Publications

Pre-Prints

  1. Falese, James P.; McFadden, Emily J.; D’Inzeo, Christopher A.; Hargrove, Amanda E.* “Structural analysis of the lncRNA SChLAP1 reveals protein binding interfaces and a conformationally heterogenous retroviral insertion.” [bioRxiv (preprint) DOI: 10.1101/2021.10.21.465303] 

  2. Wicks, Sarah L.; Morgan, Brittany S.; Wilson, Alexander W.; Hargrove, Amanda E.* “Probing Bioactive Chemical Space to Discover RNA-Targeted Small Molecules.” [bioRxiv (preprint) DOI: 10.1101/2023.07.31.551350]

Peer-Reviewed Manuscripts

Corresponding author (*), Co-first author (†), Undergraduate Authors (underlined)

  1. Bailey, Morgan A.;† Martyr, Justin G.;† Hargrove, Amanda E.;* Fitzgerald, Michael C.* “Stability-based Proteomics for Investigation of Structured RNA-protein Interactions.” Analytical Chemistry. 2024, 96(7), 3044–3053. DOI: 10.1021/acs.analchem.3c04978

  2. Davila-Calderon, Jesse; Li, Mei-Ling; Penumutchu, Srinivasa R.; Haddad, Christina; Malcolm, Linzy; King, Josephine; Hargrove, Amanda E;* Brewer, Gary;* Tolbert, Blanton S.* “Enterovirus Evolution Reveals the Mechanism of an RNA-Targeted Antiviral and Determinants of Viral Replication.” Science Advances. 2024. 10(7), eadg3060. DOI: 10.1126/sciadv.adg306

  3. Hymon, Daniel; Martins, Jason; Richter, Christian; Sreeramulu, Sridhar; Wacker, Anna; Ferner, Jan; Patwardhan, Neeraj N.; Hargrove, Amanda E.; Schwalbe, Harald.* “NMR 1H,19F-based screening of the four stem-looped structure 5_SL1–SL4 located in the 5′-untranslated region of SARS-CoV 2 RNA.” RSC Medicinal Chemistry. 2024, 15, 165-177. DOI: 10.1039/D3MD00322A

  4. Vögele, Jennifer; Hymon, Daniel; Martins, Jason; Ferner, Jan; Jonker, Hendrick RA; Hargrove, Amanda E; Weigand, Julia E; Wacker, Anna; Schwalbe, Harald; Wöhnert, Jens; Duchardt-Ferner, Elke.* “High-resolution structure of stem-loop 4 from the 5′-UTR of SARS-CoV-2 solved by solution state NMR.” Nucleic Acids Research. 2023, 51, 11318–11331. DOI: 10.1093/nar/gkad762

  5. Bagnolini, Greta;† Luu, TinTin B.;† Hargrove, Amanda E.* “Recognizing the power of machine learning and other computational methods to accelerate progress in small molecule targeting of RNA.” RNA. 2023, 29, 473-488. DOI: 10.1261/rna.079497.122

  6. Zafferani, Martina; Martyr, Justin G.; Muralidharan, Dhanasheel; Montalvan, Nadeska I.; Cai, Zhengguo; Hargrove, Amanda E.* “Multi-assay profiling of a focused small molecule library reveals predictive bidirectional modulation of the lncRNA MALAT1 triplex stability in vitro.” ACS Chemical Biology. 2022, 17(9), 2437–2447. DOI: 10.1021/acschembio.2c00124

  7. Zafferani, Martina; Muralidharan, Dhanasheel; Montalvan, Nadeska I.; Hargrove, Amanda E.* “RT-qPCR as a screening platform for mutational and small molecule impacts on structural stability of RNA tertiary structures.” RSC Chemical Biology. 2022, 3, 905-915. DOI: 10.1039/D2CB00015F

