New assay technologies for high-throughput screening

Exploring the Relationships between Structure and Antimicrobial Potency of Quinolinequinones

Microorganisms are responsible for hospital infections, and methicillin-resistant Staphylococcus aureus is one of them. In looking for the most effective lead structures to cope with the rise of antimicrobial (antibiotic) resistance, we evaluated the antimicrobial profile of quinolinequinones for potential antimicrobial applications. 1,4-quinone molecules fused with heteroatom have been studied extensively for many years as a source of drugs and lead structures. The aims of this study were to evaluate the antimicrobial activity of quinolinequinones against bacterial and fungal strains, and to probe for potential lead structures. For this reason, the activity of these compounds against three different strains of Candida fungi (C. albicans, C. parapsilosis, and C. tropicalis) and Gram-positive and Gram-negative pathogenic bacteria were investigated, searching for potential lead compounds. Five of nine quinolinequinones showed activity mainly against the Gram-positive strains with a minimal inhibitory concentration within the Clinical and Laboratory Standards Institute (CLSI) levels. The results revealed that quinolinequinones have significant activity against bacteria including Staphylococcus aureus and Staphylococcus epidermidis, and fungi including Candida albicans and Candida parapsilosis. QQ1, QQ2, QQ3, QQ5, and QQ6 exhibited the highest growth inhibition against two essential species of the Gram-positive strains (Staphylococcus epidermidis and Staphylococcus aureus). Among these, four molecules (QQ2, QQ3, QQ5, and QQ6) were also active against Enterococcus faecalis, the other member of the Gram-positive strains. The antifungal profile of two quinolinequinones (QQ7 and QQ8) indicated that they were as effective as the reference drug Clotrimazole against Candida albicans. The same molecules also have potential inhibitory antifungal activity against Candida tropicalis. For better understanding, the most active two quinolinequinones (QQ2 and QQ6) were examined for biofilm inhibition and a time-kill kinetic study.

Automated affinity selection for rapid discovery of peptide binders

In-solution affinity selection (AS) of large synthetic peptide libraries affords identification of binders to protein targets through access to an expanded chemical space. Standard affinity selection methods, however, can be time-consuming, low-throughput, or provide hits that display low selectivity to the target. Here we report an automated bio-layer interferometry (BLI)-assisted affinity selection platform. When coupled with tandem mass spectrometry (MS), this method enables both rapid de novo discovery and affinity maturation of known peptide binders with high selectivity. The BLI-assisted AS-MS technology also features real-time monitoring of the peptide binding during the library selection process, a feature unattainable by current selection approaches. We show the utility of the BLI AS-MS platform toward rapid identification of novel nanomolar (dissociation constant, K_D < 50 nM) non-canonical binders to the leukemia-associated oncogenic protein menin. To our knowledge, this is the first application of BLI to the affinity selection of synthetic peptide libraries. We believe our approach can significantly accelerate the use of synthetic peptidomimetic libraries in drug discovery.

This work reports an automated affinity selection-mass spectrometry (AS-MS) approach amenable to both de novo peptide binder discovery and affinity maturation of known binders in a high-throughput and selective manner.

2D and 3D inkjet printing of biopharmaceuticals - A review of trends and future perspectives in research and manufacturing

There is an ongoing global shift in pharmaceutical business models from small molecule drugs to biologics. This increase in complexity is in response to advancements in our diagnoses and understanding of diseases. With the more targeted approach coupled with its inherently more costly development and manufacturing, 2D and 3D printing are being explored as suitable techniques to deliver more personalised and affordable routes to drug discovery and manufacturing. In this review, we explore first the business context underlying this shift to biopharmaceuticals and provide an update on the latest work exploring discovery and pharmaceutics. We then draw on multiple disciplines to help reveal the shared challenges facing researchers and firms aiming to develop biopharmaceuticals, specifically when using the most commonly explored manufacturing routes of drop-on-demand inkjet printing and pneumatic extrusion. This includes separating out how to consider mechanical and chemical influences during manufacturing, the role of the chosen hardware and the challenges of aqueous formulation based on similar challenges being faced by the printing industry. Together, this provides a review of existing work and guidance for researchers and industry to help with the de-risking and rapid development of future biopharmaceutical products.

Flavonoids: A complementary approach to conventional therapy of COVID-19?

