Sperm binding to oviduct epithelial spheroids varies among males and ejaculates but not among females in pigs

The elimination of ejaculates and males with low fertility despite good sperm motility and morphology is crucial to maintain high pregnancy rates after artificial insemination (AI) in farm animals. The ability of sperm to survive in the female tract is particularly crucial in pigs due to the large variation in the timing between AI and ovulation and the high number of oocytes to fertilise. The objective of this study was to characterise a new in vitro model of oviduct sperm reservoir using porcine oviduct epithelial spheroids (OES) and to assess the variability in sperm binding to OES among gilts, boars and their ejaculates. Isthmic mucosa fragments were collected from gilt oviducts at a slaughterhouse, and after 48 h of culture, the OES that had spontaneously formed were sorted according to their vesicle shape and size (150-200 μm in diameter) for characterisation and sperm binding assays. The OES contained viable, cytokeratin-positive and vimentin-negative cells, of which 36.4 ± 2.0% were multiciliated. The average proportion of multiciliated cells per OES did not change among culture replicates. After co-incubation with boar fresh semen, only sperm of normal morphology were found to bind, by their head, to cilia of OES. The density of sperm bound to the OES surface increased linearly with sperm concentration. The bound sperm density on OES was used to assess the binding capacity of fresh ejaculates collected from Pietrain boars. For a given ejaculate, the bound sperm density did not vary among pools of OES female donors. The analysis of five successive ejaculates from nine boars indicated significant differences in bound sperm densities on the OES among individual boars and their ejaculates (P < 0.01). There was no correlation between the sperm bound density and sperm parameters measured by computer-assisted sperm analysis or the initial dilution of the ejaculate. In conclusion, the OES characterised in this study offered physiological conditions to study sperm binding to the isthmic reservoir and evidenced that sperm from different ejaculates and different boars vary in their ability to bind to these oviduct spheroids despite homogeneous motility and morphology.

A convenient assay for soluble Dectin-1 lectin domain binding to insoluble β-glucans

β-Glucan is a homopolymer with a backbone of β-1,3-linked glucose residues. The solubility and biological activity of β-glucan can be influenced by the length of the backbone and the length/interval of the β-1,6 branches. Dectin-1 is crucial in innate immunity through its binding to exogenous β-glucans. However, there are few quantitative binding affinities available and there is no comprehensive comparative analysis of the binding of Dectin-1 to insoluble β-glucans. Here, we have developed a simple binding assay for the interaction between Dectin-1 lectin domain (Dectin-1 CTLD) and insoluble β-glucans. We utilized the paramylon particle as a model of insoluble β-glucans. Dectin-1 CTLD bound to paramylon (particle size 3.1 μm) was separated from unbound Dectin-1 CTLD by centrifugation using a membrane filter (pore size 0.2 μm). The protein in the filtrate was quantified by SDS-PAGE and densitometry. The amount decreased in proportion to the amount of paramylon in the mixture. A control experiment using the Dectin-1 CTLD inactive mutant W221A showed that the mutant passes through the filter without binding paramylon. These results are evidence of site-specific binding of Dectin-1 CTLD to paramylon and demonstrate that the separation of paramylon-bound/unbound Dectin-1 CTLD is achievable through centrifugation using a filter. The assay was extended to other insoluble β-glucans including curdlan. Additionally, it can be utilized in competitive inhibition experiments with soluble short-chain β-glucans such as laminarin. The assay system allows for quantitative comparison of the affinities between insoluble and soluble β-glucans and Dectin-1 CTLD, and should be useful because of its low-tech convenience.

Acridinium-Based Chemiluminescent Receptor-Ligand Binding Assay for Protein/Peptide Hormones

Chemiluminescent acridinium esters (AE) have been extensively used for oligonucleotide probing and peptide-binding assays in molecular research due to labeling efficiency, lack of radioactivity, and ease of application. In addition to being a powerful and reliable alternative to radiolabeling, AE can be directly bound to the target molecule, with high specificity. Here, we describe an AE-based protein/peptide labeling method and the use of the labeled protein/peptide in a ligand-binding assay.

Direct evaluation of polarity of the ligand binding pocket in retinoid X receptor using a fluorescent solvatochromic agonist

High selectivity of small-molecule drug candidates for their target molecule is important to minimize potential side effects. One factor that contributes to the selectivity is the internal polarity of the ligand-binding pocket (LBP) in the target molecule, but this is difficult to measure. Here, we first confirmed that the retinoid X receptor (RXR) agonist 6-(ethyl(1-isobutyl-2-oxo-4-(trifluoromethyl)-1,2-dihydroquinolin-7-yl)amino)nicotinic acid (NEt-iFQ, 1) exhibits fluorescence solvatochromism, i.e., its Stokes shift depends on the polarity of the solvent, and then we utilized this property to directly measure the internal polarity of the RXRα-LBP. The Stokes shift of 1 when bound to the RXRα-LBP corresponded to that of 1 in chloroform solution. This finding is expected to be helpful for designing RXR-selective ligands. A similar approach should be appliable to evaluate the internal polarity of the LBPs of other receptors.

Identification and functional analysis of odorant-binding proteins of the parasitoid wasp Scleroderma guani reveal a chemosensory synergistic evolution with the host Monochamus alternatus

Scleroderma guani is a generalist ectoparasitoid of wood-boring insects. The chemosensory genes expressed in its antennae play crucial roles in host-seeking. In the present study, we identified 14 OBP genes for the first time from the antennae transcriptomes and genomic data of S. guani. The expression profiles of 14 OBPs were tested by RT-qPCR, and the RT-qPCR results showed that SguaOBP2/5/6/11/12/13 were specifically highly expressed in the female antennae. Then we performed ligand binding assays to test the interactions between six selected SguaOBPs with host specific chemical compounds from M. alternatus and pines. The binding results indicated that SguaOBP12 had a higher binding affinity with longifolene, β-caryophyllene, α-pinene, β-pinene, myrcene, butylated hydroxytoluene, and 3-carene. SguaOBP11 had a high or medium binding affinity with them. Furthermore, both SguaOBP11 and SguaOBP12 had a medium binding affinity with the aggregation pheromone of Monochamus species, 2-undecyloxy-1-ethanol. Finally, by using molecular docking and RNAi, we further explored the molecular interactions and behavioral functions of SguaOBP11 and SguaOBP12 with these vital odor molecules. Our study contributes to the further understanding of chemical communications between S. guani and its host, and further exploration for its role as a more effective biological control agent.

GPR160 is not a receptor of anorexigenic cocaine- and amphetamine-regulated transcript peptide

COCAINE: and amphetamine-regulated transcript peptide (CARTp) is an anorexigenic neuropeptide whose receptor is undisclosed. Previously, we reported the specific binding of CART(61-102) to pheochromocytoma PC12 cells, where CART(61-102) affinity and the number of binding sites per cell corresponded to ligand-receptor binding. Recently, Yosten et al. designated orphan GPR160 as the CARTp receptor, because the GPR160 antibody abolished neuropathic pain and anorexigenic effects induced by CART(55-102) and exogenous CART(55-102) coimmunoprecipitated with GPR160 in KATOIII cells. As no direct evidence that CARTp is a ligand for GPR160 has been described, we decided to verify this hypothesis by testing CARTp affinity to the GPR160 receptor. We investigated the GPR160 expression in PC12 cells since it is cell line known to specifically bind CARTp. Moreover, we examined the specific CARTp binding in THP1 cells, with high endogenous GPR160 expression and GPR160-transfected cell lines U2OS and U-251 MG. In PC12 cells, the GPR160 antibody did not compete for specific binding with ¹²⁵I-CART(61-102) or with ¹²⁵I-CART(55-102), and GPR160 mRNA expression and GPR160 immunoreactivity were not detected. Moreover, THP1 cells did not show any ¹²⁵I-CART(61-102) or ¹²⁵I-CART(55-102) specific binding despite GPR160 detection by fluorescent immunocytochemistry (ICC). Finally, no ¹²⁵I-CART(61-102) or ¹²⁵I-CART(55-102) specific binding in the GPR160-transfected cell lines U2OS and U-251 MG, selected due to their negligible endogenous expression of GPR160, was detected, despite the detection of GPR160 by fluorescent ICC. Our binding studies clearly demonstrated that GPR160 cannot be a receptor for CARTp. Further studies are needed to identify true CARTp receptors.

