Pietro Ciceri

A quantitative analysis of kinase inhibitor selectivity.

Kinase inhibitors are a new class of therapeutics with a propensity to inhibit multiple targets. The biological consequences of multi-kinase activity are poorly defined, and an important step toward understanding the relationship between selectivity, efficacy and safety is the exploration of how inhibitors interact with the human kinome. We present interaction maps for 38 kinase inhibitors across a panel of 317 kinases representing >50% of the predicted human protein kinome. The data constitute the most comprehensive study of kinase inhibitor selectivity to date and reveal a wide diversity of interaction patterns. To enable a global analysis of the results, we introduce the concept of a selectivity score as a general tool to quantify and differentiate the observed interaction patterns. We further investigate the impact of panel size and find that small assay panels do not provide a robust measure of selectivity.

A small molecule–kinase interaction map for clinical kinase inhibitors

Kinase inhibitors show great promise as a new class of therapeutics. Here we describe an efficient way to determine kinase inhibitor specificity by measuring binding of small molecules to the ATP site of kinases. We have profiled 20 kinase inhibitors, including 16 that are approved drugs or in clinical development, against a panel of 119 protein kinases. We find that specificity varies widely and is not strongly correlated with chemical structure or the identity of the intended target. Many novel interactions were identified, including tight binding of the p38 inhibitor BIRB-796 to an imatinib-resistant variant of the ABL kinase, and binding of imatinib to the SRC-family kinase LCK. We also show that mutations in the epidermal growth factor receptor (EGFR) found in gefitinib-responsive patients do not affect the binding affinity of gefitinib or erlotinib. Our results represent a systematic small molecule-protein interaction map for clinical compounds across a large number of related proteins.

Dual kinase-bromodomain inhibitors for rationally designed polypharmacology.

Concomitant inhibition of multiple cancer-driving kinases is an established strategy to improve the durability of clinical responses to targeted therapies. The difficulty of discovering kinase inhibitors with an appropriate multi-target profile has, however, necessitated the application of combination therapies, which can pose significant clinical development challenges. Epigenetic reader domains of the bromodomain family have recently emerged as novel targets for cancer therapy. Here we report that several clinical kinase inhibitors also inhibit bromodomains with therapeutically relevant potencies and are best classified as dual kinase/bromodomain inhibitors. Nanomolar activity on BRD4 by BI-2536 and TG-101348, clinical PLK1 and JAK2/FLT3 kinase inhibitors, respectively, is particularly noteworthy as these combinations of activities on independent oncogenic pathways exemplify a novel strategy for rational single agent polypharmacological targeting. Furthermore, structure-activity relationships and co-crystal structures identify design features that enable a general platform for the rational design of dual kinase/bromodomain inhibitors.

Activation State-Dependent Binding of Small Molecule Kinase Inhibitors: Structural Insights from Biochemistry

Interactions between kinases and small molecule inhibitors can be activation state dependent. A detailed understanding of inhibitor binding therefore requires characterizing interactions across multiple activation states. We have systematically explored the effects of ABL1 activation loop phosphorylation and PDGFR family autoinhibitory juxtamembrane domain docking on inhibitor binding affinity. For a diverse compound set, the affinity patterns correctly classify inhibitors as having type I or type II binding modes, and we show that juxtamembrane domain docking can have dramatic negative effects on inhibitor affinity. The results have allowed us to associate ligand-induced conformational changes observed in cocrystal structures with specific energetic costs. The approach we describe enables investigation of the complex relationship between kinase activation state and compound binding affinity and should facilitate strategic inhibitor design.

Abstract 4238: BROMOscan - a high throughput, quantitative ligand binding platform identifies best-in-class bromodomain inhibitors from a screen of mature compounds targeting other protein classes.

Post-translationally appended acetyllysine marks on histone tails are key regulatory features of the epigenetic code. Bromodomains are “readers” of this specific lysine acetylation code, playing an important role in chromatin remodeling and regulation of gene expression. Bromodomains have emerged as an important new druggable target class in small-molecule inhibitor drug discovery, and several bromodomain-containing proteins have been associated with disease. There are 57 bromodomains contained in 41 different proteins; however, few small molecule bromodomain inhibitors have been reported. One primary factor limiting the discovery of new inhibitors is the absence of a comprehensive biochemical bromodomain screening platform. Here we describe the application of DiscoveRx Corporation9s proven ligand binding assay technology (KINOMEscan) to the development of quantitative ligand binding assays for human bromodomains (BROMOscan). We have developed a carefully validated assay panel that covers >30 percent of the human bromodomain family, and this panel is suitable for HTS, selectivity profiling, and quantitative affinity (Kd) assessment. We have used this panel internally to identify novel bromodomain inhibitors and, remarkably, have demonstrated that known, mature inhibitors thought to be selective for targets from other protein families have best in class affinity for bromodomains as well. These data shall be presented, as will a description of the BROMOscan panel replete with extensive assay validation data. Citation Format: Elizabeth Quinn, Lisa Wodicka, Pietro Ciceri, Gabriel Pallares, Elyssa Pickle, Adam Torrey, Mark Floyd, Jeremy Hunt, Daniel Treiber. BROMOscan - a high throughput, quantitative ligand binding platform identifies best-in-class bromodomain inhibitors from a screen of mature compounds targeting other protein classes. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4238. doi:10.1158/1538-7445.AM2013-4238

Abstract LB-390: High throughput, quantitative ligand binding assays for human bromodomains

Post translationally appended acetyl-lysine marks on histone tails are key regulatory features of the epigenetic code. Bromodomains are “readers” of this specific lysine acetylation code, playing an important role in chromatin remodeling and regulation of gene expression. Bromodomains have emerged as an important new druggable target class in small-molecule inhibitor drug discovery, and several bromodomain-containing proteins have been associated with disease. There are 57 bromodomains contained in 41 different proteins, however, few small molecule inhibitors of bromodomains have been identified to date. The primary factor limiting the discovery of new inhibitors is the absence of a comprehensive, biochemical screening platform for bromodomains. Here we describe the application of DiscoveRx Corporation9s novel competitive binding assay technology (used to build the KINOMEscan panel of >450 kinase assays) to the development of quantitative ligand binding assays for human bromodomains. By applying our established methodologies, we have rapidly developed an assay panel that covers >15% of the bromodomain family, with the ultimate goal of developing a comprehensive panel, comparable to the KINOMEscan kinase assay panel. A robust bromodomain assay panel suitable for high throughput screening that delivers quantitative ligand binding data will facilitate the identification and optimization of potent and selective small molecule bromodomain inhibitors suitable for both pharmaceutical use and as tool compounds to further elucidate the roles of bromodomains in human disease. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-390. doi:1538-7445.AM2012-LB-390