Background:In-feed antibiotics are being phased out in livestock production worldwide.Alternatives to antibiotics are urgently needed to maintain animal health and production performance.Host defense peptides(HDPs)are...Background:In-feed antibiotics are being phased out in livestock production worldwide.Alternatives to antibiotics are urgently needed to maintain animal health and production performance.Host defense peptides(HDPs)are known for their broad-spectrum antimicrobial and immunomodulatory capabilities.Enhancing the synthesis of endogenous HDPs represents a promising antibiotic alternative strategy to disease control and prevention.Methods:To identify natural products with an ability to stimulate the synthesis of endogenous HDPs,we performed a high-throughput screening of 1261 natural products using a newly-established stable luciferase reporter cell line known as IPEC-J2/pBD3-luc.The ability of the hit compounds to induce HDP genes in porcine IPEC-J2 intestinal epithelial cells,3D4/31 macrophages,and jejunal explants were verified using RT-qPCR.Augmentation of the antibacterial activity of porcine 3D4/31 macrophages against a Gram-negative bacterium(enterotoxigenic E.coli)and a Gram-positive bacterium(Staphylococcus aureus)were further confirmed with four selected HDP-inducing compounds.Results:A total of 48 natural products with a minimum Z-score of 2.0 were identified after high-throughput screening,with 21 compounds giving at least 2-fold increase in luciferase activity in a follow-up dose-response experiment.Xanthohumol and deoxyshikonin were further found to be the most potent in inducing pBD3 mRNA expression,showing a minimum 10-fold increase in IPEC-J2,3D4/31 cells,and jejunal explants.Other compounds such as isorhapontigenin and calycosin also enhanced pBD3 mRNA expression by at least 10-fold in both IPEC-J2 cells and jejunal explants,but not 3D4/31 cells.In addition to pBD3,other porcine HDP genes such as pBD2,PG1-5,and pEP2C were induced to different magnitudes by xanthohumol,deoxyshikonin,isorhapontigenin,and calycosin,although clear gene-and cell type-specific patterns of regulation were observed.Desirably,these four compounds had a minimum effect on the expression of several representative inflammatory cytokine genes.Furthermore,when used at HDP-inducing concentrations,these compounds showed no obvious direct antibacterial activity,but significantly augmented the antibacterial activity of 3D4/31 macrophages(P<0.05)against both Gram-negative and Gram-positive bacteria.Conclusions:Our results indicate that these newly-identified natural HDP-inducing compounds have the potential to be developed as novel alternatives to antibiotics for prophylactic and therapeutic treatment of infectious diseases in livestock production.展开更多
Single atomic catalysts(SACs),especially metal-nitrogen doped carbon(M-NC)catalysts,have been extensively explored for the electrochemical oxygen reduction reaction(ORR),owing to their high activity and atomic utiliza...Single atomic catalysts(SACs),especially metal-nitrogen doped carbon(M-NC)catalysts,have been extensively explored for the electrochemical oxygen reduction reaction(ORR),owing to their high activity and atomic utilization efficiency.However,there is still a lack of systematic screening and optimization of local structures surrounding active centers of SACs for ORR as the local coordination has an essential impact on their electronic structures and catalytic performance.Herein,we systematic study the ORR catalytic performance of M-NC SACs with different central metals and environmental atoms in the first and second coordination sphere by using density functional theory(DFT)calculation and machine learning(ML).The geometric and electronic informed overpotential model(GEIOM)based on random forest algorithm showed the highest accuracy,and its R^(2) and root mean square errors(RMSE)were 0.96 and 0.21,respectively.30 potential high-performance catalysts were screened out by GEIOM,and the RMSE of the predicted result was only 0.12 V.This work not only helps us fast screen high-performance catalysts,but also provides a low-cost way to improve the accuracy of ML models.展开更多
A stably transfected CHO cell line coexpressing G551D-CFTR and iodide-sensitive yellow fluorescent protein mutant EYFP-H148Q-I152L was successfully established and used as assay model to identify small-molecule activa...A stably transfected CHO cell line coexpressing G551D-CFTR and iodide-sensitive yellow fluorescent protein mutant EYFP-H148Q-I152L was successfully established and used as assay model to identify small-molecule activators of G551D-CFTR chloride channel from 100000 diverse combinatorial compounds by high throughput screening on a customized Beckman robotic system. A bicyclooctane compound was identified to activate G551D-CFTR chloride channel with high-affinity(K d=1.8 μmol/L). The activity of the bicyclooctane compound is G551D-CFTR-specific, reversible and non-toxic. The G551D-CFTR activator may be useful as a tool to study the mutant G551D-CFTR chloride channel structure and transport properties and as a candidate drug to cure cystic fibrosis caused by G551D-CFTR mutation.展开更多
A novel solid phase organic synthesis resin was synthesized for combinatorial high-throughput screening,which based on FTIR spectra self-encoding functional resin technology. A new deconvolution strategy termed positi...A novel solid phase organic synthesis resin was synthesized for combinatorial high-throughput screening,which based on FTIR spectra self-encoding functional resin technology. A new deconvolution strategy termed position encoding deconvolution had illustrated and was compared with some popular combinatorial deconvolution strategies in efficiency and information content. The mimic high throughput screening of hexapeptide library successfully proved the applying of the self-encoding functional resin technology and the position encoding deconvolution strategy.展开更多
The glycine-to-aspartic acid missense mutation at the codon 551(G551D) of the cystic fibrosis transmembrane conductance regulator(CFTR) is one of the five most frequent cystic fibrosis(CF) mutations associated with a ...The glycine-to-aspartic acid missense mutation at the codon 551(G551D) of the cystic fibrosis transmembrane conductance regulator(CFTR) is one of the five most frequent cystic fibrosis(CF) mutations associated with a severe CF phenotype. To explore the feasibility of pharmacological correction of disrupted activation of CFTR chloride channel caused by G551D mutation, we developed a halide-sensitive fluorescence miniassay for G551D-CFTR in Fisher rat thyroid(FRT) epithelial cells for the discovery of novel activators of G551D-CFTR. A class of bicyclooctane small molecule compounds that efficiently stimulate G551D-CFTR chloride channel activity was identified by high throughput screening via the FRT cell-based assay. This class of compounds selectively activates G551D-CFTR with a high affinity, whereas little effect of the compounds on wildtype CFTR can be seen. The discovery of a class of bicyclooctane G551D-CFTR activators will permit the analysis of structure-activity relationship of the compounds to identify ideal leads for in vivo therapeutic studies.展开更多
In this article, we introduce the system of high throughput screening (HTS). Its role in new drug study and current development is described. The relationship between research achievements of genome study and new type...In this article, we introduce the system of high throughput screening (HTS). Its role in new drug study and current development is described. The relationship between research achievements of genome study and new type screening model of new drugs is emphasized. The personal opinions of current problems about HTS study in China are raised.展开更多