Chemical Synthesis and Molecular Interaction Analysis of α-Galactosyl Ceramide Derivatives as CD1d Ligands

CD1d is a non-classical major histocompatibility complex (MHC) protein, responsible for lipid antigen presentation, which presents lipids to natural killer T (NKT) cells. Various CD1d lipid ligands have been reported, including microbial and endogenous glycolipids/phospholipids. Among them, an α-galactosylceramide (α-GalCer), a representative CD1d ligand, is one of the most potent ligands and its derivatives have been developed. In this chapter, the chemistry of α-GalCer and its derivatives are described with an emphasis on their chemical syntheses and molecular interaction analysis with CD1d are described.

Fluorescence Polarization-Based Competition Assays to Evaluate Histone Deacetylase 6 Inhibitors

Histone deacetylase 6 (HDAC6) is an emerging clinical target for the treatment of several hematological cancers and central nervous system disorders. HDAC6 catalyzes the deacetylation of lysine residues on substrates such as tubulin, with profound implications in key cellular processes, including cellular motility and migration. This critical deacetylation activity occurs at the catalytic domain 2 (CD2) of HDAC6, and small molecule inhibitors of HDAC6 are designed to target CD2. We briefly highlight previously reported strategies for recombinant bacterial expression and purification of the HDAC6 CD2. We aim to discuss competition assays that have been used to evaluate the potency of potential HDAC6 inhibitors against CD2 via displacement of pre-bound fluorescent HDAC-probes. Moreover, we elaborate on previous protocols that have been employed in inhibitor screening and present an HDAC6-selective probe that also enables rapid and reliable high-throughput screening of new chemical entities designed to target the HDAC6 CD2.

Characterization of PAMAM Dendrimers for the Delivery of Nucleic Acid Nanoparticles

The protocols described in this book chapter are meant to be used as an outline and guideline to explore the use of a cationic, polymeric, and synthetic carrier-poly (amidoamine) (PAMAM) dendrimers. The amine-terminated, hyperbranched structures have been identified as a vehicle for the delivery of nucleic acids. As such, clear protocols for the optimization of dendrimer usage should be set in place. This chapter details the experiments used to determine the ratio that dendrimers and nucleic acids should be complexed at through the use of binding assays, nuclease protection assays, and competitive binding assays.

Scintillation Proximity Assay (SPA)-Based Radioligand Binding for PPARα, PPARγ, and PPARδ Receptors

Peroxisome proliferator-activated receptors (PPARs) have been exploited as drug targets for combating multiple diseases. Several activators with different selectivity for the PPAR α, γ, and δ subtypes have been introduced into the market or have reached advanced clinical trials. Binding assays are of utmost importance for the discovery and profiling of such PPAR ligands. Binding assays are often based on radioligands, in particular, tritiated molecules are applied. We developed synthetic procedures for tritiating various PPAR agonists and applied these radioligands for setting up a scintillation proximity assay (SPA) for PPAR α, γ, and δ. These SPAs allow to assess the binding affinities of PPAR α, γ, and δ ligands, along with their respective subtype selectivity profiles. Therefore, SPA is an important tool for hit discovery and lead optimization campaigns aimed at identifying next-generation PPAR ligands.

Immobilization-Free Determination of Dissociation Constants Independent of Ligand Size Using MicroScale Thermophoresis

The quantitative characterization of aptamer-ligand interactions is an important step in the aptamer development process. However, certain pitfalls impede K_D determination, especially when working with small molecule ligands. These include altered binding behavior caused by ligand immobilization. Further, the compulsory requirement for major differences in size between the bound and unbound state makes small molecule ligands ineligible for separation-based methods. MicroScale Thermophoresis circumvents such limitations as binding is accurately quantified with both binding partners free in solution and independent of ligand size. In this chapter, we present a protocol for the characterization of a DNA aptamer binding to its small molecule ligand daunorubicin.

Involvement of muscarinic receptors in psychomotor hyperactivity in dopamine-deficient mice

Dopamine-deficient (DD) mice exhibit psychomotor hyperactivity that might be related to a decrease in muscarinic signaling. In the present study, muscarinic acetylcholine receptor M2 (CHRM2) density decreased in the cortex in DD mice. This is significant because cortical CHRM2 acts as an autoreceptor; therefore, changes in CHRM2 levels could alter acetylcholine in DD mice. We also found that the CHRM1/CHRM4 agonist xanomeline and CHRM2 agonist arecaidine propargyl ester tosylate inhibited hyperactivity in DD mice, suggesting that postsynaptic CHRM1 and CHRM2 and presynaptic CHRM2 may be involved in hyperactivity in DD mice.

Production of human embryonic kidney 293T cells stably expressing C-X-C chemokine receptor type 4 (CXCR4) as a screening tool for anticancer lead compound targeting CXCR4

AIM

The C-X-C chemokine-receptor type 4 (CXCR4) is an emerging target for cancer drug discovery due to its high expression in cancer cells. The present study aimed to produce CXCR4 overexpressing HEK293T cells for a non-radioactive binding assay as a platform to identify drug candidates targeting CXCR4.

MAIN METHODS

HEK293T cells stably expressing human CXCR4 were constructed by transfection of CXCR4 plasmids from the human CXCR4 gene. The CXCR4 overexpressing HEK293T cells were obtained by fluorescence-activated sorting and verified by conducting the competition binding assay of a known CXCR4 inhibitor, AMD3100 (plerixafor), to determine the IC₅₀ value against monoclonal anti-human CD184 (hCD184) antibody tagged with fluorescence probe, phycoerythrin (PE). The non-radioactive binding assay using CXCR4 overexpressing HEK293T cells and PE-anti hCD184 was applied as a platform for identifying the target of natural compounds that exhibited cytotoxicity against cancer cell lines.

KEY FINDINGS

The CXCR4 overexpressing HEK293T cells were produced with high expression (99.8%). The IC₅₀ value of plerixafor determined by fluorescence tagged antibody-based competition assay using our developed cells agree with previously reported values using a radioligand binding assay. We observed no significant displacement of bound PE-anti-hCD184 by the test natural compounds which could be due to non-specific binding to other functional targets or organelles, low potency of the natural compounds, or binding to CXCR4 at deeper pockets.

SIGNIFICANCE

The verified non-radioactive binding assay can serve as an alternative screening tool for anticancer lead compounds targeting CXCR4 and an essential tool for proof of mechanism study in the drug discovery.

Natural LILRB1 D1-D2 variants show frequency differences in populations and bind to HLA class I with various avidities

Leukocyte immunoglobulin-like receptor B1 (LILRB1) is widely expressed on various immune cells and the engagement of LILRB1 to HLA class I and pathogen-derived proteins can modulate the immune response. In the current study, 108 LILRB1 alleles were identified by screening the LILRB1 locus from the 1000 Genomes Phase 3 database. Forty-six alleles that occurred in three or more individuals encode 28 LILRB1 allotypes, and the inferred LILRB1 allotypes were then grouped into 9 LILRB1 D1-D2 variants for further analysis. We found that variants 1, 2, and 3 represent the three most frequent LILRB1 D1-D2 variants and the nine variants show frequency differences in populations. The binding assay demonstrated that variant 1 bound to HLA class I with the highest avidity, and all tested LILRB1 D1-D2 variants bound to HLA-C with lower avidity than to HLA-A and -B. Locus-specific polymorphisms at positions 183, 189, and 268 in HLA class I and dimorphisms in HLA-A (positions 207 and 253) and in HLA-B (position 194) affect their binding to LILRB1. Notably, the electrostatic interaction plays a critical role in the binding of LILRB1 to HLA class I as revealed by electrostatic analysis and by comparison of different binding avidities caused by polymorphisms at positions 72 and 103 of LILRB1. In this paper, we present a comprehensive study of the population genetics and binding abilities of LILRB1. The data will help us better understand the LILRB1-related diversity of the immune system and lay a foundation for functional studies.

