Targeted Investigational Oncology Agents in the NCI-60: A Phenotypic Systems-based Resource

The NCI-60 human tumor cell line panel has proved to be a useful tool for the global cancer research community in the search for novel chemotherapeutics. The publicly available cell line characterization and compound screening data from the NCI-60 assay have significantly contributed to the understanding of cellular mechanisms targeted by new oncology agents. Signature sensitivity/resistance patterns generated for a given chemotherapeutic agent against the NCI-60 panel have long served as fingerprint presentations that encompass target information and the mechanism of action associated with the tested agent. We report the establishment of a new public NCI-60 resource based on the cell line screening of a large and growing set of 175 FDA-approved oncology drugs (AOD) plus >825 clinical and investigational oncology agents (IOA), representing a diverse set (>250) of therapeutic targets and mechanisms. This data resource is available to the public (https://ioa.cancer.gov) and includes the raw data from the screening of the IOA and AOD collection along with an extensive set of visualization and analysis tools to allow for comparative study of individual test compounds and multiple compound sets.

Comparative Analysis of Drug-like EP300/CREBBP Acetyltransferase Inhibitors

The human acetyltransferase paralogues EP300 and CREBBP are master regulators of lysine acetylation whose activity has been implicated in various cancers. In the half-decade since the first drug-like inhibitors of these proteins were reported, three unique molecular scaffolds have taken precedent: an indane spiro-oxazolidinedione (A-485), a spiro-hydantoin (iP300w), and an aminopyridine (CPI-1612). Despite increasing use of these molecules to study lysine acetylation, the dearth of data regarding their relative biochemical and biological potencies makes their application as chemical probes a challenge. To address this gap, here we present a comparative study of drug-like EP300/CREBBP acetyltransferase inhibitors. First, we determine the biochemical and biological potencies of A-485, iP300w, and CPI-1612, highlighting the increased potencies of the latter two compounds at physiological acetyl-CoA concentrations. Cellular evaluation shows that inhibition of histone acetylation and cell growth closely aligns with the biochemical potencies of these molecules, consistent with an on-target mechanism. Finally, we demonstrate the utility of comparative pharmacology by using it to investigate the hypothesis that increased CoA synthesis caused by knockout of PANK4 can competitively antagonize the binding of EP300/CREBBP inhibitors and demonstrate proof-of-concept photorelease of a potent inhibitor molecule. Overall, our study demonstrates how knowledge of the relative inhibitor potency can guide the study of EP300/CREBBP-dependent mechanisms and suggests new approaches to target delivery, thus broadening the therapeutic window of these preclinical epigenetic drug candidates.

Multicellular Complex Tumor Spheroid Response to DNA Repair Inhibitors in Combination with DNA-damaging Drugs

Multicellular spheroids comprised of malignant cells, endothelial cells, and mesenchymal stem cells served as an in vitro model of human solid tumors to investigate the potentiation of DNA-damaging drugs by pharmacologic modulation of DNA repair pathways. The DNA-damaging drugs, topotecan, trabectedin, and temozolomide were combined with varied inhibitors of DNA damage response enzymes including PARP (olaparib or talazoparib), ATM (ataxia telangiectasia mutated; AZD-1390), ATR (ataxia telangiectasia and Rad3-related protein; berzosertib or elimusertib), and DNA-PK (DNA-dependent protein kinase; nedisertib or VX-984). A range of clinically achievable concentrations were tested up to the clinical Cmax, if known. Mechanistically, the types of DNA damage induced by temozolomide, topotecan, and trabectedin are distinct, which was apparent from the response of spheroids to combinations with various DNA repair inhibitors. Although most combinations resulted in additive cytotoxicity, synergistic activity was observed for temozolomide combined with PARP inhibitors as well as combinations of the ATM inhibitor AZD-1390 with either topotecan or trabectedin. These findings might provide guidance for the selection of anticancer agent combinations worthy of further investigation.

Significance

Clinical efficacy of DNA-damaging anticancer drugs can be influenced by the DNA damage response in tumor cells. The potentiation of DNA-damaging drugs by pharmacologic modulation of DNA repair pathways was assessed in multicellular tumor spheroids. Although most combinations demonstrated additive cytotoxicity, synergistic cytotoxicity was observed for several drug combinations.

Comparative analysis of drug-like EP300/CREBBP acetyltransferase inhibitors

The human acetyltransferase paralogs EP300 and CREBBP are master regulators of lysine acetylation whose activity has been implicated in various cancers. In the half-decade since the first drug-like inhibitors of these proteins were reported, three unique molecular scaffolds have taken precedent: an indane spiro-oxazolidinedione (A-485), a spiro-hydantoin (iP300w), and an aminopyridine (CPI-1612). Despite increasing use of these molecules to study lysine acetylation, the dearth of data regarding their relative biochemical and biological potencies makes their application as chemical probes a challenge. To address this gap, here we present a comparative study of drug-like EP300/CREBBP acetyltransferase inhibitors. First, we determine the biochemical and biological potencies of A-485, iP300w, and CPI-1612, highlighting the increased potency of the latter two compounds at physiological acetyl-CoA concentrations. Cellular evaluation shows that inhibition of histone acetylation and cell growth closely aligns with the biochemical potencies of these molecules, consistent with an on-target mechanism. Finally, we demonstrate the utility of comparative pharmacology by using it to investigate the hypothesis that increased CoA synthesis caused by knockout of PANK4 can competitively antagonize binding of EP300/CREBBP inhibitors and demonstrate proof-of-concept photorelease of a potent inhibitor molecule. Overall, our study demonstrates how knowledge of relative inhibitor potency can guide the study of EP300/CREBBP-dependent mechanisms and suggests new approaches to target delivery, thus broadening the therapeutic window of these preclinical epigenetic drug candidates.

Abstract 5720: Combination therapies in matched 3D in vitro and in vivo preclinical models of rare and recalcitrant cancers from the National Cancer Institute’s Patient-Derived Models Repository

There is a major need in oncology drug development to establish predictive preclinical assays with high translational relevance to patient responses. The National Cancer Institute’s Patient-Derived Models Repository (https://pdmr.cancer.gov) offers a collection of highly characterized models from a variety of cancer types including rare and recalcitrant malignancies and tumors from patients of diverse ancestry. This collection includes matched sets of patient-derived cell lines, organoids, and xenografts (PDXs), which allows comparisons of drug responses from in vitro and in vivo assays performed with the same patient-derived tumor model. A high-throughput screen was conducted using matched sets of patient-derived organoids and cell lines. Patient-derived cell lines were grown as 3D multicellular spheroids mixed with endothelial cells and mesenchymal stem cells. The patient-derived organoids were 100% tumor cells and were plated in 5% basement membrane extract supplemented with growth factors and cytokines. All drugs were tested at concentrations up to their reported clinical Cmax values and cell viability for individual drug treatments and drug combinations were assayed using CellTiter-Glo 3D after seven days drug exposure. Prior to the endpoint viability measurements, growth curves for spheroid median volume and organoid median surface area were calculated from a series of non-invasive brightfield images collected every 12 hours. For some drug combinations, differential responses were observed between the matched organoids and multicellular spheroids, potentially reflecting the contribution of the stromal component in the spheroids. Overall, the drug-dependent growth responses observed from the two 3D in vitro models (i.e., multicellular spheroids and organoids) were frequently comparable to those observed in vivo from PDXs. For example, the in vitro activities of several drug combinations including: BAY1895344 + temozolomide, erlotinib + cediranib, entinostat + talazoparib, and selumetinib + abemaciclib, demonstrated good agreement with the responses observed in vivo. However, among the drug combinations tested ixazomib + panobinostat showed the greatest cytotoxicity in vitro but had no activity in the matched PDX models. The availability of matched patent-derived cell lines, organoids and PDXs provides an opportunity to learn about the features of assay methodologies and data analyses that influence the successful translation of preclinical results between in vitro and in vivo systems. The results of this study are encouraging, but also highlight discrepancies that will be important to investigate, understand and address in order to improve translational capacity of future assays. This project was funded in part with federal funds from the NCI, NIH, under contract no. HHSN261201500003I.