Background Early embryo development plays a pivotal role in determining pregnancy outcomes,postnatal development,and lifelong health.Therefore,the strategic selection of functional nutrients to enhance embryo developm...Background Early embryo development plays a pivotal role in determining pregnancy outcomes,postnatal development,and lifelong health.Therefore,the strategic selection of functional nutrients to enhance embryo development is of paramount importance.In this study,we established a stable porcine trophectoderm cell line expressing dual fluorescent reporter genes driven by the CDX2 and TEAD4 gene promoter segments using lentiviral transfection.Results Three amino acid metabolites—kynurenic acid,taurine,and tryptamine—met the minimum z-score criteria of 2.0 for both luciferase and Renilla luciferase activities and were initially identified as potential metabolites for embryo development,with their beneficial effects validated by qPCR.Given that the identified metabolites are closely related to methionine,arginine,and tryptophan,we selected these three amino acids,using lysine as a standard,and employed response surface methodology combined with our high-throughput screening cell model to efficiently screen and optimize amino acid combination conducive to early embryo development.The optimized candidate amino acid system included lysine(1.87 mmol/L),methionine(0.82 mmol/L),tryptophan(0.23 mmol/L),and arginine(3 mmol/L),with the ratio of 1:0.43:0.12:1.60.In vitro experiments confirmed that this amino acid system enhances the expression of key genes involved in early embryonic development and improves in vitro embryo adhesion.Transcriptomic analysis of blastocysts suggested that candidate amino acid system enhances early embryo development by regulating early embryonic cell cycle and differentiation,as well as improving nutrient absorption.Furthermore,based on response surface methodology,400 sows were used to verify this amino acid system,substituting arginine with the more cost-effective N-carbamoyl glutamate(NCG),a precursor of arginine.The optimal dietary amino acid requirement was predicted to be 0.71%lysine,0.32%methionine,0.22%tryptophan,and 0.10%NCG for sows during early gestation.The optimized amino acid system ratio of the feed,derived from the peripheral release of essential amino acids,was found to be 1:0.45:0.13,which is largely consistent with the results obtained from the cell model optimization.Subsequently,we furtherly verified that this optimal dietary amino acid system significantly increased total litter size,live litter size and litter weight in sows.Conclusions In summary,we successfully established a dual-fluorescent high-throughput screening cell model for the efficient identification of potential nutrients that would promote embryo development and implantation.This innovative approach overcomes the limitations of traditional amino acid nutrition studies in sows,providing a more effective model for enhancing reproductive outcomes.展开更多
Due to their immunomodulatory function,mesenchymal stromal cells(MSCs)are a promising therapeutic with the potential to treat neuroinflammation associated with neurodegenerative diseases.This function is mediated by s...Due to their immunomodulatory function,mesenchymal stromal cells(MSCs)are a promising therapeutic with the potential to treat neuroinflammation associated with neurodegenerative diseases.This function is mediated by secreted extracellular vesicles(MSC-EVs).Despite established safety,MSC clinical translation has been unsuccessful due to inconsistent clinical outcomes resulting from functional heterogeneity.Current approaches to mitigate functional heterogeneity include‘priming’MSCs with inflammatory signals to enhance function.However,comprehensive evaluation of priming and its effects on MSC-EV function has not been performed.Furthermore,clinical translation of MSC-EV therapies requires significant manufacturing scale-up,yet few studies have investigated the effects of priming in bioreactors.As MSC morphology has been shown to predict their immunomodulatory function,we screened MSC morphological response to an array of priming signals and evaluated MSC-EV identity and potency in response to priming in flasks and bioreactors.We identified unique priming conditions corresponding to distinct morphologies.These conditions demonstrated a range of MSC-EV preparation quality and lipidome,allowing us to discover a novel MSC-EV manufacturing condition,as well as gain insight into potential mechanisms of MSC-EV microglia modulation.Our novel screening approach and application of priming to MSC-EV bioreactor manufacturing informs refinement of larger-scale manufacturing and enhancement of MSC-EV function.展开更多
While the human genome is pervasively transcribed,<2%of the human genome is transcribed into protein-coding mRNAs,leaving most of the transcripts as noncoding RNAs,such as microRNAs and long-noncoding RNAs(lncRNAs)...While the human genome is pervasively transcribed,<2%of the human genome is transcribed into protein-coding mRNAs,leaving most of the transcripts as noncoding RNAs,such as microRNAs and long-noncoding RNAs(lncRNAs),which are critical components of epigenetic regulation.lncRNAs are emerging as critical regulators of gene expression and genomic stability.However,it remains largely unknown about how lncRNAs are regulated.Here,we develop a highly sensitive and dynamic reporter that allows us to identify and/or monitor negative modulators of lncRNA transcript levels in a high throughput fashion.Specifically,we engineer a fluorescent fusion protein by fusing three copies of the PEST destruction domain of mouse ornithine decarboxylase(MODC)to the C-terminal end of the codon-optimized bilirubin-inducible fluorescent protein,designated as dBiFP,and show that the dBiFP protein is highly destabilized,compared with the commonly-used eGFP protein.We further demonstrate that the dBiFP signal is effectively down-regulated when the dBiFP and mouse lncRNA H19 chimeric transcript is silenced by mouse H19-specific siRNAs.Therefore,our results strongly suggest that the dBiFP fusion protein may serve as a sensitive and dynamic transcript reporter to monitor the inhibition of lncRNAs by microRNAs,synthetic regulatory RNA molecules,RNA binding proteins,and/or small molecule inhibitors so that novel and efficacious inhibitors targeting the epigenetic circuit can be discovered to treat human diseases such as cancer and other chronic disorders.展开更多
Alphaviruses,which contain a variety of mosquito-borne pathogens,are important pathogens of emerging/reemerging infectious diseases and potential biological weapons.Currently,no specific antiviral drugs are available ...Alphaviruses,which contain a variety of mosquito-borne pathogens,are important pathogens of emerging/reemerging infectious diseases and potential biological weapons.Currently,no specific antiviral drugs are available for the treatment of alphaviruses infection.For most highly pathogenic alphaviruses are classified as risk group-3 agents,the requirement of biosafety level 3(BSL-3)facilities limits the live virus-based antiviral study.To facilitate the antiviral development of alphaviruses,we developed a high throughput screening(HTS)platform based on a recombinant Semliki Forest virus(SFV)which can be manipulated in BSL-2 laboratory.Using the reverse genetics approach,the recombinant SFV and SFV reporter virus expressing eGFP(SFV-eGFP)were successfully rescued.The SFV-eGFP reporter virus exhibited robust eGFP expression and remained relatively stable after four passages in BHK-21 cells.Using a broad-spectrum alphavirus inhibitor ribavirin,we demonstrated that the SFV-eGFP can be used as an effective tool for antiviral study.The SFV-eGFP reporter virus-based HTS assay in a 96-well format was then established and optimized with a robust Z0 score.A section of reference compounds that inhibit highly pathogenic alphaviruses were used to validate that the SFV-eGFP reporter virus-based HTS assay enables rapid screening of potent broad-spectrum inhibitors of alphaviruses.This assay provides a safe and convenient platform for antiviral study of alphaviruses.展开更多
