Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Streamlined analysis of drug targets by proteome integral solubility alteration indicates organ-specific engagement

ABSTRACT: Proteins are the primary targets of almost all small molecule drugs. However, even the most selectively designed drugs can potentially target several unknown proteins. Identification of potential drug targets can facilitate design of new drugs and repurposing of existing ones. Current state-of-the-art proteomics methodologies enable screening of thousands of proteins against a limited number of drug molecules. Here we report the development of a label-free quantitative proteomics approach that enables proteome-wide screening of small organic molecules in a scalable, reproducible, and rapid manner by streamlining the proteome integral solubility alteration (PISA) assay. We used rat organs ex-vivo to determine organ specific targets of medical drugs and enzyme inhibitors to identify novel drug targets for common drugs such as Ibuprofen. Finally, global drug profiling revealed overarching trends of how small molecules affect the proteome through either direct or indirect protein interactions.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Rattus Norvegicus (rat) Homo Sapiens (human)

TISSUE(S): Spleen, Brain, Liver, Cell Culture, Kidney, Hela Cell

SUBMITTER: Tanveer Batth

LAB HEAD: Jesper Velgaard

PROVIDER: PXD050784 | Pride | 2024-10-16

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	DIA-NN_analysis.zip	Other
	FASTA_and_spectral_libraries.zip	Other
	PISA_HeLa_HepG2.zip	Other
	Pilot_experiments.zip	Other
	Rat_organ_Cancer_Drugs.zip	Other

Items per page:

1 - 5 of 7

Similar Datasets

Barcode sequencing of Saccharomyces cerevisiae deletion libraries, SYBARIS project

Project description:A systematic approach allowing the identification of the molecular way-of-action of novel potential drugs represents the golden-tool for drug-discovery. While high-throughput screening technologies of large libraries is now well established, the assessment of the drug targets and mechanism of action is still under development. Taking advantage of the yeast model Saccharomyces cerevisiae, we herein applied BarSeq, a Next Generation Sequencing-based method to the analysis of both haploinsufficiency and homozygous fitness effects of a novel antifungal drug ('089') compared to the well-known antifungal ketoconazole. '089' was a novel compound identified in during a screen for antifungal drugs, as it was showing fungicidal effects, and able to affect the yeast fitness at the mitochondrial level (Stefanini et al., 2010. (Dissection of the Effects of Small Bicyclic Peptidomimetics on a Panel of Saccharomyces cerevisiae Mutants;.J Biol Chem, 285: 23477-23485.) Integrative bioinformatic analysis of BarSeq, whole genome expression analysis and classical biological assays identified the target and cell pathways affected by the novel antifungal. Confirmation of the effects observed in the yeast model and in pathogenic fungi further demonstrated the reliability of the multi-sided approach and the novelty of the targets and way-of-action of the new class of molecules studied representing a valuable source of novel antifungals.

2016-04-30 | E-SYBR-6 | biostudies-arrayexpress

Rapid discovery of drug target engagement by isothermal shift assay

Project description:Determining protein targets directly bound by drug molecules remains challenging. Here we present the isothermal shift assay, iTSA, for rapid unbiased identification of drug targets. Compared with thermal proteome profiling, the prevailing method for target engagement, iTSA offers a simplified workflow, 4- fold higher throughput, and a multiplexed experimental design with higher replication. We demonstrate its application to determination of target engagement for several kinase inhibitors in lysates and living cells.

2019-03-28 | MSV000083640 | MassIVE

Ultrahigh-throughput discovery of modified aptamers as specific and potent enzyme inhibitors

Project description:Enzymes are instrumental to life and key actors of pathologies, making them relevant drug targets. Most enzyme inhibitors consist of small molecules. Although efficient, their development is long, costly and can come with unwanted off-targeting. Substantial gain in specificity and discovery efficiency is possible using biologicals. Best exemplified by antibodies, these drugs derived from living systems display high specificity and their development is eased by harnessing natural evolution. Aptamers are nucleic acids sharing functional similarities with antibodies while being deprived of many of their limitations. Yet, the success rate of inhibitory aptamer discovery remained hampered by the lack of an efficient discovery pipeline. In this work, we addressed this issue by introducing an ultrahigh-throughput strategy combining in vitro selection, microfluidic screening and bioinformatics. We demonstrate its efficiency by discovering a modified aptamer that specifically and strongly inhibits SPM-1, a beta-lactamase that remained recalcitrant to the development of potent inhibitors.

2024-09-15 | E-MTAB-14407 | biostudies-arrayexpress

Gene expression analysis upon exposure of hESCs to novel set of self-renewal and differentiation compounds

Project description:Here we present a strategy to adapt hESCs to high-throughput screening (HTS) conditions, resulting in an assay suitable for the discovery of small molecules that drive hESC self-renewal or differentiation. Use of this new assay has led to the identification of several currently marketed drugs and natural compounds promoting short-term hESC maintenance and compounds directing early lineage choice. Global gene expression analysis upon drug treatment reveals overlapping and novel pathways correlated to hESC self-renewal and differentiation. Our results demonstrate feasibility of hESC-based HTS and enhance the available repertoire of chemical compounds for manipulating hESC fate. Keywords: Global gene expression analysis, drug response, human ES cells, pluripotency, differentiation, self-renewal