Citation Format: Thomas S. Dexheimer, Thomas Silvers, Rene Delosh, Russell Reinhart, Chad Ogle, Zahra Davoudi, Eric Jones, Debbie Trail, John Carter, Justine Mills, Kyle Georgius, Howard Stotler, Michelle Norris, Shannon Uzelac, Suzanne Borgel, Tiffanie Minor, Luke Stockwin, Michael Mullendore, Kevin Plater, Keegan Kalmbach, Jessica Steed, Matthew Murphy, Gareth Bliss, Carrie Bonomi, Kelly Dougherty, Marion Gibson, Kevin Cooper, Dianne Newton, Cindy R. Timme, Yvonne A. Evrard, Melinda G. Hollingshead, Nathan P. Coussens, Ralph E. Parchment, James H. Doroshow, Beverly A. Teicher. Combination therapies in matched 3D in vitro and in vivo preclinical models of rare and recalcitrant cancers from the National Cancer Institute’s Patient-Derived Models Repository. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5720.

Discovery of Novel Small-Molecule Scaffolds for the Inhibition and Activation of WIP1 Phosphatase from a RapidFire Mass Spectrometry High-Throughput Screen

Wild-type P53-induced phosphatase 1 (WIP1), also known as PPM1D or PP2Cδ, is a serine/threonine protein phosphatase induced by P53 after genotoxic stress. WIP1 inhibition has been proposed as a therapeutic strategy for P53 wild-type cancers in which it is overexpressed, but this approach would be ineffective in P53-negative cancers. Furthermore, there are several cancers with mutated P53 where WIP1 acts as a tumor suppressor. Therefore, activating WIP1 phosphatase might also be a therapeutic strategy, depending on the P53 status. To date, no specific, potent WIP1 inhibitors with appropriate pharmacokinetic properties have been reported, nor have WIP1-specific activators. Here, we report the discovery of new WIP1 modulators from a high-throughput screen (HTS) using previously described orthogonal biochemical assays suitable for identifying both inhibitors and activators. The primary HTS was performed against a library of 102 277 compounds at a single concentration using a RapidFire mass spectrometry assay. Hits were further evaluated over a range of 11 concentrations with both the RapidFire MS assay and an orthogonal fluorescence-based assay. Further biophysical, biochemical, and cell-based studies of confirmed hits revealed a WIP1 activator and two inhibitors, one competitive and one uncompetitive. These new scaffolds are prime candidates for optimization which might enable inhibitors with improved pharmacokinetics and a first-in-class WIP1 activator.

Abstract 3091: Patient-derived organoid drug responses corroborate known target-drug interactions for selected anticancer agents

Patient-derived organoids (PDOrgs) are heterogeneous three-dimensional cellular clusters that have been shown to recapitulate the tumor histology and genetic alterations of their originating tissue. Numerous studies suggest the in vitro drug responses of tumor organoids align with in vivo responses. In this study, we evaluated fourteen anticancer agents against a cohort of PDOrgs from three disease histologies: colon, pancreatic, and non-small cell lung adenocarcinoma. The PDOrgs were obtained from the National Cancer Institute’s Patient-Derived Models Repository (https://pdmr.cancer.gov): a resource that offers clinically annotated and molecularly characterized models. The PDOrg models were selected for specific genetic variants of KRAS and BRAF, or different RNA levels of ABCB1, an ATP-dependent efflux pump. The approved and investigational agents were selected to target specific genetic variants and pathways: KRAS G12C covalent inhibitors (sotorasib and MRTX-1257), RAS pathway inhibitors (BAY-293, BI-3406 and TNO-155), BRAF V600E/K inhibitors (dabrafenib and encorafenib), ABCB1 substrates (paclitaxel, doxorubicin, 5-FU, AZD-1775, and SN-38), and ABCB1 non-substrates (gemcitabine and trametinib). The goal of the study was to assess whether the sensitivities of PDOrgs to therapeutic agents matched these genetic profiles under standard in vitro conditions. PDOrgs were seeded into 384-well microplates, in a semi-automated fashion, and exposed to nine concentrations of each anticancer agent for six days followed by cell viability assessment by CellTiter-Glo 3D. Data analysis was performed using GRmetrics, an R package for calculation and visualization of concentration-response metrics based on growth rate inhibition (https://git.bioconductor.org/packages/GRmetrics). These data demonstrated that PDOrgs harboring a KRAS G12C variant were uniquely sensitive to sotorasib and MRTX-1257 and were, overall, more sensitive to the other RAS pathway targeting agents. Conversely, PDOrgs harboring wild type RAS and other KRAS variants were largely unresponsive to these targeted agents. Likewise, only PDOrgs harboring the BRAF V600E variant were sensitive to dabrafenib and encorafenib. For the majority of PDOrgs, the pharmacological responses to agents that are ABCB1 substrates inversely correlated with ABCB1 RNA expression. This study demonstrates the ability of organoids to serve as useful models for evaluating therapeutic responses to anticancer agents, including identifying known target-drug associations. Moreover, the technical conditions, as well as the selected PDOrgs and therapeutic agents, may be used as a reference set for the validation of a fully automated PDOrg screening system. This project was funded in part with federal funds from the NCI, NIH, under contract no. HHSN261201500003I.

Citation Format: Curtis Hose, Erik Harris, John Connelly, Petreena S. Campbell, Mariaestela Ortiz, Eric Jones, Dianne Newton, Yvonne A. Evrard, Melinda Hollingshead, Ralph Parchment, Beverly A. Teicher, Nathan P. Coussens, James H. Doroshow, Annamaria Rapisarda. Patient-derived organoid drug responses corroborate known target-drug interactions for selected anticancer agents [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3091.

Abstract 1055: Screens of targeted agents combined with the ubiquitin activating enzyme inhibitor TAK-243 or the pan-Akt inhibitor ipatasertib identified combinations that are effective in patient-derived complex spheroids

Combinations of targeted chemotherapeutics can provide new options to treat cancer; however, the preclinical discovery of potentially beneficial therapeutic combinations is challenging given the heterogeneity of cancer. Complex tumor spheroids, consisting of combined patient-derived tumor cells and stromal cells (human umbilical vein endothelial cells and mesenchymal stem cells) serve as a physiologically relevant in vitro model of solid tumors that is amenable to high-throughput screening. In this study, ten anticancer agents with a range of targets including MEK, mTOR, RAF, PI3K, and the proteasome, were tested both alone and in combination with the ubiquitin activating enzyme inhibitor, TAK-243, or the pan-Akt inhibitor, ipatasertib. All anticancer agents were tested over a 3 log range of concentrations up to their clinical Cmax value, if known. The activities of single agents and combinations were evaluated in complex spheroids grown from patient-derived tumor cells from the National Cancer Institute’s Patient-Derived Models Repository (https://pdmr.cancer.gov), including ten colon and six pancreatic adenocarcinoma and four melanoma cell lines. The spheroids were allowed to grow for three days prior to the addition of anticancer agents and cell viability was measured seven days later using CellTiter-Glo 3D. TAK-243 was cytotoxic against all six pancreatic adenocarcinoma spheroids and all four melanoma spheroids, as well as several colon adenocarcinoma spheroids. The single agent BRAF V600E-selective inhibitor, vemurafenib, showed selective cytotoxicity against melanoma spheroids with the BRAF V600E/K variant. TAK-243 in combination with vemurafenib produced greater than additive cytotoxicity in most complex spheroid models. The overall cytotoxicity of the TAK-243 and vemurafenib combination was similar in melanoma spheroids containing WT BRAF and the BRAF V600E/K variant. The activity of vemurafenib and the BRAF V600E-selective inhibitor dabrafenib were not equivalent in this combination screen and greater than additive cytotoxicity was observed more frequently when TAK-243 was combined with vemurafenib than with dabrafenib. The combination of ipatasertib and vemurafenib had additive and greater than additive cytotoxicity in more than half of the complex spheroid models tested. Other notable agents combined with ipatasertib included the MEK inhibitors trametinib and selumetinib, both of which produced greater than additive cytotoxicity in spheroids derived from pancreatic cancer metastases. These results might inform the prioritization of drug combinations for further investigation by in vivo studies. This project was funded in part with federal funds from the NCI, NIH, under contract no. HHSN261201500003I.

