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1.
J Chem Inf Model ; 61(9): 4156-4172, 2021 09 27.
Artigo em Inglês | MEDLINE | ID: mdl-34318674

RESUMO

A common strategy for identifying molecules likely to possess a desired biological activity is to search large databases of compounds for high structural similarity to a query molecule that demonstrates this activity, under the assumption that structural similarity is predictive of similar biological activity. However, efforts to systematically benchmark the diverse array of available molecular fingerprints and similarity coefficients have been limited by a lack of large-scale datasets that reflect biological similarities of compounds. To elucidate the relative performance of these alternatives, we systematically benchmarked 11 different molecular fingerprint encodings, each combined with 13 different similarity coefficients, using a large set of chemical-genetic interaction data from the yeast Saccharomyces cerevisiae as a systematic proxy for biological activity. We found that the performance of different molecular fingerprints and similarity coefficients varied substantially and that the all-shortest path fingerprints paired with the Braun-Blanquet similarity coefficient provided superior performance that was robust across several compound collections. We further proposed a machine learning pipeline based on support vector machines that offered a fivefold improvement relative to the best unsupervised approach. Our results generally suggest that using high-dimensional chemical-genetic data as a basis for refining molecular fingerprints can be a powerful approach for improving prediction of biological functions from chemical structures.


Assuntos
Aprendizado de Máquina , Máquina de Vetores de Suporte , Bases de Dados Factuais
2.
Plant Biotechnol J ; 17(8): 1567-1581, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-30672092

RESUMO

Sclerotinia sclerotiorum, a predominately necrotrophic fungal pathogen with a broad host range, causes a significant yield-limiting disease of soybean called Sclerotinia stem rot. Resistance mechanisms against this pathogen in soybean are poorly understood, thus hindering the commercial deployment of resistant varieties. We used a multiomic approach utilizing RNA-sequencing, gas chromatography-mass spectrometry-based metabolomics and chemical genomics in yeast to decipher the molecular mechanisms governing resistance to S. sclerotiorum in soybean. Transcripts and metabolites of two soybean recombinant inbred lines, one resistant and one susceptible to S. sclerotiorum were analysed in a time course experiment. The combined results show that resistance to S. sclerotiorum in soybean is associated in part with an early accumulation of JA-Ile ((+)-7-iso-jasmonoyl-L-isoleucine), a bioactive jasmonate, increased ability to scavenge reactive oxygen species, and importantly, a reprogramming of the phenylpropanoid pathway leading to increased antifungal activities. Indeed, we noted that phenylpropanoid pathway intermediates, such as 4-hydroxybenzoate, cinnamic acid, ferulic acid and caffeic acid, were highly accumulated in the resistant line. In vitro assays show that these metabolites and total stem extracts from the resistant line clearly affect S. sclerotiorum growth and development. Using chemical genomics in yeast, we further show that this antifungal activity targets ergosterol biosynthesis in the fungus, by disrupting enzymes involved in lipid and sterol biosynthesis. Overall, our results are consistent with a model where resistance to S. sclerotiorum in soybean coincides with an early recognition of the pathogen, leading to the modulation of the redox capacity of the host and the production of antifungal metabolites.


Assuntos
Ascomicetos/patogenicidade , Resistência à Doença/genética , Ergosterol/biossíntese , Glycine max/genética , Glycine max/microbiologia , Doenças das Plantas/genética , Regulação da Expressão Gênica de Plantas , Doenças das Plantas/microbiologia , Regulação para Cima
3.
Bioinformatics ; 34(7): 1251-1252, 2018 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-29206899

RESUMO

Summary: Chemical-genomic approaches that map interactions between small molecules and genetic perturbations offer a promising strategy for functional annotation of uncharacterized bioactive compounds. We recently developed a new high-throughput platform for mapping chemical-genetic (CG) interactions in yeast that can be scaled to screen large compound collections, and we applied this system to generate CG interaction profiles for more than 13 000 compounds. When integrated with the existing global yeast genetic interaction network, CG interaction profiles can enable mode-of-action prediction for previously uncharacterized compounds as well as discover unexpected secondary effects for known drugs. To facilitate future analysis of these valuable data, we developed a public database and web interface named MOSAIC. The website provides a convenient interface for querying compounds, bioprocesses (Gene Ontology terms) and genes for CG information including direct CG interactions, bioprocesses and gene-level target predictions. MOSAIC also provides access to chemical structure information of screened molecules, chemical-genomic profiles and the ability to search for compounds sharing structural and functional similarity. This resource will be of interest to chemical biologists for discovering new small molecule probes with specific modes-of-action as well as computational biologists interested in analysing CG interaction networks. Availability and implementation: MOSAIC is available at http://mosaic.cs.umn.edu. Contact: hisyo@riken.jp, yoshidam@riken.jp, charlie.boone@utoronto.ca or chadm@umn.edu. Supplementary information: Supplementary data are available at Bioinformatics online.


