Mapping the high throughput SEREX technology screening for novel tumor antigens

Advances in novel tumor-associated antigen (TAA) screening strategy have accelerated the identification and characterization of biomarkers and potential target molecules for tumor subtyping, diagnosis and therapeutics, which may facilitate early detection and diagnosis of the diseases individually and enhance treatment approaches for cancer. Over the past decades, a plethora of non-invasive methodologies dedicated to identify novel target molecules have been primarily focusing on the discovery of human tumor antigens recognized by the autologous antibody repertoire or cytotoxic T lymphocytes, among which serological analysis of recombinant cDNA expression libraries (SEREX) technology is chronologically first established and is of outstanding sensitivity and antigen coverage. This approach involves immunoscreening cDNA libraries extracted from fresh tumor tissues with sera from cancer patients to identify gene products recognized by IgG antibody. SEREX-defined clones can be directly sequenced and their expression profiles can be readily determined, allowing for immediate structural definition of the antigenic target and subsequent identification of TAAs and their cognate autoantibodies. This review is not only devoted to outline the SEREX technology and its advantages, drawbacks and recent modifications currently available for discovering provocative tumor antigens, but also to translate these SEREX-defined peptides into valuable cancer-specific signatures that would aid in the development of diagnostics, prognostics and therapeutics for cancer patients.     

Discovery of a new family of chromium ethylene polymerisation catalysts using high throughput screening methodology

Following a discovery that salicylaldimines bearing bulky ortho-phenoxy substituents and small imine substituents give very active chromium catalysts for ethylene polymerisation, High Throughput Screening (HTS) methodology has been employed to facilitate a further discovery of exceptionally active catalysts based on tridentate salicylaldimine ligands with bulky triptycenyl groups.     

Discovery and evaluation of highly active imidotitanium ethylene polymerisation catalysts using high throughput catalyst screening

A family of ca. 50 imidotitanium precatalysts [Ti(NR)(Me(3)[9]aneN(3))Cl(2)](R = alkyl or aryl; Me(3)[9]aneN(3)= 1,4,7-trimethyltriazacyclononane) were prepared in good yields using semi-automated procedures; high-throughput screening techniques identified seven highly active ethylene polymerisation precatalysts with activities in the range ca. 3 400 to 10 000 kg(PE) mol(-1) h(-1) bar(-1).     

Discovery of novel catalytic materials for emissions control using high throughput scanning mass spectrometry

High-throughput approaches were applied to the discovery of more efficient catalysts for various applications in emissions control. The screening approach was based on a hierarchy of qualitative or semi-quantitative primary screens for discovery of hits and quantitative secondary screens for confirmation and scale-up of leads. In this work, primary screening was carried out by fast scanning mass spectrometry (SMS) for NO(x) abatement, low temperature CO oxidation, VOC removal, CO(x) methanation and the water gas shift (WGS) reaction.     

Retroviral display and high throughput screening

Retroviruses distinguish themselves from all other mammalian viruses by their abilities to infect and propagate in mammalian cells without causing a cytopathic effect and to stably integrate their genetic information into the genome of the host cell. These unique properties make them an ideal platform for the display and directed evolution of proteins in a mammalian cell environment. This review will describe the essentials about retrovirus biology and then discuss in detail display and screening strategies that have been developed during the past 15 years of retroviral display technology.     

Beta galactosidase enzyme fragment complementation as a novel technology for high throughput screening

In this review, the applications of beta galactosidase complementation are described. alpha Complementation is a naturally occurring process in bacteria and in engineered cells, and can also occur in eukaryotic cells. Two forms of alpha complementation have been used in high throughput screening (HTS), in which interacting fragments complement with either low or high affinity. Low affinity complementation is used to monitor protein protein interactions, such as those occurring in homodimerization of the epidermal growth factor receptor (EGFR), and provides a robust screen for detection of EGFR inhibitors. High affinity complementation provides the basis for several HTS assays, in which analytes, such as cAMP or IP(3), are detected in crude cell lysates. A development of the latter approach is protein labeling, providing for measurement of cell protein expression and trafficking. Collectively, the use of beta galactosidase complementation provides a novel and flexible technology for highly sensitive, homogeneous HTS assay development.     