COVID-19, the highly contagious novel disease caused by SARS-CoV-2, has become a major international concern as it has spread quickly all over the globe. However, scientific knowledge and therapeutic treatment options for this new coronavirus remain limited. Although previous outbreaks of human coronaviruses (CoVs) such as SARS and MERS stimulated research, there are, to date, no antiviral therapeutics available that specifically target these kinds of viruses. Natural compounds with a great diversity of chemical structures may provide an alternative approach for the discovery of new antivirals. In fact, numerous flavonoids were found to have antiviral effects against SARS-and MERS-CoV by mainly inhibiting the enzymes 3-chymotrypsin-like protease (3CLpro) and papain-like protease (PLpro). In this review, we specifically focused on the search for flavonoids, polyphenolic compounds, which are proven to be effective against human CoVs. We therefore summarized and analyzed the latest progress in research to identify flavonoids for antiviral therapy and proposed strategies for future work on medicinal plants against coronaviruses such as SARS-CoV-2. We discovered quercetin, herbacetin, and isobavachalcone as the most promising flavonoids with anti-CoV potential.

Microflow-based dynamic combinatorial chemistry: a microscale synthesis and screening platform for the rapid and accurate identification of bioactive molecules

The first flow-based synthesis and screening platform that integrates both microflow chemistry and protein-directed dynamic combinatorial chemistry into a single modular unit was disclosed and validated by a case study.

Identification of inhibitors for vascular endothelial growth factor receptor by using dynamic combinatorial chemistry

The novel analysis method consisting of size-exclusion chromatography (SEC) and HRMS analysis was firstly applied in the discovery of potential inhibitors towards cancer drug targets. With vascular endothelial growth factor receptor (VEGFR-2) as a target, dynamic combinatorial libraries (DCLs) were prepared by reacting aldehydes with amines. Four sensitive binders targeted VEGFR-2 were directly isolated from the library. Antitumor activity test in vitro and inhibition experiments toward angiogenesis were also carried out.

Inkjet printing for pharmaceutics - A review of research and manufacturing

Global regulatory, manufacturing and consumer trends are driving a need for change in current pharmaceutical sector business models, with a specific focus on the inherently expensive research costs, high-risk capital-intensive scale-up and the traditional centralised batch manufacturing paradigm. New technologies, such as inkjet printing, are being explored to radically transform pharmaceutical production processing and the end-to-end supply chain. This review provides a brief summary of inkjet printing technologies and their current applications in manufacturing before examining the business context driving the exploration of inkjet printing in the pharmaceutical sector. We then examine the trends reported in the literature for pharmaceutical printing, followed by the scientific considerations and challenges facing the adoption of this technology. We demonstrate that research activities are highly diverse, targeting a broad range of pharmaceutical types and printing systems. To mitigate this complexity we show that by categorising findings in terms of targeted business models and Active Pharmaceutical Ingredient (API) chemistry we have a more coherent approach to comparing research findings and can drive efficient translation of a chosen drug to inkjet manufacturing.

Prospects for multitarget lipid-raft-coated silica beads: a remarkable online biomaterial for discovering multitarget antitumor lead compounds

Application of lipid raft biomaterial with multiple cancer-related receptors for screening novel multitarget antitumour lead compounds.

Techniques used for the discovery of therapeutic compounds: The case of SARS

Severe acute respiratory syndrome coronavirus (SARS-CoV) is the etiological agent of SARS disease, which has ever severely menaced humans from the end of 2002 to June 2003. To date, great efforts have been made for the discovery of therapeutic compounds by using various technologies. In this report, we present a survey of these techniques and their applications in the development of promising anti-SARS agents.:

Discovering Echinococcus granulosus thioredoxin glutathione reductase inhibitors through site-specific dynamic combinatorial chemistry

In this study, we report a strategy using dynamic combinatorial chemistry for targeting the thioredoxin (Trx)-reductase catalytic site on Trx glutathione reductase (TGR), a pyridine nucleotide thiol-disulfide oxido-reductase. We chose Echinococcus granulosus TGR since it is a bottleneck enzyme of platyhelminth parasites and a validated pharmacological target. A dynamic combinatorial library (DCL) was constructed based on thiol-disulfide reversible exchange. We demonstrate the use of 5-thio-2-nitrobenzoic acid (TNB) as a non-covalent anchor fragment in a DCL templated by E. granulosus TGR. The heterodimer of TNB and bisthiazolidine (2af) was identified, upon library analysis by HPLC (IC50 = 24 μM). Furthermore, 14 analogs were synthetically prepared and evaluated against TGR. This allowed the study of a structure-activity relationship and the identification of a disulfide TNB-tricyclic bisthiazolidine (2aj) as the best enzyme inhibitor in these series, with an IC50 = 24 μM. Thus, our results validate the use of DCL for targeting thiol-disulfide oxido-reductases.