High throughput screening(HTS)is a widely used effective approach in genome-wide association and large scale protein expression studies,drug discovery,and biomedical imaging research.How to accurately identify candid...High throughput screening(HTS)is a widely used effective approach in genome-wide association and large scale protein expression studies,drug discovery,and biomedical imaging research.How to accurately identify candidate‘targets’or biologically meaningful features with a high degree of confidence has led to extensive statistical research in an effort to minimize both false-positive and false-negative rates.A large body of literature on this topic with in-depth statistical contents is available.We examine currently available statistical methods on HTS and aim to summarize some selected methods into a concise,easy-tofollow introduction for experimental biologists.展开更多
The utilization of phosphorescent metal complexes as emissive dopants for organic light-emitting diodes(OLEDs)has been the subject of intense research.Cyclometalated Pt(Ⅱ)complexes are particularly popular triplet em...The utilization of phosphorescent metal complexes as emissive dopants for organic light-emitting diodes(OLEDs)has been the subject of intense research.Cyclometalated Pt(Ⅱ)complexes are particularly popular triplet emitters due to their color-tunable emissions.To make them viable for practical applications as OLED emitters,it is essential to develop Pt(Ⅱ)complexes with high radiative decay rate constants(k_(r))and photoluminescence quantum yields(PLQY).To this end,an efficient and accurate prediction tool is highly desirable.In this work,we propose a general yet powerful protocol achieving metal complex generation,high throughput virtual screening(HTVS),and fast predictions with high accuracy.More than 3600 potential structures are generated in a synthesis-friendly manner.Moreover,three HTVS-machine learning(ML)models are established using different algorithms with carefully designed features that are suitable for metal complexes.Specifically,30 potential candidates are filtered out by HTVS-ML models with a three-tier screening rule and put into accurate predictions with experimental calibrationΔ-learning method.The highly accurate prediction approach further reduces the stress of experiments and inspires greater confidence in identifying the most promising complexes as excellent emitters.As a result,12 promising complexes(k_(r)>10^(5) s^(−1) and PLQY>0.6)with the same superior core structures are confirmed from over 3600 Pt-complexes.Experiments revealed that two very close complexes have excellent emission properties and are consistent with the prediction results,providing strong evidence for the efficacy of the proposed protocol.We expect this protocol will become a valuable tool,expediting the rational design and rapid development of novel OLED materials with desired properties.展开更多
Cardiac fibrosis has emerged as the primary cause of morbidity,disability,and even mortality in numerous nations.In light of the advancements in precision medicine strategies,substantial attention has been directed to...Cardiac fibrosis has emerged as the primary cause of morbidity,disability,and even mortality in numerous nations.In light of the advancements in precision medicine strategies,substantial attention has been directed toward the development of a practical and precise drug screening platform customized for individual patients.In this study,we introduce a biomimetic cardiac fibrosis-on-a-chip incorporating structural color hydrogels(SCHs)to enable optical high-throughput drug screening.By cocultivating a substantial proportion of cardiac fibroblasts(CFBs)with cardiomyocytes on the SCH,this biomimetic fibrotic microtissue successfully replicates the structural components and biomechanical properties associated with cardiac fibrosis.More importantly,the structural color shift observed in the SCH can be indicative of cardiac contraction and relaxation,making it a valuable tool for evaluating fibrosis progression.By incorporating such fibrotic microtissue into a microfluidic gradient chip,we develop a biomimetic optical cardiac fibrosis-on-a-chip platform that accurately and efficiently screens potential anti-fibrotic drugs.These characteristics suggest that this microphysiological platform possesses the capability to establish a preclinical framework for screening cardiac drugs,and may even contribute to the advancement ofprecisionmedicine.展开更多
Traditional Chinese medicine(TCM) has been widely used in China and other Asia countries for thousands of years to treat or prevent human diseases. Chinese herbal medicine, one of the most important components of TCM,...Traditional Chinese medicine(TCM) has been widely used in China and other Asia countries for thousands of years to treat or prevent human diseases. Chinese herbal medicine, one of the most important components of TCM, has unique diversities in chemical components, and thus results in a wide range of biological activities. However, pharmaceutical industry is facing a major challenge to develop a large population of novel natural products and drugs, and considerable efforts have not resulted in highvolume of novel drug discovery and productivity. At present, increasing attention has been paid to Chinese herb medicine modernization in combination with the cutting-age technologies of drug discovery, especially the high throughput selection. High content imaging is an image-based high throughput screening method by using automated microscopy and image analysis software to capture and analyze phenotypes at a large scale to investigate multiple biological features simultaneously in the biological complex. Here, we described the pipeline of the state-of-the-art high content imaging technology, summarized the applications of the high content imaging technology in drug discovery from traditional Chinese herbal medicine, and finally discussed the current challenges and future perspectives for development of high throughput image-based screening technology in novel drug research and discovery.展开更多
OBJECTIVE Dopamine receptors(DRs) are involved in the development and treatment of many neuropsychiatric disorders.Currently available dopaminergic drugs modulate both DRD2 and DRD3,leading to side effects and uncerta...OBJECTIVE Dopamine receptors(DRs) are involved in the development and treatment of many neuropsychiatric disorders.Currently available dopaminergic drugs modulate both DRD2 and DRD3,leading to side effects and uncertainty as to the roles each DR subtype plays physiologically.Our lab employed high throughput screening paradigms to discover highly selective modulators for the DRD3.METHODS The NIH Molecular Libraries Program 400,000 + small molecule library was screened using the Discove Rx Path Hunter?β-arrestin assay for compounds that activate the DRD3 without effects on the DRD2.Confirmation and counter-screens assessed selectivity and mechanisms of action.We identified 62 potential agonists,and chose the most promising to perform a structure-activity relationship(SAR) study to increase potency while maintaining selectivity.The lead compound identified through this process,ML417,was also characterized using bioluminescence resonance energy transfer(BRET)-based β-arrestin recruitment and G-protein activation assays as well as p-ERK assays.Potential neuroprotective properties of this compound were assessed using a SHSY5 Y neuronal cell model.RESULTS ML417 displays potent,DRD3-selective agonist activity in multiple functional assays.Binding and functional GPCR screens(>165 receptors) show ML417 has limited cross-reactivity with other GPCRs.ML417 also displays superior(compared to the reference compound pramipexole),dose-dependent protection against a decrease in neurite length induced by 10 μmol·L^(-1) of the neurotoxin,6-hydroxydopamine,in the SHSY5 Y cell model.CONCLUSION We have discovered and characterized ML417,a potent and highly selective DRD3 agonist.This compound will be useful as a research tool,and may prove useful as a therapeutic drug lead.展开更多
