Given the high attrition rates, substantial costs and slow pace of new drug discovery and development, repurposing of 'old' drugs to treat both common and rare diseases is increasingly becoming an attractive proposition because it involves the use of de-risked compounds, with potentially lower overall development costs and shorter development timelines. Various data-driven and experimental approaches have been suggested for the identification of repurposable drug candidates; however, there are also major technological and regulatory challenges that need to be addressed. In this Review, we present approaches used for drug repurposing (also known as drug repositioning), discuss the challenges faced by the repurposing community and recommend innovative ways by which these challenges could be addressed to help realize the full potential of drug repurposing.

Drug repurposing: progress, challenges and recommendations

A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles.

The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb, http://www.guidetopharmacology.org) provides expert-curated molecular interactions between successful and potential drugs and their targets in the human genome. Developed by the International Union of Basic and Clinical Pharmacology (IUPHAR) and the British Pharmacological Society (BPS), this resource, and its earlier incarnation as IUPHAR-DB, is described in our 2014 publication. This update incorporates changes over the intervening seven database releases. The unique model of content capture is based on established and new target class subcommittees collaborating with in-house curators. Most information comes from journal articles, but we now also index kinase cross-screening panels. Targets are specified by UniProtKB IDs. Small molecules are defined by PubChem Compound Identifiers (CIDs); ligand capture also includes peptides and clinical antibodies. We have extended the capture of ligands and targets linked via published quantitative binding data (e.g. Ki, IC50 or Kd). The resulting pharmacological relationship network now defines a data-supported druggable genome encompassing 7% of human proteins. The database also provides an expanded substrate for the biennially published compendium, the Concise Guide to PHARMACOLOGY. This article covers content increase, entity analysis, revised curation strategies, new website features and expanded download options.

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The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands

Interactions between proteins and small molecules are an integral part of biological processes in living organisms. Information on these interactions is dispersed over many databases, texts and prediction methods, which makes it difficult to get a comprehensive overview of the available evidence. To address this, we have developed STITCH ('Search Tool for Interacting Chemicals') that integrates these disparate data sources for 430 000 chemicals into a single, easy-to-use resource. In addition to the increased scope of the database, we have implemented a new network view that gives the user the ability to view binding affinities of chemicals in the interaction network. This enables the user to get a quick overview of the potential effects of the chemical on its interaction partners. For each organism, STITCH provides a global network; however, not all proteins have the same pattern of spatial expression. Therefore, only a certain subset of interactions can occur simultaneously. In the new, fifth release of STITCH, we have implemented functionality to filter out the proteins and chemicals not associated with a given tissue. The STITCH database can be downloaded in full, accessed programmatically via an extensive API, or searched via a redesigned web interface at http://stitch.embl.de.

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STITCH 5: augmenting protein–chemical interaction networks with tissue and affinity data

The judicious application of ligand or binding efficiency metrics, which quantify the molecular properties required to obtain binding affinity for a drug target, is gaining traction in the selection and optimization of fragments, hits and leads. Retrospective analysis of recently marketed oral drugs shows that they frequently have highly optimized ligand efficiency values for their targets. Optimizing ligand efficiency metrics based on both molecular mass and lipophilicity, when set in the context of the specific target, has the potential to ameliorate the inflation of these properties that has been observed in current medicinal chemistry practice, and to increase the quality of drug candidates.

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The role of ligand efficiency metrics in drug discovery

We tested the interaction of 72 kinase inhibitors with 442 kinases covering >80% of the human catalytic protein kinome. Our data show that, as a class, type II inhibitors are more selective than type I inhibitors, but that there are important exceptions to this trend. The data further illustrate that selective inhibitors have been developed against the majority of kinases targeted by the compounds tested. Analysis of the interaction patterns reveals a class of 'group-selective' inhibitors broadly active against a single subfamily of kinases, but selective outside that subfamily. The data set suggests compounds to use as tools to study kinases for which no dedicated inhibitors exist. It also provides a foundation for further exploring kinase inhibitor biology and toxicity, as well as for studying the structural basis of the observed interaction patterns. Our findings will help to realize the direct enabling potential of genomics for drug development and basic research about cellular signaling.

Comprehensive analysis of kinase inhibitor selectivity.

Provided herein are heterocyclic compounds for treatment of CSFIR, FLT3, KIT, and/or PDGFRβ kinase mediated diseases. Also provided are pharmaceutical compositions comprising the compounds and methods of using the compounds and compositions.

Heterocyclic compounds and use thereof as modulators of type iii receptor tyrosine kinases

Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC

Tumor-associated macrophages (TAMs) are thought to be regulators of solid tumor development based on their capacity to enhance metastatic, invasive, and angiogenic programming of neoplastic tissue. Colony stimulating factor-1 (CSF-1) is a key cytokine involved in recruitment and activation of tissue macrophages, exerting these effects through binding to a high-affinity receptor tyrosine kinase, the

CSF-1 receptor. We have developed a small molecule CSF1R inhibitor AC708 in an attempt to impact the TAM-related progression of human tumors. Here we demonstrate that AC708 possesses significant specificity for CSF1R relative to the rest of the kinome, and to the closely related PDGFR family receptors PDGFRα and β, FLT3, and KIT. In cell based assays, AC708 potently inhibited CSF1R phosphorylation mediated by CSF-1 (IC50

= 26 nM) and by IL-34 (IC50 = 33 nM). It also inhibited the viability of growth-factor dependent cells cultured in CSF-1 (IC50 = 38 nM) or

IL-34 (IC50 = 40 nM), and inhibited the CSF-1-mediated differentiation and survival of primary human osteoclast with an IC50 of 15 nM. In cytokine release experiments where enriched human monocytes were stimulated with either CSF-1 or IL-34, AC708 inhibited MCP-1 release with nearly identical IC50 regardless of which cytokine was used (CSF-1 (93 nM),

