FDA-approved Small-molecule Drugs Research Articles

A Virtual Docking Screen at 23 SARS‐CoV‐2 Proteins Identifies Drug Repurposing Candidates at New Sites and Targets

The ongoing severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) pandemic requires treatments with rapid clinical translatability. As such, several studies have screened FDA‐approved drugs in silico at a limited number of classical antiviral sites for anti‐SARS‐CoV‐2 activity. We hypothesized that an extensive in‐silico drug repurposingscreen against a wide range of SARS‐COV‐2 proteins could identify novel antiviral drugs and help elucidate mechanisms of drug action of hits from in vitro screens. We selected 48 known or predicted drug sites across 23 SARS‐COV‐2 proteins using homology models and crystal structures based on known antiviral drug sites (i.e., polymerase or protease active sites), computational predictions, and protein‐protein interfaces. Then, using the software GOLD, we docked 1268 FDA‐approved small‐molecule drugs into each site. Virtual hits were prioritized based on their anti‐SARS‐COV‐2 activity found in a recent phenotypic drug‐repurposing screen using human huh‐7 epithelial cells. This resulted in the identification of a range of drugs acting at a variety of targets and sites. Several compelling drug/site pairs were identified, including sites on the Spike protein, which mediates viral entry. For example, we identified hits with anti‐SARS‐CoV2 activity in vitro, at a putative allosteric site that incorporates two functionalities required for viral entry, namely the Spike S2’ cleavage site – which a host protease must cleave for viral entry, and the critical ‘fusion peptide’ domain – which injects itself into the host membrane during viral entry. Moreover, these in silico results identify possible mechanisms for in vitro drug repurposing hits, potential additional targets for known drugs, and a starting point to test drug combinations that may have better activity by acting at different steps in the viral cycle activity in combination than on their own.8.5.5

A graphene oxide-based fluorescent nanosensor to identify antiviral agents via a drug repurposing screen

Currently, there are no approved therapeutics for Dengue virus (DENV) infection, even though it can cause fatal complications. Understanding DENV infection and its propagation process in host cells is necessary to develop specific antiviral therapeutics. Here, we developed a graphene oxide-based fluorescent system (Graphene Oxide-based Viral RNA Analysis system, GOViRA) that enables sensitive and quantitative real-time monitoring of the intracellular viral RNA level in living cells. The GOViRA system consists of a fluorescent dye-labeled peptide nucleic acid (PNA) with a complementary sequence to the DENV genome and a dextran-coated reduced graphene oxide nanocolloid (DRGON). When the dye labeled PNA is adsorbed onto DRGON, the fluorescence of the dye is effectively quenched. The quenched fluorescence signal is recovered when the dye labeled PNA forms interaction with intracellular viral RNA in DENV infected host cells. We demonstrated the successful use of the GOViRA platform for high-throughput screening to discover novel antiviral compounds. Through a cell-based high-throughput screening of FDA-approved small-molecule drugs, we identified ulipristal, a selective progesterone receptor modulator (SPRM), as a potent inhibitor against DENV infection. The anti-DENV activity of ulipristal was confirmed both in vitro and in vivo. Moreover, we suggest that the mode of action of ulipristal is mediated by inhibiting viral entry into the host cells.

Molecular and Clinical Data Integration Identifies an Association Between Decreased Colectomy Rates and Atorvastatin Exposure in Ulcerative Colitis Patients: A Retrospective Cohort Study

