scholarly journals Towards next generation antisense oligonucleotides: mesylphosphoramidate modification improves therapeutic index and duration of effect of gapmer antisense oligonucleotides

2021 ◽  
Vol 49 (16) ◽  
pp. 9026-9041
Author(s):  
Brooke A Anderson ◽  
Graeme C Freestone ◽  
Audrey Low ◽  
Cheryl L De-Hoyos ◽  
William J Drury III ◽  
...  
Keyword(s):  
Protein Binding ◽  
Antisense Oligonucleotides ◽  
Rna Binding ◽  
Therapeutic Index ◽  
Next Generation ◽  
Binding Properties ◽  
Duration Of Effect ◽  
Extended Duration ◽  
Inflammatory Profile ◽  
Reduced Activity

Abstract The PS modification enhances the nuclease stability and protein binding properties of gapmer antisense oligonucleotides (ASOs) and is one of very few modifications that support RNaseH1 activity. We evaluated the effect of introducing stereorandom and chiral mesyl-phosphoramidate (MsPA) linkages in the DNA gap and flanks of gapmer PS ASOs and characterized the effect of these linkages on RNA-binding, nuclease stability, protein binding, pro-inflammatory profile, antisense activity and toxicity in cells and in mice. We show that all PS linkages in a gapmer ASO can be replaced with MsPA without compromising chemical stability and RNA binding affinity but these designs reduced activity. However, replacing up to 5 PS in the gap with MsPA was well tolerated and replacing specific PS linkages at appropriate locations was able to greatly reduce both immune stimulation and cytotoxicity. The improved nuclease stability of MsPA over PS translated to significant improvement in the duration of ASO action in mice which was comparable to that of enhanced stabilized siRNA designs. Our work highlights the combination of PS and MsPA linkages as a next generation chemical platform for identifying ASO drugs with improved potency and therapeutic index, reduced pro-inflammatory effects and extended duration of effect.

scholarly journals DeepCLIP: Predicting the effect of mutations on protein-RNA binding with Deep Learning

2019 ◽  
Author(s):  
Alexander Gulliver Bjørnholt Grønning ◽  
Thomas Koed Doktor ◽  
Simon Jonas Larsen ◽  
Ulrika Simone Spangsberg Petersen ◽  
Lise Lolle Holm ◽  
...  
Keyword(s):  
Deep Learning ◽  
Protein Binding ◽  
Binding Sites ◽  
Antisense Oligonucleotides ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
List Type ◽  
Link Type ◽  
Sequence Variations

ABSTRACTNucleotide variants can cause functional changes by altering protein-RNA binding in various ways that are not easy to predict. This can affect processes such as splicing, nuclear shuttling, and stability of the transcript. Therefore, correct modelling of protein-RNA binding is critical when predicting the effects of sequence variations. Many RNA-binding proteins recognize a diverse set of motifs and binding is typically also dependent on the genomic context, making this task particularly challenging. Here, we present DeepCLIP, the first method for context-aware modeling and predicting protein binding to nucleic acids using exclusively sequence data as input. We show that DeepCLIP outperforms existing methods for modelling RNA-protein binding. Importantly, we demonstrate that DeepCLIP is able to reliably predict the functional effects of contextually dependent nucleotide variants in independent wet lab experiments. Furthermore, we show how DeepCLIP binding profiles can be used in the design of therapeutically relevant antisense oligonucleotides, and to uncover possible position-dependent regulation in a tissue-specific manner. DeepCLIP can be freely used at http://deepclip.compbio.sdu.dk.HighlightsWe have designed DeepCLIP as a simple neural network that requires only CLIP binding sites as input. The architecture and parameter settings of DeepCLIP makes it an efficient classifier and robust to train, making high performing models easy to train and recreate.Using an extensive benchmark dataset, we demonstrate that DeepCLIP outperforms existing tools in classification. Furthermore, DeepCLIP provides direct information about the neural network’s decision process through visualization of binding motifs and a binding profile that directly indicates sequence elements contributing to the classification.To show that DeepCLIP models generalize to different datasets we have demonstrated that predictions correlate with in vivo and in vitro experiments using quantitative binding assays and minigenes.Identifying the binding sites for regulatory RNA-binding proteins is fundamental for efficient design of (therapeutic) antisense oligonucleotides. Employing a reported disease associated mutation, we demonstrate that DeepCLIP can be used for design of therapeutic antisense oligonucleotides that block regions important for binding of regulatory proteins and correct aberrant splicing.Using DeepCLIP binding profiles, we uncovered a possible position-dependent mechanism behind the reported tissue-specificity of a group of TDP-43 repressed pseudoexons.We have made DeepCLIP available as an online tool for training and application of proteinRNA binding deep learning models and prediction of the potential effects of clinically detected sequence variations (http://deepclip.compbio.sdu.dk/). We also provide DeepCLIP as a configurable stand-alone program (http://www.github.com/deepclip).

Absorption, Metabolic Stability and Protein Binding Properties of Sutherlandioside B from Sutherlandia frutescens

Planta Medica ◽  
2008 ◽  
Vol 74 (03) ◽  
Author(s):  
VLM Madgula ◽  
B Avula ◽  
X Fu ◽  
XC Li ◽  
TJ Smillie ◽  
...  
Keyword(s):  
Protein Binding ◽  
Metabolic Stability ◽  
Binding Properties ◽  
Sutherlandia Frutescens

The DNA- and protein-binding properties and cytotoxicity of a new copper(II) hydrazone Schiff base complex

2021 ◽  
pp. 1-23
Author(s):  
Niladri Biswas ◽  
Sandeepta Saha ◽  
Barun Kumar Biswas ◽  
Manas Chowdhury ◽  
Ashikur Rahaman ◽  
...  
Keyword(s):  
Schiff Base ◽  
Protein Binding ◽  
Schiff Base Complex ◽  
Binding Properties ◽  
Base Complex

Nickel(ii) complexes with a flexible piperazinyl moiety: studies on DNA and protein binding and catecholase like properties

2015 ◽  
Vol 44 (5) ◽  
pp. 2299-2310 ◽  
Author(s):  
Mriganka Das ◽  
Rajendar Nasani ◽  
Manideepa Saha ◽  
Shaikh M Mobin ◽  
Suman Mukhopadhyay
Keyword(s):  
Protein Binding ◽  
Nickel Complexes ◽  
Boat Conformation ◽  
Binding Properties

Nickel complexes with a flexible piperazinyl moiety are showing interesting DNA and protein binding properties and catecholase like activity in the boat conformation.

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