Citation Format: Nathan P. Coussens, John J. Wright, Ralph E. Parchment, René Delosh, Julie Laudeman, Russell Reinhart, Chad Ogle, Thomas Silvers, Thomas S. Dexheimer, Joel Morris, James H. Doroshow, Beverly A. Teicher. Screens of targeted agents combined with the ubiquitin activating enzyme inhibitor TAK-243 or the pan-Akt inhibitor ipatasertib identified combinations that are effective in patient-derived complex spheroids [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1055.

Abstract 3079: Development of an automated platform for screening patient-derived organoid models

One of the major challenges in preclinical cancer therapeutic development is establishing physiologically relevant in vitro assays that correlate with the in vivo responses of patient tumors to anticancer agents. By incorporating tumor cell heterogeneity and three-dimensional morphological features, patient-derived organoids provide an improved in vivo relevancy compared to established tumor cell lines grown as monolayers. However, organoids grow while embedded in an extracellular matrix material with complex media formulations, which poses challenges for culture scale-up and automated drug screening methods. Organoid models derived from a variety of human solid tumor types are distributed by the National Cancer Institute’s Patient-Derived Models Repository program (https://pdmr.cancer.gov). A panel of human patient-derived colon adenocarcinoma organoid models was assembled to evaluate an automated high-throughput screening (HTS) platform. The organoid panel members were characterized for their reproducible growth and expansion capacity in culture, recovery from cryopreservation, and amenability to operations associated with HTS. Short tandem repeat profiling was performed regularly throughout the process to authenticate each sample. Among the organoid models, variations were observed in morphology (assessed by brightfield imaging) and growth rate (measured by population doublings). Most models expanded well in culture for greater than sixty days and all models demonstrated a sufficient recovery from cryopreservation. The aims in adapting organoid cultures to a HTS platform included minimizing the operational complexity, maximizing the process throughput, and maintaining high organoid viability. Assay conditions for all panel members were selected in conjunction with automated methods, instrumentation, and endpoint measurements. Details such as the optimal sample preparation steps, media formulation, and inoculation density varied among the organoid models. However, other aspects such as liquid handling procedures for organoid inoculation and drug delivery, microwell plate type, assay duration, and endpoint measurements were selected for their suitability to all organoid models tested. Using a custom-designed automated screening system, the refined methods were validated by screening the panel of patient-derived colon adenocarcinoma organoids against a library of oncology drugs approved by the United States Food and Drug Administration (https://dtp.cancer.gov/organization/dscb/obtaining/default.htm). Assay performance metrics and pharmacological data demonstrate the robust performance of this organoid screening platform. Future efforts will establish additional patient-derived organoid panels for expanded HTS using this platform. This project was funded in part with federal funds from the NCI, NIH, under contract no. HHSN261201500003I.

Citation Format: Siddhartha Paul, Curtis Hose, Eric Jones, Erik Harris, John Connelly, Petreena Campbell, Mariaestela Ortiz, Thomas S. Dexheimer, Thomas Silvers, Penny Sellers Brady, Julie Grams, Tiffany Nikirk Rohrer, Karen Martin, Patricia Ramsey, Lori Bowles, Annamaria Rapisarda, Ralph E. Parchment, Beverly A. Teicher, James H. Doroshow, Nathan P. Coussens. Development of an automated platform for screening patient-derived organoid models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3079.

Abstract 1881: Drug combination screening of Ipatasertib and Abemaciclib with other targeted agents in complex multicellular tumor spheroids from the NCI-60 and the National Cancer Institute’s Patient-Derived Models Repository

Drug combinations are frequently used to improve clinical efficacy, to minimize toxicity, and to reduce the development of drug resistance. Here, we investigated the growth inhibitory activities of the pan-Akt inhibitor ipatasertib and the CDK4/6 inhibitor abemaciclib in combination with other targeted agents. Twelve well-characterized patient-derived cancer cell lines from the National Cancer Institute’s Patient-Derived Models Repository (https://pdmr.cancer.gov/models/database.htm) and seven established cell lines from the NCI-60 tumor cell line panel (https://dtp.cancer.gov/discovery_development/nci-60/cell_list.htm) were grown as multicellular 3D complex spheroids. The complex spheroids, a mixture of tumor cells (60%), endothelial cells (25%), and mesenchymal stem cells (15%), were grown for 3 days before drug(s) were added. All agents were tested both alone and in combinations at multiple concentrations up to their reported clinical Cmax value and cell viability was assayed using CellTiter-Glo 3D seven days after drug exposure. While abemaciclib had minimal activity as a single agent, ipatasertib was noticeably selective for tumor cells harboring activating PI3K/AKT/mTOR pathway variants. Dual inhibition of the PI3K/AKT/mTOR and RAS/MEK/ERK pathways was one of the most effective combinations. For example, the combination of ipatasertib with the MEK inhibitor selumetinib or the ERK inhibitor ravoxertinib resulted in additive and/or synergistic cytotoxicity in over half the complex spheroid models screened. The V600E variant-specific BRAF inhibitor vemurafenib and the KRAS G12C selective inhibitor sotorasib in combination with ipatasertib showed activity in the one BRAF V600E and two KRAS G12C variant containing complex spheroid models, respectively. Another effective ipatasertib combination was vertical inhibition of the PI3K/AKT/mTOR pathway with the mTORC1/2 kinase inhibitor sapanisertib, which demonstrated additive and/or synergistic responses across multiple complex spheroid models. For abemaciclib, the most successful combination was with the CDK2/7/9 inhibitor BMS-387032, which achieved greater than one log of cytotoxicity in the majority of the complex spheroid models. For the combination of abemaciclib and selumetinib, there was a high correlation between the responses of two patient-derived cell lines grown as complex spheroids and their corresponding patient-derived xenografts (PDX). Additional PDX studies are planned for promising drug combinations from this in vitro screen. This project was funded in part with federal funds from the NCI, NIH, under contract no. HHSN261201500003I.

Citation Format: Thomas Steven Dexheimer, Thomas Silvers, Rene Delosh, Julie Laudeman, Russell Reinhart, Chad Ogle, Siddhartha Paul, Nathan P. Coussens, Ralph E. Parchment, Joel Morris, John Wright, Naoko Takebe, Beverly A. Teicher, James H. Doroshow. Drug combination screening of Ipatasertib and Abemaciclib with other targeted agents in complex multicellular tumor spheroids from the NCI-60 and the National Cancer Institute’s Patient-Derived Models Repository [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1881.

