scholarly journals An in silico map of the SARS-CoV-2 RNA Structurome

2020 ◽  
Author(s):  
Ryan J. Andrews ◽  
Jake M. Peterson ◽  
Hafeez S. Haniff ◽  
Jonathan Chen ◽  
Christopher Williams ◽  
...  
Keyword(s):  
Small Molecules ◽  
Rna Structure ◽  
Drug Targets ◽  
Rna Binding ◽  
Rna Virus ◽  
Human Pathogens ◽  
Public Database ◽  
Positive Sense ◽  
Basic Biology ◽  
Potential Drug Targets

AbstractSARS-CoV-2 is a positive-sense single-stranded RNA virus that has exploded throughout the global human population. This pandemic coronavirus strain has taken scientists and public health researchers by surprise and knowledge of its basic biology (e.g. structure/function relationships in its genomic, messenger and template RNAs) and modes for therapeutic intervention lag behind that of other human pathogens. In this report we used a recently-developed bioinformatics approach, ScanFold, to deduce the RNA structural landscape of the SARS-CoV-2 transcriptome. We recapitulate known elements of RNA structure and provide a model for the folding of an essential frameshift signal. Our results find that the SARS-CoV-2 is greatly enriched in unusually stable and likely evolutionarily ordered RNA structure, which provides a huge reservoir of potential drug targets for RNA-binding small molecules. Our results also predict regions that are accessible for intermolecular interactions, which can aid in the design of antisense therapeutics. All results are made available via a public database (the RNAStructuromeDB) where they may hopefully drive drug discovery efforts to inhibit SARS-CoV-2 pathogenesis.

scholarly journals A map of the SARS-CoV-2 RNA structurome

2021 ◽  
Vol 3 (2) ◽  
Author(s):  
Ryan J Andrews ◽  
Collin A O’Leary ◽  
Van S Tompkins ◽  
Jake M Peterson ◽  
Hafeez S Haniff ◽  
...  
Keyword(s):  
Experimental Data ◽  
Rna Structure ◽  
Drug Targets ◽  
Rna Binding ◽  
Large Reservoir ◽  
Model Comparisons ◽  
Functional Regions ◽  
Structure Probing ◽  
Genome Wide ◽  
Potential Drug Targets

Abstract SARS-CoV-2 has exploded throughout the human population. To facilitate efforts to gain insights into SARS-CoV-2 biology and to target the virus therapeutically, it is essential to have a roadmap of likely functional regions embedded in its RNA genome. In this report, we used a bioinformatics approach, ScanFold, to deduce the local RNA structural landscape of the SARS-CoV-2 genome with the highest likelihood of being functional. We recapitulate previously-known elements of RNA structure and provide a model for the folding of an essential frameshift signal. Our results find that SARS-CoV-2 is greatly enriched in unusually stable and likely evolutionarily ordered RNA structure, which provides a large reservoir of potential drug targets for RNA-binding small molecules. Results are enhanced via the re-analyses of publicly-available genome-wide biochemical structure probing datasets that are broadly in agreement with our models. Additionally, ScanFold was updated to incorporate experimental data as constraints in the analysis to facilitate comparisons between ScanFold and other RNA modelling approaches. Ultimately, ScanFold was able to identify eight highly structured/conserved motifs in SARS-CoV-2 that agree with experimental data, without explicitly using these data. All results are made available via a public database (the RNAStructuromeDB: https://structurome.bb.iastate.edu/sars-cov-2) and model comparisons are readily viewable at https://structurome.bb.iastate.edu/sars-cov-2-global-model-comparisons.

