Label-free drug discovery

Current drug discovery is dominated by label-dependent molecular approaches, which screen drugs in the context of a predefined and target-based hypothesis in vitro. Given that target-based discovery has not transformed the industry, phenotypic screen that identifies drugs based on a specific phenotype of cells, tissues, or animals has gained renewed interest. However, owing to the intrinsic complexity in drug-target interactions, there is often a significant gap between the phenotype screened and the ultimate molecular mechanism of action sought. This paper presents a label-free strategy for early drug discovery. This strategy combines label-free cell phenotypic profiling with computational approaches, and holds promise to bridge the gap by offering a kinetic and holistic representation of the functional consequences of drugs in disease relevant cells that is amenable to mechanistic deconvolution.

The development of label-free cellular assays for drug discovery

INTRODUCTION

The need to improve drug research and development productivity continues to drive innovation in pharmacological assays. Technologies that can leverage the advantages of both molecular and phenotypic assays would hold great promise for discovery of new medicines.

AREAS COVERED

This article briefly reviews current label-free platforms for cell-based assays and is primarily focused on fundamental aspects of these assays using dynamic mass redistribution technology as an example. The article also presents strategies for relating label-free profiles to molecular modes of actions of drugs.

EXPERT OPINION

Emerging evidence suggests that label-free cellular assays are phenotypic in nature, yet permit molecular mechanistic deconvolution. Together with unique competency in throughput, sensitivity and pathway coverages, label-free cellular assays allow users to screen drugs against endogenous receptors in native cells (including disease relevant primary cells) and determine the molecular modes of action of drug molecules. However, there are challenges for label-free in both basic research and drug discovery: the deconvolution of the cellular and molecular mechanisms for the biosensor signatures of receptor-drug interactions, new methodologies for data analysis and the development of new biosensor technologies. These challenges will need to be met for the wide adoption of these assays in drug discovery.

Anti-inflammatory gallic Acid and wedelolactone are G protein-coupled receptor-35 agonists

G protein-coupled receptor-35 (GPR35) has been shown to be a target of the asthma drugs cromolyn disodium and nedocromil sodium. Gallic acid and caffeic acids are reported to modulate allergic reactions via unknown mode(s) of action. Here we attempt to elucidate whether both phenolic acids share a common mode of action with the two asthma drugs. Label-free dynamic mass redistribution (DMR) assays showed that both phenolic acids triggered robust DMR signals in HT-29 cells, whose characteristics were similar to that of cromolyn disodium. Both phenolic acids resulted in detectable β-arrestin translocation signals in an engineered U2OS cell line stably expressing a C-terminal-modified GPR35, but with lower efficacy than cromolyn disodium. Antiallergic wedelolactone was found to be a potent β-arrestin-biased GPR35 agonist. These results suggest that certain anti-inflammatory phytochemicals including gallic acid and wedelolactone may modulate inflammatory allergic action via their agonism at GPR35. GPR35 may represent a target for the treatment of allergic disorders including asthma.

Label-free integrative pharmacology on-target of drugs at the β(2)-adrenergic receptor

We describe a label-free integrative pharmacology on-target (iPOT) method to assess the pharmacology of drugs at the β(2)-adrenergic receptor. This method combines dynamic mass redistribution (DMR) assays using an array of probe molecule-hijacked cells with similarity analysis. The whole cell DMR assays track cell system-based, ligand-directed, and kinetics-dependent biased activities of the drugs, and translates their on-target pharmacology into numerical descriptors which are subject to similarity analysis. We demonstrate that the approach establishes an effective link between the label-free pharmacology and in vivo therapeutic indications of drugs.

