Microscale thermophoresis provides insights into mechanism and thermodynamics of ribozyme catalysis

Gaffarogullari, Ece C.; Krause, André; Balbo, Jessica; Herten, Dirk‐Peter; Jäschke, Andres

doi:10.4161/rna.27101

Cited by 19 publications

(17 citation statements)

References 32 publications

(44 reference statements)

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“…MST results revealed weak affinity in comparison to control (HMGA1). Furthermore, Gaffarogullari et al [73] used MST to investigate the interaction of small-molecule substrate to RNA enzyme known as Diels-Alderase ribozyme (DAse) while, previous approaches using FCS technique failed to quantitate the binding event due to interference with small-molecule labeling procedures for maleimide dienophiles substrate. MST approach used via two experimental sets: the first analyzed the binding interactions between DAse and diene substrates that was successfully investigated by FCS to access the suitability of MST, which exhibited good agreement with FCS measurements.…”

Section: Mst Of Nucleic Acids Interactionsmentioning

confidence: 99%

Thermophoresis for characterizing biomolecular interaction

Asmari

Ratih

Alhazmi

et al. 2018

Methods

101

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The study of biomolecular interactions is crucial to get more insight into the biological system. The interactions of protein-protein, protein-nucleic acids, protein-sugars, nucleic acid-nucleic acids and protein-small molecules are supporting therapeutics and technological developments. Recently, the development in a large number of analytical techniques for characterizing biomolecular interactions reflect the promising research investments in this field. In this review, microscale thermophoresis technology (MST) is presented as an analytical technique for characterizing biomolecular interactions. Recent years have seen much progress and several applications established. MST is a powerful technique in quantitation of binding events based on the movement of molecules in microscopic temperature gradient. Simplicity, free solutions analysis, low sample volume, short analysis time, and immobilization free are the MST advantages over other competitive techniques. A wide range of studies in biomolecular interactions have been successfully carried out using MST, which tend to the versatility of the technique to use in screening binding events in order to save time, cost and obtained high data quality.

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Section: Mst Of Nucleic Acids Interactionsmentioning

confidence: 99%

Thermophoresis for characterizing biomolecular interaction

Asmari

Ratih

Alhazmi

et al. 2018

Methods

101

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“…The myristoyl pocket in protein kinase A (PKA) is located in the C-terminal domain, in a different area from the c-Abl myristoyl pocket, and myristate binding here appears to activate membrane association with PKA. 51 This pocket has received less attention than the myristoyl pocket in c-Abl, and does not appear to be targeted by any known inhibitors, but based on the mapping results of PKA structures, the PKA myristoyl pocket appears to be highly druggable.…”

Section: Pmp (Pka Myristoyl Pocket)mentioning

confidence: 99%

Kinase Atlas: Druggability Analysis of Potential Allosteric Sites in Kinases

Yueh¹,

Rettenmaier

Xia³

et al. 2019

J. Med. Chem.

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The inhibition of kinases has been pursued by the pharmaceutical industry for over 20 years. While the locations of the sites that bind type II and III inhibitors at or near the ATP binding sites are well defined, the literature describes ten different regions that were reported as regulatory hot spots in some kinases and thus are potential target sites for type IV inhibitors. Kinase Atlas is a systematic collection of binding hot spots located at the above ten sites in 4910 structures of 376 distinct kinases available in the Protein Data Bank. The hot spots are identified by FTMap, a computational analogue of experimental fragment screening. Users of Kinase Atlas (https://kinaseatlas.bu.edu) may view summarized results for all structures of a particular kinase, such as which binding sites are present and how druggable they are, or they may view hot spot information for a particular kinase structure of interest.

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“…4C). [186][187][188][189][190][191][192] To quantify the intermolecular interactions, infrared-lasers are used to achieve precise microscale temperature gradients within the glass capillaries filled with the targeted solution, e.g. cell lysate, serum or bioliquids.…”

Section: Microscale Thermophoresis (Mst)mentioning

confidence: 99%

Unveiling the druggable RNA targets and small molecule therapeutics

Sztuba-Solińska

Chávez-Calvillo

Cline

2019

Bioorganic & Medicinal Chemistry

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Keywords:RNA structure and function RNA interactions Epitranscriptomics Small molecules RNA-based therapeutics RNA in disease Drug target A B S T R A C T The increasing appreciation for the crucial roles of RNAs in infectious and non-infectious human diseases makes them attractive therapeutic targets. Coding and non-coding RNAs frequently fold into complex conformations which, if effectively targeted, offer opportunities to therapeutically modulate numerous cellular processes, including those linked to undruggable protein targets. Despite the considerable skepticism as to whether RNAs can be targeted with small molecule therapeutics, overwhelming evidence suggests the challenges we are currently facing are not outside the realm of possibility. In this review, we highlight the most recent advances in molecular techniques that have sparked a revolution in understanding the RNA structure-to-function relationship. We bring attention to the application of these modern techniques to identify druggable RNA targets and to assess small molecule binding specificity. Finally, we discuss novel screening methodologies that support RNA drug discovery and present examples of therapeutically valuable RNA targets. RNA as a drug targetThe vast diversity of RNAs expanding beyond coding transcripts to several classes of ncRNAs that vary in length, biogenesis, polarity, and putative functions, increases the repertoire of druggable targets. 19,20 Here, specific RNA properties contribute to its attractive, yet challenging makeup as a target molecule. RNA can form complex three-dimensional structures through canonical Watson-Crick base pairing and complex tertiary interactions that are mediated by non-canonical bonds. Such structures can be as intricate and stable as those formed by proteins and can recognize small-molecule ligands, other nucleic acids, and/or proteins with high affinity and specificity. [21][22][23][24] At the same time, the highly dynamic conformation and repetitive character of its surface presents difficulties for drug design. 25,26 In addition, many putative small molecule-binding pockets in RNA are much more polar and solvent exposed than binding sites on proteins, complicating ligand design efforts. Compounding these issues, most target RNAs are expressed at low levels, with the exception of ribosomal (rRNA) and transfer (tRNA) RNAs, which constitute 80-90% and 10-15% of total cellular RNA, respectively. 27 Other abundant RNAs, such as messenger (mRNA), small nuclear (snRNA), and small nucleolar (snoRNA) are present at levels that are about 1-2 orders of magnitude lower than rRNA and tRNA. Certain small RNAs, such as micro (miRNA) and piwi (piRNAs) can be present at very high levels; however, this appears to be cell type dependent. One should keep in mind that if the RNA has catalytic activity or if it acts as a scaffold to regulate https://doi.

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Microscale thermophoresis provides insights into mechanism and thermodynamics of ribozyme catalysis

Cited by 19 publications

References 32 publications

Thermophoresis for characterizing biomolecular interaction

Thermophoresis for characterizing biomolecular interaction

Kinase Atlas: Druggability Analysis of Potential Allosteric Sites in Kinases

Unveiling the druggable RNA targets and small molecule therapeutics

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