Assuntos
Biologia Computacional/métodos , Bases de Dados Factuais , Descoberta de Drogas/métodos , Regulação Fúngica da Expressão Gênica , Interação Gene-Ambiente , Saccharomyces cerevisiae/genética , Redes Reguladoras de Genes , Internet , Modelos Genéticos , Saccharomyces cerevisiae/efeitos dos fármacos , Saccharomyces cerevisiae/metabolismo
4.
Nat Chem Biol ; 13(9): 982-993, 2017 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-28759014

RESUMO

Chemical-genetic approaches offer the potential for unbiased functional annotation of chemical libraries. Mutations can alter the response of cells in the presence of a compound, revealing chemical-genetic interactions that can elucidate a compound's mode of action. We developed a highly parallel, unbiased yeast chemical-genetic screening system involving three key components. First, in a drug-sensitive genetic background, we constructed an optimized diagnostic mutant collection that is predictive for all major yeast biological processes. Second, we implemented a multiplexed (768-plex) barcode-sequencing protocol, enabling the assembly of thousands of chemical-genetic profiles. Finally, based on comparison of the chemical-genetic profiles with a compendium of genome-wide genetic interaction profiles, we predicted compound functionality. Applying this high-throughput approach, we screened seven different compound libraries and annotated their functional diversity. We further validated biological process predictions, prioritized a diverse set of compounds, and identified compounds that appear to have dual modes of action.


Assuntos
Sistemas de Liberação de Medicamentos , Bibliotecas de Moléculas Pequenas , Avaliação Pré-Clínica de Medicamentos , Perfilação da Expressão Gênica , Estrutura Molecular
7.
PLoS Comput Biol ; 14(10): e1006532, 2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-30376562

RESUMO

Chemical-genetic interactions-observed when the treatment of mutant cells with chemical compounds reveals unexpected phenotypes-contain rich functional information linking compounds to their cellular modes of action. To systematically identify these interactions, an array of mutants is challenged with a compound and monitored for fitness defects, generating a chemical-genetic interaction profile that provides a quantitative, unbiased description of the cellular function(s) perturbed by the compound. Genetic interactions, obtained from genome-wide double-mutant screens, provide a key for interpreting the functional information contained in chemical-genetic interaction profiles. Despite the utility of this approach, integrative analyses of genetic and chemical-genetic interaction networks have not been systematically evaluated. We developed a method, called CG-TARGET (Chemical Genetic Translation via A Reference Genetic nETwork), that integrates large-scale chemical-genetic interaction screening data with a genetic interaction network to predict the biological processes perturbed by compounds. In a recent publication, we applied CG-TARGET to a screen of nearly 14,000 chemical compounds in Saccharomyces cerevisiae, integrating this dataset with the global S. cerevisiae genetic interaction network to prioritize over 1500 compounds with high-confidence biological process predictions for further study. We present here a formal description and rigorous benchmarking of the CG-TARGET method, showing that, compared to alternative enrichment-based approaches, it achieves similar or better accuracy while substantially improving the ability to control the false discovery rate of biological process predictions. Additional investigation of the compatibility of chemical-genetic and genetic interaction profiles revealed that one-third of observed chemical-genetic interactions contributed to the highest-confidence biological process predictions and that negative chemical-genetic interactions overwhelmingly formed the basis of these predictions. We also present experimental validations of CG-TARGET-predicted tubulin polymerization and cell cycle progression inhibitors. Our approach successfully demonstrates the use of genetic interaction networks in the high-throughput functional annotation of compounds to biological processes.