Discovery of Small-Molecule VapC1 Nuclease Inhibitors by Virtual Screening and Scaffold Hopping from an Atomic Structure Revealing Protein-Protein Interactions with a Native VapB1 Inhibitor

Nontypeable Haemophilus influenzae (NTHi) are clinically important Gram-negative bacteria that are responsible for various human mucosal diseases, including otitis media (OM). Recurrent OM caused by NTHi is common, and infections that recur less than 2 weeks following antimicrobial therapy are largely attributable to the recurrence of the same strain of bacteria. Toxin-antitoxin (TA) modules encoded by bacteria enable rapid responses to environmental stresses and are thought to facilitate growth arrest, persistence, and tolerance to antibiotics. The vapBC-1 locus of NTHi encodes a type II TA system, comprising the ribonuclease toxin VapC1 and its cognate antitoxin VapB1. The activity of VapC1 has been linked to the survival of NTHi during antibiotic treatment both in vivo and ex vivo. Therefore, inhibitors of VapC1 might serve as adjuvants to antibiotics, preventing NTHi from entering growth arrest and surviving; however, none have been reported to date. A truncated VapB1 peptide from a crystal structure of the VapBC-1 complex was used to generate pharmacophore queries to facilitate a scaffold hopping approach for the identification of small-molecule VapC1 inhibitors. The National Center for Advancing Translational Sciences small-molecule library was virtually screened using the shape-based method rapid overlay of chemical structures (ROCS), and the top-ranking hits were docked into the VapB1 binding pocket of VapC1. Two hundred virtual screening hits with the best docking scores were selected and tested in a biochemical VapC1 activity assay, which confirmed eight compounds as VapC1 inhibitors. An additional 60 compounds were selected with structural similarities to the confirmed VapC1 inhibitors, of which 20 inhibited VapC1 activity. Intracellular target engagement of five inhibitors was indicated by the destabilization of VapC1 within bacterial cells from a cellular thermal shift assay; however, no impact on bacterial growth was observed. Thus, this virtual screening and scaffold hopping approach enabled the discovery of VapC1 ribonuclease inhibitors that might serve as starting points for preclinical development.

Complex Tumor Spheroids, a Tissue-Mimicking Tumor Model, for Drug Discovery and Precision Medicine

Malignant tumors are complex tissues composed of malignant cells, vascular cells, structural mesenchymal cells including pericytes and carcinoma-associated fibroblasts, infiltrating immune cells, and others, collectively called the tumor stroma. The number of stromal cells in a tumor is often much greater than the number of malignant cells. The physical associations among all these cell types are critical to tumor growth, survival, and response to therapy. Most cell-based screens for cancer drug discovery and precision medicine validation use malignant cells in isolation as monolayers, embedded in a matrix, or as spheroids in suspension. Medium- and high-throughput screening with multiple cell lines requires a scalable, reproducible, robust cell-based assay. Complex spheroids include malignant cells and two normal cell types, human umbilical vein endothelial cells and highly plastic mesenchymal stem cells, which rapidly adapt to the malignant cell microenvironment. The patient-derived pancreatic adenocarcinoma cell line, K24384-001-R, was used to explore complex spheroid structure and response to anticancer agents in a 96-well format. We describe the development of the complex spheroid assay as well as the growth and structure of complex spheroids over time. Subsequently, we demonstrate successful assay miniaturization to a 384-well format and robust performance in a high-throughput screen. Implementation of the complex spheroid assay was further demonstrated with 10 well-established pancreatic cell lines. By incorporating both human stromal and tumor components, complex spheroids might provide an improved model for tumor response in vivo.

Abstract P222: Combinations of receptor tyrosine kinase inhibitors targeting the tumor and stromal cells of complex spheroids from the National Cancer Institute’s Patient-Derived Models Repository (PDMR; https://pdmr.cancer.gov/)

Tumor stroma is critical in shaping the tumor microenvironment and promoting tumor growth and metastasis. Six stroma-targeted kinase inhibitors (cediranib, vandetanib, axitinib, pazopanib, cabozantinib, and lenvatinib) were tested both as single agents and in combination with five tumor cell-targeted kinase inhibitors (erlotinib, gefitinib, osimertinib, rociletinib, and erdafitinib)using a complex spheroid cell culture model. Complex spheroids, containing 60% tumor cells, 25% endothelial cells (HUVEC) and 15% mesenchymal stem cells (MSC), serve as a cell culture model of human solid tumors incorporating both malignant and stromal cells. Seventeen tumor cell lines were grown as complex spheroids, including varied sarcoma and non-small cell lung cancer types. Drug sensitivities of the HUVEC and MSC were also evaluated, both individually as monolayers and mixed as monolayers and spheroids. Overall, the HUVEC and MSC were more sensitive to the VEGFR inhibitors than to the EGFR inhibitors. Growth as complex spheroids reduced the sensitivity of HUVEC and MSC to several kinase inhibitors compared to each cell type alone or in mixed monolayer culture. A significant correlation was observed between the EGFR mRNA expression in patient-derived tumor lines and their sensitivity to the EGFR inhibitors. In combination regimens, Erlotinib was most effective when combined with the VEGFR inhibitors pazopanib, vandetanib and cediranib, which produced more than one log of cell killing at concentrations less than the clinical Cmax of each drug. Osimertinib and rociletinib, which irreversibly target EGFR variants, were more cytotoxic towards complex spheroids of NCI-H1975 NSCLC (EGFR L858R, T790M) than NCI-H522 NSCLC (EGFR wildtype). Combinations of the mutant-selective EGFR inhibitors with a VEGFR inhibitor (especially, vandetanib, lenvatinib or cediranib) increased the cytotoxicity in complex spheroids containing EGFR mutant and wildtype tumor lines. Highly effective combinations included erdafitinib with vandetanib and erlotinib with cediranib. The combination of cediranib and erlotinib was also evaluated in nine patient-derived xenograft (PDX) models and resulted in two partial responses in a penile squamous carcinoma and uterine sarcoma, while the remainder showed stable, slowed, or progressive disease. Using >1 log of cell kill at drug concentrations less than the mouse Cmax concentration for each drug as a predictor for in vivo responsiveness, the complex spheroid assay was 88% accurate in predicting response or progressive disease in the PDX models. This criteria for predicting in vivo activity from in vitro model results will be further explored. This project was funded in part with federal funds from the NCI, NIH, under contract no. HHSN261200800001E.

Citation Format: Thomas S. Dexheimer, Julie Laudeman, Thomas Silvers, Rene Delosh, Russell Reinhart, Chad Ogle, Eric Jones, Nathan P. Coussens, Beverly A. Teicher, Naoko Takebe, Alice Chen, James H. Doroshow. Combinations of receptor tyrosine kinase inhibitors targeting the tumor and stromal cells of complex spheroids from the National Cancer Institute’s Patient-Derived Models Repository (PDMR; https://pdmr.cancer.gov/) [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P222.

Addressing Compound Reactivity and Aggregation Assay Interferences: Case Studies of Biochemical High-Throughput Screening Campaigns Benefiting from the National Institutes of Health Assay Guidance Manual Guidelines

Compound-dependent assay interferences represent a continued burden in drug and chemical probe discovery. The open-source National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS) Assay Guidance Manual (AGM) established an "Assay Artifacts and Interferences" section to address different sources of artifacts and interferences in biological assays. In addition to the frequent introduction of new chapters in this important topic area, older chapters are periodically updated by experts from academia, industry, and government to include new technologies and practices. Section chapters describe many best practices for mitigating and identifying compound-dependent assay interferences. Using two previously reported biochemical high-throughput screening campaigns for small-molecule inhibitors of the epigenetic targets Rtt109 and NSD2, the authors review best practices and direct readers to high-yield resources in the AGM and elsewhere for the mitigation and identification of compound-dependent reactivity and aggregation assay interferences.

