High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor
Not Available
60 APPLIED LIFE SCIENCES↗
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Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography
Since early 2020, COVID-19 has grown to affect the lives of billions globally. A worldwide investigation has been ongoing for characterizing the virus and also for finding an effective drug and developing vaccines. As time has been of the essence, a crucial part of this research has been drug repurposing; therefore, confirmation of in silico drug screening studies have been carried out for this purpose. Here we demonstrated the possibility of screening a variety of drugs efficiently by leveraging a high data collection rate of 120 images/second with the new low-noise, high dynamic range ePix10k2M Pixel Array Detector installed at the Macromolecular Femtosecond Crystallography (MFX) instrument at the Linac Coherent Light Source (LCLS). The X-ray Free-Electron Laser (XFEL) is used for remote high-throughput data collection for drug repurposing of the main protease (Mpro) of SARS-CoV-2 at ambient temperature with mitigated X-ray radiation damage. We obtained multiple structures soaked with nine drug candidate molecules in two crystal forms. Although our drug binding attempts failed, we successfully established a high-throughput Serial Femtosecond X-ray crystallographic (SFX) data collection protocol.
60 APPLIED LIFE SCIENCES↗
Smart Microbial Cells Couple Catalysis and Sensing to Provide High-Throughput Selection of an Organophosphate Hydrolase
Enzyme engineering for gain of function requires navigating a large combinatorial sequence space efficiently. Typically, many mutations are needed to get significant improvements, while a single “bad” mutation can inactivate the enzyme. To establish high-throughput screening and achieve enhanced resolution between two variants, genetic libraries of the organophosphate hydrolase enzyme paraoxonase 1 (PON 1 ) were rapidly screened via an engineered positive-feedback circuit: a p-nitrophenol (PNP)-specific transcription factor (TF) regulated expression of PON 1 , which catalyzed paraoxon breakdown and PNP production. Rare active mutant colonies, picked by simple visual fluorescence of a PON 1 –green fluorescent protein (GFP) fusion, were characterized. Furthermore, in a single screening round, high (library-scale) throughput enabled the discovery of enhanced paraoxon degradation activity in PON 1 , including structurally unexpected mutations.
59 BASIC BIOLOGICAL SCIENCES↗
An Innovative High Throughput Genome Releaser for Rapid and Efficient PCR Screening
High-throughput PCR screening is vital in synthetic biology and metabolic engineering as it allows researchers to rapidly analyze and detect numerous targeted genetic mutation in the genome. Current challenges for high-throughput PCR screening in synthetic biology include efficiently preparing genomic DNA, optimizing protocols for diverse sample types, managing contamination risks, and effectively analyzing the large volumes of data generated while ensuring consistent and accurate results. In this study, we present the development of a High Throughput Genome Releaser (HTGR), an innovative device addressing common challenges in screening PCR. This genome DNA releaser is designed based on a squash method for rapid, cost-effective, and efficient DNA release, optimized for subsequent PCR reactions. After experimenting with various synthetic materials, we selected a plastic that closely replicates the smooth surface and compression properties of microscope slides, ensuring reliable performance. We engineered a device featuring a 96-Well Plate and a shear applicator, operable both manually and automatically, and compatible with standard liquid-handling robot platform. This compatibility enhances ease of use in high-throughput PCR workflows. Additionally, we developed software to support its automatic functions. Our results demonstrated that the specially engineered 96-Well Plate and HTGR can effectively squash fungal spores , which release enough genome DNA for PCR screening. The genome releaser facilitates the preparation of PCR-amplifiable genomic DNA substrate from 96 samples within minutes, eliminates the need for extraction buffers, and is adaptable to a wide range of microorganisms and cells, which could significantly advance biomanufacturing processes.
