Molecular Libraries Screening Center Network Research Articles

Diversity-Oriented Library Synthesis from Steviol and Isosteviol-Derived Scaffolds.

The readily available natural product stevioside provides a unique diterpene core structure that can be explored for small molecule library development by diversity-oriented synthesis and functional group transformations. Validation arrays were prepared from steviol, isosteviol, and related analogues, derived from stevioside, to produce over 90 compounds. These compounds were submitted to the NIH Molecular Libraries Small Molecule Repository for screening in the Molecular Libraries Screening Center Network. Micromolar hits were identified in multiple high-throughput assays for several library members. A cheminformatics analysis of the compounds was performed that verified the expected diversity and complexity of this set of compounds. The screening results indicate that scaffolds-derived natural products can provide screening hits against multiple target proteins.

Optimization of a Novel D2 Dopamine Receptor Antagonist Scaffold Reveals Exceptionally Selective and Potent Lead Molecules

FDA‐approved antipsychotics are primarily D2 dopamine receptor (D2R) antagonists, however they generally lack receptor selectivity and interact with other GPCRs, including D3Rs. Despite its clear clinical importance, there are few compounds that selectively modulate the D2R. This is due to structural similarities in the orthosteric binding sites of the D2‐like receptors (D2R, D3R, and D4R), as well as other biogenic amine receptors. To find better therapeutic candidates, as well as probe compounds to investigate D2R pathophysiology, we sought to identify highly selective D2R antagonists by implementing a high‐throughput screening (HTS) campaign using more than 400,000 unique compounds in the Molecular Libraries Screening Center Network library. Most of the hit compounds that were identified as antagonists of the D2R were also antagonists of the closely related D3R. However, several compounds were found to exhibit high affinity for the D2R with low affinity for the D3R. One such compound (MLS6916) served as our lead scaffold for optimization. MLS6916 is ~700 fold selective for the D2R vs. D3R as determined in functional β‐arrestin recruitment assays and radioligand binding competition assays. Importantly, MLS6916 was also examined for functional activity at 168 different GPCRs and showed no agonist activity on any GPCR tested, and only exhibited antagonist activity at the D2‐like receptors. Preliminary investigations, however, revealed that this initial hit compound was metabolically unstable. To optimize this hit scaffold, we conducted an iterative medicinal chemistry campaign with the goals of increasing selectivity, potency, and engendering metabolic stability. Over 70 analogs of the MLS6916 parent compound were synthesized to dissect the influence of various constituents of the molecule and to construct structure‐activity relationships. Analogs were analyzed for activity on D2R, D3R, and D4R using both radioligand binding and functional assays to determine affinities and potencies for the D2‐like receptors. In addition, analogs were tested for solubility, permeability, and stability. Several lead compounds were identified with Ki values of < 50 nM for the D2R with > 1,000‐fold selectivity vs. the D3R. These selectivity trends were confirmed in functional β‐arrestin recruitment assays. Importantly, lead compounds with enhanced metabolic stability and permeability were identified. Further analysis and optimization of these lead compounds will provide new insight into highly selective D2R antagonists for the treatment and understanding of dopamine‐related disorders.Support or Funding InformationNINDS Intramural Research Program

Identification and characterization of a novel dopamine receptor antagonist with high selectivity for the D2 dopamine receptor