Analysis of High-Dimensional Structure-Activity Screening Datasets Using the Optimal Bit String Tree

A new classification method called the Optimal Bit String Tree is proposed to identify quantitative structure-activity relationships (QSARs). The method introduces the concept of a chromosome to describe the presence/absence context of a combination of descriptors. A descriptor set and its optimal chromosome form the splitting variable. A new stochastic searching scheme that contains a weighted sampling scheme, simulated annealing, and a trimming procedure optimizes the choice of splitting variable. Simulation studies and an application to screening monoamine oxidase (MAO) inhibitors show that OBSTree is advantageous in accurately and effectively identifying QSAR rules and finding different classes of active compounds. Details of the algorithm, SAS code, and simulated and real datasets are available online as supplementary materials.

Robotic implementation of assays: tissue-nonspecific alkaline phosphatase (TNAP) case study

Laboratory automation and robotics have "industrialized" the execution and completion of large-scale, enabling high-capacity and high-throughput (100 K-1 MM/day) screening (HTS) campaigns of large "libraries" of compounds (>200 K-2 MM) to complete in a few days or weeks. Critical to the success these HTS campaigns is the ability of a competent assay development team to convert a validated research-grade laboratory "benchtop" assay suitable for manual or semi-automated operations on a few hundreds of compounds into a robust miniaturized (384- or 1,536-well format), well-engineered, scalable, industrialized assay that can be seamlessly implemented on a fully automated, fully integrated robotic screening platform for cost-effective screening of hundreds of thousands of compounds. Here, we provide a review of the theoretical guiding principles and practical considerations necessary to reduce often complex research biology into a "lean manufacturing" engineering endeavor comprising adaption, automation, and implementation of HTS. Furthermore we provide a detailed example specifically for a cell-free in vitro biochemical, enzymatic phosphatase assay for tissue-nonspecific alkaline phosphatase that illustrates these principles and considerations.

Interaction between pheromone and its receptor of the fission yeast Schizosaccharomyces pombe examined by a force spectroscopy study

Interaction between P-factor, a peptide pheromone composed of 23 amino acid residues, and its pheromone receptor, Mam2, on the cell surface of the fission yeast Schizosaccharomyces pombe was examined by an atomic force microscope (AFM). An AFM tip was modified with P-factor derivatives to perform force curve measurements. The specific interaction force between P-factor and Mam2 was calculated to be around 120 pN at a probe speed of 1.74 μm/s. When the AFM tip was modified with truncated P-factor derivative lacking C-terminal Leu, the specific interaction between the tip and the cell surface was not observed. These results were also confirmed with an assay system using a green fluorescent protein (GFP) reporter gene to monitor the activation level of signal transduction following the interaction of Mam2 with P-factor.

Fully automated microinjection system for Xenopus laevis oocytes with integrated sorting and collection

Microinjection is the most flexible transfection method in terms of choice of reagents to inject into cells. But this method lacks the high throughput to compete with less flexible methods like chemical- or viral-based approaches. Various approaches have been pursued to increase the throughput by automating the microinjection process. However, these approaches focused solely on the microinjection itself and disregarded the tasks before and after the injection, which also belong to the critical time path of the whole process, that is, sorting out viable cells from a cell suspension, placing the cell for injection, and collecting the cell after the injection. In the approach with our XenoFactor, we demonstrate a system capable of running the whole process automatically. By optimizing the XenoFactor for Xenopus laevis oocytes, we could demonstrate the successful automated injection. Starting from a suspension with a mixture of defolliculated oocytes at different stages and quality levels, the manual approach requires 1 day in total for the preparation of 400 microinjected oocytes. The XenoFactor takes only 4h for the same amount and delivers injected oocytes of reproducible quality and without the fatigue symptoms experienced during the manual approach.