Carbon-supported transition metal single atoms are promising oxygen reduction reaction(ORR)electrocatalyst.Since there are many types of carbon supports and transition metals,the accurate prediction of the components ...Carbon-supported transition metal single atoms are promising oxygen reduction reaction(ORR)electrocatalyst.Since there are many types of carbon supports and transition metals,the accurate prediction of the components with high activity through theoretical calculations can greatly save experimental time and costs.In this work,the ORR catalytic properties of 180 types single-atom catalysts(SACs)composed of the eight representative carbon-based substrates(graphdiyne,C_(2)N,C_(3)N_(4),phthalocyanine,C-coordination graphene,N-coordination graphene,covalent organic frameworks and metal-organic frameworks)and 3d,4d,and 5d transition metal elements are investigated by density functional theory(DFT).The adsorption free energy of OH^(*) is proved a universal descriptor capable of accurately prediction of the ORR catalytic activity.It is found that the oxygen reduction reaction overpotentials of all the researched SACs follow one volcano shape very well with the adsorption free energy of OH^(*).Phthalocyanine,N-coordination graphene and metal-organic frameworks stand out as the promising supports for single metal atom due to the relatively lower overpotentials.Notably,the Co-doped metal-organic frameworks,Ir-doped phthalocyanine,Co-doped N-coordination graphene,Co-doped graphdiyne and Rh-doped phthalocyanine show extremely low overpotentials comparable to that of Pt(111).The study provides a guideline for design and selection of carbon-supported SACs toward oxygen reduction reaction.展开更多
CONSPECTUS:In this Account,we present a comprehensive overview of recent advancements in applying data-driven combinatorial design for developing novel highenergy-density materials.Initially,we outline the progress in...CONSPECTUS:In this Account,we present a comprehensive overview of recent advancements in applying data-driven combinatorial design for developing novel highenergy-density materials.Initially,we outline the progress in energetic materials(EMs)development within the framework of the four scientific paradigms,with particular emphasis on the opportunities afforded by the evolution of computer and data science,which has propelled the theoretical design of EMs into a new era of data-driven development.We then discuss the structural features of typical EMs such as TNT,RDX,HMX,and CL-20,namely,a“scaffolds+functional groups”characteristic,underscoring the efficacy of the combinatorial design approach in constructing novel EMs.It has been discerned that those modifications to the scaffolds are the primary driving force behind the enhancement of EMs’properties.Subsequently,we introduce three distinct data-driven design strategies for EMs,each with a different approach to scaffold construction.These strategies are as follows:(1)the known scaffold strategy to identify fused cyclic scaffolds containing oxazole or oxadiazole structures from other fields via database screening and employ a high-throughput combinatorial approach with functional groups to design oxazole(and oxadiazole)-based fused cyclic EMs;(2)the semiknown scaffold strategy to construct semiknown scaffolds by integrating known scaffolds and realize the design of bridged cyclic EMs through a high-throughput combination of functional groups;(3)the unknown scaffold strategy to build caged structural models for quantitative characterization,high-throughput screening caged scaffolds from the database,construct unknown caged scaffolds by substituting atoms or substructures,and combine functional groups to design zero oxygen balance caged EMs.Employing the proposed strategies,the design capacity for EMs reaches an impressive scale of 10^(7) molecules,significantly increasing the probability of obtaining high-performance EMs.Furthermore,the incorporation of property assessment models based on machine learning and density functional theory has achieved a balance between computational accuracy and computational speed.Statistical analysis of the virtual screening has revealed the advantages of bicyclic tri-and tetrasubstituted position scaffolds in the construction of high-energy and easily synthesizable fused cyclic EMs.Additionally,the proposed strategies have been successfully applied to design multifunctional modular energetic materials,resulting in the successful synthesis of three target compounds,validating the effectiveness of data-driven combinatorial design approaches.Lastly,we discuss the current state of high-throughput combinatorial design and,in light of the multifaceted criteria required for the design of EMs,explore the feasibility of multiobjective optimization methods such as Pareto optimization.Moreover,we envision the application of generative models in the subsequent design and development of EMs.We anticipate that this Account will provide valuable insights into the theoretical design of EMs,and we envision the integration of new technologies and methodologies that could play an increasingly significant role in the future discovery of EMs.展开更多
In silico computational methods have been widely utilized to study enzyme catalytic mechanisms and design enzyme performance,including molecular docking,molecular dynamics,quantum mechanics,and multiscale QM/MM approa...In silico computational methods have been widely utilized to study enzyme catalytic mechanisms and design enzyme performance,including molecular docking,molecular dynamics,quantum mechanics,and multiscale QM/MM approaches.However,the manual operation associated with these methods poses challenges for simulating enzymes and enzyme variants in a high‐throughput manner.We developed the NAC4ED,a high‐throughput enzyme mutagenesis computational platform based on the“near‐attack conformation”design strategy for enzyme catalysis substrates.This platform circumvents the complex calculations involved in transition‐state searching by representing enzyme catalytic mechanisms with parameters derived from near‐attack conformations.NAC4ED enables the automated,high‐throughput,and systematic computation of enzyme mutants,including protein model construction,complex structure acquisition,molecular dynamics simulation,and analysis of active conformation populations.Validation of the accuracy of NAC4ED demonstrated a prediction accuracy of 92.5%for 40 mutations,showing strong consistency between the computational predictions and experimental results.The time required for automated determination of a single enzyme mutant using NAC4ED is 1/764th of that needed for experimental methods.This has significantly enhanced the efficiency of predicting enzyme mutations,leading to revolutionary breakthroughs in improving the performance of high‐throughput screening of enzyme variants.NAC4ED facilitates the efficient generation of a large amount of annotated data,providing high‐quality data for statistical modeling and machine learning.展开更多
Current in vitro assays for the activity of HIV-RT(reverse transcriptase)require radio-labeled or chemically modified nucleotides to detect reaction products.However,these assays are inherently end-point measurements ...Current in vitro assays for the activity of HIV-RT(reverse transcriptase)require radio-labeled or chemically modified nucleotides to detect reaction products.However,these assays are inherently end-point measurements and labor intensive.Here we describe a novel non-radioactive assay based on the principle of pyrosequencing coupledenzyme system to monitor the activity of HIV-RT by indirectly measuring the release of pyrophosphate(PPi),which is generated during nascent strand synthesis.The results show that our assay could monitor HIV-RT activity with high sensitivity and is suitable for rapid highthroughput drug screening targeting anti-HIV therapies due to its high speed and convenience.Moreover,this assay can be used to measure primase activity in an easy and sensitive manner,which suggests that this novel approach could be wildly used to analyze the activity of PPi-generated and ATP-free enzyme reactions.展开更多