Assuntos
Ciclo Celular , Descoberta de Drogas/métodos , Redes Reguladoras de Genes , Bibliotecas de Moléculas Pequenas , Biologia de Sistemas/métodos , Ciclo Celular/efeitos dos fármacos , Ciclo Celular/genética , Colchicina/farmacologia , Redes Reguladoras de Genes/efeitos dos fármacos , Redes Reguladoras de Genes/genética , Multimerização Proteica/efeitos dos fármacos , Reprodutibilidade dos Testes , Tubulina (Proteína)/efeitos dos fármacos , Tubulina (Proteína)/metabolismo , Moduladores de Tubulina/farmacologia , Leveduras/efeitos dos fármacos , Leveduras/genética , Leveduras/fisiologia
9.
Microb Cell Fact ; 17(1): 5, 2018 Jan 12.
Artigo em Inglês | MEDLINE | ID: mdl-29329531

RESUMO

BACKGROUND: Gamma valerolactone (GVL) treatment of lignocellulosic bomass is a promising technology for degradation of biomass for biofuel production; however, GVL is toxic to fermentative microbes. Using a combination of chemical genomics with the yeast (Saccharomyces cerevisiae) deletion collection to identify sensitive and resistant mutants, and chemical proteomics to monitor protein abundance in the presence of GVL, we sought to understand the mechanism toxicity and resistance to GVL with the goal of engineering a GVL-tolerant, xylose-fermenting yeast. RESULTS: Chemical genomic profiling of GVL predicted that this chemical affects membranes and membrane-bound processes. We show that GVL causes rapid, dose-dependent cell permeability, and is synergistic with ethanol. Chemical genomic profiling of GVL revealed that deletion of the functionally related enzymes Pad1p and Fdc1p, which act together to decarboxylate cinnamic acid and its derivatives to vinyl forms, increases yeast tolerance to GVL. Further, overexpression of Pad1p sensitizes cells to GVL toxicity. To improve GVL tolerance, we deleted PAD1 and FDC1 in a xylose-fermenting yeast strain. The modified strain exhibited increased anaerobic growth, sugar utilization, and ethanol production in synthetic hydrolysate with 1.5% GVL, and under other conditions. Chemical proteomic profiling of the engineered strain revealed that enzymes involved in ergosterol biosynthesis were more abundant in the presence of GVL compared to the background strain. The engineered GVL strain contained greater amounts of ergosterol than the background strain. CONCLUSIONS: We found that GVL exerts toxicity to yeast by compromising cellular membranes, and that this toxicity is synergistic with ethanol. Deletion of PAD1 and FDC1 conferred GVL resistance to a xylose-fermenting yeast strain by increasing ergosterol accumulation in aerobically grown cells. The GVL-tolerant strain fermented sugars in the presence of GVL levels that were inhibitory to the unmodified strain. This strain represents a xylose fermenting yeast specifically tailored to GVL produced hydrolysates.


Assuntos
Engenharia Genética/métodos , Genômica/métodos , Lactonas/farmacologia , Saccharomyces cerevisiae/efeitos dos fármacos , Saccharomyces cerevisiae/genética , Biocatálise , Biocombustíveis , Biomassa , Carboxiliases/deficiência , Carboxiliases/genética , Farmacorresistência Fúngica , Ergosterol/metabolismo , Etanol/metabolismo , Etanol/farmacologia , Fermentação , Lignina/metabolismo , Mutação , Proteômica , Saccharomyces cerevisiae/metabolismo , Xilose/metabolismo
10.
Proc Natl Acad Sci U S A ; 112(12): E1490-7, 2015 Mar 24.
Artigo em Inglês | MEDLINE | ID: mdl-25775513

RESUMO

A rise in resistance to current antifungals necessitates strategies to identify alternative sources of effective fungicides. We report the discovery of poacic acid, a potent antifungal compound found in lignocellulosic hydrolysates of grasses. Chemical genomics using Saccharomyces cerevisiae showed that loss of cell wall synthesis and maintenance genes conferred increased sensitivity to poacic acid. Morphological analysis revealed that cells treated with poacic acid behaved similarly to cells treated with other cell wall-targeting drugs and mutants with deletions in genes involved in processes related to cell wall biogenesis. Poacic acid causes rapid cell lysis and is synergistic with caspofungin and fluconazole. The cellular target was identified; poacic acid localized to the cell wall and inhibited ß-1,3-glucan synthesis in vivo and in vitro, apparently by directly binding ß-1,3-glucan. Through its activity on the glucan layer, poacic acid inhibits growth of the fungi Sclerotinia sclerotiorum and Alternaria solani as well as the oomycete Phytophthora sojae. A single application of poacic acid to leaves infected with the broad-range fungal pathogen S. sclerotiorum substantially reduced lesion development. The discovery of poacic acid as a natural antifungal agent targeting ß-1,3-glucan highlights the potential side use of products generated in the processing of renewable biomass toward biofuels as a source of valuable bioactive compounds and further clarifies the nature and mechanism of fermentation inhibitors found in lignocellulosic hydrolysates.


