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Publisher Correction: A mass spectrometry-based proteome map of drug action in lung cancer cell lines.

Benjamin Ruprecht, Julie Di Bernardo, Zhao Wang, Xuan Mo, Oleg Ursu, Matthew Christopher, Rafael B Fernandez, Li Zheng, Brian D Dill, Huijun Wang, Yuting Xu, Andy Liaw, Jonathan D Mortison, Nirodhini Siriwardana, Brian Andresen, Meir Glick, James R Tata, Victoria Kutilek, Ivan Cornella-Taracido, An Chi,

An amendment to this paper has been published and can be accessed via a link at the top of the paper. ... Read more >>

Nat Chem Biol (Nature chemical biology)
[2020, 16(10):1149]

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A mass spectrometry-based proteome map of drug action in lung cancer cell lines.

Benjamin Ruprecht, Julie Di Bernardo, Zhao Wang, Xuan Mo, Oleg Ursu, Matthew Christopher, Rafael B Fernandez, Li Zheng, Brian D Dill, Huijun Wang, Yuting Xu, Andy Liaw, Jonathan D Mortison, Nirodhini Siriwardana, Brian Andresen, Meir Glick, James R Tata, Victoria Kutilek, Ivan Cornella-Taracido, An Chi,

Mass spectrometry-based discovery proteomics is an essential tool for the proximal readout of cellular drug action. Here, we apply a robust proteomic workflow to rapidly profile the proteomes of five lung cancer cell lines in response to more than 50 drugs. Integration of millions of quantitative protein-drug associations substantially improved ... Read more >>

Nat. Chem. Biol. (Nature chemical biology)
[2020, 16(10):1111-1119]

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Novel drug targets in 2018.

Oleg Ursu, Meir Glick, Tudor Oprea,

Nat Rev Drug Discov (Nature reviews. Drug discovery)
[2019, :]

Cited: 1 time

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How to Prepare a Compound Collection Prior to Virtual Screening.

Cristian G Bologa, Oleg Ursu, Tudor I Oprea,

Virtual screening is a well-established technique that has proven to be successful in the identification of novel biologically active molecules, including drug repurposing. Whether for ligand-based or for structure-based virtual screening, a chemical collection needs to be properly processed prior to in silico evaluation. Here we describe our step-by-step procedure ... Read more >>

Methods Mol. Biol. (Methods in molecular biology (Clifton, N.J.))
[2019, 1939:119-138]

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DrugCentral 2018: an update.

Oleg Ursu, Jayme Holmes, Cristian G Bologa, Jeremy J Yang, Stephen L Mathias, Vasileios Stathias, Dac-Trung Nguyen, Stephan Schürer, Tudor Oprea,

DrugCentral is a drug information resource (http://drugcentral.org) open to the public since 2016 and previously described in the 2017 Nucleic Acids Research Database issue. Since the 2016 release, 103 new approved drugs were updated. The following new data sources have been included: Food and Drug Administration (FDA) Adverse Event Reporting ... Read more >>

Nucleic Acids Res. (Nucleic acids research)
[2019, 47(D1):D963-D970]

Cited: 11 times

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Activation of Rho Family GTPases by Small Molecules.

Charuta C Palsuledesai, Zurab Surviladze, Anna Waller, T Fabiola Miscioscia, Yuna Guo, Yang Wu, Jake Strouse, Elsa Romero, Virginia M Salas, Ramona Curpan, Susan Young, Mark Carter, Terry Foutz, Zhanna Galochkina, Harold Ames, Mark K Haynes, Bruce S Edwards, Orazio Nicolotti, Li Luo, Oleg Ursu, Cristian G Bologa, Tudor I Oprea, Angela Wandinger-Ness, Larry A Sklar,

Ras and Ras-related small GTPases are key regulators of diverse cellular functions that impact cell growth, survival, motility, morphogenesis, and differentiation. They are important targets for studies of disease mechanisms as well as drug discovery. Here, we report the characterization of small molecule agonists of one or more of six ... Read more >>

ACS Chem. Biol. (ACS chemical biology)
[2018, 13(6):1514-1524]

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Unexplored therapeutic opportunities in the human genome.

