Publications of Amanda Hargrove

Books

  1. Hargrove, AE, "Preface"January,, 2019, 623, xv-xvii [doi].

Journal Articles

  1. Bailey, MA; Martyr, JG; Hargrove, AE; Fitzgerald, MC, "Stability-Based Proteomics for Investigation of Structured RNA-Protein Interactions.", Analytical chemistryFebruary,, 2024 [doi] [abs].

  2. Hymon, D; Martins, J; Richter, C; Sreeramulu, S; Wacker, A; Ferner, J; Patwardhan, NN; Hargrove, AE; Schwalbe, H, "NMR <sup>1</sup>H,<sup>19</sup>F-based screening of the four stem-looped structure 5_SL1-SL4 located in the 5'-untranslated region of SARS-CoV 2 RNA.", RSC medicinal chemistryJanuary,, 2024, 15(1), 165-177, Royal Society of Chemistry (RSC) [doi] [abs].

  3. Vögele, J; Hymon, D; Martins, J; Ferner, J; Jonker, HRA; Hargrove, AE; Weigand, JE; Wacker, A; Schwalbe, H; Wöhnert, J; Duchardt-Ferner, E, "High-resolution structure of stem-loop 4 from the 5'-UTR of SARS-CoV-2 solved by solution state NMR.", Nucleic acids researchNovember,, 2023, 51(20), 11318-11331 [doi] [abs].

  4. Bagnolini, G; Luu, TB; Hargrove, AE, "Recognizing the power of machine learning and other computational methods to accelerate progress in small molecule targeting of RNA.", RNA (New York, N.Y.)April,, 2023, 29(4), 473-488, Cold Spring Harbor Laboratory [doi] [abs].

  5. Davila-Calderon, J; Li, M-L; Penumutchu, SR; Haddad, C; Malcolm, L; Hargrove, AE; Brewer, G; Tolbert, BS, "Enterovirus Evolution Reveals the Mechanism of an RNA-Targeted Antiviral and Determinants of Viral Replication", in Cold Spring Harbor LaboratoryFebruary,, 2023, 10(7), eadg3060, American Association for the Advancement of Science (AAAS) [doi] [abs].

  6. Zafferani, M; Martyr, JG; Muralidharan, D; Montalvan, NI; Cai, Z; Hargrove, AE, "Multiassay Profiling of a Focused Small Molecule Library Reveals Predictive Bidirectional Modulation of the lncRNA MALAT1 Triplex Stability In Vitro.", ACS chemical biologySeptember,, 2022, 17(9), 2437-2447 [doi] [abs].

  7. Zafferani, M; Muralidharan, D; Montalvan, NI; Hargrove, AE, "RT-qPCR as a screening platform for mutational and small molecule impacts on structural stability of RNA tertiary structures.", RSC chemical biologyJuly,, 2022, 3(7), 905-915 [doi] [abs].

  8. Donlic, A; Swanson, EG; Chiu, L-Y; Wicks, SL; Juru, AU; Cai, Z; Kassam, K; Laudeman, C; Sanaba, BG; Sugarman, A; Han, E; Tolbert, BS; Hargrove, AE, "R-BIND 2.0: An Updated Database of Bioactive RNA-Targeting Small Molecules and Associated RNA Secondary Structures.", ACS chemical biologyJune,, 2022, 17(6), 1556-1566 [doi] [abs].

  9. Cai, Z; Zafferani, M; Akande, OM; Hargrove, AE, "Quantitative Structure-Activity Relationship (QSAR) Study Predicts Small-Molecule Binding to RNA Structure.", Journal of medicinal chemistryMay,, 2022, 65(10), 7262-7277 [doi] [abs].

  10. Haddad, C; Tolbert, BS; Hargrove, AE; Brewer, G; Li, ML, "The Discovery of Antivirals and Targets for SARS-CoV-2 and EV-A71", FASEB journal : official publication of the Federation of American Societies for Experimental BiologyMay,, 2022, 36 [doi] [abs].

  11. Cai, Z; Zafferani, M; Akande, O; Hargrove, A, "Quantitative Structure Activity Relationship (QSAR) study predicts small molecule binding to RNA structure"December,, 2021 [doi] [abs].

