Quantitative High Throughput Screening for Small Molecules Targeting CD47 in Cancer

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SCIENTIFIC ABSTRACT CD47 is an immune checkpoint molecule that downregulates key aspects of both the innate and adaptive anti- tumor immune response via the inhibitory receptor SIRPα on tumor associated myeloid cells including macrophage and myeloid-derived suppressor cells. CD47 is expressed at higher levels in solid and hematological tumors than nonmalignant tissues and correlates with treatment resistance and poor prognosis. This has led to the development of biologics such as humanized CD47 antibodies that block SIRPα engagement which are being tested in clinical trials. Unfortunately, toxicological issues, including anemia related to ubiquitous CD47 expression and poor tumor microenvironment (TME) selectivity vs normal cells, are barriers to their clinical advancement. Additional SIRPα-CD47 blocking modalities are needed to realize the full potential of this critical immunotherapy target. We hypothesize that using small molecules targeting SIRPα to block SIRPα-CD47 interaction will result in better TME selectivity, lower toxicity, enhanced solid tumor penetration, and lead to greater anti-tumor efficacy. To address this hypothesis, we built an innovative multidisciplinary program to develop the first SIRPα-targeting small molecules and made substantial progress toward this goal with our current NIH award. Like many immune checkpoints, SIRPα-CD47 is a protein-protein interaction complex and is challenging to target using small molecules as we described. However, using a combination of X-ray crystallography fragment screening, protein-observed Heteronuclear Single Quantum Coherence (HSQC) NMR, and Homogeneous Time Resolved Fluorescence (HTRF), we identified chemotypes that bound SIRPα. These molecules dramatically altered the conformation of SIRPα regions at the CD47 interface, providing a mechanism for disruption of the complex. We subsequently improved these initial X-ray screening hits into highly ligand-efficient (LE = 0.45) probes that bound SIRPα and inhibited CD47 interaction. These novel SIRPα-binding molecules have been validated by HTRF, AlphaScreen, isothermal calorimetry, HSQC NMR, and X-ray crystallography, yielding a consistent SAR profile and provide a springboard to a high impact hit to lead campaign. Using our unique molecular design tools, we developed a structure-based strategy to further optimize our hits into potent and selective lead-like molecules. To support this campaign, we established an innovative set of biological in vitro characterization assays to test their anti-tumor immune activity and mechanism of action. The overall objective of this MERIT award extension application is to continue the development of our validated SIRPα-targeting hits into potent biologically active lead molecules ready for in vivo evaluation according to the following specific aims: Aim 4. Design, synthesis, and biochemical evaluation of potent and selective CD47-SIRPα inhibiting small molecules from validated SIRPα-bound fragment hits. The goal of this aim is to generate multiple candidate molecules by local optimization of the hit core and growing into adjacent subpockets with sufficient potency to establish their biological activity in Aim 5. Aim 5. Evaluation and optimization of CD47-SIRPα inhibiting small molecule activities in clinically-relevant models. To determine the potency necessary for small molecule SIRPα-CD47 inhibitors to elicit biological activity, we will evaluate their in vitro activity and target selectivity using a series of validated biological mechanism of action assays and tumor-immune interaction characterization systems. The successful completion of these aims will result in lead candidate molecules for subsequent evaluation of anti-tumor immune activity evaluation using well-characterized indication-specific animal models. Our novel approach to this compelling target will create first of their kind chemical probes to interrogate the mechanisms of SIRPα-CD47-mediated tumor cell killing. It will lay the foundation for further development of a best-in-class immunotherapy for cancer patients with significant advantages over other CD47-targeted cancer immunotherapies now in development.