Scholars@Duke
Amanda Hargrove

Amanda Hargrove

Research Professor of Chemistry
Chemistry
amanda.hargrove@duke.edu
124 Science Drive, Box 90346, 3219 French Sci Center, Durham, NC 27708-0346
3219 French Science Center, Box 90346, Durham, NC 27708

Selected Publications

Chemical matter that binds RNA

Chapter · July 5, 2024 The recent "RNA revolution" has spurred the growth of studies focused on targeting disease-relevant RNAs with various chemical probes, from sequence-based antisense oligonucleotides to structure-based small molecules. Among these, small molecules attracted ... Full text Cite

Stability-Based Proteomics for Investigation of Structured RNA-Protein Interactions.

Journal Article Analytical chemistry · February 2024 RNA-protein interactions are essential to RNA function throughout biology. Identifying the protein interactions associated with a specific RNA, however, is currently hindered by the need for RNA labeling or costly tiling-based approaches. Conventional stra ... Full text Cite

Enterovirus evolution reveals the mechanism of an RNA-targeted antiviral and determinants of viral replication.

Journal Article Science advances · February 2024 Selective pressures on viruses provide opportunities to establish target site specificity and mechanisms of antivirals. Enterovirus (EV)-A71 with resistant mutations in the stem loop (SL) II internal ribosome entry site (IRES) (SLIIresist) were ... Full text Cite

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.

Journal Article RSC medicinal chemistry · January 2024 Development of new antiviral medication against the beta-coronavirus SARS-CoV-2 (SCoV2) is actively being pursued. Both NMR spectroscopy and crystallography as structural screening technologies have been utilised to screen the viral proteome for binding to ... Full text Cite

High-resolution structure of stem-loop 4 from the 5'-UTR of SARS-CoV-2 solved by solution state NMR.

Journal Article Nucleic acids research · November 2023 We present the high-resolution structure of stem-loop 4 of the 5'-untranslated region (5_SL4) of the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) genome solved by solution state nuclear magnetic resonance spectroscopy. 5_SL4 adopts an ... Full text Cite

Recognizing the power of machine learning and other computational methods to accelerate progress in small molecule targeting of RNA.

Journal Article RNA (New York, N.Y.) · April 2023 RNA structures regulate a wide range of processes in biology and disease, yet small molecule chemical probes or drugs that can modulate these functions are rare. Machine learning and other computational methods are well poised to fill gaps in knowledge and ... Full text Cite

Multiassay Profiling of a Focused Small Molecule Library Reveals Predictive Bidirectional Modulation of the lncRNA MALAT1 Triplex Stability In Vitro.

Journal Article ACS chemical biology · September 2022 The rapidly accelerating characterization of RNA tertiary structures has revealed their pervasiveness and active roles in human diseases. Small molecule-mediated modulation of RNA tertiary structures constitutes an attractive avenue for the development of ... Full text Cite

RT-qPCR as a screening platform for mutational and small molecule impacts on structural stability of RNA tertiary structures.

Journal Article RSC chemical biology · July 2022 The exponential increase in the discovery and characterization of RNA tertiary structures has highlighted their active role in a variety of human diseases, yet often their interactome and specific function remain unknown. Small molecules offer opportunitie ... Full text Cite

R-BIND 2.0: An Updated Database of Bioactive RNA-Targeting Small Molecules and Associated RNA Secondary Structures.

Journal Article ACS chemical biology · June 2022 Discoveries of RNA roles in cellular physiology and pathology are increasing the need for new tools that modulate the structure and function of these biomolecules, and small molecules are proving useful. In 2017, we curated the RNA-targeted BI Full text Cite

The Discovery of Antivirals and Targets for SARS-CoV-2 and EV-A71

Conference FASEB journal : official publication of the Federation of American Societies for Experimental Biology · May 1, 2022 Positive Strand RNA (PSR) viruses, such as coronaviruses and enteroviruses, cause serious health and economic threats worldwide, as currently seen with the COVID-19 pandemic. This has drawn attention to the importance of identifying new antivirals and mole ... Full text Cite

Quantitative Structure-Activity Relationship (QSAR) Study Predicts Small-Molecule Binding to RNA Structure.

Journal Article Journal of medicinal chemistry · May 2022 The diversity of RNA structural elements and their documented role in human diseases make RNA an attractive therapeutic target. However, progress in drug discovery and development has been hindered by challenges in the determination of high-resolution RNA ... Full text Cite

Quantitative Structure Activity Relationship (QSAR) study predicts small molecule binding to RNA structure

Journal Article · December 27, 2021 The diversity of RNA structural elements and their documented role in human diseases make RNA an attractive therapeutic target. However, progress in drug discovery and development has been hindered by challenges in the determination of high-resolut ... Full text Cite

Noncoding RNAs: biology and applications-a Keystone Symposia report.