The Therapeutic Potential of 2-{[4-(2-methoxyphenyl)piperazin-1-yl]alkyl}-1H-benzo[d]imidazoles as Ligands for Alpha1-Adrenergic Receptor - Comparative In Silico and In Vitro Study

Adrenergic receptors are among the most studied G protein-coupled receptors. Activation or blockade of these receptors is a major therapeutic approach for the treatment of numerous disorders such as cardiac hypertrophy, congestive heart failure, hypertension, angina pectoris, cardiac arrhythmias, depression, benign prostate hyperplasia, anaphylaxis, asthma, and hyperthyroidism. Among all nine cloned adrenoceptor subtypes and the subsequent development of animal models, a significant target for various neurological conditions treatment is alpha1-adrenergic receptors. 2-{[4-(2-Methoxyphenyl)piperazin-1-yl]alkyl}-1H-benzo[d]imidazoles, their 5 substituted derivatives, and structurally similar, arylpiperazine based alpha1-adrenergic receptors antagonists (trazodone, naftopidil, and urapidil) have been subjects of comparative analysis. Most of the novel compounds showed alpha1-adrenergic affinity in the range from 22 nM to 250 nM. The in silico docking and molecular dynamics simulations, binding data together with absorption, distribution, metabolism, and excretion (ADME) calculations identified the promising lead compounds. The results brought out the conclusions which allowed us to propose a rationale for the activity of these molecules and to highlight six compounds (2-5, 8, and 12) that exhibited an acceptable pharmacokinetic profile to the advanced investigation as the potential alpha1-adrenergic receptor antagonists.

Competitive chrodrimanin B interactions with rat brain GABAA receptors revealed by radioligand binding assays

Meroterpenoid compounds chrodrimanins produced by Talaromyces sp. YO-2 have been shown to act as competitive antagonists of silkworm larval GABA_A receptors using electrophysiology, yet no further evidence has been provided to support such an action. We have investigated the actions of chrodrimanin B on rat brain GABA_A receptors by binding assays with non-competitive ligand of GABA_A receptors [³H]EBOB and competitive ligands [³H]gabazine and [³H]muscimol. Chrodrimanin B did not significantly affect the binding of [³H]EBOB while reducing the binding of [³H]gabazine and [³H]muscimol to the rat membrane preparations. Chrodrimanin B increased the dissociation constant K_d of [³H]gabazine and [³H]muscimol without significantly affecting the maximum binding, pointing to competitive interactions of chrodrimanin B with rat GABA_A receptors in support of our previous observation that the compound acts as a competitive antagonist on the silkworm larval GABA receptor.

Approaches for the detection and analysis of anti-drug antibodies to biopharmaceuticals: A review

Antibody-based therapeutic agents and other biopharmaceuticals are now used in the treatment of many diseases. However, when these biopharmaceuticals are administrated to patients, an immune reaction may occur that can reduce the drug's efficacy and lead to adverse side effects. The immunogenicity of biopharmaceuticals can be evaluated by detecting and measuring antibodies that have been produced against these drugs, or anti-drug antibodies (ADAs). Methods for ADA detection and analysis can be important during the selection of a therapeutic approach based on such drugs and is crucial when developing and testing new biopharmaceuticals. This review examines approaches that have been used for ADA detection, measurement, and characterization. Many of these approaches are based on immunoassays and antigen binding tests, including homogeneous mobility shift assays. Other techniques that have been used for the analysis of ADAs are capillary electrophoresis, reporter gene assays, surface plasmon resonance spectroscopy, and liquid chromatography-mass spectrometry. The general principles of each approach will be discussed, along with their recent applications with regards to ADA analysis. This article is protected by copyright. All rights reserved.

The spike-ACE2 binding assay: An in vitro platform for evaluating vaccination efficacy and for screening SARS-CoV-2 inhibitors and neutralizing antibodies

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 has become a worldwide pandemic, and there is a pressing need for the rapid development of novel therapeutic strategies. SARS-CoV-2 viral entry is mediated by interaction between the receptor binding domain (RBD) of the SARS-CoV-2 Spike protein and host cellular receptor, human angiotensin converting enzyme 2 (ACE2). The lack of a high throughput screening (HTS) platform for candidate drug screening means that no targeted COVID-19 treatments have been developed to date. To overcome this limitation, we developed a novel, rapid, simple, and HTS binding assay platform to screen potential inhibitors of the RBD-ACE2 complex. Three “neutralizing” mouse monoclonal antibodies capable of blocking the RBD-ACE2 interaction were identified using our binding assay and pseudovirus neutralization assay followed by further validation with the Focus Reduction Neutralization Test (FRNT), which analyzes the neutralization capacity of samples in the presence of live SARS-CoV-2. Furthermore, the consistency of our binding assay and FRNT results (R² = 0.68) was demonstrated by patients' serum, of which were COVID-19 positive (n = 34) and COVID-19 negative (n = 76). Several small molecules selected for their potential to inhibit the Spike-ACE2 complex in silico were also confirmed with the binding assay. In addition, we have evaluated vaccine efficacy using binding assay platform and validated through pseudovirus neutralization assay. The correlation between binding assay & psuedovirus assay of the post vaccinated serum showed well correlated (R² = 0.09) Moreover, our binding assay platform successfully validated different Spike RBD mutants. These results indicate that our binding assay can be used as a platform for in vitro screening of small molecules and monoclonal antibodies, and high-throughput assessment of antibody levels after vaccination. When conducting drug screening, computer virtual screening lacks actual basis, construction of pseudoviruses is relatively complicated, and even FRNT requires a P3 laboratory. There are few methods to determine the competitiveness of the target drug and SRBD or ACE2. Our binding assay can fill this gap and accelerate the process and efficiency of COVID-19 drug screening.

Activation of Bacillus thuringiensis Cry1I to a 50 kDa stable core impairs its full toxicity to Ostrinia nubilalis

Bacillus thuringiensis Cry1I insecticidal proteins are structurally similar to other three-domain Cry proteins, although their size, activity spectrum, and expression at the stationary phase are unique among other members of the Cry1 family. The mode of action of Cry1 proteins is not completely understood but the existence of an activation step prior to specific binding is widely accepted. In this study, we attempted to characterize and determine the importance of the activation process in the mode of action of Cry1I, as Cry1Ia protoxin or its partially processed form showed significantly higher toxicity to Ostrinia nubilalis than the fully processed protein either activated with trypsin or with O. nubilalis midgut juice. Oligomerization studies showed that Cry1Ia protoxin, in solution, formed dimers spontaneously, and the incubation of Cry1Ia protoxin with O. nubilalis brush border membrane vesicles (BBMV) promoted the formation of dimers of the partially processed form. While no oligomerization of fully activated proteins after incubation with BBMV was detected. The results of the in vitro competition assays showed that both the Cry1Ia protoxin and the approx. 50 kDa activated proteins bind specifically to the O. nubilalis BBMV and compete for the same binding sites. Accordingly, the in vivo binding competition assays show a decrease in toxicity following the addition of an excess of 50 kDa activated protein. Consequently, as full activation of Cry1I protein diminishes its toxicity against lepidopterans, preventing or decelerating proteolysis might increase the efficacy of this protein in Bt-based products. KEY POINTS: • Processing Cry1I to a 50 kDa stable core impairs its full toxicity to O. nubilalis • Partially processed Cry1Ia protoxin retains the toxicity of protoxin vs O. nubilalis • Protoxin and its final processed forms compete for the same functional binding sites.

