Stepwise frontal affinity chromatography model for drug and protein interaction

Screening and evaluation of the hit compound from a DNA-encoded library derived from natural products based on immobilized endothelin receptor A

The enormous growing demand for drug candidates binding to endothelin receptor A (ETA) has made it necessary to continuously pursue new strategies for ligand screening and early evaluation. This work achieved the one-step immobilization of ETA based on the bioorthogonal chemistry between the epidermal growth factor receptor tag (EGFR-tag) and ibrutinib. Comprehensive characterizations including Western blot analysis are performed to realize the morphology, antibody/ligand recognition activity, and specificity of the immobilized ETA. Taking macitentan, ambrisentan, and bosentan as an example, we utilized the immobilized ETA to construct a thermodynamic model for the evaluation of the specific ligands binding to ETA. Using this model, we screened the potential compound NP845 from a DNA-encoded library with 10,686 members derived from natural products and calculated the association constant as (2.24 ± 0.15) × 105 M-1 at 37 °C, thereby demonstrating the good pharmacological activity of NP845. The entropy change (∆Sθ), enthalpy change (∆Hθ), and Gibbs free energy (∆Gθ) were 1.75 J/mol·K, -31.1 kJ/mol, and -31.6 kJ/mol at 37 °C, whereby we recognized the electrostatic force was the driving force of the interaction between NP845 and ETA. In vitro cell tests proved that NP845 can downregulate the expression level of PKA, B-Raf, MEK, and ERK1 in VSMC. Our results indicated that NP845 was a potential lead compound for fighting the ailments mediated by ETA.

New liquid chromatography columns for highlighting the interaction of ligand candidates with humic acid

Humic acid was the main compound in soil and reduced the availability of some organic compounds in soils. In this work, humic acid was immobilized for the first time on a homemade neutravidin poly(glycidyl methacrylate-co-ethylene dimethacrylate) capillary column with a 20 μm i.d. for the screening of potential ligands to humic acid and the evaluation of their molecular recognition mechanism. This homemade humic acid column enabling it to work at very low backpressure (0.60 MPa at 20 nl/min flow rate), had a long lifetime, excellent repeatability, and negligible non-specific binding sites. The performance of this affinity humic acid column was demonstrated by the evaluation of recognition assay for a series of known ligands of humic acid (a series of rodenticide molecules) which is the heart of the fragment-based drug design. In addition, this column was used successfully for highlighting the binding mechanism to humic acid of the severe acute respiratory syndrome coronavirus-2-spike protein. As well this new humic acid miniaturized liquid chromatography column developed in this work could be used in the feature for another solute molecule-humic acid binding studies or for a separative mode.

Development of a new heparan sulfate proteoglycan (HSPG) chromolith LC column to study the pH dependence binding of peptide vaccines to HSPG and role of human serum albumin on its binding

Heparan sulfate proteoglycan (HSPG) expressed on immune cell surface participate in antitumor T-cell responses generated in the acidic lymph node (LN) microenvironment. In this work, HSPG was immobilized for the first time on a HPLC chromolith support for studying the effect of extra cellular acidosis in LNs on the binding to HSPG of two peptide vaccines (universal cancer peptide UCP2 and UCP4). This home-made HSPG column enabling to work at high flow-rates, was resistance to change in pH, had a long - life time, an excellent repeatability and negligible non-specific binding sites. The performance of this affinity HSPG column was confirmed by the evaluation of recognition assay for a series of known ligand of HSPG. It was shown that at 37 °C, the UCP2 binding to HSPG versus pH described a sigmoidal shape while UCP4 remained relatively constant in the pH range 5.0-7.5 and lower than the one of UCP2. By the use of an HSA HPLC column, it was shown at 37 °C and in acidic conditions a loss of affinity of UCP2 and UCP4 to HSA. It was demonstrated that upon UCP2/HSA binding, the protonation of the histidine residue in the cluster R(arg) Q(Gln) Hist (H) of the UCP2 peptide allowed to expose more favorably than UCP4 its polar and cationic groups to the negative net charge of HSPG on immune cells. Acidic pHs led to the protonation of the UCP2 residue histidine by flipping the His switch to the on position with a concomitant increase in affinity for the negative net charge of HSPG confirming that UCP2 was more immunogenic than UCP4. As well this HSPG chromolith LC column developed in this work could be used in the feature for other protein - HSPG binding studies or for a separative mode.

