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Veríssimo NVP, Mussagy CU, Bento HBS, Pereira JFB, Santos-Ebinuma VDC. Ionic liquids and deep eutectic solvents for the stabilization of biopharmaceuticals: A review. Biotechnol Adv 2024; 71:108316. [PMID: 38199490 DOI: 10.1016/j.biotechadv.2024.108316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/12/2024]
Abstract
Biopharmaceuticals have allowed the control of previously untreatable diseases. However, their low solubility and stability still hinder their application, transport, and storage. Hence, researchers have applied different compounds to preserve and enhance the delivery of biopharmaceuticals, such as ionic liquids (ILs) and deep eutectic solvents (DESs). Although the biopharmaceutical industry can employ various substances for enhancing formulations, their effect will change depending on the properties of the target biomolecule and environmental conditions. Hence, this review organized the current state-of-the-art on the application of ILs and DESs to stabilize biopharmaceuticals, considering the properties of the biomolecules, ILs, and DESs classes, concentration range, types of stability, and effect. We also provided a critical discussion regarding the potential utilization of ILs and DESs in pharmaceutical formulations, considering the restrictions in this field, as well as the advantages and drawbacks of these substances for medical applications. Overall, the most applied IL and DES classes for stabilizing biopharmaceuticals were cholinium-, imidazolium-, and ammonium-based, with cholinium ILs also employed to improve their delivery. Interestingly, dilute and concentrated ILs and DESs solutions presented similar results regarding the stabilization of biopharmaceuticals. With additional investigation, ILs and DESs have the potential to overcome current challenges in biopharmaceutical formulation.
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Affiliation(s)
- Nathalia Vieira Porphirio Veríssimo
- Department of Bioprocess Engineering and Biotechnology, School of Pharmaceutical Sciences, São Paulo State University, CEP: 14801-902 Araraquara, SP, Brazil; Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences, São Paulo University, CEP: 14040-020 Ribeirão Preto, SP, Brazil.
| | - Cassamo Usemane Mussagy
- Escuela de Agronomía, Facultad de Ciencias Agronómicas y de los Alimentos, Pontificia Universidad Católica de Valparaíso, Quillota 2260000, Chile.
| | - Heitor Buzetti Simões Bento
- Department of Bioprocess Engineering and Biotechnology, School of Pharmaceutical Sciences, São Paulo State University, CEP: 14801-902 Araraquara, SP, Brazil.
| | | | - Valéria de Carvalho Santos-Ebinuma
- Department of Bioprocess Engineering and Biotechnology, School of Pharmaceutical Sciences, São Paulo State University, CEP: 14801-902 Araraquara, SP, Brazil.
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2
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Stulz R, Lerche M, Luige O, Taylor A, Geschwindner S, Ghidini A. An enhanced biophysical screening strategy to investigate the affinity of ASOs for their target RNA. RSC Chem Biol 2023; 4:1123-1130. [PMID: 38033730 PMCID: PMC10685824 DOI: 10.1039/d3cb00072a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 10/03/2023] [Indexed: 12/02/2023] Open
Abstract
The recent and rapid increase in the discovery of new RNA therapeutics has created the perfect terrain to explore an increasing number of novel targets. In particular, antisense oligonucleotides (ASOs) have long held the promise of an accelerated and effective drug design compared to other RNA-based therapeutics. Although ASOs in silico design has advanced distinctively in the past years, especially thanks to the several predictive frameworks for RNA folding, it is somehow limited by the wide approximation of calculating sequence affinity based on RNA-RNA/DNA sequences. None of the ASO modifications are taken into consideration, losing hybridization information particularly fundamental to ASOs that elicit their function through RNase H1-mediated mechanisms. Here we present an inexpensive and enhanced biophysical screening strategy to investigate the affinity of ASOs for their target RNA using several biophysical techniques such as high throughput differential scanning fluorimetry (DSF), circular dichroism (CD), isothermal calorimetry (ITC), surface plasmon resonance (SPR) and small-angle X-ray scattering (SAXS).
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Affiliation(s)
- Rouven Stulz
- Oligonucleotide Chemistry, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Gothenburg Sweden
| | - Michael Lerche
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca Gothenburg Sweden
| | - Olivia Luige
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo Huddinge 14183 Sweden
- Early Chemical Development, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca Gothenburg Sweden
| | - Agnes Taylor
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca Gothenburg Sweden
| | - Stefan Geschwindner
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Gothenburg Sweden
| | - Alice Ghidini
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Gothenburg Sweden
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3
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Kallert E, Behrendt M, Frey A, Kersten C, Barthels F. Non-covalent dyes in microscale thermophoresis for studying RNA ligand interactions and modifications. Chem Sci 2023; 14:9827-9837. [PMID: 37736627 PMCID: PMC10510756 DOI: 10.1039/d3sc02993j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/27/2023] [Indexed: 09/23/2023] Open
Abstract
Microscale Thermophoresis (MST) is a powerful biophysical technique that measures the mobility of biomolecules in response to a temperature gradient, making it useful for investigating the interactions between biological molecules. This study presents a novel methodology for studying RNA-containing samples using non-covalent nucleic acid-sensitive dyes in MST. This "mix-and-measure" protocol uses non-covalent dyes, such as those from the Syto or Sybr series, which lead to the statistical binding of one fluorophore per RNA oligo showing key advantages over traditional covalent labelling approaches. This new approach has been successfully used to study the binding of ligands to RNA molecules (e.g., SAM- and PreQ1 riboswitches) and the identification of modifications (e.g., m6A) in short RNA oligos which can be written by the RNA methyltransferase METTL3/14.
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Affiliation(s)
- Elisabeth Kallert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University of Mainz Staudingerweg 5 55128 Mainz Germany
| | - Malte Behrendt
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University of Mainz Staudingerweg 5 55128 Mainz Germany
| | - Ariane Frey
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University of Mainz Staudingerweg 5 55128 Mainz Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University of Mainz Staudingerweg 5 55128 Mainz Germany
| | - Fabian Barthels
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University of Mainz Staudingerweg 5 55128 Mainz Germany
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4
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Llowarch P, Usselmann L, Ivanov D, Holdgate GA. Thermal unfolding methods in drug discovery. BIOPHYSICS REVIEWS 2023; 4:021305. [PMID: 38510342 PMCID: PMC10903397 DOI: 10.1063/5.0144141] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 04/13/2023] [Indexed: 03/22/2024]
Abstract
Thermal unfolding methods, applied in both isolated protein and cell-based settings, are increasingly used to identify and characterize hits during early drug discovery. Technical developments over recent years have facilitated their application in high-throughput approaches, and they now are used more frequently for primary screening. Widespread access to instrumentation and automation, the ability to miniaturize, as well as the capability and capacity to generate the appropriate scale and quality of protein and cell reagents have all played a part in these advances. As the nature of drug targets and approaches to their modulation have evolved, these methods have broadened our ability to provide useful chemical start points. Target proteins without catalytic function, or those that may be difficult to express and purify, are amenable to these methods. Here, we provide a review of the applications of thermal unfolding methods applied in hit finding during early drug discovery.
