Novel Naphthalene-Based Inhibitors of Trypanosoma brucei RNA Editing Ligase 1
Publication Date
August 24, 2010
Journal
PLOS Neglected Tropical Diseases
Authors
Jacob D. Durrant, Laurence Hall, Robert V. Swift, Melissa Landon, et al
Volume
4
Issue
8
Pages
e803
DOI
https://dx.plos.org/10.1371/journal.pntd.0000803
Publisher URL
http://journals.plos.org/plosntds/article?id=10.1371%2Fjournal.pntd.0000803
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/20808768
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2927429
Europe PMC
http://europepmc.org/abstract/MED/20808768
Web of Science
000281443200031
Scopus
78149265785
Mendeley
http://www.mendeley.com/research/novel-naphthalenebased-inhibitors-trypanosoma-brucei-rna-editing-ligase-1
Events
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Mendeley | Further Information

{"title"=>"Novel naphthalene-based inhibitors of Trypanosoma brucei RNA editing ligase 1", "type"=>"journal", "authors"=>[{"first_name"=>"Jacob D.", "last_name"=>"Durrant", "scopus_author_id"=>"12239804300"}, {"first_name"=>"Laurence", "last_name"=>"Hall", "scopus_author_id"=>"36159556200"}, {"first_name"=>"Robert V.", "last_name"=>"Swift", "scopus_author_id"=>"23989825500"}, {"first_name"=>"Melissa", "last_name"=>"Landon", "scopus_author_id"=>"7103383479"}, {"first_name"=>"Achim", "last_name"=>"Schnaufer", "scopus_author_id"=>"6603584837"}, {"first_name"=>"Rommie E.", "last_name"=>"Amaro", "scopus_author_id"=>"8730822500"}], "year"=>2010, "source"=>"PLoS Neglected Tropical Diseases", "identifiers"=>{"isbn"=>"1935-2735 (Electronic)\\r1935-2727 (Linking)", "pmid"=>"20808768", "doi"=>"10.1371/journal.pntd.0000803", "pui"=>"359899861", "issn"=>"1935-2735", "sgr"=>"78149265785", "scopus"=>"2-s2.0-78149265785"}, "id"=>"2431ca3d-ce39-3b1b-a080-683e5c82ed4d", "abstract"=>"BACKGROUND: Neglected tropical diseases, including diseases caused by trypanosomatid parasites such as Trypanosoma brucei, cost tens of millions of disability-adjusted life-years annually. As the current treatments for African trypanosomiasis and other similar infections are limited, new therapeutics are urgently needed. RNA Editing Ligase 1 (REL1), a protein unique to trypanosomes and other kinetoplastids, was identified recently as a potential drug target.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: Motivated by the urgent need for novel trypanocidal therapeutics, we use an ensemble-based virtual-screening approach to discover new naphthalene-based TbREL1 inhibitors. The predicted binding modes of the active compounds are evaluated within the context of the flexible receptor model and combined with computational fragment mapping to determine the most likely binding mechanisms. Ultimately, four new low-micromolar inhibitors are presented. Three of the four compounds may bind to a newly revealed cleft that represents a putative druggable site not evident in any crystal structure.\\n\\nCONCLUSIONS/SIGNIFICANCE: Pending additional optimization, the compounds presented here may serve as precursors for future novel therapies useful in the fight against several trypanosomatid pathogens, including human African trypanosomiasis, a devastating disease that afflicts the vulnerable patient populations of sub-Saharan Africa.", "link"=>"http://www.mendeley.com/research/novel-naphthalenebased-inhibitors-trypanosoma-brucei-rna-editing-ligase-1", "reader_count"=>61, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>5, "Researcher"=>19, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>16, "Student > Postgraduate"=>1, "Other"=>3, "Student > Master"=>5, "Student > Bachelor"=>5, "Professor"=>5}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>5, "Researcher"=>19, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>16, "Student > Postgraduate"=>1, "Other"=>3, "Student > Master"=>5, "Student > Bachelor"=>5, "Professor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Biochemistry, Genetics and Molecular Biology"=>7, "Agricultural and Biological Sciences"=>31, "Medicine and Dentistry"=>2, "Pharmacology, Toxicology and Pharmaceutical Science"=>2, "Chemistry"=>10, "Social Sciences"=>1, "Computer Science"=>4, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Chemistry"=>{"Chemistry"=>10}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>31}, "Computer Science"=>{"Computer Science"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}, "Unspecified"=>{"Unspecified"=>3}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>2}}, "reader_count_by_country"=>{"United States"=>2, "Japan"=>1, "United Kingdom"=>2, "India"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/834288"], "description"=>"<p>Coils are colored gray, sheets are colored cyan, and helices are colored ice blue. A) Residues lining the deep end of the binding pocket used for RMSD clustering are shown in a licorice graphical representation. Residues from the centroid of the first, second, and third most populated clusters are shown in red, blue, and green, respectively. Residues from the crystal structure are shown in purple. B) E60 and R111 conformational variability. Coloring is as in A). The orientation of E60 in the centroids of the top two most populated clusters differs from that of the third cluster, as well as from that of the crystal structure. C) Consensus binding sites of the organic solvent probes used in the computational fragment mapping analysis. Solvent probe clusters are colored to match the coloring in A) and B).