Background: Ulcerative colitis (UC) is a chronic inflammatory disorder of the gastrointestinal tract with limited effective therapeutic options for long-term treatment and disease maintenance. We hypothesized that multi-cohort analysis of independent cohorts representing real-world heterogeneity of patients with UC would identify a robust transcriptomic signature to improve identification of FDA-approved drugs that can be repurposed to treat patients with UC. Methods: We performed a multi-cohort analysis of transcriptome profiles of 272 colon biopsies across 11 publicly available datasets to identify a robust UC gene signature. We compared the gene signature with in vitro transcriptomic profiles induced by 781 FDA-approved small-molecule drugs to identify potential drug targets. We used a retrospective cohort study design modeled after a target trial to evaluate the protective effect of atorvastatin on colectomy risk in patients with UC from the Stanford Research Repository (STARR) database and Optum Clinformatics DataMart. Findings: The transcriptomic profile of atorvastatin treatment had the highest inverse-correlation with the UC gene signature among any non-oncolytic therapy. In both the STARR(n=827) and Optum(n=7821) cohorts, atorvastatin use was significantly associated with a decreased risk of colectomy, a marker of treatment-refractory disease in patients with UC, compared to patients prescribed a comparator drug (STARR: HR=0.47, p=0.03; Optum: HR=0.66, p=0.03), irrespective of age and length of atorvastatin treatment. Interpretations: These findings suggest that atorvastatin might serve as a novel therapeutic option for ameliorating disease in patients with UC. Importantly, we provide a systematic framework for integrating publicly available heterogeneous molecular data with similarly heterogeneous clinical data at a large scale to repurpose existing FDA-approved drugs for a wide range of human diseases. Funding Statement: LB is funded by the Stanford Bio-X Graduate Fellowship. MKDS is funded in part by the National Heart, Lung, and Blood Institute (F30:HL149252) and The Stanford University Medical Scientist Training Program (T32GM007365). PK is funded in part by the Bill and Melinda Gates Foundation (OPP1113682); the National Institute of Allergy and Infectious Diseases (NIAID) grants 1U19AI109662, U19AI057229, and 5R01AI125197; Department of Defense contracts W81XWH-18-1-0253 and W81XWH1910235; and the Ralph & Marian Falk Medical Research Trust, outside of this work. Declaration of Interests: Authors declare no conflicts of interest. Ethics Approval Statement: Access was permitted through a previously approved IRB.

Direct control of CAR T cells through small molecule-regulated antibodies

Antibody-based therapeutics have experienced a rapid growth in recent years and are now utilized in various modalities spanning from conventional antibodies, antibody-drug conjugates, bispecific antibodies to chimeric antigen receptor (CAR) T cells. Many next generation antibody therapeutics achieve enhanced potency but often increase the risk of adverse events. Antibody scaffolds capable of exhibiting inducible affinities could reduce the risk of adverse events by enabling a transient suspension of antibody activity. To demonstrate this, we develop conditionally activated, single-module CARs, in which tumor antigen recognition is directly modulated by an FDA-approved small molecule drug. The resulting CAR T cells demonstrate specific cytotoxicity of tumor cells comparable to that of traditional CARs, but the cytotoxicity is reversibly attenuated by the addition of the small molecule. The exogenous control of conditional CAR T cell activity allows continual modulation of therapeutic activity to improve the safety profile of CAR T cells across all disease indications.

Structure-Property Relationships and Machine Learning Models for Addressing CYP3A4-Mediated Victim Drug-Drug Interaction Risk in Drug Discovery.

Among the FDA-approved small molecule drugs (2005-2016) that are primarily metabolized by cytochrome P450 (CYP), 64% are primarily metabolized by CYP3A4. As the proportion of an individual drug's fraction metabolized through CYP3A4 increases, the risk for the drug to be a victim of an interaction with CYP3A4 inhibitors or inducers increases. Therefore, it is important to assess the extent of involvement of individual CYP enzymes in the overall clearance for a scaffold early in discovery and mitigate the CYP3A4-mediated victim-drug-drug interaction (DDI) risk, if warranted by the desired clinical profile of the drug. To mitigate the CYP3A4-mediated victim DDI risk in discovery, we analyzed the physicochemical properties of the CYP3A4 substrates and found that molecular weight was the property that provided the best separation of the CYP3A4 substrates from other CYP substrates. In addition, neutral and basic compounds with MW ≥ 360 g/mol tend to be primarily metabolized by CYP3A4, whereas acidic compounds with MW < 360 g/mol are most likely to be primarily metabolized by other CYP enzymes. We then developed Support Vector Machine based on fingerprints (SVM-FP) and Deep-Learning (DL) models to predict if a molecule will be primarily metabolized by CYP3A4. Our models were trained on 2306 compounds, which is the largest training set among published models for this endpoint. Both models showed positive predictive values (PPV) > 80% in predicting a CYP3A4 substrate on a prospective testing set. Given the high PPV of the models, project teams can confidently deprioritize compounds predicted to be CYP3A4 substrates to avoid the potential liability of CYP3A4 victim DDI. Teams can then focus time and resources on synthesizing compounds that are predicted to have a lower dependency on CYP3A4 metabolism and confirm that experimentally. Through such iterative in silico-in vitro learning circles, drug discovery teams can decide if metabolism through non-CYP3A4 pathways could be achieved in the SAR of a chemical series to mitigate the CYP3A4 victim DDI risk.

