waveRAPID—A Robust Assay for High-Throughput Kinetic Screens with the Creoptix WAVEsystem

2021 ◽  
pp. 247255522110138
Author(s):  
Önder Kartal ◽  
Fabio Andres ◽  
May Poh Lai ◽  
Rony Nehme ◽  
Kaspar Cottier
Keyword(s):  
Drug Discovery ◽  
Fold Increase ◽  
Microtiter Plate ◽  
Experimental Conditions ◽  
Short Pulses ◽  
Cycle Times ◽  
Fragment Screening ◽  
New Instrument ◽  
Single Well ◽  
Compound Screening

Surface-based biophysical methods for measuring binding kinetics of molecular interactions, such as surface plasmon resonance (SPR) or grating-coupled interferometry (GCI), are now well established and widely used in drug discovery. Increasing throughput is an often-cited need in the drug discovery process and this has been achieved with new instrument generations where multiple interactions are measured in parallel, shortening the total measurement times and enabling new application areas within the field. Here, we present the development of a novel technology called waveRAPID for a further—up to 10-fold—increase in throughput, consisting of an injection method using a single sample. Instead of sequentially injecting increasing analyte concentrations for constant durations, the analyte is injected at a single concentration in short pulses of increasing durations. A major advantage of the new method is its ability to determine kinetics from a single well of a microtiter plate, making it uniquely suitable for kinetic screening. We present the fundamentals of this approach using a small-molecule model system for experimental validation and comparing kinetic parameters to traditional methods. By varying experimental conditions, we furthermore assess the robustness of this new technique. Finally, we discuss its potential for improving hit quality and shortening cycle times in the areas of fragment screening, low-molecular-weight compound screening, and hit-to-lead optimization.

scholarly journals waveRAPID® - a robust assay for high-throughput kinetic screens with the Creoptix® WAVEsystem

2021 ◽  
Author(s):  
Önder Kartal ◽  
Fabio Andres ◽  
May Poh Lai ◽  
Rony Nehme ◽  
Kaspar Cottier
Keyword(s):  
Drug Discovery ◽  
Fold Increase ◽  
Experimental Conditions ◽  
Short Pulses ◽  
Cycle Times ◽  
Fragment Screening ◽  
Novel Technology ◽  
New Instrument ◽  
Single Well ◽  
Compound Screening

AbstractSurface-based biophysical methods for measuring binding kinetics of molecular interactions, such as Surface Plasmon Resonance (SPR) or Grating-Coupled Interferometry (GCI), are now well established and widely used in drug discovery. Increasing throughput is an often-cited need in the drug discovery process, and this has been achieved with new instrument generations where multiple interactions are measured in parallel, shortening the total measurement times and enabling new application areas within the field. Here, we present the development of a novel technology called waveRAPID for a further - up to ten-fold - increase in throughput, consisting of an injection method using a single sample. Instead of sequentially injecting increasing analyte concentrations for constant durations, the analyte is injected at a single concentration in short pulses of increasing durations. A major advantage of the new method is its ability to determine kinetics from a single well of a micro-titer plate, making it uniquely suitable for kinetic screening. We present the fundamentals of this approach using a small molecule model system for experimental validation and comparing kinetic parameters to traditional methods. By varying experimental conditions, we furthermore assess the robustness of this new technique.Finally, we discuss its potential for improving hit quality and shortening cycle times in the areas of fragment screening, low molecule weight compound screening, and hit-to-lead optimization.

scholarly journals A prospective compound screening contest identified broader inhibitors for Sirtuin 1

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Shuntaro Chiba ◽  
Masahito Ohue ◽  
Anastasiia Gryniukova ◽  
Petro Borysko ◽  
Sergey Zozulya ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Inhibitory Action ◽  
Enzyme Inhibitors ◽  
Sirtuin 1 ◽  
Compound Library ◽  
Experimental Conditions ◽  
Computer Aided ◽  
Compound Screening ◽  
Single Method ◽  
Potential Inhibitors