The role of IL-17 promotes spinal cord neuroinflammation via activation of the transcription factor STAT3 after spinal cord injury in the rat

Study Design. In this study, we investigated the role of IL-17 via activation of STAT3 in the pathophysiology of SCI. Objective. The purpose of the experiments is to study the expression of IL-17 and related cytokines via STAT3 signaling pathways, which is caused by the acute inflammatory response following SCI in different periods via establishing an acute SCI model in rat. Methods. Basso, Beattie, and Bresnahan hind limb locomotor rating scale was used to assess the rat hind limb motor function. Immunohistochemistry was used to determine the expression levels of IL-17 and p-STAT3 in spinal cord tissues. Western blotting analysis was used to determine the protein expression of p-STAT3 in spinal cord tissue. RT-PCR was used to analyze the mRNA expression of IL-17 and IL-23p19 in the spleen tissue. ELISA was used to determine the peripheral blood serum levels of IL-6, IL-21, and IL-23. Results. Compared to the sham-operated group, the expression levels of IL-17, p-STAT3, IL-6, IL-21, and IL-23 were significantly increased and peaked at 24 h after SCI. The increased levels of cytokines were correlated with the SCI disease stages. Conclusion. IL-17 may play an important role in promoting spinal cord neuroinflammation after SCI via activation of STAT3.

Evaluation of dynamic mass redistribution technology for pharmacological studies of recombinant and endogenously expressed g protein-coupled receptors

The Epic cell assay technology (Corning Inc., Corning, NY) uses a resonant waveguide grating optical biosensor to measure cellular response to ligands manifested through dynamic mass redistribution (DMR) of cellular contents. The DMR measurement is a noninvasive, label-free assay that can be used to assess the pharmacological properties of compounds. In this study, a panel of 12 compounds was evaluated against two G protein-coupled receptor (GPCR) targets in recombinant expressed cell lines using the Corning Epic system in 384-well microplates. The evaluation was performed in a double-blinded fashion such that the identity and properties of both the GPCR targets and compounds were unknown to the researchers at the time of the study. Analysis of the DMR response from cell stimulation was used to identify compounds that functioned as agonists or antagonists and to evaluate the associated efficacy and potency. DMR results were shown to have good agreement with data obtained from cyclic AMP and calcium flux assays for compounds evaluated. A further analysis was performed and successfully identified the signaling pathways that the two GPCRs activated. In addition, the DMR measurement was able to detect responses from an endogenous receptor in these cells. The Epic DMR technology provides a generic platform amenable to pharmacological evaluation of cellular responses to GPCR activation in a label-free live cell assay format.

The growth of bilayer defects and the induction of interdigitated domains in the lipid-loss process of supported phospholipid bilayers

The lipid-loss process has been studied with in situ atomic force microscopy (AFM) at six different temperatures for supported dipalmitoylphosphatidylcholine (DPPC) bilayers. A typical structural characteristic is the creation and the growth of bilayer defects as lipid molecules are lost from the bilayer. The rate of the lipid loss has an Arrhenius behavior, with an activation energy of 37 kT, where kT is the thermal energy at room temperature. For the lipid-loss processes at temperatures above 45 degrees C, interdigitated membrane domains are induced and are mostly in contact with some bilayer defects. These domains disappear at the increase of the area of bilayer defects. Possible mechanisms of these phenomena are discussed.

Cationic silanes stabilize intermediates in DNA condensation

In vitro condensation of DNA has been widely studied to gain insight into the mechanisms of DNA compaction in biological systems such as chromosomes and phage heads and has been used to produce nanostructured particles with novel material and functional properties. Here we report on the condensation of DNA in aqueous solutions by cationic silanes, which combine the condensing properties of polyamines with the cross-linking chemistry of silanes. DNA can be reversibly condensed into classical toroidal and rod-shaped structures with these agents. At low silane concentrations DNA forms a variety of looped structures with well-defined characteristics, including flower- and sausage-shaped forms. These structures suggest that at low silane concentrations a DNA-DNA contact in which the strands are at very large angles to each other is stabilized. Changes in these structures observed as a function of silane concentration suggest possible pathways for the formation of toroids and rods.

Tyrphostin analogs are GPR35 agonists

GPR35 is an orphan G protein-coupled receptor that is not well-characterized. Here we employ dynamic mass redistribution (DMR) assays to discover new GPR35 agonists. DMR assays identified tyrphostin analogs as GPR35 agonists, which were confirmed with receptor internalization, Tango β-arrestin translocation, and extracellular-signal-regulated kinase phosphorylation assays. These agonists provide pharmacological tools to study the biology and function of GPR35.