Tudor I Oprea, Cristian G Bologa, Søren Brunak, Allen Campbell, Gregory N Gan, Anna Gaulton, Shawn M Gomez, Rajarshi Guha, Anne Hersey, Jayme Holmes, Ajit Jadhav, Lars Juhl Jensen, Gary L Johnson, Anneli Karlson, Andrew R Leach, Avi Ma'ayan, Anna Malovannaya, Subramani Mani, Stephen L Mathias, Michael T McManus, Terrence F Meehan, Christian von Mering, Daniel Muthas, Dac-Trung Nguyen, John P Overington, George Papadatos, Jun Qin, Christian Reich, Bryan L Roth, Stephan C Schürer, Anton Simeonov, Larry A Sklar, Noel Southall, Susumu Tomita, Ilinca Tudose, Oleg Ursu, Dušica Vidovic, Anna Waller, David Westergaard, Jeremy J Yang, Gergely Zahoránszky-Köhalmi,

A large proportion of biomedical research and the development of therapeutics is focused on a small fraction of the human genome. In a strategic effort to map the knowledge gaps around proteins encoded by the human genome and to promote the exploration of currently understudied, but potentially druggable, proteins, the ... Read more >>

Nat Rev Drug Discov (Nature reviews. Drug discovery)
[2018, 17(5):317-332]

Cited: 26 times

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Unexplored therapeutic opportunities in the human genome.

Tudor I Oprea, Cristian G Bologa, Søren Brunak, Allen Campbell, Gregory N Gan, Anna Gaulton, Shawn M Gomez, Rajarshi Guha, Anne Hersey, Jayme Holmes, Ajit Jadhav, Lars Juhl Jensen, Gary L Johnson, Anneli Karlson, Andrew R Leach, Avi Ma'ayan, Anna Malovannaya, Subramani Mani, Steven L Mathias, Michael T McManus, Terrence F Meehan, Christian von Mering, Daniel Muthas, Dac-Trung Nguyen, John P Overington, George Papadatos, Jun Qin, Christian Reich, Bryan L Roth, Stephan C Schürer, Anton Simeonov, Larry A Sklar, Noel Southall, Susumu Tomita, Ilinca Tudose, Oleg Ursu, Dušica Vidovic, Anna Waller, David Westergaard, Jeremy J Yang, Gergely Zahoránszky-Köhalmi,

This corrects the article DOI: 10.1038/nrd.2018.14. ... Read more >>

Nat Rev Drug Discov (Nature reviews. Drug discovery)
[2018, 17(5):377]

Cited: 5 times

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High-Throughput Flow Cytometry Screening of Multidrug Efflux Systems.

Mark K Haynes, Matthew Garcia, Ryan Peters, Anna Waller, Pietro Tedesco, Oleg Ursu, Cristian G Bologa, Radleigh G Santos, Clemencia Pinilla, Terry H Wu, Julie A Lovchik, Tudor I Oprea, Larry A Sklar, George P Tegos,

The resistance nodulation cell division (RND) family of proteins are inner membrane transporters that associate with periplasmic adaptor proteins and outer membrane porins to affect substrate transport from the cytosol and periplasm in Gram-negative bacteria. Various structurally diverse compounds are substrates of RND transporters. Along with their notable role in ... Read more >>

Methods Mol. Biol. (Methods in molecular biology (Clifton, N.J.))
[2018, 1700:293-318]

Cited: 3 times

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TIN-X: target importance and novelty explorer.

