scholarly journals Anti-frameshifting ligand active against SARS coronavirus-2 is resistant to natural mutations of the frameshift-stimulatory pseudoknot

2020 ◽  
Author(s):  
Krishna Neupane ◽  
Sneha Munshi ◽  
Meng Zhao ◽  
Dustin B. Ritchie ◽  
Sandaru M. Ileperuma ◽  
...  
Keyword(s):  
Small Molecule ◽  
Viral Proteins ◽  
Therapeutic Strategies ◽  
Base Pairing ◽  
Sars Coronavirus ◽  
Ribosomal Frameshifting ◽  
Expression Levels ◽  
Viral Propagation ◽  
Small Molecule Ligands ◽  
Rna Pseudoknot

The coronavirus SARS-CoV-2 causing the COVID-19 pandemic uses −1 programmed ribosomal frameshifting (−1 PRF) to control the expression levels of key viral proteins. Because modulating −1 PRF can attenuate viral propagation, ligands binding to the viral RNA pseudoknot that stimulates −1 PRF may prove useful as therapeutics. Mutations in the pseudoknot have been observed over the course of the pandemic, but how they affect −1 PRF and the activity of inhibitors is unknown. Cataloguing natural mutations in all parts of the SARS-CoV-2 pseudoknot, we studied a panel of 6 mutations in key structural regions. Most mutations left the −1 PRF efficiency unchanged, even when base-pairing was disrupted, but one led to a remarkable three-fold decrease, suggesting that SARS-CoV-2 propagation may be less sensitive to modulation of −1 PRF efficiency than some other viruses. Examining the effects of one of the few small-molecule ligands known to suppress −1 PRF significantly in SARS-CoV, we found that it did so by similar amounts in all SARS-CoV-2 mutants tested, regardless of the basal −1 PRF efficiency, indicating that the activity of anti-frameshifting ligands can be resistant to natural pseudoknot mutations. These results have important implications for therapeutic strategies targeting SARS-CoV-2 through modulation of −1 PRF.

scholarly journals Small-molecule ligands can inhibit −1 programmed ribosomal frameshifting in a broad spectrum of coronaviruses

2021 ◽  
Author(s):  
Sneha Munshi ◽  
Krishna Neupane ◽  
Sandaru M Ileperuma ◽  
Matthew TJ Halma ◽  
Jamie A Kelly ◽  
...  
Keyword(s):  
Small Molecule ◽  
Broad Spectrum ◽  
Viral Proteins ◽  
Serine Protease Inhibitor ◽  
Viral Mrna ◽  
Ribosomal Frameshifting ◽  
Small Molecule Ligands ◽  
Spectrum Activity ◽  
Negative Controls ◽  
Broad Spectrum Activity

Recurrent outbreaks of novel zoonotic coronavirus (CoV) diseases since 2000 have high-lighted the importance of developing therapeutics with broad-spectrum activity against CoVs. Because all CoVs use −1 programmed ribosomal frameshifting (−1 PRF) to control expression of key viral proteins, the frameshift signal in viral mRNA that stimulates −1 PRF provides a promising potential target for such therapeutics. To test the viability of this strategy, we explored a group of 6 small-molecule ligands, evaluating their activity against the frameshift signals from a panel of representative bat CoVs—the most likely source of future zoonoses—as well as SARS-CoV-2 and MERS-CoV. We found that whereas some ligands had notable activity against only a few of the frameshift signals, the serine protease inhibitor nafamostat suppressed −1 PRF significantly in several of them, while having limited to no effect on −1 PRF caused by frameshift signals from other viruses used as negative controls. These results suggest it is possible to find small-molecule ligands that inhibit −1 PRF specifically in a broad spectrum of CoVs, establishing the frameshift signal as a viable target for developing pan-coronaviral therapeutics.

scholarly journals Modeling the structure of the frameshift stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers

2020 ◽  
Author(s):  
Sara Ibrahim Omar ◽  
Meng Zhao ◽  
Rohith Vedhthaanth Sekar ◽  
Sahar Arbabi Moghadam ◽  
Jack A. Tuszynski ◽  
...  
Keyword(s):  
Single Molecule ◽  
Structural Models ◽  
Viral Proteins ◽  
Single Molecule Force Spectroscopy ◽  
Ribosomal Frameshifting ◽  
Structural Prediction ◽  
Prediction Tools ◽  
Dynamics Simulations ◽  
Rna Pseudoknot ◽  
Stem Structure

The coronavirus causing the COVID-19 pandemic, SARS-CoV-2, uses −1 programmed ribosomal frameshifting (−1 PRF) to control the relative expression of viral proteins. As modulating −1 PRF can inhibit viral replication, the RNA pseudoknot stimulating −1 PRF may be a fruitful target for therapeutics treating COVID-19. We modeled the unusual 3-stem structure of the stimulatory pseudoknot of SARS-CoV-2 computationally, using multiple blind structural prediction tools followed by μs-long molecular dynamics simulations. The results were compared for consistency with nuclease-protection assays and single-molecule force spectroscopy measurements of the SARS-CoV-1 pseudoknot, to determine the most likely conformations. We found several possible conformations for the SARS-CoV-2 pseudoknot, all having an extended stem 3 but with different packing of stems 1 and 2. Several conformations featured rarely-seen threading of a single strand through the junction formed between two helices. These structural models may help interpret future experiments and support efforts to discover ligands inhibiting −1 PRF in SARS-CoV-2.