Despite its clinical importance in the treatment of a number of neuropsychiatric disorders, such as Parkinson's disease and schizophrenia, there are few compounds, either agonists or antagonists that are highly selective for the D2 dopamine receptor (D2R). Most compounds with activity at the D2R also exhibit significant affinity for the D3 or D4 dopamine receptors (D3R or D4R), or other G protein‐coupled receptors (GPCRs). Development of D2R‐selective ligands has proven especially problematic due to the high structural similarities of the orthosteric binding sites of the D2‐like receptors (D2R, D3R and D4R). Importantly, highly selective D2R antagonists could represent improved therapeutics for treating the positive symptoms of schizophrenia with potentially fewer side effects due to off‐target activities. Thus, in order to identify selective antagonists of the D2R, we implemented a high‐throughput screening (HTS) campaign to interrogate over 400,000 unique compounds in the Molecular Libraries Screening Center Network library. Not surprisingly, most of the compounds that were identified as antagonists of the D2R were also antagonists of the closely related D3R. However, a small pool of antagonist compounds that exhibited significant D2R>D3R selectivity was identified. These compounds were characterized using orthogonal D2R and D3R functional assays (including several G protein‐mediated assays and b‐arrestin recruitment) as well as radioligand binding assays. One compound, MLS1946, was found to exhibit high affinity for the D2R (Ki ~100 nM) without measurable affinity for the D3R (Ki > 40 mM). This compound was further characterized using a number of D2R and D3R signaling assays and found to exert no activity an the D3R, while exhibiting potent antagonism of the D2R. Follow‐up studies were performed using an analog of the hit compound and a functional screen (b‐arrestin recruitment) of a panel of 168 different GPCRs. We found that the hit compound analog was completely devoid of agonist activity within this panel of GPCRs. In contrast, at the dose tested, the compound was found to completely antagonize dopamine stimulation of the D2R while exhibiting partial antagonism of the D4R. Surprisingly, the compound was devoid of significant antagonist activity at the remaining 166 GPCRs. These results suggest that the MLS1946 scaffold displays a highly selective D2R antagonist profile. We are currently engaged in a chemical optimization campaign to synthesize analogs around this scaffold to both interrogate structure‐activity relationships and optimize compounds for in vivo testing. It is anticipated that further development of the MLS1946 scaffold may lead to an optimized D2R‐selective antagonist with drug‐like properties for the treatment and understanding of dopamine‐related pathologies.Support or Funding InformationNINDS Intramural Research Program

HCS campaign to identify selective inhibitors of IL-6-induced STAT3 pathway activation in head and neck cancer cell lines.

Signal transducer and activator of transcription factor 3 (STAT3) is hyperactivated in head and neck squamous cell carcinomas (HNSCC). Cumulative evidence indicates that IL-6 production by HNSCC cells and/or stromal cells in the tumor microenvironment activates STAT3 and contributes to tumor progression and drug resistance. A library of 94,491 compounds from the Molecular Library Screening Center Network (MLSCN) was screened for the ability to inhibit interleukin-6 (IL-6)-induced pSTAT3 activation. For contractual reasons, the primary high-content screening (HCS) campaign was conducted over several months in 3 distinct phases; 1,068 (1.1%) primary HCS actives remained after cytotoxic or fluorescent outliers were eliminated. One thousand one hundred eighty-seven compounds were cherry-picked for confirmation; actives identified in the primary HCS and compounds selected by a structural similarity search of the remaining MLSCN library using hits identified in phases I and II of the screen. Actives were confirmed in pSTAT3 IC50 assays, and an IFNγ-induced pSTAT1 activation assay was used to prioritize selective inhibitors of STAT3 activation that would not inhibit STAT1 tumor suppressor functions. Two hundred three concentration-dependent inhibitors of IL-6-induced pSTAT3 activation were identified and 89 of these also produced IC50s against IFN-γ-induced pSTAT1 activation. Forty-nine compounds met our hit criteria: they reproducibly inhibited IL-6-induced pSTAT3 activation by ≥70% at 20 μM; their pSTAT3 activation IC50s were ≤25 μM; they were ≥2-fold selective for pSTAT3 inhibition over pSTAT1 inhibition; a cross target query of PubChem indicated that they were not biologically promiscuous; and they were ≥90% pure. Twenty-six chemically tractable hits that passed filters for nuisance compounds and had acceptable drug-like and ADME-Tox properties by computational evaluation were purchased for characterization. The hit structures were distributed among 5 clusters and 8 singletons. Twenty-four compounds inhibited IL-6-induced pSTAT3 activation with IC50s ≤20 μM and 13 were ≥3-fold selective versus inhibition of pSTAT1 activation. Eighteen hits inhibited the growth of HNSCC cell lines with average IC50s ≤ 20 μM. Four chemical series were progressed into lead optimization: the guanidinoquinazolines, the triazolothiadiazines, the amino alcohols, and an oxazole-piperazine singleton.