Yuan, Guoliang [BATTELLE (PACIFIC NW LAB)]↗
Microscale thermophoresis as a powerful tool for screening glycosyltransferases involved in cell wall biosynthesis
Background: Identification and characterization of key enzymes associated with cell wall biosynthesis and modification is fundamental to gain insights into cell wall dynamics. However, it is a challenge that activity assays of glycosyltransferases are very low throughput and acceptor substrates are generally not available. Results: We optimized and validated microscale thermophoresis (MST) to achieve high throughput screening for glycosyltransferase substrates. MST is a powerful method for the quantitative analysis of protein-ligand interactions with low sample consumption. The technique is based on the motion of molecules along local temperature gradients, measured by fluorescence changes. We expressed glycosyltransferases as YFP-fusion proteins in tobacco and optimized the MST method to allow the determination of substrate binding affinity without purification of the target protein from the cell lysate. The application of this MST method to the β-1,4-galactosyltransferase AtGALS1 validated the capability to screen both nucleotide-sugar donor substrates and acceptor substrates. We also expanded the application to members of glycosyltransferase family GT61 in sorghum for substrate screening and function prediction. Conclusions: This method is rapid and sensitive to allow determination of both donor and acceptor substrates of glycosyltransferases. MST enables high throughput screening of glycosyltransferases for likely substrates, which will narrow down their in vivo function and help to select candidates for further studies. Additionally, this method gives insight into biochemical mechanism of glycosyltransferase function.
59 BASIC BIOLOGICAL SCIENCES↗
acCRISPR: an activity-correction method for improving the accuracy of CRISPR screens
Abstract High throughput CRISPR screens are revolutionizing the way scientists unravel the genetic underpinnings of engineered and evolved phenotypes. One of the critical challenges in accurately assessing screening outcomes is accounting for the variability in sgRNA cutting efficiency. Poorly active guides targeting genes essential to screening conditions obscure the growth defects that are expected from disrupting them. Here, we develop acCRISPR, an end-to-end pipeline that identifies essential genes in pooled CRISPR screens using sgRNA read counts obtained from next-generation sequencing. acCRISPR uses experimentally determined cutting efficiencies for each guide in the library to provide an activity correction to the screening outcomes via calculation of an optimization metric, thus determining the fitness effect of disrupted genes. CRISPR-Cas9 and -Cas12a screens were carried out in the non-conventional oleaginous yeast Yarrowia lipolytica and acCRISPR was used to determine a high-confidence set of essential genes for growth under glucose, a common carbon source used for the industrial production of oleochemicals. acCRISPR was also used in screens quantifying relative cellular fitness under high salt conditions to identify genes that were related to salt tolerance. Collectively, this work presents an experimental-computational framework for CRISPR-based functional genomics studies that may be expanded to other non-conventional organisms of interest.
59 BASIC BIOLOGICAL SCIENCES↗
High Throughput Electrochemical Screening of Phosphate-Rich Nonflammable Electrolytes in Lithium-Ion Batteries
Frequent fires and explosions in lithium-ion batteries (LIBs) used in grid energy storage systems (ESS) highlight the necessity of revisiting nonflammable phosphate electrolytes as alternatives to the currently used flammable carbonates. However, previous studies have shown the difficulty of integrating phosphate solvents into LIB electrolytes due to compatibility issues with graphite. In this work, we developed a high-throughput (HTP) electrochemical characterization method, akin to pH test paper, to rapidly screen potential phosphate electrolytes and graphite materials. Through HTP screening, we identified 101 promising combinations out of 1,740. This number was reduced to 26 after testing in Li/Graphite half cells. The optimized phosphate-rich electrolyte (60 v% phosphate) with cosolvents demonstrated 300 stable cycles at 0.1 C in Graphite/LiFePO 4 (LFP) full cells with thick electrodes (∼3.0 mAh cm −2 ), surpassing prior research findings. This unique HTP method provides a powerful tool to expedite the development of safe LIBs for ESS applications.