Metformin coordinates osteoblast/osteoclast differentiation associated with ischemic osteonecrosis.

In this study, we aimed to identify a candidate drug that can activate endogenous Angiopoietin 1 (Ang1) expression via drug repositioning as a pharmacological treatment for avascular osteonecrosis. After incubation with 821 drugs from the Food and Drug Administration (FDA)-approved drug library, Ang1 expression in U2OS cell culture media was examined by ELISA. Metformin, the first-line medication for treatment of type 2 diabetes, was selected as a candidate for in vitro and in vivo experimental evaluation. Ang1 was induced, and alkaline phosphatase activity was increased by metformin treatment in U2OS and MG63 cells. Wound healing and migration assay showed increased osteoblastic cell mobility by metformin treatment in U2OS and MG63 cells. Metformin upregulated expression of protein markers for osteoblastic differentiation in U2OS and MG63 cells but inhibited osteoclastic differentiation in Raw264.7 cells. Metformin (25 mg/kg) protected against ischemic necrosis in the epiphysis of the rat femoral head by maintaining osteoblast/osteocyte function and vascular density but inhibiting osteoclast activity in the necrotic femoral head. These findings provide novel insight into the specific biomarkers that are targeted and regulated by metformin in osteoblast differentiation and contribute to understanding the effects of these FDA-approved small-molecule drugs as novel therapeutics for ischemic osteonecrosis.

Dasatinib regulates LPS-induced microglial and astrocytic neuroinflammatory responses by inhibiting AKT/STAT3 signaling

BackgroundThe FDA-approved small-molecule drug dasatinib is currently used as a treatment for chronic myeloid leukemia (CML). However, the effects of dasatinib on microglial and/or astrocytic neuroinflammatory responses and its mechanism of action have not been studied in detail.MethodsBV2 microglial cells, primary astrocytes, or primary microglial cells were treated with dasatinib (100 or 250 nM) or vehicle (1% DMSO) for 30 min or 2 h followed by lipopolysaccharide (LPS; 200 ng/ml or 1 μg/ml) or PBS for 5.5 h. RT-PCR, real-time PCR; immunocytochemistry; subcellular fractionation; and immunohistochemistry were subsequently conducted to determine the effects of dasatinib on LPS-induced neuroinflammation. In addition, wild-type mice were injected with dasatinib (20 mg/kg, intraperitoneally (i.p.) daily for 4 days or 20 mg/kg, orally administered (p.o.) daily for 4 days or 2 weeks) or vehicle (4% DMSO + 30% polyethylene glycol (PEG) + 5% Tween 80), followed by injection with LPS (10 mg/kg, i.p.) or PBS. Then, immunohistochemistry was performed, and plasma IL-6, IL-1β, and TNF-α levels were analyzed by ELISA.ResultsDasatinib regulates LPS-induced proinflammatory cytokine and anti-inflammatory cytokine levels in BV2 microglial cells, primary microglial cells, and primary astrocytes. In BV2 microglial cells, dasatinib regulates LPS-induced proinflammatory cytokine levels by regulating TLR4/AKT and/or TLR4/ERK signaling. In addition, intraperitoneal injection and oral administration of dasatinib suppress LPS-induced microglial/astrocyte activation, proinflammatory cytokine levels (including brain and plasma levels), and neutrophil rolling in the brains of wild-type mice.ConclusionsOur results suggest that dasatinib modulates LPS-induced microglial and astrocytic activation, proinflammatory cytokine levels, and neutrophil rolling in the brain.

