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β-Alanine (3-aminopropionic acid) holds great potential in industrial application. It can be obtained through a chemical synthesis route, which is hazardous to the environment. It is well known that l-aspartate-α-decarboxylase (ADC) can convert l-aspartate to β-alanine in bacteria. However, due to the low activity of ADC, industrial production of β-alanine through the green biological route remains unclear. Thus, improving the activity of ADC is critical to reduce the cost of β-alanine production. In this study, we established a dual-fluorescence high-throughput system for efficient ADC screening. By measuring the amount of β-alanine and the expression level of ADC using two different fluorescence markers, we can rapidly quantify the relative activity of ADC variants. From a mutagenesis library containing 2000 ADC variants, we obtained a mutant with 33% increased activity. Further analysis revealed that mutations of K43R and P103Q in ADC significantly improved the yield of β-alanine produced by the whole-cell biocatalysis. Compared with the previous single-fluorescence method, our system can not only quantify the amount of β-alanine but also measure the expression level of ADC with different fluorescence, making it able to effectively screen out ADC variants with improved relative activity. The dual-fluorescence high-throughput system for rapid screening of ADC provides a good strategy for industrial production of β-alanine via the biological conversion route in the future.

High-throughput screening based on CRISPR-Cas9 libraries has become an attractive and powerful technique to identify target genes for functional studies. However, accessibility of public data is limited due to the lack of user-friendly utilities and up-to-date resources covering experiments from third parties. Here, we describe iCSDB, an integrated database of CRISPR screening experiments using human cell lines. We compiled two major sources of CRISPR-Cas9 screening: the DepMap portal and BioGRID ORCS. DepMap portal itself is an integrated database that includes three large-scale projects of CRISPR screening. We additionally aggregated CRISPR screens from BioGRID ORCS that is a collection of screening results from PubMed articles. Currently, iCSDB contains 1375 genome-wide screens across 976 human cell lines, covering 28 tissues and 70 cancer types. Importantly, the batch effects from different CRISPR libraries were removed and the screening scores were converted into a single metric to estimate the knockout efficiency. Clinical and molecular information were also integrated to help users to select cell lines of interest readily. Furthermore, we have implemented various interactive tools and viewers to facilitate users to choose, examine and compare the screen results both at the gene and guide RNA levels. iCSDB is available at https://www.kobic.re.kr/icsdb/.

The high incidence of diabetes mellitus has caused widespread concern around the world, and has quickly become one of the most prevalent and costly chronic diseases. Alpha-glucosidase has been considered as the main target enzyme in the prevention and treatment of type 2 diabetes, and the inhibition of alpha-glucosidase activity can control postprandial blood glucose levels of diabetics and keep blood glucose levels normal. However, most of the current antidiabetic drugs in the clinic have many side effects. Recently, the screening of alpha-glucosidase inhibitors, from natural products, with excellent activity and less side effects has been successfully achieved, which also proposes more requirements and challenges for the approaches of alpha-glucosidase inhibitor (AGI) screening because of the trace level of active compounds in natural products, large-scale sample screening, and complex matrix of natural products. In this review, we comprehensively summarized the available strategies for the assay of alpha-glucosidase activity and AGI screening for the first time, including classic strategies such as high throughput screening methods (e.g. capillary electrophoresis strategies, HPLC/LC-MS strategies), emerging sensing strategies (e.g. colorimetric sensing, fluorescence sensing, electrochemical sensing, and surface plasmon resonance sensing) and other strategies. Finally, future opportunities and challenges in future research are tentatively proposed.

OBJECTIVES Serum repositories are foundations for seroepidemiological data, revealing targeted information about morbidities and existing heterogeneity in human populations. With the recent technological advances, we can perform high-throughput screening at an affordable cost using minimal plasma. Monitoring brain health after an injury is critical since mild Traumatic Brain Injury (mTBI) and other neurological symptoms are under-diagnosed. Our objective in this study is to present our preliminary serological data from one of our ongoing studies on mTBI. METHODS In this retrospective study, we used stored plasma samples to understand biomarkers of mTBI. We compared plasma samples from five patients with mTBI following their first concussive episode to five gender and age-matched healthy controls. We assessed multiple biomarkers to show the importance of biorepositories. RESULTS Most of the estimated plasma factors in mTBI subjects at baseline were comparable to normal healthy individuals except for the astroglial markers S100B and glial fibrillary acidic protein. Fluctuations of these biomarkers can affect the homeostasis of brain parenchyma by altering the neural network signaling, which in turn may result in intermittent behavioral symptoms. CONCLUSION Biorepositories are powerful resources for understanding the spectrum of morbidity. Biomarkers serve as a valuable diagnostic and therapeutic tool.