DNA Conjugates as Tool Compounds for DEL Selections

DEL selections are designed to discover novel small molecule compounds attached to DNA that bind to a target protein. A known small molecule or peptide ligand that binds to the target protein can be conjugated to DNA to mimic compounds contained in DEL libraries. The conjugate can be used as a ligand in preselection binding assays to validate a target protein and optimize selection methods and serve as a positive control in selection experiments. In this chapter, the design, synthesis, and use of DNA conjugate tool compounds are discussed. As an example, I describe the design of a DNA conjugate of a ligand to the CCR5 receptor and its use to optimize selection conditions and as a spike-in positive control in a DEL selection experiment. These methods are broadly applicable to both soluble protein targets and to targets that are displayed on the cell surface and to various types of compounds that can be conjugated to DNA.

2-[125I]iodomelatonin and [3H]melatonin Binding Assays for Melatonin Receptors

The radioligand binding assay is a powerful method to study the interaction of a ligand with its target. This technique allows not only to determine different pharmacological key parameters such as the affinity and the association and dissociation constants but also to estimate the amount of target expressed in recombinant or endogenous cells or tissues. The current detailed protocols describe the different binding assays (saturation, kinetic, and competition) that can be performed on melatonin receptors using their most commonly used and validated radioligands 2-[¹²⁵I]-iodomelatonin (2-[¹²⁵I]-MLT) and [³H]-melatonin ([³H]-MLT).

A TXTL-Based Assay to Rapidly Identify PAMs for CRISPR-Cas Systems with Multi-Protein Effector Complexes

Type I CRISPR-Cas systems represent the most common and diverse type of these prokaryotic defense systems and are being harnessed for a growing set of applications. As these systems rely on multi-protein effector complexes, their characterization remains challenging. Here, we report a rapid and straightforward method to characterize these systems in a cell-free transcription-translation (TXTL) system. A ribonucleoprotein complex is produced and binds to its target next to a recognized PAM, thereby preventing the targeted sequence from being cleaved by a restriction enzyme. Selection for uncleaved targeted plasmids leads to an enrichment of recognized sequences within a PAM library. This assay will aid the exploration of CRISPR-Cas diversity and evolution and help contribute new systems for CRISPR technologies and applications.

Surface Plasmon Resonance Analysis of PfEMP1 Interaction with Receptors

A detailed understanding of the interaction between the highly variant Plasmodium falciparum erythrocyte membrane proteins 1 (PfEMP1) and their human binding partners is essential to explain their roles in disease development in malaria, as well as to understand how antibodies can inhibit these interactions and how the parasite manages to evade such an immune response. This chapter focuses on using surface plasmon resonance (SPR) as a reproducible, high-throughput method to quantitatively characterize these interactions. We describe how to utilize protein A or A/G and streptavidin for protein immobilization on SPR sensor chips and provide instructions on how to biotinylate proteins for this purpose and how to use SPR for binding competition assays. Since these experiments rely on recombinant proteins, we also present a method to verify their structural integrity using circular dichroism spectroscopy.

In vitro characterization of [3H]VAT in cells, animal and human brain tissues for vesicular acetylcholine transporter

Vesicular acetylcholine transporter plays a crucial role in the cholinergic system, and its alterations is implicated in several neurodegenerative disorders. We recently developed a PET imaging tracer [¹⁸F]VAT to target VAChT in vivo with high affinity and selectivity. Here we report in vitro characterization of [³H]VAT, a tritiated counterpart of [¹⁸F]VAT. Using human VAChT-rich cell membrane extracts, a saturated binding curve was obtained for [³H]VAT with K_d = 6.5 nM and B_max = 22.89 pmol/mg protein. In the [³H]VAT competition-binding assay with a panel of CNS ligands, binding inhibition of [³H]VAT was observed using VAChT ligands, the K_i values ranged from 5.41 to 33.3 nM. No inhibition was detected using a panel of other CNS ligands. In vitro [³H]VAT autoradiography of rat brain sections showed strong signals in the striatum, moderate to high signals in vermis, thalamus, cortex, and hippocampus, and weak signals in cerebellum. Strong [³H]VAT ARG signals were also observed from striatal sections of normal nonhuman primates and human brains. Competitive ARG study with human striatal sections demonstrated strong ARG signals of [³H]VAT in caudate and putamen were blocked significantly by either VAChT ligand TZ659 or (-)-vesamicol, but not by the σ₁ receptor ligand Yun-122. ARG study also indicated that signal in the striatal sections from PSP human brains was lower than normal human brains. These data provide solid evidence supporting [¹⁸F]VAT as a suitable PET radiotracer for quantitative assessment of VAChT levels in vivo.

New insights into the mechanism of Keap1-Nrf2 interaction based on cancer-associated mutations

AIMS

Keap1-Nrf2 signaling pathway is one of the most important antioxidant signaling pathways, and its abnormal activation is related to cancer metastasis and drug resistance. Many studies have shown Keap1 and Nrf2 mutations are closely associated with cancer occurrence. However, few studies focus on Keap1-Nrf2 binding characteristics of cancer-associated mutations. The study investigated the molecular mechanism between Keap1/Nrf2 mutations and cancer.

MAIN METHODS

We have determined the crystal structure of the Keap1-Kelch domain with Nrf2 25-mer peptide. What's more, we clarified the molecular effects of Nrf2^Thr80 and Nrf2^Pro85 on the binding of Keap1 by the method isothermal titration calorimetry (ITC), differential scanning fluorimetry (DSF) and electrophoretic mobility shift assay (EMSA). Especially, we confirmed the effect of Thr80 and Pro85 mutations on Keap1/Nrf2 signaling pathway in HEK293T cells by RT-PCR and western blot (WB). Finally, we verified the effect of six cancer-related high-frequency somatic mutations Keap1^G364C, Keap1^D422N, Keap1^R470C, Keap1^G480W, Keap1^E493Q and Keap1^R601L on binding with Nrf2 through ITC experiments.

KEY FINDINGS

Nrf2^Thr80 and Nrf2^Pro85 play a vital role in the Keap1-Nrf2 interaction. Mutant or modification at position Thr80 will disrupt the interaction. Especially, Nrf2^Thr80 and Nrf2^Pro85 mutations activate the expression of cytoprotective genes in HEK293T cells. As for Keap1, except G364C, the binding affinity of other cancer-related mutants to Nrf2 hardly changed, which means that Keap1 mutants can activate Nrf2 without disrupting the binding to Nrf2.

SIGNIFICANCE

The study provides new insight into Keap1/Nrf2 signaling pathway and cancer.

A new class of sensing elements for sensors: Clamp peptides for Zika virus

The design of a new class of selective and high affinity antibody mimetics termed clamp peptide (CP) that incorporate three short peptides structurally and mechanically mimicking a clamp is proposed as sensing elements for a reliable detection sensor platform. The CPs consist of two short peptides functioning as arms that recognize two different epitopes in the target protein and are connected by a third short peptide that acts as a hinge between the peptide arms. For the construction of CPs, we employed a rational design combined with computational methods. To illustrate our approach, we designed a CP that binds selectively to the envelope protein of the Zika virus (ZIKV). The virtual docking cycles were run maximizing the discrimination between ZIKV and Dengue virus (DENV) envelope proteins. DENV was chosen among the flavivirus family because it has high structural similarity with ZIKV. When employed in a colorimetric binding assay or in label-free electrochemical impedance sensor format, the CP was selective for ZIKV vs DENV particles showing detection limit under 10⁴ copies/mL, comparable to anti-ZIKV antibodies. Apparent dissociation binding constants (Kd) confirmed a better performance of CPs than mono-arm peptides (Kd of best CP = 162 nM ± 23 nM; Kd of best mono-arm peptide = 11.15 ± 2.76 μM). The performance of the assays based on CPs was also verified in serum and urine (diluted 1:10 and 1:1 respectively). The detection limits of CPs decreased about one order of magnitude for ZIKV detection in serum or urine, with a distinct analytical signal starting from 10⁵ copies/mL of ZIKV.