Questioning a publication bias between industry-funded and non-industry-funded randomized controlled trials on biological and small molecule therapy for rheumatoid arthritis

BackgroundThere has been a significant increase in financial support of clinical research by the pharmaceutical industry. MethodsWe performed a comprehensive systematic literature review to determine whether there is publication bias for rheumatoid arthritis (RA) studies between industry-funded and non-industry funded randomized controlled trials (RCTs), and between RCTs with positive results (PRs) and those with negative results (NRs) of FDAapproved biological and small molecule drug therapy for RA. Each RCT was classified as having either a PR or a NR, and as having received commercial funding or not. ResultsMost (297/349, 85.18%) of the RCTs were commercially funded. There was no significant difference in PRs or association with publication between commercially and noncommercially funded RCTs. Sample size was significantly larger in commercially funded RCTs and in those with PRs, and it was the only significant parameter that predicted publication in higher impact factor journals in the field of RA. ConclusionThere is no significant association between commercial funding and the publication of positive results or the publication of an RCT in higher impact factor journals.

Abstract A220: Destabilizing domain technology facilitates exogenous regulation of IL15 and IL12 for adaptive T-cell therapy

Abstract Cytokines are messenger molecules that act as regulators of innate and adaptive immunity by propagating cell-cell immune signaling. Several cytokines have been approved for the treatment of metastatic renal cell cancer, advanced melanoma, and hairy cell leukemia (HCL) and can be particularly effective when combined with adoptive cell therapy. However, systemic delivery or constitutive expression of cytokines even at moderate levels can potentially lead to significant toxicity. These hurdles to enabling cytokine-enhanced adoptive cell therapy motivated us to implement destabilizing domain (DD) technology for regulating cytokines in chimeric antigen receptor (CAR) reprogrammed T-cells. The ability of CAR-T-cells to traffic to tumor sites enables localized co-delivery of cytokines for enhanced CAR-T-cell antitumor activity while improving safety. Obsidian Therapeutics’ DD technology enables titratable and reversible regulation of a protein of interest with FDA-approved small-molecule drugs in a time- and dose-dependent manner. Protein-fused DDs are misfolded in the absence of a stabilizing small-molecule ligand and are rapidly degraded by the proteasome. However, the addition of ligand restores the folding, stability, and function of the DD-protein fusion. We have generated IL-12 and membrane-bound IL15-IL15Ra (mbIL15) fused to DDs such as FK506 binding protein (FKBP), Escherichia coli dihydrofolate reductase (ecDHFR), as well as human protein substrates (huDDs) with clinically approved ligands. DD-IL12 and DD-mbIL15 fusions displayed ligand-dependent regulation of cytokine secretion or cell surface expression, respectively, in cell lines and primary human T-cells. We then tested DD regulation of IL12 or mbIL15 in vivo by injecting T-cells engineered with cytokine-fused DDs into NSG mice, followed by oral administration of vehicle or corresponding ligand. Vehicle-treated mice displayed low level expression of the respective cytokines, whereas ligand treatment robustly induced the expression of target cytokine within 4-6 hours after treatment. Cytokine expression returned to baseline levels 24 hours following ligand administration. These data demonstrate the feasibility of exogenous control over transgene-derived protein expression in primary human T-cells for the development of next-generation CAR-T-cell products with enhanced efficacy and more favorable safety profiles. Citation Format: Karen Tran, Kutlu Elpek, Tucker Ezell, Scott Heller, Mara Inniss, Abhishek Kulkarni, Dan Jun Li, Grace Olinger, Michelle Ols, Christopher Reardon, Dexue Sun, Tariq Kassum, Michael Briskin, Celeste Richardson, Vipin Suri, Steven Shamah, Michael Gilman. Destabilizing domain technology facilitates exogenous regulation of IL15 and IL12 for adaptive T-cell therapy [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr A220.