An estimated 130 million people worldwide are chronically infected with hepatitis C virus (HCV) making it a leading cause of liver disease worldwide. Because the currently available therapy of pegylated interferon-alp...An estimated 130 million people worldwide are chronically infected with hepatitis C virus (HCV) making it a leading cause of liver disease worldwide. Because the currently available therapy of pegylated interferon-alpha and ribavirin is only effective in a subset of patients, the development of new HCV antivirals is a healthcare imperative. This review discusses the experimental models available for HCV antiviral drug research, recent advances in HCV antiviral drug development, as well as active research being pursued to facilitate development of new HCV-specific therapeutics.展开更多
基金supported by the National Natural Science Foundation of China(31972576)the Beijing Natural Science Foundation(6202004)+2 种基金the Special Program on Science and Technology Innovation Capacity Building of BAAFS(KJCX20180414 and KJCX201914)the USDA National Institute of Food and Agriculture(2018-68003-27462 and 2018-33610-28252)the Oklahoma Center for the Advancement of Science and Technology(AR19-27)。
文摘Background:In-feed antibiotics are being phased out in livestock production worldwide.Alternatives to antibiotics are urgently needed to maintain animal health and production performance.Host defense peptides(HDPs)are known for their broad-spectrum antimicrobial and immunomodulatory capabilities.Enhancing the synthesis of endogenous HDPs represents a promising antibiotic alternative strategy to disease control and prevention.Methods:To identify natural products with an ability to stimulate the synthesis of endogenous HDPs,we performed a high-throughput screening of 1261 natural products using a newly-established stable luciferase reporter cell line known as IPEC-J2/pBD3-luc.The ability of the hit compounds to induce HDP genes in porcine IPEC-J2 intestinal epithelial cells,3D4/31 macrophages,and jejunal explants were verified using RT-qPCR.Augmentation of the antibacterial activity of porcine 3D4/31 macrophages against a Gram-negative bacterium(enterotoxigenic E.coli)and a Gram-positive bacterium(Staphylococcus aureus)were further confirmed with four selected HDP-inducing compounds.Results:A total of 48 natural products with a minimum Z-score of 2.0 were identified after high-throughput screening,with 21 compounds giving at least 2-fold increase in luciferase activity in a follow-up dose-response experiment.Xanthohumol and deoxyshikonin were further found to be the most potent in inducing pBD3 mRNA expression,showing a minimum 10-fold increase in IPEC-J2,3D4/31 cells,and jejunal explants.Other compounds such as isorhapontigenin and calycosin also enhanced pBD3 mRNA expression by at least 10-fold in both IPEC-J2 cells and jejunal explants,but not 3D4/31 cells.In addition to pBD3,other porcine HDP genes such as pBD2,PG1-5,and pEP2C were induced to different magnitudes by xanthohumol,deoxyshikonin,isorhapontigenin,and calycosin,although clear gene-and cell type-specific patterns of regulation were observed.Desirably,these four compounds had a minimum effect on the expression of several representative inflammatory cytokine genes.Furthermore,when used at HDP-inducing concentrations,these compounds showed no obvious direct antibacterial activity,but significantly augmented the antibacterial activity of 3D4/31 macrophages(P<0.05)against both Gram-negative and Gram-positive bacteria.Conclusions:Our results indicate that these newly-identified natural HDP-inducing compounds have the potential to be developed as novel alternatives to antibiotics for prophylactic and therapeutic treatment of infectious diseases in livestock production.
基金financially supported by the National Key Research and Development Program of China (2018YFA0702002)the Beijing Natural Science Foundation (Z210016)the National Natural Science Foundation of China (21935001)。
文摘Single atomic catalysts(SACs),especially metal-nitrogen doped carbon(M-NC)catalysts,have been extensively explored for the electrochemical oxygen reduction reaction(ORR),owing to their high activity and atomic utilization efficiency.However,there is still a lack of systematic screening and optimization of local structures surrounding active centers of SACs for ORR as the local coordination has an essential impact on their electronic structures and catalytic performance.Herein,we systematic study the ORR catalytic performance of M-NC SACs with different central metals and environmental atoms in the first and second coordination sphere by using density functional theory(DFT)calculation and machine learning(ML).The geometric and electronic informed overpotential model(GEIOM)based on random forest algorithm showed the highest accuracy,and its R^(2) and root mean square errors(RMSE)were 0.96 and 0.21,respectively.30 potential high-performance catalysts were screened out by GEIOM,and the RMSE of the predicted result was only 0.12 V.This work not only helps us fast screen high-performance catalysts,but also provides a low-cost way to improve the accuracy of ML models.
基金the Start- up Fund for Returned Overseas Scholars from Northeast Normal U niversity,National ScienceFund for Distinguished Young Scholars (No. 30 32 5 0 11) ,Distinguished Young Scholars Fund of Jilin Province(No.2 0 0 30 112 ) ,Excellent Young Teachers
文摘A stably transfected CHO cell line coexpressing G551D-CFTR and iodide-sensitive yellow fluorescent protein mutant EYFP-H148Q-I152L was successfully established and used as assay model to identify small-molecule activators of G551D-CFTR chloride channel from 100000 diverse combinatorial compounds by high throughput screening on a customized Beckman robotic system. A bicyclooctane compound was identified to activate G551D-CFTR chloride channel with high-affinity(K d=1.8 μmol/L). The activity of the bicyclooctane compound is G551D-CFTR-specific, reversible and non-toxic. The G551D-CFTR activator may be useful as a tool to study the mutant G551D-CFTR chloride channel structure and transport properties and as a candidate drug to cure cystic fibrosis caused by G551D-CFTR mutation.
文摘A novel solid phase organic synthesis resin was synthesized for combinatorial high-throughput screening,which based on FTIR spectra self-encoding functional resin technology. A new deconvolution strategy termed position encoding deconvolution had illustrated and was compared with some popular combinatorial deconvolution strategies in efficiency and information content. The mimic high throughput screening of hexapeptide library successfully proved the applying of the self-encoding functional resin technology and the position encoding deconvolution strategy.
基金the Start- up Fund for Returned Overseas Scholars from Northeast Normal U niversity,National ScienceFund for Distinguished Young Scholars(No.30 32 5 0 11) ,Distinguished Young Scholars Fund of Jilin Province(No.2 0 0 30 112 ) ,Excellent Young Teachers Pr
文摘The glycine-to-aspartic acid missense mutation at the codon 551(G551D) of the cystic fibrosis transmembrane conductance regulator(CFTR) is one of the five most frequent cystic fibrosis(CF) mutations associated with a severe CF phenotype. To explore the feasibility of pharmacological correction of disrupted activation of CFTR chloride channel caused by G551D mutation, we developed a halide-sensitive fluorescence miniassay for G551D-CFTR in Fisher rat thyroid(FRT) epithelial cells for the discovery of novel activators of G551D-CFTR. A class of bicyclooctane small molecule compounds that efficiently stimulate G551D-CFTR chloride channel activity was identified by high throughput screening via the FRT cell-based assay. This class of compounds selectively activates G551D-CFTR with a high affinity, whereas little effect of the compounds on wildtype CFTR can be seen. The discovery of a class of bicyclooctane G551D-CFTR activators will permit the analysis of structure-activity relationship of the compounds to identify ideal leads for in vivo therapeutic studies.
文摘In this article, we introduce the system of high throughput screening (HTS). Its role in new drug study and current development is described. The relationship between research achievements of genome study and new type screening model of new drugs is emphasized. The personal opinions of current problems about HTS study in China are raised.