The STINT-NMR method for studying in-cell protein-protein interactions

This unit describes critical components and considerations required to study protein-protein structural interactions inside a living cell by using NMR spectroscopy (STINT-NMR). STINT-NMR entails sequentially expressing two (or more) proteins within a single bacterial cell in a time-controlled manner and monitoring their interactions using in-cell NMR spectroscopy. The resulting spectra provide a complete titration of the interaction and define structural details of the interacting surfaces at the level of single amino acid residues. The advantages and limitations of STINT-NMR are discussed, along with the differences between studying macromolecular interactions in vitro and in vivo (in-cell). Also described are considerations in the design of STINT-NMR experiments, focusing on selecting appropriate overexpression plasmid vectors, sample requirements and instrumentation, and the analysis of STINT-NMR data, with specific examples drawn from published works. Applications of STINT-NMR, including an in-cell methodology to post-translationally modify interactor proteins and an in-cell NMR assay for screening small molecule interactor libraries (SMILI-NMR) are presented.

Bioluminescence assays: multicolor luciferase assay, secreted luciferase assay and imaging luciferase assay

IMPORTANCE OF THE FIELD

By selecting the most appropriate bioluminescence assay, the researcher can study the underlying molecular mechanisms of a physiological system and the effects of a drug throughout the body.

AREAS COVERED IN THIS REVIEW

This review covers three luciferase assay systems: the multicolor luciferase assay, secreted luciferase assay and imaging luciferase assay. These assays are applied to drug screening in vitro, in cellulo and in vivo.

WHAT THE READER WILL GAIN

Different solutions for reporter assay in vitro, in cellulo and in vivo are presented. A suitable bioluminescence system depending on the assay purpose is also discussed.

TAKE HOME MESSAGE

Bioluminescence is a manifold system based on the different types of luciferin and its luciferase. Namely, luciferin catalyzed by corresponding luciferases resulted in the production of different color lights. We must understand the manifold mechanisms of bioluminescence reaction.

Screening the bioactive compounds in aqueous extract of Coptidis rhizoma which specifically bind to rabbit lung tissues beta2-adrenoceptor using an affinity chromatographic selection method

A receptor affinity chromatographic selection method was developed for screening the bioactive compounds binding to beta(2)-adrenoceptor (beta(2)-AR) in Coptidis rhizome. The bioactive compounds were analyzed by molecular recognition with a beta(2)-AR affinity column. The retention compounds eluted from the beta(2)-AR column were separated online with reverse-phase high-performance liquid chromatography by column switching technology, and identified by a coupled ion-trap mass spectrometer. Four compounds were screened as the bioactive compounds of Coptidis rhizome and identified as 2,9,10-trimethoxy-3-hydroxyl-protoberberine (jateorhizine), 2,3-methylenedioxy-9-methoxy-protoberberine, 2,3,9,10-tetramethoxy-protoberberine (palmatine) and 2,3-methylenedioxy-9,10-dimethoxy-protoberberine (berberine). The association constants of jatrorrhizine, palmatine and berberine to the beta(2)-AR were determined by the zonal elution method with standards. Berberine and palmatine had only one type of binding site on the immobilized beta(2)-AR. Their association constants were (2.28+/-0.11)x10(4)/M and (3.00+/-0.10)x10(4)/M, respectively. Jatrorrhizine had at least two type of binding sites on the immobilized beta(2)-AR, and the corresponding association constants were (2.20+/-0.09)x10(-4)/M and (6.78+/-0.001)x10(5)/M.

Nonpeptide ligands for peptidergic G protein-coupled receptors

Neuropeptides play essential roles in many physiological systems in vertebrates and invertebrates. Peptides per se are difficult to use as therapeutic agents, as they are generally very unstable in biological fluid environments and cross biological membranes poorly. Recognition that nonpeptide ligands for peptide receptors have clinical utility came from the discovery that opiates (such as morphine) act by binding to G protein-coupled receptors (GPCRs) for which the endogenous ligands are a family of neuropeptides (enkephalins and endorphins). Basic research has revealed a very large number of distinct neuropeptides that influence virtually every aspect of mammalian physiology and considerable effort has been expended in the pursuit of new drugs that act through peptidergic signaling systems. Although useful drugs have been found to affect various aspects ofneuropeptide biology, most work has been devoted to the discovery of nonpeptide ligands that act as agonists or antagonists at peptidergic GPCRs. Similar opportunities are apparent for the discovery of nonpeptide ligands that act on invertebrate GPCRs. A consideration of the knowledge gained from the process as conducted for mammalian peptidergic systems can inform and illuminate promising strategies for the discovery of new drugs for the treatment and control of pests and parasites.

