Imaging-based phenotypic screening uses cellular phenotypes to describe the drug performance, which generally focuses on single cellular feature, lacking of a comprehensive characterization. Here, we propose a high co...Imaging-based phenotypic screening uses cellular phenotypes to describe the drug performance, which generally focuses on single cellular feature, lacking of a comprehensive characterization. Here, we propose a high content phenotypic screening method based on expansion microscopy(ExM) assisted cell painting, which enables multi-channel imaging with approximately 50 nm resolution. As a demonstration, we applied this method to a phenotypic screening involving five drugs. The morphological attributes of three subcellular structures were summarized to consist a “fingerprint” describing the drug effect. The proposed method can provide comprehensive and detailed clues for drug evaluation, enriching the content of phenotypic screening.展开更多
F-box proteins are components of the SCF （SkpA-Cullin 1-F-box） E3 ligase complexes, acting as the specificity-determinants in targeting substrate proteins for ubiquitination and degradation. In humans, at least 22 o...F-box proteins are components of the SCF （SkpA-Cullin 1-F-box） E3 ligase complexes, acting as the specificity-determinants in targeting substrate proteins for ubiquitination and degradation. In humans, at least 22 out of 75 F-box proteins have experimentally documented substrates, whereas in Drosophila 12 F-box proteins have been characterized with known substrates. To systematically investigate the genetic and molecular functions of F-box proteins in Drosophila, we performed a survey of the literature and databases. We identified 45 Drosophila genes that encode proteins containing at least one F-box domain. We collected publically available RNAi lines against these genes and used them in a tissue-specific RNAi-based phenotypic screen. Here, we present our systematic phenotypic dataset from the eye, the wing and the notum. This dataset is the first of its kind and represents a useful resource for future studies of the molecular and genetic functions of F-box genes in Drosophila. Our results show that, as expected, F-box genes in Drosophila have regulatory roles in a diverse array of processes including cell proliferation, cell growth, signal transduction, and cellular and animal survival.展开更多
Despite advancements in the areas of omics and chemoinformatics,potent novel biotherapeutic molecules with new modes of actions are needed for leishmaniasis.The socioeconomic burden of leishmaniasis remains alarming i...Despite advancements in the areas of omics and chemoinformatics,potent novel biotherapeutic molecules with new modes of actions are needed for leishmaniasis.The socioeconomic burden of leishmaniasis remains alarming in endemic regions.Currently,reports from existing endemic areas such as Nepal,Iran,Brazil,India,Sudan and Afghanistan,as well as newly affected countries such as Peru,Bolivia and Somalia indicate concerns of chemoresistance to the classical antimonial treatment.As a result,effective antileishmanial agents which are safe and affordable are urgently needed.Natural products from both flora and fauna have contributed immensely to chemotherapeutics and serve as vital sources of new chemical agents.This review focuses on a systematic cross-sectional view of all characterized anti-leishmanial compounds from natural sources over the last decade.Furthermore,IC_(50)/EC_(50),cytotoxicity and suggested mechanisms of action of some of these natural products are provided.The natural product classification includes alkaloids,terpenes,terpenoids,and phenolics.The plethora of reported mechanisms involve calcium channel inhibition,immunomodulation and apoptosis.Making avail-able enriched data pertaining to bioactivity and mechanisms of natural products complement current efforts geared towards unraveling potent leishmanicides of therapeutic relevance.展开更多
Chinese herbal medicines(CHMs)serve as the cornerstone of traditional Chinese medicine(TCM)practices and are vital sources of inspiration for novel drug discovery.Many landmark drugs,including artemisinin,ephedrine,bi...Chinese herbal medicines(CHMs)serve as the cornerstone of traditional Chinese medicine(TCM)practices and are vital sources of inspiration for novel drug discovery.Many landmark drugs,including artemisinin,ephedrine,bicyclol,berberine,and dl-3-nbutylphthalide,originated from CHMs.Nevertheless,only 23.5%of the new drugs approved by the US Food and Drug Administration(FDA)over the past four decades have stemmed from botanical drugs,natural products,or their derivatives[1].展开更多