  8. Donlic, Anita; Swanson, Emily G.; Chiu, Liang-Yuan; Wicks, Sarah L.; Umuhire Juru, Aline; Cai, Zhengguo; Kassam, Kamillah; Laudeman, Chris; Sanaba, Bilva G.; Sugarman, Andrew; Han, Eunseong; Tolbert, Blanton S.*; Hargrove, Amanda E.* “R-BIND 2.0: An Updated Database of Bioactive RNA Targeting Small Molecules and Associated RNA Secondary Structures.” ACS Chemical Biology. 2022, 17(6), 1556-1566. DOI: 10.1021/acschembio.2c00224

  9. Cai, Zhengguo; Zafferani, Martina; Akande, Olanrewaju M.; Hargrove, Amanda E.* “Quantitative Structure Activity Relationship (QSAR) study predicts small molecule binding to RNA structure.” Journal of Medicinal Chemistry. 2022, 65(10), 7262–7277. DOI: 10.1021/acs.jmedchem.2c00254

  10. Zafferani, Martina; Haddad, Christina; Luo, Le; Davila-Calderon, Jesse; Yuan-Chiu, Liang; Shema Mugisha, Christian; Monaghan, Adeline G.; Kennedy, Andrew A.; Yesselman, Joseph D.; Gifford, Robert R.; Tai, Andrew W.; Kutluay, Sebla B.; Li, Mei-Ling*; Brewer, Gary*; Tolbert, Blanton S.*; Hargrove, Amanda E.* “Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures.” Science Advances. 2021, 7(48), eabl6096. DOI: 10.1126/sciadv.abl6096
    This work was featured on Duke’s Research Blog, Indy week and the New York Times

  11. Zafferani, Martina; Hargrove, Amanda E.* “Small Molecule Targeting of Biologically Relevant RNA Tertiary and Quaternary Structures.” Cell Chemical Biology. 2021, 28(5), 594-609. DOi: 10.1016/j.chembiol.2021.03.003 

  12. Falese, James P.; Donlic, Anita; Hargrove, Amanda E.* “Tutorial Review: Targeting RNA with small molecules: from fundamental principles towards the clinic.” Chemical Society Reviews. 2021, 50(4), 2224-2243. DOI: 10.1039/D0CS01261K.

  13. Umuhire Juru, Aline; Hargrove, Amanda E.* "Frameworks for targeting RNA with small molecules.” Journal of Biological Chemistry, 2021, 296, 100191. DOi: 10.1074/jbc.REV120.015203 

  14. Hargrove, Amanda E.* “Small molecule-RNA targeting: Starting with the fundamentals.” Chemical Communications, 2020, 56, 14744-14756. DOi: 10.1039/D0CC06796B
    This article is part of the themed collection: 2020 Emerging Investigators

  15. Davila-Calderon, Jesse; Patwardhan, Neeraj N.; Chiu, Liang-Yuan; Sugarman, Andrew L.; Cai, Zhengguo; Penutmutchu, Srinivasa R.; Li, Mei-Ling; Brewer, Gary;* Hargrove, Amanda E.;* Tolbert, Blanton S.* “IRES-targeting small molecule inhibits enterovirus 71 replication via allosteric stabilization of a ternary complex.” Nature Communications, 2020, 11, 4775. DOI: 10.1038/s41467-020-18594-3
    This work was featured on Duke’s Research Blog and United Press International

  16. Donlic, Anita; Zafferani, Martina; Padroni, Giacomo; Puri, Malavika; Hargrove, Amanda E.* “Regulation of MALAT1 triple helix stability and in vitro degradation by diphenylfurans.” Nucleic Acids Research, 2020, 48(14), 7653–7664. DOI: 10.1093/nar/gkaa585

  17. Padroni, Giacomo; Patwardhan, Neeraj N.; Schapira, Matthieu; Hargrove, Amanda E.* “Systematic analysis of the interactions driving small molecule–RNA recognition.” RSC Medicinal Chemistry, 2020,11, 802-813. DOi: 10.1039/D0MD00167H

  18. Umuhire Juru, Aline; Cai, Zhengguo; Jan, Adina; Hargrove, Amanda E.* "Template-guided selection of RNA ligands using imine-based dynamic combinatorial chemistry.” Chemical Communications. 2020, 56, 3555-3558. DOI: 10.1039/d0cc00266f