A radioligand receptor binding assay for measuring of insulin secreted by MIN6 cells after stimulation with glucose, arginine, ornithine, dopamine, and serotonin

We adapted a radioligand receptor binding assay for measuring insulin levels in unknown samples. The assay enables rapid and accurate determination of insulin concentrations in experimental samples, such as from insulin-secreting cells. The principle of the method is based on the binding competition of insulin in a measured sample with a radiolabeled insulin for insulin receptor (IR) in IM-9 cells. Both key components, radiolabeled insulin and IM-9 cells, are commercially available. The IR binding assay was used to determine unknown amounts of insulin secreted by MIN6 β cell line after stimulation with glucose, arginine, ornithine, dopamine, and serotonin. The experimental data obtained by the IR binding assay were compared to the results determined by RIA kits and both methods showed a very good agreement of results. We observed the stimulation of glucose-induced insulin secretion from MIN6 cells by arginine, weaker stimulation by ornithine, but inhibitory effects of dopamine. Serotonin effects were either stimulatory or inhibitory, depending on the concentration of serotonin used. The results will require further investigation. The study also clearly revealed advantages of the IR binding assay that allows the measuring of a higher throughput of measured samples, with a broader range of concentrations than in the case of RIA kits. The IR binding assay can provide an alternative to standard RIA and ELISA assays for the determination of insulin levels in experimental samples and can be especially useful in scientific laboratories studying insulin production and secretion by β cells and searching for new modulators of insulin secretion.

Identification of novel target molecules of l-menthol

The present study used a binding assay to identify novel target biomolecules of l-menthol ([−]-menthol) that promote mouse ambulation. Among 88 different ligands to specific biomolecules examined, 0.1 mM l-menthol inhibited the binding of 13 ligands with relatively high inhibition rates. The assays showed that l-menthol acts on calcium channels, sodium channels, γ-aminobutyric acid type A (GABA_A) receptor, GABA transporter, dopamine transporter, dopamine D4 receptor, adenosine A2a receptor, α2A-adrenergic receptor, histamine H2 receptor, bombesin receptor, angiotensin AT1 receptor, vasopressin V2 receptor, and leukotriene B4 receptor over a similar concentration range. The inhibition constant (K_i) for l-menthol inhibition of binding of [³H]-WIN35,428 to the human recombinant dopamine transporter was 6.15 × 10⁻⁴ mol/L. The K_i for l-menthol inhibition of binding of [³H]-ethynylbicycloorthobenzoate (EBOB), a ligand of GABA_A receptor picrotoxin site, was 2.88 × 10⁻⁴ mol/L. These results should aid future research by providing clues for investigating the mechanisms underlying l-menthol activities, including the ambulation-promoting effect. The present results suggest that the dopamine transporter, adenosine A2a receptor, dopamine D4 receptor, α2A-adrenergic receptor, and GABA_A receptor are promising candidate molecules that are involved in the mechanisms underlying the psychostimulant-like effect of l-menthol.

Interaction of 8-anilinonaphthalene-1-sulfonate with SARS-CoV-2 main protease and its application as a fluorescent probe for inhibitor identification

The 3C-like main protease of SARS-CoV-2 (3CLPro) is responsible for the cleavage of the viral polyprotein. This process is essential for the viral life cycle. Therefore, 3CLPro is a promising target to develop antiviral drugs for COVID-19 prevention and treatment. Traditional enzymatic assays for the identification of 3CLPro inhibitors rely on peptide-based colorimetric or fluorogenic substrates. However, the COVID-19 pandemic has limit or delay access to these substrates, especially for researchers in developing countries attempting to screen natural product libraries. We explored the use of the fluorescent probe 8-anilinonaphthalene-1-sulfonate (ANS) as an alternative assay for inhibitor identification. Fluorescence enhancement upon binding of ANS to 3CLPro was observed, and this interaction was competitive with a peptide substrate. The utility of ANS-based competitive binding assay to identify 3CLPro inhibitors was demonstrated with the flavonoid natural products baicalein and rutin. The molecular nature of ANS and rutin interaction with 3CLPro was explored with molecular modeling. Our results suggested that ANS could be employed in a competitive binding assay to facilitate the identification of novel SARS-CoV-2 antiviral compounds.

Characterization, expression and function analysis of the TLR3 gene in golden pompano (Trachinotus ovatus)

Toll-like receptors (TLRs)are pattern recognition receptors (PRRs) that are important in invertebrate innate immunity for the recognition and elimination of pathogens. Although they were reported in many fishes, Toll-like receptors subfamily contain a large number of members with different functions that need to research in deep. In the present study, the full-length cDNA of TLR3 from the golden pompano, Trachinotus ovatus, was cloned and characterized. The full length of ToTLR3 cDNA was 3710 bp including an open reading frame of 2760 bp encoding a peptide of 919 amino acids. The derived amino acids sequence comprised of 14 leucine-rich repeats (LRR), capped with LRRCT followed by transmembrane domain and cytoplasmic Toll/IL-1R domain (TIR). Multiple sequence alignment and phylogenetic analysis revealed that ToTLR3 shared the highest similarity to the teleost fish and suggested ToTLR3 is fairly conservative in evolution process. Tissues distribution analysis indicated that ToTLR3 showed a tissue-specific variation with high expression in blood and liver. After the fish were stimulated by poly(I:C), flagellin and LPS, ToTLR3 expression in the liver, intestine, blood, kidney, skin and muscle was significantly upregulated in a time-depended manner, especially in immune related tissues such as liver, blood and kidney. Binding assay revealed the specificity of rToTLR3 for pathogen-associated molecular patterns (PAMPs) and bacteria that included Vibrio harveyi, V. vulnificus, V. anguillarum, Photobacterium damselae, Escherichia coli, Aeromonas hydrophila, Staphylococcus aureus and PolyI:C, LPS, Flagellin, and PGN. In addition, a luciferase reporter assay showed that overexpression ToTLR3 significantly increased NF-κB activity. Collectively, our results suggested that ToTLR3 might play an important role as a pattern recognition receptor (PRR) in the immune response towards pathogen infections, and transmiss the danger signal to downstream signaling pathways.

Synthesis of 4,6-diphenylpyrimidin-2-ol derivatives as new benzodiazepine receptor ligands

Benzodiazepines (BZDs) have been widely used in neurological disorders such as insomnia, anxiety, and epilepsy. The use of classical BZDs, e.g., diazepam, has been limited due to adverse effects such as interaction with alcohol, ataxia, amnesia, psychological and physical dependence, and tolerance. In the quest for new benzodiazepine agonists with more selectivity and low adverse effects, novel derivatives of 4,6-diphenylpyrimidin-2-ol were designed, synthesized, and evaluated. In this series, compound 2, 4-(2-(benzyloxy)phenyl)-6-(4-fluorophenyl)pyrimidin-2-ol, was the most potent analogue in radioligand binding assay with an IC₅₀ value of 19 nM compared to zolpidem (IC₅₀ = 48 nM), a nonbenzodiazepine central BZD receptor (CBR) agonist. Some compounds with a variety of affinities in radioligand receptor binding assay were selected for in vivo evaluations. Compound 3 (IC₅₀ = 25 nM), which possessed chlorine instead of fluorine in position 4 of the phenyl ring, exhibited an excellent ED₅₀ value in most in vivo tests. Proper sedative-hypnotic effects, potent anticonvulsant activity, appropriate antianxiety effect, and no memory impairment probably served compound 3, a desirable candidate as a benzodiazepine agonist. The pharmacological effects of compound 3 were antagonized by flumazenil, a selective BZD receptor antagonist, confirming the BZD receptors' involvement in the biological effects of the novel ligand.