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Affiliation(s)
- Poppy Llowarch
- High Throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Laura Usselmann
- High Throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Delyan Ivanov
- High Throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Geoffrey A. Holdgate
- High Throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
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5
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Real-Hohn A, Groznica M, Kontaxis G, Zhu R, Chaves OA, Vazquez L, Hinterdorfer P, Kowalski H, Blaas D. Stabilization of the Quadruplex-Forming G-Rich Sequences in the Rhinovirus Genome Inhibits Uncoating-Role of Na + and K . Viruses 2023; 15:1003. [PMID: 37112983 PMCID: PMC10141139 DOI: 10.3390/v15041003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Rhinoviruses (RVs) are the major cause of common cold, a respiratory disease that generally takes a mild course. However, occasionally, RV infection can lead to serious complications in patients debilitated by other ailments, e.g., asthma. Colds are a huge socioeconomic burden as neither vaccines nor other treatments are available. The many existing drug candidates either stabilize the capsid or inhibit the viral RNA polymerase, the viral proteinases, or the functions of other non-structural viral proteins; however, none has been approved by the FDA. Focusing on the genomic RNA as a possible target for antivirals, we asked whether stabilizing RNA secondary structures might inhibit the viral replication cycle. These secondary structures include G-quadruplexes (GQs), which are guanine-rich sequence stretches forming planar guanine tetrads via Hoogsteen base pairing with two or more of them stacking on top of each other; a number of small molecular drug candidates increase the energy required for their unfolding. The propensity of G-quadruplex formation can be predicted with bioinformatics tools and is expressed as a GQ score. Synthetic RNA oligonucleotides derived from the RV-A2 genome with sequences corresponding to the highest and lowest GQ scores indeed exhibited characteristics of GQs. In vivo, the GQ-stabilizing compounds, pyridostatin and PhenDC3, interfered with viral uncoating in Na+ but not in K+-containing phosphate buffers. The thermostability studies and ultrastructural imaging of protein-free viral RNA cores suggest that Na+ keeps the encapsulated genome more open, allowing PDS and PhenDC3 to diffuse into the quasi-crystalline RNA and promote the formation and/or stabilization of GQs; the resulting conformational changes impair RNA unraveling and release from the virion. Preliminary reports have been published.
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Affiliation(s)
- Antonio Real-Hohn
- Center of Medical Biochemistry, Vienna Biocenter, Max Perutz Laboratories, Medical University of Vienna, Dr. Bohr Gasse 9/3, 1030 Vienna, Austria; (M.G.)
| | - Martin Groznica
- Center of Medical Biochemistry, Vienna Biocenter, Max Perutz Laboratories, Medical University of Vienna, Dr. Bohr Gasse 9/3, 1030 Vienna, Austria; (M.G.)
- Institut Pasteur, CEDEX 15, 75724 Paris, France
| | - Georg Kontaxis
- Vienna Biocenter, Max Perutz Laboratories, Department of Structural and Computational Biology, University of Vienna, Campus Vienna BioCenter 5, 1030 Vienna, Austria;
| | - Rong Zhu
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, 4020 Linz, Austria; (R.Z.)
| | - Otávio Augusto Chaves
- Immunopharmacology Laboratory, Oswaldo Cruz Institute (IOC/Fiocruz), Av. Brasil, 4365, Rio de Janeiro 21040-360, Brazil
| | - Leonardo Vazquez
- Immunopharmacology Laboratory, Oswaldo Cruz Institute (IOC/Fiocruz), Av. Brasil, 4365, Rio de Janeiro 21040-360, Brazil
| | - Peter Hinterdorfer
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, 4020 Linz, Austria; (R.Z.)
| | - Heinrich Kowalski
- Center of Medical Biochemistry, Vienna Biocenter, Max Perutz Laboratories, Medical University of Vienna, Dr. Bohr Gasse 9/3, 1030 Vienna, Austria; (M.G.)
| | - Dieter Blaas
- Center of Medical Biochemistry, Vienna Biocenter, Max Perutz Laboratories, Medical University of Vienna, Dr. Bohr Gasse 9/3, 1030 Vienna, Austria; (M.G.)
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6
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Furtado D, Cortez-Jugo C, Hung YH, Bush AI, Caruso F. mRNA Treatment Rescues Niemann-Pick Disease Type C1 in Patient Fibroblasts. Mol Pharm 2022; 19:3987-3999. [PMID: 36125338 DOI: 10.1021/acs.molpharmaceut.2c00463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Messenger RNA (mRNA) holds great potential as a disease-modifying treatment for a wide array of monogenic disorders. Niemann-Pick disease type C1 (NP-C1) is an ultrarare monogenic disease that arises due to loss-of-function mutations in the NPC1 gene, resulting in the entrapment of unesterified cholesterol in the lysosomes of affected cells and a subsequent reduction in their capacity for cholesterol esterification. This causes severe damage to various organs including the brain, liver, and spleen. In this work, we describe the use of NPC1-encoded mRNA to rescue the protein insufficiency and pathogenic phenotype caused by biallelic NPC1 mutations in cultured fibroblasts derived from an NP-C1 patient. We first evaluated engineering strategies for the generation of potent mRNAs capable of eliciting high protein expression across multiple cell types. We observed that "GC3" codon optimization, coupled with N1-methylpseudouridine base modification, yielded an mRNA that was approximately 1000-fold more potent than wild-type, unmodified mRNA in a luciferase reporter assay and consistently superior to other mRNA variants. Our data suggest that the improved expression associated with this design strategy was due in large part to the increased secondary structure of the designed mRNAs. Both codon optimization and base modification appear to contribute to increased secondary structure. Applying these principles to the engineering of NPC1-encoded mRNA, we observed a normalization in NPC1 protein levels after mRNA treatment, as well as a rescue of the mutant phenotype. Specifically, mRNA treatment restored the cholesterol esterification capacity of patient cells to wild-type levels and induced a significant reduction in both unesterified cholesterol levels (>57% reduction compared to Lipofectamine-treated control in a cholesterol esterification assay) and lysosome size (157 μm2 reduction compared to Lipofectamine-treated control). These findings show that engineered mRNA can correct the deficit caused by NPC1 mutations. More broadly, they also serve to further validate the potential of this technology to correct diseases associated with loss-of-function mutations in genes coding for large, complex, intracellular proteins.