Viral RNA structural equilibria and their interactions with host proteins

2019 ◽  
Author(s):  
◽  
Samantha Elizabeth Brady
Keyword(s):  
Reverse Transcription ◽  
Rna Structure ◽  
Drug Targets ◽  
Rna Viruses ◽  
Rna Virus ◽  
Protein Translation ◽  
Viral Rna ◽  
Primer Binding Site ◽  
In Vitro Techniques

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT REQUEST OF AUTHOR.] Understanding viral RNA structure and how it functions is crucial in elucidating new drug targets. There are many kinds of viruses that utilize RNA as a critical component of their life cycle, such as retroviruses, single-stranded plus or minus sense RNA viruses, and double-stranded RNA viruses. Two viruses that are studied in this thesis are human immunodeficiency virus (HIV), which is a retrovirus, and hepatitis C virus (HCV), which is a single-stranded plus sense RNA virus. It has been previously reported that a human host factor, RNA helicase A (RHA), is packaged into HIV virions by binding to the primer binding site (PBS) segment of the 5'untranslated region in the HIV genomic RNA. We determined RHA is required for efficient reverse transcription prior to capsid uncoating by utilizing cell based and in vitro techniques. It has also been suggested that RHA plays other roles during HIV infection besides reverse transcription. Utilizing NMR, we demonstrated that RHA binds to the monomeric 5'UTR at the bottom of the TAR hairpin, which is different from how it binds during viral packaging. Next, we employed NMR techniques to probe the 3'end of the HCV genome called 3'X. We determined that the 3'X is in structural equilibrium between two states: an open conformation and a closed conformation. These two conformations have been suggested to play a role in minus sense synthesis and viral protein translation, respectively. Taken together, my thesis work has elucidated how many viruses manipulate and utilize their RNA structure to modulate their outcome.

scholarly journals Symbiosis Comes of Age at the 10th Biennial Meeting of Wolbachia Researchers

2019 ◽  
Vol 85 (8) ◽  
Author(s):  
Irene L. G. Newton ◽  
Barton E. Slatko
Keyword(s):  
Cell Biology ◽  
Rna Virus ◽  
Host Cells ◽  
Human Pathogens ◽  
Content Type ◽  
New Science ◽  
Successful Infection ◽  
Filarial Nematodes ◽  
Insect Populations ◽  
Basic Biology

ABSTRACT Wolbachia pipientis is an alphaproteobacterial obligate intracellular microbe and arguably the most successful infection on our planet, colonizing 40% to 60% of insect species. Wolbachia spp. are also present in most, but not all, filarial nematodes, where they are obligate mutualists and are the targets for antifilarial drug discovery. Although Wolbachia spp. are related to important human pathogens, they do not infect mammals but instead are well known for their reproductive manipulations of insect populations, inducing the following phenotypes: male killing, feminization, parthenogenesis induction, and cytoplasmic incompatibility (CI). The most common of these, CI, results in a sperm-egg incompatibility and increases the relative fecundity of infected females in a population. In the last decade, Wolbachia spp. have also been shown to provide a benefit to insects, where the infection can inhibit RNA virus replication within the host. Wolbachia spp. cannot be cultivated outside host cells, and no genetic tools are available in the symbiont, limiting approaches available for their study. This means that many questions fundamental to our understanding of Wolbachia basic biology remained unknown for decades. The 10th biennial international Wolbachia conference, Wolbachia Evolution, Ecology, Genomics and Cell Biology: A Chronicle of the Most Ubiquitous Symbiont, was held on 17 to 22 June 2018 in Salem, MA. In this review, we highlight the new science presented at the meeting, link it to prior efforts to answer these questions across the Wolbachia genus, and present the importance of these findings to the field of symbiosis. The topics covered in this review are based on the presentations at the conference.

scholarly journals Integrated Analysis Identifies Interaction Patterns between Small Molecules and Pathways

2014 ◽  
Vol 2014 ◽  
pp. 1-10 ◽  
Author(s):  
Yan Li ◽  
Weiguo Li ◽  
Xin Chen ◽  
Hong Jiang ◽  
Jiatong Sun ◽  
...  
Keyword(s):  
Gene Expression ◽  
Small Molecules ◽  
Drug Targets ◽  
Cancer Cell Line ◽  
Integrated Analysis ◽  
Interaction Patterns ◽  
Drug Candidates ◽  
Molecularly Targeted Therapy ◽  
Topological Characteristics ◽  
Potential Drug Targets