2008-06-05 | GSE11302 | GEO

Functional metabolic molecules were identified as novel therapeutic targets to facilitate gemcitabine treatment against pancreatic cancer (Cells metabolomics)

Project description:With the development of frontier technologies in system biology, traditional omics-drove phenotypic studies are insufficient to decipher the diseases. Therefore, for a thorough understanding of the molecular mechanisms of diseases to investigate novel drug targets, traditional phenotypic studies must be broken through to the functional exploration of molecules. Meanwhile, the intuitive role of small molecule compounds (metabolites) in pathogenesis, precision diagnosis and therapy are gradually recognized compared to macromolecules such as DNA, RNA and proteins. Therefore, we pioneeringly proposed Spatial Temporal Operative Real Metabolomics (STORM) strategy that established a relationship between metabolic phenotypes and functions to accurately character abnormal metabolisms and further identify operative functional molecules as novel therapeutic targets. Here, given the difficulty of pancreatic cancer (PC) treatment and the high resistance of clinical drugs, we were committed to explore new targets and drugs of pancreatic cancer from a small molecular functional perspective via STORM strategy. Fortunately, based on targeted metabolomics, we found that gemcitabine, one of the most effective clinical anti-PC drugs, served as a dual modulator that promote the accumulation of functional metabolic molecules in purine metabolism to activate down-streamed kinases. And the quantitative consequences of related enzymes annotated the unique molecular mechanisms of purine metabolism regulations by gemcitabine. Collectively, we broadened the cognitions of gemcitabine in tumor inhibition, providing potential strategies for treating PC with small molecules modification. Even more importantly, with the integration of multiple frontier technologies, the STORM strategy has proven to be well adapted to the phenotypic era of functional molecules devoted to innovate molecule mechanism annotation and therapeutic discovery.

2022-03-25 | ST002122 | MetabolomicsWorkbench

Functional metabolic molecule were identified as novel therapeutic targets to facilitate gemcitabine treatment against pancreatic cancer (Tumor tissues metabolomics)

2022-03-25 | ST002121 | MetabolomicsWorkbench

Functional metabolic molecules were identified as novel therapeutic targets to facilitate gemcitabine treatment against pancreatic cancer (Cells metabolomics with ATP)

2022-08-04 | ST002255 | MetabolomicsWorkbench

Partitioning of cancer therapeutics in nuclear condensates

Project description:The nucleus contains diverse phase-separated condensates that compartmentalize and concentrate biomolecules with distinct physicochemical properties. Here we consider whether condensates concentrate small molecule cancer therapeutics such that their pharmacodynamic properties are altered. We found that antineoplastic drugs become concentrated in specific protein condensates in vitro and that this occurs through physicochemical properties independent of the drug target. This behavior was also observed in tumor cells, where drug partitioning influenced drug activity. Altering the properties of the condensate was found to impact the concentration and activity of drugs. These results suggest that selective partitioning and concentration of small molecules within condensates contributes to drug pharmacodynamics and that further understanding of this phenomenon may facilitate advances in disease therapy.

2020-04-27 | GSE149085 | GEO

Targeting Xist with compounds that disrupt RNA structure and X-inactivation

Project description:Although >98% of our genome is noncoding, nearly all drugs on the market target one of ~700 disease-related proteins. The historical reluctance to invest in noncoding RNA stems partly from requirements for drug targets to adopt a single stable conformation. Most RNAs can adopt several conformations of similar stabilities. RNA structures also remain challenging to determine. Nonetheless, an increasing number of diseases is now being attributed to noncoding RNA and the ability to target them would vastly expand the chemical space for drug development. Here we devise a screening strategy and identify small molecules that hit the non-coding RNA prototype, Xist. The X1 compound has drug-like properties and binds specifically to Xist’s RepA motif in vitro and in vivo. SAXS analysis reveals that RepA can adopt multiple conformations but favors one structure in solution. X1 binding reduces RepA’s conformational space, displaces cognate interacting protein factors (PRC2, SPEN), suppresses H3K27 trimethylation, and blocks initiation of X-inactivation. X1 inhibits cell differentiation and growth in a female-specific manner. Thus, RNA can be systematically targeted by drug-like compounds that disrupt RNA structure and epigenetic function.

2022-03-30 | GSE141683 | GEO

Ligand and Target Discovery by Fragment-Based Screening in Human Cells

Project description:Advances in the synthesis and screening of small-molecule libraries have accelerated the discovery of chemical probes for studying biological processes. Still, only a small fraction of the human proteome has chemical ligands, and the full complement of proteins with potential to be targeted by small molecules remains unknown. Here, we describe a platform that marries fragment-based ligand discovery with quantitative chemical proteomics to map thousands of reversible small molecule-protein interactions directly in human cells, many of which can be site-specifically determined. We advance this knowledge to create ligands that affect the activity of proteins heretofore lacking chemical probes and to identify by phenotypic screening small molecules that promote adipocyte differentiation by engaging the poorly characterized membrane protein PGRMC2. Fragment-based screening in human cells thus provides an extensive proteome-wide map of protein ligandability and facilitates the coordinated discovery of bioactive small molecules and their molecular targets.

2017-01-24 | GSE90731 | GEO