In vitro functional characterization of biosimilar therapeutic antibodies

The key factor in successful development and marketing of biosimilar antibodies is a deep understanding of their critical quality attributes and the ability to control them. Comprehensive functional characterization is therefore at the heart of the process and is a crucial part of regulatory requirements. Establishment of a scientifically sound molecule-specific functional in vitro assay panel requires diligent planning and high flexibility in order to respond to both regulatory requirements and the ever-changing demands relevant to the different stages of the development and production process. Relevance of the chosen assays to the in vivo mechanism of action is of key importance to the stepwise evidence-based demonstration of biosimilarity. Use of a sound interdisciplinary approach and orthogonal state-of-the-art techniques is also unavoidable for gaining in-depth understanding of the biosimilar candidate. The aim of the present review is to give a snapshot on the methodic landscape as depicted by the available literature discussing the in vitro techniques used for the functional characterization of approved biosimilar therapeutic antibodies. Emerging hot topics of the field and relevant structure-function relationships are also highlighted.

High-Throughput Protein-Nucleic Acid Interaction Assay Based on Protein-Induced Fluorescence Enhancement

Molecular processes involved in gene expression encompass multitudes of interactions between proteins and nucleic acids. Quantitative description of these interactions is crucial for delineating the mechanisms governing transcription, genome duplication, and translation. Here we describe a detailed protocol for the quantitative analysis of protein-nucleic acid interactions based on protein-induced fluorescence enhancement (PIFE). While PIFE has mainly been used in single-molecule studies, we modified its application for bulk measurement of protein-nucleic acid interactions in microwell plates using standard fluorescent plate readers. The microwell plate PIFE assay (mwPIFE) is simple, does not require laborious protein labeling, and is high throughput. These properties predispose mwPIFE to become a method of choice for routine applications that require multiple parallel measurements such as buffer optimization, competition experiments, or screening chemical libraries for binding modulators.

Development of a nano-luciferase based assay to measure the binding of SARS-CoV-2 spike receptor binding domain to ACE-2

To identify drugs that could potentially be used to treat infection with SARS-CoV-2, a high throughput 384-well assay was developed to measure the binding of the receptor binding domain (RBD) of the viral S1 protein to its main receptor, angiotensin converting enzyme 2 (ACE2). The RBD was fused to both a HiBIT tag and an IL6 secretion signal to enable facile collection from the cell culture media. The addition of culture media containing this protein, termed HiBIT-RBD, to cells expressing ACE2 led to binding that was specific to ACE2 and both time and concentration dependant, Binding could be inhibited by both RBD expressed in E. coli and by a full length S1 - Fc fusion protein (Fc-fused S1) expressed in eukaryotic cells. The mutation of residues that are known to play a role in the interaction of RBD with ACE2 also reduced binding. This assay may be used to identify drugs which inhibit the viral uptake into cells mediated by binding to ACE2.

1.A high-throughput, 384-well plate assay was developed to measure the binding S1 RBD to ACE2;

2.HiBIT-RBD binds to cells expressing ACE2 specifically and in a time dependant fashion;

3.The binding of HiBIT-RBD to ACE2 can be inhibited using recombinantly expressed SARS-CoV-2 RBD and full-length, Spike S1;

4.Site specific mutations within the RBD demonstrate the specificity of this assay.

Identification of novel Urotensin-II receptor antagonists with potent inhibition of U-II induced pressor response in mice

Urotensin II (U-II) has been found to be one of the most potent vasoconstrictor (Ames et al., 1999; Bohm et al., 2002) reported till date. U-II exerts its response via activation of a G-protein coupled receptor, Urotensin II receptor(UT). Binding of U-II to UT leads to an instant increase in the inositol phosphate turnover and intracellular Ca²⁺. Such an instant Ca²⁺ release and potent vasoconstriction exerted by U-II is expected to have an important role in the progression of cardiac diseases. We have previously shown that UT antagonist DS37001789 prevents U-II induced blood pressure elevation in mice (Nishi et al., 2019) in a dose dependent manner, with potent efficacy at 30 and 100 mg/kg. Further to this, we have also shown that DS37001789 ameliorates mortality in pressure-overload mice with heart failure (Nishi et al., 2020). We therefore conducted an extensive structure-activity relationship studies to identify molecules with superior efficacy. In the present manuscript, we report the identification of two potent, non-peptide small molecule antagonists of Urotensin II receptor (UT), RCI-0879 and RCI-0298 which blocked the action of U-II, both in vitro and in vivo. These molecules were found to be very potent in in vitro Ca²⁺ and radioligand binding assays using human and mouse UT over-expressing CHO cells. RCI-0879 and RCI-0298 also exhibited superior efficacy in in vivo mouse pressor response model using C57BL/6 mice, compared to our initial molecules (Nishi et al., 2019) and demonstrated ED₅₀ values of 3.2 mg/kg and 6.8 mg/kg respectively. Our findings reported herewith, further strengthen our concept and belief in UT antagonization as a potential therapeutic approach for the management of chronic heart failure.

Affinity, potency, efficacy, selectivity, and molecular modeling of substituted fentanyls at opioid receptors

Substituted fentanyls are abused and cause rapid fatal overdose. As their pharmacology is not well characterized, we examined in vitro pharmacology and structure-activity relationships of 22 substituted fentanyls with modifications of the fentanyl propyl group, and conducted in silico receptor/ligand modeling. Affinities for mu, kappa, and delta opioid receptors (MOR, KOR, and DOR, respectively) heterologously expressed in mammalian cells were assessed in agonist radioligand binding assays. At MOR, furanyl fentanyl had higher affinity than fentanyl, while acryl, isobutyryl and cyclopropyl fentanyls had similar affinities. Comparing affinities, thiophene and methoxyacetyl fentanyls had highest selectivity for MOR (2520- and 2730-fold compared to KOR and DOR, respectively). Functional activities were assessed using [³⁵S]GTPγS binding assays. At MOR, furanyl fentanyl had higher potency and 11 substituted fentanyls had similar high potencies compared to fentanyl. Eight compounds were full agonists of MOR and twelve compounds were partial agonists, with efficacies from 8.8% (phenyl fentanyl) to 60.2% (butyryl fentanyl). All efficacious compounds had selective functional potency for MOR. The predicted binding poses of flexible fentanyl and rigid morphine against MOR show partially overlapping binding pockets, with fentanyl maintaining additional interaction with the transmembrane (TM) 2 helix. Subsequent molecular dynamics simulations revealed a predominant fentanyl binding pose involving various TM interactions. The piperidine nitrogen of substituted fentanyls establishes a salt-bridge with the conserved D-147^3.32 residue and the propanamide carbonyl group establishes a hydrogen bond with the indole side-chain (-NH) of W-318^7.35. The simulation suggests theN-linked phenethyl group may regulate the rotameric switch of W-293^6.48. The predicted binding pose, in conjunction with in vitro binding affinity, clarified the molecular basis of the binding/selectivity profile of furanyl fentanyl and other derivatives at the sequence level. In summary, substituted fentanyls with high MOR potencies, selectivities, and efficacies are likely to have abuse and overdose potential. The work presented here is a prototype to investigate fentanyl derivatives and their abuse potential.

The inorganic polymer, polyphosphate, blocks binding of SARS-CoV-2 spike protein to ACE2 receptor at physiological concentrations

Inorganic polyphosphate (polyP) is a morphogenetically active and metabolic energy-delivering physiological polymer that is released from blood platelets. Here, we show that polyP efficiently inhibits the binding of the envelope spike (S)-protein of the coronavirus SARS-CoV-2, the causative agent of COVID-19, to its host cell receptor ACE2 (angiotensin-converting enzyme 2). To stabilize polyP against the polyP-degrading alkaline phosphatase, the soluble polymer was encapsulated in silica/polyP nanoparticles. Applying a binding assay, soluble Na-polyP (sizes of 40 P_i and of 3 P_i units) as well as silica-nanoparticle-associated polyP significantly inhibit the interaction of the S-protein with ACE2 at a concentration of 1 µg/mL, close to the level present in blood. This inhibition is attributed to an interaction of polyP with a basic amino acid stretch on the surface of the receptor binding domain of S-protein. PolyP retains its activity in a flushing solution, opening a new strategy for the prevention and treatment of SARS-CoV-2 infection in the oropharyngeal cavity. The data suggest that supplementation of polyP might contribute to a strengthening of the human innate immunity system in compromised, thrombocytopenic COVID-19 patients.