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Affiliation(s)
- Denzil Furtado
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Christina Cortez-Jugo
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ya Hui Hung
- Melbourne Dementia Research Centre, The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Ashley I Bush
- Melbourne Dementia Research Centre, The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Frank Caruso
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
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7
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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 Chem Biol 2022; 17:2437-2447. [PMID: 35984959 PMCID: PMC9741926 DOI: 10.1021/acschembio.2c00124] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
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 tools for therapeutically targeting and/or uncovering the pathways associated with these RNA motifs. This potential has been highlighted by targeting of the triple helix present at the 3'-end of the noncoding RNA MALAT1, a transcript implicated in several human diseases. This triplex has been reported to decrease the susceptibility of the transcript to degradation and promote its cellular accumulation. While small molecules have been shown to bind to and impact the stability of the MALAT1 triple helix, the small molecule properties that lead to these structural modulations are not well understood. We designed a library utilizing the diminazene scaffold, which is underexplored but precedented for nucleic acid binding, to target the MALAT1 triple helix. We employed multiple assays to holistically assess what parameters, if any, could predict the small molecule affinity and effect on triplex stability. We designed and/or optimized competition, calorimetry, and thermal shift assays as well as an enzymatic degradation assay, the latter of which led to the discovery of bidirectional modulators of triple helix stability within the scaffold-centric library. Determination of quantitative structure-activity relationships afforded predictive models for both affinity- and stability-based assays. This work establishes a suite of powerful orthogonal biophysical tools for the evaluation of small molecule:RNA triplex interactions that generate predictive models and will allow small molecule interrogation of the growing body of disease-associated RNA triple helices.
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Affiliation(s)
- Martina Zafferani
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27705, United States
| | - Justin G Martyr
- Department of Biochemistry, Duke University School of Medicine, Nanaline H. Duke, Durham, North Carolina, 27710, United States
| | - Dhanasheel Muralidharan
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27705, United States
| | - Nadeska I Montalvan
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27705, United States
| | - Zhengguo Cai
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27705, United States
| | - Amanda E Hargrove
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27705, United States
- Department of Biochemistry, Duke University School of Medicine, Nanaline H. Duke, Durham, North Carolina, 27710, United States
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8
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Barthels F, Hammerschmidt SJ, Fischer TR, Zimmer C, Kallert E, Helm M, Kersten C, Schirmeister T. A low-cost 3D-printable differential scanning fluorometer for protein and RNA melting experiments. HARDWAREX 2022; 11:e00256. [PMID: 35509940 PMCID: PMC9058602 DOI: 10.1016/j.ohx.2022.e00256] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/02/2021] [Accepted: 01/01/2022] [Indexed: 06/14/2023]
Abstract
Differential scanning fluorimetry (DSF) is a widely used biophysical technique with applications to drug discovery and protein biochemistry. DSF experiments are commonly performed in commercial real-time polymerase chain reaction (qPCR) thermal cyclers or nanoDSF instruments. Here, we report the construction, validation, and example applications of an open-source DSF system for 176 €, which, in addition to protein-DSF experiments, also proved to be a versatile biophysical instrument for less conventional RNA-DSF experiments. Using 3D-printed parts made of polyoxymethylene, we were able to fabricate a thermostable machine chassis for protein-melting experiments. The combination of blue high-power LEDs as the light source and stage light foil as filter components was proven to be a reliable and affordable alternative to conventional optics equipment for the detection of SYPRO Orange or Sybr Gold fluorescence. The ESP32 microcontroller is the core piece of this openDSF instrument, while the in-built I2S interface was found to be a powerful analog-to-digital converter for fast acquisition of fluorescence and temperature data. Airflow heating and inline temperature control by thermistors enabled high-accuracy temperature management in PCR tubes (±0.1 °C) allowing us to perform high-resolution thermal shift assays (TSA) from exemplary biological applications.
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9
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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 Chem Biol 2022; 3:905-915. [PMID: 35866161 PMCID: PMC9257624 DOI: 10.1039/d2cb00015f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/25/2022] [Indexed: 11/21/2022] Open
Abstract
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 opportunities to both decode these cellular roles and develop therapeutics, however there are few examples of small molecules that target biologically relevant RNA tertiary structures. While RNA triple helices are a particularly attractive target, discovery of triple helix modulators has been hindered by the lack of correlation between small molecule affinity and effect on structural modulation, thereby limiting the utility of affinity-based screening as a primary filtering method. To address this challenge, we developed a high-throughput RT-qPCR screening platform that reports on the effect of mutations and additives, such as small molecules, on the stability of triple helices. Using the 3′-end of the oncogenic long non-coding RNA MALAT1 as a proof-of-concept, we demonstrated the applicability of both a two-step and a one-pot method to assess the impact of mutations and small molecules on the stability of the triple helix. We demonstrated the adaptability of the assay to diverse RNA tertiary structures by applying it to the SARS-CoV-2 pseudoknot, a key viral RNA structure recently identified as an attractive therapeutic target for the development of antivirals. Employment of a functional high-throughput assay as a primary screen will significantly expedite the discovery of probes that modulate the structural landscape of RNA structures and, consequently, help gain insight into the roles of these pervasive structures. RT-qPCR can be harnessed as a small molecule screening platform to read out the effect of small molecules on the structural stability of a variety of RNA targets.![]()
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Affiliation(s)
- Martina Zafferani
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27705, USA
| | | | - Nadeska I. Montalvan
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27705, USA
| | - Amanda E. Hargrove
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27705, USA
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10
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Alexander Harrison J, Pruška A, Oganesyan I, Bittner P, Zenobi R. Temperature-Controlled Electrospray Ionization: Recent Progress and Applications. Chemistry 2021; 27:18015-18028. [PMID: 34632657 PMCID: PMC9298390 DOI: 10.1002/chem.202102474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Indexed: 11/11/2022]
Abstract
Native electrospray ionization (ESI) and nanoelectrospray ionization (nESI) allow researchers to analyze intact biomolecules and their complexes by mass spectrometry (MS). The data acquired using these soft ionization techniques provide a snapshot of a given biomolecules structure in solution. Over the last thirty years, several nESI and ESI sources capable of controlling spray solution temperature have been developed. These sources can be used to elucidate the thermodynamics of a given analyte, as well as provide structural information that cannot be readily obtained by other, more commonly used techniques. This review highlights how the field of temperature-controlled mass spectrometry has developed.