Comparative virtual screening and novelty detection for NMDA-GlycineB antagonists

Identification of novel compound classes for a drug target is a challenging task for cheminformatics and drug design when considerable research has already been undertaken and many potent lead structures have been identified, which leaves limited unclaimed chemical space for innovation. We validated and successfully applied different state-of-the-art techniques for virtual screening (Bayesian machine learning, automated molecular docking, pharmacophore search, pharmacophore QSAR and shape analysis) of 4.6 million unique and readily available chemical structures to identify promising new and competitive antagonists of the strychnine-insensitive Glycine binding site (Glycine(B) site) of the NMDA receptor. The novelty of the identified virtual hits was assessed by scaffold analysis, putting a strong emphasis on novelty detection. The resulting hits were tested in vitro and several novel, active compounds were identified. While the majority of the computational methods tested were able to partially discriminate actives from structurally similar decoy molecules, the methods differed substantially in their prospective applicability in terms of novelty detection. The results demonstrate that although there is no single best computational method, it is most worthwhile to follow this concept of focused compound library design and screening, as there still can new bioactive compounds be found that possess hitherto unexplored scaffolds and interesting variations of known chemotypes.

A general electrochemical method for label-free screening of protein-small molecule interactions

Here we report a versatile method by which the interaction between a protein and a small molecule, and the disruption of that interaction by competition with other small molecules, can be monitored electrochemically directly in complex sample matrices.

Screening of small molecule interactor library by using in-cell NMR spectroscopy (SMILI-NMR)

We developed an in-cell NMR assay for screening small molecule interactor libraries (SMILI-NMR) for compounds capable of disrupting or enhancing specific interactions between two or more components of a biomolecular complex. The method relies on the formation of a well-defined biocomplex and utilizes in-cell NMR spectroscopy to identify the molecular surfaces involved in the interaction at atomic scale resolution. Changes in the interaction surface caused by a small molecule interfering with complex formation are used as a read-out of the assay. The in-cell nature of the experimental protocol insures that the small molecule is capable of penetrating the cell membrane and specifically engaging the target molecule(s). Utility of the method was demonstrated by screening a small dipeptide library against the FKBP-FRB protein complex involved in cell cycle arrest. The dipeptide identified by SMILI-NMR showed biological activity in a functional assay in yeast.

Managing evaporation for more robust microscale assays. Part 2. Characterization of convection and diffusion for cell biology

Cell based microassays allow the screening of a multitude of culture conditions in parallel, which can be used for various applications from drug screening to fundamental cell biology research. Tubeless microfluidic devices based on passive pumping are a step towards accessible high throughput microassays, however they are vulnerable to evaporation. In addition to volume loss, evaporation can lead to the generation of small flows. Here, we focus on issues of convection and diffusion for cell culture in microchannels and particularly the transport of soluble factors secreted by cells. We find that even for humidity levels as high as 95%, convection in a passive pumping channel can significantly alter distributions of these factors and that appropriate system design can prevent convection.

Peptide-based Biopolymers in Biomedicine and Biotechnology

Peptides are emerging as a new class of biomaterials due to their unique chemical, physical, and biological properties. The development of peptide-based biomaterials is driven by the convergence of protein engineering and macromolecular self-assembly. This review covers the basic principles, applications, and prospects of peptide-based biomaterials. We focus on both chemically synthesized and genetically encoded peptides, including poly-amino acids, elastin-like polypeptides, silk-like polymers and other biopolymers based on repetitive peptide motifs. Applications of these engineered biomolecules in protein purification, controlled drug delivery, tissue engineering, and biosurface engineering are discussed.