IL-34 (88 nM)), and with a lower IC50 than that obtained with the benchmark compound GW-2580 (CSF-1 (148 nM), IL-34 (140 nM)). In vivo, AC708 was assessed for its ability to inhibit the intraperitoneal growth of M-NFS-60 cells in mice. In these experiments, AC708 inhibited M-NFS-60 growth in a dose-dependent manner, with a greater than 80% reduction in cell number at 100 mg/kg, similar to that achieved with the benchmark compound Ki-20227. Two assays were employed to assess the ability of AC708 to modulate endogenous CSF1R. In the first model, AC708 inhibited CSF-1-mediated MCP-1 release in vivo by 60% when dosed at 100 mg/kg. In the second model, plasma levels of TRAP5b were determined following injection of recombinant Parathyroid hormone-related protein (PTHrP) with or without co-administration of AC708. PTHrP-induced increases of plasma TRAP5b were reduced by AC708 in a dose-dependent manner, with levels falling to below baseline in the 100 mg/kg dose group.

Lastly to assess the ability of AC708 to modulate TAMs we utilized the 4T-1 breast cancer line implanted orthotopically.

Although primary tumor growth was relatively unchanged by AC708 treatment in this model, administration of drug for two weeks resulted in a dose-dependent reduction of tumor resident macrophages, with a 70% reduction at the 100 mg/kg dose relative to vehicle control. AC708 impact on tumor angiogenesis and metastatic potential is currently under investigation and will be reported. These studies further validate CSF1R as a potential target in cancer, and support the development of AC708 as a therapeutic in oncology.

Citation Format: Robert C. Armstrong, Barbara Belli, Martin W. Rowbottom, Ron R. Nepomuceno, Alan Q. Dao, Allison M. Rooks, Dan Brigham, Craig W. McMannus, Michael D. Hocker, Mark W. Holladay, Gang Liu. AC708 is a potent and selective inhibitor of CSF1R and reduces tumor associated macrophage infiltration in a breast tumor model . [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 903. doi:10.1158/1538-7445.AM2013-903

Abstract 903: AC708 is a potent and selective inhibitor of CSF1R and reduces tumor associated macrophage infiltration in a breast tumor model .

Provided herein are heterocyclic compounds for treatment of CSF1R, FLT3, KIT, and/or PDGFRβ kinase mediated diseases. Also provided are pharmaceutical compositions comprising the compounds and methods of using the compounds and compositions.

Heterocyclic compounds and methods of use thereof

Background: Targeted protein degradation (TPD) using the endogenous ubiquitin (Ub) proteasome system (UPS) is a rapidly growing drug discovery approach to eliminate pathogenic proteins. Strategies for TPD have focused on designing heterobifunctional PROTACs that utilize ligand binding to select E3 ligases (e.g., cereblon and VHL), often resulting in compounds with poor drug-like properties. Monovalent degraders represent an alternative approach, in which small molecules are designed to bind the target protein and induce its degradation through the recruitment of an E3 ligase complex. Monovalent degraders generally have better physico-chemical properties than PROTACs; however, designing compounds to induce degradation is not well precedented and relies on serendipitous discovery. Methods: An E3 ligase agnostic chemical library was screened using our ultra-high throughput cell-based screening (uHTS) platform. Hits were identified by measuring protein degradation of BRD4 using immunofluorescence. A Ub pathway focused CRISPR screen was used to identify the E3 ligase responsible for compound-induced degradation of BRD4. The degradation mechanism was validated using western blot, luciferase-based protein-protein interaction (PPI) and mutational analyses. In vitro antitumor activity was assessed by proliferation and apoptosis assays. NOD/ SCID mice were implanted sub-Q with acute myeloid leukemia (AML) xenograft model MV-4-11 and treated with compounds administered QD. Results: uHTS resulted in identification of selective monovalent degraders that target the bromodomain extra-terminal (BET) protein, BRD4. Degrader series optimization produced PLX-3618, which demonstrated potent degradation of BRD4, without depleting BET family members BRD2 and BRD3. Proteasome and neddylation inhibitors confirmed degradation was mediated via the UPS, and a Ub-focused CRISPR screen identified CUL4DCAF11 as the E3 complex responsible for PLX-3618 induced degradation of BRD4. PPI studies verified a BRD4/PLX-3618/DCAF11 ternary complex; BRD4 point mutational analyses provided further insights into the DCAF11-mediated degradation mechanism. Degradation of BRD4 by PLX-3618 resulted in downregulation of the MYC oncogene and potent anti-proliferative activity against a panel of tumor cell lines, with high sensitivity observed in AML. in vivo, PLX-3618 resulted in complete tumor regression, whereas a pan-BET inhibitor only resulted in tumor growth inhibition without regression. PK/PD analyses provided insight into the unique exposure/response profile of targeted protein degraders. Conclusion: These results demonstrate the efficient discovery of novel monovalent degraders using our proprietary platform. Characterization of the degradation mechanism highlights the discovery of DCAF11 as a novel E3 ligase substrate receptor amenable to recruitment and degradation of BRD4. No conflict of interest. 

Michael D. Hocker

Papers

Comprehensive analysis of kinase inhibitor selectivity.

Heterocyclic compounds and use thereof as modulators of type iii receptor tyrosine kinases

Abstract 903: AC708 is a potent and selective inhibitor of CSF1R and reduces tumor associated macrophage infiltration in a breast tumor model .

Heterocyclic compounds and methods of use thereof

Discovery of novel small molecules that recruit DCAF11 for selective degradation of BRD4