Abstract 2644: Comparison of PDMR cell line complex spheroid response and PDX response to trametinib

The NCI is engaged in developing a large resource of well-characterized patient-derived xenografts and corresponding cell lines and organoid cultures which are available to the global cancer research community (https://pdmr.cancer.gov/models/database.htm). The current study explored trametinib in PDMR models including cell lines and PDX tumors. Trametinib is a selective reversible allosteric inhibitor of MEK1 and MEK2 activity. The RAS-RAF-MEK-ERK pathway is important in cell proliferation and differentiation and is active in many cancers. Twenty-one PDMR lines were grown as complex spheroids, tumor cells mixed with HUVEC and MSC, to model human solid tumors. Complex spheroids were established for 3 days before drug was added. Seven days after drug addition the experiment was terminated with CellTiter-Glo 3D. Cell viability was determined relative to vehicle treated control and IC50 values calculated from concentration response data. Response to trametinib was assessed over a concentration range (0.0001 - 0.03 μM) achievable in patients. The clinical Cmax concentration for trametinib is 0.021 μM. 3 cell lines did not reach an IC50 at 0.02 μM. PDX studies were performed in 5 PDMR models. Three lines were derived from one pancreatic cancer patient: 521955-158-R2-J5 was from a liver metastasis; 521955-158-R6-J3 was from a myometrium metastasis; and 521955-158-R7-J2 was from a colon metastasis. The trametinib IC50 values for the 521955-158-R2, 521955-158-R7 and 128128-338-R lines ranged from 0.001 - 0.0015 μM. The 521955-158-R6 line was resistant with an IC50 of 0.03 μM. The 349418-098-R NSCLC line, which harbors a BRAF V600E mutation, was sensitive to trametinib with an IC50 value of 0.0002 μM. PDX studies had 8-15 mice in control groups and 6-15 mice in treated groups. The PDX models, 128128-338-R, 521955-158-R6, 521955-158-R7, 877537-175-T-J1 and 349418-098-R, responded rapidly to trametinib but had modest to moderate responses with all 5 tumors reaching maximal responses ranging between 25 and 50% of control tumor volume. The PDX tumors had a range of growth rates taking between 14 and 45 days to reach volumes of 150-200 mm3, to begin treatment. Trametinib was administered, in 10% DMSO/5% Cremophor orally once daily for 28 days. During the treatment period tumor quadrupling times were 128128-338-R, controls 21days and treated 36 days; 521955-158-R6, controls 15 days and treated 40 days; 521955-158-R7, controls 17 days and treated 35 days; 977537-175-T-J1, controls 6 days and treated 18 days and 349418-098-R, controls 19 days and treated 32 days. The differences in tumor response were not sufficient to find a correlation with spheroid response, although the 128128-338-R model which had the lowest IC50 value also had the greatest tumor response as determined by T/C volume ratio. This project was funded in part with federal funds from the NCI, NIH, under contract no. HHSN261200800001E.

Citation Format: Beverly A. Teicher, Nathan P. Coussens, Melinda Hollingshead, John Wright, Thomas Silvers, Rene Delosh, Julie Laudeman, Russell Reinhart, Chad Ogle, James Doroshow. Comparison of PDMR cell line complex spheroid response and PDX response to trametinib [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2644.

Abstract 1028: Combination screening of KRASG12C specific inhibitors with other targeted therapies in patient-derived multicellular tumor spheroids

KRAS is one of the most frequently mutated oncogenes in cancer and efforts to directly target KRAS have been challenging. However, covalent inhibitors targeting a specific KRASG12C (Gly12 to Cys12) variant have recently been developed and have demonstrated encouraging clinical activity in patients with tumors driven by the mutant protein. Drug combinations are used to improve clinical efficacy, to minimize toxicity, and to reduce the development of resistance. Here, we investigate the growth inhibitory activity of two KRASG12C variant-specific inhibitors, AMG-510 and MRTX-1257, in combination with other targeted therapies. Twenty patient-derived cancer cell lines, which have been well-characterized for their KRAS status and related targets and are available from NCI, were grown as multicellular 3D complex spheroids (https://pdmr.cancer.gov/models/database.htm). The complex spheroids, a mixture of tumor cells, endothelial cells and mesenchymal stem cells, were established for 3 days before drug(s) were added. All agents were tested at concentrations up to their reported clinical Cmax values and cell viability for each individual drug treatment and drug combination was assayed using CellTiter-Glo 3D seven days after drug exposure. As single agents, AMG-510 and MRTX-1257 showed selectivity for the KRASG12C variant containing cancer cell lines. The pancreatic cancer cell line 323965-272-R-J2 carrying a KRASG12C variant exhibited an enhanced sensitivity to the combination of the mTOR inhibitor everolimus and a low concentration of either AMG-510 or MRTX-1257. Additive to greater than additive cytotoxicity for the combination of everolimus and the KRASG12C inhibitors was also observed in the KRASG12C variant melanoma cell line 299254-011-R-J1, while no effect was detected in cell lines with wildtype or other KRAS mutations. Similarly, combining the mTOR kinase inhibitor sapanisertib, which blocks both mTORC1 and mTORC2 activities, with MTRX-1257 also led to a notable reduction in cell viability in all three KRASG12C-containing cell lines. In the KRASG12C variant melanoma cell line 299254-011-R-J1, targeting of the upstream receptor tyrosine kinase FGFR with erdafitinib in combination with the KRASG12C inhibitors produced greater than additive cell killing over the concentration range from 0.1 to 10 µM. Lastly, both KRASG12C inhibitors and abemaciclib, demonstrated additive to greater than additive cytotoxicity in the pancreatic cancer cell line 323965-272-R-J2, but this outcome was not observed with the CDK4/6 inhibitor, palbociclib, or in the other KRASG12C variant cell lines. These preclinical findings provide guidance regarding selection of combination regimens with KRASG12C inhibitors that may result in increased clinical efficacy. This project was funded in part with federal funds from the NCI, NIH, under contract no. HHSN261200800001E.

Citation Format: Thomas S. Dexheimer, Thomas Silvers, René Delosh, Julie Laudeman, Russell Reinhart, Chad Ogle, Nathan P. Coussens, John Wright, Beverly A. Teicher, James H. Doroshow. Combination screening of KRASG12C specific inhibitors with other targeted therapies in patient-derived multicellular tumor spheroids [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1028.

Abstract 1072: Combination screening of DNA damaging agents temozolomide and trabectedin with inhibitors of DNA repair using a complex spheroid model with a panel of patient-derived and established tumor cell lines

DNA-damaging agents are important anticancer therapeutics but are rarely curative. The current study combines the DNA-damaging agents trabectedin and temozolomide with varied DNA repair inhibitors to identify combinations that increase malignant cell kill and therefore might improve therapeutic benefit. Twenty-seven tumor cell lines focused on sarcoma and small cell lung cancer (https://pdmr.cancer.gov/models/database.htm) were grown as complex spheroids containing 60% tumor cells, 25% endothelial cells and 15% mesenchymal stem cells as an in vitro model for human solid tumors. After 3 days of growth, the complex spheroids were screened using a 3-log concentration range with the highest concentration at the clinical Cmax for each agent. The spheroids were treated with temozolomide or trabectedin as single agents or in combination with a PARP inhibitor (olaparib or talazoparib), an ATM inhibitor (AZD-1390), an ATR inhibitor (berzosertib (M6620) or BAY-1895344), a DNA-PK inhibitor (nedisertib (M3814) or VX984) or a BET bromodomain inhibitor (birabresib). Seven days after drug exposure, ATP was measured with CellTiter-Glo 3D. Olaparib or talazoparib produced additive to greater than additive cell killing in combination with either trabectedin or temozolomide. Whereas cell killing with temozolomide alone was modest, greater than 1 log of cell killing was achieved in combination with either olaparib or talazoparib. The ATM inhibitor AZD-1390 in combination with trabectedin showed greater than additive responses in most models and approximately 3 logs of cell killing in sarcoma and small cell lung cancer models at higher trabectedin concentrations. The ATR inhibitors BAY-1895344 and berzosertib had additive and greater than additive responses in combination with temozolomide or trabectedin among the small cell lung cancer models tested and produced greater than 2 logs of cell kill in many models when combined with temozolomide. When combined with trabectedin, the DNA-PK inhibitor VX-984 had additive responses, whereas nedisertib had greater than additive responses in most models. The BET inhibitor birabresib had greater than additive responses in many models when combined with trabectedin and additive responses with temozolomide. Overall, greater than additive responses were observed more frequently with trabectedin combinations containing the ATM inhibitor AZD-1390 or the DNA-PK inhibitor nedisertib, as well as temozolomide combinations with the PARP inhibitors olaparib or talazoparib or the ATR inhibitor BAY-1895344, particularly among sarcoma and small cell lung cancer models. These results might inform the prioritization of drug combinations for further investigation. This project was funded in part with federal funds from the NCI, NIH, under contract no. HHSN261200800001E.