Phenotypic screening has played an important role in discovering innovative small-molecule drugs and clinical candidates with unique molecular mechanisms of action.However,conducting cell-based high-throughput screeni...Phenotypic screening has played an important role in discovering innovative small-molecule drugs and clinical candidates with unique molecular mechanisms of action.However,conducting cell-based high-throughput screening from vast compound libraries is extremely time-consuming and expensive.Fortunately,deep learning has provided a new paradigm for identifying compounds with specific phenotypic properties.Herein,we developed a data-driven classification-generation cascade model to discover new chemotype antitumor drugs.Through wet-lab validation,WJ0976 and WJ0909 were identified as tetrahydrocarbazole derivatives and displayed potent broad-spectrum antitumor activity as well as growth inhibitory properties against multidrug-resistant cancer cells.Furthermore,the R-(−)-WJ0909(WJ0909B),demonstrated optimal antitumor efficacy in vitro and ex vivo patient-derived organoids(PDOs).Further investigations revealed that WJ0909B upregulates p53 expression and cause mitochondria-dependent endogenous apoptosis.Moreover,WJ0909B and the click-activated prodrug WJ0909B-TCO potently inhibited tumor growth in cell-derived xenograft models.This research highlights the significant potential of deep learning-guided approach to phenotypic drug discovery for anticancer drugs and the strategy of click-activated prodrug for targeted cancer therapy.展开更多
Metastasis is the leading cause of death from cutaneous melanoma.Identifying metastasisrelated targets and developing corresponding therapeutic strategies are major areas of focus.While functional genomics strategies ...Metastasis is the leading cause of death from cutaneous melanoma.Identifying metastasisrelated targets and developing corresponding therapeutic strategies are major areas of focus.While functional genomics strategies provide powerful tools for target discovery,investigations at the protein level can directly decode the bioactive epitopes on functional proteins.Aptamers present a promising avenue as they can explore membrane proteomes and have the potential to interfere with cell function.Herein,we developed a target and epitope discovery platform,termed functional aptamer evolution-enabled target identification(FAETI),by integrating affinity aptamer acquisition with phenotype screening and target protein identification.Utilizing the aptamer XH3C,which was screened for its migration-inhibitory function,we identified the Chondroitin Sulfate Proteoglycan 4(CSPG4),as a potential target involved in melanoma migration.Further evidence demonstrated that XH3C induces cytoskeletal rearrangement by blocking the interaction between the bioactive epitope of CSPG4 and integrin a4.Taken together,our study demonstrates the robustness of aptamer-based molecular tools for target and epitope discovery.Additionally,XH3C is an affinity and functional molecule that selectively binds to a unique epitope on CSPG4,enabling the development of innovative therapeutic strategies.展开更多
Genes that are expressed ubiquitously throughout all developmental stages are thought to be necessary for basic biological or cellular functions. Therefore, determining their biological roles is a great challenge. We ...Genes that are expressed ubiquitously throughout all developmental stages are thought to be necessary for basic biological or cellular functions. Therefore, determining their biological roles is a great challenge. We identified 4034 of these genes in rice after studying the results of Agilent 44K and Affymetrix meta- anatomical expression profiles. Among 105 genes that were characterized by loss-of-function analysis, 79 were classified as members of gene families, the majority of which were predominantly expressed. Using T-DNA insertional mutants, we examined 43 genes and found that loss of expression of six genes caused developing seedor seedling-defective phenotypes. Of these, three are singletons without similar family members and defective phenotypes are expected from mutations. Phylogenomic analyses integrating genome-wide transcriptome data revealed the functional dominance of three ubiquitously expressed fam- ily genes. Among them, we investigated the function of OsO3g19890, which is involved in ATP generation within the mitochondria during endosperm development. We also created and evaluated functional net- works associated with this gene to understand the molecular mechanism. Our study provides a useful strategy for pheonome analysis of ubiquitously expressed genes in rice.展开更多
基金supported by the National Key R&D Program of China(No.2022YFC2409603)the Tianjin Municipal Science and Technology Program(No.23JCZXJC00340)the Beijing-Tianjin-Hebei Fundamental Research Cooperation Project(No.J230001)。
文摘Imaging-based phenotypic screening uses cellular phenotypes to describe the drug performance, which generally focuses on single cellular feature, lacking of a comprehensive characterization. Here, we propose a high content phenotypic screening method based on expansion microscopy(ExM) assisted cell painting, which enables multi-channel imaging with approximately 50 nm resolution. As a demonstration, we applied this method to a phenotypic screening involving five drugs. The morphological attributes of three subcellular structures were summarized to consist a “fingerprint” describing the drug effect. The proposed method can provide comprehensive and detailed clues for drug evaluation, enriching the content of phenotypic screening.