Protocol for Peptide Synthesis on Spectrally Encoded Beads for MRBLE-pep Assays

Every living cell relies on signal transduction pathways comprised of protein-protein interactions (PPIs). In many cases, these PPIs are between a folded protein domain and a short linear motif (SLiM) within an unstructured region of a protein. As a result of this small interaction interface (3-10 amino acids), the affinities of SLiM-mediated interactions are typically weak (K _ds of ~1-10 µM), allowing physiologically relevant changes in cellular concentrations of either protein partner to dictate changes in occupancy and thereby transmit cellular signals. However, these weak affinities also render detection and quantitative measurement of these interactions challenging and labor intensive. To address this, we recently developed MRBLE-pep, a technology that employs peptide libraries synthesized on spectrally encoded hydrogel beads to allow multiplexed affinity measurements between a protein and many different peptides in parallel. This approach dramatically reduces both the amount of protein and peptide as well as the time required to measure protein-peptide affinities compared to traditional methods. Here, we provide a detailed protocol describing how to: (1) functionalize polyethylene glycol diacrylate (PEG-DA) MRBLE beads with free amine groups, (2) synthesize peptide libraries on functionalized MRBLEs, (3) validate synthesized peptide sequences via MALDI mass spectrometry and quantify evenness of peptide coverage on MRBLEs, (4) use MRBLE-bound peptide libraries in multiplexed protein binding assays, and (5) analyze binding data to determine binding affinities. We anticipate that this protocol should prove useful for other researchers seeking to use MRBLE-pep in their own laboratories as well as for researchers broadly interested in solid-phase peptide synthesis and protein-protein binding assay development.

In vitro assay for the development of small molecule inhibitors targeting PD-1/PD-L1

Cancer immunotherapy has recently emerged as one of the hot research field since clinical successes achieved by antibody drugs of immune checkpoints, among which PD-1 and its ligand PD-L1 are the well established molecules. PD-1/PD-L1 pathway induces immune tolerance and immune evasion, especially in tumor microenvironment, cancer cell is capable to escape the immune surveillance by up-regulating the expression level of PD-1 or PD-L1. Blockade of PD-1/PD-L1 can unleash the anti-tumor activity, and the strategy shows great successes in the treatment of various cancer types in the late stage. Beside antibody drugs, many other molecules such as peptides, high affinity PD(L)-1 mutants, chemical compounds, and DNA aptamers are designed for inhibitors of PD-1/PD-L1 pathway. Each modulators show their pros and cons based on their own physiochemical properties. Here we introduced the methods for identifying low molecular weight inhibitors of PD-1/PD-L1 and mainly discussed the cell-based blocking test.

MS binding assays for GlyT1 based on Org24598 as nonlabelled reporter ligand

In this study an alternative to radioligand binding assays addressing the glycine transporter 1 (GlyT1) based on quantification of a nonlabelled reporter ligand by means of mass spectrometry (MS) is presented. The established MS Binding Assays employ the GlyT1 inhibitor Org24598 as reporter ligand for which a highly sensitive LC-ESI-MS/MS (liquid chromatography electrospray ionization tandem mass spectrometry) method was developed. A validation of this LC-ESI-MS/MS method with respect to selectivity, linearity, accuracy and precision according to the FDA guidance demonstrated its reliability for quantification of Org24598 in binding experiments. For the implementation of GlyT1 binding experiments conditions in accordance to known GlyT1 radioligand binding assays and already known filtration based MS Binding Assays were chosen. In saturation experiments the affinity of Org24598 towards GlyT1 could be characterized with an equilibrium dissociation constant (K_d) of 16.8 ± 2.2 nM that is well in agreement with the affinity determined in radioligand binding assays. Finally, several known GlyT ligands were studied in competition experiments and the determined inhibition constants (K_i) compared with results from radioligand binding and uptake assays. The almost perfect correlation of the affinities obtained in the MS based binding experiments with results from literature clearly indicates that the established GlyT1 MS Binding Assays are a powerful substitute for the GlyT1 radioligand binding assays so far used for affinity profiling and screening. This article is part of the issue entitled 'Special Issue on Neurotransmitter Transporters'.

Measuring Low-Picomolar Apparent Binding Affinities by Minigel Electrophoretic Mobility Shift

Measuring protein/DNA interactions that have apparent binding affinity constants in the low-picomolar range presents a unique experimental challenge. To probe the sequence specificity of telomere binding proteins, our laboratory has developed an electrophoretic mobility shift assay protocol that allows for the routine measurement of K _D,app values in the 1-20 pM range. Here, we describe the protocol and highlight the particular considerations that should be made to successfully and reproducibly measure high-affinity interactions between proteins and single-stranded DNA.

In vitro and in vivo activity of cyclopeptide Dmt-c[d-Lys-Phe-Asp]NH2, a mu opioid receptor agonist biased toward β-arrestin

Morphine and related drugs, which are the most effective analgesics for the relief of severe pain, act through activating opioid receptors. The endogenous ligands of these receptors are opioid peptides which cannot be used as antinociceptive agents due to their low bioactivity and stability in biological fluids. The major goal of opioid research is to understand the mechanism of action of opioid receptor agonists in order to improve therapeutic utility of opioids. Analgesic effects of morphine are mediated mostly through activation of the mu opioid receptor. However, in the search for safer and more effective drug candidates, analogs with mixed opioid receptor profile gained a lot of interest. Recently, the concept of biased agonists able to differentially activate GPCR downstream pathways, became a new approach in the design of novel drug candidates. It is hypothesized that compounds promoting G-protein signaling may produce analgesia while β-arrestin recruitment may be responsible for opioid side effects. In this report we showed that replacement of the tyrosine residue in the mu-selective ligand Tyr-c[d-Lys-Phe-Asp]NH₂ with 2',6'-dimethyltyrosine (Dmt) produced a cyclopeptide Dmt-c[d-Lys-Phe-Asp]NH₂ with mu/delta opioid receptor agonist profile. This analog showed improved antinociception in the hot-plate test, probably due to the simultaneous activation of mu and delta receptors but also significantly inhibited the gastrointestinal transit. Using the bioluminescence resonance energy transfer (BRET) assay it was shown that this analog was a mu receptor agonist biased toward β-arrestin. β-Arrestin-dependent signaling is most likely responsible for the observed inhibition of gastrointestinal motility exerted by the novel cyclopeptide.

Development of a novel ligand binding assay for relaxin family peptide receptor 3 and 4 using NanoLuc complementation

Relaxin family peptides perform a variety of biological functions by binding and activating relaxin family peptide receptor 1-4 (RXFP1-4), four A-class G protein-coupled receptors. In the present work, we developed a novel ligand binding assay for RXFP3 and RXFP4 based on NanoLuc complementation technology (NanoBiT). A synthetic ligation version of the low-affinity small complementation tag (SmBiT) was efficiently ligated to the A-chain N terminus of recombinant chimeric agonist R3/I5 using recombinant circular sortase A. After the ligation product R3/I5-SmBiT was mixed with human RXFP3 or RXFP4 genetically fused with a secretory large NanoLuc fragment (sLgBiT) at the N terminus, NanoLuc complementation was induced by high-affinity ligand-receptor binding. Binding kinetics and affinities of R3/I5-SmBiT with sLgBiT-fused RXFP3 and RXFP4 were conveniently measured according to the complementation-induced bioluminescence. Using R3/I5-SmBiT and the sLgBiT-fused receptor as a complementation pair, binding potencies of various ligands with RXFP3 and RXFP4 were quantitatively measured without the cumbersome washing step. The novel NanoBiT-based ligand binding assay is convenient for use and suitable for automation, thus will facilitate interaction studies of RXFP3 and RXFP4 with ligands in future. This assay can also be applied to some other plasma membrane receptors for pharmacological characterization of ligands in future studies.