AbstractPotential inhibitors of a target biomolecule, NAD-dependent deacetylase Sirtuin 1, were identified by a contest-based approach, in which participants were asked to propose a prioritized list of 400 compounds from a designated compound library containing 2.5 million compounds using in silico methods and scoring. Our aim was to identify target enzyme inhibitors and to benchmark computer-aided drug discovery methods under the same experimental conditions. Collecting compound lists derived from various methods is advantageous for aggregating compounds with structurally diversified properties compared with the use of a single method. The inhibitory action on Sirtuin 1 of approximately half of the proposed compounds was experimentally accessed. Ultimately, seven structurally diverse compounds were identified.

scholarly journals LED Illumination Spectrum Manipulation for Increasing the Yield of Sweet Basil (Ocimum basilicum L.)

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 344
Author(s):  
Md Momtazur Rahman ◽  
Mikhail Vasiliev ◽  
Kamal Alameh
Keyword(s):  
Growth Rate ◽  
Fold Increase ◽  
Photosynthetic Photon Flux Density ◽  
Ocimum Basilicum ◽  
Photon Flux ◽  
Photon Flux Density ◽  
White Led ◽  
Experimental Conditions ◽  
Sweet Basil ◽  
Optimal Illumination

Manipulation of the LED illumination spectrum can enhance plant growth rate and development in grow tents. We report on the identification of the illumination spectrum required to significantly enhance the growth rate of sweet basil (Ocimum basilicum L.) plants in grow tent environments by controlling the LED wavebands illuminating the plants. Since the optimal illumination spectrum depends on the plant type, this work focuses on identifying the illumination spectrum that achieves significant basil biomass improvement compared to improvements reported in prior studies. To be able to optimize the illumination spectrum, several steps must be achieved, namely, understanding plant biology, conducting several trial-and-error experiments, iteratively refining experimental conditions, and undertaking accurate statistical analyses. In this study, basil plants are grown in three grow tents with three LED illumination treatments, namely, only white LED illumination (denoted W*), the combination of red (R) and blue (B) LED illumination (denoted BR*) (relative red (R) and blue (B) intensities are 84% and 16%, respectively) and a combination of red (R), blue (B) and far-red (F) LED illumination (denoted BRF*) (relative red (R), blue (B) and far-red (F) intensities are 79%, 11%, and 10%, respectively). The photosynthetic photon flux density (PPFD) was set at 155 µmol m−2 s−1 for all illumination treatments, and the photoperiod was 20 h per day. Experimental results show that a combination of blue (B), red (R), and far-red (F) LED illumination leads to a one-fold increase in the yield of a sweet basil plant in comparison with only white LED illumination (W*). On the other hand, the use of blue (B) and red (R) LED illumination results in a half-fold increase in plant yield. Understanding the effects of LED illumination spectrum on the growth of plant sweet basil plants through basic horticulture research enables farmers to significantly improve their production yield, thus food security and profitability.

scholarly journals High-throughput crystallographic fragment screening for drug discovery

2018 ◽  
Vol 74 (a2) ◽  
pp. e24-e24
Author(s):  
Alexander Metz ◽  
Franziska Huschmann ◽  
Johannes Schiebel ◽  
Uwe Müller ◽  
Manfred Weiss ◽  
...  
Keyword(s):  
Drug Discovery ◽  
High Throughput ◽  
Fragment Screening

Scalable Microfluidic Platform for Flexible Configuration of and Experiments with Microtissue Multiorgan Models

2018 ◽  
Vol 24 (1) ◽  
pp. 79-95 ◽  
Author(s):  
Christian Lohasz ◽  
Nassim Rousset ◽  
Kasper Renggli ◽  
Andreas Hierlemann ◽  
Olivier Frey
Keyword(s):  
Large Scale ◽  
Plastic Material ◽  
Microtiter Plate ◽  
Scale Production ◽  
Experimental Conditions ◽  
Precise Control ◽  
Open Design ◽  
Gravity Driven ◽  
Gravity Driven Flow