  12. Cable, J; Heard, E; Hirose, T; Prasanth, KV; Chen, L-L; Henninger, JE; Quinodoz, SA; Spector, DL; Diermeier, SD; Porman, AM; Kumar, D; Feinberg, MW; Shen, X; Unfried, JP; Johnson, R; Chen, C-K; Wilusz, JE; Lempradl, A; McGeary, SE; Wahba, L; Pyle, AM; Hargrove, AE; Simon, MD; Marcia, M; Przanowska, RK; Chang, HY; Jaffrey, SR; Contreras, LM; Chen, Q; Shi, J; Mendell, JT; He, L; Song, E; Rinn, JL; Lalwani, MK; Kalem, MC; Chuong, EB; Maquat, LE; Liu, X, "Noncoding RNAs: biology and applications-a Keystone Symposia report.", Annals of the New York Academy of SciencesDecember,, 2021, 1506(1), 118-141 [doi] [abs].

  13. Zafferani, M; Haddad, C; Luo, L; Davila-Calderon, J; Chiu, L-Y; Mugisha, CS; Monaghan, AG; Kennedy, AA; Yesselman, JD; Gifford, RJ; Tai, AW; Kutluay, SB; Li, M-L; Brewer, G; Tolbert, BS; Hargrove, AE, "Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures.", Science advancesNovember,, 2021, 7(48), eabl6096, American Association for the Advancement of Science (AAAS) [doi] [abs].

  14. Cai, Z; Zafferani, M; Hargrove, A, "Ensemble learning-based quantitative structure-activity relationship platform predicts binding behavior of RNA-targeted small molecules"July,, 2021 [doi] [abs].

  15. Zafferani, M; Hargrove, AE, "Small molecule targeting of biologically relevant RNA tertiary and quaternary structures.", Cell chemical biologyMay,, 2021, 28(5), 594-609, Elsevier BV [doi] [abs].

  16. Falese, JP; Donlic, A; Hargrove, AE, "Targeting RNA with small molecules: from fundamental principles towards the clinic.", Chemical Society reviewsMarch,, 2021, 50(4), 2224-2243 [doi] [abs].

  17. Umuhire Juru, A; Hargrove, AE, "Frameworks for targeting RNA with small molecules.", The Journal of biological chemistryJanuary,, 2021, 296, 100191 [doi] [abs].

  18. Falese, J; McFadden, E; D’Inzeo, C; Hargrove, A, "Structural analysis of the lncRNA SChLAP1 reveals protein binding interfaces and a conformationally heterogenous retroviral insertion", 2021 [doi] [abs].

  19. Martina, Z; Christina, H; Le, L; Jesse, D-C; Liang, Y-C; Christian, SM; Monaghan, AG; Kennedy, AA; Yesselman, JD; Gifford, RR; Tai, AW; Kutluay, SB; Li, M-L; Brewer, G; Tolbert, BS; Hargrove, AE, "Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures.", bioRxivDecember,, 2020 [doi] [abs].

  20. Hargrove, AE, "Small molecule-RNA targeting: starting with the fundamentals.", Chemical communications (Cambridge, England)November,, 2020, 56(94), 14744-14756 [doi] [abs].

  21. Davila-Calderon, J; Patwardhan, NN; Chiu, L-Y; Sugarman, A; Cai, Z; Penutmutchu, SR; Li, M-L; Brewer, G; Hargrove, AE; Tolbert, BS, "IRES-targeting small molecule inhibits enterovirus 71 replication via allosteric stabilization of a ternary complex.", Nature communicationsSeptember,, 2020, 11(1), 4775, Springer Science and Business Media LLC [doi] [abs].

  22. Donlic, A; Zafferani, M; Padroni, G; Puri, M; Hargrove, AE, "Regulation of MALAT1 triple helix stability and in vitro degradation by diphenylfurans.", Nucleic acids researchAugust,, 2020, 48(14), 7653-7664 [doi] [abs].

  23. Padroni, G; Patwardhan, NN; Schapira, M; Hargrove, AE, "Systematic analysis of the interactions driving small molecule-RNA recognition.", RSC medicinal chemistryJuly,, 2020, 11(7), 802-813 [doi] [abs].