Discovery of atorvastatin as a tetramer stabilizer of nuclear receptor RXRα through structure-based virtual screening

Retinoid X receptor alpha (RXRα), a central member of the nuclear receptor superfamily and a key regulator of many signal transduction pathways, has been an attractive drug target. We previously discovered that an N-terminally truncated form of RXRα can be induced by specific ligands to form homotetramers, which, as a result of conformational selection, forms the basis for inhibiting the nongenomic activation of RXRα. Here, we report the identification and characterization of atorvastatin as a new RXRα tetramer stabilizer by using structure-based virtual screening and demonstrate that virtual library screening can be used to aid in identifying RXRα ligands that can induce its tetramerization. In this study, docking was applied to screen the FDA-approved small molecule drugs in the DrugBank 4.0 collection. Two compounds were selected and purchased for testing. We showed that the selected atorvastatin could bind to RXRα to promote RXRα-LBD tetramerization. We also showed that atorvastatin possessed RXRα-dependent apoptotic effects. In addition, we used a chemical approach to aid in the studies of the binding mode of atorvastatin.

Repositioning Tacrolimus: Evaluation of the Effect of Short-Term Tacrolimus Treatment on Osteoprogenitor Cells and Primary Cells for Bone Regenerative Engineering.

Small-molecule-based bone regenerative engineering is an encouraging strategy for repair and regeneration of skeletal tissue. Using osteogenic small molecules for engineering bone tissue has several potential benefits over polypeptide-based approaches. Interestingly, hundreds of such small molecules possess the capability to promote osteogenesis, and several of these are already approved by the FDA for use in other applications, indicating their safety for human use. However, the need for their use at a high frequency and/or duration, due to their short half-life and nonspecificity, is still problematic. We, and others, have identified several non-FDA-approved small-molecule-based compounds that induce long-lasting osteogenic effects following short-term (<24 h) treatment. In this study, however, we have performed a proactive screen to investigate and compare the osteogenic effects of several preselected FDA-approved small-molecule drugs in vitro using osteoprogenitor MC3T3-E1 cells. Our results demonstrate that treatment with the small-molecule drug tacrolimus (FK-506) for 24 h significantly enhanced long-lasting osteogenic responses in both osteoprogenitor cells and primary cell cultures. In addition, we tested whether a short-term treatment with FK-506 is able to induce osteogenic differentiation of cells seeded on a polymeric scaffold in vitro. Using an osteogenic small molecule that has long-lasting effects despite a short duration of exposure to cells may alleviate the undesirable effects often seen with many osteogenic small molecules.

Ibrutinib suppresses LPS-induced neuroinflammatory responses in BV2 microglial cells and wild-type mice

BackgroundThe FDA-approved small-molecule drug ibrutinib is an effective targeted therapy for patients with chronic lymphocytic leukemia (CLL). Ibrutinib inhibits Bruton’s tyrosine kinase (BTK), a kinase involved in B cell receptor signaling. However, the potential regulation of neuroinflammatory responses in the brain by ibrutinib has not been comprehensively examined.MethodsBV2 microglial cells were treated with ibrutinib (1 μM) or vehicle (1% DMSO), followed by lipopolysaccharide (LPS; 1 μg/ml) or PBS. RT-PCR, immunocytochemistry, and subcellular fractionation were performed to examine the effects of ibrutinib on neuroinflammatory responses. In addition, wild-type mice were sequentially injected with ibrutinib (10 mg/kg, i.p.) or vehicle (10% DMSO, i.p.), followed by LPS (10 mg/kg, i.p.) or PBS, and microglial and astrocyte activations were assessed using immunohistochemistry.ResultsIbrutinib significantly reduced LPS-induced increases in proinflammatory cytokine levels in BV2 microglial and primary microglial cells but not in primary astrocytes. Ibrutinib regulated TLR4 signaling to alter LPS-induced proinflammatory cytokine levels. In addition, ibrutinib significantly decreased LPS-induced increases in p-AKT and p-STAT3 levels, suggesting that ibrutinib attenuates LPS-induced neuroinflammatory responses by inhibiting AKT/STAT3 signaling pathways. Interestingly, ibrutinib also reduced LPS-induced BV2 microglial cell migration by inhibiting AKT signaling. Moreover, ibrutinib-injected wild-type mice exhibited significantly reduced microglial/astrocyte activation and COX-2 and IL-1β proinflammatory cytokine levels.ConclusionsOur data provide insights on the mechanisms of a potential therapeutic strategy for neuroinflammation-related diseases.