  19. Ganser, Laura R.; Kelly, Megan L.; Patwardhan, Neeraj N.; Hargrove, Amanda E.; Al-Hashimi, Hashim M.* “Demonstration that small molecules can bind and stabilize low-abundance short-lived RNA excited conformational states.” J. Mol. Bio. 2020, 432, 1297-1304. DOI: 10.1016/j.jmb.2019.12.009

  20. Morgan, Brittany S.; Sanaba, Bilva; Donlic, Anita; Karloff, Diane; Forte, Jordan E; Zhang, Yuqi; Hargrove, Amanda E.* “R-BIND: An Interactive Database for Exploring and Developing RNA-Targeted Chemical Probes.” ACS Chemical Biology. 2019, 14(12), 2691-2700. DOI: 10.1021/acschembio.9b00631

  21. Patwardhan, Neeraj N.; Cai, Zhengguo; Umuhire Juru, Aline; Hargrove, Amanda E.* “Driving factors in amiloride recognition of HIV RNA targets.” Organic & Biomolecular Chemistry. 2019, 17, 9313-9320. DOI: 10.1039/C9OB01702J

  22. Umuhire Juru, Aline; Patwardhan, Neeraj N.; Hargrove, Amanda E.* “Understanding the contributions of conformational changes, thermodynamics, and kinetics of RNA-small molecule interactions.” ACS Chemical Biology. 2019, 14(5), 824-838. DOI: 10.1021/acschembio.8b00945

  23. Wicks, Sarah L.; Hargrove, Amanda E.* “Fluorescent indicator displacement assays to identify and characterize small molecule interactions with RNA.” Methods. 2019, 167, 3-14.  DOI: 10.1016/j.ymeth.2019.04.018

  24. Eubanks, Christopher S.; Zhao, Bo; Patwardhan, Neeraj N.; Thompson, Rhese; Zhang, Qi; Hargrove, Amanda E.* “Visualizing RNA conformational changes via Pattern Recognition of RNA by Small Molecules.” Journal of the American Chemical Society. 2019, 141(14), 5692–5698. DOI: 10.1021/jacs.8b09665

  25. Eubanks, Christopher S.; Hargrove, Amanda E.* “RNA structural differentiation: Opportunities with pattern recognition. Biochemistry. 2019, 58(4), 199–213. DOI: 10.1021/acs.biochem.8b01090
    Special Issue:     Future of Biochemistry: International Issue.

  26. Patwardhan, Neeraj N.; Cai, Zhengguo; Newson, Colby; Hargrove, Amanda E.* “Fluorescent peptide displacement as a general assay for screening small molecule libraries against RNA.” Organic & Biomolecular Chemistry. 2019, 17, 1778-1786. DOI: 10.1039/c8ob02467g
    This article is part of themed collections: New Talent and Chemical Biology in OBC and was highlighted in the Organic and Biomolecular Chemistry blog

  27. Donlic, Anita; Morgan, Brittany S.; Xu, Jason L.; Liu, Anqi; Roble, Carlos Jr.; Hargrove, Amanda E.* “Discovery of small molecule ligands for MALAT1 by tuning an RNA-binding scaffold.” Angewandte Chemie, International Edition. 2018, 57, 13242-13247. DOI: 10.1002/anie.201808823
    Chen, G. and Edwards, N: F1000Prime Recommendation of Evaluation [Donlic A et al., Angew Chem Int Ed Engl 2018 57(40):13242-13247]. In F1000Prime, 21 Nov 2018;     10.3410/f.733852452.793552881

  28. Morgan, Brittany S.; Forte, Jordan E.; Hargrove, Amanda E.* “Insights into the development of chemical probes for RNA.” Nucleic Acids Research. 2018, 46(16), 8025-8037. DOI: 10.1093/nar/gky718
    Chaires J: F1000Prime Recommendation of Evaluation [Morgan BS et al., Nucleic Acids Res 2018 46(16):8025-8037]. In F1000Prime, 04 Sep 2018;     10.3410/f.733808492.793550119