  24. Umuhire Juru, A; Cai, Z; Jan, A; Hargrove, AE, "Template-guided selection of RNA ligands using imine-based dynamic combinatorial chemistry.", Chemical communications (Cambridge, England)March,, 2020, 56(24), 3555-3558 [doi] [abs].

  25. Ganser, LR; Kelly, ML; Patwardhan, NN; Hargrove, AE; Al-Hashimi, HM, "Demonstration that Small Molecules can Bind and Stabilize Low-abundance Short-lived RNA Excited Conformational States.", J Mol BiolFebruary,, 2020, 432(4), 1297-1304 [doi] [abs].

  26. Hargrove, AE, "The next 20 years of Medicinal Research Reviews.", Medicinal research reviewsJanuary,, 2020, 40(1), 7-8 [doi].

  27. Davila-Calderon, J; Patwardhan, N; Chiu, L-Y; Sugarman, A; Cai, Z; Penutmutchu, S; Li, M-L; Brewer, G; Hargrove, A; Tolbert, B, "Small Molecule Targeting IRES Domain Inhibits Enterovirus 71 Replication via an Allosteric Mechanism that Stabilizes a Ternary Complex", 2020 [doi] [abs].

  28. Morgan, BS; Sanaba, BG; Donlic, A; Karloff, DB; Forte, JE; Zhang, Y; Hargrove, AE, "R-BIND: An Interactive Database for Exploring and Developing RNA-Targeted Chemical Probes.", ACS chemical biologyDecember,, 2019, 14(12), 2691-2700 [doi] [abs].

  29. Patwardhan, NN; Cai, Z; Umuhire Juru, A; Hargrove, AE, "Driving factors in amiloride recognition of HIV RNA targets.", Organic & biomolecular chemistryOctober,, 2019, 17(42), 9313-9320 [doi] [abs].

  30. Wicks, SL; Hargrove, AE, "Fluorescent indicator displacement assays to identify and characterize small molecule interactions with RNA.", Methods (San Diego, Calif.)September,, 2019, 167, 3-14 [doi] [abs].

  31. Umuhire Juru, A; Patwardhan, NN; Hargrove, AE, "Understanding the Contributions of Conformational Changes, Thermodynamics, and Kinetics of RNA-Small Molecule Interactions.", ACS chemical biologyMay,, 2019, 14(5), 824-838 [doi] [abs].

  32. Donlic, A; Morgan, BS; Xu, JL; Liu, A; Roble, C; Hargrove, AE, "Corrigendum: Discovery of Small Molecule Ligands for MALAT1 by Tuning an RNA-Binding Scaffold.", Angewandte Chemie (International ed. in English)April,, 2019, 58(17), 5482 [doi] [abs].

  33. Eubanks, CS; Zhao, B; Patwardhan, NN; Thompson, RD; Zhang, Q; Hargrove, AE, "Visualizing RNA Conformational Changes via Pattern Recognition of RNA by Small Molecules.", Journal of the American Chemical SocietyApril,, 2019, 141(14), 5692-5698 [doi] [abs].

  34. Patwardhan, NN; Cai, Z; Newson, CN; Hargrove, AE, "Fluorescent peptide displacement as a general assay for screening small molecule libraries against RNA.", Organic & biomolecular chemistryFebruary,, 2019, 17(7), 1778-1786 [doi] [abs].

  35. Eubanks, CS; Hargrove, AE, "RNA Structural Differentiation: Opportunities with Pattern Recognition.", BiochemistryJanuary,, 2019, 58(4), 199-213 [doi] [abs].

  36. Donlic, A; Morgan, BS; Xu, JL; Liu, A; Roble, C; Hargrove, AE, "Discovery of Small Molecule Ligands for MALAT1 by Tuning an RNA-Binding Scaffold.", Angewandte Chemie (International ed. in English)October,, 2018, 57(40), 13242-13247 [doi] [abs].

  37. Donlic, A; Morgan, BS; Xu, JL; Liu, A; Roble, C; Hargrove, AE, "Discovery of Small Molecule Ligands for MALAT1 by Tuning an RNA‐Binding Scaffold", Angewandte ChemieOctober,, 2018, 130(40), 13426-13431, Wiley [doi] [abs].

  38. Morgan, BS; Forte, JE; Hargrove, AE, "Insights into the development of chemical probes for RNA.", Nucleic acids researchSeptember,, 2018, 46(16), 8025-8037 [doi] [abs].

  39. Donlic, A; Hargrove, AE, "Targeting RNA in mammalian systems with small molecules.", Wiley interdisciplinary reviews. RNAJuly,, 2018, 9(4), e1477 [doi] [abs].

  40. Eubanks, CS; Hargrove, AE, "Sensing the impact of environment on small molecule differentiation of RNA sequences.", Chemical communications (Cambridge, England)December,, 2017, 53(100), 13363-13366 [doi] [abs].

  41. Morgan, BS; Forte, JE; Culver, RN; Zhang, Y; Hargrove, AE, "Discovery of Key Physicochemical, Structural, and Spatial Properties of RNA-Targeted Bioactive Ligands.", Angewandte Chemie (International ed. in English)October,, 2017, 56(43), 13498-13502, Wiley [doi] [abs].

  42. Patwardhan, NN; Ganser, LR; Kapral, GJ; Eubanks, CS; Lee, J; Sathyamoorthy, B; Al-Hashimi, HM; Hargrove, AE, "Amiloride as a new RNA-binding scaffold with activity against HIV-1 TAR.", MedchemcommMay,, 2017, 8(5), 1022-1036 [doi] [abs].

  43. Eubanks, CS; Forte, JE; Kapral, GJ; Hargrove, AE, "Small Molecule-Based Pattern Recognition To Classify RNA Structure.", Journal of the American Chemical SocietyJanuary,, 2017, 139(1), 409-416 [doi] [abs].

  44. McFadden, EJ; Hargrove, AE, "Biochemical Methods To Investigate lncRNA and the Influence of lncRNA:Protein Complexes on Chromatin.", BiochemistryMarch,, 2016, 55(11), 1615-1630 [doi] [abs].

  45. Burg, JM; Link, JE; Morgan, BS; Heller, FJ; Hargrove, AE; McCafferty, DG, "KDM1 class flavin-dependent protein lysine demethylases.", BiopolymersJuly,, 2015, 104(4), 213-246 [doi] [abs].

  46. Morgan, BS; Hargrove, AE, "Synthetic receptors for oligonucleotides and nucleic acids", Monographs in Supramolecular ChemistryJanuary,, 2015, 2015-January(14), 253-325.

  47. Hargrove, AE; Martinez, TF; Hare, AA; Kurmis, AA; Phillips, JW; Sud, S; Pienta, KJ; Dervan, PB, "Tumor Repression of VCaP Xenografts by a Pyrrole-Imidazole Polyamide.", edited by Agoulnik, IU , PloS oneJanuary,, 2015, 10(11), e0143161 [doi] [abs].

  48. Nickols, NG; Szablowski, JO; Hargrove, AE; Li, BC; Raskatov, JA; Dervan, PB, "Activity of a Py-Im polyamide targeted to the estrogen response element.", Molecular cancer therapeuticsMay,, 2013, 12(5), 675-684 [doi] [abs].

  49. Raskatov, JA; Nickols, NG; Hargrove, AE; Marinov, GK; Wold, B; Dervan, PB, "Gene expression changes in a tumor xenograft by a pyrrole-imidazole polyamide.", Proceedings of the National Academy of Sciences of the United States of AmericaOctober,, 2012, 109(40), 16041-16045 [doi] [abs].

  50. Hargrove, AE; Raskatov, JA; Meier, JL; Montgomery, DC; Dervan, PB, "Characterization and solubilization of pyrrole-imidazole polyamide aggregates.", Journal of medicinal chemistryJune,, 2012, 55(11), 5425-5432 [doi] [abs].

  51. Raskatov, JA; Hargrove, AE; So, AY; Dervan, PB, "Pharmacokinetics of Py-Im polyamides depend on architecture: cyclic versus linear.", Journal of the American Chemical SocietyMay,, 2012, 134(18), 7995-7999 [doi] [abs].

  52. Hargrove, AE; Nieto, S; Zhang, T; Sessler, JL; Anslyn, EV, "Artificial receptors for the recognition of phosphorylated molecules.", Chemical reviewsNovember,, 2011, 111(11), 6603-6782 [doi].

  53. Hargrove, AE; Ellington, AD; Anslyn, EV; Sessler, JL, "Chemical functionalization of oligodeoxynucleotides with multiple boronic acids for the polyvalent binding of saccharides.", Bioconjugate chemistryMarch,, 2011, 22(3), 388-396 [doi] [abs].

  54. Hargrove, AE; Reyes, RN; Riddington, I; Anslyn, EV; Sessler, JL, "Boronic acid porphyrin receptor for ginsenoside sensing.", Organic lettersNovember,, 2010, 12(21), 4804-4807 [doi] [abs].

  55. Hargrove, AE; Zhong, Z; Sessler, JL; Anslyn, EV, "Algorithms for the determination of binding constants and enantiomeric excess in complex host : guest equilibria using optical measurements.", New journal of chemistry = Nouveau journal de chimieJanuary,, 2010, 34(2), 348-354, Royal Society of Chemistry (RSC) [doi] [abs].

  56. Collins, BE; Sorey, S; Hargrove, AE; Shabbir, SH; Lynch, VM; Anslyn, EV, "Probing intramolecular B-N interactions in ortho-aminomethyl arylboronic acids.", The Journal of organic chemistryJune,, 2009, 74(11), 4055-4060, American Chemical Society (ACS) [doi] [abs].

  57. Pikulski, M; Hargrove, A; Shabbir, SH; Anslyn, EV; Brodbelt, JS, "Sequencing and characterization of oligosaccharides using infrared multiphoton dissociation and boronic acid derivatization in a quadrupole ion trap.", Journal of the American Society for Mass SpectrometryDecember,, 2007, 18(12), 2094-2106 [doi] [abs].

  58. Spence, JD; Hargrove, AE; Crampton, HL; Thomas, DW, "Porphyrenediynes: synthesis and cyclization of meso-enediynylporphyrins", Tetrahedron LettersJanuary,, 2007, 48(4), 725-728, Elsevier BV [doi] [abs].

  59. Sessler, JL; Lee, JT; Ou, Z; Köhler, T; Hargrove, AE; Cho, WS; Lynch, V; Kadish, KM, "Chemical and electrochemical oxidation of N-alkyl cyclo[n]-pyrroles", Journal of Porphyrins and PhthalocyaninesJanuary,, 2006, 10(12), 1329-1336, World Scientific Pub Co Pte Lt [doi] [abs].

Chapter in Book

  1. Hay, EGS; Cai, Z; Hargrove, AE, "Chemical matter that binds RNA", in RNA as a Drug Target: The Next Frontier for Medicinal ChemistryJuly,, 2024, 93-117 [doi] [abs].

  2. Zewde, B; Atoyebi, O; Zvonkina, IJ; Thomspon, T; Hargrove, A; Scott, A; Raghavan, D, "Biopolymer Nanocomposites and Their Applications", in World Scientific Series in Nanoscience and NanotechnologyJanuary,, 2020, 20, 45-108 [doi] [abs].

  3. Hargrove, AE, "RNA Recognition", in RNA RECOGNITION, edited by Hargrove, AE January,, 2019, 623, XV-XVII, ACADEMIC PRESS LTD-ELSEVIER SCIENCE LTD.

  4. Padroni, G; Eubanks, CS; Hargrove, AE, "Differentiation and classification of RNA motifs using small molecule-based pattern recognition.", in Methods in EnzymologyJanuary,, 2019, 623, 101-130 [doi] [abs].

  5. Hargrove, AE, "Preface.", 2019, 623, xv-xvii [doi].

  6. Morgan, BS; Hargrove, AE, "Chapter 7. Synthetic Receptors for Oligonucleotides and Nucleic Acids", in Monographs in Supramolecular Chemistry, 2015, 253-325, Royal Society of Chemistry [doi].