Abstract 776: Utilising genetic susceptibility and big data to inform novel cancer therapies

Abstract Despite a move towards personalised medicine, attrition rates for new cancer drugs remain unacceptably high. The pharmaceutical industry has also shown a preference for well-studied targets and pathways, as evidenced by ‘me too' drugs. Together with the challenge of inadequate pre-clinical models, this indicates a need for novel, evidence-based therapeutic targets. Genome-wide association studies (GWAS) have identified over 450 robust genetic variants associated with increased cancer risk. Genes implicated through GWAS are often mutated somatically and therefore represent attractive therapeutic targets. Examples include the target of venetoclax in chronic lymphocytic leukaemia, BCL2. We exploit this principle more generally by integrating genetic associations for common cancers with drug target data and druggability using the canSAR drug discovery knowledgebase (https://cansar.icr.ac.uk). By harnessing the power of Big Data we aim to both identify opportunities for repurposing of existing drugs, and prioritise novel targets for cancer drug discovery. We mined the NHGRI-EBI Catalog of published GWAS for all cancer risk SNPs. We annotated candidate target genes through overlapping topologically associating domains (TADs), a more sensitive technique than previously published methods using linkage disequilibrium. We used canSAR to identify target genes for which there is no FDA-approved small molecule drug, and the resource Probe Miner to identify targets for which high-quality chemical probes exist. We also utilised canSAR's machine learning algorithms to assess the druggability of target genes by structure-, ligand-, precedence- and network-based approaches. We additionally analysed results from cancer drug databases to ascertain whether there is an enrichment of ‘drug target-indication pairs' at successive stages of the drug development pathway for which supporting evidence from GWAS exists: this indicates potential ‘stumbling blocks' that may present a risk for future drug development projects. 7 257 protein-coding genes mapped within TADs overlapping cancer risk SNPs. Of these, 98 were pre-existing targets for which there is an FDA-approved small molecule drug. For the remaining 7 159 genes we performed multi-faceted druggability analyses incorporating assessments of the 3D structure of the target and any protein complexes it exists in, chemical properties of known ligands of the target, and the target's position and role within the human interactome. We comprehensively rank our target-indication pairings by criteria including novelty relative to existing targets and predicted attrition risk. Mapping approved drug targets back to cancer GWAS signals enables identification of both novel drug targets and patient populations. Collectively our findings show the value of investigating germline cancer genetics as part of interdisciplinary, data-driven approaches to inform drug discovery. Citation Format: Elizabeth A. Coker, Ben Kinnersley, Amit Sud, Patrizio Di Micco, Bissan Al-Lazikani, Richard Houlston. Utilising genetic susceptibility and big data to inform novel cancer therapies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 776.