Journal Article Annals of the New York Academy of Sciences · December 2021 The human transcriptome contains many types of noncoding RNAs, which rival the number of protein-coding species. From long noncoding RNAs (lncRNAs) that are over 200 nucleotides long to piwi-interacting RNAs (piRNAs) of only 20 nucleotides, noncoding RNAs ... Full text Cite

Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures.

Journal Article Science advances · November 2021 Featured Publication The SARS-CoV-2 pandemic, and the likelihood of future coronavirus pandemics, emphasized the urgent need for development of novel antivirals. Small-molecule chemical probes offer both to reveal aspects of virus replication and to serve as leads for antivira ... Full text Open Access Cite

Ensemble learning-based quantitative structure-activity relationship platform predicts binding behavior of RNA-targeted small molecules

Journal Article · July 23, 2021 The diversity of RNA structural elements and their documented role in human diseases make RNA an attractive therapeutic target. However, progress in drug discovery and development has been hindered by a limited understanding of the parameters that ... Full text Cite

Small molecule targeting of biologically relevant RNA tertiary and quaternary structures.

Journal Article Cell chemical biology · May 2021 Initial successes in developing small molecule ligands for non-coding RNAs have underscored their potential as therapeutic targets. More recently, these successes have been aided by advances in biophysical and structural techniques for identification and c ... Full text Cite

Targeting RNA with small molecules: from fundamental principles towards the clinic.

Journal Article Chemical Society reviews · March 2021 Recent advances in our understanding of RNA biology have uncovered crucial roles for RNA in multiple disease states, ranging from viral and bacterial infections to cancer and neurological disorders. As a result, multiple laboratories have become interested ... Full text Cite

Frameworks for targeting RNA with small molecules.

Conference The Journal of biological chemistry · January 2021 Since the characterization of mRNA in 1961, our understanding of the roles of RNA molecules has significantly grown. Beyond serving as a link between DNA and proteins, RNA molecules play direct effector roles by binding to various ligands, including protei ... Full text Cite

Structural analysis of the lncRNA SChLAP1 reveals protein binding interfaces and a conformationally heterogenous retroviral insertion

Journal Article · 2021 ABSTRACT The lncRNA Second Chromosome Locus Associated with Prostate 1 (SChLAP1) was previously identified as a predictive biomarker and potential driver of aggressive prostate cancer. Recent work suggests that SChLAP1 may bind the SWI/SNF chromat ... Full text Cite

Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures.

Journal Article bioRxiv · December 6, 2020 The SARS-CoV-2 pandemic, and the likelihood of future coronavirus pandemics, has rendered our understanding of coronavirus biology more essential than ever. Small molecule chemical probes offer to both reveal novel aspects of virus replication and to serve ... Full text Link to item Cite

Small molecule-RNA targeting: starting with the fundamentals.

Journal Article Chemical communications (Cambridge, England) · November 2020 The structural and regulatory elements in therapeutically relevant RNAs offer many opportunities for targeting by small molecules, yet fundamental understanding of what drives selectivity in small molecule:RNA recognition has been a recurrent challenge. In ... Full text Cite

IRES-targeting small molecule inhibits enterovirus 71 replication via allosteric stabilization of a ternary complex.

Journal Article Nature communications · September 2020 Featured Publication Enterovirus 71 (EV71) poses serious threats to human health, particularly in Southeast Asia, and no drugs or vaccines are available. Previous work identified the stem loop II structure of the EV71 internal ribosomal entry site as vital to viral translation ... Full text Cite

Regulation of MALAT1 triple helix stability and in vitro degradation by diphenylfurans.

Journal Article Nucleic acids research · August 2020 Small molecule-based modulation of a triple helix in the long non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) has been proposed as an attractive avenue for cancer treatment and a model system for understanding small molecule: ... Full text Cite

Systematic analysis of the interactions driving small molecule-RNA recognition.

Journal Article RSC medicinal chemistry · July 2020 RNA molecules are becoming an important target class in drug discovery. However, the principles for designing RNA-binding small molecules are yet to be fully uncovered. In this study, we examined the Protein Data Bank (PDB) to highlight privileged interact ... Full text Cite

Template-guided selection of RNA ligands using imine-based dynamic combinatorial chemistry.