基金supported by National Natural Science Foundation of China (32172747 and 32425052)
文摘Background Early embryo development plays a pivotal role in determining pregnancy outcomes,postnatal development,and lifelong health.Therefore,the strategic selection of functional nutrients to enhance embryo development is of paramount importance.In this study,we established a stable porcine trophectoderm cell line expressing dual fluorescent reporter genes driven by the CDX2 and TEAD4 gene promoter segments using lentiviral transfection.Results Three amino acid metabolites—kynurenic acid,taurine,and tryptamine—met the minimum z-score criteria of 2.0 for both luciferase and Renilla luciferase activities and were initially identified as potential metabolites for embryo development,with their beneficial effects validated by qPCR.Given that the identified metabolites are closely related to methionine,arginine,and tryptophan,we selected these three amino acids,using lysine as a standard,and employed response surface methodology combined with our high-throughput screening cell model to efficiently screen and optimize amino acid combination conducive to early embryo development.The optimized candidate amino acid system included lysine(1.87 mmol/L),methionine(0.82 mmol/L),tryptophan(0.23 mmol/L),and arginine(3 mmol/L),with the ratio of 1:0.43:0.12:1.60.In vitro experiments confirmed that this amino acid system enhances the expression of key genes involved in early embryonic development and improves in vitro embryo adhesion.Transcriptomic analysis of blastocysts suggested that candidate amino acid system enhances early embryo development by regulating early embryonic cell cycle and differentiation,as well as improving nutrient absorption.Furthermore,based on response surface methodology,400 sows were used to verify this amino acid system,substituting arginine with the more cost-effective N-carbamoyl glutamate(NCG),a precursor of arginine.The optimal dietary amino acid requirement was predicted to be 0.71%lysine,0.32%methionine,0.22%tryptophan,and 0.10%NCG for sows during early gestation.The optimized amino acid system ratio of the feed,derived from the peripheral release of essential amino acids,was found to be 1:0.45:0.13,which is largely consistent with the results obtained from the cell model optimization.Subsequently,we furtherly verified that this optimal dietary amino acid system significantly increased total litter size,live litter size and litter weight in sows.Conclusions In summary,we successfully established a dual-fluorescent high-throughput screening cell model for the efficient identification of potential nutrients that would promote embryo development and implantation.This innovative approach overcomes the limitations of traditional amino acid nutrition studies in sows,providing a more effective model for enhancing reproductive outcomes.
基金supported by the National Science Foundation under BIO-2036968,cooperative agreement EEC-1648035(RAM),and UGA Research Foundation startup funds(KMH)supported in part by the Glycosciences Training Grant Program(NIH T32 GM145467)。
文摘Due to their immunomodulatory function,mesenchymal stromal cells(MSCs)are a promising therapeutic with the potential to treat neuroinflammation associated with neurodegenerative diseases.This function is mediated by secreted extracellular vesicles(MSC-EVs).Despite established safety,MSC clinical translation has been unsuccessful due to inconsistent clinical outcomes resulting from functional heterogeneity.Current approaches to mitigate functional heterogeneity include‘priming’MSCs with inflammatory signals to enhance function.However,comprehensive evaluation of priming and its effects on MSC-EV function has not been performed.Furthermore,clinical translation of MSC-EV therapies requires significant manufacturing scale-up,yet few studies have investigated the effects of priming in bioreactors.As MSC morphology has been shown to predict their immunomodulatory function,we screened MSC morphological response to an array of priming signals and evaluated MSC-EV identity and potency in response to priming in flasks and bioreactors.We identified unique priming conditions corresponding to distinct morphologies.These conditions demonstrated a range of MSC-EV preparation quality and lipidome,allowing us to discover a novel MSC-EV manufacturing condition,as well as gain insight into potential mechanisms of MSC-EV microglia modulation.Our novel screening approach and application of priming to MSC-EV bioreactor manufacturing informs refinement of larger-scale manufacturing and enhancement of MSC-EV function.
基金The reported work was supported in part by research grants from the National Institutes of Health(AT004418,DE020140 to TCH and RRR)the US Department of Defense(OR130096 to JMW)+5 种基金the Scoliosis Research Society(TCH and MJL)the National Key Research and Development Program of China(2016YFC1000803 and 2011CB707906 to TCH)the National Natural Science Foundation of China(#81201916 to XW)ZZ was a recipient of protectorate fellowship from China Scholarship CouncilThis project was also supported in part by The University of Chicago Cancer Center Support Grant(P30CA014599)the National Center for Advancing Translational Sciences of the National Institutes of Health through Grant Number UL1 TR000430.
文摘While the human genome is pervasively transcribed,<2%of the human genome is transcribed into protein-coding mRNAs,leaving most of the transcripts as noncoding RNAs,such as microRNAs and long-noncoding RNAs(lncRNAs),which are critical components of epigenetic regulation.lncRNAs are emerging as critical regulators of gene expression and genomic stability.However,it remains largely unknown about how lncRNAs are regulated.Here,we develop a highly sensitive and dynamic reporter that allows us to identify and/or monitor negative modulators of lncRNA transcript levels in a high throughput fashion.Specifically,we engineer a fluorescent fusion protein by fusing three copies of the PEST destruction domain of mouse ornithine decarboxylase(MODC)to the C-terminal end of the codon-optimized bilirubin-inducible fluorescent protein,designated as dBiFP,and show that the dBiFP protein is highly destabilized,compared with the commonly-used eGFP protein.We further demonstrate that the dBiFP signal is effectively down-regulated when the dBiFP and mouse lncRNA H19 chimeric transcript is silenced by mouse H19-specific siRNAs.Therefore,our results strongly suggest that the dBiFP fusion protein may serve as a sensitive and dynamic transcript reporter to monitor the inhibition of lncRNAs by microRNAs,synthetic regulatory RNA molecules,RNA binding proteins,and/or small molecule inhibitors so that novel and efficacious inhibitors targeting the epigenetic circuit can be discovered to treat human diseases such as cancer and other chronic disorders.
基金supported by the Creative Research Group Program of Natural Science Foundation of Hubei Province (2022CFA021)National Natural Science Foundation of China (81702005).
文摘Alphaviruses,which contain a variety of mosquito-borne pathogens,are important pathogens of emerging/reemerging infectious diseases and potential biological weapons.Currently,no specific antiviral drugs are available for the treatment of alphaviruses infection.For most highly pathogenic alphaviruses are classified as risk group-3 agents,the requirement of biosafety level 3(BSL-3)facilities limits the live virus-based antiviral study.To facilitate the antiviral development of alphaviruses,we developed a high throughput screening(HTS)platform based on a recombinant Semliki Forest virus(SFV)which can be manipulated in BSL-2 laboratory.Using the reverse genetics approach,the recombinant SFV and SFV reporter virus expressing eGFP(SFV-eGFP)were successfully rescued.The SFV-eGFP reporter virus exhibited robust eGFP expression and remained relatively stable after four passages in BHK-21 cells.Using a broad-spectrum alphavirus inhibitor ribavirin,we demonstrated that the SFV-eGFP can be used as an effective tool for antiviral study.The SFV-eGFP reporter virus-based HTS assay in a 96-well format was then established and optimized with a robust Z0 score.A section of reference compounds that inhibit highly pathogenic alphaviruses were used to validate that the SFV-eGFP reporter virus-based HTS assay enables rapid screening of potent broad-spectrum inhibitors of alphaviruses.This assay provides a safe and convenient platform for antiviral study of alphaviruses.
基金This work is supported in part by NIH P50-CA70907,NIH U24CA126608,and NASA NNJ05HD36G.