High throughput screening methods, measuring the sensitivity and resistance of tumor cells to drug treatments have been rapidly evolving. Not only do these screens allow correlating response profiles to tumor genomic features for developing novel predictors of treatment response, but they can also add evidence for therapy decision making in precision oncology. Recent analysis methods developed for either assessing single agents or combination drug efficacies enable quantification of dose-response curves with restricted symmetric fit settings. Here, we introduce iTReX, a user-friendly and interactive Shiny/R application, for both the analysis of mono- and combination therapy responses. The application features an extended version of the drug sensitivity score (DSS) based on the integral of an advanced five-parameter dose-response curve model and a differential DSS for combination therapy profiling. Additionally, iTReX includes modules that visualize drug target interaction networks and support the detection of matches between top therapy hits and the sample omics features to enable the identification of druggable targets and biomarkers. iTReX enables the analysis of various quantitative drug or therapy response readouts (e.g. luminescence, fluorescence microscopy) and multiple treatment strategies (drug treatments, radiation). Using iTReX we validate a cost-effective drug combination screening approach and reveal the application’s ability to identify potential sample-specific biomarkers based on drug target interaction networks. The iTReX web application is accessible at ( https://itrex.kitz-heidelberg.de ).

As the importance of protein–protein interactions (PPIs) in human health and disease has become broadly recognized, interest in identifying inhibitors of PPIs has increased substantially. High throughput screening (HTS) is one of several strategies that have been implemented to identify PPI inhibitors. In this chapter, HTS methods are surveyed and situated within the broader context of PPI inhibitor discovery.

RNA-binding proteins (RBPs) are involved in regulating all aspects of RNA metabolism, including processing, transport, translation, and degradation. Dysregulation of RNA metabolism is linked to a plethora of diseases, such as cancer, neurodegenerative diseases, and neuromuscular disorders. Recent years have seen a dramatic shift in the knowledge base, with RNA increasingly being recognised as an attractive target for precision medicine therapies. In this article, we are going to review current RNA-targeted therapies. Furthermore, we will scrutinise a range of drug discoveries targeting protein-RNA interactions. In particular, we will focus on the interplay between Lin28 and let-7, splicing regulatory proteins and survival motor neuron (SMN) pre-mRNA, as well as HuR, Musashi, proteins and their RNA targets. We will highlight the mechanisms RBPs utilise to modulate RNA metabolism and discuss current high-throughput screening strategies. This review provides evidence that we are entering a new era of RNA-targeted medicine.

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Bull fertility is crucial for efficient, profitable, and sustainable agriculture of cattle. Despite the fact that the uses of sperm from low fertility bulls cause millions of dollars economic losses, conventional methods available to accurately predict bull fertility are still of limited use. Although breeding bulls produce billions of sperm mostly with normal motility and morphology, some bulls are afflicted with poor fertility due to molecular or cellular defects in the sperm. Sperm functional genome including transcriptome, proteome, and metabolome influence bull fertility. Through high throughput screening methods of metabolomics, specific small molecules have been described both for seminal plasma and sperm. Compared to sperm, seminal plasma contains much higher numbers and levels of metabolites. Although the identities and functions of many of these metabolites are known, such knowledge is still yet to be generated for a greater number of metabolites of sperm and seminal plasma. Once validated as fertility markers, sperm, and seminal plasma metabolites can be used to evaluate semen quality and predict bull fertility, and/or used in assisted reproductive technologies. This review describes the possibility to use small molecules (in the review called metabolites) as fertility predictors.

Directed evolution and rational design are powerful strategies in protein engineering to tailor enzyme properties to meet the demands in academia and industry. Traditional approaches for enzyme engineering and directed evolution are often experimentally driven, in particular when the protein structure-function relationship is not available. Though they have been successfully applied to engineer many enzymes, these methods are still facing significant challenges due to the tremendous size of the protein sequence space and the combinatorial problem. It can be ascertained that current experimental techniques and computational techniques might never be able to sample through the entire protein sequence space and benefit from nature's full potential for the generation of better enzymes. With advancements in next generation sequencing, high throughput screening methods, the growth of protein databases and artificial intelligence, especially machine learning (ML), data-driven enzyme engineering is emerging as a promising solution to these challenges. To date, ML-assisted approaches have efficiently and accurately determined the quantitative structure-property/activity relationship for the prediction of diverse enzyme properties. In addition, enzyme engineering can be accelerated much faster than ever through the combination of experimental library generation and ML-based prediction. In this chapter, we review the recent progresses in ML-assisted enzyme engineering and highlight several successful examples (e.g., to enhance activity, enantioselectivity, or thermostability). Herein we explain enzyme engineering strategies that combine random or (semi-)rational approaches with ML methods and allow an effective reengineering of enzymes to improve targeted properties. We further discuss the main challenges to solve in order to realize the full potential of ML methods in enzyme engineering. Finally, we describe the current limitations of ML-assisted enzyme engineering, and our perspective on future opportunities in this growing field.