  29. Donlic, Anita; Hargrove, Amanda E.* "Targeting RNA in mammalian systems with small molecules." WIREs RNA. 2018, 9(4), e1477. Top 20 Most Read Article, 2017-2018. DOI: 10.1002/wrna.1477
    This article was featured in     Advanced Science News

  30. Eubanks, Christopher S.; Hargrove, Amanda E.* “Sensing the impact of environment on small molecule differentiation of RNA sequences.” Chemical Communications. 2017, 53, 13363-13366. DOI: 10.1039/C7CC07157D
    This article is part of the themed collection:     Chemosensors and Molecular Logic

  31. Morgan, Brittany S.; Forte, Jordan E.; Culver, Rebecca N.; Zhang, Yuqi; Hargrove, Amanda E.* "Discovery of key physicochemical, structural, and spatial properties of RNA-targeted bioactive ligands." Angewandte Chemie, International Edition.  2017, 56(43), 13498-13502. DOI: 10.1002/anie.201707641

  32. Patwardhan, Neeraj N.; Ganser, Laura R.; Kapral, Gary J.; Eubanks, Christopher S.; Lee, Janghyun; Sathyamoorthy, Bharathwaj; Al-Hashimi, Hashim M.; Hargrove, Amanda E.* “Amiloride as a new RNA binding scaffold with activity against HIV-1 TAR.” MedChemComm. 2017, 8, 1022-1036. Designated “2017 Hot Article in MedChemComm.” DOI: 10.1039/C6MD00729E
    This article is part of the themed collection: 2017 Hot Articles in MedChemComm

  33. Eubanks, Christopher S.; Forte, Jordan E.; Kapral, Gary J.; Hargrove, Amanda E.* "Small molecule-based pattern recognition to classify RNA structure." Journal of the American Chemical Society. 2017, 139, 409-416. DOI: 10.1021/jacs.6b11087
    Arora P and Barros S: F1000Prime Recommendation of Evaluation [Eubanks CS et al., J Am Chem Soc 2017 139(1):409-416]. In F1000Prime, 07 Jun 2017;     10.3410/f.727137423.793532776
    Bujnicki J and Almeida C: F1000Prime Recommendation of Evaluation [Eubanks CS et al., J Am Chem Soc 2017 139(1):409-416]. In F1000Prime, 21 Jun 2017;     10.3410/f.727137423.793533363

  34. McFadden, Emily J.; Hargrove, Amanda E.* “Biochemical methods to investigate lncRNA and the influence of lncRNA:protein complexes on chromatin.” Biochemistry. 2016, 55 (11), 1615-1630. DOI: 10.1021/acs.biochem.5b01141

Book Chapters

  1. Swanson Hay, Emily G; Cai, Zhengguo; Hargrove, Amanda E. “Chemical Matter That Binds RNA.” In RNA as a Drug Target: The Next Frontier for Medicinal Chemistry, Schneekloth John; Pettersson, Martin, Eds. WILEY-VCH GmbH: 2024; pp 93-117.

  2. Padroni, Giacomo; Eubanks, Christopher S.; Hargrove, Amanda E. “Chapter Six - Differentiation and classification of RNA motifs using small molecule-based pattern recognition.” In Methods in Enzymology, Hargrove, A. E., Ed. Academic Press: 2019; Vol. 623, pp 101-130.

  3. Morgan, Brittany S.; Hargrove, Amanda E. "Chapter Seven - Synthetic Receptors for Oligonucleotides and Nucleic Acids." In Synthetic Receptors for Biomolecules: Design Principles and Applications; Smith, B. D., Ed.; The Royal Society of Chemistry: Cambridge, 2015, pp 253-325. 

Books Edited

Methods in Enzymology: Volume 623: RNA Recognition. Hargrove, Amanda E., Ed. Academic Press: 2019. ISBN: 9780128168318.