Abstract 3580: Enhancing adoptive cell therapies through exogenous regulation

Abstract Adoptive cell therapy with chimeric antigen receptor (CAR) modified T cells has demonstrated remarkable clinical efficacy in the treatment of certain B cell malignancies and more recently in multiple myeloma. However, in solid tumors, CAR-T therapy has been far less successful, likely due to the lack of robust CAR-T cell expansion, the immunosuppressive microenvironment, and clonal heterogeneity within these tumors. The trafficking of CAR-T cells to tumor sites provides an opportunity for selective delivery of cargo that can enhance CAR-T cell activity at the site of the tumor. Interleukin-12 (IL12) and membrane tethered interleukin-15 (mbIL15) have previously been shown to enhance CAR-T activity, yet the unregulated expression of either compromises safety and/or efficacy. The Obsidian Therapeutics platform equips engineered immune cells with new functionalities whose activity can be regulated via the administration of FDA-approved small-molecule drugs, putting dosing control back in the hands of the treating physician. We utilize small, fully human protein sequences called destabilizing domains (DDs) that confer reversible destabilization to a fused target protein. In the absence of ligand the fusion protein is degraded, whereas the presence of small molecule ligand restores expression and functionality. Furthermore, stabilization is titratable with small molecule ligand dose, providing finely tuned control over target protein expression and function. We have applied our technology to create DD-IL12 and DD-mbIL15 “cassettes” that provide exogenous regulation of cytokine activity when transduced into CAR-Ts for enhanced cellular function. We describe here the successful implementation of the DD technology in engineered primary human T cells and show small-molecule ligand controlled regulation of DD-IL12 and DD-mbIL15 protein expression in vivo in mouse models. These data demonstrate the feasibility of exogenous control over protein expression in primary human T cells for the development of next-generation CAR-T cell products with enhanced efficacy and more favorable safety profiles. Citation Format: Celeste Richardson, Kutlu Elpek, Michelle Ols, Tariq Kassum, Steve Shamah. Enhancing adoptive cell therapies through exogenous regulation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3580.

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 statementThe 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.

Discovery of Key Physicochemical, Structural, and Spatial Properties of RNA-Targeted Bioactive Ligands.

While a myriad non-coding RNAs are known to be essential in cellular processes and misregulated in diseases, the development of RNA-targeted small molecule probes has met with limited success. To elucidate the guiding principles for selective small molecule/RNA recognition, we analyzed cheminformatic and shape-based descriptors for 104 RNA-targeted ligands with demonstrated biological activity (RNA-targeted BIoactive ligaNd Database, R-BIND). We then compared R-BIND to both FDA-approved small molecule drugs and RNA ligands without reported bioactivity. Several striking trends emerged for bioactive RNA ligands, including: 1) Compliance to medicinal chemistry rules, 2) distinctive structural features, and 3) enrichment in rod-like shapes over others. This work provides unique insights that directly facilitate the selection and synthesis of RNA-targeted libraries with the goal of efficiently identifying selective small molecule ligands for therapeutically relevant RNAs.

Abstract 5014: Drug discovery for NF1-associated malignant peripheral nerve sheath tumors using the zebrafish model

Abstract Children and young adults with type 1 neurofibromatosis (NF1) are at risk to develop plexiform neurofibromas, which can undergo malignant transformation to malignant peripheral nerve sheath tumors (MPNSTs). MPNSTs are among the most frequently occurring sarcomas in children and young adults and are especially problematic in NF1 patients. Currently, complete surgical excision is the only curative therapy for NF1-associated MPNST, but these tumors are often not completely resectable. Therefore, it is very important to identify promising drugs that can be rapidly moved into clinical trials to improve the therapy of patients with MPNSTs. We have developed a faithful zebrafish model of NF1-associated MPNST by using genome engineering to develop zebrafish lines harboring loss-of-function mutations of the duplicated nf1a and nf1b genes and p53. Our nf1 and p53 deficient zebrafish models develop MPNSTs that are very similar to human NF1-associated MPNST, and thus are ideal for experiments to test the efficacy of FDA-approved small molecule drugs in vivo. To test the FDA-approved drugs for activity against MPNST tumor cells, about 100 Sox10:mCherry expressed MPNST primary tumor cells were transplanted into dechorionized 2 day-post-fertilization (dpf) larval fish using a micro-injector. MPNST-implanted embryos were exposed to individual test compounds added to the fish water at a range of concentrations and to the vehicle control. After 4-days of treatment, quantitative assessment of the remaining mCherry-labeled tumor cell numbers were measured using the ImageJ software for each treated embryo. Currently, trametinib and sunitinib caused marked antitumor effects indicated by reduced numbers of mCherry-labeled nf1-deficient MPNST cells compared to the DMSO control in this study. We are now applying this embryonic implantation assay to identify combinations of FDA-approved drugs that have a high degree of efficacy against MPNST and can be rapidly “repurposed” to improve the treatment of this disease. Citation Format: Dong Hyuk Ki, Shuning He, A. Thomas Look. Drug discovery for NF1-associated malignant peripheral nerve sheath tumors using the zebrafish model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5014. doi:10.1158/1538-7445.AM2017-5014

