Dataset Information

Compound Interaction Screen on a Photoactivatable Cellulose Membrane (CISCM) Identifies Drug Targets.

ABSTRACT: Identifying the protein targets of drugs is an important but tedious process. Existing proteomic approaches enable unbiased target identification but lack the throughput needed to screen larger compound libraries. Here, we present a compound interaction screen on a photoactivatable cellulose membrane (CISCM) that enables target identification of several drugs in parallel. To this end, we use diazirine-based undirected photoaffinity labeling (PAL) to immobilize compounds on cellulose membranes. Functionalized membranes are then incubated with protein extract and specific targets are identified via quantitative affinity purification and mass spectrometry. CISCM reliably identifies known targets of natural products in less than three hours of analysis time per compound. In summary, we show that combining undirected photoimmobilization of compounds on cellulose with quantitative interaction proteomics provides an efficient means to identify the targets of natural products.

SUBMITTER: Melder FTI

PROVIDER: S-EPMC9826412 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Compound Interaction Screen on a Photoactivatable Cellulose Membrane (CISCM) Identifies Drug Targets.

Melder F Teresa I FTI Lindemann Peter P Welle Alexander A Trouillet Vanessa V Heißler Stefan S Nazaré Marc M Selbach Matthias M

ChemMedChem 20220920 19

Identifying the protein targets of drugs is an important but tedious process. Existing proteomic approaches enable unbiased target identification but lack the throughput needed to screen larger compound libraries. Here, we present a compound interaction screen on a photoactivatable cellulose membrane (CISCM) that enables target identification of several drugs in parallel. To this end, we use diazirine-based undirected photoaffinity labeling (PAL) to immobilize compounds on cellulose membranes. F ...[more]

PMID: 35867055

Similar Datasets

Project description:Purpose: BCR-ABL-positive acute lymphoid leukemia (ALL) has a dire prognosis. Despite improved disease-free survival due to implementation of TKIs in front-line therapy, patient survival remains unsatisfactory and there exists a need for new treatments. Therefore, we performed a drug screen based on competition between untransformed cells and BCR-Abl-transformed cells, and identified several compounds that selectively reduce the competitive fitness of BCR-Abl-transformed cells. Using a systems approach we discovered that one of these compounds, DJ34, induces potent activation of p53 and rapid degradation of c-Myc, which is frequently deregulated in leukemia. DJ34 treatment induced apoptosis, cell cycle arrest and cell differentiation and inhibited survival of primary AML cells, both ex vivo and in a zebrafish PDX model. The goals of this study is to check the effect of DJ34 on transcriptome profile of BCR-Abl expressing BaF3 cells. Methods: mRNA profiles of BaF3 cells expressing BCR-Abl treated with DMSO or 20µM DJ34 for 6hrs were generated by Illumina Hiseq 4000 SE50, in triplicate. Then, clean reads (as provided by BGI) were mapped to the GRCm38.85 genome assembly using Tophat2 (v. 2.1.1) [1] using default options BAM files were indexed using SAMtools [2]. Differential expression data was produced using cuffquant and cuffdiff with default options, from the cufflinks suite (v 2.2.1 / SVN rev 4237) [3]. Reference genome for the primary assembly and gene annotations used are revision 85 of GRCm38, from ensembl.org. The .Bam and .tdf files were used for quantification and visualization in IGV respectively. [1] Kim, Daehwan, et al. "TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions." Genome biology 14.4 (2013): R36. [2] Li, Heng, et al. "The sequence alignment/map format and SAMtools." Bioinformatics 25.16 (2009): 2078-2079. [3] Trapnell, Cole, et al. "Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks." Nature protocols 7.3 (2012): 562. Results: Using data analysis workflow described above, we identified differentially expressed genes in the control and DJ34 treated BaF3 cells expressing BCR-Abl cells. Conclusions: Competition based drug screening has identified DJ34 that selectively erradicates BCR-Abl expressing BaF3 cells. Our RNa-seq basaed transcriptome analysis shows that DJ34 induces potent activation of p53 and rapid degradation of c-Myc, which is frequently deregulated in leukemia.

Dataset Information

Compound Interaction Screen on a Photoactivatable Cellulose Membrane (CISCM) Identifies Drug Targets.

Publications

Compound Interaction Screen on a Photoactivatable Cellulose Membrane (CISCM) Identifies Drug Targets.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets