Discovery of Selective Inhibitors Against EBNA1 via High Throughput In Silico Virtual Screening
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{"title"=>"Discovery of selective inhibitors against ebna1 via high throughput in silico virtual screening", "type"=>"journal", "authors"=>[{"first_name"=>"Ning", "last_name"=>"Li", "scopus_author_id"=>"36014373300"}, {"first_name"=>"Scott", "last_name"=>"Thompson", "scopus_author_id"=>"57199221704"}, {"first_name"=>"David C.", "last_name"=>"Schultz", "scopus_author_id"=>"7202619896"}, {"first_name"=>"Weiliang", "last_name"=>"Zhu", "scopus_author_id"=>"7404232989"}, {"first_name"=>"Hualiang", "last_name"=>"Jiang", "scopus_author_id"=>"34868049700"}, {"first_name"=>"Cheng", "last_name"=>"Luo", "scopus_author_id"=>"26324947200"}, {"first_name"=>"Paul M.", "last_name"=>"Lieberman", "scopus_author_id"=>"7102065006"}], "year"=>2010, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-77956332699", "pui"=>"359482083", "doi"=>"10.1371/journal.pone.0010126", "isbn"=>"1932-6203 (Electronic) 1932-6203 (Linking)", "sgr"=>"77956332699", "pmid"=>"20405039"}, "id"=>"13dfc6df-2244-3853-8dc6-934b017cdd4d", "abstract"=>"BACKGROUND: Epstein-Barr Virus (EBV) latent infection is associated with several human malignancies and is a causal agent of lymphoproliferative diseases during immunosuppression. While inhibitors of herpesvirus DNA polymerases, like gancyclovir, reduce EBV lytic cycle infection, these treatments have limited efficacy for treating latent infection. EBNA1 is an EBV-encoded DNA-binding protein required for viral genome maintenance during latent infection.\\n\\nMETHODOLOGY: Here, we report the identification of a new class of small molecules that inhibit EBNA1 DNA binding activity. These compounds were identified by virtual screening of 90,000 low molecular mass compounds using computational docking programs with the solved crystal structure of EBNA1. Four structurally related compounds were found to inhibit EBNA1-DNA binding in biochemical assays with purified EBNA1 protein. Compounds had a range of 20-100 microM inhibition of EBNA1 in fluorescence polarization assays and were further validated for inhibition using electrophoresis mobility shift assays. These compounds exhibited no significant inhibition of an unrelated DNA binding protein. Three of these compounds inhibited EBNA1 transcription activation function in cell-based assays and reduced EBV genome copy number when incubated with a Burkitt lymphoma cell line.\\n\\nCONCLUSIONS: These experiments provide a proof-of-principle that virtual screening can be used to identify specific inhibitors of EBNA1 that may have potential for treatment of EBV latent infection.", "link"=>"http://www.mendeley.com/research/discovery-selective-inhibitors-against-ebna1-via-high-throughput-silico-virtual-screening", "reader_count"=>35, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>4, "Researcher"=>12, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>6, "Student > Postgraduate"=>1, "Student > Master"=>7, "Other"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>4, "Researcher"=>12, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>6, "Student > Postgraduate"=>1, "Student > Master"=>7, "Other"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Biochemistry, Genetics and Molecular Biology"=>6, "Agricultural and Biological Sciences"=>15, "Medicine and Dentistry"=>4, "Arts and Humanities"=>1, "Neuroscience"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Chemistry"=>1, "Computer Science"=>2, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>4}, "Neuroscience"=>{"Neuroscience"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>15}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Unspecified"=>{"Unspecified"=>3}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"United States"=>3, "Norway"=>1, "China"=>1, "United Kingdom"=>1, "Russia"=>1}, "group_count"=>3}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/854437"], "description"=>"<p>The EBNA1/DNA crystal structure was computationally fitted into a 6 Å grid containing every residue of the EBNA1 DNA-binding pocket was used to dock a library of compounds from the SPECS database. Compounds were preselected for solubility in an aqueous solution using a log <i>S</i> value of greater than −4. A database of ∼90,000 small-molecule compounds were then analyzed by one primary docking programs and three score functions to calculate the free energy of binding. 5000 candidates were then re-examined using Xscore, Slide, and AutoDock programs to select 30 top candidates. The top 30 compounds from 15 manually classified groups were selected for experimental DNA binding and cell-based bioassays.</p>", "links"=>[], "tags"=>["discovering", "ebna1"], "article_id"=>524894, "categories"=>["Virology", "Biochemistry"], "users"=>["Ning Li", "Scott Thompson", "David C. Schultz", "Weiliang Zhu", "Hualiang Jiang", "Cheng Luo", "Paul M. Lieberman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0010126.g001", "stats"=>{"downloads"=>3, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Flow_chart_of_virtual_and_experimental_screening_strategy_for_discovering_EBNA1_inhibitors_/524894", "title"=>"Flow chart of virtual and experimental screening strategy for discovering EBNA1 inhibitors.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 01:51:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/854594"], "description"=>"<p>Candidate inhibitors SC7, SC11, SC19, and SC27 were assayed by fluorescence polarization (FP) for inhibition of EBNA1-DNA binding (panel A) and for inhibition of Zta-DNA binding (panel B). IC50 values were calculated for each isotherm. Inhibitor concentrations were diluted 2-fold from 833 to 7 µM for each compound. Inhibitors were also assayed using a secondary EMSA assay to monitor EBNA1-DNA binding (panel C) or Zta-DNA binding (panel D) using the same concentrations of inhibitor compounds (two fold dilutions from 833 to 7 µM) as that shown for FP assays in panels A and B, above.</p>", "links"=>[], "tags"=>["inhibition", "ebna1-dna", "binding"], "article_id"=>525051, "categories"=>["Virology", "Biochemistry"], "users"=>["Ning Li", "Scott Thompson", "David C. Schultz", "Weiliang Zhu", "Hualiang Jiang", "Cheng Luo", "Paul M. Lieberman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0010126.g003", "stats"=>{"downloads"=>1, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Physical_inhibition_of_EBNA1_DNA_binding_assays_/525051", "title"=>"Physical inhibition of EBNA1-DNA binding assays.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 01:52:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/854726"], "description"=>"<p>Soluble compounds SC7, SC11, and SC19 were assayed for their ability to inhibit either EBNA1 or Zta-dependent transcription activation in transfected 293T cells. Cells were transfected with vector or EBNA1 expression plasmid and the OriP-Cp-Luciferase reporter plasmid in the presence of 5 µM SC7, SC11, SC19 or DMSO control. 100% inhibition was equivalent to basal expression levels of OriP-Cp-Luc in the absence of ectopic EBNA1 expression. In parallel experiments, the same compounds were also assayed for inhibition of Zta transcription activation of the BHLF1-Luciferase reporter plasmid. Percent inhibition of Zta is shown in grey. Percent inhibition of EBNA1 is shown in black. Error bars represent standard deviation from the mean for at least three experimental replicates.</p>", "links"=>[], "tags"=>["ebna1", "transcription", "activation", "cell-based"], "article_id"=>525178, "categories"=>["Virology", "Biochemistry"], "users"=>["Ning Li", "Scott Thompson", "David C. Schultz", "Weiliang Zhu", "Hualiang Jiang", "Cheng Luo", "Paul M. Lieberman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0010126.g004", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Inhibition_of_EBNA1_transcription_activation_function_in_cell_based_assays_/525178", "title"=>"Inhibition of EBNA1 transcription activation function in cell-based assays.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 01:52:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/854908"], "description"=>"<p>(A) Interactions of SC7 with the EBNA1 binding Pocket; (B) Interaction analysis between SC7 and EBNA1 calculated by LIGPLOT program; (C) Interactions of SC19 with the EBNA1 binding Pocket; (D) Interaction analysis between SC19 and EBNA1 calculated by LIGPLOT program; (E) The comparison between the binding mode of SC7/EBNA1 and DNA/EBNA1 crystal complex structure, SC7 is shown in yellow stick and DNA is shown in magenta stick.</p>", "links"=>[], "tags"=>["simulation", "hits", "ebna1"], "article_id"=>525364, "categories"=>["Virology", "Biochemistry"], "users"=>["Ning Li", "Scott Thompson", "David C. Schultz", "Weiliang Zhu", "Hualiang Jiang", "Cheng Luo", "Paul M. Lieberman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0010126.g006", "stats"=>{"downloads"=>2, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Docking_simulation_of_two_best_hits_SC7_and_SC19_in_the_EBNA1_site_/525364", "title"=>"Docking simulation of two best hits (SC7 and SC19) in the EBNA1 site.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 01:53:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/854517"], "description"=>"<p>The chemical structure of four related compounds identified by virtual screening that were validated for physical inhibition of EBNA1-DNA binding.</p>", "links"=>[], "tags"=>["compounds", "validated", "inhibition", "ebna1-dna"], "article_id"=>524975, "categories"=>["Virology", "Biochemistry"], "users"=>["Ning Li", "Scott Thompson", "David C. Schultz", "Weiliang Zhu", "Hualiang Jiang", "Cheng Luo", "Paul M. Lieberman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0010126.g002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_chemical_structure_of_four_related_compounds_identified_by_virtual_screening_that_were_validated_for_physical_inhibition_of_EBNA1_DNA_binding_/524975", "title"=>"The chemical structure of four related compounds identified by virtual screening that were validated for physical inhibition of EBNA1-DNA binding.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 01:51:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/854807"], "description"=>"<p>EBV-positive Raji Burkitt lymphoma cell lines were treated with 10 µM SC7, SC11, or SC19 or DMSO control for six days. EBV genome copy number was determined by quantitative real-time PCR analysis of EBV DNA (DS) relative to cellular DNA (actin). Error bars represent standard deviation from the mean for at least three experimental replicates.</p>", "links"=>[], "tags"=>["ebv", "genomes", "burkitt", "lymphoma"], "article_id"=>525259, "categories"=>["Virology", "Biochemistry"], "users"=>["Ning Li", "Scott Thompson", "David C. Schultz", "Weiliang Zhu", "Hualiang Jiang", "Cheng Luo", "Paul M. Lieberman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0010126.g005", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Elimination_of_EBV_genomes_from_Burkitt_lymphoma_cell_lines_/525259", "title"=>"Elimination of EBV genomes from Burkitt lymphoma cell lines.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 01:53:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/855045"], "description"=>"<p>(A) Corresponding position of three modification sites within the DNA binding pocket of EBNA1; (B) Base scaffold with three possible positions for modification.</p>", "links"=>[], "tags"=>["ebna1", "inhibitors", "greater", "potency"], "article_id"=>525500, "categories"=>["Virology", "Biochemistry"], "users"=>["Ning Li", "Scott Thompson", "David C. Schultz", "Weiliang Zhu", "Hualiang Jiang", "Cheng Luo", "Paul M. Lieberman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0010126.g007", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Design_strategy_for_EBNA1_inhibitors_with_greater_potency_and_specificity_/525500", "title"=>"Design strategy for EBNA1 inhibitors with greater potency and specificity.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 01:54:41"}

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