{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T02:13:40Z","timestamp":1760148820523,"version":"build-2065373602"},"reference-count":63,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2023,6,14]],"date-time":"2023-06-14T00:00:00Z","timestamp":1686700800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100008569","name":"OCAST","doi-asserted-by":"publisher","award":["HR20-002","R01 CA242845","P20 GM103640","P30 GM145423","P30 CA225520"],"award-info":[{"award-number":["HR20-002","R01 CA242845","P20 GM103640","P30 GM145423","P30 CA225520"]}],"id":[{"id":"10.13039\/100008569","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["HR20-002","R01 CA242845","P20 GM103640","P30 GM145423","P30 CA225520"],"award-info":[{"award-number":["HR20-002","R01 CA242845","P20 GM103640","P30 GM145423","P30 CA225520"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"the Presbyterian Health Foundation","award":["HR20-002","R01 CA242845","P20 GM103640","P30 GM145423","P30 CA225520"],"award-info":[{"award-number":["HR20-002","R01 CA242845","P20 GM103640","P30 GM145423","P30 CA225520"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Mitochondrial RNA editing in trypanosomes represents an attractive target for developing safer and more efficient drugs for treating infections with trypanosomes because this RNA editing pathway is not found in humans. Other workers have targeted several enzymes in this editing system, but not the RNA. Here, we target a universal domain of the RNA editing substrate, which is the U-helix formed between the oligo-U tail of the guide RNA and the target mRNA. We selected a part of the U-helix that is rich in G-U wobble base pairs as the target site for the virtual screening of 262,000 compounds. After chemoinformatic filtering of the top 5000 leads, we subjected 50 representative complexes to 50 nanoseconds of molecular dynamics simulations. We identified 15 compounds that retained stable interactions in the deep groove of the U-helix. The microscale thermophoresis binding experiments on these five compounds show low-micromolar to nanomolar binding affinities. The UV melting studies show an increase in the melting temperatures of the U-helix upon binding by each compound. These five compounds can serve as leads for drug development and as research tools to probe the role of the RNA structure in trypanosomal RNA editing.<\/jats:p>","DOI":"10.3390\/ijms241210110","type":"journal-article","created":{"date-parts":[[2023,6,15]],"date-time":"2023-06-15T01:32:57Z","timestamp":1686792777000},"page":"10110","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Targeting RNA Structure to Inhibit Editing in Trypanosomes"],"prefix":"10.3390","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4534-9156","authenticated-orcid":false,"given":"Francis A.","family":"Acquah","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8181-8987","authenticated-orcid":false,"given":"Blaine H. 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Treat. Options Infect. Dis."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"818","DOI":"10.1016\/j.pt.2018.08.006","article-title":"The long wait for a new drug for Human African Trypanosomiasis","volume":"34","author":"Baker","year":"2018","journal-title":"Trends Parasitol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/j.pt.2012.12.005","article-title":"Drug resistance in African trypanosomiasis: The melarsoprol and pentamidine story","volume":"29","author":"Baker","year":"2013","journal-title":"Trends Parasitol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1007\/s00018-010-0538-9","article-title":"When you can\u2019t trust the DNA: RNA editing changes transcript sequences","volume":"68","author":"Knoop","year":"2011","journal-title":"Cell. Mol. Life Sci."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1016\/0092-8674(86)90063-2","article-title":"Major transcript of the frameshifted coxII gene from trypanosome mitochondria contains four nucleotides that are not encoded in the DNA","volume":"46","author":"Benne","year":"1986","journal-title":"Cell"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"17278","DOI":"10.1073\/pnas.0805820105","article-title":"Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei","volume":"105","author":"Amaro","year":"2008","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"2435","DOI":"10.1261\/rna.2347310","article-title":"Identification of specific inhibitors for a trypanosomatid RNA editing reaction","volume":"16","author":"Liang","year":"2010","journal-title":"RNA"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1016\/0092-8674(90)90375-O","article-title":"Guide RNAs in kinetoplastid mitochondria have a nonencoded 3\u2032 Oligo(U) tail involved in recognition of the preedited region","volume":"62","author":"Blum","year":"1990","journal-title":"Cell"},{"key":"ref_10","first-page":"1803","article-title":"Interactions of mRNAs and gRNAs involved in trypanosome mitochondrial RNA editing: Structure probing of an mRNA bound to its cognate gRNA","volume":"7","author":"Leung","year":"2001","journal-title":"RNA"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Reifur, L., Yu, L.E., Cruz-Reyes, J., Vanhartesvelt, M., and Koslowsky, D.J. (2010). The impact of mRNA structure on guide RNA targeting in kinetoplastid RNA editing. PLoS ONE, 5.","DOI":"10.1371\/journal.pone.0012235"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1261\/rna.2880311","article-title":"The crystal structure of an oligo(U):pre-mRNA duplex from a trypanosome RNA editing substrate","volume":"17","author":"Mooers","year":"2011","journal-title":"RNA"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1007\/978-1-4939-1896-6_13","article-title":"Structural studies of a double-stranded RNA from trypanosome RNA editing by small-angle X-ray scattering","volume":"Volume 1240","author":"Criswell","year":"2015","journal-title":"RNA-RNA Interactions"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"804","DOI":"10.1073\/pnas.73.3.804","article-title":"Sequence-specific recognition of double helical nucleic acids by proteins","volume":"73","author":"Seeman","year":"1976","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"2324","DOI":"10.1021\/acs.jcim.5b00559","article-title":"ZINC 15\u2014ligand discovery for everyone","volume":"55","author":"Sterling","year":"2015","journal-title":"J. Chem. Inf. Model."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1002\/jcc.21334","article-title":"AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading","volume":"31","author":"Trott","year":"2010","journal-title":"J. Comput. Chem."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1038\/nprot.2016.051","article-title":"Computational protein-ligand docking and virtual drug screening with the AutoDock suite","volume":"11","author":"Forli","year":"2016","journal-title":"Nat. Protoc."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1021\/ci9803381","article-title":"Unsupervised database clustering based on Daylight\u2019s fingerprint and Tanimoto similarity: A fast and automated way to cluster small and large data sets","volume":"39","author":"Butina","year":"1999","journal-title":"J. Chem. Inf. Comput. Sci."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/j.ymeth.2015.08.023","article-title":"Studying small molecule-aptamer interactions using microscale thermophoresis (MST)","volume":"97","author":"Entzian","year":"2016","journal-title":"Methods"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Leeder, W.M., Reuss, A.J., Brecht, M., Kratz, K., Wachtveitl, J., and Goringer, H.U. (2015). Charge reduction and thermodynamic stabilization of substrate RNAs inhibit RNA editing. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0118940"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1146\/annurev.bb.24.060195.001535","article-title":"Nucleic acid hybridization: Triplex stability and energetics","volume":"24","author":"Plum","year":"1995","journal-title":"Annu. Rev. Biophys. Biomol. Struct."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"869","DOI":"10.1016\/S0300-9084(02)01460-8","article-title":"Rational ligand design for RNA: The role of static structure and conformational flexibility in target recognition","volume":"84","author":"Hermann","year":"2002","journal-title":"Biochimie"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"2821","DOI":"10.1046\/j.1432-1033.2002.02970.x","article-title":"Temperature dependence of thermodynamic properties for DNA\/DNA and RNA\/DNA duplex formation","volume":"269","author":"Wu","year":"2002","journal-title":"Eur. J. Biochem."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1038\/311584a0","article-title":"Z-RNA\u2014A left-handed RNA double helix","volume":"311","author":"Hall","year":"1984","journal-title":"Nature"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"9008","DOI":"10.1021\/acs.jpca.6b08023","article-title":"Similarities and differences between RNA and DNA double-helical structures in circular dichroism spectroscopy: A SAC-CI study","volume":"120","author":"Miyahara","year":"2016","journal-title":"J. Phys. Chem. A"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1016\/j.ijpddr.2011.10.003","article-title":"Inhibitors of RNA editing as potential chemotherapeutics against trypanosomatid pathogens","volume":"2","author":"Salavati","year":"2012","journal-title":"Int. J. Parasitol. Drugs Drug Resist."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Durrant, J.D., Hall, L., Swift, R.V., Landon, M., Schnaufer, A., and Amaro, R.E. (2010). Novel naphthalene-based inhibitors of Trypanosoma brucei RNA editing ligase 1. PLoS Negl. Trop. Dis., 4.","DOI":"10.1371\/journal.pntd.0000803"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1329","DOI":"10.1016\/j.bbagen.2016.12.023","article-title":"Identification of G-quadruplex DNA\/RNA binders: Structure-based virtual screening and biophysical characterization","volume":"1861","author":"Rocca","year":"2017","journal-title":"Biochim. Biophys. Acta Gen. Subj."