ACE2 and SARS-CoV-2-Main Protease Capillary Columns for Affinity Chromatography: Testimony of the Binding of Dexamethasone and its Carbon Nanotube Nanovector

In this paper, each of the two following proteins, the angiotensin-converting enzyme 2 (ACE2) and the Main protease (Main pro) of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) were grafted for the first time on homemade neutravidin poly(GMA-co-EDMA) capillary columns for the research of their ligands. The effect of the column diameter on the quantity of immobilized biotinylated protein was studied. For a capillary length of 40 mm, when its internal diameter varied from 75 to 25 μm, the grafted quantity of ACE2 decreased by 85% (from 1.50 to 0.24 μg). Among all the studied ligands, a particular vigilance has been given for dexamethasone, a widely used molecule today for adult patients hospitalized with SARS-CoV-2. Competition experiments were performed with SARS-CoV-2 Receptor Binding Domain used as reference molecule with the ACE2 affinity column to assess the orthosteric binding site of dexamethasone (Dex) on ACE2. This ligand was then immobilized on Multiwall Carbon Nanotubes (Dex/MWCNT). By comparison of the normalized breakthrough curves measured for Dex and Dex/MWCNT on both the ACE2 and Main pro affinity columns, it was showed for the first time that nanovectorisation of Dex with MWCNT enhanced and stabilized its binding to both ACE2 and Main pro. This last result reinforced the use of Dex and the interest of MWCNT for boosting immune health against COVID 19.

The importance of plasma protein and tissue binding in a drug discovery program to successfully deliver a preclinical candidate

Plasma protein binding and tissue binding are arguably two of the most critical parameters that are measured as part of a drug discovery program since, according to the free drug hypothesis, it is the free drug that is responsible for both efficacy and toxicity. This chapter aims to deconstruct the role of plasma protein and tissue binding in drug discovery programs, and to consider the conclusion made by Pfizer and Genentech/Depomed a decade ago that optimising plasma protein binding as an independent parameter does not significantly influence efficacy. This chapter will also examine how binding metrics are applied in drug discovery programs and explore circumstances where optimising plasma protein or tissue binding can be an effective strategy to deliver a candidate molecule for preclinical development with an early indication of sufficient therapeutic index.

Development of nano Bio LC columns for the search of acethylcholinesterase molecular targets

A novel acetylcholinesterase (AChE) Nano LC capillary column (75μm i.d * 50 mm length) was developed for the fast screening of AChE inhibitors and the evaluation of their molecular recognition mechanism. Biotinylated AChE was immobilized on a streptavidin Nano LC capillary column. Because of the very strong streptavidin biotin interaction, the AChE immobilization step performed by frontal analysis is very fast (required less than 10 min) and the amount of immobilized AChE was in the microgram range (1μg). The yellow anion obtained from the enzymatic reaction detected at 412 nm was achieved within 60 s and the immobilized acetylcholinesterase retained 96% of the initial activity beyond 90 days. This column was successfully applied for the discrimination of weak affinity ligands to AChE from non-binders which is the heart of the Fragment Based Drug Design (FBDD). This column was used for the determination of the IC₅₀ values of a series of inhibitor molecules. In addition, it was demonstrated that competitive experiments could be performed with our miniaturized system to confirm the existence and the binding pocket of a ligand to AChE contained in a methanol plant extract. The results revealed that our AChE Nano LC capillary column developed in this work represents a useful tool for the rapid screening of inhibitor candidates and evaluation of action mechanism. This article is protected by copyright. All rights reserved.

Immobilization of the SARS-CoV-2-receptor binding domain onto methacrylate-based monoliths for nano LC at 30 nL min-1 and application for research of its ligands

For the design of novel potent molecules against therapeutic protein targets produced in a low quantity or that are very expensive, the development of miniaturized analytical techniques is of crucial importance. One challenging target is the receptor binding domain (RBD) of the SARS-CoV-2-spike protein (S), which mediates the binding of the virus to host cells. In the present study, the RBD protein was thus immobilized on polymethacrylate monoliths prepared in a miniaturized capillary column (25 μm internal diameter; 70 mm length) by in situ polymerization, which could offer low backpressure in Nano LC at 30 nL min^-1. The immobilized quantity of the expensive RBD protein on the organic monolith was very low, in the submicrogram range, i.e., 0.060 μg. The immobilization method reduced non-selective interactions between the ligand and the organic monolith matrix and maintained the functionality of RBD due to the high activity rate (96%). The performance of this miniaturized affinity capillary column was demonstrated for the rapid evaluation of a recognition assay induced by 1,2,3,4,6-pentagalloyl glucose (PGG), a known ligand of RBD, and by five other molecules. In addition, it was demonstrated that competitive experiments could be performed with our miniaturized system to reveal the existence of only one type of binding site for three ligands of RBD, namely carbenoxolone, simeprevir and irinotecan. All these results showed the potential of our analytical miniaturized affinity system for the determination of interactions between potential ligands and immobilized RBD of SARS-CoV-2 to aid in the battle against COVID-19.