Citation Format: Nathan P. Coussens, Ralph E. Parchment, Jeffrey A. Moscow, L. Austin Doyle, René Delosh, Julie Laudeman, Russell Reinhart, Chad Ogle, Thomas Silvers, Thomas S. Dexheimer, Joel Morris, Beverly A. Teicher, James H. Doroshow. Combination screening of DNA damaging agents temozolomide and trabectedin with inhibitors of DNA repair using a complex spheroid model with a panel of patient-derived and established tumor cell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1072.

Interaction of the N terminus of ADP-ribosylation factor with the PH domain of the GTPase-activating protein ASAP1 requires phosphatidylinositol 4,5-bisphosphate

Arf GAP with Src homology 3 domain, ankyrin repeat, and pleckstrin homology (PH) domain 1 (ASAP1) is a multidomain GTPase-activating protein (GAP) for ADP-ribosylation factor (ARF)-type GTPases. ASAP1 affects integrin adhesions, the actin cytoskeleton, and invasion and metastasis of cancer cells. ASAP1's cellular function depends on its highly-regulated and robust ARF GAP activity, requiring both the PH and the ARF GAP domains of ASAP1, and is modulated by phosphatidylinositol 4,5-bisphosphate (PIP₂). The mechanistic basis of PIP₂-stimulated GAP activity is incompletely understood. Here, we investigated whether PIP₂ controls binding of the N-terminal extension of ARF1 to ASAP1's PH domain and thereby regulates its GAP activity. Using [Δ17]ARF1, lacking the N terminus, we found that PIP₂ has little effect on ASAP1's activity. A soluble PIP₂ analog, dioctanoyl-PIP₂ (diC8PIP₂), stimulated GAP activity on an N terminus-containing variant, [L8K]ARF1, but only marginally affected activity on [Δ17]ARF1. A peptide comprising residues 2-17 of ARF1 ([2-17]ARF1) inhibited GAP activity, and PIP₂-dependently bound to a protein containing the PH domain and a 17-amino acid-long interdomain linker immediately N-terminal to the first β-strand of the PH domain. Point mutations in either the linker or the C-terminal α-helix of the PH domain decreased [2-17]ARF1 binding and GAP activity. Mutations that reduced ARF1 N-terminal binding to the PH domain also reduced the effect of ASAP1 on cellular actin remodeling. Mutations in the ARF N terminus that reduced binding also reduced GAP activity. We conclude that PIP₂ regulates binding of ASAP1's PH domain to the ARF1 N terminus, which may partially regulate GAP activity.

The Opioid Crisis and the Future of Addiction and Pain Therapeutics

Opioid misuse and addiction are a public health crisis resulting in debilitation, deaths, and significant social and economic impact. Curbing this crisis requires collaboration among academic, government, and industrial partners toward the development of effective nonaddictive pain medications, interventions for opioid overdose, and addiction treatments. A 2-day meeting, The Opioid Crisis and the Future of Addiction and Pain Therapeutics: Opportunities, Tools, and Technologies Symposium, was held at the National Institutes of Health (NIH) to address these concerns and to chart a collaborative path forward. The meeting was supported by the NIH Helping to End Addiction Long-Term^SM (HEAL) Initiative, an aggressive, trans-agency effort to speed scientific solutions to stem the national opioid crisis. The event was unique in bringing together two research disciplines, addiction and pain, in order to create a forum for crosscommunication and collaboration. The output from the symposium will be considered by the HEAL Initiative; this article summarizes the scientific presentations and key takeaways. Improved understanding of the etiology of acute and chronic pain will enable the discovery of novel targets and regulatable pain circuits for safe and effective therapeutics, as well as relevant biomarkers to ensure adequate testing in clinical trials. Applications of improved technologies including reagents, assays, model systems, and validated probe compounds will likely increase the delivery of testable hypotheses and therapeutics to enable better health outcomes for patients. The symposium goals were achieved by increasing interdisciplinary collaboration to accelerate solutions for this pressing public health challenge and provide a framework for focused efforts within the research community. SIGNIFICANCE STATEMENT: This article summarizes key messages and discussions resulting from a 2-day symposium focused on challenges and opportunities in developing addiction- and pain-related medications. Speakers and attendees came from 40 states in the United States and 15 countries, bringing perspectives from academia, industry, government, and healthcare by researchers, clinicians, regulatory experts, and patient advocates.

Physiologically relevant orthogonal assays for the discovery of small-molecule modulators of WIP1 phosphatase in high-throughput screens

WT P53-Induced Phosphatase 1 (WIP1) is a member of the magnesium-dependent serine/threonine protein phosphatase (PPM) family and is induced by P53 in response to DNA damage. In several human cancers, the WIP1 protein is overexpressed, which is generally associated with a worse prognosis. Although WIP1 is an attractive therapeutic target, no potent, selective, and bioactive small-molecule modulator with favorable pharmacokinetics has been reported. Phosphatase enzymes are among the most challenging targets for small molecules because of the difficulty of achieving both modulator selectivity and bioavailability. Another major obstacle has been the availability of robust and physiologically relevant phosphatase assays that are suitable for high-throughput screening. Here, we describe orthogonal biochemical WIP1 activity assays that utilize phosphopeptides from native WIP1 substrates. We optimized an MS assay to quantify the enzymatically dephosphorylated peptide reaction product in a 384-well format. Additionally, a red-shifted fluorescence assay was optimized in a 1,536-well format to enable real-time WIP1 activity measurements through the detection of the orthogonal reaction product, P_i. We validated these two optimized assays by quantitative high-throughput screening against the National Center for Advancing Translational Sciences (NCATS) Pharmaceutical Collection and used secondary assays to confirm and evaluate inhibitors identified in the primary screen. Five inhibitors were further tested with an orthogonal WIP1 activity assay and surface plasmon resonance binding studies. Our results validate the application of miniaturized physiologically relevant and orthogonal WIP1 activity assays to discover small-molecule modulators from high-throughput screens.

Assay Guidance Manual: Quantitative Biology and Pharmacology in Preclinical Drug Discovery

The Assay Guidance Manual (AGM) is an eBook of best practices for the design, development, and implementation of robust assays for early drug discovery. Initiated by pharmaceutical company scientists, the manual provides guidance for designing a “testing funnel” of assays to identify genuine hits using high‐throughput screening (HTS) and advancing them through preclinical development. Combined with a workshop/tutorial component, the overall goal of the AGM is to provide a valuable resource for training translational scientists.

High-throughput screening with nucleosome substrate identifies small-molecule inhibitors of the human histone lysine methyltransferase NSD2

The histone lysine methyltransferase nuclear receptor-binding SET domain protein 2 (NSD2, also known as WHSC1/MMSET) is an epigenetic modifier and is thought to play a driving role in oncogenesis. Both NSD2 overexpression and point mutations that increase its catalytic activity are associated with several human cancers. Although NSD2 is an attractive therapeutic target, no potent, selective, and bioactive small molecule inhibitors of NSD2 have been reported to date, possibly due to the challenges of developing high-throughput assays for NSD2. Here, to establish a platform for the discovery and development of selective NSD2 inhibitors, we optimized and implemented multiple assays. We performed quantitative high-throughput screening with full-length WT NSD2 and a nucleosome substrate against a diverse collection of bioactive small molecules comprising 16,251 compounds. We further interrogated 174 inhibitory compounds identified in the primary screen with orthogonal and counter assays and with activity assays based on the clinically relevant NSD2 variants E1099K and T1150A. We selected five confirmed inhibitors for follow-up, which included a radiolabeled validation assay, surface plasmon resonance studies, methyltransferase profiling, and histone methylation in cells. We found that all five NSD2 inhibitors bind the catalytic SET domain and one exhibited apparent activity in cells, validating the workflow and providing a template for identifying selective NSD2 inhibitors. In summary, we have established a robust discovery pipeline for identifying potent NSD2 inhibitors from small-molecule libraries.