Assuntos
Ácidos Cumáricos/química , Fungicidas Industriais/química , Poaceae/química , Saccharomyces cerevisiae/efeitos dos fármacos , Estilbenos/química , beta-Glucanas/química , Caspofungina , Membrana Celular/metabolismo , Parede Celular/metabolismo , Relação Dose-Resposta a Droga , Sinergismo Farmacológico , Equinocandinas/química , Genômica , Hidrólise , Concentração Inibidora 50 , Lignina/química , Lipopeptídeos , Extratos Vegetais/química , Saccharomyces cerevisiae/metabolismo
11.
Mol Biol Evol ; 32(9): 2317-27, 2015 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-25953281

RESUMO

How populations that inhabit the same geographical area become genetically differentiated is not clear. To investigate this, we characterized phenotypic and genetic differences between two populations of Saccharomyces cerevisiae that in some cases inhabit the same environment but show relatively little gene flow. We profiled stress sensitivity in a group of vineyard isolates and a group of oak-soil strains and found several niche-related phenotypes that distinguish the populations. We performed bulk-segregant mapping on two of the distinguishing traits: The vineyard-specific ability to grow in grape juice and oak-specific tolerance to the cell wall damaging drug Congo red. To implicate causal genes, we also performed a chemical genomic screen in the lab-strain deletion collection and identified many important genes that fell under quantitative trait loci peaks. One gene important for growth in grape juice and identified by both the mapping and the screen was SSU1, a sulfite-nitrite pump implicated in wine fermentations. The beneficial allele is generated by a known translocation that we reasoned may also serve as a genetic barrier. We found that the translocation is prevalent in vineyard strains, but absent in oak strains, and presents a postzygotic barrier to spore viability. Furthermore, the translocation was associated with a fitness cost to the rapid growth rate seen in oak-soil strains. Our results reveal the translocation as a dual-function locus that enforces ecological differentiation while producing a genetic barrier to gene flow in these sympatric populations.


Assuntos
Saccharomyces cerevisiae/genética , Adaptação Fisiológica , Proteínas de Transporte de Ânions/genética , Proteínas de Transporte de Ânions/metabolismo , Ecossistema , Fermentação , Genes Fúngicos , Pleiotropia Genética , Escore Lod , Fenótipo , Locos de Características Quantitativas , Quercus/microbiologia , Saccharomyces cerevisiae/crescimento & desenvolvimento , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Análise de Sequência de DNA , Microbiologia do Solo , Vitis/microbiologia
12.
Microb Cell Fact ; 15: 17, 2016 Jan 20.
Artigo em Inglês | MEDLINE | ID: mdl-26790958

RESUMO

BACKGROUND: Imidazolium ionic liquids (IILs) underpin promising technologies that generate fermentable sugars from lignocellulose for future biorefineries. However, residual IILs are toxic to fermentative microbes such as Saccharomyces cerevisiae, making IIL-tolerance a key property for strain engineering. To enable rational engineering, we used chemical genomic profiling to understand the effects of IILs on S. cerevisiae. RESULTS: We found that IILs likely target mitochondria as their chemical genomic profiles closely resembled that of the mitochondrial membrane disrupting agent valinomycin. Further, several deletions of genes encoding mitochondrial proteins exhibited increased sensitivity to IIL. High-throughput chemical proteomics confirmed effects of IILs on mitochondrial protein levels. IILs induced abnormal mitochondrial morphology, as well as altered polarization of mitochondrial membrane potential similar to valinomycin. Deletion of the putative serine/threonine kinase PTK2 thought to activate the plasma-membrane proton efflux pump Pma1p conferred a significant IIL-fitness advantage. Conversely, overexpression of PMA1 conferred sensitivity to IILs, suggesting that hydrogen ion efflux may be coupled to influx of the toxic imidazolium cation. PTK2 deletion conferred resistance to multiple IILs, including [EMIM]Cl, [BMIM]Cl, and [EMIM]Ac. An engineered, xylose-converting ptk2∆ S. cerevisiae (Y133-IIL) strain consumed glucose and xylose faster and produced more ethanol in the presence of 1 % [BMIM]Cl than the wild-type PTK2 strain. We propose a model of IIL toxicity and resistance. CONCLUSIONS: This work demonstrates the utility of chemical genomics-guided biodesign for development of superior microbial biocatalysts for the ever-changing landscape of fermentation inhibitors.