scholarly journals Augmented base pairing networks encode RNA-small molecule binding preferences

2019 ◽  
Author(s):  
Carlos Oliver ◽  
Vincent Mallet ◽  
Roman Sarrazin Gendron ◽  
Vladimir Reinharz ◽  
William L. Hamilton ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Small Molecule ◽  
Binding Sites ◽  
Rna Binding ◽  
Graph Representation ◽  
Learning Approaches ◽  
Base Pairing ◽  
Binding Prediction ◽  
Structural Patterns ◽  
Small Molecule Ligands

AbstractMotivationThe binding of small molecules to RNAs is an important mechanism which can stabilize 3D structures or activate key molecular functions. To date, computational and experimental efforts toward small molecule binding prediction have primarily focused on protein targets. Considering that a very large portion of the genome is transcribed into non-coding RNAs but only few regions are translated into proteins, successful annotations of RNA elements targeted by small-molecule would likely uncover a vast repertoire of biological pathways and possibly lead to new therapeutic avenues.ResultsOur work is a first attempt at bringing machine learning approaches to the problem of RNA drug discovery. RNAmigos takes advantage of the unique structural properties of RNA to predict small molecule ligands for unseen binding sites. A key feature of our model is an efficient representation of binding sites as augmented base pairing networks (ABPNs) aimed at encoding important structural patterns. We subject our ligand predictions to two virtual screen settings and show that we are able to rank the known ligand on average in the 73rd percentile, showing a significant improvement over several baselines. Furthermore, we observe that graphs which are augmented with non-Watson Crick (a.k.a non-canonical) base pairs are the only representation which is able to retrieve a significant signal, suggesting that non-canonical interactions are an necessary source of binding specificity in RNAs. We also find that an auxiliary graph representation task significantly boosts performance by providing efficient structural embeddings to the low data setting of ligand prediction. RNAmigos shows that RNA binding data contains structural patterns with potential for drug discovery, and provides methodological insights which can be applied to other structure-function learning tasks.AvailabilityCode and data is freely available at http://csb.cs.mcgill.ca/[email protected]

scholarly journals Crystal structure of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) frameshifting pseudoknot

RNA ◽  
2021 ◽  
pp. rna.078825.121
Author(s):  
Christopher P Jones ◽  
Adrian R Ferre-D'Amare
Keyword(s):  
Crystal Structure ◽  
Severe Acute Respiratory Syndrome ◽  
Small Molecule ◽  
Viral Protein ◽  
Open Reading Frame ◽  
Ribosomal Frameshifting ◽  
Reading Frame ◽  
X Ray ◽  
Rna Pseudoknot ◽  
Small Molecule Therapeutics

SARS-CoV-2 produces two long viral protein precursors from one open reading frame using a highly conserved RNA pseudoknot that enhances programmed -1 ribosomal frameshifting. The 1.3 Å-resolution X-ray structure of the pseudoknot reveals three coaxially stacked helices buttressed by idiosyncratic base triples from loop residues. This structure represents a frameshift-stimulating state that must be deformed by the ribosome, and exhibits base-triple-adjacent pockets that could be targeted by future small-molecule therapeutics.

scholarly journals Modeling the structure of the frameshift-stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers

2021 ◽  
Vol 17 (1) ◽  
pp. e1008603
Author(s):  
Sara Ibrahim Omar ◽  
Meng Zhao ◽  
Rohith Vedhthaanth Sekar ◽  
Sahar Arbabi Moghadam ◽  
Jack A. Tuszynski ◽  
...  
Keyword(s):  
Single Molecule ◽  
Structural Models ◽  
Viral Proteins ◽  
Single Molecule Force Spectroscopy ◽  
Ribosomal Frameshifting ◽  
Structural Prediction ◽  
Prediction Tools ◽  
Dynamics Simulations ◽  
Rna Pseudoknot ◽  
Stem Structure

The coronavirus causing the COVID-19 pandemic, SARS-CoV-2, uses −1 programmed ribosomal frameshifting (−1 PRF) to control the relative expression of viral proteins. As modulating −1 PRF can inhibit viral replication, the RNA pseudoknot stimulating −1 PRF may be a fruitful target for therapeutics treating COVID-19. We modeled the unusual 3-stem structure of the stimulatory pseudoknot of SARS-CoV-2 computationally, using multiple blind structural prediction tools followed by μs-long molecular dynamics simulations. The results were compared for consistency with nuclease-protection assays and single-molecule force spectroscopy measurements of the SARS-CoV-1 pseudoknot, to determine the most likely conformations. We found several possible conformations for the SARS-CoV-2 pseudoknot, all having an extended stem 3 but with different packing of stems 1 and 2. Several conformations featured rarely-seen threading of a single strand through junctions formed between two helices. These structural models may help interpret future experiments and support efforts to discover ligands inhibiting −1 PRF in SARS-CoV-2.

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