文摘High throughput screening(HTS)is a widely used effective approach in genome-wide association and large scale protein expression studies,drug discovery,and biomedical imaging research.How to accurately identify candidate‘targets’or biologically meaningful features with a high degree of confidence has led to extensive statistical research in an effort to minimize both false-positive and false-negative rates.A large body of literature on this topic with in-depth statistical contents is available.We examine currently available statistical methods on HTS and aim to summarize some selected methods into a concise,easy-tofollow introduction for experimental biologists.
基金supported by the RGC General Research Fund under Grant No.17309620Hong Kong Quantum AI Lab Limited and Air@InnoHK of Hong Kong Government+4 种基金the support from National Natural Science Foundation of China(Grant Nos.22073007 and 22473022)Shenzhen Basic Research Key Project Fund(Grant No.JCYJ20220818103200001)National Natural Science Foundation of China(No.22273010)Department of Science and Technology of Jilin Province(20210402075GH)C-M C and F-F H acknowledge Guangdong Major Project of Basic and Applied Basic Research(Grant No.2019B030302009).
文摘The utilization of phosphorescent metal complexes as emissive dopants for organic light-emitting diodes(OLEDs)has been the subject of intense research.Cyclometalated Pt(Ⅱ)complexes are particularly popular triplet emitters due to their color-tunable emissions.To make them viable for practical applications as OLED emitters,it is essential to develop Pt(Ⅱ)complexes with high radiative decay rate constants(k_(r))and photoluminescence quantum yields(PLQY).To this end,an efficient and accurate prediction tool is highly desirable.In this work,we propose a general yet powerful protocol achieving metal complex generation,high throughput virtual screening(HTVS),and fast predictions with high accuracy.More than 3600 potential structures are generated in a synthesis-friendly manner.Moreover,three HTVS-machine learning(ML)models are established using different algorithms with carefully designed features that are suitable for metal complexes.Specifically,30 potential candidates are filtered out by HTVS-ML models with a three-tier screening rule and put into accurate predictions with experimental calibrationΔ-learning method.The highly accurate prediction approach further reduces the stress of experiments and inspires greater confidence in identifying the most promising complexes as excellent emitters.As a result,12 promising complexes(k_(r)>10^(5) s^(−1) and PLQY>0.6)with the same superior core structures are confirmed from over 3600 Pt-complexes.Experiments revealed that two very close complexes have excellent emission properties and are consistent with the prediction results,providing strong evidence for the efficacy of the proposed protocol.We expect this protocol will become a valuable tool,expediting the rational design and rapid development of novel OLED materials with desired properties.
基金supported by the National Key Research and Development Program of China(2020YFA0710800 and 2020YFA0908200)the Key Program of the National Natural Science Foundation of China(81930043 and 82330055)+2 种基金the National Natural Science Foundation of China(T2225003,82001719,52073060,and 61927805)the Nanjing Medical Science and Technique Development Foundation(ZKX21019)the Clinical Trials from Nanjing Drum Tower Hospital(2022-LCYJ-ZD-01).
文摘Cardiac fibrosis has emerged as the primary cause of morbidity,disability,and even mortality in numerous nations.In light of the advancements in precision medicine strategies,substantial attention has been directed toward the development of a practical and precise drug screening platform customized for individual patients.In this study,we introduce a biomimetic cardiac fibrosis-on-a-chip incorporating structural color hydrogels(SCHs)to enable optical high-throughput drug screening.By cocultivating a substantial proportion of cardiac fibroblasts(CFBs)with cardiomyocytes on the SCH,this biomimetic fibrotic microtissue successfully replicates the structural components and biomechanical properties associated with cardiac fibrosis.More importantly,the structural color shift observed in the SCH can be indicative of cardiac contraction and relaxation,making it a valuable tool for evaluating fibrosis progression.By incorporating such fibrotic microtissue into a microfluidic gradient chip,we develop a biomimetic optical cardiac fibrosis-on-a-chip platform that accurately and efficiently screens potential anti-fibrotic drugs.These characteristics suggest that this microphysiological platform possesses the capability to establish a preclinical framework for screening cardiac drugs,and may even contribute to the advancement ofprecisionmedicine.
文摘Traditional Chinese medicine(TCM) has been widely used in China and other Asia countries for thousands of years to treat or prevent human diseases. Chinese herbal medicine, one of the most important components of TCM, has unique diversities in chemical components, and thus results in a wide range of biological activities. However, pharmaceutical industry is facing a major challenge to develop a large population of novel natural products and drugs, and considerable efforts have not resulted in highvolume of novel drug discovery and productivity. At present, increasing attention has been paid to Chinese herb medicine modernization in combination with the cutting-age technologies of drug discovery, especially the high throughput selection. High content imaging is an image-based high throughput screening method by using automated microscopy and image analysis software to capture and analyze phenotypes at a large scale to investigate multiple biological features simultaneously in the biological complex. Here, we described the pipeline of the state-of-the-art high content imaging technology, summarized the applications of the high content imaging technology in drug discovery from traditional Chinese herbal medicine, and finally discussed the current challenges and future perspectives for development of high throughput image-based screening technology in novel drug research and discovery.
基金supported by National Institute of Neurological Disorders and Stroke Intramural Research Program
文摘OBJECTIVE Dopamine receptors(DRs) are involved in the development and treatment of many neuropsychiatric disorders.Currently available dopaminergic drugs modulate both DRD2 and DRD3,leading to side effects and uncertainty as to the roles each DR subtype plays physiologically.Our lab employed high throughput screening paradigms to discover highly selective modulators for the DRD3.METHODS The NIH Molecular Libraries Program 400,000 + small molecule library was screened using the Discove Rx Path Hunter?β-arrestin assay for compounds that activate the DRD3 without effects on the DRD2.Confirmation and counter-screens assessed selectivity and mechanisms of action.We identified 62 potential agonists,and chose the most promising to perform a structure-activity relationship(SAR) study to increase potency while maintaining selectivity.The lead compound identified through this process,ML417,was also characterized using bioluminescence resonance energy transfer(BRET)-based β-arrestin recruitment and G-protein activation assays as well as p-ERK assays.Potential neuroprotective properties of this compound were assessed using a SHSY5 Y neuronal cell model.RESULTS ML417 displays potent,DRD3-selective agonist activity in multiple functional assays.Binding and functional GPCR screens(>165 receptors) show ML417 has limited cross-reactivity with other GPCRs.ML417 also displays superior(compared to the reference compound pramipexole),dose-dependent protection against a decrease in neurite length induced by 10 μmol·L^(-1) of the neurotoxin,6-hydroxydopamine,in the SHSY5 Y cell model.CONCLUSION We have discovered and characterized ML417,a potent and highly selective DRD3 agonist.This compound will be useful as a research tool,and may prove useful as a therapeutic drug lead.