Ligand-directed functional selectivity at the mu opioid receptor revealed by label-free integrative pharmacology on-target

Development of new opioid drugs that provide analgesia without producing dependence is important for pain treatment. Opioid agonist drugs exert their analgesia effects primarily by acting at the mu opioid receptor (MOR) sites. High-resolution differentiation of opioid ligands is crucial for the development of new lead drug candidates with better tolerance profiles. Here, we use a label-free integrative pharmacology on-target (iPOT) approach to characterize the functional selectivity of a library of known opioid ligands for the MOR. This approach is based on the ability to detect dynamic mass redistribution (DMR) arising from the activation of the MOR in living cells. DMR assays were performed in HEK-MOR cells with and without preconditioning with probe molecules using label-free resonant waveguide grating biosensors, wherein the probe molecules were used to modify the activity of specific signaling proteins downstream the MOR. DMR signals obtained were then translated into high resolution heat maps using similarity analysis based on a numerical matrix of DMR parameters. Our data indicate that the iPOT approach clearly differentiates functional selectivity for distinct MOR signaling pathways among different opioid ligands, thus opening new avenues to discover and quantify the functional selectivity of currently used and novel opioid receptor drugs.

Acoustofluidic chemical waveform generator and switch

Eliciting a cellular response to a changing chemical microenvironment is central to many biological processes including gene expression, cell migration, differentiation, apoptosis, and intercellular signaling. The nature and scope of the response is highly dependent upon the spatiotemporal characteristics of the stimulus. To date, studies that investigate this phenomenon have been limited to digital (or step) chemical stimulation with little control over the temporal counterparts. Here, we demonstrate an acoustofluidic (i.e., fusion of acoustics and microfluidics) approach for generating programmable chemical waveforms that permits continuous modulation of the signal characteristics including the amplitude (i.e., sample concentration), shape, frequency, and duty cycle, with frequencies reaching up to 30 Hz. Furthermore, we show fast switching between multiple distinct stimuli, wherein the waveform of each stimulus is independently controlled. Using our device, we characterized the frequency-dependent activation and internalization of the β2-adrenergic receptor (β2-AR), a prototypic G-protein coupled receptor (GPCR), using epinephrine. The acoustofluidic-based programmable chemical waveform generation and switching method presented herein is expected to be a powerful tool for the investigation and characterization of the kinetics and other dynamic properties of many biological and biochemical processes.

Agonist-directed desensitization of the β2-adrenergic receptor

The β(2)-adrenergic receptor (β(2)AR) agonists with reduced tachyphylaxis may offer new therapeutic agents with improved tolerance profile. However, receptor desensitization assays are often inferred at the single signaling molecule level, thus ligand-directed desensitization is poorly understood. Here we report a label-free biosensor whole cell assay with microfluidics to determine ligand-directed desensitization of the β(2)AR. Together with mechanistic deconvolution using small molecule inhibitors, the receptor desensitization and resensitization patterns under the short-term agonist exposure manifested the long-acting agonism of salmeterol, and differentiated the mechanisms of agonist-directed desensitization between a full agonist epinephrine and a partial agonist pindolol. This study reveals the cellular mechanisms of agonist-selective β(2)AR desensitization at the whole cell level.

G-protein-coupled receptor microarrays

Membrane-bound proteins represent the single most important class of drug targets. Arraying these proteins is difficult because they typically need to be embedded in membranes to maintain their correctly folded conformations. We describe here the fabrication of microarrays consisting of G-protein-coupled receptors (GPCRs)--the single largest family of membrane-bound proteins-by robotic pin-printing on slides, and demonstrate assays for screening of ligands on these arrays.

Probing cytoskeleton modulation by optical biosensors

This paper reported the use of resonant waveguide grating biosensors for studying the cytoskeleton structure in cells. This was achieved by measuring the changes in mass within the bottom portion of cells upon exposure to saponin in the absence and presence of cytoskeleton modulators. Treatment of Chinese hamster ovary cells with saponin led to a dose-dependent and dynamic mass changes. When a higher concentration of saponin (> 60 microg/ml) was used, a net loss in mass was observed. This is probably resulted from the diffusion of soluble intracellular materials away from the bottom portion of cells after pore formation in the cell plasma membranes by saponin. The pretreatment of cells with actin disruption agents, cytochalasin B and latrunculin A, led to significantly increased loss in cell mass induced by either 75 or 125 microg/ml saponin. These results suggested that optical biosensors provide an attractive means to study the cytoskeleton structure and screen modulators that affect the cytoskeleton structure.

Troubleshooting and deconvoluting label-free cell phenotypic assays in drug discovery

INTRODUCTION

Central to drug discovery and development is to comprehend the target(s), potency, efficacy and safety of drug molecules using pharmacological assays. Owing to their ability to provide a holistic view of drug actions in native cells, label-free biosensor-enabled cell phenotypic assays have been emerging as new generation phenotypic assays for drug discovery. Despite the benefits associated with wide pathway coverage, high sensitivity, high information content, non-invasiveness and real-time kinetics, label-free cell phenotypic assays are often viewed to be a blackbox in the era of target-centric drug discovery.

METHODS

This article first reviews the biochemical and biological complexity of drug-target interactions, and then discusses the key characteristics of label-free cell phenotypic assays and presents a five-step strategy to troubleshooting and deconvoluting the label-free cell phenotypic profiles of drugs.

RESULTS

Drug-target interactions are intrinsically complicated. Label-free cell phenotypic signatures of drugs mirror the innate complexity of drug-target interactions, and can be effectively deconvoluted using the five-step strategy.

DISCUSSION

The past decades have witnessed dramatic expansion of pharmacological assays ranging from molecular to phenotypic assays, which is coincident with the realization of the innate complexity of drug-target interactions. The clinical features of a drug are defined by how it operates at the system level and by its distinct polypharmacology, ontarget, phenotypic and network pharmacology. Approaches to examine the biochemical, cellular and molecular mechanisms of action of drugs are essential to increase the efficiency of drug discovery and development. Label-free cell phenotypic assays and the troubleshooting and deconvoluting approach presented here may hold great promise in drug discovery and development.

The Role of 6-Gingerol on Inhibiting Amyloid β Protein-Induced Apoptosis in PC12 Cells

Our previous study suggests that ginger root extract can reverse behavioral dysfunction and prevent Alzheimer's disease (AD)-like symptoms induced by the amyloid-β protein (Aβ) in a rat model. 6-Gingerol is the major gingerol in ginger rhizomes, but its effect on the treatment of AD remains unclear. In this study, we aimed to determine if 6-gingerol had a protective effect on Aβ1-42-induced damage and apoptotic death in rat pheochromocytoma cells (PC12 cells) and to investigate the underlying mechanisms by which 6-gingerol may exert its neuroprotective effects. Our results indicated that pre-treatment with 6-gingerol significantly increased cell viability and reduced cell apoptosis in Aβ1-42-treated cells. Moreover, 6-gingerol pretreatment markedly reduced the level of intracellular reactive oxygen species (ROS) and malondialdehyde (MDA), the production of nitric oxide (NO), and the leakage of lactate dehydrogenase (LDH) and increased superoxide dismutase (SOD) activity compared with the Aβ1-42 treatment group. In addition, 6-gingerol pretreatment also significantly enhanced the protein levels of phosphorylated Akt (p-Akt) and glycogen synthase kinase-3β (p-GSK-3β). Overall, these results indicate that 6-gingerol exhibited protective effects on apoptosis induced by Aβ1-42 in cultured PC12 cells by reducing oxidative stress and inflammatory responses, suppressing the activation of GSK-3β and enhancing the activation of Akt, thereby exerting neuroprotective effects. Therefore, 6-gingerol may be useful in the prevention and/or treatment of AD.

Duplexed label-free G protein--coupled receptor assays for high-throughput screening

This article describes duplexed label-free optical biosensor cellular assays for simultaneously assaying 2 endogenous receptors, the G(q)-coupled histamine receptor (H( 1)) and the G(s)-coupled beta(2)-adrenergic receptor (beta(2)AR), in A431 cells. The biosensor cellular assays consist of 2 sequential steps-an initial agonist screening using Sigma LOPAC (Library of Pharmaceutically Active Compounds) and a subsequent antagonist screening using a solution mixture containing the H(1) agonist histamine and the beta(2)AR agonist epinephrine. Results showed that costimulating A431 cells with histamine and epinephrine led to an optical response additive to individual responses. The agonist screening not only identified all full agonists for both the H(1) and beta(2) receptors, but also detected pathway-biased ligands for the beta(2)AR. Furthermore, the succeeding antagonist screening documented all known antagonists in the library for either the H(1) or beta(2) receptors. This is the 1st demonstration of a single cellular assay that is capable of screening ligands against 2 GPCRs coupled to distinct G proteins, and highlights the power of pathway-unbiased and label-free biosensor cellular assays for GPCR screens.