</p>", "links"=>[], "tags"=>["centroids", "populated", "rmsd", "clusters", "aligned"], "article_id"=>504648, "categories"=>["Physics", "Medicine", "Pharmacology", "Computational Biology", "Biophysics"], "users"=>["Jacob D. Durrant", "Laurence Hall", "Robert V. Swift", "Melissa Landon", "Achim Schnaufer", "Rommie E. Amaro"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0000803.g004", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_centroids_of_the_three_most_populated_RMSD_clusters_aligned_to_the_Tb_REL1_crystal_structure_/504648", "title"=>"The centroids of the three most populated RMSD clusters aligned to the <i>Tb</i>REL1 crystal structure.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-08-24 01:17:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/833822"], "description"=>"<p>A) The core 4,5-dihydroxynaphthalene-2,7-disulfonate scaffold of three previously identified <i>Tb</i>REL1 inhibitors. B) Naphthalene-2-sulfonic acid. C) 2-naphthoic acid. D) 2-nitronaphthalene. V1-V4) The four low-micromolar inhibitors identified in the current work.</p>", "links"=>[], "tags"=>["biophysics/theory and simulation", "computational biology/molecular dynamics", "infectious diseases/neglected tropical diseases", "infectious diseases/protozoal infections", "pharmacology/drug development"], "article_id"=>504188, "categories"=>["Physics", "Medicine", "Pharmacology", "Computational Biology", "Biophysics"], "users"=>["Jacob D. Durrant", "Laurence Hall", "Robert V. Swift", "Melissa Landon", "Achim Schnaufer", "Rommie E. Amaro"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0000803.g001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Substructures_and_novel_inhibitors_/504188", "title"=>"Substructures and novel inhibitors.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-08-24 01:09:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/833966"], "description"=>"<p>Solid black lines represent hydrogen bonds. Positively charged residues and ions (Mg<sup>2+</sup>) at the active-site periphery are highlighted in yellow. The carbons of the F209 phenyl ring are shown in licorice. Portions of the protein are not visualized to improve clarity. A) ATP binding. B) The predicted binding pose of naphthalene-2,7-disulfonate.</p>", "links"=>[], "tags"=>["biophysics/theory and simulation", "computational biology/molecular dynamics", "infectious diseases/neglected tropical diseases", "infectious diseases/protozoal infections", "pharmacology/drug development"], "article_id"=>504330, "categories"=>["Physics", "Medicine", "Pharmacology", "Computational Biology", "Biophysics"], "users"=>["Jacob D. Durrant", "Laurence Hall", "Robert V. Swift", "Melissa Landon", "Achim Schnaufer", "Rommie E. Amaro"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0000803.g002", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Tb_REL1_binding_/504330", "title"=>"<i>Tb</i>REL1 binding.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-08-24 01:12:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/834391"], "description"=>"<p>IC<sub>50</sub> and EC<sub>50</sub> are measures (in µM) of the inhibition of REL1 activity and parasite growth, respectively; AutoDock<sub>Crystal</sub> is the predicted binding energy, in kcal/mol, to the crystal structure; Rank<sub>Crystal</sub> is the rank of the ligand when all 588 compounds are ordered by their respective AutoDock<sub>Crystal</sub> values; AutoDock<sub>Ensemble</sub> is the average predicted binding energy to the 33 representative protein-receptor conformations obtained <i>via</i> QR factorization, plus or minus the standard deviation; Rank<sub>Ensemble</sub> is the rank of the ligand when the top 45 compounds are ordered by their respective AutoDock<sub>Ensemble</sub> values; % Expected Pose is the percentage of the 33 representative protein structures amenable to deep-pocket binding, in which the naphthalene core is docked deep into the binding pocket; AutoDock<sub>Ensemble/Expected</sub> is the average predicted binding energy when only those members of the ensemble amenable to deep-pocket binding are considered; AutoDock<sub>Ensemble/Unexpected</sub> is the average predicted binding energy when only the remaining members of the ensemble are considered; and AutoDock<sub>Ensemble/Best</sub> is the predicted binding energy of the ligand to the “optimal protein conformation” from the ensemble. All predicted energies are in kcal/mol.