Daniel C Cannon, Jeremy J Yang, Stephen L Mathias, Oleg Ursu, Subramani Mani, Anna Waller, Stephan C Schürer, Lars Juhl Jensen, Larry A Sklar, Cristian G Bologa, Tudor I Oprea,

The increasing amount of peer-reviewed manuscripts requires the development of specific mining tools to facilitate the visual exploration of evidence linking diseases and proteins.We developed TIN-X, the Target Importance and Novelty eXplorer, to visualize the association between proteins and diseases, based on text mining data processed from scientific literature. In ... Read more >>

Bioinformatics (Bioinformatics (Oxford, England))
[2017, 33(16):2601-2603]

Cited: 1 time

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Drug target ontology to classify and integrate drug discovery data.

Yu Lin, Saurabh Mehta, Hande Küçük-McGinty, John Paul Turner, Dusica Vidovic, Michele Forlin, Amar Koleti, Dac-Trung Nguyen, Lars Juhl Jensen, Rajarshi Guha, Stephen L Mathias, Oleg Ursu, Vasileios Stathias, Jianbin Duan, Nooshin Nabizadeh, Caty Chung, Christopher Mader, Ubbo Visser, Jeremy J Yang, Cristian G Bologa, Tudor I Oprea, Stephan C Schürer,

BACKGROUND:One of the most successful approaches to develop new small molecule therapeutics has been to start from a validated druggable protein target. However, only a small subset of potentially druggable targets has attracted significant research and development resources. The Illuminating the Druggable Genome (IDG) project develops resources to catalyze the ... Read more >>

J Biomed Semantics (Journal of biomedical semantics)
[2017, 8(1):50]

Cited: 5 times

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Formalizing drug indications on the road to therapeutic intent.

Stuart J Nelson, Tudor I Oprea, Oleg Ursu, Cristian G Bologa, Amrapali Zaveri, Jayme Holmes, Jeremy J Yang, Stephen L Mathias, Subramani Mani, Mark S Tuttle, Michel Dumontier,

Therapeutic intent, the reason behind the choice of a therapy and the context in which a given approach should be used, is an important aspect of medical practice. There are unmet needs with respect to current electronic mapping of drug indications. For example, the active ingredient sildenafil has 2 distinct ... Read more >>

J Am Med Inform Assoc (Journal of the American Medical Informatics Association : JAMIA)
[2017, 24(6):1169-1172]

Cited: 2 times

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High-Throughput Screening Approach for Identifying Compounds That Inhibit Nonhomologous End Joining.

Andrea L Bredemeyer, Bruce S Edwards, Mark K Haynes, Abigail J Morales, Yinan Wang, Oleg Ursu, Anna Waller, Larry A Sklar, Barry P Sleckman,

DNA double-strand breaks (DSBs) are repaired primarily by homologous recombination (HR) or nonhomologous end joining (NHEJ). Compounds that modulate HR have shown promise as cancer therapeutics. The V(D)J recombination reaction, which assembles antigen receptor genes in lymphocytes, is initiated by the introduction of DNA DSBs at two recombining gene segments ... Read more >>

SLAS Discov (SLAS discovery : advancing life sciences R & D)
[2018, 23(7):624-633]

Cited: 3 times

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Drug Target Ontology to Classify and Integrate Drug Discovery Data

Yu Lin, Saurabh Mehta, Hande Küçük-McGinty, John Paul Turner, Dusica Vidovic, Michele Forlin, Amar Koleti, Dac-Trung Nguyen, Lars Juhl Jensen, Rajarshi Guha, Stephen Mathias, Oleg Ursu, Vasileios Stathias, Jianbin Duan, Nooshin Nabizadeh, Caty Chung, Christopher Mader, Ubbo Visser, Jeremy Yang, Cristian Bologa, Tudor Oprea, Stephan Schürer,

Abstract Background One of the most successful approaches to develop new small molecule therapeutics has been to start from a validated druggable protein target. However, only a small subset of potentially druggable targets has attracted significant research and development resources. The Illuminating the Druggable Genome (IDG) project develops resources to ... Read more >>

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Chronic obstructive pulmonary disease phenotypes using cluster analysis of electronic medical records.