Assuntos
Líquidos Iônicos/metabolismo , Saccharomyces cerevisiae/metabolismo , Xilose/metabolismo , Fermentação/fisiologia
13.
Angew Chem Int Ed Engl ; 53(43): 11583-6, 2014 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-25197007

RESUMO

Forazoline A, a novel antifungal polyketide with in vivo efficacy against Candida albicans, was discovered using LCMS-based metabolomics to investigate marine-invertebrate-associated bacteria. Forazoline A had a highly unusual and unprecedented skeleton. Acquisition of (13)C-(13)C gCOSY and (13)C-(15)N HMQC NMR data provided the direct carbon-carbon and carbon-nitrogen connectivity, respectively. This approach represents the first example of determining direct (13)C-(15)N connectivity for a natural product. Using yeast chemical genomics, we propose that forazoline A operated through a new mechanism of action with a phenotypic outcome of disrupting membrane integrity.


Assuntos
Antifúngicos/farmacologia , Bactérias/química , Policetídeos/farmacologia , Animais , Antifúngicos/isolamento & purificação , Candida albicans/efeitos dos fármacos , Espectroscopia de Ressonância Magnética Nuclear de Carbono-13 , Espectroscopia de Ressonância Magnética , Biologia Marinha , Espectrometria de Massas , Camundongos , Testes de Sensibilidade Microbiana , Estrutura Molecular , Policetídeos/isolamento & purificação
14.
Front Microbiol ; 14: 1281058, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-38075883

RESUMO

Metal(loid) salts were used to treat infectious diseases in the past due to their exceptional biocidal properties at low concentrations. However, the mechanism of their toxicity has yet to be fully elucidated. The production of reactive oxygen species (ROS) has been linked to the toxicity of soft metal(loid)s such as Ag(I), Au(III), As(III), Cd(II), Hg(II), and Te(IV). Nevertheless, few reports have described the direct, or ROS-independent, effects of some of these soft-metal(loid)s on bacteria, including the dismantling of iron-sulfur clusters [4Fe-4S] and the accumulation of porphyrin IX. Here, we used genome-wide genetic, proteomic, and biochemical approaches under anaerobic conditions to evaluate the direct mechanisms of toxicity of these metal(loid)s in Escherichia coli. We found that certain soft-metal(loid)s promote protein aggregation in a ROS-independent manner. This aggregation occurs during translation in the presence of Ag(I), Au(III), Hg(II), or Te(IV) and post-translationally in cells exposed to Cd(II) or As(III). We determined that aggregated proteins were involved in several essential biological processes that could lead to cell death. For instance, several enzymes involved in amino acid biosynthesis were aggregated after soft-metal(loid) exposure, disrupting intracellular amino acid concentration. We also propose a possible mechanism to explain how soft-metal(loid)s act as proteotoxic agents.

15.
BMC Evol Biol ; 12: 46, 2012 Apr 02.
Artigo em Inglês | MEDLINE | ID: mdl-22471618

RESUMO

BACKGROUND: Interspecific hybridization occurs in every eukaryotic kingdom. While hybrid progeny are frequently at a selective disadvantage, in some instances their increased genome size and complexity may result in greater stress resistance than their ancestors, which can be adaptively advantageous at the edges of their ancestors' ranges. While this phenomenon has been repeatedly documented in the field, the response of hybrid populations to long-term selection has not often been explored in the lab. To fill this knowledge gap we crossed the two most distantly related members of the Saccharomyces sensu stricto group, S. cerevisiae and S. uvarum, and established a mixed population of homoploid and aneuploid hybrids to study how different types of selection impact hybrid genome structure. RESULTS: As temperature was raised incrementally from 31°C to 46.5°C over 500 generations of continuous culture, selection favored loss of the S. uvarum genome, although the kinetics of genome loss differed among independent replicates. Temperature-selected isolates exhibited greater inherent and induced thermal tolerance than parental species and founding hybrids, and also exhibited ethanol resistance. In contrast, as exogenous ethanol was increased from 0% to 14% over 500 generations of continuous culture, selection favored euploid S. cerevisiae x S. uvarum hybrids. Ethanol-selected isolates were more ethanol tolerant than S. uvarum and one of the founding hybrids, but did not exhibit resistance to temperature stress. Relative to parental and founding hybrids, temperature-selected strains showed heritable differences in cell wall structure in the forms of increased resistance to zymolyase digestion and Micafungin, which targets cell wall biosynthesis. CONCLUSIONS: This is the first study to show experimentally that the genomic fate of newly-formed interspecific hybrids depends on the type of selection they encounter during the course of evolution, underscoring the importance of the ecological theatre in determining the outcome of the evolutionary play.