Background Pulmonary arterial hypertension (PAH) is characterized by enhanced proliferation of pulmonary artery smooth muscle cells (PASMCs) accompanying increased production of inflammatory factors and adaptation of mitochondrial metabolism to a hyperproliferative state. However, at present, since all the drugs in clinical use target pulmonary vascular dilatation, they may not be so effective for patients with advanced PAH. Purposes We aimed to discover a novel drug for PAH that inhibits PASMC proliferation. Methods In the first screening, we examined 5,562 compounds from our original library using high-throughput screening system to discover a compound that inhibits proliferation of PASMCs from PAH patients (PAH-PASMCs). In the second screening, we performed concentration-dependent assays and counter assays with PAH-PASMCs and PASMCs from healthy donors. We also performed apoptosis assays and mechanistic analysis for inflammation, reactive oxygen species (ROS), and mitochondrial function. Results We found that celastramycin, a benzoyl pyrrole-type compound originally found in a bacteria extract, inhibited the proliferation of PAH-PASMCs in a dose-dependent manner with minimal effects on PASMCs from healthy donors. Moreover, celastramycin inhibited proliferation with minimal increase in apoptosis and low rate of cell death. Then, we synthesized 25 analogues of celastramycin, and finally selected the lead compound that significantly inhibited proliferation of PAH-PASMCs and reduced cytosolic ROS levels. Mechanistic analysis demonstrated that celastramycin reduced the protein levels of hypoxia-inducible factor-1α, which was abnormally activated in PAH-PASMCs and impaired aerobic metabolism, and nuclear factor-κB, which induces pro-inflammatory signals, in PAH-PASMCs compared with vehicle controls, leading to reduced secretion of inflammatory cytokines. Importantly, celastramycin treatment reduced the ROS levels in PAH-PASMCs with increased protein levels of NF-E2-related factor 2 (Nrf2), a master regulator of cellular response against oxidative stress. Furthermore, celastramycin treatment improved mitochondrial energy metabolism with recovered mitochondrial network formation in PAH-PASMCs. We also discovered that celastramycin-mediated effects on these transcriptional modulators could be regulated by zinc finger C3H1 domain-containing protein, which is a binding partner of celastramycin. Finally, celastramycin treatment ameliorated pulmonary hypertension in three experimental animal models of PH in mice and rats, accompanied by reduced inflammatory changes in the lungs. Conclusions These results indicate that celastramycin ameliorates pulmonary hypertension through inhibition of excessive proliferation of PAH-PASMCs, for which its anti-inflammatory and beneficial effects on mitochondrial energy metabolism may be involved. Thus, celastramycin could be a novel drug for PAH as it exerts anti-proliferative effects on PAH-PASMCs.

BACKGROUND Glioma and glioblastoma comprise 28% of all primary central nervous system tumors and cause the majority of primary brain tumor deaths. Despite substantial research into the molecular pathogenesis and genetic landscape of glioma, no currently approved therapies are curative for any glioma or glioblastoma. Patients with glioblastoma have an average survival time of 12-15 months, while patients with grade III gliomas have an average survival time of 3-5 years, and patients with grade II gliomas have an average survival time of 8-15 years. The lack of a curative treatment for these tumors necessitates additional research into novel therapies. METHODS In this study, we developed a high-throughput drug screen and culture system to identify existing FDA-approved therapies with the potential to inhibit glioma viability. RESULTS In total, we screened 39 tumors: 21 glioblastoma, 10 oligodendroglioma, and 8 astrocytoma. Carfilzomib was the most effective compound across the cohort, decreasing the average tumor viability to 39.0% +/- 16.5%SD. Regardless of tumor grade, MGMT methylation, EGFR amplification, tumor recurrence and etiology, tumor histology, prior treatment, and patient gender, carfilzomib significantly reduced cell viability in every tumor; though was not necessarily the most effective compound in each of these groups. We found HDAC inhibition to be the most effective treatment in grade 1 astrocytomas. However, HDAC inhibition was surpassed by carfilzomib and RNA transcription inhibitors in all higher grades. Interestingly, EGFR inhibition, while significantly effective in 36 tumors, was consistently less effective than carfilzomib across the cohort, though did surpass the effectiveness of HDAC inhibition in grade III gliomas. CONCLUSIONS FDA approved compounds can effectively inhibit glioma tumor viability. Specifically, carfilizomib holds great promise. Further in vivo studies are needed to confirm these findings.

Enzymes have been used for millennia in food applications, well before the nature of these catalysts was even hinted. The increasing knowledge on structure and function of enzymes, together with high throughput screening methods and genetic engineering coupled to an increasing demand for greener production methods and healthy food, has significantly propelled the use of enzymes in food and also in feed. Developments have focused on increasing the efficiency in the production/processing of well-established goods but also in the development of processes for manufacturing new goods. The present work aims to give a brief overview of the historic background, provide insight on the current applications and recent developments of enzymes in food and feed, the rationale underlying such use, and the prospective advances in this area. This encompasses: a comprehensive description of the role played by enzymes in key processes and goods production in food and feed; the requirements on the enzyme properties and formulations assigned for such role; insight on the strategies undertaken towards the design and inception of improved or novel enzymes leading to more effective processes and/or new goods. The multidisciplinary nature of these strategies currently used will be highlighted.