High impact technologies for natural products screening

Natural products have historically been a rich source of lead molecules in drug discovery. However, natural products have been de-emphasized as high throughput screening resources in the recent past, in part because of difficulties in obtaining high quality natural products screening libraries, or in applying modern screening assays to these libraries. In addition, natural products programs based on screening of extract libraries, bioassay-guided isolation, structure elucidation and subsequent production scale-up are challenged to meet the rapid cycle times that are characteristic of the modern HTS approach. Fortunately, new technologies in mass spectrometry, NMR and other spectroscopic techniques can greatly facilitate the first components of the process - namely the efficient creation of high-quality natural products libraries, bimolecular target or cell-based screening, and early hit characterization. The success of any high throughput screening campaign is dependent on the quality of the chemical library. The construction and maintenance of a high quality natural products library, whether based on microbial, plant, marine or other sources is a costly endeavor. The library itself may be composed of samples that are themselves mixtures - such as crude extracts, semi-pure mixtures or single purified natural products. Each of these library designs carries with it distinctive advantages and disadvantages. Crude extract libraries have lower resource requirements for sample preparation, but high requirements for identification of the bioactive constituents. Pre-fractionated libraries can be an effective strategy to alleviate interferences encountered with crude libraries, and may shorten the time needed to identify the active principle. Purified natural product libraries require substantial resources for preparation, but offer the advantage that the hit detection process is reduced to that of synthetic single component libraries. Whether the natural products library consists of crude or partially fractionated mixtures, the library contents should be profiled to identify the known components present - a process known as dereplication. The use of mass spectrometry and HPLC-mass spectrometry together with spectral databases is a powerful tool in the chemometric profiling of bio-sources for natural product production. High throughput, high sensitivity flow NMR is an emerging tool in this area as well. Whether by cell based or biomolecular target based assays, screening of natural product extract libraries continues to furnish novel lead molecules for further drug development, despite challenges in the analysis and prioritization of natural products hits. Spectroscopic techniques are now being used to directly screen natural product and synthetic libraries. Mass spectrometry in the form of methods such as ESI-ICRFTMS, and FACS-MS as well as NMR methods such as SAR by NMR and STD-NMR have been utilized to effectively screen molecular libraries. Overall, emerging advances in mass spectrometry, NMR and other technologies are making it possible to overcome the challenges encountered in screening natural products libraries in today's drug discovery environment. As we apply these technologies and develop them even further, we can look forward to increased impact of natural products in the HTS based drug discovery.

Identification of five human novel genes associated with cell proliferation by cell-based screening from an expressed cDNA ORF library

The development of functional profiling technologies provides opportunity for high-throughput functional genomics studies. We describe a cell-based screening system to identify novel human genes associated with cell proliferation. The method integrates luciferase reporter gene activity, fluorescence stain, automated microscopy and cellular phenotype assays. We successfully used the system to screen 409 novel human genes cloned by our lab and found that 27 genes significantly up-regulated promoter-Renilla luciferase reporter plasmid (pRL) activity. Among them, five genes, TRAF3IP3, ZNF306, ZNF250, SGOL1, and ZNF434, were determined through morphological observation, calcein AM fluorescence stain, MTT assay and cell cycle analysis to be associated with cell proliferation. Furthermore, we showed that the gene TRAF3IP3, which initially was identified to specifically interact with TRAF3, stimulated cell growth by modulating the c-Jun N-terminal kinase (JNK) pathway, and RNAi of TRAF3IP3 confirmed that the effect was physiological and necessary. In summary, we integrated a rapid and efficient system for screening novel growth regulatory genes. Using the new screening system we identified five genes associated with cell proliferation for the first time.

Neurochemical bases of visceral nociception: mathematical model

A mathematical model of visceral perception was constructed, comprising primary sensory, motor, intestinofugal and principal neurons, interstitial cells of Cajal and smooth muscle elements that are arranged in a functional circuit through chemical synapses. The mathematical description of constructive elements was based on detailed morphological, anatomical, electrophysiological and neuropharmacological characteristics of cells and chemical processes of electrochemical coupling. Emphasis was given to signal transduction mechanisms that involved multiple neurotransmitters and receptor polymodality. The role of co-transmission by acetylcholine (ACh), serotonin (5-HT), noradrenalin (NA), N-methyl-d-aspartate (NMDA) and alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) and their corresponding receptors-muscarinic and nicotinic type ACh receptors, beta-adrenoceptors, 5-HT(3/4) type serotonergic receptors, NMDA and AMPA receptors in pathogenesis of nociception was studied numerically. Results of computer simulations reproduced patterns of electrical activity of neurons and mechanical responses of the smooth muscle similar to those observed in in vivo and in vitro experiments when ACh, 5-HT, NA, NMDA and AMPA were acting either alone or co-jointly. The results provide neurochemical bases for explanation of pathophysiological mechanisms of visceral nociception, which cannot be elucidated by existing experimental methods. Care should be taken though when extrapolating the numerical results onto the actual system because of limiting assumptions of the model.