Assuntos
Adaptação Biológica/genética , Genoma Fúngico/genética , Hibridização Genética/genética , Saccharomyces/genética , Seleção Genética/genética , Hibridização Genômica Comparativa , Etanol , Cariótipo , Densidade Demográfica , Especificidade da Espécie , Temperatura
16.
Bioorg Med Chem ; 20(6): 1952-60, 2012 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-22261022

RESUMO

Chemical-genomic (CG) profiling of bioactive compounds is a powerful approach for drug target identification and mode of action studies. Within the last decade, research focused largely on the development and application of CG approaches in the model yeast Saccharomyces cerevisiae. The success of these methods has sparked interest in transitioning CG profiling to other biological systems to extend clinical and evolutionary relevance. Additionally, CG profiling has proven to enhance drug-synergy screens for developing combinatorial therapies. Herein, we briefly review CG profiling, focusing on emerging cross-species technologies and novel drug-synergy applications, as well as outlining needs within the field.


Assuntos
Descoberta de Drogas/métodos , Genômica/métodos , Animais , Antifúngicos/farmacologia , Sinergismo Farmacológico , Perfilação da Expressão Gênica/métodos , Redes Reguladoras de Genes/efeitos dos fármacos , Humanos , Micoses/tratamento farmacológico , Saccharomyces cerevisiae/efeitos dos fármacos , Saccharomyces cerevisiae/genética
17.
NPJ Syst Biol Appl ; 8(1): 3, 2022 01 27.
Artigo em Inglês | MEDLINE | ID: mdl-35087094

RESUMO

Morphological profiling is an omics-based approach for predicting intracellular targets of chemical compounds in which the dose-dependent morphological changes induced by the compound are systematically compared to the morphological changes in gene-deleted cells. In this study, we developed a reliable high-throughput (HT) platform for yeast morphological profiling using drug-hypersensitive strains to minimize compound use, HT microscopy to speed up data generation and analysis, and a generalized linear model to predict targets with high reliability. We first conducted a proof-of-concept study using six compounds with known targets: bortezomib, hydroxyurea, methyl methanesulfonate, benomyl, tunicamycin, and echinocandin B. Then we applied our platform to predict the mechanism of action of a novel diferulate-derived compound, poacidiene. Morphological profiling of poacidiene implied that it affects the DNA damage response, which genetic analysis confirmed. Furthermore, we found that poacidiene inhibits the growth of phytopathogenic fungi, implying applications as an effective antifungal agent. Thus, our platform is a new whole-cell target prediction tool for drug discovery.


Assuntos
Descoberta de Drogas , Saccharomyces cerevisiae , Reprodutibilidade dos Testes , Saccharomyces cerevisiae/genética
18.
G3 (Bethesda) ; 11(8)2021 08 07.
Artigo em Inglês | MEDLINE | ID: mdl-33956138

RESUMO

Momilactone B is a natural product with dual biological activities, including antimicrobial and allelopathic properties, and plays a major role in plant chemical defense against competitive plants and pathogens. The pharmacological effects of momilactone B on mammalian cells have also been reported. However, little is known about the molecular and cellular mechanisms underlying its broad bioactivity. In this study, the genetic determinants of momilactone B sensitivity in yeast were explored to gain insight into its mode of action. We screened fission yeast mutants resistant to momilactone B from a pooled culture containing genome-wide gene-overexpressing strains in a drug-hypersensitive genetic background. Overexpression of pmd1, bfr1, pap1, arp9, or SPAC9E9.06c conferred resistance to momilactone B. In addition, a drug-hypersensitive, barcoded deletion library was newly constructed and the genes that imparted altered sensitivity to momilactone B upon deletion were identified. Gene Ontology and fission yeast phenotype ontology enrichment analyses predicted the biological pathways related to the mode of action of momilactone B. The validation of predictions revealed that momilactone B induced abnormal phenotypes such as multiseptated cells and disrupted organization of the microtubule structure. This is the first investigation of the mechanism underlying the antifungal activity of momilactone B against yeast. The results and datasets obtained in this study narrow the possible targets of momilactone B and facilitate further studies regarding its mode of action.