基金supported by the National Natural Science Foundation of China(No.51371017)。
文摘Carbon-supported transition metal single atoms are promising oxygen reduction reaction(ORR)electrocatalyst.Since there are many types of carbon supports and transition metals,the accurate prediction of the components with high activity through theoretical calculations can greatly save experimental time and costs.In this work,the ORR catalytic properties of 180 types single-atom catalysts(SACs)composed of the eight representative carbon-based substrates(graphdiyne,C_(2)N,C_(3)N_(4),phthalocyanine,C-coordination graphene,N-coordination graphene,covalent organic frameworks and metal-organic frameworks)and 3d,4d,and 5d transition metal elements are investigated by density functional theory(DFT).The adsorption free energy of OH^(*) is proved a universal descriptor capable of accurately prediction of the ORR catalytic activity.It is found that the oxygen reduction reaction overpotentials of all the researched SACs follow one volcano shape very well with the adsorption free energy of OH^(*).Phthalocyanine,N-coordination graphene and metal-organic frameworks stand out as the promising supports for single metal atom due to the relatively lower overpotentials.Notably,the Co-doped metal-organic frameworks,Ir-doped phthalocyanine,Co-doped N-coordination graphene,Co-doped graphdiyne and Rh-doped phthalocyanine show extremely low overpotentials comparable to that of Pt(111).The study provides a guideline for design and selection of carbon-supported SACs toward oxygen reduction reaction.
基金support from National Natural Science Foundation of China(Nos.22275145 and 21875184)Natural Science Foundation of Shaanxi Province(Nos.2022JC-10 and 2024JC-YBQN-0112).
文摘CONSPECTUS:In this Account,we present a comprehensive overview of recent advancements in applying data-driven combinatorial design for developing novel highenergy-density materials.Initially,we outline the progress in energetic materials(EMs)development within the framework of the four scientific paradigms,with particular emphasis on the opportunities afforded by the evolution of computer and data science,which has propelled the theoretical design of EMs into a new era of data-driven development.We then discuss the structural features of typical EMs such as TNT,RDX,HMX,and CL-20,namely,a“scaffolds+functional groups”characteristic,underscoring the efficacy of the combinatorial design approach in constructing novel EMs.It has been discerned that those modifications to the scaffolds are the primary driving force behind the enhancement of EMs’properties.Subsequently,we introduce three distinct data-driven design strategies for EMs,each with a different approach to scaffold construction.These strategies are as follows:(1)the known scaffold strategy to identify fused cyclic scaffolds containing oxazole or oxadiazole structures from other fields via database screening and employ a high-throughput combinatorial approach with functional groups to design oxazole(and oxadiazole)-based fused cyclic EMs;(2)the semiknown scaffold strategy to construct semiknown scaffolds by integrating known scaffolds and realize the design of bridged cyclic EMs through a high-throughput combination of functional groups;(3)the unknown scaffold strategy to build caged structural models for quantitative characterization,high-throughput screening caged scaffolds from the database,construct unknown caged scaffolds by substituting atoms or substructures,and combine functional groups to design zero oxygen balance caged EMs.Employing the proposed strategies,the design capacity for EMs reaches an impressive scale of 10^(7) molecules,significantly increasing the probability of obtaining high-performance EMs.Furthermore,the incorporation of property assessment models based on machine learning and density functional theory has achieved a balance between computational accuracy and computational speed.Statistical analysis of the virtual screening has revealed the advantages of bicyclic tri-and tetrasubstituted position scaffolds in the construction of high-energy and easily synthesizable fused cyclic EMs.Additionally,the proposed strategies have been successfully applied to design multifunctional modular energetic materials,resulting in the successful synthesis of three target compounds,validating the effectiveness of data-driven combinatorial design approaches.Lastly,we discuss the current state of high-throughput combinatorial design and,in light of the multifaceted criteria required for the design of EMs,explore the feasibility of multiobjective optimization methods such as Pareto optimization.Moreover,we envision the application of generative models in the subsequent design and development of EMs.We anticipate that this Account will provide valuable insights into the theoretical design of EMs,and we envision the integration of new technologies and methodologies that could play an increasingly significant role in the future discovery of EMs.
基金supported by the National Key R&D Program of China(grant No.2019YFA0905200)Science and Technology Commission of Shanghai Municipality(grant No.23HC1400500)+1 种基金Agricultural Science and Technology Innovation System of Shanghai,China(grant No.T2023217)Shanghai Frontiers Science Center of Molecule Intelligent Syntheses.
文摘In silico computational methods have been widely utilized to study enzyme catalytic mechanisms and design enzyme performance,including molecular docking,molecular dynamics,quantum mechanics,and multiscale QM/MM approaches.However,the manual operation associated with these methods poses challenges for simulating enzymes and enzyme variants in a high‐throughput manner.We developed the NAC4ED,a high‐throughput enzyme mutagenesis computational platform based on the“near‐attack conformation”design strategy for enzyme catalysis substrates.This platform circumvents the complex calculations involved in transition‐state searching by representing enzyme catalytic mechanisms with parameters derived from near‐attack conformations.NAC4ED enables the automated,high‐throughput,and systematic computation of enzyme mutants,including protein model construction,complex structure acquisition,molecular dynamics simulation,and analysis of active conformation populations.Validation of the accuracy of NAC4ED demonstrated a prediction accuracy of 92.5%for 40 mutations,showing strong consistency between the computational predictions and experimental results.The time required for automated determination of a single enzyme mutant using NAC4ED is 1/764th of that needed for experimental methods.This has significantly enhanced the efficiency of predicting enzyme mutations,leading to revolutionary breakthroughs in improving the performance of high‐throughput screening of enzyme variants.NAC4ED facilitates the efficient generation of a large amount of annotated data,providing high‐quality data for statistical modeling and machine learning.
基金the National Natural Science Foundation of China(Grant Nos.30221003,30720022)the Ministry of Science and Technology 973 Project(Grant No.2006CB806503)+2 种基金the Ministry of Science and Technology National High Technology Research and Development Program("863"Program)(Grant No.2006AA02A322)the Ministry of Science and Technology International Cooperation Project(Grant No.2006DFB32420)the Chinese Academy of Sciences Knowledge Innovation Project(Grant No.KSCX1-YW-R-05)。
文摘Current in vitro assays for the activity of HIV-RT(reverse transcriptase)require radio-labeled or chemically modified nucleotides to detect reaction products.However,these assays are inherently end-point measurements and labor intensive.Here we describe a novel non-radioactive assay based on the principle of pyrosequencing coupledenzyme system to monitor the activity of HIV-RT by indirectly measuring the release of pyrophosphate(PPi),which is generated during nascent strand synthesis.The results show that our assay could monitor HIV-RT activity with high sensitivity and is suitable for rapid highthroughput drug screening targeting anti-HIV therapies due to its high speed and convenience.Moreover,this assay can be used to measure primase activity in an easy and sensitive manner,which suggests that this novel approach could be wildly used to analyze the activity of PPi-generated and ATP-free enzyme reactions.
基金supported by National Institutes of Health grants AI070827 and CA33266American Cancer Society grant RSG-09-076-01 and the UIC Walter Payton Center GUILD
文摘An estimated 130 million people worldwide are chronically infected with hepatitis C virus (HCV) making it a leading cause of liver disease worldwide. Because the currently available therapy of pegylated interferon-alpha and ribavirin is only effective in a subset of patients, the development of new HCV antivirals is a healthcare imperative. This review discusses the experimental models available for HCV antiviral drug research, recent advances in HCV antiviral drug development, as well as active research being pursued to facilitate development of new HCV-specific therapeutics.