High‐throughput screening for novel allosteric modulators of the D1 dopamine receptor (662.4)

Dopamine is a critically important neurotransmitter in the CNS and peripheral nervous system, with five receptor subtypes mediating its effects. Importantly, D1 receptor (D1R)‐selective agents may prove beneficial in the treatment of many neuropsychiatric disorders. In an effort to identify novel selective allosteric modulators of the D1R we used a high throughput screening approach. 380,000 small molecules in the NIH Molecular Libraries Screening Center Network library were screened using a cell line expressing the D1R coupled to G15 resulting in a robust Ca2+ signal upon receptor stimulation. Hit compounds were triaged through secondary functional and radioligand displacement binding assays to determine subtype selectivity and their allosteric versus orthosteric nature. We initially identified 96 putative positive allosteric modulator (PAM) hits that enhanced the EC20 activity of dopamine in the Ca2+ response ‐ 6 of these were subsequently confirmed during triage and were chosen for further characterization. In addition we found approximately 115 agonist and 125 antagonist hits that failed to completely inhibit radioligand binding and have been classified as potential allosteric agonists and antagonists or negative allosteric modulators (NAMs). These compounds are currently being characterized using additional assays to confirm their selectivity, activity, and classification.Grant Funding Source: NINDS Intramural Program

Abstract 733: Synthesis and biological evaluation of inhibitors of Rho protein kinase

Abstract Rho GTPases are small G-proteins which play a critical role in signaling pathways and control cell growth and division. Rho-associated protein kinase (known as ROCK or Rho kinase) is a Ser/Thr protein kinase activated by GTP-bound Rho and phosphorylates important signalling proteins. Rho/ROCK mediated signalling pathways are implicated in cell morphology, moltility, smooth muscle contraction, formation of stress fiber, focal adhesion, cell transformation and cytokineses. ROCKs have been subject to growing attention, having been implicated in a range of therapeutic areas including cancer. Further, the pharmacological inhibition of ROCKs has been suggested as a promising strategy in the prevention of cell invasion, a central event in the process of metastasis. We describe the identification of potent ROCK inhibitors from data mining of the Molecular Libraries Screening Center Network (MLSCN) data available through PubChem and in-house HTS screening. Libraries of compounds have been designed to aid the hit-to-lead process and probe structure activity relationships. Molecular modeling and crystallography have been used to aid the design of potent ROCK inhibitors. Compounds were first assessed for in vitro ROCK1 inhibitory activity using a Z-lyte kinase assay. Selected compounds were also screened against the isoform ROCK2. Selectivity trends will be discussed. The overall process has led to the improvement of activity of compounds from high micromolar activity to low nanomolar activity. Structure activity relationship studies led to the identification of highly potent and cell-permeable analogues that were shown to inhibit selected substrates of ROCK such as MYPT1 in cell assays and are the subject of ongoing antitumor studies. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 733.

Oxime esters as selective, covalent inhibitors of the serine hydrolase retinoblastoma-binding protein 9 (RBBP9)

We recently described a fluorescence polarization platform for competitive activity-based protein profiling (fluopol-ABPP) that enables high-throughput inhibitor screening for enzymes with poorly characterized biochemical activity. Here, we report the discovery of a class of oxime ester inhibitors for the unannotated serine hydrolase RBBP9 from a full-deck (200,000+ compound) fluopol-ABPP screen conducted in collaboration with the Molecular Libraries Screening Center Network (MLSCN). We show that these compounds covalently inhibit RBBP9 by modifying enzyme’s active site serine nucleophile and, based on competitive ABPP in cell and tissue proteomes, are selective for RBBP9 relative to other mammalian serine hydrolases.

Antituberculosis activity of the molecular libraries screening center network library

There is an urgent need for the discovery and development of new antitubercular agents that target novel biochemical pathways and treat drug-resistant forms of the disease. One approach to addressing this need is through high-throughput screening of drug-like small molecule libraries against the whole bacterium in order to identify a variety of new, active scaffolds that will stimulate additional biological research and drug discovery. Through the Molecular Libraries Screening Center Network, the NIAID Tuberculosis Antimicrobial Acquisition and Coordinating Facility tested a 215,110-compound library against Mycobacterium tuberculosis strain H37Rv. A medicinal chemistry survey of the results from the screening campaign is reported herein.

Small-Molecule Modulators of the NF-κB Pathway Newly Identified by a Translocation-Based Cellular Assay

Nuclear factor kappa B (NF-kappaB) is an important transcription factor. Aberrant regulation of the NF-kappaB pathway is frequently observed in a number of major ailments such as cancer and inflammatory diseases. Hence NF-kappaB modulators have been intensely pursued for their potential therapeutic applications. Numerous reviews have described recent progress in the development of these agents. More recently, a variety of structurally and functionally novel small molecules, identified through high-throughput screens conducted within the Molecular Libraries Screening Center Network (MLSCN) of the NIH Roadmap for Medical Research, have been added to the current list of NF-kappaB regulators. This review will discuss the inhibitors and activators newly discovered by Columbia's Molecular Libraries Screening Center (MLSC) using a well-designed and stable cellular assay.

Editorial [Hot topic: Medicinal Chemistry in the Pilot Phase of the Molecular Libraries Screening Center Network (Guest Editor: Donna M. Huryn)

Editorial [Hot topic: Medicinal Chemistry in the Pilot Phase of the Molecular Libraries Screening Center Network (Guest Editor: Donna M. Huryn)

Discovery and validation of new antitubercular compounds as potential drug leads and probes

Increasing multidrug resistance in Mycobacterium tuberculosis continues to diminish the number of effective drugs available for treatment of active tuberculosis. Although there are four new products (representing three new chemical classes) in clinical development, an active, robust pipeline of new chemical entities is critical to discovery of medicines to dramatically improve or shorten length of therapy via new mechanisms of action. In the absence of major pharmaceutical industry activity in tuberculosis drug development, the National Institute of Allergy and Infectious Diseases (NIAID) has supported the development of a high throughput screen for growth inhibitors of M. tuberculosis using a chemically diverse commercial library, a compound library available through the NIH Roadmap, Molecular Libraries Screening Center Network, and other compound sources. The rationale for these screens and suggested approaches for follow-up studies to identify compounds for advanced preclinical studies and as chemical probes of critical functions in M. tuberculosis, are discussed.

Identification and Characterization of Novel Tissue-Nonspecific Alkaline Phosphatase Inhibitors with Diverse Modes of Action

Tissue-nonspecific alkaline phosphatase (TNAP) is a ubiquitous enzyme expressed at high levels in bone, liver, and kidney. It appears involved in dephosphorylation of numerous phosphate monoesters, but only 2 of them, pyrophosphate and pyridoxal phosphate, have yet been unequivocally documented. Discovery and characterization of other substrates could be considerably facilitated if specific and potent modulators of TNAP activity with various modes of action were available. Here, the authors describe in detail a high-throughput screening campaign to identify inhibitors of TNAP, performed within the Molecular Library Screening Center Network (MLSCN). A novel homogeneous luminescent TNAP assay was developed and optimized with respect to the enzyme and substrate concentrations, enabling identification of a large number of compounds overlooked by a conventional colorimetric assay. Several new chemical series were identified from screening the Molecular Libraries Small Molecule Repository (MLSMR) collection and demonstrated to have diverse selectivity and mode of inhibition profiles. The nanomolar potency of some of these scaffolds surpasses currently known inhibitors. This article provides an example of a success where the Roadmap Initiative collaborative model, sponsored by the National Institutes of Health, brought together a deep knowledge of target biology from a principal investigator's laboratory, a well-designed compound collection from the MLSMR, and an industrial-level screening facility and staff at the MLSCN center to identify pharmacologically active compounds, with outstanding selectivity data from a panel of more than 200 publicly accessible assays, through a high-throughput screen.

Cdc25B Dual-Specificity Phosphatase Inhibitors Identified in a High-Throughput Screen of the NIH Compound Library