A decade of fragment-based drug design: strategic advances and lessons learned

Since the early 1990s, several technological and scientific advances - such as combinatorial chemistry, high-throughput screening and the sequencing of the human genome - have been heralded as remedies to the problems facing the pharmaceutical industry. The use of these technologies in some form is now well established at most pharmaceutical companies; however, the return on investment in terms of marketed products has not met expectations. Fragment-based drug design is another tool for drug discovery that has emerged in the past decade. Here, we describe the development and evolution of fragment-based drug design, analyse the role that this approach can have in combination with other discovery technologies and highlight the impact that fragment-based methods have made in progressing new medicines into the clinic.

An efficient approach for the rapid assessment of oral rat exposures for new chemical entities in drug discovery

Present study aims to improve efficiency and capacity of in vivo rat pharmacokinetic studies for rapid assessment of systemic exposure (AUC and C(max)) of new chemical entities. Plasma concentration-time profiles in rats from structurally diverse compounds were extracted from the Pfizer database. AUC(0-8) was calculated with 7 data points or a reduced subset of 3 data points. AUC values determined with 7 data points were compared to subset AUC values. A < or = 30% difference in values for 90% of cases was acceptance criteria. In parallel, samples were analyzed individually and pooled at each time point across compounds. For 96% of cases, AUC values estimated using 1, 4, and 8 h were comparable to AUC values obtained from 7 data points suggesting 1, 4, and 8 h sampling should be sufficient to estimate AUC. For C(max), the difference between 1, 4, and 8 h data-point analysis versus 7 data-point analysis is less than 30% for 72% of cases. Concentrations from individual versus pooled sample analysis were found to be equivalent. A rapid rat PK screening paradigm was created by the combination of 1, 4, and 8 h sampling and pooled sample analysis, which improves throughput and cycle time of in vivo PK studies.

JX401, A p38α Inhibitor Containing a 4-Benzylpiperidine Motif, Identified via a Novel Screening System in Yeast

In vivo screening of compounds for potential pharmacological activity is more advantageous than in vitro screening. In vivo screens eliminate the isolation of compounds that cannot cross biological membranes, are cytotoxic, or are not specific to the target. However, animal-based or even cell-based systems are usually expensive, time-consuming, and laborious. Here we describe the identification of inhibitors of the mitogen-activated protein kinase p38alpha via a high throughput screen using yeast cells. p38alpha is hyperactive in inflammatory diseases, and various indications suggest that its inhibition would reverse inflammation. However, there are currently no p38alpha inhibitors in clinical use. Because the human p38alpha imposes severe growth retardation when expressed in yeast, we screened a library of 40,000 randomly selected small molecules for compounds that would restore a normal growth rate. We identified two compounds; both share a structural motif of 4-benzylpiperidine, and both were shown to be efficient and selective p38alpha inhibitors in vitro. They were also active in mammalian cells, as manifested by their ability to reversibly inhibit myoblast differentiation. Thus, the yeast screen identified efficient and specific p38alpha inhibitors that are capable of crossing biological membranes, are not toxic, and function in mammalian cells. The rapid and cost-efficient high-throughput screening used here could be applied for isolation of inhibitors of various targets.

Cell-based screening and validation of human novel genes associated with cell viability

In the present study, a cell-based high-throughput assay is established to identify novel human genes associated with cell viability. The assay relies on the down-regulation of Renilla luciferase (pRL) activity in a 96-well format. In addition, 2-color fluorescence probes were used to distinguish living and dead cells. As the positive control, the authors used the expression vectors encoding Bax, TNFRSF1A, and TAJ, which were widely known to effectively induce programmed cell death. They screened 409 novel genes (including alternative mRNA splicing forms) cloned in their laboratory and found that 39 genes could significantly down-regulate pRL activity. A subsequent fluorescence-based assay revealed that 4 of the 39 genes (PIP5KL1, OLFM1, RNF122, FAM26B) were associated with cell viability. Further function assays validated that the 4 genes were able to induce both necrosis and apoptosis. These results therefore indicate that a rapid and effective screening system has been developed, which should shed light on some functions of novel genes.