</p>", "links"=>[], "tags"=>["computational"], "article_id"=>504758, "categories"=>["Physics", "Medicine", "Pharmacology", "Computational Biology", "Biophysics"], "users"=>["Jacob D. Durrant", "Laurence Hall", "Robert V. Swift", "Melissa Landon", "Achim Schnaufer", "Rommie E. Amaro"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0000803.t001", "stats"=>{"downloads"=>2, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_summary_of_the_computational_and_experimental_results_/504758", "title"=>"A summary of the computational and experimental results.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-08-24 01:19:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/415419", "https://ndownloader.figshare.com/files/415435", "https://ndownloader.figshare.com/files/415458", "https://ndownloader.figshare.com/files/415479"], "description"=>"<div><h3>Background</h3><p>Neglected tropical diseases, including diseases caused by trypanosomatid parasites such as <em>Trypanosoma brucei</em>, cost tens of millions of disability-adjusted life-years annually. As the current treatments for African trypanosomiasis and other similar infections are limited, new therapeutics are urgently needed. RNA Editing Ligase 1 (REL1), a protein unique to trypanosomes and other kinetoplastids, was identified recently as a potential drug target.</p><h3>Methodology/Principal Findings</h3><p>Motivated by the urgent need for novel trypanocidal therapeutics, we use an ensemble-based virtual-screening approach to discover new naphthalene-based <em>Tb</em>REL1 inhibitors. The predicted binding modes of the active compounds are evaluated within the context of the flexible receptor model and combined with computational fragment mapping to determine the most likely binding mechanisms. Ultimately, four new low-micromolar inhibitors are presented. Three of the four compounds may bind to a newly revealed cleft that represents a putative druggable site not evident in any crystal structure.</p><h3>Conclusions/Significance</h3><p>Pending additional optimization, the compounds presented here may serve as precursors for future novel therapies useful in the fight against several trypanosomatid pathogens, including human African trypanosomiasis, a devastating disease that afflicts the vulnerable patient populations of sub-Saharan Africa.</p></div>", "links"=>[], "tags"=>["naphthalene-based", "inhibitors", "rna", "editing", "ligase"], "article_id"=>142017, "categories"=>["Physics", "Medicine", "Pharmacology", "Biological Sciences", "Biophysics"], "users"=>["Jacob D. Durrant", "Laurence Hall", "Robert V. Swift", "Melissa Landon", "Achim Schnaufer", "Rommie E. Amaro"], "doi"=>["https://dx.doi.org/10.1371/journal.pntd.0000803.s001", "https://dx.doi.org/10.1371/journal.pntd.0000803.s002", "https://dx.doi.org/10.1371/journal.pntd.0000803.s003", "https://dx.doi.org/10.1371/journal.pntd.0000803.s004"], "stats"=>{"downloads"=>11, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Novel_Naphthalene_Based_Inhibitors_of_Trypanosoma_brucei_RNA_Editing_Ligase_1/142017", "title"=>"Novel Naphthalene-Based Inhibitors of <em>Trypanosoma brucei</em> RNA Editing Ligase 1", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2010-08-24 00:33:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/834138"], "description"=>"<p>The <i>Tb</i>REL1 crystal structure is shown in mesh. The E60 and R111 residues of the optimal conformations are labeled directly, and the E60 residue of the crystal structure is labeled with an arrow. In all four cases, the closed position of the crystal-structure E60 residue would have prevented optimal ligand binding. A) V1. B) V2. C) V3. D) V4.</p>", "links"=>[], "tags"=>["binding", "inhibitors", "respective", "optimal", "conformation"], "article_id"=>504498, "categories"=>["Physics", "Medicine", "Pharmacology", "Computational Biology", "Biophysics"], "users"=>["Jacob D. Durrant", "Laurence Hall", "Robert V. Swift", "Melissa Landon", "Achim Schnaufer", "Rommie E. Amaro"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0000803.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Predicted_binding_of_the_identified_inhibitors_to_the_respective_optimal_protein_conformation_from_the_ensemble_/504498", "title"=>"Predicted binding of the identified inhibitors to the respective optimal protein conformation from the ensemble.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-08-24 01:14:58"}

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