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Affiliation(s)
- Julian Alexander Harrison
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland
| | - Adam Pruška
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland
| | - Irina Oganesyan
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland
| | - Philipp Bittner
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland
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11
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De Bisschop G, Allouche D, Frezza E, Masquida B, Ponty Y, Will S, Sargueil B. Progress toward SHAPE Constrained Computational Prediction of Tertiary Interactions in RNA Structure. Noncoding RNA 2021; 7:71. [PMID: 34842779 PMCID: PMC8628965 DOI: 10.3390/ncrna7040071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 01/04/2023] Open
Abstract
As more sequencing data accumulate and novel puzzling genetic regulations are discovered, the need for accurate automated modeling of RNA structure increases. RNA structure modeling from chemical probing experiments has made tremendous progress, however accurately predicting large RNA structures is still challenging for several reasons: RNA are inherently flexible and often adopt many energetically similar structures, which are not reliably distinguished by the available, incomplete thermodynamic model. Moreover, computationally, the problem is aggravated by the relevance of pseudoknots and non-canonical base pairs, which are hardly predicted efficiently. To identify nucleotides involved in pseudoknots and non-canonical interactions, we scrutinized the SHAPE reactivity of each nucleotide of the 188 nt long lariat-capping ribozyme under multiple conditions. Reactivities analyzed in the light of the X-ray structure were shown to report accurately the nucleotide status. Those that seemed paradoxical were rationalized by the nucleotide behavior along molecular dynamic simulations. We show that valuable information on intricate interactions can be deduced from probing with different reagents, and in the presence or absence of Mg2+. Furthermore, probing at increasing temperature was remarkably efficient at pointing to non-canonical interactions and pseudoknot pairings. The possibilities of following such strategies to inform structure modeling software are discussed.
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Affiliation(s)
- Grégoire De Bisschop
- Université de Paris, CNRS, UMR 8038/CiTCoM, F-75006 Paris, France; (G.D.B.); (D.A.); (E.F.)
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Delphine Allouche
- Université de Paris, CNRS, UMR 8038/CiTCoM, F-75006 Paris, France; (G.D.B.); (D.A.); (E.F.)
- Institut Necker-Enfants Malades (INEM), Inserm U1151, 156 rue de Vaugirard, CEDEX 15, 75015 Paris, France
| | - Elisa Frezza
- Université de Paris, CNRS, UMR 8038/CiTCoM, F-75006 Paris, France; (G.D.B.); (D.A.); (E.F.)
| | - Benoît Masquida
- Université de Strasbourg, CNRS UMR7156 GMGM, 67084 Strasbourg, France;
| | - Yann Ponty
- Ecole Polytechnique, CNRS UMR 7161, LIX, 91120 Palaiseau, France; (Y.P.); (S.W.)
| | - Sebastian Will
- Ecole Polytechnique, CNRS UMR 7161, LIX, 91120 Palaiseau, France; (Y.P.); (S.W.)
| | - Bruno Sargueil
- Université de Paris, CNRS, UMR 8038/CiTCoM, F-75006 Paris, France; (G.D.B.); (D.A.); (E.F.)
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12
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Rapisarda A, Bargiela A, Llamusi B, Pont I, Estrada-Tejedor R, Garcia-España E, Artero R, Perez-Alonso M. Defined D-hexapeptides bind CUG repeats and rescue phenotypes of myotonic dystrophy myotubes in a Drosophila model of the disease. Sci Rep 2021; 11:19417. [PMID: 34593893 PMCID: PMC8484449 DOI: 10.1038/s41598-021-98866-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 09/14/2021] [Indexed: 11/17/2022] Open
Abstract
In Myotonic Dystrophy type 1 (DM1), a non-coding CTG repeats rare expansion disease; toxic double-stranded RNA hairpins sequester the RNA-binding proteins Muscleblind-like 1 and 2 (MBNL1 and 2) and trigger other DM1-related pathogenesis pathway defects. In this paper, we characterize four d-amino acid hexapeptides identified together with abp1, a peptide previously shown to stabilize CUG RNA in its single-stranded conformation. With the generalized sequence cpy(a/t)(q/w)e, these related peptides improved three MBNL-regulated exon inclusions in DM1-derived cells. Subsequent experiments showed that these compounds generally increased the relative expression of MBNL1 and its nuclear-cytoplasmic distribution, reduced hyperactivated autophagy, and increased the percentage of differentiated (Desmin-positive) cells in vitro. All peptides rescued atrophy of indirect flight muscles in a Drosophila model of the disease, and partially rescued muscle function according to climbing and flight tests. Investigation of their mechanism of action supports that all four compounds can bind to CUG repeats with slightly different association constant, but binding did not strongly influence the secondary structure of the toxic RNA in contrast to abp1. Finally, molecular modeling suggests a detailed view of the interactions of peptide-CUG RNA complexes useful in the chemical optimization of compounds.
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Affiliation(s)
- Anna Rapisarda
- Department of Genetics, University Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Dr. Moliner, 50, 46100, Burjasot, Valencia, Spain.,Translational Genomics Group, INCLIVA Biomedical Research Institute, 46010, Valencia, Spain
| | - Ariadna Bargiela
- Department of Genetics, University Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Dr. Moliner, 50, 46100, Burjasot, Valencia, Spain. .,Translational Genomics Group, INCLIVA Biomedical Research Institute, 46010, Valencia, Spain.