The University of Pittsburgh Molecular Library Screening Center (Pittsburgh, PA) conducted a screen with the National Institutes of Health compound library for inhibitors of in vitro cell division cycle 25 protein (Cdc25) B activity during the pilot phase of the Molecular Library Screening Center Network. Seventy-nine (0.12%) of the 65,239 compounds screened at 10 muM met the active criterion of > or =50% inhibition of Cdc25B activity, and 25 (31.6%) of these were confirmed as Cdc25B inhibitors with 50% inhibitory concentration (IC(50)) values <50 microM. Thirteen of the Cdc25B inhibitors were represented by singleton chemical structures, and 12 were divided among four clusters of related structures. Thirteen (52%) of the Cdc25B inhibitor hits were quinone-based structures. The Cdc25B inhibitors were further characterized in a series of in vitro secondary assays to confirm their activity, to determine their phosphatase selectivity against two other dual-specificity phosphatases, mitogen-activated protein kinase phosphatase (MKP)-1 and MKP-3, and to examine if the mechanism of Cdc25B inhibition involved oxidation and inactivation. Nine Cdc25B inhibitors did not appear to affect Cdc25B through a mechanism involving oxidation because they did not generate detectable amounts of H(2)O(2) in the presence of dithiothreitol, and their Cdc25B IC(50) values were not significantly affected by exchanging the dithiothreitol for beta-mercaptoethanol or reduced glutathione or by adding catalase to the assay. Six of the nonoxidative hits were selective for Cdc25B inhibition versus MKP-1 and MKP-3, but only the two bisfuran-containing hits, PubChem substance identifiers 4258795 and 4260465, significantly inhibited the growth of human MBA-MD-435 breast and PC-3 prostate cancer cell lines. To confirm the structure and biological activity of 4260465, the compound was resynthesized along with two analogs. Neither of the substitutions to the two analogs was tolerated, and only the resynthesized hit 26683752 inhibited Cdc25B activity in vitro (IC(50) = 13.83 +/- 1.0 microM) and significantly inhibited the growth of the MBA-MD-435 breast and PC-3 prostate cancer cell lines (IC(50) = 20.16 +/- 2.0 microM and 24.87 +/- 2.25 microM, respectively). The two bis-furan-containing hits identified in the screen represent novel nonoxidative Cdc25B inhibitor chemotypes that block tumor cell proliferation. The availability of non-redox active Cdc25B inhibitors should provide valuable tools to explore the inhibition of the Cdc25 phosphatases as potential mono- or combination therapies for cancer.

Parallel synthesis of a library of symmetrically- and dissymmetrically-disubstituted imidazole-4,5-dicarboxamides bearing amino acid esters.

The imidazole-4,5-dicarboxylic acid scaffold is readily derivatized with amino acid esters to afford symmetrically- and dissymmetrically-disubstituted imidazole-4,5-dicarboxamides with intramolecularly hydrogen bonded conformations that predispose the presentation of amino acid pharmacophores. In this work, a total of 45 imidazole-4,5-dicarboxamides bearing amino acid esters were prepared by parallel synthesis. The library members were purified by column chromatography on silica gel and the purified compounds characterized by LC-MS with LC detection at 214 nm. A selection of the final compounds was also analyzed by 1H-NMR spectroscopy. The analytically pure final products have been submitted to the Molecular Library Small Molecule Repository (MLSMR) for screening in the Molecular Library Screening Center Network (MLSCN) as part of the NIH Roadmap.

Parallel synthesis of an imidazole-4,5-dicarboxamide library bearing amino acid esters and alkanamines.

The imidazole-4,5-dicarboxylic acid scaffold is readily derivatized with amino acid esters and alkanamines to afford compounds with intramolecularly hydrogen bonded conformations that mimic substituted purines and therefore are hypothesized to be potential inhibitors of kinases through competitive binding to the ATP site. In this work, a total of 126 dissymmetrically disubstituted imidazole-4,5-dicarboxamides with amino acid ester and alkanamide substituents were prepared by parallel synthesis. The library members were purified by column chromatography on silica gel and the purified compounds characterized by LC-MS with LC detection at 214 nm. A selection of the final compounds was also analyzed by 1H-NMR spectroscopy. The analytically pure final products have been submitted to the Molecular Library Small Molecule Repository (MLSMR) for screening in the Molecular Library Screening Center Network (MLSCN) as part of the NIH Roadmap.

A Comparative Analysis of Standard Microtiter Plate Reading Versus Imaging in Cellular Assays

We evaluated the performance of two plate readers (the Beckman Coulter [Fullerton, CA] DTX and the PerkinElmer [Wellesley, MA] EnVision) and a plate imager (the General Electric [Fairfield, CT] IN Cell 1000 Analyzer) in a primary fluorescent cellular screen of 10,000 Molecular Libraries Screening Center Network library compounds for up- and down-regulation of vascular cell adhesion molecule (VCAM)-1, which has been shown to be up-regulated in atherothrombotic vascular disease and is a general indicator of chronic inflammatory disease. Prior to screening, imaging of a twofold, six-step titration of fluorescent cells in a 384-well test plate showed greater consistency, sensitivity, and dynamic range of signal detection curves throughout the detection range, as compared to the plate readers. With the same 384-well test plate, the detection limits for fluorescent protein-labeled cells on the DTX and EnVision instruments were 2,250 and 560 fluorescent cells per well, respectively, as compared to 280 on the IN Cell 1000. During VCAM screening, sensitivity was critical for detection of antagonists, which reduced brightness of the primary immunofluorescence readout; inhibitor controls yielded Z' values of 0.41 and 0.16 for the IN Cell 1000 and EnVision instruments, respectively. The best 1% of small molecule inhibitors from all platforms were visually confirmed using images from the IN Cell 1000. The EnVision and DTX plate readers mutually identified approximately 57% and 21%, respectively, of the VCAM-1 inhibitors visually confirmed in the IN Cell best 1% of inhibitors. Furthermore, the plate reader hits were largely exclusive, with only 6% agreement across all platforms (three hits out of 47). Taken together, the imager outperformed the plate readers at hit detection in this bimodal assay because of superior sensitivity and had the advantage of speeding hit confirmation during post-acquisition analysis.