Better living through chemistry: Addressing emerging antibiotic resistance

The increasing emergence of multidrug-resistant bacteria is recognized as a major threat to human health worldwide. While the use of small molecule antibiotics has enabled many modern medical advances, it has also facilitated the development of resistant organisms. This minireview provides an overview of current small molecule drugs approved by the US Food and Drug Administration (FDA) for use in humans, the unintended consequences of antibiotic use, and the mechanisms that underlie the development of drug resistance. Promising new approaches and strategies to counter antibiotic-resistant bacteria with small molecules are highlighted. However, continued public investment in this area is critical to maintain an edge in our evolutionary "arms race" against antibiotic-resistant microorganisms. Impact statement The alarming increase in antibiotic-resistant microorganisms is a rapidly emerging threat to human health throughout the world. Historically, small molecule drugs have played a major role in controlling bacterial infections and they continue to offer tremendous potential in countering resistant organisms. This minireview provides a broad overview of the relevant issues, including the diversity of FDA-approved small molecule drugs and mechanisms of drug resistance, unintended consequences of antibiotic use, the current state of development for small molecule antibacterials and financial challenges that impact progress towards novel therapies. The content will be informative to diverse stakeholders, including clinicians, basic scientists, translational scientists and policy makers, and may be used as a bridge between these key players to advance the development of much-needed therapeutics.

Irreversible inhibition of cytosolic thioredoxin reductase 1 as a mechanistic basis for anticancer therapy

Cancer cells adapt to their inherently increased oxidative stress through activation of the glutathione (GSH) and thioredoxin (TXN) systems. Inhibition of both of these systems effectively kills cancer cells, but such broad inhibition of antioxidant activity also kills normal cells, which is highly unwanted in a clinical setting. We therefore evaluated targeting of the TXN pathway alone and, more specifically, selective inhibition of the cytosolic selenocysteine-containing enzyme TXN reductase 1 (TXNRD1). TXNRD1 inhibitors were discovered in a large screening effort and displayed increased specificity compared to pan-TXNRD inhibitors, such as auranofin, that also inhibit the mitochondrial enzyme TXNRD2 and additional targets. For our lead compounds, TXNRD1 inhibition correlated with cancer cell cytotoxicity, and inhibitor-triggered conversion of TXNRD1 from an antioxidant to a pro-oxidant enzyme correlated with corresponding increases in cellular production of H2O2 In mice, the most specific TXNRD1 inhibitor, here described as TXNRD1 inhibitor 1 (TRi-1), impaired growth and viability of human tumor xenografts and syngeneic mouse tumors while having little mitochondrial toxicity and being better tolerated than auranofin. These results display the therapeutic anticancer potential of irreversibly targeting cytosolic TXNRD1 using small molecules and present potent and selective TXNRD1 inhibitors. Given the pronounced up-regulation of TXNRD1 in several metastatic malignancies, it seems worthwhile to further explore the potential benefit of specific irreversible TXNRD1 inhibitors for anticancer therapy.

Small-Molecule Screens: A Gateway to Cancer Therapeutic Agents with Case Studies of Food and Drug Administration-Approved Drugs

High-throughput screening (HTS) of small-molecule libraries accelerates the discovery of chemical leads to serve as starting points for probe or therapeutic development. With this approach, thousands of unique small molecules, representing a diverse chemical space, can be rapidly evaluated by biologically and physiologically relevant assays. The origins of numerous United States Food and Drug Administration-approved cancer drugs are linked to HTS, which emphasizes the value in this methodology. The National Institutes of Health Molecular Libraries Program made HTS accessible to the public sector, enabling the development of chemical probes and drug-repurposing initiatives. In this work, the impact of HTS in the field of oncology is considered among both private and public sectors. Examples are given for the discovery and development of approved cancer drugs. The importance of target validation is discussed, and common assay approaches for screening are reviewed. A rigorous examination of the PubChem database demonstrates that public screening centers are contributing to early-stage drug discovery in oncology by focusing on new targets and developing chemical probes. Several case studies highlight the value of different screening strategies and the potential for drug repurposing.

Structure of a heterogeneous, glycosylated, lipid-bound, in vivo-grown protein crystal at atomic resolution from the viviparous cockroach Diploptera punctata

Macromolecular crystals for X-ray diffraction studies are typically grown in vitro from pure and homogeneous samples; however, there are examples of protein crystals that have been identified in vivo. Recent developments in micro-crystallography techniques and the advent of X-ray free-electron lasers have allowed the determination of several protein structures from crystals grown in cellulo. Here, an atomic resolution (1.2 Å) crystal structure is reported of heterogeneous milk proteins grown inside a living organism in their functional niche. These in vivo-grown crystals were isolated from the midgut of an embryo within the only known viviparous cockroach, Diploptera punctata. The milk proteins crystallized in space group P1, and a structure was determined by anomalous dispersion from the native S atoms. The data revealed glycosylated proteins that adopt a lipocalin fold, bind lipids and organize to form a tightly packed crystalline lattice. A single crystal is estimated to contain more than three times the energy of an equivalent mass of dairy milk. This unique storage form of nourishment for developing embryos allows access to a constant supply of complete nutrients. Notably, the crystalline cockroach-milk proteins are highly heterogeneous with respect to amino-acid sequence, glycosylation and bound fatty-acid composition. These data present a unique example of protein heterogeneity within a single in vivo-grown crystal of a natural protein in its native environment at atomic resolution.

Wake me when it's over - Bacterial toxin-antitoxin proteins and induced dormancy

Toxin-antitoxin systems are encoded by bacteria and archaea to enable an immediate response to environmental stresses, including antibiotics and the host immune response. During normal conditions, the antitoxin components prevent toxins from interfering with metabolism and arresting growth; however, toxin activation enables microbes to remain dormant through unfavorable conditions that might continue over millions of years. Intense investigations have revealed a multitude of mechanisms for both regulation and activation of toxin-antitoxin systems, which are abundant in pathogenic microorganisms. This minireview provides an overview of the current knowledge regarding type II toxin-antitoxin systems along with their clinical and environmental implications.

Fluorescence polarization assays in high-throughput screening and drug discovery: a review

The sensitivity of fluorescence polarization (FP) and fluorescence anisotropy (FA) to molecular weight changes has enabled the interrogation of diverse biological mechanisms, ranging from molecular interactions to enzymatic activity. Assays based on FP/FA technology have been widely utilized in high-throughput screening (HTS) and drug discovery due to the homogenous format, robust performance and relative insensitivity to some types of interferences, such as inner filter effects. Advancements in assay design, fluorescent probes, and technology have enabled the application of FP assays to increasingly complex biological processes. Herein we discuss different types of FP/FA assays developed for HTS, with examples to emphasize the diversity of applicable targets. Furthermore, trends in target and fluorophore selection, as well as assay type and format, are examined using annotated HTS assays within the PubChem database. Finally, practical considerations for the successful development and implementation of FP/FA assays for HTS are provided based on experience at our center and examples from the literature, including strategies for flagging interference compounds among a list of hits.

AlphaScreen-Based Assays: Ultra-High-Throughput Screening for Small-Molecule Inhibitors of Challenging Enzymes and Protein-Protein Interactions

AlphaScreen technology has been routinely utilized in high-throughput screening assays to quantify analyte accumulation or depletion, bimolecular interactions, and post-translational modifications. The high signal-to-background, dynamic range, and sensitivity associated with AlphaScreens as well as the homogenous assay format and reagent stability make the technology particularly well suited for high-throughput screening applications. Here, we describe the development of AlphaScreen assays to identify small-molecule inhibitors of enzymes and protein-protein interactions using the highly miniaturized 1536-well format. The subsequent implementation of counter assays to identify false-positive compounds is also discussed.