| | - Beatriz Llamusi
- Department of Genetics, University Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Dr. Moliner, 50, 46100, Burjasot, Valencia, Spain.,Translational Genomics Group, INCLIVA Biomedical Research Institute, 46010, Valencia, Spain.,Arthex Biotech S.L. Catedrático Agustín Escardino 9, Parc Scientific University of Valencia, Paterna, Valencia, Spain
| | - Isabel Pont
- Instituto de Ciencia Molecular (ICMol), Departamento de Química Inorgánica, C. Catedrático José Beltrán 2, Universidad de Valencia, 46980, Paterna, Spain
| | | | - Enrique Garcia-España
- Instituto de Ciencia Molecular (ICMol), Departamento de Química Inorgánica, C. Catedrático José Beltrán 2, Universidad de Valencia, 46980, Paterna, Spain
| | - Ruben Artero
- Department of Genetics, University Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Dr. Moliner, 50, 46100, Burjasot, Valencia, Spain.,Translational Genomics Group, INCLIVA Biomedical Research Institute, 46010, Valencia, Spain
| | - Manuel Perez-Alonso
- Department of Genetics, University Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Dr. Moliner, 50, 46100, Burjasot, Valencia, Spain.,Translational Genomics Group, INCLIVA Biomedical Research Institute, 46010, Valencia, Spain
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13
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Lundquist KP, Panchal V, Gotfredsen CH, Brenk R, Clausen MH. Fragment-Based Drug Discovery for RNA Targets. ChemMedChem 2021; 16:2588-2603. [PMID: 34101375 DOI: 10.1002/cmdc.202100324] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Indexed: 12/26/2022]
Abstract
Rapid development within the fields of both fragment-based drug discovery (FBDD) and medicinal targeting of RNA provides possibilities for combining technologies and methods in novel ways. This review provides an overview of fragment-based screening (FBS) against RNA targets, including a discussion of the most recently used screening and hit validation methods such as NMR spectroscopy, X-ray crystallography, and virtual screening methods. A discussion of fragment library design based on research from small-molecule RNA binders provides an overview on both the currently limited guidelines within RNA-targeting fragment library design, and future possibilities. Finally, future perspectives are provided on screening and hit validation methods not yet used in combination with both fragment screening and RNA targets.
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Affiliation(s)
- Kasper P Lundquist
- Center for Nanomedicine and Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kgs. Lyngby, Denmark
| | - Vipul Panchal
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5020, Bergen, Norway
| | - Charlotte H Gotfredsen
- NMR Center ⋅ DTU, Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kgs. Lyngby, Denmark
| | - Ruth Brenk
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5020, Bergen, Norway
| | - Mads H Clausen
- Center for Nanomedicine and Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kgs. Lyngby, Denmark
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14
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Kawaguchi D, Kodama A, Abe N, Takebuchi K, Hashiya F, Tomoike F, Nakamoto K, Kimura Y, Shimizu Y, Abe H. Phosphorothioate Modification of mRNA Accelerates the Rate of Translation Initiation to Provide More Efficient Protein Synthesis. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Daisuke Kawaguchi
- Chemistry Department Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Ayumi Kodama
- Chemistry Department Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Naoko Abe
- Chemistry Department Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
- Research Center for Materials Science Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Kei Takebuchi
- Chemistry Department Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Fumitaka Hashiya
- Research Center for Materials Science Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Fumiaki Tomoike
- Research Center for Materials Science Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Kosuke Nakamoto
- Chemistry Department Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Yasuaki Kimura
- Chemistry Department Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Yoshihiro Shimizu
- Biodynamics Research Center (BDR) RIKEN 6-2-3, Furuedai Suita Osaka 565-0874 Japan
| | - Hiroshi Abe
- Chemistry Department Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
- Research Center for Materials Science Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
- CREST (Japan) Science and Technology Agency 7, Gobancho, Chiyoda-ku Tokyo 102-0076 Japan
- Institute for Glyco-core Research Tokai National Higher Education and Research System Furo-cho, Chikusa-ku Nagoya Aichi 464-8601 Japan
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15
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Haniff HS, Knerr L, Chen JL, Disney MD, Lightfoot HL. Target-Directed Approaches for Screening Small Molecules against RNA Targets. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2020; 25:869-894. [PMID: 32419578 PMCID: PMC7442623 DOI: 10.1177/2472555220922802] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
RNA molecules have a variety of cellular functions that can drive disease pathologies. They are without a doubt one of the most intriguing yet controversial small-molecule drug targets. The ability to widely target RNA with small molecules could be revolutionary, once the right tools, assays, and targets are selected, thereby defining which biomolecules are targetable and what constitutes drug-like small molecules. Indeed, approaches developed over the past 5-10 years have changed the face of small molecule-RNA targeting by addressing historic concerns regarding affinity, selectivity, and structural dynamics. Presently, selective RNA-protein complex stabilizing drugs such as branaplam and risdiplam are in clinical trials for the modulation of SMN2 splicing, compounds identified from phenotypic screens with serendipitous outcomes. Fully developing RNA as a druggable target will require a target engagement-driven approach, and evolving chemical collections will be important for the industrial development of this class of target. In this review we discuss target-directed approaches that can be used to identify RNA-binding compounds and the chemical knowledge we have today of small-molecule RNA binders.
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Affiliation(s)
- Hafeez S. Haniff
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Laurent Knerr
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Jonathan L. Chen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
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16
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Donlic A, Zafferani M, Padroni G, Puri M, Hargrove A. Regulation of MALAT1 triple helix stability and in vitro degradation by diphenylfurans. Nucleic Acids Res 2020; 48:7653-7664. [PMID: 32667657 PMCID: PMC7430642 DOI: 10.1093/nar/gkaa585] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 05/18/2020] [Accepted: 07/09/2020] [Indexed: 12/23/2022] Open
Abstract
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:RNA recognition. To elucidate fundamental recognition principles and structure-function relationships, we designed and synthesized nine novel analogs of a diphenylfuran-based small molecule DPFp8, a previously identified lead binder of MALAT1. We investigated the role of recognition modalities in binding and in silico studies along with the relationship between affinity, stability and in vitro enzymatic degradation of the triple helix. Specifically, molecular docking studies identified patterns driving affinity and selectivity, including limited ligand flexibility, as observed by ligand preorganization and 3D shape complementarity for the binding pocket. The use of differential scanning fluorimetry allowed rapid evaluation of ligand-induced thermal stabilization of the triple helix, which correlated with decreased in vitro degradation of this structure by the RNase R exonuclease. The magnitude of stabilization was related to binding mode and selectivity between the triple helix and its precursor stem loop structure. Together, this work demonstrates the value of scaffold-based libraries in revealing recognition principles and of raising broadly applicable strategies, including functional assays, for small molecule-RNA targeting.
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Affiliation(s)
- Anita Donlic
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
| | - Martina Zafferani
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
| | - Giacomo Padroni
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
| | - Malavika Puri
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
| | - Amanda E Hargrove
- To whom correspondence should be addressed. Tel: +1 919 660 1522; Fax: +1 919 660 1522;
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17
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Kawaguchi D, Kodama A, Abe N, Takebuchi K, Hashiya F, Tomoike F, Nakamoto K, Kimura Y, Shimizu Y, Abe H. Phosphorothioate Modification of mRNA Accelerates the Rate of Translation Initiation to Provide More Efficient Protein Synthesis. Angew Chem Int Ed Engl 2020; 59:17403-17407. [PMID: 32627275 DOI: 10.1002/anie.202007111] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Indexed: 01/19/2023]
Abstract
Messenger RNAs (mRNAs) with phosphorothioate modification (PS-mRNA) to the phosphate site of A, G, C, and U with all 16 possible combinations were prepared, and the translation reaction was evaluated using an E. coli cell-free translation system. Protein synthesis from PS-mRNA increased in 12 of 15 patterns when compared with that of unmodified mRNA. The protein yield increased 22-fold when the phosphorothioate modification at A/C sites was introduced into the region from the 5'-end to the initiation codon. Single-turnover analysis of PS-mRNA translation showed that phosphorothioate modification increases the number of translating ribosomes, thus suggesting that the rate of translation initiation (rate of ribosome complex formation) is positively affected by the modification. The method provides a new strategy for improving translation by using non-natural mRNA.