25 ENERGY STORAGE↗
Machine learning-enabled discovery of ionic liquid–solvent electrolytes exhibiting high ionic conductivity
Ionic liquids (ILs), which are a class of materials with versatile nature and growing popularity, are facing impediments toward widespread usage as electrolytes due to various factors such as low ionic conductivity, high viscosity, high market price etc. One of the ways these limitations can be addressed is by mixing ILs with a molecular solvent. In a combinatorial sense, there exists an immense number of specific IL–solvent combinations. An exhaustive experimental or even simulation-based investigation of the chemical space spanned by such combinations can be extremely time-consuming, expensive, and nearly impossible. An alternative approach is to employ machine learning-based models developed from available databases. Although there exists prior literature that integrates machine learning to investigate mixtures of specific solvents with ILs, these models lack generalization necessitating development of a large number of ML models to handle various solvents. To remedy this shortcoming, as a part of designing green electrolytes with high ionic conductivity that can have potential applications in next-generation batteries and solar cells, this work aims to develop a unified machine learning model to predict ionic conductivity of any IL–solvent mixture system. In this regard, three models, namely, Random Forest, extreme gradient boosting (XGBoost), and artificial neural network (ANN) were formulated using the NIST ILThermo database. The dataset contained 549 unique ionic liquids from 16 cation families and 81 unique solvents, representing a total of 23 712 datapoints. SHAPLEY additive explanation (SHAP) method was used to assess the impact of various features on model prediction and their significance was compared with literature to gain physical insight about the model behavior. Finally, using the developed models, approximately 2.5 million IL–solvent mixtures at five different compositions were screened at room temperature. The high-throughput screening yielded nearly 19 000 IL–solvent mixtures for which ionic conductivity was found to exceed the ionic conductivity of conventional Li-ion battery electrolyte.
25 ENERGY STORAGE↗
Machine Learning for the Discovery, Design, and Engineering of Materials
Machine learning (ML) has become a part of the fabric of high-throughput screening and computational discovery of materials. Despite its increasingly central role, challenges remain in fully realizing the promise of ML. This is especially true for the practical acceleration of the engineering of robust materials and the development of design strategies that surpass trial and error or high-throughput screening alone. Depending on the quantity being predicted and the experimental data available, ML can either outperform physics-based models, be used to accelerate such models, or be integrated with them to improve their performance. We cover recent advances in algorithms and in their application that are starting to make inroads toward ( a) the discovery of new materials through large-scale enumerative screening, ( b) the design of materials through identification of rules and principles that govern materials properties, and ( c) the engineering of practical materials by satisfying multiple objectives. We conclude with opportunities for further advancement to realize ML as a widespread tool for practical computational materials design.
Chemistry↗
Electron-phonon coupling strength from ab initio frozen-phonon approach
In this work, we propose a fast method for high-throughput screening of potential superconducting materials. The method is based on calculating metallic screening of zone-center phonon modes, which provides an accurate estimate for the electron-phonon coupling strength. This method is complementary to the recently proposed Rigid Muffin Tin (RMT) method, which amounts to integrating the electronphonon coupling over the entire Brillouin zone (as opposed to the zone center), but in a relatively inferior approximation. We illustrate the use of this method by applying it to MgB 2 , where the high-temperature superconductivity is known to be driven largely by the zone-center modes, and compare it to a sister compound AlB 2 . We further illustrate the usage of this descriptor by screening a large number of binary hydrides, for which accurate first-principle calculations of electron-phonon coupling have been recently published. Together with the RMT descriptor, this method opens a way to perform initial high-throughput screening in search of conventional superconductors via machine learning or data mining.
36 MATERIALS SCIENCE↗
Isomerization and Selective Hydrogenation of Propyne: Screening of Metal–Organic Frameworks Modified by Atomic Layer Deposition
Various metal oxide clusters upward of 8 atoms (Cu, Cd, Co, Fe, Ga, Mn, Mo, Ni, Sn, W, Zn, In, and Al) were incorporated into the pores of the metal–organic framework (MOF) NU-1000 via atomic layer deposition (ALD) and tested via high-throughput screening for catalytic isomerization and selective hydrogenation of propyne. Cu and Co were found to be the most active for propyne hydrogenation to propylene, and synergistic bimetallic combinations of Co and Zn, along with standalone Zn and Cd, were established as the most active for conversion to the isomerized product, propadiene. The combination of Co and Zn in NU-1000 diminished the propensity for full hydrogenation to propane as well as coking compared to its individual components. Finally, this study highlights the potential for high-throughput screening to survey monometallic and bimetallic cluster combinations that best affect the efficient transformation of small molecules, while discerning mechanistic differences in isomerization and hydrogenation by different metals.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Pose Classification Using Three-Dimensional Atomic Structure-Based Neural Networks Applied to Ion Channel–Ligand Docking