Two Original Experimental Setups for Staircase Frontal Affinity Chromatography at the Miniaturized Scale

Frontal affinity chromatography is a powerful, underappreciated technique for the qualitative (screening) and quantitative (K_d determination) evaluation of biological interactions. Its development has been previously hampered by its sample consumption, limited throughput, and lack of dedicated instrumentation especially at a miniaturized scale. This work describes two original experimental devices allowing nano-frontal affinity chromatography titrations (nano-FAC) to be automatically implemented in the time-saving staircase mode. The first nano-FAC system utilizes a capillary electrophoresis device (7100 CE Agilent system) in the pressurization mode with in situ UV detection. The second nano-FAC experimental setup implements a nano-LC device (Ultimate 3000 Thermo) modified with a 10-port valve equipped with two superloops (loop volume, 5 μL) operating alternatively and automatically in a single run. The benefits and drawbacks of each approach are exemplified using two model protein-ligand interactions (concanavalin A-mannose and concanavalin A-glucose). The two methods result in concordant dissociation constants (K_d) and number of active site (B_act) values, obtained in a fully automated manner, with low sample consumption and good throughput.

Development of a multi-layering protein grafting process on miniaturized monolithic columns for weak affinity nano liquid chromatography application purposes

Affinity chromatography is a powerful technique to identify and quantify weak ligand-protein interactions (Kd in the range of mM to 0.1µM). In some fields such as Fragment Based Drug Discovery, the detection of very weak affinities (mM) is of utmost importance since weak ligands can be good starting points for the conception of high affinity ligands. However, the identification of such weak ligands can be hampered by the limited bulk density of active target grafted onto the support. At the same time, downscaling the chromatographic column is of utmost interest when scarce and/or expensive proteins are targeted. In this context, we herein present a novel approach of protein immobilization to improve the bulk density of active protein grafted onto organic capillary monolithic columns. The proposed approach is based on the streptavidin-biotin interaction and consists of successive grafting steps of biotinylated target protein onto streptavidin layers through a multi-layering process. Concanavalin A was used as model protein. The study focuses on the optimization of the grafting conditions to maximize the amount of active protein during the multi-layering process and highlights the impact of the biotinylation ratio of the protein. It is demonstrated that a 3-layer grafting process allows to improve the bulk density of active sites by a 2-fold factor compared to a single layer. This improvement in protein density allows to increase the affinity range of this technique to the millimolar range.

[Advances in chromatography in the study of drug-plasma protein interactions]

小分子药物进入人体血液循环系统后与人血清白蛋白(HSA)、α₁ -酸性糖蛋白(AGP)等血浆蛋白存在广泛的相互作用,这些相互作用深刻影响药物在体内的分布及其与靶标蛋白的结合,进而影响药物效应的发挥。深入探究药物与血浆蛋白间的相互作用对于候选药物的成药性优化、新药研发、联合用药的风险评控等意义重大。而发展高效、灵敏、准确的分析检测方法是开展药物-血浆蛋白相互作用研究的关键。近年来,色谱技术由于其高通量、高分离性能、高灵敏度等特点在该领域得到了广泛的应用,包括测定血浆蛋白翻译后修饰对药物结合的影响,多种药物的竞争性结合等。其中,高效亲和色谱(HPAC)和毛细管电泳(CE)应用最为广泛,能够通过多种分析方法获取结合常数、结合位点数、解离速率常数等相互作用信息。该文着重综述了HPAC和CE在药物-血浆蛋白相互作用研究中的常用策略及最新研究进展,包括HPAC中常用的前沿色谱法、竞争洗脱法、超快亲和提取法、峰值分析法和峰衰减分析法,以及CE中常用的亲和毛细管电泳法(ACE)和毛细管电泳前沿分析法(CE-FA)等。最后,该文还对当前色谱方法存在的不足进行了总结,并对色谱技术在药物-血浆蛋白相互作用研究领域的应用前景和发展方向进行了展望。

The distinct binding modes of pesticides affect the phase transitions of lysozyme

Studying the aggregation and nucleation of proteins in the presence of organic molecules is helpful for disclosing the mechanisms of protein crystallization.

Application of a stepwise frontal analysis method in cell membrane chromatography

Bio-affinity chromatography is used in the study of drug-receptor interactions. A stepwise frontal analysis (SFA) method was developed based on frontal analysis (FA). A high expression alpha 1A adrenergic receptor (α_1A AR) cell membrane chromatography (CMC) method was then developed and combined with SFA to investigate the affinity of three model α_1A AR-binding drugs towards α_1A AR. Equilibrium dissociation constant (K_d) values for drug-receptor interactions were determined by FA and SFA; results showed that these methods were highly consistent. The results demonstrate that the CMC/SFA method is a time-saving and less wasteful method than traditional method for the evaluation of drug-receptor binding characteristics, and could be used to study the interactions between drugs and membrane receptors.