In vivo functional assay of a recombinant aquaporin in Pichia pastoris

The water channel protein PvTIP3;1 (alpha-TIP) is a member of the major intrinsic protein (MIP) membrane channel family. We overexpressed this eukaryotic aquaporin in the methylotrophic yeast Pichia pastoris, and immunogold labeling of cellular cryosections showed that the protein accumulated in the plasma membrane, as well as vacuolar and other intracellular membranes. We then developed an in vivo functional assay for water channel activity that measures the change in optical absorbance of spheroplasts following an osmotic shock. Spheroplasts of wild-type P. pastoris displayed a linear relationship between absorbance and osmotic shock level. However, spheroplasts of P. pastoris expressing PvTIP3;1 showed a break in this linear relationship corresponding to hypo-osmotically induced lysis. It is the difference between control and transformed spheroplasts under conditions of hypo-osmotic shock that forms the basis of our aquaporin activity assay. The aquaporin inhibitor mercury chloride blocked water channel activity but had no effect on wild-type yeast. Osmotically shocked yeast cells were affected only slightly by expression of the Escherichia coli glycerol channel GlpF, which belongs to the MIP family but is a weak water channel. The important role that aquaporins play in human physiology has led to a growing interest in their potential as drug targets for treatment of hypertension and congestive heart failure, as well as other fluid overload states. The simplicity of this assay that is specific for water channel activity should enable rapid screening for compounds that modulate water channel activity.

Interference by naturally occurring fatty acids in a noncellular enzyme-based aromatase bioassay

Natural product drug discovery efforts frequently utilize noncellular screening assays. Fatty acids are commonly found in natural product extracts, and some have been shown to interfere with noncellular assays. Several pure fatty acids were tested using a noncellular aromatase assay, with the unsaturated analogues showing strong inhibitory activity, while the saturated analogues were inactive. Unsaturated fatty acids were further tested against SK-BR-3 hormone-independent human breast cancer cells that overexpress aromatase and were found to be inactive. In natural product screening efforts, especially using plant seeds, it is recommended that extracts active in noncellular bioassays should be dereplicated for the presence of fatty acids prior to bioassay-guided fractionation.

High-throughput fluorescence polarization method for identifying ligands of LOX-1

AIM

To develop and optimize a competitive fluorescence polarization (FP) method, and use it as a high-throughput screening (HTS) assay for drug discovery.

METHODS

Human lectin-like oxidized low-density lipoprotein receptor-1 (hLOX-1) and oxidized low-density lipoprotein (oxLDL) were used to establish a high-throughput fluorescence polarization assay to screen ligands of human LOX-1. A 96-well plate assay was performed with a fast plate reader. Three fluorescein isothiocyanate-labeled hLOX-1 concentrations (100, 200, and 400 nmol/L) were selected to be titrated by oxLDL (from 0.05 nmol/L to 100 micromol/L) in order to obtain optimal reactive concentrations. The concentration of Me2SO used (0%, 1%, 3%, 5%) and incubation time (15 min, 30 min, 1 h, 2 h) were optimized. The Z' factor was calculated to estimate the quality of FP-based HTS.

RESULTS

Concentrations of 200 nmol/L for human LOX-1 and 50 micromol/L for oxLDL were used in the actual assay. Concentrations of 0% to 5% Me2SO and different reaction times did not affect the FP-based HTS. The Z' value was 0.66. By using this detection and screening system, 12 700 compounds were screened and 3 ligands with an IC50 of less than 4.5 micromol/L were found.

CONCLUSION

The established competitive FP-based assay is sensitive, stable, highly reproducible and robust, and suitable for HTS for ligands of the hLOX-1 receptor.

Creation of GPCR-based chemical sensors by directed evolution in yeast

G protein-coupled receptors (GPCRs) form a class of biological chemical sensors with an enormous diversity in ligand binding and sensitivity. To explore structural aspects of ligand recognition, we subjected the human UDP-glucose receptor (P2Y14) functionally expressed in the yeast Saccharomyces to directed evolution. We sought to generate new receptor subtypes with ligand-binding properties that would be useful in the development of practical biosensors. Mutagenesis of the entire UDP-glucose receptor gene yielded receptors with increased activity but similar ligand specificities, while random mutagenesis of residues in the immediate vicinity of the ligand-binding pocket yielded mutants with altered ligand specificity. By first sensitizing the P2Y14 receptor and then redirecting ligand specificity, we were able to create mutant receptors suitable for a simple biosensor. Our results demonstrate the feasibility of altering receptor ligand-binding properties via a directed evolution strategy, using standard yeast genetic techniques. The novel receptor mutants can be used to detect chemical ligands in complex mixtures and to discriminate among chemically or stereochemically related compounds. Specifically, we demonstrate how engineered receptors can be applied in a pairwise manner to differentiate among several chemical analytes that would be indistinguishable with a single receptor. These experiments demonstrate the feasibility of a combinatorial approach to detector design based on the principles of olfaction.