Tuberculosis affects about 100 million people worldwide and causes nearly 2 million deaths annually. It has been estimated that one third of all humans is infected with latent Mycobacterium tuberculosis (Mtb). Moreover, Mtb has become increasingly resistant to available antibiotics. Consequently, it is important to identify and characterize new therapeutic targets in Mtb and to synthesize selective inhibitors. ClpP1, ClpP2 and their associated regulatory ATPases, ClpX and ClpC1 are required for the growth of Mtb and for its virulence during murine infection and are highly attractive drug targets, especially since they are not present in the cytosol of mammalian cells, and they differ markedly from the mitochondrial ClpP complex. The importance of these proteins in Mtb is emphasized by the existence of several natural antibiotics targeting this system. In order to find new inhibitors of ClpC1P1P2 system, we developed an assay based on the ATP-dependent degradation of a fluorescent protein substrate. The hits obtained were further characterized with a set of secondary assays to identify precise targets within a complex. A large library of compounds was screened and led to the identification of a ClpC1 ATPase inhibitor demonstrating that this approach can be used in future searches for anti-TB agents.

Objectives To develop a method to enable the large-scale antimicrobial susceptibility screening of Orientia tsutsugamushi clinical isolates, using one timepoint and one concentration of antibiotics to considerably speed up the time to result. Methods Growth, harvesting, multiplicity of infection (moi) and the day to determine the MICs were optimized using five O. tsutsugamushi reference strains [susceptible (Karp, Kato and Gilliam) and putatively resistant (AFC-3 and AFSC-4)], one clinical isolate (UT76) and one rodent isolate (TA763). Subsequently, the MICs of azithromycin, chloramphenicol and doxycycline for these strains and 51 clinical isolates including AFSC-7 were determined. An optimal concentration was calculated using the epidemiological cut-off value. Results The conditions for O. tsutsugamushi infection, growth and harvesting were determined to be an moi of 100:1 and trypsinization with the peak growth on day 10. The resulting MICs were in line with previously published susceptibility data for all reference strains, except for Karp and AFSC-4, which showed azithromycin MICs of 0.0156 and 0.0313 mg/L, compared with 0.0078 and 0.0156 mg/L, respectively, in previous reports. The MIC of doxycycline for AFC-3 was 0.125 mg/L compared with >4 mg/L in earlier reports. The final single screening concentrations were identified as: azithromycin, 0.125 mg/L; chloramphenicol, 8 mg/L; and doxycycline, 1 mg/L. Conclusions This simplified procedure facilitates the simultaneous screening of 48 isolates for actively monitoring potential resistance of this important fever pathogen, with an 8-fold throughput improvement over early methods. The data do not support the existence of doxycycline- and chloramphenicol-resistant scrub typhus.

Structure-formulation-property relationships for crosslinkable core-shell latexes were studied initially using high throughput screening methods and then using conventional experimental methods to determine optimum coating formulations. Two approaches that are used within coatings technology to improve sustainability are reduction in volatile organic compounds (VOC) and reduction in energy needed to cure coatings. Hybrid crosslinkable core-shell latexes have shown potential in meeting these challenges where film properties provided by particle coalescence are not sufficient and chemical crosslinking is needed. However, with numerous parameters involved such as latex particle architecture, nature and amount of crosslinker, and curing conditions, the screening of formulations via conventional coating testing methods becomes laborious and time-consuming. The results from high-throughput dye extraction and puncture testing were compared to data from conventional testing methods such as chemical resistance (MEK double rubs), pendulum hardness, and tensile testing to identify correlations. The dye extraction results have shown a strong correlation to solvent resistance and pendulum hardness data whereas toughness from puncture testing data correlated to tensile testing. Both high throughput dye extraction and puncture testing methods can be used for the accelerated screening of crosslinkable coating formulations to optimize curing parameters to achieve the best coating performance.

Feruloyl esterases (FAEs) are a diverse group of hydrolases widely distributed in plants and microorganisms which catalyzes the cleavage and formation of ester bonds between plant cell wall polysaccharides and phenolic acids. FAEs have gained importance in biofuel, medicine and food industries due to their capability of acting on a large range of substrates for cleaving ester bonds and synthesizing highadded value molecules through esterification and transesterification reactions. During the past two decades extensive studies have been carried out on the production, characterization and classification of FAEs, however only a few reports of suitable High Throughput Screening assays for this kind of enzymes have been reported. This review is focused on a concise but complete revision of classical to High Throughput Screening methods for FAEs, highlighting its advantages and disadvantages, and finally suggesting future perspectives for this important research field.

Actinomycetes have provided many industrially important bioactive compounds having great economic importance and always being a curious organism for secondary metabolite production. Actinomycetes have long been recognized as prolific producers of enzymes, antibiotics, anti cancerous agents and play important role in recycling of organic matter. Numerous methods have been advocated for isolation of actinomycetes to facilitate the discovery of natural compounds specially antibiotics. Isolation of actinomycetes can fulfill all the novel essentialities associated with actinomycetes. Actinomycetes are widely distributed in the natural habitats, hence various methods like pretreatments, enrichment, combinations of antibiotics, specific isolation media and some novel methods has been adapted for isolation. Marine actinomycetes were also isolated by various methods and found to be important source for novel secondary metabolites. Rare actinomycetes isolated by providing combinations of methods or high throughput screening methods. Endophytic actinomycetes can be isolated by mostly chemical treatment for surface sterilization followed by serial dilution. Strategy for a range of isolation methods have been mentioned in this review for discovery of various genera of actinomycetes. K e y w o r d s Actinomycetes, antibiotics, isolation methods, Enrichment