NIH Grant Watch

BioTechniquesVol. 44, No. 4 NIH Grant WatchOpen AccessNIH Grant WatchK. Nybo† & B. Perry†K. Nybo††K. Nybo is assistant editor ofBioTechniques. B. Perry is president of NIH Sales, Rockville, MD.Search for more papers by this author & B. Perry††K. Nybo is assistant editor ofBioTechniques. B. Perry is president of NIH Sales, Rockville, MD.Search for more papers by this authorPublished Online:16 May 2018https://doi.org/10.2144/000112787AboutSectionsPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinkedInRedditEmail Cell SignalingBioTechniques and NIH Sales reviewed grants made over the past year to find those that focused on cell-signaling studies. The search returned 3575 funded grants, which together received just over $1.1 billion. The National Institute of General Medical Sciences supported 17.4% of these projects, followed closely by the National Cancer Institute (17.1%), the National Heart Lung and Blood Institute (14.8%), and the National Institute of Diabetes and Digestive and Kidney Diseases (10.4%). Featured here are some of the projects that won the highest levels of support.The Penn Center for Molecular Discovery $4,145,170(5U54HG003915-03, National Human Genome Research Institute)Scott L. Diamond (University Of Pennsylvania, Philadelphia, PA)Goal: To organize 14 faculty and 9 consultants into five core functions (assay implementation, high-throughput screening, synthesis, informatics, and administration) comprising the “Center for Molecular Discovery.” Research conducted in the center will focus on proteolytic enzymes, transcriptional activation, and protein assembly, folding, and degradation.Emory Chemistry-Biology Center in the Molecular Libraries Screening Center Network (MLSCN) $4,088,558(5U54HG003918-03, National Human Genome Research Institute)Raymond J. Dingledine (Emory University, Atlanta, GA)Goal: To develop the methods for identifying and providing 20 probes annually for novel protein interaction studies, thus facilitating the MLSCN mission to research protein-protein interactions for small molecule discovery. Results will be added to chemical libraries, annotated with their biological functions, and organized for public sharing and analysis.New Mexico Molecular Libraries Screening Center (RMI) $3,789,015(5U54MH074425-03, National Institute of Mental Health)Larry A. Sklar (University of New Mexico, Albuquerque, NM)Goal: To develop a screening center composed of three teams: assay optimization, screening and automation, and cheminformatics and chemistry. The center will use its innovative flow-cytometric tools—which enable homogeneous analysis of ligand binding and protein-protein interaction, high-throughput sample handling, high-content analysis, and real-time measurements of cell response—to further develop assays for drug discovery, proteomics, and real-time analysis of molecular interactions.Vanderbilt Screen Center: GPCRs and Ion Channels (RMI) $3,746,663(5U54MH074427-03, National Institute of Mental Health)C. David Weaver (Vanderbilt University, Nashville, TN)Goal: To generate chemical tools to study G-protein coupled receptors, ion channels, and transporters. Information from the center will be free from any commercial interests, ensuring timely publication of small molecules and their protein partners for basic and translational research.Nation Center Multi-Scale Study: Cellular Networks (RMI) $3,638,557(5U54CA121852-03, National Cancer Institute)Andrea Califano (Columbia University Health Sciences, New York, NY)Goal: To catalog molecular interactions in the cell into a map that is searchable for relevant biological processes. All tools developed will be made accessible to the biomedical research community.Systems Biology of Morphogenesis and Spatial Information Flow $3,067,892(1P50GM076516-01A1, National Institute of General Medical Sciences)Arthur D. Lander (University of California Irvine, Irvine, CA)Goal: To research how spatial information contributes to morphogenesis. Research projects will focus on developmental pattern formation, control of epithelial proliferation, and spatial aspects of intracellular signaling with concurrent development of the mathematical, computational, and optical biology tools needed to advance the studies.Center for Quantitative Biology $2,808,866(5P50GM071508-04, National Institute of General Medical Sciences)David Botstein (Princeton University, Princeton, NJ)Goal: To establish a center for collaboration between quantitative biological science researchers from different departments. Quantitative research and education at the center will focus primarily on spatial patterning during development, intracellular signaling and transcriptional networks, and virus-host interaction.FiguresReferencesRelatedDetails Vol. 44, No. 4 Follow us on social media for the latest updates Metrics Downloaded 89 times History Published online 16 May 2018 Published in print April 2008 Information© 2008 Author(s)PDF download