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Affiliation(s)
- Daisuke Kawaguchi
- Chemistry Department, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Ayumi Kodama
- Chemistry Department, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Naoko Abe
- Chemistry Department, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.,Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Kei Takebuchi
- Chemistry Department, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Fumitaka Hashiya
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Fumiaki Tomoike
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Kosuke Nakamoto
- Chemistry Department, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Yasuaki Kimura
- Chemistry Department, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Yoshihiro Shimizu
- Biodynamics Research Center (BDR), RIKEN, 6-2-3, Furuedai, Suita, Osaka, 565-0874, Japan
| | - Hiroshi Abe
- Chemistry Department, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.,Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.,CREST (Japan) Science and Technology Agency, 7, Gobancho, Chiyoda-ku, Tokyo, 102-0076, Japan.,Institute for Glyco-core Research, Tokai National Higher Education and Research System, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
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18
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Increased Muscleblind levels by chloroquine treatment improve myotonic dystrophy type 1 phenotypes in in vitro and in vivo models. Proc Natl Acad Sci U S A 2019; 116:25203-25213. [PMID: 31754023 DOI: 10.1073/pnas.1820297116] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a life-threatening and chronically debilitating neuromuscular disease caused by the expansion of a CTG trinucleotide repeat in the 3' UTR of the DMPK gene. The mutant RNA forms insoluble structures capable of sequestering RNA binding proteins of the Muscleblind-like (MBNL) family, which ultimately leads to phenotypes. In this work, we demonstrate that treatment with the antiautophagic drug chloroquine was sufficient to up-regulate MBNL1 and 2 proteins in Drosophila and mouse (HSALR) models and patient-derived myoblasts. Extra Muscleblind was functional at the molecular level and improved splicing events regulated by MBNLs in all disease models. In vivo, chloroquine restored locomotion, rescued average cross-sectional muscle area, and extended median survival in DM1 flies. In HSALR mice, the drug restored muscular strength and histopathology signs and reduced the grade of myotonia. Taken together, these results offer a means to replenish critically low MBNL levels in DM1.
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19
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Ageeli AA, McGovern-Gooch KR, Kaminska MM, Baird NJ. Finely tuned conformational dynamics regulate the protective function of the lncRNA MALAT1 triple helix. Nucleic Acids Res 2019; 47:1468-1481. [PMID: 30462290 PMCID: PMC6379651 DOI: 10.1093/nar/gky1171] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 10/28/2018] [Accepted: 11/03/2018] [Indexed: 12/21/2022] Open
Abstract
Nucleic acid triplexes may regulate many important biological processes. Persistent accumulation of the oncogenic 7-kb long noncoding RNA MALAT1 is dependent on an unusually long intramolecular triple helix. This triplex structure is positioned within a conserved ENE (element for nuclear expression) motif at the lncRNA 3′ terminus and protects the entire transcript from degradation in a polyA-independent manner. A requisite 3′ maturation step leads to triplex formation though the precise mechanism of triplex folding remains unclear. Furthermore, the contributions of several peripheral structural elements to triplex formation and protective function have not been determined. We evaluated the stability, conformational fluctuations, and function of this MALAT1 ENE triple helix (M1TH) protective element using in vitro mutational analyses coupled with biochemical and biophysical characterizations. Using fluorescence and UV melts, FRET, and an exonucleolytic decay assay we define a concerted mechanism for triplex formation and uncover a metastable, dynamic triplex population under near-physiological conditions. Structural elements surrounding the triplex regulate the dynamic M1TH conformational variability, but increased triplex dynamics lead to M1TH degradation. Taken together, we suggest that finely tuned dynamics may be a general mechanism regulating triplex-mediated functions.
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Affiliation(s)
- Abeer A Ageeli
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA 19143, USA
| | | | - Magdalena M Kaminska
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA 19143, USA
| | - Nathan J Baird
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA 19143, USA
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20
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McGovern-Gooch KR, Baird NJ. Fluorescence-based investigations of RNA-small molecule interactions. Methods 2019; 167:54-65. [PMID: 31129289 DOI: 10.1016/j.ymeth.2019.05.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/08/2019] [Accepted: 05/20/2019] [Indexed: 12/17/2022] Open
Abstract
Interrogating non-coding RNA structures and functions with small molecules is an area of rapidly increasing interest among biochemists and chemical biologists. However, many biochemical approaches to monitoring RNA structures are time-consuming and low-throughput, and thereby are only of limited utility for RNA-small molecule studies. Fluorescence-based techniques are powerful tools for rapid investigation of RNA conformations, dynamics, and interactions with small molecules. Many fluorescence methods are amenable to high-throughput analysis, enabling library screening for small molecule binders. In this review, we summarize numerous fluorescence-based approaches for identifying and characterizing RNA-small molecule interactions. We describe in detail a high-information content dual-reporter FRET assay we developed to characterize small molecule-induced conformational and stability changes. Our assay is uniquely suited as a platform for both small molecule discovery and thorough characterization of RNA-small molecule binding mechanisms. Given the growing recognition of non-coding RNAs as attractive targets for therapeutic intervention, we anticipate our FRET assay and other fluorescence-based techniques will be indispensable for the development of potent and specific small molecule inhibitors targeting RNA.
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Affiliation(s)
- Kayleigh R McGovern-Gooch
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA 19104 United States
| | - Nathan J Baird
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA 19104 United States.
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21
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Unger C, Lokmer N, Lehmann D, Axmann IM. Detection of phenol contamination in RNA samples and its impact on qRT-PCR results. Anal Biochem 2019; 571:49-52. [PMID: 30742799 DOI: 10.1016/j.ab.2019.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/06/2019] [Accepted: 02/06/2019] [Indexed: 12/14/2022]
Abstract
Residual phenol, carried over from RNA purification, can alter RNA concentration measurements and is assumed to inhibit PCR. Here, we demonstrate that Impurities A260 values of spectral content profiling (SCP) UV/Vis measurements correlated with phenol concentration, whereas absorbance ratios of classical UV/Vis systems failed to reliably detect phenol in RNA samples. Phenol contamination led to over- or underestimation of RNA concentration on UV/Vis systems, whereas it had no influence on fluorometry quantification. Wrong RNA concentration results led to altered template input in qRT-PCR and consequently caused quantification cycle (Cq) shifts, although ≤ 0.01% phenol had no direct influence.