Rodrigo Vazquez Guillamet, Oleg Ursu, Gary Iwamoto, Pope L Moseley, Tudor Oprea,

Chronic obstructive pulmonary disease is a heterogeneous disease. In this retrospective study, we hypothesize that it is possible to identify clinically relevant phenotypes by applying clustering methods to electronic medical records. We included all the patients >40 years with a diagnosis of chronic obstructive pulmonary disease admitted to the University of ... Read more >>

Health Informatics J (Health informatics journal)
[2018, 24(4):394-409]

Cited: 1 time

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A comprehensive map of molecular drug targets.

Rita Santos, Oleg Ursu, Anna Gaulton, A Patrícia Bento, Ramesh S Donadi, Cristian G Bologa, Anneli Karlsson, Bissan Al-Lazikani, Anne Hersey, Tudor I Oprea, John P Overington,

The success of mechanism-based drug discovery depends on the definition of the drug target. This definition becomes even more important as we try to link drug response to genetic variation, understand stratified clinical efficacy and safety, rationalize the differences between drugs in the same therapeutic class and predict drug utility ... Read more >>

Nat Rev Drug Discov (Nature reviews. Drug discovery)
[2017, 16(1):19-34]

Cited: 287 times

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CHEMICAL AND BIOLOGICAL DESCRIPTOR INTEGRATION IMPROVES COMPUTATIONAL MODELING OF IN VIVO RAT TOXICITY.

Cristian G Bologa, Oleg Ursu, Liliana Halip, Ramona Curpăn, Tudor I Oprea,

Computational toxicology is a new discipline in the area of computational molecular sciences, which is rapidly developing as a result of the public interest stirred by several European and US initiatives. Here, we report the use of primary high throughput screening (HTS) data as biological descriptors to complement the chemical ... Read more >>

(Revue roumaine du chimie)
[2015, 60(2-3):219-226]

Cited: 0 times

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DrugCentral: online drug compendium.

Oleg Ursu, Jayme Holmes, Jeffrey Knockel, Cristian G Bologa, Jeremy J Yang, Stephen L Mathias, Stuart J Nelson, Tudor I Oprea,

DrugCentral (http://drugcentral.org) is an open-access online drug compendium. DrugCentral integrates structure, bioactivity, regulatory, pharmacologic actions and indications for active pharmaceutical ingredients approved by FDA and other regulatory agencies. Monitoring of regulatory agencies for new drugs approvals ensures the resource is up-to-date. DrugCentral integrates content for active ingredients with pharmaceutical formulations, ... Read more >>

Nucleic Acids Res. (Nucleic acids research)
[2017, 45(D1):D932-D939]

Cited: 46 times

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Pharos: Collating protein information to shed light on the druggable genome.

Dac-Trung Nguyen, Stephen Mathias, Cristian Bologa, Soren Brunak, Nicolas Fernandez, Anna Gaulton, Anne Hersey, Jayme Holmes, Lars Juhl Jensen, Anneli Karlsson, Guixia Liu, Avi Ma'ayan, Geetha Mandava, Subramani Mani, Saurabh Mehta, John Overington, Juhee Patel, Andrew D Rouillard, Stephan Schürer, Timothy Sheils, Anton Simeonov, Larry A Sklar, Noel Southall, Oleg Ursu, Dusica Vidovic, Anna Waller, Jeremy Yang, Ajit Jadhav, Tudor I Oprea, Rajarshi Guha,

The 'druggable genome' encompasses several protein families, but only a subset of targets within them have attracted significant research attention and thus have information about them publicly available. The Illuminating the Druggable Genome (IDG) program was initiated in 2014, has the goal of developing experimental techniques and a Knowledge Management ... Read more >>

Nucleic Acids Res. (Nucleic acids research)
[2017, 45(D1):D995-D1002]

Cited: 43 times

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Erratum to: Impact of similarity threshold on the topology of molecular similarity networks and clustering outcomes.