Under the influence: Proof‐of‐concept chemical probe discovery in academia

The Scripps Research Institute Molecular Screening Center is a Molecular Libraries Screening Center Network (MLSCN) facility that spans the Scripps campuses in La Jolla, California and Jupiter in Palm Beach County, Florida. Scripps has brought together an integrated combination of infrastructure, people and technologies that support the identification of proof‐of‐concept small molecules in the academic setting. By this we mean chemical probes of adequate potency, selectivity, physical properties and stability to show robust activities in cell‐based assays and in vivo, allowing pre‐competitive advancement to fields of breaking biology. Chemical probes developed for POC studies the sphingolipid receptors in physiology and pathology will be presented.

Data Mining a Small Molecule Drug Screening Representative Subset from NIH PubChem

PubChem is a scientific showcase of the NIH Roadmap Initiatives. It is a compound repository created to facilitate information exchange and data sharing among the NIH Roadmap-funded Molecular Library Screening Center Network (MLSCN) and the scientific community. However, PubChem has more than 10 million records of compound information. It will be challenging to conduct a drug screening of the whole database of millions of compounds. Thus, the purpose of the present study was to develop a data mining cheminformatics approach in order to construct a representative and structure-diverse sublibrary from the large PubChem database. In this study, a new chemical diverse representative subset, rePubChem, was selected by whole-molecule chemistry-space matrix calculation using the cell-based partition algorithm. The representative subset was generated and was then subjected to evaluations by compound property analyses based on 1D and 2D molecular descriptors. The new subset was also examined and assessed for self-similarity analysis based on 2D molecular fingerprints in comparing with the source compound library. The new subset has a much smaller library size (540K compounds) with minimum similarity and redundancy without loss of the structural diversity and basic molecular properties of its parent library (5.3 million compounds). The new representative subset library generated could be a valuable structure-diverse compound resource for in silico virtual screening and in vitro HTS drug screening. In addition, the established subset generation method of using the combined cell-based chemistry-space partition metrics with pairwised 2D fingerprint-based similarity search approaches will also be important to a broad scientific community interested in acquiring structurally diverse compounds for efficient drug screening, building representative virtual combinatorial chemistry libraries for syntheses, and data mining large compound databases like the PubChem library in general.

Utilizing high throughput screening data for predictive toxicology models: protocols and application to MLSCN assays

Computational toxicology is emerging as an encouraging alternative to experimental testing. The Molecular Libraries Screening Center Network (MLSCN) as part of the NIH Molecular Libraries Roadmap has recently started generating large and diverse screening datasets, which are publicly available in PubChem. In this report, we investigate various aspects of developing computational models to predict cell toxicity based on cell proliferation screening data generated in the MLSCN. By capturing feature-based information in those datasets, such predictive models would be useful in evaluating cell-based screening results in general (for example from reporter assays) and could be used as an aid to identify and eliminate potentially undesired compounds. Specifically we present the results of random forest ensemble models developed using different cell proliferation datasets and highlight protocols to take into account their extremely imbalanced nature. Depending on the nature of the datasets and the descriptors employed we were able to achieve percentage correct classification rates between 70% and 85% on the prediction set, though the accuracy rate dropped significantly when the models were applied to in vivo data. In this context we also compare the MLSCN cell proliferation results with animal acute toxicity data to investigate to what extent animal toxicity can be correlated and potentially predicted by proliferation results. Finally, we present a visualization technique that allows one to compare a new dataset to the training set of the models to decide whether the new dataset may be reliably predicted.