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Affiliation(s)
- Conny Unger
- QIAGEN GmbH, Qiagen Strasse 1, 40724, Hilden, Germany; Institute for Synthetic Microbiology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, Düsseldorf, 40225, Germany.
| | - Nicole Lokmer
- QIAGEN GmbH, Qiagen Strasse 1, 40724, Hilden, Germany
| | | | - Ilka M Axmann
- Institute for Synthetic Microbiology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, Düsseldorf, 40225, Germany
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22
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Insights into Catalytic and tRNA Recognition Mechanism of the Dual-Specific tRNA Methyltransferase from Thermococcus kodakarensis. Genes (Basel) 2019; 10:genes10020100. [PMID: 30704107 PMCID: PMC6410153 DOI: 10.3390/genes10020100] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 01/30/2023] Open
Abstract
The tRNA methyltransferase Trm10, conserved throughout Eukarya and Archaea, catalyzes N1-methylation of purine residues at position 9 using S-adenosyl methionine as the methyl donor. The Trm10 family exhibits diverse target nucleotide specificity, with some homologs that are obligate m¹G₉ or m¹A₉-specific enzymes, while others are bifunctional enzymes catalyzing both m¹G₉ and m¹A₉. This variability is particularly intriguing given different chemical properties of the target N1 atom of guanine and adenine. Here we performed an extensive kinetic and mutational analysis of the m¹G₉ and m¹A₉-catalyzing Trm10 from Thermococcus kodakarensis to gain insight into the active site that facilitates this unique bifunctionality. These results suggest that the rate-determining step for catalysis likely involves a conformational change to correctly position the substrate tRNA in the active site. In this model, kinetic preferences for certain tRNA can be explained by variations in the overall stability of the folded substrate tRNA, consistent with tRNA-specific differences in metal ion dependence. Together, these results provide new insight into the substrate recognition, active site and catalytic mechanism of m¹G/m¹A catalyzing bifunctional enzymes.
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23
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Pedro AQ, Pereira P, Quental MJ, Carvalho AP, Santos SM, Queiroz JA, Sousa F, Freire MG. Cholinium-based Good's buffers ionic liquids as remarkable stabilizers and recyclable preservation media for recombinant small RNAs. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2018; 6:16645-16656. [PMID: 30949418 PMCID: PMC6443033 DOI: 10.1021/acssuschemeng.8b03900] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
RNA is a biopolymer of high relevance in the biopharmaceuticals field and in fundamental and applied research; however, the preservation of the RNA stability is still a remarkable challenge. Herein, we demonstrate the enhanced potential of aqueous solutions of self-buffering cholinium-based Good's buffers ionic liquids (GB-ILs), at 20 and 50 % (w/w), as alternative preservation media of recombinant small RNAs. The thermal stability of RNA is highly enhanced by GB-ILs, with an increase of 14 °C in the biopolymer melting temperature - the highest increase observed up to date with ILs. Most GB-ILs investigated improve the stability of RNA at least up to 30-days, both at 25 °C and at 4 °C, without requiring the typical samples freezing. Molecular dynamics simulations were applied to better understand the molecular-level mechanisms responsible for the observed RNA improved stability. The number of IL cations surrounding the RNA chain is similar, yet with differences found for the IL anions, which are responsible for the overall charge of the biopolymer first solvation sphere. No cytotoxicity of the studied solutions containing RNA and ILs at 20 % (w/w) was observed onto two distinct human cell lines, reinforcing their potential to act as preservation media when foreseeing biopharmaceutical applications. Finally, RNA was successfully recovered from the ILs aqueous solutions, without changes in its structural integrity, and the ILs successfully recycled and reused.
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Affiliation(s)
- Augusto Q. Pedro
- CICECO – Aveiro Institute of Materials, Chemistry Department, University of Aveiro, Complexo de Laboratórios Tecnológicos, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Patrícia Pereira
- CICS-UBI – Health Sciences Research Centre, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Maria J. Quental
- CICECO – Aveiro Institute of Materials, Chemistry Department, University of Aveiro, Complexo de Laboratórios Tecnológicos, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - André P. Carvalho
- CICECO – Aveiro Institute of Materials, Chemistry Department, University of Aveiro, Complexo de Laboratórios Tecnológicos, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Sérgio M. Santos
- CICECO – Aveiro Institute of Materials, Chemistry Department, University of Aveiro, Complexo de Laboratórios Tecnológicos, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - João A. Queiroz
- CICS-UBI – Health Sciences Research Centre, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - Fani Sousa
- CICS-UBI – Health Sciences Research Centre, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
- Corresponding Authors: ; Tel: +351-234-401422; Fax: +351-234-370084; ; Tel: +351-275-329074
| | - Mara G. Freire
- CICECO – Aveiro Institute of Materials, Chemistry Department, University of Aveiro, Complexo de Laboratórios Tecnológicos, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
- Corresponding Authors: ; Tel: +351-234-401422; Fax: +351-234-370084; ; Tel: +351-275-329074
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24
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Chakraborty M, Sellier C, Ney M, Pascal V, Charlet-Berguerand N, Artero R, Llamusi B. Daunorubicin reduces MBNL1 sequestration caused by CUG-repeat expansion and rescues cardiac dysfunctions in a Drosophila model of myotonic dystrophy. Dis Model Mech 2018; 11:dmm.032557. [PMID: 29592894 PMCID: PMC5963859 DOI: 10.1242/dmm.032557] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 03/14/2018] [Indexed: 01/09/2023] Open
Abstract
Myotonic dystrophy (DM) is a dominantly inherited neuromuscular disorder caused by expression of mutant myotonin-protein kinase (DMPK) transcripts containing expanded CUG repeats. Pathogenic DMPK RNA sequesters the muscleblind-like (MBNL) proteins, causing alterations in metabolism of various RNAs. Cardiac dysfunction represents the second most common cause of death in DM type 1 (DM1) patients. However, the contribution of MBNL sequestration in DM1 cardiac dysfunction is unclear. We overexpressed Muscleblind (Mbl), the DrosophilaMBNL orthologue, in cardiomyocytes of DM1 model flies and observed a rescue of heart dysfunctions, which are characteristic of these model flies and resemble cardiac defects observed in patients. We also identified a drug – daunorubicin hydrochloride – that directly binds to CUG repeats and alleviates Mbl sequestration in Drosophila DM1 cardiomyocytes, resulting in mis-splicing rescue and cardiac function recovery. These results demonstrate the relevance of Mbl sequestration caused by expanded-CUG-repeat RNA in cardiac dysfunctions in DM1, and highlight the potential of strategies aimed at inhibiting this protein-RNA interaction to recover normal cardiac function. Summary: MBNL protein sequestration by expanded CUG RNA contributes towards cardiac dysfunction in a myotonic dystrophy Drosophila model. Here, the authors identify the anticancer drug daunorubicin as a candidate therapeutic for the disease.
