scholarly journals Targeted-Protein Silencing Tools: Overview and Future Perspectives

2020 ◽  
Author(s):  
Yuri Prozzillo ◽  
Gaia Fattorini ◽  
Maria Virginia Santopietro ◽  
Luigi Suglia ◽  
Alessandra Ruggiero ◽  
...  
Keyword(s):  
Rna Interference ◽  
Protein Degradation ◽  
Protein Function ◽  
Target Protein ◽  
Future Perspectives ◽  
Target Effects

Targeted Protein Silencing (TPS) is an elegant approach to investigate protein function and its role in the cellular landscape, overcoming limitations of genetic perturbation strategies. In contrast to CRISPR/Cas9 and RNA interference, these systems act in a reversible manner and reduce off-target effects. Several TPS have been developed and wisely improved, including compartment delocalization tools and protein degradation systems. In this review, we focus on Anchor-Away, deGradFP, auxin inducible degron (AID) and dTAG technologies, and discuss their recent applications and advances. Finally, we propose Nano-Grad, a novel nanobody-based protein degradation tool to specifically proteolyze endogenous tag-free target protein.

scholarly journals Targeted Protein Degradation Tools: Overview and Future Perspectives

Biology ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 421
Author(s):  
Yuri Prozzillo ◽  
Gaia Fattorini ◽  
Maria Virginia Santopietro ◽  
Luigi Suglia ◽  
Alessandra Ruggiero ◽  
...  
Keyword(s):  
Rna Interference ◽  
Protein Degradation ◽  
Protein Function ◽  
Signal Sequence ◽  
The Other ◽  
Future Perspectives ◽  
Wild Type ◽  
Design And Optimization ◽  
Protein Inactivation ◽  
Target Effects

Targeted protein inactivation (TPI) is an elegant approach to investigate protein function and its role in the cellular landscape, overcoming limitations of genetic perturbation strategies. These systems act in a reversible manner and reduce off-target effects exceeding the limitations of CRISPR/Cas9 and RNA interference, respectively. Several TPI have been developed and wisely improved, including compartment delocalization tools and protein degradation systems. However, unlike chemical tools such as PROTACs (PROteolysis TArgeting Chimeras), which work in a wild-type genomic background, TPI technologies require adding an aminoacidic signal sequence (tag) to the protein of interest (POI). On the other hand, the design and optimization of PROTACs are very laborious and time-consuming. In this review, we focus on anchor-away, deGradFP, auxin-inducible degron (AID) and dTAG technologies and discuss their recent applications and advances. Finally, we propose nano-grad, a novel nanobody-based protein degradation tool, which specifically proteolyzes endogenous tag-free target protein.

scholarly journals Phthalimide conjugation as a strategy for in vivo target protein degradation

Science ◽  
2015 ◽  
Vol 348 (6241) ◽  
pp. 1376-1381 ◽  
Author(s):  
G. E. Winter ◽  
D. L. Buckley ◽  
J. Paulk ◽  
J. M. Roberts ◽  
A. Souza ◽  
...  
Keyword(s):  
Protein Degradation ◽  
Target Protein

scholarly journals Annotating proteins with generalized functional linkages

2008 ◽  
Vol 105 (46) ◽  
pp. 17700-17705 ◽  
Author(s):  
Richard Llewellyn ◽  
David S. Eisenberg
Keyword(s):  
Protein Function ◽  
Biological Process ◽  
Computational Method ◽  
Majority Voting ◽  
Target Protein ◽  
Biological Processes ◽  
Gene Products ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Networks

As genome sequencing outstrips the rate of high-quality, low-throughput biochemical and genetic experimentation, accurate annotation of protein function becomes a bottleneck in the progress of the biomolecular sciences. Most gene products are now annotated by homology, in which an experimentally determined function is applied to a similar sequence. This procedure becomes error-prone between more divergent sequences and can contaminate biomolecular databases. Here, we propose a computational method of assignment of function, termed Generalized Functional Linkages (GFL), that combines nonhomology-based methods with other types of data. Functional linkages describe pairwise relationships between proteins that work together to perform a biological task. GFL provides a Bayesian framework that improves annotation by arbitrating a competition among biological process annotations to best describe the target protein. GFL addresses the unequal strengths of functional linkages among proteins, the quality of existing annotations, and the similarity among them while incorporating available knowledge about the cellular location or individual molecular function of the target protein. We demonstrate GFL with functional linkages defined by an algorithm known as zorch that quantifies connectivity in protein–protein interaction networks. Even when using proteins linked only by indirect or high-throughput interactions, GFL predicts the biological processes of many proteins in Saccharomyces cerevisiae, improving the accuracy of annotation by 20% over majority voting.