Nitrilases have been widely acknowledged as important alternatives to chemical catalysts, as they have been proved to transform an immense variety of nitriles under mild conditions and often in a stereoselective or regioselective manner. In the discovery of new nitrilases to establish viable industrial processes, screening plays an important role in identifying which subset of candidates contains a nitrilase of interest from a collection of organisms, clone banks, or enzyme libraries. However, the traditional methods for evaluating the nitrilases are a time-consuming, laborious, and costly process and have been regarded as a bottleneck in developing these nitrilases as industrial biocatalysts. In the past few years, a number of high-throughput screening methods have been developed for rapid evaluation and identification of nitrilases. Here, we review the various methodologies developed for high-throughput screening of nitrilases and focus on their advantages and limitations.

Drug discovery programs that generate hundreds of new molecular entities need efficient methodologies for physicochemical profiling. Several high-throughput methods for pK screening have been developed in the last 15 years to determine this key physicochemical parameter. Separation techniques such as HPLC–MS or capillary electrophoresis are particularly well-suited due to their high throughput and capacity to deal with impure or complex samples. In addition, potentiometric and (mostly) UV-metric-based methods (plate-based and automated systems), find their place as very precise methodologies for pK determination despite of somewhat lower throughput. Finally, pK prediction software packages are useful estimator tools but, to date, they cannot replace experimental measurements when accurate pK values are required., This work was funded by the Spanish Ministerio de Economia y Competitividad (SAF2015-66690-R). P.L.A. Popelier is acknowledged for his comments of the manuscript

Low aqueous solubility of active pharmaceutical ingredients (APIs) is one of the most important challenges facing drug development researchers today [1, 2]. With the development of computational chemistry and high throughput screening methods it is possible to obtain a large number of compounds with attractive therapeutic activity. However, at the same time the selection of novel active molecules with suitable biopharmaceutical properties (like solubility, intestinal permeability) becomes a great challenge and a bottleneck in drug development. Statistically, more than 40% of approved drugs and even 70–90% of those under investigations are poorly water-soluble and additional efforts are required to improve their water solubility [3–5].

High-throughput screening (HTS) has been integrated into the drug discovery process, and multiple assay formats have been widely used in many different disease areas but with limited focus on infectious agents. In recent years, there has been an increase in the number of HTS campaigns using infectious wild-type pathogens rather than surrogates or biochemical pathogen-derived targets. Concurrently, enhanced emerging pathogen surveillance and increased human mobility have resulted in an increase in the emergence and dissemination of infectious human pathogens with serious public health, economic, and social implications at global levels. Adapting the HTS drug discovery process to biocontainment laboratories to develop new drugs for these previously uncharacterized and highly pathogenic agents is now feasible, but HTS at higher biosafety levels (BSL) presents a number of unique challenges. HTS has been conducted with multiple bacterial and viral pathogens at both BSL-2 and BSL-3, and pilot screens have recently been extended to BSL-4 environments for both Nipah and Ebola viruses. These recent successful efforts demonstrate that HTS can be safely conducted at the highest levels of biological containment. This review outlines the specific issues that must be considered in the execution of an HTS drug discovery program for high-containment pathogens. We present an overview of the requirements for HTS in high-level biocontainment laboratories.

Background: The development of novel anesthetics has historically been a process of combined serendipity and empiricism, with most recent new anesthetics developed via modification of existing anesthetic structures. Methods: Using a novel high-throughput screen employing the fluorescent anesthetic 1-aminoanthracene and apoferritin as a surrogate for on-pathway anesthetic protein target(s), we screened a 350,000 compound library for competition with 1-aminoanthracene–apoferritin binding. Hit compounds meeting structural criteria had their binding affinities for apoferritin quantified with isothermal titration calorimetry and were tested for γ-aminobutyric acid type A receptor binding using a flunitrazepam binding assay. Chemotypes with a strong presence in the top 700 and exhibiting activity via isothermal titration calorimetry were selected for medicinal chemistry optimization including testing for anesthetic potency and toxicity in an in vivo Xenopus laevis tadpole assay. Compounds with low toxicity and high potency were tested for anesthetic potency in mice. Results: From an initial chemical library of more than 350,000 compounds, we identified 2,600 compounds that potently inhibited 1-aminoanthracene binding to apoferritin. A subset of compounds chosen by structural criteria (700) was successfully reconfirmed using the initial assay. Based on a strong presence in both the initial and secondary screens the 6-phenylpyridazin-3(2H)-one chemotype was assessed for anesthetic activity in tadpoles. Medicinal chemistry efforts identified four compounds with high potency and low toxicity in tadpoles, two were found to be effective novel anesthetics in mice. Conclusion: The authors demonstrate the first use of a high-throughput screen to successfully identify a novel anesthetic chemotype and show mammalian anesthetic activity for members of that chemotype.