Functional GPCR Microarrays

This paper describes G-protein-coupled receptor (GPCR) microarrays on porous glass substrates and functional assays based on the binding of a europium-labeled GTP analogue. The porous glass slides were made by casting a glass frit on impermeable glass slides and then coating with gamma-aminopropyl silane (GAPS). The emitted fluorescence was captured on an imager with a time-gated intensified CCD detector. Microarrays of the neurotensin receptor 1, the cholinergic receptor muscarinic 2, the opioid receptor mu, and the cannabinoid receptor 1 were fabricated by pin printing. The selective agonism of each of the receptors was observed. The screening of potential antagonists was demonstrated using a cocktail of agonists. The amount of activation observed was sufficient to permit determinations of EC50 and IC50. Such microarrays could potentially streamline drug discovery by helping integrate primary screening with selectivity and safety screening without compromising the essential functional information obtainable from cellular assays.

Label-free cell phenotypic assessment of the biased agonism and efficacy of agonists at the endogenous muscarinic M3 receptors

INTRODUCTION

Efficacy describes the property of a ligand that enables the receptor to change its behavior towards the host cell, while biased agonism defines the ability of a ligand to differentially activate some of the vectorial pathways over others mediated through the receptor. However, little is known about the molecular basis defining the efficacy of ligands at G protein-coupled receptors. Here we characterize the biased agonism and cell phenotypic efficacy of seven agonists at the endogenous muscarinic M3 receptors in six different cell lines including HT-29, PC-3, HeLa, SF268, CCRF-CEM and HCT-15 cells.

METHODS

Quantitative real-time PCR and multiple label-free whole cell dynamic mass redistribution (DMR) assays were used to determine the functional muscarinic receptors in each cell line. DMR pathway deconvolution assay was used to determine the pathway biased activity of the muscarinic agonists. Operational agonism model was used to quantify the pathway bias, while macro-kinetic data reported in literature was used to analyze the biochemical mechanism of action of these agonists.

RESULTS

Quantitative real-time PCR and ligand pharmacology studies showed that all the native cell lines endogenously express functional M3 receptors. Furthermore, different agonists triggered distinct DMR signals in a specific cell line as well as in different cell lines. DMR pathway deconvolution using known G protein modulators revealed that the M3 receptor in all the six cell lines signals through multiple G protein-mediated pathways, and certain agonists display biased agonism in a cell line-dependent manner. The whole cell efficacy and potency of these agonists were found to be sensitive to the assay time as well as the cell background. Correlation analysis suggested that the whole cell efficacy of agonists is correlated well with their macro-dissociation rate constants.

DISCUSSION

This study implicates that the endogenous M3 receptors are coupled to multiple pathways, and the muscarinic agonists can display distinct biased agonism and whole cell phenotypic efficacy.

Automated sizing of DNA fragments in atomic force microscope images

Current techniques used to measure lengths of DNA fragments in atomic force microscope (AFM) images require a user to operate interactive software and execute tedious error-prone cursor selections. An algorithm is proposed which provides an automated method for determining DNA fragment lengths from AFM images without interaction from the computer operator (e.g. cursor selections or mouse clicks). The approach utilises image processing techniques tailored to characteristics of AFM images of DNA fragments. The automated measurements have a mean absolute deviation of less than 1 pixel when compared to manual image-based measurements. The DNA length determined from the histogram of calculated lengths is accurate to within 3% of the actual DNA length in solution. For fragments that are 250 base-pairs long, the precision is estimated to be within 17 nm, which is about 20% of the total length. This precision was confirmed when the algorithm easily resolved fragments in one image that differed by only 17 nm. Fragment sizes up to 2000 base-pairs have been tested and successfully sized. This algorithm is being developed as part of a new solid-state DNA sizing technique for applications such as genotyping and construction of physical genome maps.