Integrated fragment-based phenotypic screening and chemoproteomics for identification of novel small cell lung cancer-specific targets

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PROJECT ABSTRACT Despite major successes in lung cancer therapy over the last two decades, there are still many patients who do not receive any benefit from targeted or immunotherapies. This is particularly true for small cell lung cancer (SCLC), a recalcitrant cancer for which there are currently no effective targeted therapies. Although SCLC patients initially respond well to conventional chemo- and immune therapy, drug resistance develops rapidly illustrating the need for new therapeutic targets and drugs. Traditional drug discovery often prioritize known targets and operates in limited biological and chemical space. Smaller fragment-like compounds are significantly better suited to enter previously unrecognized binding sites thereby probing uncharted biological target space and identifying novel targets. We hypothesize that cell-based screening of fragment-like probe molecules combined with chemoproteomics for target identification will enable the simultaneous identification of (i) novel, highly SCLC- specific targets and (ii) new lead compounds as modulators of these targets. We propose to specifically interrogate SCLC cells in comparison to NSCLC and non-cancerous cells and screen a library of small fragment-like molecules. Combination with innovative proteomics technology can subsequently identify new actionable targets, which will be functionally validated and will serve as starting points for novel SCLC-specific drug discovery projects. Aim 1: To identify actionable targets and associated chemical hit compounds in SCLC vs NSCLC cancer cells. We will screen a 15,000 fragment-like compound library (~estimated to the equivalent of >100,000 lead-like compounds) in several SCLC, which represent different molecular subtypes, and control (NSCLC and non-cancerous lung epithelial) cell lines. The most SCLC-specific or SCLC subtype-specific hits will be validated regarding selective viability and apoptosis effects, also in combination with standard of care chemotherapy drugs. Aim 2: To identify and validate novel and selective, actionable targets in SCLC cells. Using a diverse panel of fragment-like compounds with ‘privileged’ BioCore motifs and SCLC-selective screening hits from Aim 1 we will perform mass spectrometry-based chemoproteomics through UV-mediated photocrosslinking and copper-catalyzed ‘click’ chemistry in SCLC cell lines. High confidence protein target candidates, based on comparison with control compounds/cell lines and DEPMAP database mining, will be validated using appropriate biochemical and signaling readouts, as well as RNAi- and CRISPR-based genetic modulation in an expanded cell line panel. Medicinal chemistry optimization of hits will be done by 1) chemoinformatic and structure-network similarity analysis and 2) synthesis of analogs based on the SAR of both library and synthesized compounds. Leads will be characterized using biochemical and cell-based binding assays (e.g. affinity-immunoblotting, SPR, nanoBRET). The expected outcome is the identification of novel SCLC- and/or SCLC subtype-specific targets and chemical starting points for dedicated drug discovery efforts that through further elucidation of the biological context and in vivo validation produce desperately needed new therapeutics for SCLC.