Journal Article Chemical communications (Cambridge, England) · March 2020 This study establishes the applicability of imine-based dynamic combinatorial chemistry to discover non-covalent ligands for RNA targets. We elucidate properties underlying the reactivity of arylamines and demonstrate target-guided amplification of tight b ... Full text Cite

Demonstration that Small Molecules can Bind and Stabilize Low-abundance Short-lived RNA Excited Conformational States.

Journal Article J Mol Biol · February 14, 2020 Many promising RNA drug targets have functions that require the formation of RNA-protein complexes, but inhibiting RNA-protein interactions can prove difficult using small molecules. Regulatory RNAs have been shown to transiently form excited conformationa ... Full text Link to item Cite

The next 20 years of Medicinal Research Reviews.

Journal Article Medicinal research reviews · January 2020 Full text Cite

Small Molecule Targeting IRES Domain Inhibits Enterovirus 71 Replication via an Allosteric Mechanism that Stabilizes a Ternary Complex

Journal Article · 2020 We herein report an RNA-targeting antiviral small molecule that reduces replication of the human enterovirus 71 (EV71) via stabilization of an inhibitory small molecule-RNA-protein ternary complex. The EV71 virus poses serious threats to human health, part ... Full text Cite

Biopolymer Nanocomposites and Their Applications

Chapter · January 1, 2020 Biomaterials, both natural and synthetic, attract growing attention in the fields of biomedical devices, tissue engineering, and gene therapy applications. Recent trends call for use of degradable polymers as the preferred candidates for developing therape ... Full text Cite

R-BIND: An Interactive Database for Exploring and Developing RNA-Targeted Chemical Probes.

Journal Article ACS chemical biology · December 2019 While the opportunities available for targeting RNA with small molecules have been widely appreciated, the challenges associated with achieving specific RNA recognition in biological systems have hindered progress and prevented many researchers from enteri ... Full text Cite

Driving factors in amiloride recognition of HIV RNA targets.

Journal Article Organic & biomolecular chemistry · October 2019 Noncoding RNAs are increasingly promising drug targets yet ligand design is hindered by a paucity of methods that reveal driving factors in selective small molecule : RNA interactions, particularly given the difficulties of high-resolution structural chara ... Full text Cite

Fluorescent indicator displacement assays to identify and characterize small molecule interactions with RNA.

Journal Article Methods (San Diego, Calif.) · September 2019 Fluorescent indicator displacement (FID) assays are an advantageous approach to convert receptors into optical sensors that can detect binding of various ligands. In particular, the identification of ligands that bind to RNA receptors has become of increas ... Full text Cite

Understanding the Contributions of Conformational Changes, Thermodynamics, and Kinetics of RNA-Small Molecule Interactions.

Journal Article ACS chemical biology · May 2019 The implication of RNA in multiple cellular processes beyond protein coding has revitalized interest in the development of small molecules for therapeutically targeting RNA and for further probing its cellular biology. However, the process of rationally de ... Full text Cite

Corrigendum: Discovery of Small Molecule Ligands for MALAT1 by Tuning an RNA-Binding Scaffold.

Journal Article Angewandte Chemie (International ed. in English) · April 2019 Full text Cite

Visualizing RNA Conformational Changes via Pattern Recognition of RNA by Small Molecules.

Journal Article Journal of the American Chemical Society · April 2019 Conformational changes in RNA play vital roles in the regulation of many biological systems, yet these changes can be challenging to visualize. Previously, we demonstrated that Pattern Recognition of RNA by Small Molecules (PRRSM) can unbiasedly cluster de ... Full text Cite

Fluorescent peptide displacement as a general assay for screening small molecule libraries against RNA.

Journal Article Organic & biomolecular chemistry · February 2019 A prominent hurdle in developing small molecule probes against RNA is the relative scarcity of general screening methods. In this study, we demonstrate the application of a fluorescent peptide displacement assay to screen small molecule probes against four ... Full text Cite

RNA Structural Differentiation: Opportunities with Pattern Recognition.

Journal Article Biochemistry · January 2019 Our awareness and appreciation of the many regulatory roles of RNA have dramatically increased in the past decade. This understanding, in addition to the impact of RNA in many disease states, has renewed interest in developing selective RNA-targeted small ... Full text Cite

Differentiation and classification of RNA motifs using small molecule-based pattern recognition.

