Dataset Information

Methotrexate-based PROTACs as DHFR chemical probes

ABSTRACT: Methotrexate (MTX) is a potent inhibitor of dihydrofolate reductase (DHFR), where is it used as both an antineoplastic and an immunosuppressant. Mechanisms of MTX resistance in cancers include MTX polyglutamylation and upregulation of DHFR. A series of MTX-based PROteolysis TArgeting Chimeras (PROTACs) were designed to selectively degrade human DFHR. These on-target, cell-active PROTACs show proteosome- and E3 ligase-dependent DHFR degradation, selective degradation of DHFR by proteomics, and interpretable structure-activity relationships. Importantly, these PROTACs produced distinct, less-lethal phenotypes compared to MTX, indicating these compounds can complement conventional DFHR enzymatic inhibitors as tool compounds. This chemical probe set, composed of the PROTAC (Diruotrexate), its ester pro-drug (Diruotrexate-ester) and negative control analogs (Diruotrexate-IA1, -IA2), should serve as useful tools for studying one-carbon biochemistry.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Dingyin Tao

LAB HEAD: Dingyin Tao

PROVIDER: PXD030140 | Pride | 2025-05-06

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

Items per page:

1 - 5 of 18

Publications

Methotrexate-based PROTACs as DHFR-specific chemical probes.

Rana Sandeep S Dranchak Patricia P Dahlin Jayme L JL Lamy Laurence L Li Wenqing W Oliphant Erin E Shrimp Jonathan H JH Rajacharya Girish H GH Tharakan Ravi R Holland David O DO Whitten Apryl S AS Wilson Kelli M KM Singh Pankaj K PK Durum Scott K SK Tao Dingyin D Rai Ganesha G Inglese James J

Cell chemical biology 20231023 2

Methotrexate (MTX) is a tight-binding dihydrofolate reductase (DHFR) inhibitor, used as both an antineoplastic and immunosuppressant therapeutic. MTX, like folate undergoes folylpolyglutamate synthetase-mediated γ-glutamylation, which affects cellular retention and target specificity. Mechanisms of MTX resistance in cancers include a decrease in MTX poly-γ-glutamylation and an upregulation of DHFR. Here, we report a series of potent MTX-based proteolysis targeting chimeras (PROTACs) to investiga ...[more]

PMID: 37875111

Similar Datasets

Project description:The response regulator HrrA belonging to the HrrSA two-component system (previously named CgtSR11) is known to be repressed by the global iron-dependent regulator DtxR in Corynebacterium glutamicum. Sequence analysis indicated an involvement of the HrrSA system in heme-dependent gene expression. Growth experiments revealed that the non-pathogenic soil bacterium C. glutamicum is able to use hemin or hemoglobin as sole iron source. In DNA microarray analyses a putative operon encoding the hemin-binding protein HtaA and the putative hemin ABC transporter HmuTUV showed a strong upregulation in heme-grown cells. Deletion of the hmu operon clearly affects heme utilization, but does not completely abolish growth on heme or hemoglobin. As a central part of this study, we investigated the regulon of the response regulator HrrA via comparative transcriptome analysis of a hrrA deletion mutant and C. glutamicum wild type in combination with DNA-protein interaction studies with purified HrrA protein. Our data provide evidence for a heme-dependent transcriptional activation of heme oxygenase (hmuO), an enzyme involved in the utilization of heme as iron source. Besides hmuO, HrrA was shown to activate the expression of heme-containing components of the respiratory chain, namely ctaD and the ctaE-qcrCAB operon encoding subunits I and III of cytochrome aa3 oxidase and three subunits of the cytochrome bc1 complex. Furthermore, HrrA represses almost all genes involved in heme biosynthesis, including glutamyl-tRNA reductase (hemA), uroporphyrinogen decarboxylase (hemE), and ferrochelatase (hemH). Thus, our data clearly emphasize a central role of the HrrSA system in the control of heme homeostasis in C. glutamicum. Three biological replicates of each experiment were performed. Experiment 1: Transcriptome comparison of wild type grown und FeSO4 or heme as iron source; Exp. 2: WT vs. hrrA deletion mutant grown on FeSO4; Exp. 3: WT vs. hrrA mutant grown on heme. For analysis via DNA microarraysose RNA was isolated from exponentially growing cells cultivated in CgXII medium containing glucose as carbon source and either 2.5 uM FeSO4 or 2.5 uM heme as iron source.

Project description:Metaproteomic analysis of air particulate matter provides information about the properties of bioaerosols in the atmosphere and their influence on climate and public health. In this work, a new method for the extraction and analysis of proteins in airborne particulate matter from quartz microfiber filters was developed. Different protein extraction procedures were tested in order to select the best extraction protocol in terms of protein recovery. The optimized method was tested for extraction of proteins from spores of ubiquitous bacteria species and used for the first time for the metaproteomics characterization of filters from work environment. In particular, ambient aerosol samples were collected in different working environments, i.e. a composting plant, wastewater treatment plant and agricultural holding. One-hundred seventy-nine, 15, 205 and 444 proteins were successfully identified in composting plant, wastewater treatment plant, and agricultural holding, respectively. All identified proteins were mainly originate from fungi, bacteria and plants which is in line with the major categories of primary biological aerosol particles. The paper is the first metaproteomic study applied to bioaereosol samples collected in occupationally relevant environmental sites providing interesting information on the composting, wastewater treatment and feed blending processes. Significance This manuscript describes the metaproteomic analysis of aerosol samples collected in work enviroments. This is a novel use of aereosol samples and is needed as there is no really comprehensive way of analysing aereosol samples from a metaproteomic point of view. This paper could help to advance methods for metaproteomic analysis of bioaersols, specifically by comparing protein extraction protocols and pairing the best performing extraction protocol with a gel-free protein separation procedure applied for the first time for analysis of bioaerosol samples. The obtained data showed as bioaerosol was essentially made of fungi, bacteria and plant proteins, many of which could be associated to possible aerosolisation and could be a major health concern for workers on site and to the populations residing in neighbouring area.

			Action	DRS
	HBL_DMSO1ugB01.raw	Raw
	HBL_DMSO1ugB02.raw	Raw
	HBL_DMSO1ugB03.raw	Raw
	HBL_FMTX1ugB01.raw	Raw
	HBL_FMTX1ugB02.raw	Raw