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Affiliation(s)
- Mouli Chakraborty
- Translational Genomics Group, Incliva Health Research Institute, Valencia, Spain.,Department of Genetics and Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), University of Valencia, Valencia 46100, Spain.,CIPF-INCLIVA Joint Unit, Valencia 46100, Spain
| | - Chantal Sellier
- Translational Medicine and Neurogenetics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, University of Strasbourg, 1 Rue Laurent Fries, 67400 Illkirch-Graffenstaden, France
| | - Michel Ney
- Translational Medicine and Neurogenetics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, University of Strasbourg, 1 Rue Laurent Fries, 67400 Illkirch-Graffenstaden, France
| | - Villa Pascal
- PCBIS Plate-forme de Chimie Biologique Intégrative de Strasbourg CNRS UMS 3286, Labex Medalis, ESBS, Université de Strasbourg, 300 Boulevard Sébastien Brant, 67412 Illkirch, France
| | - Nicolas Charlet-Berguerand
- Translational Medicine and Neurogenetics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, University of Strasbourg, 1 Rue Laurent Fries, 67400 Illkirch-Graffenstaden, France
| | - Ruben Artero
- Translational Genomics Group, Incliva Health Research Institute, Valencia, Spain .,Department of Genetics and Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), University of Valencia, Valencia 46100, Spain.,CIPF-INCLIVA Joint Unit, Valencia 46100, Spain
| | - Beatriz Llamusi
- Translational Genomics Group, Incliva Health Research Institute, Valencia, Spain.,Department of Genetics and Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), University of Valencia, Valencia 46100, Spain.,CIPF-INCLIVA Joint Unit, Valencia 46100, Spain
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25
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Lehner F, Kudlinzki D, Richter C, Müller-Werkmeister HM, Eberl KB, Bredenbeck J, Schwalbe H, Silvers R. Impact of Azidohomoalanine Incorporation on Protein Structure and Ligand Binding. Chembiochem 2017; 18:2340-2350. [DOI: 10.1002/cbic.201700437] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Florian Lehner
- Organic Chemistry and Chemical Biology; Goethe University Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Denis Kudlinzki
- Organic Chemistry and Chemical Biology; Goethe University Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
- German Cancer Consortium; DKTK; German Cancer Research Center; DKFZ; Im Neuenheimer Feld 280 69120 Heidelberg Germany
| | - Christian Richter
- Organic Chemistry and Chemical Biology; Goethe University Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | | | - Katharina B. Eberl
- Institute for Biophysics; Goethe University Frankfurt; Max-von-Laue-Strasse 1 60438 Frankfurt am Main Germany
| | - Jens Bredenbeck
- Institute for Biophysics; Goethe University Frankfurt; Max-von-Laue-Strasse 1 60438 Frankfurt am Main Germany
| | - Harald Schwalbe
- Organic Chemistry and Chemical Biology; Goethe University Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Robert Silvers
- Organic Chemistry and Chemical Biology; Goethe University Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
- Present address: Francis Bitter Magnet Laboratory; Massachusetts Institute of Technology; Cambridge MA 02139 USA
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26
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Schnieders R, Richter C, Warhaut S, de Jesus V, Keyhani S, Duchardt-Ferner E, Keller H, Wöhnert J, Kuhn LT, Breeze AL, Bermel W, Schwalbe H, Fürtig B. Evaluation of 15N-detected H-N correlation experiments on increasingly large RNAs. JOURNAL OF BIOMOLECULAR NMR 2017; 69:31-44. [PMID: 28879611 DOI: 10.1007/s10858-017-0132-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/30/2017] [Indexed: 06/07/2023]
Abstract
Recently, 15N-detected multidimensional NMR experiments have been introduced for the investigation of proteins. Utilization of the slow transverse relaxation of nitrogen nuclei in a 15N-TROSY experiment allowed recording of high quality spectra for high molecular weight proteins, even in the absence of deuteration. Here, we demonstrate the applicability of three 15N-detected H-N correlation experiments (TROSY, BEST-TROSY and HSQC) to RNA. With the newly established 15N-detected BEST-TROSY experiment, which proves to be the most sensitive 15N-detected H-N correlation experiment, spectra for five RNA molecules ranging in size from 5 to 100 kDa were recorded. These spectra yielded high resolution in the 15N-dimension even for larger RNAs since the increase in line width with molecular weight is more pronounced in the 1H- than in the 15N-dimension. Further, we could experimentally validate the difference in relaxation behavior of imino groups in AU and GC base pairs. Additionally, we showed that 15N-detected experiments theoretically should benefit from sensitivity and resolution advantages at higher static fields but that the latter is obscured by exchange dynamics within the RNAs.
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Affiliation(s)
- Robbin Schnieders
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Sven Warhaut
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Vanessa de Jesus
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Sara Keyhani
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Elke Duchardt-Ferner
- Institute for Molecular Biosciences, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt, Germany
| | - Heiko Keller
- Institute for Molecular Biosciences, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt, Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt, Germany
| | - Lars T Kuhn
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Alexander L Breeze
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Silberstreifen 4, 76287, Rheinstetten, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany.
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany.
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27
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Haque L, Bhuiya S, Tiwari R, Pradhan AB, Das S. Biophysical insight into the interaction of the bioflavonoid kaempferol with triple and double helical RNA and the dual fluorescence behaviour of kaempferol. RSC Adv 2016. [DOI: 10.1039/c6ra12445c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Binding of kaempferol with triple and double helical RNA.
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Affiliation(s)
- Lucy Haque
- Department of Chemistry
- Jadavpur University
- Jadavpur
- India
| | | | - Richa Tiwari
- Department of Chemistry
- Jadavpur University
- Jadavpur
- India
| | | | - Suman Das
- Department of Chemistry
- Jadavpur University
- Jadavpur
- India
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