Chapter · January 2019 Understanding how to design small molecules that target coding and non-coding RNA has the potential to exponentially increase the number of therapeutically-relevant druggable targets, which are currently mostly proteins. However, there is limited informati ... Full text Cite

Preface

Book · January 1, 2019 Full text Cite

RNA Recognition

Chapter · January 1, 2019 Link to item Cite

Discovery of Small Molecule Ligands for MALAT1 by Tuning an RNA-Binding Scaffold.

Journal Article Angewandte Chemie (International ed. in English) · October 2018 Structural studies of the 3'-end of the oncogenic long non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) confirmed a unique triple-helix structure. This structure enables accumulation of the transcript, and high levels of MALAT ... Full text Cite

Discovery of Small Molecule Ligands for MALAT1 by Tuning an RNA‐Binding Scaffold

Journal Article Angewandte Chemie · October 2018 AbstractStructural studies of the 3′‐end of the oncogenic long non‐coding RNA metastasis‐associated lung adenocarcinoma transcript 1 (MALAT1) confirmed a unique triple‐helix structure. This structure enables accumulation of ... Full text Cite

Insights into the development of chemical probes for RNA.

Journal Article Nucleic acids research · September 2018 Over the past decade, the RNA revolution has revealed thousands of non-coding RNAs that are essential for cellular regulation and are misregulated in disease. While the development of methods and tools to study these RNAs has been challenging, the power an ... Full text Cite

Targeting RNA in mammalian systems with small molecules.

Journal Article Wiley interdisciplinary reviews. RNA · July 2018 The recognition of RNA functions beyond canonical protein synthesis has challenged the central dogma of molecular biology. Indeed, RNA is now known to directly regulate many important cellular processes, including transcription, splicing, translation, and ... Full text Cite

Sensing the impact of environment on small molecule differentiation of RNA sequences.

Journal Article Chemical communications (Cambridge, England) · December 2017 Using pattern recognition of RNA with small molecules (PRRSM) with fluorescent RNA chemosensors and aminoglycosides, we reveal the impact of changing environmental conditions on the differentiation of a range of RNA structures as well as the ability to pre ... Full text Cite

Discovery of Key Physicochemical, Structural, and Spatial Properties of RNA‐Targeted Bioactive Ligands

Journal Article Angewandte Chemie · October 16, 2017 AbstractWhile a myriad non‐coding RNAs are known to be essential in cellular processes and misregulated in diseases, the development of RNA‐targeted small molecule probes has met with limited success. To elucidate the guidi ... Full text Cite

Discovery of Key Physicochemical, Structural, and Spatial Properties of RNA-Targeted Bioactive Ligands.

Journal Article Angewandte Chemie (International ed. in English) · October 2017 While a myriad non-coding RNAs are known to be essential in cellular processes and misregulated in diseases, the development of RNA-targeted small molecule probes has met with limited success. To elucidate the guiding principles for selective small molecul ... Full text Cite

Amiloride as a new RNA-binding scaffold with activity against HIV-1 TAR.

Journal Article Medchemcomm · May 1, 2017 Diversification of RNA-targeted scaffolds offers great promise in the search for selective ligands of therapeutically relevant RNA such as HIV-1 TAR. We herein report the establishment of amiloride as a novel RNA-binding scaffold along with synthetic route ... Full text Link to item Cite

Small Molecule-Based Pattern Recognition To Classify RNA Structure.

Journal Article Journal of the American Chemical Society · January 2017 Three-dimensional RNA structures are notoriously difficult to determine, and the link between secondary structure and RNA conformation is only beginning to be understood. These challenges have hindered the identification of guiding principles for small mol ... Full text Cite

Biochemical Methods To Investigate lncRNA and the Influence of lncRNA:Protein Complexes on Chromatin.

Journal Article Biochemistry · March 2016 Long noncoding RNAs (lncRNAs), defined as nontranslated transcripts greater than 200 nucleotides in length, are often differentially expressed throughout developmental stages, tissue types, and disease states. The identification, visualization, and suppres ... Full text Cite

KDM1 class flavin-dependent protein lysine demethylases.

Journal Article Biopolymers · July 2015 Flavin-dependent, lysine-specific protein demethylases (KDM1s) are a subfamily of amine oxidases that catalyze the selective posttranslational oxidative demethylation of methyllysine side chains within protein and peptide substrates. KDM1s participate in t ... Full text Cite

Synthetic receptors for oligonucleotides and nucleic acids

Journal Article Monographs in Supramolecular Chemistry · January 1, 2015 Cite

Tumor Repression of VCaP Xenografts by a Pyrrole-Imidazole Polyamide.