In addition to antibodies with the classical composition of heavy and light chains, the adaptive immune repertoire of sharks also includes a heavy-chain only isotype, where antigen binding is mediated exclusively by a small and highly stable domain, referred to as vNAR. In recent years, due to their high affinity and specificity combined with their small size, high physicochemical stability and low-cost of production, vNAR fragments have evolved as promising target-binding scaffolds that can be tailor-made for applications in medicine and biotechnology. This review highlights the structural features of vNAR molecules, addresses aspects of their generation using immunization or in vitro high throughput screening methods and provides examples of therapeutic, diagnostic and other biotechnological applications.

Approaches to drug development have changed significantly over the last decade in response to the continued decline in productivity of the current discovery model. Here, we highlight exciting findings and promising approaches in the recent literature in which researchers integrate advanced micro-engineering, design, and analytical strategies to improve the relevance and utility of high-throughput screening in the drug discovery pipeline.

Natural products or their related derivatives were the most important source of officially approved drugs owning to the huge chemical structure diversities and their biodiversities Compared with traditional combinatorial chemistries and high throughput screening methods genomics driven natural product discovery is a rational and an efficient alternative for the discovery of novel structures In this mini review process of genomics driven natural product discovery is highlighted including the main steps the relevant technologies and bioinformatics tools

Background: The search for new natural or synthetic products with antioxidant activity is commonly based on methods that involve reduction of either 2,2-diphenyl-1-picrylhydrazyl (DPPH) or 2-2-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS). However, the reported values of the effective concentrations are highly variable, even in controls. Herein, we optimize and validate both meth-ods of determining antiradical activity. Methods: Optimization was carried out using both a fractionated factorial design and a basic sequential simplex method, by monitoring the reduction percentage. Quercetin or Trolox were used as positive con-trol. Furthermore, for each method, linearity, precision, accuracy, robustness, plate uniformity, signal variability, and Z factor, were established. Results: The optimized conditions for the DPPH method were: DPPH 280 μM in ethanol and 15 min of reaction time in the dark. The linear range was between 7 and 140 μM with an R2 value of 0.9987. The optimized conditions for the ABTS method were: ABTS adjusted to 0.7 absorbance units, 70% concen-tration in ethanol, and a reaction time of 6 min in the dark. The linear range was found to be between 1 and 70% with an R2 = 0.9991. For both methods, the accuracy and precision were within limits and the Z factor value was higher than 0.89. The applicability of each method was assessed by analyzing eight plant extracts. Conclusion: The DPPH and ABTS reduction methods were optimized and validated on a microscale and could be expected to be implemented in any laboratory.

Malignant glioma is the most common primary brain tumor in adults, where ~70% of newly diagnosed cases represent glioblastoma. As a result, development of novel therapies has focused on this tumor rather than lower-grade gliomas. Mutations of isocitrate dehydrogenase (IDH) genes have been found in ~10% of glioblastomas and ~80% of grade II-III gliomas. Lack of pre-clinical animal models and patient-derived glioma cultures has prevented development of therapies targeting IDH mutant gliomas. Furthermore, IDH1 mutation is emerging as a poor therapeutic target. Instead of targeting highly expressed/amplified targets in glioma, hypermethylation resulting in down-regulation of proteins in IDH1 mutant glioma cells provides a unique opportunity to identify targets that are suppressed, and when inhibited, will sensitize tumors to therapies. To identify novel therapeutics targeting IDH1 mutant glioma cells, we have used the RCAS-Tva system to generate a pre-clinical glioma mouse model and patient-derived cultures displaying IDH1 mutation. We confirmed previous reports demonstrating that IDH1 mutant cells were sensitized to ionizing radiation and showed reduced DNA repair response compared to IDH1 wild-type cells. To repurpose existing therapeutics, we performed high-throughput screening of 2,177 approved compounds in IDH1 wild-type and mutant glioma cultures. We identified families of compounds that showed specificity in reducing cell viability of IDH1 mutant glioma cells, including topoisomerase, HDAC, ATM, BCL2, HSP90, and PI3K/mTOR inhibitors. In contrast, IDH1 wild-type glioma cells showed sensitivity to diverse families of compounds, including those targeting growth factor signaling pathways, PLK1, and HMG-CoA reductase. Identified candidate compounds are currently being validated in vitro and in pre-clinical glioma models. In conclusion, we have identified a number of approved compounds that can quickly be translated from bench to bedside to improve outcome for patients diagnosed with IDH mutant gliomas.