Microphysiological systems hold the promise to increase the predictive and translational power of in vitro substance testing owing to their faithful recapitulation of human physiology. However, the implementation of academic developments in industrial settings remains challenging. We present an injection-molded microfluidic microtissue (MT) culture chip that features two channels with 10 MT compartments each and that was designed in compliance with microtiter plate standard formats. Polystyrene as a chip material enables reliable, large-scale production and precise control over experimental conditions due to low adsorption or absorption of small, hydrophobic molecules at or into the plastic material in comparison with predecessor chips made of polydimethylsiloxane. The chip is operated by tilting, which actuates gravity-driven flow between reservoirs at both ends of every channel, so that the system does not require external tubing or pumps. The flow rate can be modulated by adjusting the tilting angle on demand. The top-open design of the MT compartment enables efficient MT loading using standard or advanced pipetting equipment, ensures oxygen availability in the chip, and allows for high-resolution imaging. Every channel can be loaded with up to 10 identical or different MTs, as demonstrated by culturing liver and tumor MTs in the same medium channel on the chip.

Flow chemistry as a tool to access novel chemical space for drug discovery

2020 ◽  
Vol 12 (17) ◽  
pp. 1547-1563
Author(s):  
Enol López ◽  
María Lourdes Linares ◽  
Jesús Alcázar
Keyword(s):  
Drug Discovery ◽  
Medicinal Chemistry ◽  
Chemical Space ◽  
Flow Chemistry ◽  
Bioactive Molecules ◽  
Complex Molecules ◽  
Cycle Times

This perspective scrutinizes flow chemistry as a useful tool for medicinal chemists to expand the current chemical capabilities in drug discovery. This technology has demonstrated his value not only for the traditional reactions used in Pharma for the last 20 years, but also for bringing back to the lab underused chemistries to access novel chemical space. The combination with other technologies, such as photochemistry and electrochemistry, is opening new avenues for reactivity that will smoothen the access to complex molecules. The introduction of all these technologies in automated platforms will improve the productivity of medicinal chemistry labs reducing the cycle times to get novel and differentiated bioactive molecules, accelerating discovery cycle times.

scholarly journals Be Aware of Aggregators in the Search for Potential Human ecto-5′-Nucleotidase Inhibitors

Molecules ◽  
2018 ◽  
Vol 23 (8) ◽  
pp. 1876 ◽  
Author(s):  
Lucas Viviani ◽  
Erika Piccirillo ◽  
Arquimedes Cheffer ◽  
Leandro de Rezende ◽  
Henning Ulrich ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Kinetic Studies ◽  
Enzyme Concentration ◽  
Experimental Conditions ◽  
Time Aggregation ◽  
Compound C ◽  
Promising Target ◽  
Ic50 Values ◽  
Potential Inhibitors ◽  
Triton X

Promiscuous inhibition due to aggregate formation has been recognized as a major concern in drug discovery campaigns. Here, we report some aggregators identified in a virtual screening (VS) protocol to search for inhibitors of human ecto-5′-nucleotidase (ecto-5′-NT/CD73), a promising target for several diseases and pathophysiological events, including cancer, inflammation and autoimmune diseases. Four compounds (A, B, C and D), selected from the ZINC-11 database, showed IC50 values in the micromolar range, being at the same time computationally predicted as potential aggregators. To confirm if they inhibit human ecto-5′-NT via promiscuous mechanism, forming aggregates, enzymatic assays were done in the presence of 0.01% (v/v) Triton X-100 and an increase in the enzyme concentration by 10-fold. Under both experimental conditions, these four compounds showed a significant decrease in their inhibitory activities. To corroborate these findings, turbidimetric assays were performed, confirming that they form aggregate species. Additionally, aggregation kinetic studies were done by dynamic light scattering (DLS) for compound C. None of the identified aggregators has been previously reported in the literature. For the first time, aggregation and promiscuous inhibition issues were systematically studied and evaluated for compounds selected by VS as potential inhibitors for human ecto-5′-NT. Together, our results reinforce the importance of accounting for potential false-positive hits acting by aggregation in drug discovery campaigns to avoid misleading assay results.

scholarly journals Differential Pulse Polarographic Determination of Procymidone in Formulations and Wine

2002 ◽  
Vol 85 (3) ◽  
pp. 731-735 ◽  
Author(s):  
Neelam Y Sreedhar ◽  
Thommandru R Babu ◽  
Kethamreddy Samatha ◽  
Devarapalli Sujatha ◽  
Thenepalli Thriveni
Keyword(s):  
Reduction Process ◽  
Differential Pulse ◽  
Differential Pulse Polarography ◽  
Experimental Conditions ◽  
Controlled Potential Electrolysis ◽  
Pulse Polarography ◽  
Half Wave ◽  
Single Well ◽  
Controlled Potential ◽  
Ph Range

Abstract The dicarboximide fungicide procymidone was studied systematically by using direct current polarography, cyclic voltammetry, differential pulse polarography (DPP), controlled potential electrolysis, and millicoulometry in the universal buffer medium with dimethylformamide as the solvent. Procymidone exhibited a single well-defined polarographic wave in the pH range 2.0–6.0, leading to the formation of the hydroxy compound. The overall reduction process was diffusion-controlled and adsorption-free. The variation of half-wave potential with pH, the concentration of the analyte, and other experimental conditions are described. The reduction mechanism proposed is an overall 4-electron process, in which the dicarboximide group is reduced. DPP was used to determine procymidone in agricultural formulations and wine at the optimum conditions found; a detection limit of 2.4 × 10−9M was estimated. The results obtained by the proposed method were also compared with those obtained by other methods.

Antimalarial drug discovery: efficacy models for compound screening

2004 ◽  
Vol 3 (6) ◽  
pp. 509-520 ◽  
Author(s):  
David A. Fidock ◽  
Philip J. Rosenthal ◽  
Simon L. Croft ◽  
Reto Brun ◽  
Solomon Nwaka
Keyword(s):  
Drug Discovery ◽  
Antimalarial Drug ◽  
Compound Screening

scholarly journals Beyond Agar: Gel Substrates with Improved Optical Clarity and Drug Efficiency and Reduced Autofluorescence for Microbial Growth Experiments

2015 ◽  
Vol 81 (16) ◽  
pp. 5639-5649 ◽  
Author(s):  
Philipp A. Jaeger ◽  
Cameron McElfresh ◽  
Lily R. Wong ◽  
Trey Ideker
Keyword(s):  
Cost Savings ◽  
Colony Growth ◽  
Microtiter Plate ◽  
Biological Properties ◽  
Genetic Screens ◽  
Experimental Conditions ◽  
Fluorescent Reporter ◽  
Content Type ◽  
Recent Developments ◽  
Support Matrix

ABSTRACTAgar, a seaweed extract, has been the standard support matrix for microbial experiments for over a century. Recent developments in high-throughput genetic screens have created a need to reevaluate the suitability of agar for use as colony support, as modern robotic printing systems now routinely spot thousands of colonies within the area of a single microtiter plate. Identifying optimal biophysical, biochemical, and biological properties of the gel support matrix in these extreme experimental conditions is instrumental to achieving the best possible reproducibility and sensitivity. Here we systematically evaluate a range of gelling agents by using the yeastSaccharomyces cerevisiaeas a model microbe. We find that carrageenan and Phytagel have superior optical clarity and reduced autofluorescence, crucial for high-resolution imaging and fluorescent reporter screens. Nutrient choice and use of refined Noble agar or pure agarose reduce the effective dose of numerous selective drugs by >50%, potentially enabling large cost savings in genetic screens. Using thousands of mutant yeast strains to compare colony growth between substrates, we found no evidence of significant growth or nutrient biases between gel substrates, indicating that researchers could freely pick and choose the optimal gel for their respective application and experimental condition.

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