Gergely Zahoránszky-Kőhalmi, Cristian G Bologa, Oleg Ursu, Tudor I Oprea,

[This corrects the article DOI: 10.1186/s13321-016-0127-5.]. ... Read more >>

(Journal of cheminformatics)
[2016, 8:28]

Cited: 0 times

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Discovery of a specific inhibitor of human GLUT5 by virtual screening and in vitro transport evaluation.

Alayna M George Thompson, Oleg Ursu, Petr Babkin, Cristina V Iancu, Alex Whang, Tudor I Oprea, Jun-yong Choe,

GLUT5, a fructose-transporting member of the facilitative glucose transporter (GLUT, SLC2) family, is a therapeutic target for diabetes and cancer but has no potent inhibitors. We virtually screened a library of 6 million chemicals onto a GLUT5 model and identified N-[4-(methylsulfonyl)-2-nitrophenyl]-1,3-benzodioxol-5-amine (MSNBA) as an inhibitor of GLUT5 fructose transport in ... Read more >>

Sci Rep (Scientific reports)
[2016, 6:24240]

Cited: 12 times

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Badapple: promiscuity patterns from noisy evidence.

Jeremy J Yang, Oleg Ursu, Christopher A Lipinski, Larry A Sklar, Tudor I Oprea, Cristian G Bologa,

BACKGROUND:Bioassay data analysis continues to be an essential, routine, yet challenging task in modern drug discovery and chemical biology research. The challenge is to infer reliable knowledge from big and noisy data. Some aspects of this problem are general with solutions informed by existing and emerging data science best practices. ... Read more >>

(Journal of cheminformatics)
[2016, 8:29]

Cited: 21 times

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BDDCS, the Rule of 5 and drugability.

Leslie Z Benet, Chelsea M Hosey, Oleg Ursu, Tudor I Oprea,

The Rule of 5 methodology appears to be as useful today in defining drugability as when it was proposed, but recognizing that the database that we used includes only drugs that successfully reached the market. We do not view additional criteria necessary nor did we find significant deficiencies in the ... Read more >>

Adv Drug Deliv Rev (Advanced drug delivery reviews)
[2016, 101:89-98]

Cited: 14 times

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Discovery of Small-Molecule Nonfluorescent Inhibitors of Fluorogen-Fluorogen Activating Protein Binding Pair.

Yang Wu, Shaun R Stauffer, Robyn L Stanfield, Phillip H Tapia, Oleg Ursu, Gregory W Fisher, Christopher Szent-Gyorgyi, Annette Evangelisti, Anna Waller, J Jacob Strouse, Mark B Carter, Cristian Bologa, Kristine Gouveia, Mike Poslusney, Alan S Waggoner, Craig W Lindsley, Jonathan W Jarvik, Larry A Sklar,

A new class of biosensors, fluorogen activating proteins (FAPs), has been successfully used to track receptor trafficking in live cells. Unlike the traditional fluorescent proteins (FPs), FAPs do not fluoresce unless bound to their specific small-molecule fluorogens, and thus FAP-based assays are highly sensitive. Application of the FAP-based assay for ... Read more >>

J Biomol Screen (Journal of biomolecular screening)
[2016, 21(1):74-87]

Cited: 1 time

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Discovering Small Molecules that Overcome Differentiation Arrest in Acute Myeloid Leukemia

David B. Sykes, Mark K. Haynes, Anna Waller, Matthew Garcia, Oleg Ursu, Kristine E. Gouveia, Larry Sklar, Timothy A. Lewis, Sivaraman Dandapani, Benito Munoz, David T. Scadden, Michelle Palmer, Stuart L. Schreiber,

Acute Myeloid Leukemia (AML) in adults is a clinically devastating disease with a 5-year survival rate of only 25%. We lack new and effective therapies for AML, and the chemotherapy standard of care remains unchanged in thirty years. One success story has been the discovery of drugs that trigger the ... Read more >>

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