The identification of promising lead compounds showing pharmacological activities toward a biological target is essential in early stage drug discovery. With the recent increase in available small-molecule databases, virtual high-throughput screening using physics-based molecular docking has emerged as an essential tool in assisting fast and cost-efficient lead discovery and optimization. However, the best scored docking poses are often suboptimal, resulting in incorrect screening and chemical property calculation. We address the pose classification problem by leveraging data-driven machine learning approaches to identify correct docking poses from AutoDock Vina and Glide screens. To enable effective classification of docking poses, we present two convolutional neural network approaches: a three-dimensional convolutional neural network (3D-CNN) and an attention-based point cloud network (PCN) trained on the PDBbind refined set. We demonstrate the effectiveness of our proposed classifiers on multiple evaluation data sets including the standard PDBbind CASF-2016 benchmark data set and various compound libraries with structurally different protein targets including an ion channel data set extracted from Protein Data Bank (PDB) and an in-house KCa3.1 inhibitor data set. Our experiments show that excluding false positive docking poses using the proposed classifiers improves virtual high-throughput screening to identify novel molecules against each target protein compared to the initial screen based on the docking scores.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Large-scale experimental validation of thermochemical water-splitting oxides discovered by defect graph neural networks
Thermochemical water-splitting (TCH) based on 2-step thermal redox cycles in metal oxides is a promising approach to generating H 2 , but state-of-the-art (SOTA) CeO 2 has several practical limitations, which has motivated continued materials discovery efforts in this field. Here, in this study, we improve upon a SOTA defect graph neural network (dGNN) surrogate model's oxygen vacancy predictions and combine them with materials project phase diagrams to down-select and discover structurally diverse, experimentally known metal oxides whose TCH performance was previously unknown. Amongst twelve candidates selected based on our high-throughput screening and down-selection criteria, we achieved ∼80% accuracy in identifying materials with stable redox cycling and hydrogen production in stagnation flow reactor water-splitting experiments. Closer to 100% accuracy can be achieved if higher-accuracy, hybrid DFT-predicted vacancy formation energies were computed and used in lieu of the most uncertain dGNN-based screening predictions, as they correct false positives to true negatives. Notably, two discovered candidates, Sr 3 PrMn 2 O 8 and Ba 2 Fe 2 O 5 , display hydrogen yields greater than CeO 2 under specific redox conditions. In conclusion, these results demonstrate our ability to computationally predict and experimentally validate promising candidate TCH materials that have the potential to compete with CeO 2 .
08 HYDROGEN↗
Metabolomic Profiling of Wild-type and Mutant Soybean Root Nodules Using Laser-ablation Electrospray Ionization Mass Spectrometry Reveals Altered Metabolism
The establishment of the nitrogen-fixing symbiosis between soybean and Bradyrhizobium japonicum is complex. In order to document the changes in plant metabolism due to the symbiosis, we utilized laser ablation electrospray ionization mass spectrometry (LAESI-MS) for in situ metabolic profiling of wild-type nodules, nodules infected with a B. japonicum nifH mutant unable to fix nitrogen, nodules doubly infected by both strains, and nodules formed on plants mutated in the stearoyl-acyl carrier protein desaturase (sacpd-c) gene, which were previously shown to have altered nodule ultrastructure. Results showed that the relative abundance of fatty acids, purines, and lipids was significantly changed in response to the symbiosis. The nifH mutant nodules had elevated levels of jasmonic acid (JA), correlating with signs of nitrogen deprivation. Nodules resulting from the mixed inoculant displayed similar, overlapping metabolic distributions within the sectors of effective (fix+) and ineffective (nifH mutant, fix-) endosymbionts. These data are inconsistent with the notion that plant sanctioning is cell autonomous. Nodules lacking sacpd-c displayed an elevation of soyasaponins and organic acids in the central necrotic regions. This study demonstrates the utility of LAESI-MS for high-throughput screening of plant phenotypes. Overall, nodules disrupted in the symbiosis were elevated in metabolites related to plant defense.
Agtuca, Beverly J.↗
High-Throughput Compatibility Screening of Materials for SF 6 -Alternative Insulation
Not provided.
Engineering↗
Diversifying Databases of Metal Organic Frameworks for High-Throughput Computational Screening
Not Available
36 MATERIALS SCIENCE↗