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"4350","DOI":"10.1021\/jm020155c","article-title":"Do structurally similar molecules have similar biological activity?","volume":"45","author":"Martin","year":"2002","journal-title":"J. Med. Chem."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1038\/nature09107","article-title":"Thousands of chemical starting points for antimalarial lead identification","volume":"465","author":"Gamo","year":"2010","journal-title":"Nature"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"W753","DOI":"10.1093\/nar\/gkac267","article-title":"TeachOpenCADD 2022: Open source and FAIR Python pipelines to assist in structural bioinformatics and cheminformatics research","volume":"50","author":"Sydow","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1002\/med.20067","article-title":"Combining docking and molecular dynamic simulations in drug design","volume":"26","author":"Alonso","year":"2006","journal-title":"Med. Res. Rev."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"4177","DOI":"10.1021\/acs.chemrev.7b00427","article-title":"RNA structural dynamics as captured by molecular simulations: A comprehensive overview","volume":"118","author":"Sponer","year":"2018","journal-title":"Chem. Rev."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"622","DOI":"10.1016\/j.coph.2009.06.008","article-title":"Biophysical techniques for ligand screening and drug design","volume":"9","author":"Renaud","year":"2009","journal-title":"Curr. Opin. Pharmacol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"2701","DOI":"10.1021\/ci4003156","article-title":"Complementarity between in silico and biophysical screening approaches in fragment-based lead discovery against the A(2A) adenosine receptor","volume":"53","author":"Chen","year":"2013","journal-title":"J. Chem. Inf. Model."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1007\/978-1-4939-9145-7_6","article-title":"In silico drug-target profiling","volume":"1953","author":"Trosset","year":"2019","journal-title":"Methods Mol. Biol."},{"key":"ref_37","first-page":"147","article-title":"Targeting the HIV RNA genome: High-hanging fruit only needs a longer ladder","volume":"389","year":"2015","journal-title":"Curr. Top. Microbiol. Immunol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"4638","DOI":"10.1021\/acs.biochem.7b01141","article-title":"Measuring RNA-ligand interactions with microscale thermophoresis","volume":"57","author":"Moon","year":"2018","journal-title":"Biochemistry"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1119","DOI":"10.1002\/med.21278","article-title":"Structure-based DNA-targeting strategies with small molecule ligands for drug discovery","volume":"33","author":"Sheng","year":"2013","journal-title":"Med. Res. Rev."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Pal, A., and Levy, Y. (2019). Structure, stability and specificity of the binding of ssDNA and ssRNA with proteins. PLoS Comput. Biol., 15.","DOI":"10.1371\/journal.pcbi.1006768"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1016\/j.jconrel.2020.03.040","article-title":"Nucleic acid-based drug delivery strategies","volume":"323","author":"Tan","year":"2020","journal-title":"J. Control Release"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1038\/222385a0","article-title":"Platinum compounds: A new class of potent antitumour agents","volume":"222","author":"Rosenberg","year":"1969","journal-title":"Nature"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1007\/s00775-022-01973-0","article-title":"DNA G-quadruplex-stabilizing metal complexes as anticancer drugs","volume":"28","author":"Zegers","year":"2023","journal-title":"J. Biol. Inorg. Chem."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1002\/prot.20035","article-title":"GEMDOCK: A generic evolutionary method for molecular docking","volume":"55","author":"Yang","year":"2004","journal-title":"Proteins"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1016\/j.compbiolchem.2018.05.008","article-title":"Computer-aided drug design and virtual screening of targeted combinatorial libraries of mixed-ligand transition metal complexes of 2-butanone thiosemicarbazone","volume":"75","author":"Khan","year":"2018","journal-title":"Comput. Biol. Chem."