Journal Article PloS one · January 2015 Pyrrole-imidazole (Py-Im) polyamides are high affinity DNA-binding small molecules that can inhibit protein-DNA interactions. In VCaP cells, a human prostate cancer cell line overexpressing both AR and the TMPRSS2-ERG gene fusion, an androgen response elem ... Full text Cite

Activity of a Py-Im polyamide targeted to the estrogen response element.

Journal Article Molecular cancer therapeutics · May 2013 Pyrrole-imidazole (Py-Im) polyamides are a class of programmable DNA minor groove binders capable of modulating the activity of DNA-binding proteins and affecting changes in gene expression. Estrogen receptor alpha (ERα) is a ligand-activated hormone recep ... Full text Cite

Gene expression changes in a tumor xenograft by a pyrrole-imidazole polyamide.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · October 2012 Gene regulation by DNA binding small molecules could have important therapeutic applications. This study reports the investigation of a DNA-binding pyrrole-imidazole polyamide targeted to bind the DNA sequence 5'-WGGWWW-3' with reference to its potency in ... Full text Cite

Characterization and solubilization of pyrrole-imidazole polyamide aggregates.

Journal Article Journal of medicinal chemistry · June 2012 To optimize the biological activity of pyrrole-imidazole polyamide DNA-binding molecules, we characterized the aggregation propensity of these compounds through dynamic light scattering and fractional solubility analysis. Nearly all studied polyamides were ... Full text Cite

Pharmacokinetics of Py-Im polyamides depend on architecture: cyclic versus linear.

Journal Article Journal of the American Chemical Society · May 2012 The pharmacokinetic properties of three pyrrole-imidazole (Py-Im) polyamides of similar size and Py-Im content but different shape were studied in the mouse. Remarkably, hairpin and cyclic oligomers programmed for the same DNA sequence 5'-WGGWWW-3' display ... Full text Cite

Chemical functionalization of oligodeoxynucleotides with multiple boronic acids for the polyvalent binding of saccharides.

Journal Article Bioconjugate chemistry · March 2011 A novel saccharide host containing four boronic acid recognition units on a single DNA duplex terminus was constructed. This construct allowed boronic acid sugar recognition in the context of double-stranded DNA to be established while highlighting the ben ... Full text Cite

Boronic acid porphyrin receptor for ginsenoside sensing.

Journal Article Organic letters · November 2010 Ginsenoside detection was pursued through the design of a porphyrin receptor containing two boronic acid units. This receptor was found to undergo different degrees of fluorescence quenching with five ginsenoside guests and an acylated derivative. The tren ... Full text Cite

Algorithms for the determination of binding constants and enantiomeric excess in complex host: Guest equilibria using optical measurements

Journal Article New Journal of Chemistry · January 1, 2010 The determination of binding constants is central to many areas of research, supramolecular chemistry in particular. Traditional nonlinear regression analysis, however, cannot be applied to complex systems unless certain assumptions are undertaken, which o ... Full text Cite

Probing intramolecular B-N interactions in ortho-aminomethyl arylboronic acids

Journal Article Journal of Organic Chemistry · June 5, 2009 (Chemical Equation Presented) This work investigates the interplay between the intramolecular B-N dative bonding and solvent insertion in various ortho-methylamino arylboronic acids in protic media. 11B NMR experiments were conducted to study the effect th ... Full text Cite

Sequencing and characterization of oligosaccharides using infrared multiphoton dissociation and boronic acid derivatization in a quadrupole ion trap.

Journal Article Journal of the American Society for Mass Spectrometry · December 2007 A simplified method for determining the sequence and branching of oligosaccharides using infrared multiphoton dissociation (IRMPD) in a quadrupole ion trap (QIT) is described. An IR-active boronic acid (IRABA) reagent is used to derivatize the oligosacchar ... Full text Cite

Porphyrenediynes: synthesis and cyclization of meso-enediynylporphyrins

Journal Article Tetrahedron Letters · January 22, 2007 Synthetic methodology to prepare porphyrinylethynyl enediynes has been developed. Compared to phenylethynyl derivatives, a bulky porphyrinic substituent on the alkyne significantly increases the thermal barrier toward Bergman cyclization and leads to multi ... Full text Cite

Chemical and electrochemical oxidation of N-alkyl cyclo[n]-pyrroles

Journal Article Journal of Porphyrins and Phthalocyanines · January 1, 2006 Cyclo[n]pyrroles (n = 6, 7, and 8), are expanded porphyrins that lack bridging meso carbon atoms. They adopt conformations that are near-planar and show features that are consistent with global aromaticity. In previous work, involving studies of cyclo[8]py ... Full text Cite