Development and validation of a bioassay to evaluate binding of adalimumab to cell membrane-anchored TNFα using flow cytometry detection

Physicochemical and structural properties of proteins used as active pharmaceutical ingredients of biopharmaceuticals are determinant to carry out their biological activity. In this regard, the assays intended to evaluate functionality of biopharmaceuticals provide confirmatory evidence that they contain the appropriate physicochemical properties and structural conformation. The validation of the methodologies used for the assessment of critical quality attributes of biopharmaceuticals is a key requirement for manufacturing under GMP environments. Herein we present the development and validation of a flow cytometry-based methodology for the evaluation of adalimumab's affinity towards membrane-bound TNFα (mTNFα) on recombinant CHO cells. This in vitro methodology measures the interaction between an in-solution antibody and its target molecule onto the cell surface through a fluorescent signal. The characteristics evaluated during the validation exercise showed that this methodology is suitable for its intended purpose. The assay demonstrated to be accurate (r² = 0.92, slope = 1.20), precise (%CV ≤ 18.31) and specific (curve fitting, r² = 0.986-0.997) to evaluate binding of adalimumab to mTNFα. The results obtained here provide evidence that detection by flow cytometry is a viable alternative for bioassays used in the pharmaceutical industry. In addition, this methodology could be standardized for the evaluation of other biomolecules acting through the same mechanism of action.

Herbicide and insect resistant Bt cotton pollen assessment finds no detrimental effects on adult honey bees

One important concern regarding the use of transgenic cotton expressing insecticidal toxins from the bacterium Bacillus thuringiensis (Bt) is its potential detrimental effect on non-target organisms. The honey bee (Apis mellifera) is the most important pollinator species worldwide and it is directly exposed to transgenic crops by the consumption of genetically modified (GM) pollen. However, the potential effects of Bt cotton on A. mellifera remain unclear. In the present study, we assessed the effects of two Bt cotton varieties; ZMSJ expressing the Cry1Ac and Cry2Ab insecticidal proteins, and ZMKCKC producing Cry1Ac and EPSPS, on A. mellifera. Feeding on pollen from two Bt cotton varieties led to detection of low levels of Cry toxins (<10 ng/g fresh weight) in the midgut of A. mellifera adults, yet expression of detoxification genes did not change significantly compared to feeding on non-Bt cotton. Binding assays showed no Cry1Ac or Cry2Ab binding to midgut brush border membrane proteins from A. mellifera adults. Taken together, these results support minimal risk for potential negative effects on A. mellifera by exposure to Bt cotton.

Isolation and functional analysis of syndecans

Syndecans comprise a major family of cell surface heparan sulfate proteoglycans (HSPGs). Syndecans are composed of sulfated glycosaminoglycans (GAGs), heparan sulfate (HS) or both HS and chondroitin sulfate (CS), attached covalently to core proteins. Syndecans regulate many cellular processes, such as adhesion, proliferation, and migration. Syndecans bind and regulate molecules primarily through their HS chains, but do not bind to all HS/heparin-binding molecules. Furthermore, mice ablated for the syndecan-1 or -4 gene do not show major developmental abnormalities, but they do show striking pathological phenotypes when challenged with infectious or inflammatory stimuli and conditions, suggesting that certain functions of syndecans are specific and cannot be compensated for by other syndecans or other HSPGs. These observations underscore the physiological importance of syndecans and indicate a need to study the activities of isolated native syndecans to define their molecular and cellular functions, and to establish their biological significance. Here we describe methods to isolate syndecans and several assays to analyze their functions.

Synthesis and activity of opioid peptidomimetics with β2- and β3-amino acids

Morphiceptin (Tyr-Pro-Phe-Pro-NH₂) is a selective ligand of the mu opioid receptor, an important target in pain regulation. In this study, morphiceptin was modified at positions 2 or 3 by introduction of β²- or β³-amino acids and additionally in position 1 by replacing Tyr by Dmt (2',6'-dimethyltyrosine), which resulted in obtaining enzymatically stable analogs with mixed opioid receptor affinity profiles. An analog of the sequence Dmt-d-Ala-(R)-β²-1-Nal-Pro-NH₂ [Nal=3-(1-naphthyl)-alanine] showed very high activity at the mu and delta receptors in the calcium mobilization functional test but did not cross the artificial membrane imitating the blood-brain barrier. In the in vivo test this analog induced strong antinociceptive effect in the writhing test in mice after intraperitioneal but also oral administration and inhibited diarrhea similarly to loperamide. Therefore, it may become an interesting lead compound in the development of peripherally restricted drugs for the treatment of gastrointestinal disorders.

"Two-in-One" approach for bioassay selection for dual specificity antibodies

Dual specific antibodies and bispecific antibodies that recognize two different antigen targets are currently being regarded as very effective therapeutics for complex human diseases. While effective, designing and developing a bioassay strategy for dual specific antibodies that is reflective of the mechanism of action (MoA) and also measures the dual activities of antibodies pose unique and exciting challenges. An important question asked while developing a bioassay for dual specific antibodies is, "How many bioassays will be needed, one bioassay or two separate bioassays?" Here we present an approach of using one bioassay for a dual specific antibody that targets two receptors in signaling pathways. The presented assay is able to measure the antibody effects on both target bindings, which would not be achievable using two separate assays. Furthermore, this assay can detect changes in the binding of either target, which impact overall efficacy of the antibody. Its improved sensitivity enables substituting two binding assays with this one bioassay for lot release and stability testing to measure any changes on either target binding, ensuring consistency between lots. This is a single-bioassay approach for a dual specific antibody that is MoA reflective of the intended therapeutic indication. The demonstrated assay development and bridging study strategy for this bioassay for a dual specific mAb1 could be applicable to the other dual specific, bispecific antibodies, and antibodies used for combination therapy.

A novel method for detection of IFN-lambda 3 binding to cells for quantifying IFN-lambda receptor expression

Type III interferons (IFN-lambdas) are important antiviral cytokines that also modulate immune responses acting through a unique IFN-λR1/IL-10R2 heterodimeric receptor. Conflicting data has been reported for which cells express the IFN-λR1 subunit and directly respond to IFN-λs. In this study we developed a novel method to measure IFN-λ3 binding to IFN-λR1/IL-10R2 on the surface of cells and relate this to a functional readout of interferon stimulated gene (ISG) activity in various cell lines. We show that Huh7.5 hepatoma cells bind IFN-λ3 at the highest levels with the lowest Kd(app), translating to the highest induction of various ISGs. Raji and Jurkat cell lines, representing B and T cells, respectively, moderately bind IFN-λ3 and have lower ISG responses. U937 cells, representing monocytes, did not bind IFN-λ3 well and therefore, did not have any ISG induction. Importantly, knockdown of IFNLR1 in Huh7.5 cells decreased our binding signal proportionally and reduced ISG induction by up to 93%. IFN-λ3 responsiveness increased over time with maximal ISG responses seen at 24h for all but one gene. These data confirm our new IFN-λ3 binding assay can be used to quantify IFN-λ receptor surface expression on a variety of cell types and reflects IFN-λ3 responsiveness.

Fluorescence polarization-based competition binding assay for c-Jun N-terminal kinases 1 and 2

In order to evaluate the isoform selectivity of novel inhibitors within the c-Jun N-terminal kinase (JNK) family, a fluorescence polarization-based competition binding assay, previously developed for JNK3, was extended to the other isoforms JNK1 and JNK2. The assay is based on the displacement of a versatile fluorescent pyridinylimidazole-based probe and was validated by testing the precursor of the probe as well as standard JNK inhibitors.