Comprehensive Modeling and Discovery of Mebendazole as a Novel TRAF2- and NCK-interacting Kinase Inhibitor

TRAF2- and NCK-interacting kinase (TNIK) represents one of the crucial targets for Wnt-activated colorectal cancer. In this study, we curated two datasets and conducted a comprehensive modeling study to explore novel TNIK inhibitors with desirable biopharmaceutical properties. With Dataset I, we derived Comparative Molecular Similarity Indices Analysis (CoMSIA) and variable-selection k-nearest neighbor models, from which 3D-molecular fields and 2D-descriptors critical for the TNIK inhibitor activity were revealed. Based on Dataset II, predictive CoMSIA-SIMCA (Soft Independent Modelling by Class Analogy) models were obtained and employed to screen 1,448 FDA-approved small molecule drugs. Upon experimental evaluations, we discovered that mebendazole, an approved anthelmintic drug, could selectively inhibit TNIK kinase activity with a dissociation constant Kd = ~1 μM. The subsequent CoMSIA and kNN analyses indicated that mebendazole bears the favorable molecular features that are needed to bind and inhibit TNIK.

In Silico Identification and In Vitro and In Vivo Validation of Anti-Psychotic Drug Fluspirilene as a Potential CDK2 Inhibitor and a Candidate Anti-Cancer Drug.

Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths worldwide. Surgical resection and conventional chemotherapy and radiotherapy ultimately fail due to tumor recurrence and HCC’s resistance. The development of novel therapies against HCC is thus urgently required. The cyclin-dependent kinase (CDK) pathways are important and well-established targets for cancer treatment. In particular, CDK2 is a key factor regulating the cell cycle G1 to S transition and a hallmark for cancers. In this study, we utilized our free and open-source protein-ligand docking software, idock, prospectively to identify potential CDK2 inhibitors from 4,311 FDA-approved small molecule drugs using a repurposing strategy and an ensemble docking methodology. Sorted by average idock score, nine compounds were purchased and tested in vitro. Among them, the anti-psychotic drug fluspirilene exhibited the highest anti-proliferative effect in human hepatocellular carcinoma HepG2 and Huh7 cells. We demonstrated for the first time that fluspirilene treatment significantly increased the percentage of cells in G1 phase, and decreased the expressions of CDK2, cyclin E and Rb, as well as the phosphorylations of CDK2 on Thr160 and Rb on Ser795. We also examined the anti-cancer effect of fluspirilene in vivo in BALB/C nude mice subcutaneously xenografted with human hepatocellular carcinoma Huh7 cells. Our results showed that oral fluspirilene treatment significantly inhibited tumor growth. Fluspirilene (15 mg/kg) exhibited strong anti-tumor activity, comparable to that of the leading cancer drug 5-fluorouracil (10 mg/kg). Moreover, the cocktail treatment with fluspirilene and 5-fluorouracil exhibited the highest therapeutic effect. These results suggested for the first time that fluspirilene is a potential CDK2 inhibitor and a candidate anti-cancer drug for the treatment of human hepatocellular carcinoma. In view of the fact that fluspirilene has a long history of safe human use, our discovery of fluspirilene as a potential anti-HCC drug may present an immediately applicable clinical therapy.

Phase I trial of the combination of bortezomib and clofarabine in adults with refractory solid tumors.

TPS2614 Background: We conducted a systematic combination drug screen across the NCI-60 cell line panel encompassing nearly all pairwise combinations of FDA-approved small-molecule cancer drugs ( >...