The linker for activation of T cells (LAT) signaling hub: from signaling complexes to microclusters

Since the cloning of the critical adapter, LAT (linker for activation of T cells), more than 15 years ago, a combination of multiple scientific approaches and techniques continues to provide valuable insights into the formation, composition, regulation, dynamics, and function of LAT-based signaling complexes. In this review, we will summarize current views on the assembly of signaling complexes nucleated by LAT. LAT forms numerous interactions with other signaling molecules, leading to cooperativity in the system. Furthermore, oligomerization of LAT by adapter complexes enhances intracellular signaling and is physiologically relevant. These results will be related to data from super-resolution microscopy studies that have revealed the smallest LAT-based signaling units and nanostructure.

Revealing the secrets of intractable cellular functions: All-in-one-well methods for studying protein interaction and secretion

Protein-based assays are essential tools for many laboratories in both industrial and academic settings. Protein targets of interest are often found at low abundance and can be complex in nature, making their analysis intractable. One of the considerable challenges when developing assays is that small sample sizes can limit the amount of relevant information that can be extracted. The ability to miniaturize an assay allows sufficient data to be collected from scarce samples, while being able to interrogate multiple proteins simultaneously through multiplexing enables researchers to extract more data from each experiment and improve the biological relevance of the results significantly. This multiplexing ability provides the opportunity to quantitatively profile multiple signaling pathways from minute samples derived from very small cell populations. Furthermore, having the tools to directly study protein target binding in cells allows biologically relevant information to be preserved, including subcellular localization, posttranslational modifications, and the occurrence of multiple interactions with different accessory proteins and other scaffolding molecules. In this webinar, two examples of such approaches will be discussed. The first is the use of a method to amplify the signal in a target engagement assay using small samples, utilized to interrogate modulators of cytokine secretion. The second involves a so-called cellular thermal shift assay (CETSA) to detect protein-ligand interactions without the need to modify either the ligand or receptor, or the necessity for recombinant cell lines.

In vivo crystallography at X-ray free-electron lasers: the next generation of structural biology?

The serendipitous discovery of the spontaneous growth of protein crystals inside cells has opened the field of crystallography to chemically unmodified samples directly available from their natural environment. On the one hand, through in vivo crystallography, protocols for protein crystal preparation can be highly simplified, although the technique suffers from difficulties in sampling, particularly in the extraction of the crystals from the cells partly due to their small sizes. On the other hand, the extremely intense X-ray pulses emerging from X-ray free-electron laser (XFEL) sources, along with the appearance of serial femtosecond crystallography (SFX) is a milestone for radiation damage-free protein structural studies but requires micrometre-size crystals. The combination of SFX with in vivo crystallography has the potential to boost the applicability of these techniques, eventually bringing the field to the point where in vitro sample manipulations will no longer be required, and direct imaging of the crystals from within the cells will be achievable. To fully appreciate the diverse aspects of sample characterization, handling and analysis, SFX experiments at the Japanese SPring-8 angstrom compact free-electron laser were scheduled on various types of in vivo grown crystals. The first experiments have demonstrated the feasibility of the approach and suggest that future in vivo crystallography applications at XFELs will be another alternative to nano-crystallography.

Strategies for assessing proton linkage to bimolecular interactions by global analysis of isothermal titration calorimetry data

Isothermal titration calorimetry (ITC) is a traditional and powerful method for studying the linkage of ligand binding to proton uptake or release. The theoretical framework has been developed for more than two decades and numerous applications have appeared. In the current work, we explored strategic aspects of experimental design. To this end, we simulated families of ITC data sets that embed different strategies with regard to the number of experiments, range of experimental pH, buffer ionization enthalpy, and temperature. We then re-analyzed the families of data sets in the context of global analysis, employing a proton linkage binding model implemented in the global data analysis platform SEDPHAT, and examined the information content of all data sets by a detailed statistical error analysis of the parameter estimates. In particular, we studied the impact of different assumptions about the knowledge of the exact concentrations of the components, which in practice presents an experimental limitation for many systems. For example, the uncertainty in concentration may reflect imperfectly known extinction coefficients and stock concentrations or may account for different extents of partial inactivation when working with proteins at different pH values. Our results show that the global analysis can yield reliable estimates of the thermodynamic parameters for intrinsic binding and protonation, and that in the context of the global analysis the exact molecular component concentrations may not be required. Additionally, a comparison of data from different experimental strategies illustrates the benefit of conducting experiments at a range of temperatures.

The LAT story: a tale of cooperativity, coordination, and choreography

The adapter molecule LAT is a nucleating site for multiprotein signaling complexes that are vital for the function and differentiation of T cells. Extensive investigation of LAT in multiple experimental systems has led to an integrated understanding of the formation, composition, regulation, dynamic movement, and function of LAT-nucleated signaling complexes. This review discusses interactions of signaling molecules that bind directly or indirectly to LAT and the role of cooperativity in stabilizing LAT-nucleated signaling complexes. In addition, it focuses on how imaging studies visualize signaling assemblies as signaling clusters and demonstrate their dynamic nature and cellular fate. Finally, this review explores the function of LAT based on the interpretation of mouse models using various LAT mutants.

Crystal structure of the Nod1 caspase activation and recruitment domain

Nod-like receptors (NLRs), Nod1 and Nod2 are cytosolic detectors of pathogen-associated molecular patterns (PAMPs). Nod1 is a three-domain protein, consisting of a caspase activation and recruitment domain (CARD), a nucleotide-binding oligomerization domain (NOD), and a leucine-rich repeat domain (LRR). The binding of PAMPs to the LRR results in the activation of signaling through homophilic CARD-CARD interactions. Several CARD structures have been determined, including a recent NMR structure of Nod1 CARD. In contrast to the reported NMR structure, the crystal structure reported here is a dimer, where the sixth helix is swapped between two monomers. While the overall structure is very similar to the known CARD structures, this is the first report of a homodimeric CARD structure. The ability of the CARD to exist in monomeric and dimeric forms suggests another level of regulation in the activation of NLR proteins.

Isolation of an endotoxin-MD-2 complex that produces Toll-like receptor 4-dependent cell activation at picomolar concentrations

Host proinflammatory responses to minute amounts of endotoxins derived from many Gram-negative bacteria require the interaction of lipopolysaccharide-binding protein (LBP), CD14, Toll-like receptor 4 (TLR4) and MD-2. Optimal sensitivity to endotoxin requires an ordered series of endotoxin-protein and protein-protein interactions. At substoichiometric concentrations, LBP facilitates delivery of endotoxin aggregates to soluble CD14 (sCD14) to form monomeric endotoxin-sCD14 complexes. Subsequent interactions of endotoxin-sCD14 with TLR4 and/or MD-2 have not been specifically defined. This study reports the purification of a stable, monomeric, bioactive endotoxin-MD-2 complex generated by treatment of endotoxin-sCD14 with recombinant MD-2. Efficient generation of this complex occurred at picomolar concentrations of endotoxin and nanogram per milliliter doses of MD-2 and required presentation of endotoxin to MD-2 as a monomeric endotoxin-CD14 complex. TLR4-dependent delivery of endotoxin to human embryonic kidney (HEK) cells and cell activation at picomolar concentrations of endotoxin occurred with the purified endotoxin-MD-2 complex, but not with purified endotoxin aggregates with or without LBP and/or sCD14. The presence of excess MD-2 inhibited delivery of endotoxin-MD-2 to HEK/TLR4 cells and cell activation. These findings demonstrate that TLR4-dependent activation of host cells by picomolar concentrations of endotoxin occurs by sequential interaction and transfer of endotoxin to LBP, CD14, and MD-2 and simultaneous engagement of endotoxin and TLR4 by MD-2.