A Photoaffinity Labeling-Based Chemoproteomics Strategy for Unbiased Target Deconvolution of Small Molecule Drug Candidates

Thomas, Jason R.; Brittain, Scott M.; Lipps, Jennifer; Llamas, Luis; Jain, Rishi K.; Schirle, Markus

doi:10.1007/978-1-4939-7201-2_1

Cited by 22 publications

(37 citation statements)

References 8 publications

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“…EN219-alkyne probe labeling in situ and pulldown studies. Experiments were performed following an adaption of a previously described protocol (Thomas et al, 2017). The 231MFP cells were treated with either DMSO vehicle or 50 μM EN219-alkyne probe for 90 min.…”

Section: Structures Of Compounds Screened Can Be Found Inmentioning

confidence: 99%

Chemoproteomics-Enabled Ligand Screening Yields Covalent RNF114-Based Degraders that Mimic Natural Product Function

Luo

Spradlin

Boike

et al. 2020

Preprint

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The translation of natural product function to fully synthetic small molecules has remained an important process in medicinal chemistry for decades resulting in numerous FDA-approved medicines. We recently discovered that the terpene natural product nimbolide can be utilized as a covalent recruiter of the E3 ubiquitin ligase RNF114 for use in targeted protein degradation (TPD) -- a powerful therapeutic modality within modern day drug discovery. Using activity-based protein profiling-enabled covalent ligand screening approaches, we herein report the discovery of fully synthetic RNF114-based recruiter molecules that can also be exploited for PROTAC applications, and demonstrate their utility in degrading therapeutically relevant targets such as BRD4 and BCR-ABL in cells. The identification of simple and easily manipulated drug-like scaffolds that can mimic the function of a complex natural product is beneficial in further expanding the toolbox of E3 ligase recruiters, an area of great importance in drug discovery and chemical biology.

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Section: Structures Of Compounds Screened Can Be Found Inmentioning

confidence: 99%

Chemoproteomics-Enabled Ligand Screening Yields Covalent RNF114-Based Degraders that Mimic Natural Product Function

Luo

Spradlin

Boike

et al. 2020

Preprint

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“…Latest technological breakthroughs have revolutionized drug development, particularly regarding screening of ligands and/or inhibitors. Thermal proteome profiling has been recently introduced, as an evolution to the traditional fluorometric/calorimetric thermal shift assay, that now, when combined with mass spectrometry, can provide insights on drug's mechanism of action through comprehensive screening in living cells . The conventional thermal shift assay is based on the investigation of protein stabilization when interacting with other biomolecules like drugs, DNA, and co‐factors.…”

Section: New Technological Advancementsmentioning

confidence: 99%

Proteomics in Drug Development: The Dawn of a New Era?

Frantzi

Latosinska

Mischak

2019

Proteomics Clinical Apps

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Mass spectrometry offers the potential of acquiring high resolution data depicting the functional status of a group of healthy or diseased individuals, according to different conditions. As most of the drugs are currently targeting proteins, proteomics has a dual value, both in the discovery of new molecules as therapeutic targets, but also as a methodology to perform high throughput drug profiling. As there is an evident need for drugs to be improved in terms of efficacy, a mechanistic insight for downstream effectors can be valuable in order to predict side effects and resistance mechanisms. Recently developed assays, like thermal proteome profiling enables comprehensive drug target profiling and is, therefore, of high value in drug discovery. In this review, a systematic literature search is conducted and the most prominent proteomics studies as implicated in assisting drug discovery and development is presented. Focus is placed on investigations that are closer to implementation, therefore particular emphasis is given in studies conducted in human diseased population and further verified in vitro or in vivo.

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“…Experiments were performed following an adaption of a previously described protocol 81 High pH Reversed Phase Separation. Tandem mass tag labeled (TMT) samples were then consolidated, and separated using high-pH reversed phase chromatography (RP-10) with fraction collection as previously described 81 . Fractions were speed-vac dried, then reconstituted to produce 24 fractions for subsequent on-line nanoLC-MS/MS analysis.…”

Section: In Situ Nimbolide-alkyne Probe Labeling and Biotin-azide Pulmentioning

confidence: 99%

Harnessing the Anti-Cancer Natural Product Nimbolide for Targeted Protein Degradation

Spradlin

Ward

et al. 2018

Preprint

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Nimbolide, a terpenoid natural product derived from the Neem tree, impairs cancer pathogenicity across many types of human cancers; however, the direct targets and mechanisms by which nimbolide exerts its effects are poorly understood. Here, we used activity-based protein profiling (ABPP) chemoproteomic platforms to discover that nimbolide reacts with a novel functional cysteine crucial for substrate recognition in the E3 ubiquitin ligase RNF114. Nimbolide impairs breast cancer cell proliferation in-part by disrupting RNF114 substrate recognition, leading to inhibition of ubiquitination and degradation of the tumor-suppressors such as p21, resulting in their rapid stabilization. We further demonstrate that nimbolide can be harnessed to recruit RNF114 as an E3 ligase in targeted protein degradation applications and show that synthetically simpler scaffolds are also capable of accessing this unique reactive site. Our study highlights the utility of ABPP platforms in uncovering unique druggable modalities accessed by natural products for cancer therapy and targeted protein degradation applications.

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A Photoaffinity Labeling-Based Chemoproteomics Strategy for Unbiased Target Deconvolution of Small Molecule Drug Candidates

Cited by 22 publications

References 8 publications

Chemoproteomics-Enabled Ligand Screening Yields Covalent RNF114-Based Degraders that Mimic Natural Product Function

Chemoproteomics-Enabled Ligand Screening Yields Covalent RNF114-Based Degraders that Mimic Natural Product Function

Proteomics in Drug Development: The Dawn of a New Era?

Harnessing the Anti-Cancer Natural Product Nimbolide for Targeted Protein Degradation

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