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1016\/S0092-8674(00)81062-4","article-title":"Direct visualization of uridylate deletion in vitro suggests a mechanism for kinetoplastid RNA editing","volume":"84","author":"Seiwert","year":"1996","journal-title":"Cell"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1107\/S2059798316001224","article-title":"Direct-methods structure determination of a trypanosome RNA-editing substrate fragment with translational pseudosymmetry","volume":"72","author":"Mooers","year":"2016","journal-title":"Acta Crystallogr. Sect. D Struct. Biol."},{"key":"ref_48","unstructured":"Delano, W. (2021). The PyMOL Molecular Graphics System, Version 2.5.1, Schrodinger, Ltd."},{"key":"ref_49","unstructured":"Landrum, G. (2023, April 30). RDKit: A Software Suite for Cheminformatics, Computational Chemistry, and Predictive Modeling. Available online: http:\/\/rdkit.org\/."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","article-title":"GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers","volume":"1\u20132","author":"Abraham","year":"2015","journal-title":"SoftwareX"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1859","DOI":"10.1002\/jcc.20945","article-title":"CHARMM-GUI: A web-based graphical user interface for CHARMM","volume":"29","author":"Jo","year":"2008","journal-title":"J. Comput. Chem."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1021\/acs.jctc.5b00935","article-title":"CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM\/OpenMM Simulations Using the CHARMM36 Additive Force Field","volume":"12","author":"Lee","year":"2016","journal-title":"J. Chem. Theory Comput."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"035103","DOI":"10.1063\/5.0012280","article-title":"CHARMM-GUI supports the Amber force fields","volume":"153","author":"Lee","year":"2020","journal-title":"J. Chem. Phys."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"3257","DOI":"10.1021\/ct300400x","article-title":"Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone phi, psi and side-chain chi(1) and chi(2) dihedral angles","volume":"8","author":"Best","year":"2012","journal-title":"J. Chem. Theory Comput."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"7182","DOI":"10.1063\/1.328693","article-title":"Polymorphic transitions in single-crystals\u2014A new molecular-dynamics method","volume":"52","author":"Parrinello","year":"1981","journal-title":"J. Appl. Phys."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1002\/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H","article-title":"LINCS: A linear constraint solver for molecular simulations","volume":"18","author":"Hess","year":"1997","journal-title":"J. Comput. Chem."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"8577","DOI":"10.1063\/1.470117","article-title":"A smooth particle mesh Ewald method","volume":"103","author":"Essmann","year":"1995","journal-title":"J. Chem. Phys."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"3314","DOI":"10.1021\/ct300418h","article-title":"MMPBSA.py: An efficient program for end-state free energy calculations","volume":"8","author":"Swails","year":"2012","journal-title":"J. Chem. Theory Comput."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"6281","DOI":"10.1021\/acs.jctc.1c00645","article-title":"gmx_MMPBSA: A New tool to perform end-state free energy calculations with GROMACS","volume":"17","author":"Valiente","year":"2021","journal-title":"J. Chem. Theory Comput."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/j.molstruc.2014.03.009","article-title":"MicroScale thermophoresis: Interaction analysis and beyond","volume":"1077","author":"Andre","year":"2014","journal-title":"J. Mol. Struct."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1177\/2472555217744728","article-title":"Using microscale thermophoresis to characterize hits from high-throughput ccreening: A european lead factory perspective","volume":"23","author":"Rainard","year":"2018","journal-title":"Slas Discov."},{"key":"ref_62","first-page":"371","article-title":"Biophysical, chemical, and functional probes of RNA structure, interactions and folding: Part A","volume":"Volume 468","author":"Herschlag","year":"2009","journal-title":"Methods in Enzymology"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"4385","DOI":"10.1038\/s41598-019-40715-2","article-title":"Thermodynamic and structural contributions of the 6-thioguanosine residue to helical properties of RNA","volume":"9","author":"Gladysz","year":"2019","journal-title":"Sci. Rep."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/24\/12\/10110\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T19:54:41Z","timestamp":1760126081000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/24\/12\/10110"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,6,14]]},"references-count":63,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2023,6]]}},"alternative-id":["ijms241210110"],"URL":"https:\/\/doi.org\/10.3390\/ijms241210110","relation":{},"ISSN":["1422-0067"],"issn-type":[{"type":"electronic","value":"1422-0067"}],"subject":[],"published":{"date-parts":[[2023,6,14]]}}}