Isolation of Peptide Aptamers to Target Protein Function

2009 ◽  
pp. 333-360 ◽  
Author(s):  
Luisa Lopez-Ochoa ◽  
Tara E. Nash ◽  
Jorge Ramirez-Prado ◽  
Linda Hanley-Bowdoin
Keyword(s):  
Protein Function ◽  
Target Protein ◽  
Peptide Aptamers

scholarly journals Delivery strategies of cancer immunotherapy: recent advances and future perspectives

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Zhongwei Zhao ◽  
Liyun Zheng ◽  
Weiqian Chen ◽  
Wei Weng ◽  
Jingjing Song ◽  
...  
Keyword(s):  
Cancer Immunotherapy ◽  
Clinical Status ◽  
Efficacy And Safety ◽  
Cytokine Release ◽  
Cytokine Release Syndrome ◽  
Future Perspectives ◽  
Vascular Leak Syndrome ◽  
Delivery Strategies ◽  
Cancer Immunotherapeutic ◽  
Target Effects

AbstractImmunotherapy has become an emerging strategy for the treatment of cancer. Immunotherapeutic drugs have been increasing for clinical treatment. Despite significant advances in immunotherapy, the clinical application of immunotherapy for cancer patients has some challenges associated with safety and efficacy, including autoimmune reactions, cytokine release syndrome, and vascular leak syndrome. Novel strategies, particularly improved delivery strategies, including nanoparticles, scaffolds, and hydrogels, are able to effectively target tumors and/or immune cells of interest, increase the accumulation of immunotherapies within the lesion, and reduce off-target effects. Here, we briefly describe five major types of cancer immunotherapy, including their clinical status, strengths, and weaknesses. Then, we introduce novel delivery strategies, such as nanoparticle-based delivery of immunotherapy, implantable scaffolds, injectable biomaterials for immunotherapy, and matrix-binding molecular conjugates, which can improve the efficacy and safety of immunotherapies. Also, the limitations of novel delivery strategies and challenges of clinical translation are discussed.

scholarly journals Non-Target Effects of Green Fluorescent Protein (GFP)-Derived Double-Stranded RNA (dsRNA-GFP) Used in Honey Bee RNA Interference (RNAi) Assays

Insects ◽  
2013 ◽  
Vol 4 (1) ◽  
pp. 90-103 ◽  
Author(s):  
Francis Nunes ◽  
Aline Aleixo ◽  
Angel Barchuk ◽  
Ana Bomtorin ◽  
Christina Grozinger ◽  
...  
Keyword(s):  
Green Fluorescent Protein ◽  
Rna Interference ◽  
Honey Bee ◽  
Fluorescent Protein ◽  
Double Stranded Rna ◽  
Green Fluorescent ◽  
Target Effects

scholarly journals Targeting the Allosteric Site of Oncoprotein BCR-ABL as an Alternative Strategy for Effective Target Protein Degradation

2017 ◽  
Vol 8 (10) ◽  
pp. 1042-1047 ◽  
Author(s):  
Kenichiro Shimokawa ◽  
Norihito Shibata ◽  
Tomoya Sameshima ◽  
Naoki Miyamoto ◽  
Osamu Ujikawa ◽  
...  
Keyword(s):  
Protein Degradation ◽  
Alternative Strategy ◽  
Target Protein ◽  
Allosteric Site

scholarly journals Synthetic Pre-miRNA-Based shRNA as Potent RNAi Triggers

2011 ◽  
Vol 2011 ◽  
pp. 1-6 ◽  
Author(s):  
Kazuya Terasawa ◽  
Kazuharu Shimizu ◽  
Gozoh Tsujimoto
Keyword(s):  
Biological Activity ◽  
Rna Interference ◽  
Gene Function ◽  
Small Interfering Rnas ◽  
Therapeutic Applications ◽  
Short Hairpin ◽  
Short Hairpin Rnas ◽  
Interferon Responses ◽  
Rnai Activity ◽  
Target Effects

RNA interference (RNAi) is a powerful tool for studying gene function owing to the ease with which it can selectively silence genes of interest, and it has also attracted attention because of its potential for therapeutic applications. Chemically synthesized small interfering RNAs (siRNAs) and DNA vector-based short hairpin RNAs (shRNAs) are now widely used as RNAi triggers. In contrast to expressed shRNAs, the use of synthetic shRNAs is limited. Here we designed shRNAs modeled on a precursor microRNA (pre-miRNA) and evaluated their biological activity. We demonstrated that chemically synthetic pre-miRNA-based shRNAs have more potent RNAi activity than their corresponding siRNAs and found that their antisense strands are more efficiently incorporated into the RNA-induced silencing complex. Although greater off-target effects and interferon responses were induced by shRNAs than by their corresponding siRNAs, these effects could be overcome by simply using a lower concentration or by optimizing and chemically modifying shRNAs similar to synthetic siRNAs. These are challenges for the future.

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