Gene expression analysis for high throughput screening applications

To meet growing needs for high throughput gene expression profiling, we established a new automated high throughput TaqMan RT-PCR method for quantitative mRNA expression analysis. In this method, the Allegro( trade mark ) (Zymark) system conducts all sample tracking and liquid handling steps, and ABI PRISM 7900 HT (Applied Biosystems) is used to conduct real-time determination of the C(t) value when amplification of PCR products is first detected and accumulation of inhibitory PCR products is unlikely to occur. The ABI PRISM 7900 HT Sequence Detection System features a real-time PCR instrument with 384-well-plate compatibility and robotic loading, and continuous wavelength detection, which enables the use of multiple fluorophores in a single reaction. The Allegro System offers an assembly line approach with a modular design that allows reconfiguration of the components to accommodate variations in the assay flow. In the present study, we have established and validated a new automated High Throughput (HT) TaqMan RT-PCR- based method for quantitative mRNA expression analysis. The data demonstrate that HT-Taqman PCR is a powerful tool that can be used for measuring low concentrations of mRNA, and is highly accurate, reproducible, and amenable to high throughput analysis. Results suggest that HT-TaqMan is a reliable method for the quantification of low-expression genes and a powerful tool with HT capability for target identification/validation, structure-activity relationship (SAR) study, compound selection for efficacy studies, and biomarker identification in drug discovery and development.     

Virtual high throughput screening in new lead identification

Drug discovery continues to be one of the greatest contemporary challenges and rational application of modelling approaches is the first important step to obtain lead compounds, which can be optimised further. Virtual high throughput screening (VHTS) is one of the efficient approaches to obtain lead structures for a given target. Strategic application of different screening filters like pharmacophore mapping, shape-based, ligand-based, molecular similarity etc., in combination with other drug design protocols provide invaluable insights in lead identification and optimization. Screening of large databases using these computational methods provides potential lead compounds, thus triggering a meaningful interplay between computations and experiments. In this review, we present a critical account on the relevance of molecular modelling approaches in general, lead optimization and virtual screening methods in particular for new lead identification. The importance of developing reliable scoring functions for non-bonded interactions has been highlighted, as it is an extremely important measure for the reliability of scoring function. The lead optimization and new lead design has also been illustrated with examples. The importance of employing a combination of general and target specific screening protocols has also been highlighted.     

Design of a compound screening collection for use in high throughput screening

In this paper we introduce a quantitative model that relates chemical structural similarity to biological activity, and in particular to the activity of lead series of compounds in high-throughput assays. From this model we derive the optimal screening collection make up for a given fixed size of screening collection, and identify the conditions under which a diverse collection of compounds or a collection focusing on particular regions of chemical space are appropriate strategies. We derive from the model a diversity function that may be used to assess compounds for acquisition or libraries for combinatorial synthesis by their ability to complement an existing screening collection. The diversity function is linked directly through the model to the goal of more frequent discovery of lead series from high-throughput screening. We show how the model may also be used to derive relationships between collection size and probabilities of lead discovery in high-throughput screening, and to guide the judicious application of structural filters.     

Recent advances in high throughput screening for ADME properties

With the increase in the numbers of molecules synthesized in a typical drug discovery program, as well as the large amount of information utilized in the selection of a drug candidate, there is a need for a plethora of drug metabolism and pharmacokinetic (DMPK) information to be regularly generated in discovery. Over the past decade, many in vitro, and even in vivo, DMPK screens have been developed and routinely deployed to generate this information in support of drug discovery efforts. In the past few years, newer methods, or adaptations to methods, have been published, and this review attempts to summarize these advances. In particular, advances have been reported for experimental approaches to metabolic clearance, CYP inhibition, in vivo exposure, and distribution, as well as in silico determinations of absorption, distribution, metabolism, and excretion (ADME) properties. Bioanalytical approaches aimed at optimizing analyte method development, sample preparation, and analyte detection, have also been reported. Future advances will further improve the ability to make decisions on molecules earlier in drug discovery.     

Fluorescence-based adenylyl cyclase assay adaptable to high throughput screening

The second messenger cAMP has been implicated in numerous cellular processes such as glycogen metabolism, muscle contraction, learning and memory, and differentiation and development. Genetic evidence suggests that the enzyme that produces cAMP, adenylyl cyclase (AC), may be involved in pathogenesis in many of these cellular processes. In addition, these data suggest that membrane-bound ACs may be valuable targets for therapeutics to treat pathogenesis of these processes. The development of a robust real-time adenylyl cyclase assay that can be scalable to high-throughput screening could help in the development of novel therapeutics. Here we report a novel fluorescence-based cyclase assay using Bodipy FL GTPgammaS (BGTPgammaS). The fluorescence of the Bodipy moiety of BGTPgammaS was dramatically enhanced by incubation with the minimal catalytic core of wild-type-AC (wt-AC) and a mutant with decreased purine selectivity (mut-AC), in an AC activation-dependent manner. No increase in fluorescence was observed using Bodipy FL ATPgammaS (BATPgammaS) as substrate for either wt-AC or mut-AC. Using BGTPgammaS, forskolin, Gsalpha.GTPgammaS and the divalent cation Mn(2+) potently enhanced the rate of fluorescence increase in a concentration-dependent manner. The fluorescence enhancement of the Bodipy moiety was inhibited by known inhibitors of AC such as 2'deoxy,3'AMP and 2',5'-dideoxy-3'ATP. Furthermore, the fluorescence assay is adaptable to 96-well and 384-well multiplate format and is thus applicable to high throughput screening methodologies.     