基金financially supported by the National Basic Research Program of China(973 Program)(No.2009CB918702)the National Natural Science Foundation of China(Nos.31071087 and 31100889)
文摘F-box proteins are components of the SCF （SkpA-Cullin 1-F-box） E3 ligase complexes, acting as the specificity-determinants in targeting substrate proteins for ubiquitination and degradation. In humans, at least 22 out of 75 F-box proteins have experimentally documented substrates, whereas in Drosophila 12 F-box proteins have been characterized with known substrates. To systematically investigate the genetic and molecular functions of F-box proteins in Drosophila, we performed a survey of the literature and databases. We identified 45 Drosophila genes that encode proteins containing at least one F-box domain. We collected publically available RNAi lines against these genes and used them in a tissue-specific RNAi-based phenotypic screen. Here, we present our systematic phenotypic dataset from the eye, the wing and the notum. This dataset is the first of its kind and represents a useful resource for future studies of the molecular and genetic functions of F-box genes in Drosophila. Our results show that, as expected, F-box genes in Drosophila have regulatory roles in a diverse array of processes including cell proliferation, cell growth, signal transduction, and cellular and animal survival.
文摘Despite advancements in the areas of omics and chemoinformatics,potent novel biotherapeutic molecules with new modes of actions are needed for leishmaniasis.The socioeconomic burden of leishmaniasis remains alarming in endemic regions.Currently,reports from existing endemic areas such as Nepal,Iran,Brazil,India,Sudan and Afghanistan,as well as newly affected countries such as Peru,Bolivia and Somalia indicate concerns of chemoresistance to the classical antimonial treatment.As a result,effective antileishmanial agents which are safe and affordable are urgently needed.Natural products from both flora and fauna have contributed immensely to chemotherapeutics and serve as vital sources of new chemical agents.This review focuses on a systematic cross-sectional view of all characterized anti-leishmanial compounds from natural sources over the last decade.Furthermore,IC_(50)/EC_(50),cytotoxicity and suggested mechanisms of action of some of these natural products are provided.The natural product classification includes alkaloids,terpenes,terpenoids,and phenolics.The plethora of reported mechanisms involve calcium channel inhibition,immunomodulation and apoptosis.Making avail-able enriched data pertaining to bioactivity and mechanisms of natural products complement current efforts geared towards unraveling potent leishmanicides of therapeutic relevance.
基金supported by the National Key Research and Development Program of China(2025YFC3507500)the National Natural Science Foundation of China(82274198)。
文摘Chinese herbal medicines(CHMs)serve as the cornerstone of traditional Chinese medicine(TCM)practices and are vital sources of inspiration for novel drug discovery.Many landmark drugs,including artemisinin,ephedrine,bicyclol,berberine,and dl-3-nbutylphthalide,originated from CHMs.Nevertheless,only 23.5%of the new drugs approved by the US Food and Drug Administration(FDA)over the past four decades have stemmed from botanical drugs,natural products,or their derivatives[1].
基金supported by CAMS Innovation Fund for Medical Sciences,China(No.2021-I2M-1-028 and No.2021-I2M-1-054,China)+6 种基金the National Natural Science Foundation of China,China(No.82303782,China)the China Postdoctoral Science Foundation,China(2024M763807,China)the 2024 China Industrial Technology Infrastructure Public Service Platform Project,China(GN2024-31-4700)The computing resources were supported by Biomedical High Performance Computing Platform,Chinese Academy of Medical Sciences,China.