Previous studies have indicated that the downstream proteins in a key pathway can be potential drug targets and that the pathway can play an important role in the action of drugs. So pathways could be considered as targets of small molecules. A link map between small molecules and pathways was constructed using gene expression profile, pathways, and gene expression of cancer cell line intervened by small molecules and then we analysed the topological characteristics of the link map. Three link patterns were identified based on different drug discovery implications for breast, liver, and lung cancer. Furthermore, molecules that significantly targeted the same pathways tended to treat the same diseases. These results can provide a valuable reference for identifying drug candidates and targets in molecularly targeted therapy.

scholarly journals Target-Directed Approaches for Screening Small Molecules against RNA Targets

2020 ◽  
Vol 25 (8) ◽  
pp. 869-894 ◽  
Author(s):  
Hafeez S. Haniff ◽  
Laurent Knerr ◽  
Jonathan L. Chen ◽  
Matthew D. Disney ◽  
Helen L. Lightfoot
Keyword(s):  
Small Molecules ◽  
Small Molecule ◽  
Drug Targets ◽  
Industrial Development ◽  
Rna Binding ◽  
Cellular Functions ◽  
Rna Molecules ◽  
The Face ◽  
Rna Binders ◽  
The Right

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.

scholarly journals Supramolecular cylinders target bulge structures in the 5’ UTR of the RNA genome of SARS-CoV-2 and inhibit viral replication

2021 ◽  
Author(s):  
Lazaros Melidis ◽  
Harriet J. Hill ◽  
Nicholas J. Coltman ◽  
Scott P. Davies ◽  
Kinga Winczura ◽  
...  
Keyword(s):  
Viral Replication ◽  
Rna Structure ◽  
Drug Targets ◽  
Rna Binding ◽  
Antiviral Agents ◽  
3D Models ◽  
Stem Loop ◽  
Dynamic Structures ◽  
Dynamics Simulations

AbstractThe untranslated regions (UTRs) of viral genomes contain a variety of conserved yet dynamic structures crucial for viral replication, providing drug targets for the development of broad spectrum anti-virals. We combine in vitro RNA analysis with Molecular Dynamics simulations to build the first 3D models of the structure and dynamics of key regions of the 5’ UTR of the SARS-CoV-2 genome. Furthermore, we determine the binding of metallo-supramolecular helicates (cylinders) to this RNA structure. These nano-size agents are uniquely able to thread through RNA junctions and we identify their binding to a 3-base bulge and the central cross 4-way junction located in the stem loop 5. Finally, we show these RNA-binding cylinders suppress SARS-CoV-2 replication, highlighting their potential as novel antiviral agents.

scholarly journals A Perspective on Extreme Open Science: Companies Sharing Compounds without Restriction

2019 ◽  
Vol 24 (5) ◽  
pp. 505-514 ◽  
Author(s):  
David H. Drewry ◽  
Carrow I. Wells ◽  
William J. Zuercher ◽  
Timothy M. Willson
Keyword(s):  
Dark Matter ◽  
Drug Discovery ◽  
Small Molecules ◽  
Drug Targets ◽  
Scientific Community ◽  
Kinase Inhibitors ◽  
Open Science ◽  
Potential Drug ◽  
Potential Drug Targets ◽  
Shed Light

Although the human genome provides the blueprint for life, most of the proteins it encodes remain poorly studied. This perspective describes how one group of scientists, in seeking new targets for drug discovery, used open science through unrestricted sharing of small molecules to shed light on dark matter of the genome. Starting initially with a single pharmaceutical company before expanding to multiple companies, a precedent was established for sharing published kinase inhibitors as chemical tools. The integration of open science and kinase chemogenomics has supported the study of many new potential drug targets by the scientific community.

Sign in / Sign up

Export Citation Format

Share Document