Chemical Proteomics Identifies Druggable Vulnerabilities in a Genetically Defined Cancer

Abstract

The transcription factor NRF2 is a master regulator of the cellular antioxidant response and is often genetically activated in Non-Small Cell Lung Cancers (NSCLCs) by, for instance, mutations in the interacting protein KEAP1. While direct pharmacological inhibition of NRF2 has proven challenging, its aberrant activation rewires biochemical networks in cancer cells that may create special vulnerabilities. Here, we use chemical proteomics to map druggable proteins that are selectively expressed in KEAP1-mutant NSCLC cells. Principal among these was NR0B1, an atypical orphan nuclear receptor that we show engages in a multimeric protein complex to regulate the transcriptional output of KEAP1-mutant NSCLC cells. We further identify small molecules that covalently target a conserved cysteine within the NR0B1 protein interaction domain and demonstrate that these compounds disrupt NR0B1 complexes and impair the anchorage-independent growth of KEAP1-mutant cancer cells. Our findings designate NR0B1 as a druggable, transcriptional regulator that supports NRF2-dependent lung cancers.

A Chemical Biology View of Bioactive Small Molecules and a Binder‐Based Approach to Connect Biology to Precision Medicines

“…This innovation has the potential to identify binders for both specific states of proteins and protein complexes, including ones that are challenging to purify – a requirement for the traditional fragment-based approach. [24] …”

A Personal Perspective on Chemical Biology: Before the Beginning

“…[51,52] For drug discovery with undruggable targets, there is a bump and hole strategy by 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 Kevan Shokat (UCSF) engineering unnatural nucleotidespecificity for tyrosine kinase [53] and activity based protein profiling by Ben Cravatt (Scripps) and his chemical strategies for the global analysis of enzyme function. [54] Finally the discovery by Doudna and coworkers (Berkeley) of the CRISPR/cas genome cutting machinery [55] followed by the protein engineering of CRISPR by David Liu (Harvard) for programmable editing of a target base in genomic DNA is driving new discovery in biology. [56] 6.…”

Targeted therapy of esophageal squamous cell carcinoma: the NRF2 signaling pathway as target

“…For example, a recent study used chemical proteomics to map druggable proteins that are selectively expressed in NRF2 high lung cancer. NR0B1 was identified as a downstream druggable target, and small molecules were found to disrupt NR0B1 protein complexes and thus inhibit NRF2‐dependent lung cancer . Several small molecule NRF2 inhibitors—halofuginone, brusatol, AEM1, and ML385—have been identified by high‐throughput screening.…”

“…NR0B1 was identified as a downstream druggable target, and small molecules were found to disrupt NR0B1 protein complexes and thus inhibit NRF2-dependent lung cancer. 111 Several small molecule NRF2 inhibitors-halofuginone, 112 brusatol, 113 AEM1, 114 and ML385 115 -have been identified by highthroughput screening. We are also in the process of screening NRF2 inhibitors from chemical libraries for NRF2 high ESCC.…”