Diamond-Blackfan Anaemia (DBA) is a rare blood cell aplasia that presents clinically at approximately 2-3 months of age and its main characteristic is reduced erythroid precursors in the bone marrow, i.e. anemia. Mutations in different ribosomal protein (RP) genes have been associated with DBA, with mutations in RPS19 accounting for 20-25% of all cases. It has been proposed that RPS19 deficiency causes perturbations in ribosome biogenesis, thus activation of the p53-dependent Nucleolar Surveillance Pathway (NSP). In this context free RPs (predominantly L5 and L11) in a complex with 5S rRNA sequester the E3 ubiquitin ligase murine double minute 2 (MDM2), leading to the accumulation of p53 and subsequent activation of its transcriptional targets mediating cell cycle arrest or apoptosis. In DBA, one of the molecular mechanisms impairing the proliferation and thus reducing the number of erythroid progenitors that can progress to mature red blood cells is an elevation of p53 protein mediating activation of the NSP. In order to identify potential therapeutics that could be repurposed to prevent the activation of NSP in DBA patients, we have screened compound libraries of clinically approved therapeutics to identify pathways implicated in the p53-dependent NSP due to RPS19 deficiency. We quantitated both cell number and the level of p53 expression, identifying compounds that can result in low and high expression of p53, the latter for potential use in cancer therapy. Using an RPS19 depleted A549 cell line as a model system, the screen successfully identified different therapeutic groups. In the DBA context, we were most interested in the compounds that reduced p53 and had no negative effect on cell number. A selection of 22 molecules were re-evaluated in vitro, again using RPS19 depleted A549 cells, through the quantification of p53 protein expression and densitometry analysis. From this, 10candidates were evaluated ex vivofor their effects on proliferation using bone marrow obtained from an inducible Rps19 knockdown (DBA) mouse model. While we are currently testing a number of compounds in vivo using the Rps19 DBA mouse model (as described), one of the compounds tested thus far has demonstrated a partial rescue of the cKit+ population, no changes in erythroid precursors but interestingly a reversal of the defect in the Granulocyte-Monocyte Progenitor (GMP) population. Impairment in lineage progression in the GMP compartment has also been reported to present in bone marrow failure Shwachman-Diamond Syndrome. We are currently evaluating the mechanism by which this drug is rescuing the c-Kit+ and GMP populations in these mice. In summary, our high-throughput screening approach and follow up studies have identified a suite of novel therapies that may be beneficial for repurposing for the treatment of bone marrow failure by increasing hematopoietic progenitor cells. We plan to evaluate this, and potentially other therapies, in a clinical trial with DBA patients. Disclosures Flygare: LU Holding: Patents & Royalties: Patent.

Safety pharmacology continues to seek to validate and refine methods for use in preclinical detection of adverse effect liability. Almost uniquely in pharmacology, drug safety assessment by safety pharmacologists is driven by the need for elaboration and validation of methods for detecting drug actions. This is the 10th consecutive year that the Journal of Pharmacological and Toxicological Methods (JPTM) has published themed issues arising from the annual meeting of the Safety Pharmacology Society (SPS), most recently held in Phoenix, AZ in 2012. The SPS is now into its 13th year as a distinct (from Pharmacology and Toxicology) discipline that integrates safety pharmacologists from industry with those in academia and the various global regulatory authorities. Some of the unique sessions of the 2012 meeting included (i) Oncology Therapies, (ii) Assessment of Cardiac Function and (iii) The Growing Role of Safety Pharmacology. This issue of JPTM reflects these themes. As with the previous 10 issues of the Journal , the manuscripts in this issue encompass a broad spectrum of safety pharmacology topics including application of state-of-the-art methods in keeping with the directive of the ICH S7A guidance document emphasizing “…the use of new technologies and methodologies in accordance with sound scientific principles…” study conduct and data analysis, processing and evaluation. This includes some exciting new applications with well validated in vitro and ex vivo safety pharmacology models, refinements in high throughput screening methods with application for use in early safety pharmacology assessments, modified supplemental safety methods meant to evaluate potential adverse pharmacodynamic effects on organ system functions not addressed by the core battery and heart rate variability in non-human primates (NHP). Additionally a series of fascinating articles examining the effects of known drugs on electrophysiological and contractile function in human induced (iPSC-CM) and embryonic (hESC-CM) stem cells are presented. A historical review on hERG channel electrophysiology and channel characterization, efforts of the HESI Cardiac Technical Safety Committee since its inception and an overview of the dynamic and vibrant Safety Pharmacology Society (SPS) are also included in this issue.

Recently, ω-transaminases have been increasingly used to synthesize amine compounds by reductive amination of prochiral ketones which are of high pharmacological significance. However, the conventional methods for evaluating these enzymes are time consuming and have often been regarded as a bottle neck in developing these enzymes as industrial biocatalysts. In the past few years, several high throughput screening methods have been developed for fast evaluation and identification of ω-transaminase. This review summarizes the various methodologies developed for rapidly screening ω-transaminases.

Hundreds of therapeutic monoclonal antibodies (mAbs) are currently in development, and many companies have multiple antibodies in their pipelines. Current methodology used in recovery processes for these molecules are reviewed here. Basic unit operations such as harvest, Protein A affinity chromatography, and additional polishing steps are surveyed. Alternative processes such as flocculation, precipitation, and membrane chromatography are discussed. We also cover platform approaches to purification methods development, use of high throughput screening methods, and offer a view on future developments in purification methodology as applied to mAbs.