High throughput drug screening by direct RNA profiling on DNA sensors

The feasibility of DNA microarray sensor technology as a routine technique of molecular pharmacology to perform high throughput drug screening and the advantages of directly labeled RNA for a high throughput experiment are presented in this paper. A novel, single-step direct chemical labeling method for DNA microarray target samples has been developed to reduce the sample amount, cost, time and error of the experiment by eliminating the need for enzyme mediated labeling. Reproducibility of the data for high throughput drug screening is demonstrated by monitoring differential gene expression of a set of 45 gene targets involved in the genotoxic stress response pathways.     

Homogeneous single-label tyrosine kinase activity assay for high throughput screening

Protein post-translational modifications (PTMs) are regulatory mechanisms carried out by different enzymes in a cell. Kinase catalyzed phosphorylation is one of the most important PTM affecting the protein activity and function. We have developed a single-label quenching resonance energy transfer (QRET) assay to monitor tyrosine phosphorylation in a homogeneous high throughput compatible format. Epidermal growth factor receptor (EGFR) induced phosphorylation was monitored using Eu³⁺-chelate labeled peptide and label-free phosphotyrosine specific antibody in presence of a soluble quencher molecule. In the QRET kinase assay, antibody binding to phosphorylated Eu³⁺-peptide protects the Eu³⁺-chelate from luminescence quenching, monitoring high time-resolved luminescence (TRL) signals. In the presence of specific kinase inhibitor, antibody recognition and Eu³⁺-chelate protection is prevented, allowing an efficient luminescence quenching. The assay functionality was demonstrated with a panel of EGFR inhibitors (AG-1478, compound 56, erlotinib, PD174265, and staurosporine). The monitored IC₅₀ values ranged from 0.08 to 155.3 nM and were comparable to those found in the literature. EGFR activity and inhibition assays were performed using low nanomolar enzyme and antibody concentration in a 384-well plate format, demonstrating its compatibility for high throughput screening (HTS).     

Microfluidics for cell-based high throughput screening platforms—A review

In the last decades, the basic techniques of microfluidics for the study of cells such as cell culture, cell separation, and cell lysis, have been well developed. Based on cell handling techniques, microfluidics has been widely applied in the field of PCR (Polymerase Chain Reaction), immunoassays, organ-on-chip, stem cell research, and analysis and identification of circulating tumor cells. As a major step in drug discovery, high-throughput screening allows rapid analysis of thousands of chemical, biochemical, genetic or pharmacological tests in parallel. In this review, we summarize the application of microfluidics in cell-based high throughput screening. The screening methods mentioned in this paper include approaches using the perfusion flow mode, the droplet mode, and the microarray mode. We also discuss the future development of microfluidic based high throughput screening platform for drug discovery.     

Surrogate docking: structure-based virtual screening at high throughput speed

Summary Structure-based screening using fully flexible docking is still too slow for large molecular libraries. High quality docking of a million molecule library can take days even on a cluster with hundreds of CPUs. This performance issue prohibits the use of fully flexible docking in the design of large combinatorial libraries. We have developed a fast structure-based screening method, which utilizes docking of a limited number of compounds to build a 2D QSAR model used to rapidly score the rest of the database. We compare here a model based on radial basis functions and a Bayesian categorization model. The number of compounds that need to be actually docked depends on the number of docking hits found. In our case studies reasonable quality models are built after docking of the number of molecules containing 50 docking hits. The rest of the library is screened by the QSAR model. Optionally a fraction of the QSAR-prioritized library can be docked in order to find the true docking hits. The quality of the model only depends on the training set size – not on the size of the library to be screened. Therefore, for larger libraries the method yields higher gain in speed no change in performance. Prioritizing a large library with these models provides a significant enrichment with docking hits: it attains the values of 13 and 35 at the beginning of the score-sorted libraries in our two case studies: screening of the NCI collection and a combinatorial libraries on CDK2 kinase structure. With such enrichments, only a fraction of the database must actually be docked to find many of the true hits. The throughput of the method allows its use in screening of large compound collections and in the design of large combinatorial libraries. The strategy proposed has an important effect on efficiency but does not affect retrieval of actives, the latter being determined by the quality of the docking method itself. Electronic supplementary material is available at http://dx.doi.org/10.1007/s10822-005-9002-6.