Stepwise frontal analysis coupled with cell membrane chromatography for affinity screening and characterization analysis of bioactive constituent from the mature fruits of schisandra chinensis

Cell membrane chromatography (CMC) is effective and widely used in drug screening, especially for the analysis of complex matrixes. However, it is time-consuming and costly given that cells or animals are employed for activity confirmation, which leads to a large amount of waste being produced if the result is negative. Stepwise frontal analysis is employed to saturate the affinity stationary phase, by using a series of low- to high-concentration solutions which resultantly form a staircase pattern. In doing so, the waste of samples, caused by the balancing process, can be avoided. In this study, stepwise frontal analysis coupled with a CMC system was performed for screening and characterizing the affinity of an active compound from wuweizi. Schizandrin A was screened and identified by α_1A AR /CMC coupled with UHPLC-MS/MS. By comparing the values obtained with those related to the equilibrium dissociation constant (K_d) calculated by zonal elution, the accuracy of the stepwise frontal analysis was verified. Subsequently, the type of affinity force between Schizandrin A and α_1A AR was studied by thermodynamic parameters. Moreover, schizandrin A showed an antagonistic effect on phenylephrine-induced contractions, which relax prostate muscle strips in a non-competitive antagonism manner. It has already suggested that the active compound, schizandrin A, could be used as a lead compound for the treatment of benign prostate hyperplasia (BPH) and should be further studied. Thus, the findings of this study are significant given that they could result in an online screening and affinity analysis method being utilized for the discovery of medicinal compounds as well as clarify the interaction characteristics between a drug and a receptor.

Recent advances in screening active components from natural products based on bioaffinity techniques

Natural products have provided numerous lead compounds for drug discovery. However, the traditional analytical methods cannot detect most of these active components, especially at their usual low concentrations, from complex natural products. Herein, we reviewed the recent technological advances (2015–2019) related to the separation and screening bioactive components from natural resources, especially the emerging screening methods based on the bioaffinity techniques, including biological chromatography, affinity electrophoresis, affinity mass spectroscopy, and the latest magnetic and optical methods. These screening methods are uniquely advanced compared to other traditional methods, and they can fish out the active components from complex natural products because of the affinity between target and components, without tedious separation works. Therefore, these new tools can reduce the time and cost of the drug discovery process and accelerate the development of more effective and better-targeted therapeutic agents.

Solid-Supported Proteins in the Liquid Chromatography Domain to Probe Ligand-Target Interactions

Ligand-target interactions play a central role in drug discovery processes because these interactions are crucial in biological systems. Small molecules-proteins interactions can regulate and modulate protein function and activity through conformational changes. Therefore, bioanalytical tools to screen new ligands have focused mainly on probing ligand-target interactions. These interactions have been evaluated by using solid-supported proteins, which provide advantages like increased protein stability and easier protein extraction from the reaction medium, which enables protein reuse. In some specific approaches, precisely in the ligand fishing assay, the bioanalytical method allows the ligands to be directly isolated from complex mixtures, including combinatorial libraries and natural products extracts without prior purification or fractionation steps. Most of these screening assays are based on liquid chromatography separation, and the binding events can be monitored through on-line or off-line methods. In the on-line approaches, solid supports containing the immobilized biological target are used as chromatographic columns most of the time. Several terms have been used to refer to such approaches, such as weak affinity chromatography, high-performance affinity chromatography, on-flow activity assays, and high-performance liquid affinity chromatography. On the other hand, in the off-line approaches, the binding event occurs outside the liquid chromatography system and may encompass affinity and activity-based assays in which the biological target is immobilized on magnetic particles or monolithic silica, among others. After the incubation step, the supernatant or the eluate from the binding assay is analyzed by liquid chromatography coupled to various detectors. Regardless of the selected bioanalytical approach, the use of solid supported proteins has significantly contributed to the development of automated and reliable screening methods that enable ligands to be isolated and characterized in complex matrixes without purification, thereby reducing costs and avoiding time-laborious steps. This review provides a critical overview of recently developed assays.

Recent applications of immobilized biomaterials in herbal analysis

Immobilization of biomaterials developed rapidly due to the great promise in improving their stability, activity and even selectivity. In this review, the immobilization strategies of biomaterials, including physical adsorption, encapsulation, covalent attachment, cross-linking and affinity linkage, were briefly introduced. Then, the major emphasis was focused on the reported various types of immobilized biomaterials, including proteins, enzymes, cell membrane and artificial membrane, living cells, carbohydrates and bacteria, used in the herbal analysis for bioactive compound screening, drug-target interaction evaluation and chiral separation. In addition, a series of carrier materials applied in biomaterials immobilization, such as magnetic nanoparticles, metal-organic frameworks, silica capillary column, cellulose filter paper, cell membrane chromatography, immobilized artificial membrane chromatography and hollow fiber, were also discussed. Perspectives on further applications of immobilized biomaterials in herbal analysis were finally presented.