Proteases constitute one of the most important groups of industrial enzymes with a worldwide value expected to reach 2.7 billion US dollars by 2019. Proteases represent a group of enzymes that hydrolyze the peptide bonds of proteins, releasing polypeptides or free amino acids. These enzymes are used in cleaning products, production of leathers, textiles, food and dairy products, in the pharmaceutical and diagnostic industries and for water treatment. Another area of interest regarding proteases is the development of drugs that act as protease inhibitors. This review will briefly describe the general methods used in the detection of proteases and the few studies in the development of high throughput screening methods of proteases and protease inhibitors.

In situ and operando techniques can play important roles in the development of better performing photoelectrodes, photocatalysts, and electrocatalysts by helping to elucidate crucial intermediates and mechanistic steps. The development of high throughput screening methods has also accelerated the evaluation of relevant photoelectrochemical and electrochemical properties for new solar fuel materials. In this chapter, several in situ and high throughput characterization tools are discussed in detail along with their impact on our understanding of solar fuel materials.

Combinatorial chemistry has been well recognized as an important tool of drug discovery. An ongoing hand is to integrate the combinatorial approach with fundamentals of medicinal chemistry and rational drug design. The last five years has seen an explosion in the exploration and adoption of combinatorial techniques. Indeed, it is difficult to identify any other topic in chemistry that has ever caught the imagination of chemists with such fervor and with the continuous development of high throughput screening methods. There is a growing need for the synthesis of a large number of molecules. Compound libraries designed to produce specific inhibitors of therapeutic target proteins have generated significant interest in drug discovery research. Combinatorial chemistry provides the opportunity to generate large libraries of compounds for biological testing. A literature search revealed that many lead compounds have indeed been discovered from libraries and this review presents a survey of combinatorial synthesis of HIV-1 reverse transcriptase inhibitors, protease inhibitors, HIV-1 function inhibitors such as adsorption inhibitors, CCR5 antagonists and HIV-1 Tat-tar inhibitors that can be developed as potential anti-HIV drugs.

One approach to accelerate the discovery process of experimentally determined products is through the use of high-throughput screening (HTS) methods. This paper presents a method for the r...

Investigators of anion channels are frequently heard bemoaning the absence of potent, specific inhibitors of their favorite channel. The lack of such blockers has been particularly frustrating for researchers investigating the cystic fibrosis transmembrane conductance regulator (CFTR) Cl− channel

Combinatorial chemistry has proven to be a valuable tool for the development of new compounds. The combinatorial methodology is well suited to the development of complex, multicomponent materials that, typically, require extensive experimentation for their development. As a result, coating development appeared to be a good candidate for the application of the combinatorial methodology. A “combinatorial factory” capable of preparing and testing over 100 coatings per day has been developed. The components of the factory consist of: (1) an automated system to prepare liquid coating formulations; (2) a novel coating application process capable of making high density arrays of coatings of controlled thickness; (3) curing of the coating arrays either thermally or with UV light; (4) testing of the coatings using newly developed high throughput screening methods; and (5) a data handling process to quickly identify the most promising coatings produced. Various aspects of the application of the combinatorial methodology to coating development are described.

The ability to image specific molecular targets in vivo would have significant impact in allowing earlier disease detection and in tailoring molecular therapies. One of the rate-limiting steps in the development of novel compounds as reporter probes has been the lack of cell-based, biologically relevant, high throughput screening methods. Here we describe the development and validation of magnetic resonance imaging (MRI) as a technique to rapidly screen compounds that are potential MR reporter agents for their interaction with specific cellular targets. We show that MR imaging can (1) evaluate thousands of samples simultaneously and rapidly, (2) provide exceedingly accurate measurements, and (3) provide receptor binding/internalization data as validated by radioactive assays. The technique allows the screening of libraries of peptide-nanoparticle conjugates against target cells and the identification of conjugates that may be subsequently used as reporter agents in vivo. The technology should greatly accelerate the development of target-specific or cell-specific MR contrast agents.

This chapter treats exclusively directed evolution of proteins, the primary focus being on recent methodology developments. During the past 25 years, numerous gene mutagenesis methods have been developed. It is difficult even for experts to make the optimal choice, because comparative studies focusing on relative efficiency are rare. A few select studies in directed evolution are reviewed in the chapter, because they allow conclusions regarding the relative merits of different mutagenesis methods and strategies. In a landmark study, single-gene DNA shuffling was applied to turn Escherichia coli β-galactosidase (BGAL) into a β-fucosidase, thereby changing the substrate scope. The enzyme hydrolyzes β-galactosyl linkages such as the β (1,4)-linkage in lactose. In principle, epPCR and DNA shuffling are independent of structural data, whereas saturation mutagenesis generally needs such knowledge to make a decision regarding the randomization sites. Alternatively, saturation mutagenesis can be applied systematically at every single amino acid position, as was reported in the thermostabilization of a xylanase. Subsequent to the first directed evolution study regarding the enantioselectivity of enzymes, which involved four cycles of epPCR in the hydrolytic kinetic resolution of a chiral ester catalyzed by a lipase, numerous academic and industrial studies have appeared that contribute to the generalization of this new approach to asymmetric catalysis. Subsequent investigations addressed the reasons for the apparent efficacy of iterative combinatorial active-site saturation testing as a form of iterative saturation mutagenesis (ISM).