug delivery. Therefore, the research on drug-receptor interaction is growing rapidly. The equilibrium dissociation constant (KD) is the basic parameter to evaluate the binding property of the drug-receptor. Thus, a variety of analytical methods have been established to determine the KD values, including radioligand binding assay, surface plasmon resonance method, fluorescence energy resonance transfer method, affinity chromatography, and isothermal titration calorimetry. With the invention and innovation of new technology and analysis method, there is a deep exploration and comprehension about drug-receptor interaction. This review discusses the different methods of determining the KD values, and analyzes the applicability and the characteristic of each analytical method. Conclusively, the aim is to provide the guidance for researchers to utilize the most appropriate analytical tool to determine the KD values.

Combined use of optical spectroscopy and computational methods to study the binding and the photoinduced conformational modification of proteins when NMR and X-ray structural determinations are not an option

The functions of proteins depend on their interactions with various ligands and these interactions are controlled by the structure of the polypeptides. If one can manipulate the structure of proteins, their functions can in principle be modulated. The issue of protein structure-function relationship is not only a central problem in biophysics, but is becoming clear that the ability to "artificially" modify the structure of proteins could be relevant in fields beyond the biomedical area to provide, for instance, light responses in proteins which would not possess such properties in their native state. This chapter presents an overview of the combination of optical electronic and vibrational spectroscopy with various computational methods to investigate the binding between photoactive ligands and proteins.

Magnetic Ligand Fishing as a Targeting Tool for HPLC-HRMS-SPE-NMR: α-Glucosidase Inhibitory Ligands and Alkylresorcinol Glycosides from Eugenia catharinae

A bioanalytical platform combining magnetic ligand fishing for α-glucosidase inhibition profiling and HPLC-HRMS-SPE-NMR for structural identification of α-glucosidase inhibitory ligands, both directly from crude plant extracts, is presented. Magnetic beads with N-terminus-coupled α-glucosidase were synthesized and characterized for their inherent catalytic activity. Ligand fishing with the immobilized enzyme was optimized using an artificial test mixture consisting of caffeine, ferulic acid, and luteolin before proof-of-concept with the crude extract of Eugenia catharinae. The combination of ligand fishing and HPLC-HRMS-SPE-NMR identified myricetin 3-O-α-L-rhamnopyranoside, myricetin, quercetin, and kaempferol as α-glucosidase inhibitory ligands in E. catharinae. Furthermore, HPLC-HRMS-SPE-NMR analysis led to identification of six new alkylresorcinol glycosides, i.e., 5-(2-oxopentyl)resorcinol 4-O-β-D-glucopyranoside, 5-propylresorcinol 4-O-β-D-glucopyranoside, 5-pentylresorcinol 4-O-[α-D-apiofuranosyl-(1→6)]-β-D-glucopyranoside, 5-pentylresorcinol 4-O-β-D-glucopyranoside, 4-hydroxy-3-O-methyl-5-pentylresorcinol 1-O-β-D-glucopyranoside, and 3-O-methyl-5-pentylresorcinol 1-O-[β-D-glucopyranosyl-(1→6)]-β-D-glucopyranoside.

Penetrable silica microspheres for immobilization of bovine serum albumin and their application to the study of the interaction between imatinib mesylate and protein by frontal affinity chromatography

In the current study, novel featured silica, named penetrable silica, simultaneously containing macropores and mesopores, was immobilized with bovine serum albumin (BSA) via Schiff base method. The obtained BSA-SiO2 was employed as the high-performance liquid chromatographic (HPLC) stationary phase. Firstly, D- and L-tryptophan were used as probes to investigate the chiral separation ability of the BSA-SiO2 stationary phase. An excellent enantioseparation factor was obtained up to 4.3 with acceptable stability within at least 1 month. Next, the BSA-SiO2 stationary phase was applied to study the interaction between imatinib mesylate (IM) and BSA by frontal affinity chromatography. A single type of binding site was found for IM with the immobilized BSA, and the hydrogen-bonding and van der Waals interactions were expected to be contributing interactions based on the thermodynamic studies, and this was a spontaneous process. Compared to the traditional silica for HPLC stationary phase, the proposed penetrable silica microsphere possessed a larger capacity to bond more BSA, minimizing column overloading effects and enhancing enantioseparation ability. In addition, the lower running column back pressure and fast mass transfer were meaningful for the column stability and lifetime. It was a good substrate to immobilize biomolecules for fast chiral resolution and screening drug-protein interactions.

Solid-phase biological assays for drug discovery

In the past 30 years, there has been a significant growth in the use of solid-phase assays in the area of drug discovery, with a range of new assays being used for both soluble and membrane-bound targets. In this review, we provide some basic background to typical drug targets and immobilization protocols used in solid-phase biological assays (SPBAs) for drug discovery, with emphasis on particularly labile biomolecular targets such as kinases and membrane-bound receptors, and highlight some of the more recent approaches for producing protein microarrays, bioaffinity columns, and other devices that are central to small molecule screening by SPBA. We then discuss key applications of such assays to identify drug leads, with an emphasis on the screening of mixtures. We conclude by highlighting specific advantages and potential disadvantages of SPBAs, particularly as they relate to particular assay formats.