Assuntos
Antifúngicos , Diterpenos , Lactonas , Proteínas de Schizosaccharomyces pombe , Schizosaccharomyces , Antifúngicos/farmacologia , Diterpenos/farmacologia , Genoma Fúngico , Lactonas/farmacologia , Schizosaccharomyces/efeitos dos fármacos , Schizosaccharomyces/genética , Proteínas de Schizosaccharomyces pombe/genética
19.
Science ; 370(6519): 974-978, 2020 11 20.
Artigo em Inglês | MEDLINE | ID: mdl-33214279

RESUMO

New antifungal drugs are urgently needed to address the emergence and transcontinental spread of fungal infectious diseases, such as pandrug-resistant Candida auris. Leveraging the microbiomes of marine animals and cutting-edge metabolomics and genomic tools, we identified encouraging lead antifungal molecules with in vivo efficacy. The most promising lead, turbinmicin, displays potent in vitro and mouse-model efficacy toward multiple-drug-resistant fungal pathogens, exhibits a wide safety index, and functions through a fungal-specific mode of action, targeting Sec14 of the vesicular trafficking pathway. The efficacy, safety, and mode of action distinct from other antifungal drugs make turbinmicin a highly promising antifungal drug lead to help address devastating global fungal pathogens such as C. auris.


Assuntos
Antifúngicos/farmacologia , Benzopiranos/farmacologia , Candida/efeitos dos fármacos , Candidíase Invasiva/tratamento farmacológico , Farmacorresistência Fúngica Múltipla , Isoquinolinas/farmacologia , Micromonospora/química , Urocordados/microbiologia , Animais , Antifúngicos/química , Antifúngicos/uso terapêutico , Benzopiranos/química , Benzopiranos/uso terapêutico , Modelos Animais de Doenças , Proteínas Fúngicas/metabolismo , Isoquinolinas/química , Isoquinolinas/uso terapêutico , Camundongos , Microbiota , Proteínas de Transferência de Fosfolipídeos/metabolismo
20.
Methods Mol Biol ; 2049: 419-444, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31602625

RESUMO

Neurodegenerative diseases (ND) represent a growing, global health crisis, one that lacks any disease-modifying therapeutic strategy. This critical need for new therapies must be met with an exhaustive approach to exploit all tools available. A yeast (Saccharomyces cerevisiae) model of α-synuclein toxicity-the protein causally linked to Parkinson's disease and other synucleinopathies-offers a powerful approach that takes advantage of the unique offerings of this system: tractable genetics, robust high-throughput screening strategies, unparalleled data repositories, powerful computational tools, and extensive evolutionary conservation of fundamental biological pathways. These attributes have enabled genetic and small molecule screens that have revealed toxic phenotypes and drug targets that translate directly to patient-derived iPSC neurons. Extending these insights, recent advances in genetic network analyses have generated the first "humanized" α-synuclein network, which has identified druggable proteins and led to validation of the toxic phenotypes in patient-derived cells. Unbiased phenotypic small molecule screens can identify compounds targeting critical proteins within α-synuclein networks. While identification of direct drug targets for phenotypic screen hits represents a bottleneck, high-throughput chemical genetic methods provide a means to uncover cellular targets and pathways for large numbers of compounds in parallel. Taken together, the yeast α-synuclein model and associated tools can reveal insights into underlying cellular pathologies, lead molecules and their cognate targets, and strategies to translate mechanisms of toxicity and cytoprotection into complex neuronal systems.


Assuntos
Saccharomyces cerevisiae/metabolismo , Sinucleinopatias/metabolismo , alfa-Sinucleína/metabolismo , Animais , Avaliação Pré-Clínica de Medicamentos , Redes Reguladoras de Genes , Humanos , Doença de Parkinson/tratamento farmacológico , Doença de Parkinson/metabolismo , Sinucleinopatias/tratamento farmacológico
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