文摘Phenotypic screening has played an important role in discovering innovative small-molecule drugs and clinical candidates with unique molecular mechanisms of action.However,conducting cell-based high-throughput screening from vast compound libraries is extremely time-consuming and expensive.Fortunately,deep learning has provided a new paradigm for identifying compounds with specific phenotypic properties.Herein,we developed a data-driven classification-generation cascade model to discover new chemotype antitumor drugs.Through wet-lab validation,WJ0976 and WJ0909 were identified as tetrahydrocarbazole derivatives and displayed potent broad-spectrum antitumor activity as well as growth inhibitory properties against multidrug-resistant cancer cells.Furthermore,the R-(−)-WJ0909(WJ0909B),demonstrated optimal antitumor efficacy in vitro and ex vivo patient-derived organoids(PDOs).Further investigations revealed that WJ0909B upregulates p53 expression and cause mitochondria-dependent endogenous apoptosis.Moreover,WJ0909B and the click-activated prodrug WJ0909B-TCO potently inhibited tumor growth in cell-derived xenograft models.This research highlights the significant potential of deep learning-guided approach to phenotypic drug discovery for anticancer drugs and the strategy of click-activated prodrug for targeted cancer therapy.
基金financially supported by the National Key Research&Development Program of China(Grant No.2022YFA1304500)the National Natural Science Foundation of China(Grant No.22227805,22374004)+2 种基金Excellent Young Scientists Fund Program(Overseas)Clinical Medicine Plus X-Young Scholars Project of Peking Universitythe Fundamental Research Funds for the Central Universities(No.PKU2024LCXQ026,China).
文摘Metastasis is the leading cause of death from cutaneous melanoma.Identifying metastasisrelated targets and developing corresponding therapeutic strategies are major areas of focus.While functional genomics strategies provide powerful tools for target discovery,investigations at the protein level can directly decode the bioactive epitopes on functional proteins.Aptamers present a promising avenue as they can explore membrane proteomes and have the potential to interfere with cell function.Herein,we developed a target and epitope discovery platform,termed functional aptamer evolution-enabled target identification(FAETI),by integrating affinity aptamer acquisition with phenotype screening and target protein identification.Utilizing the aptamer XH3C,which was screened for its migration-inhibitory function,we identified the Chondroitin Sulfate Proteoglycan 4(CSPG4),as a potential target involved in melanoma migration.Further evidence demonstrated that XH3C induces cytoskeletal rearrangement by blocking the interaction between the bioactive epitope of CSPG4 and integrin a4.Taken together,our study demonstrates the robustness of aptamer-based molecular tools for target and epitope discovery.Additionally,XH3C is an affinity and functional molecule that selectively binds to a unique epitope on CSPG4,enabling the development of innovative therapeutic strategies.
文摘Genes that are expressed ubiquitously throughout all developmental stages are thought to be necessary for basic biological or cellular functions. Therefore, determining their biological roles is a great challenge. We identified 4034 of these genes in rice after studying the results of Agilent 44K and Affymetrix meta- anatomical expression profiles. Among 105 genes that were characterized by loss-of-function analysis, 79 were classified as members of gene families, the majority of which were predominantly expressed. Using T-DNA insertional mutants, we examined 43 genes and found that loss of expression of six genes caused developing seedor seedling-defective phenotypes. Of these, three are singletons without similar family members and defective phenotypes are expected from mutations. Phylogenomic analyses integrating genome-wide transcriptome data revealed the functional dominance of three ubiquitously expressed fam- ily genes. Among them, we investigated the function of OsO3g19890, which is involved in ATP generation within the mitochondria during endosperm development. We also created and evaluated functional net- works associated with this gene to understand the molecular mechanism. Our study provides a useful strategy for pheonome analysis of ubiquitously expressed genes in rice.