Passive sampling methods for contaminated sediments: risk assessment and management

This paper details how activity-based passive sampling methods (PSMs), which provide information on bioavailability in terms of freely dissolved contaminant concentrations (Cfree ), can be used to better inform risk management decision making at multiple points in the process of assessing and managing contaminated sediment sites. PSMs can increase certainty in site investigation and management, because Cfree is a better predictor of bioavailability than total bulk sediment concentration (Ctotal ) for 4 key endpoints included in conceptual site models (benthic organism toxicity, bioaccumulation, sediment flux, and water column exposures). The use of passive sampling devices (PSDs) presents challenges with respect to representative sampling for estimating average concentrations and other metrics relevant for exposure and risk assessment. These challenges can be addressed by designing studies that account for sources of variation associated with PSMs and considering appropriate spatial scales to meet study objectives. Possible applications of PSMs include: quantifying spatial and temporal trends in bioavailable contaminants, identifying and evaluating contaminant source contributions, calibrating site-specific models, and, improving weight-of-evidence based decision frameworks. PSM data can be used to assist in delineating sediment management zones based on likelihood of exposure effects, monitor remedy effectiveness, and, evaluate risk reduction after sediment treatment, disposal, or beneficial reuse after management actions. Examples are provided illustrating why PSMs and freely dissolved contaminant concentrations (Cfree ) should be incorporated into contaminated sediment investigations and study designs to better focus on and understand contaminant bioavailability, more accurately estimate exposure to sediment-associated contaminants, and better inform risk management decisions. Research and communication needs for encouraging broader use are discussed.

Acetylcholinesterase immobilized capillary reactors coupled to protein coated magnetic beads: a new tool for plant extract ligand screening

The use of immobilized capillary enzyme reactors (ICERs) and enzymes coated to magnetic beads ((NT or CT)-MB) for ligand screening has been adopted as a new technique of high throughput screening (HTS). In this work the selected target was the enzyme acetylcholinesterase (AChE), which acts on the central nervous system and is a validated target for the treatment of Alzheimer's disease, as well as for new insecticides. A new approach for the screening of plant extracts was developed based on the ligand fishing experiments and zonal chromatography. For that, the magnetic beads were used for the ligand fishing experiments and capillary bioreactors for the activity assays. The latter was employed also under non-linear conditions to determine the affinity constants of known ligands, for the first time, as well as for the active fished ligand.

Open tubular columns containing the immobilized ligand binding domain of peroxisome proliferator-activated receptors α and γ for dual agonists characterization by frontal affinity chromatography with mass spectrometry detection

The peroxisome proliferator-activated receptors (PPARs) belong to the nuclear receptor superfamily. In the last years novel PPARs ligands have been identified and these include PPARα/γ dual agonists. To rapidly identify novel PPARs dual ligands, a robust binding assay amenable to high-throughput screening toward PPAR isoforms would be desirable. In this work we describe a parallel assay based on the principles of frontal affinity chromatography coupled to mass spectrometry (FAC-MS) that can be used to characterize dual agonists. For this purpose the ligand binding domain of PPARα receptor was immobilized onto the surface of open tubular capillaries to create new PPAR-alpha-OT columns to be used in parallel with PPAR-gamma-OT columns. The two biochromatographic systems were used in both ranking and Kd experiments toward new ureidofibrate-like dual agonists for subtype selectivity ratio determination. In order to validate the system, the Kd values determined by frontal analysis chromatography were compared to the affinity constants obtained by ITC experiments. The results of this study strongly demonstrate the specific nature of the interaction of the ligands with the two immobilized receptor subtypes.

Development of new chromatographic tools based on A2A adenosine receptor subtype for ligand characterization and screening by FAC-MS

A liquid chromatographic stationary phase containing immobilized membranes from cells expressing A(2A) adenosine receptor (A(2A)AR) is firstly described. Cellular membranes from CHO cells stably transfected with human A(2A)AR vector (A(2A)(+)) and from the same cell line transfected with the corresponding empty vector (A(2A)(-)) were entrapped on immobilized artificial membrane (IAM) support and packed into 6.6 mm I.D. glass columns to create A(2A)(+)-IAM and A(2A)(-)-IAM stationary phases. Frontal chromatography experiments on both A(2A)(+)-IAM and A(2A)(-)-IAM columns demonstrated the presence of a low specific interaction with the receptor. However, immobilized A(2A) retained its ability to specifically bind known ligands as demonstrated by the agreement of the calculated K(d) values with two different chromatographic protocols in comparison to previously reported data. In order to maximize the specific interaction, the same cellular membranes were immobilized on the inner surface of a silica capillary (40 cm × 100 μm I.D.) by non-covalent interactions using the avidin-biotin coupling system to create two open tubular columns A(2A)(+)-OT and A(2A)(-)-OT. The open tubular system was characterized by ranking experiments for affinity studies in mixture useful for the selection of new potential candidates.