Geneticin shows selective antiviral activity against SARS-CoV-2 by interfering with programmed −1 ribosomal frameshifting

Varricchio, Carmine; Mathez, Gregory; Pillonel, Trestan; Bertelli, Claire; Kaiser, Laurent; Tapparel, Caroline; Brancale, Andrea; Cagno, Valeria

doi:10.1016/j.antiviral.2022.105452

Cited by 13 publications

(28 citation statements)

References 53 publications

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“…10 Several methods have already been employed against −1 PRF, including identification of host factors, 18,30 locked nucleic acid antisense oligonucleotides, 6,22 and small molecules. 3,12,13,32,47 In conclusion, this work expands our understanding of the SARS-CoV-2 FSE by revealing its dynamic interplay with a predicted upstream multibranch loop. Our in silico studies predicted that the multibranch loop could fold independent of the FSE structure whether the FSE was in a linear or bent conformation.…”

Section: ■ Conclusionmentioning

confidence: 57%

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Structure of the SARS-CoV-2 Frameshift Stimulatory Element with an Upstream Multibranch Loop

Peterson,

Becker,

O’Leary

et al. 2024

Biochemistry

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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) frameshift stimulatory element (FSE) is necessary for programmed −1 ribosomal frameshifting (−1 PRF) and optimized viral efficacy. The FSE has an abundance of context-dependent alternate conformations, but two of the structures most crucial to −1 PRF are an attenuator hairpin and a three-stem H-type pseudoknot structure. A crystal structure of the pseudoknot alone features three RNA stems in a helically stacked linear structure, whereas a 6.9 Å cryo-EM structure including the upstream heptameric slippery site resulted in a bend between two stems. Our previous research alluded to an extended upstream multibranch loop that includes both the attenuator hairpin and the slippery site–a conformation not previously modeled. We aim to provide further context to the SARS-CoV-2 FSE via computational and medium resolution cryo-EM approaches, by presenting a 6.1 Å cryo-EM structure featuring a linear pseudoknot structure and a dynamic upstream multibranch loop.

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Section: ■ Conclusionmentioning

confidence: 57%

“…Improved RNA models can assist with therapeutic drug screening and pocket analysis . Several methods have already been employed against −1 PRF, including identification of host factors, , locked nucleic acid antisense oligonucleotides, , and small molecules. ,,,, …”

Section: Discussionmentioning

confidence: 99%

Structure of the SARS-CoV-2 Frameshift Stimulatory Element with an Upstream Multibranch Loop

Peterson,

Becker,

O’Leary

et al. 2024

Biochemistry

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“…Infection of Vero E6 with several passages was performed as described previously [ 35 ]. Briefly, Vero E6 cells (3.5 × 10 5 cells per well) were seeded on a 6-well plate.…”

Section: Methodsmentioning

confidence: 99%

“…RT-qPCRs of SARS-CoV-2 were performed with TaqPath 1-Step RT-qPCR (Thermo Fisher Scientific, Waltham, MA, USA) with primers and probe targeting the E gene (Fwd: 5′-ACAGGTACGTTAATAGTTAATAGCGT-3′, Rev: 5′-ATATTGCAGCAGTACGCACACA-3′, probe: 5′-ACACTAGCCATCCTTACTGCGCTTCG-3′) [ 37 ]. Next-generation sequencing was performed as described previously [ 35 , 38 ]. The consensus sequences represent mutations observed in more than 70% of the reads.…”

Section: Methodsmentioning

confidence: 99%

Alpha and Omicron SARS-CoV-2 Adaptation in an Upper Respiratory Tract Model

Mathez

Pillonel

Bertelli

et al. 2022

Viruses

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently causing an unprecedented pandemic. Although vaccines and antivirals are limiting the spread, SARS-CoV-2 is still under selective pressure in human and animal populations, as demonstrated by the emergence of variants of concern. To better understand the driving forces leading to new subtypes of SARS-CoV-2, we infected an ex vivo cell model of the human upper respiratory tract with Alpha and Omicron BA.1 variants for one month. Although viral RNA was detected during the entire course of the infection, infectious virus production decreased over time. Sequencing analysis did not show any adaptation in the spike protein, suggesting a key role for the adaptive immune response or adaptation to other anatomical sites for the evolution of SARS-CoV-2.

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“…Predicting and understanding frameshift inducing RNA structures in SARS-CoV-2 and related viruses is a critical target for therapeutic development [9,10]. One example is intracellular small molecule therapy [6,[11][12][13][14][15][16], a strategy to limit viral fitness by disrupting the twisted RNA structure that contacts the ribosome at multiple locations [6]. Experiments demonstrate that specific compounds can inhibit frameshift efficiency in SARS-CoV-2 [6,15] and other coronaviruses, affecting both humans and bats [17].…”

Section: Introductionmentioning

confidence: 99%

Tying the Knot: Unraveling the Intricacies of the Coronavirus Frameshift Pseudoknot

Trinity,

Stege,

Jabbari

2023

Preprint

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Understanding and targeting functional RNA structures towards treatment of coronavirus infection can help us to prepare for novel variants of SARS-CoV-2 (the virus causing COVID-19), and any other coronaviruses that could emerge via human-to-human transmission or potential zoonotic (inter-species) events. Leveraging the fact that all coronaviruses use a mechanism known as -1 programmed ribosomal frameshifting (-1 PRF) to replicate, we apply algorithms to predict the most energetically favourable secondary structures (each nucleotide involved in at most one pairing) that may be involved in regulating the -1 PRF event in coronaviruses, especially SARS-CoV-2. We compute previously unknown most stable structure predictions for the frameshift site of coronaviruses via hierarchical folding, a biologically motivated framework where initial non-crossing structure folds first, followed by subsequent, possibly crossing (pseudoknotted), structures. Using mutual information from 181 coronavirus sequences, in conjunction with the algorithm KnotAli, we compute secondary structure predictions for the frameshift site of different coronaviruses. We then utilize the Shapify algorithm to obtain most stable SARS-CoV-2 secondary structure predictions guided by frameshift sequence-specific and genome-wide experimental data. We build on our previous secondary structure investigation of the singular SARS-CoV-2 68 nt frameshift element sequence, by using Shapify to obtain predictions for 132 extended sequences and including covariation information. Previous investigations have not applied hierarchical folding to extended length SARS-CoV-2 frameshift sequences. By doing so, we simulate the effects of ribosome interaction with the frameshift site, providing insight to biological function. We contribute in-depth discussion to contextualize secondary structure dual-graph motifs for SARS-CoV-2, highlighting the energetic stability of the previously identified 3_8 motif alongside the known dominant 3_3 and 3_6 (native-type) -1 PRF structures. Integrating experimental data within minimum free energy (MFE) hierarchical folding algorithms provides novel structure predictions to distill the relationship between RNA structure and function. In particular, fully categorizing most stable secondary structure predictions via hierarchical folding supports our identification of motif transitions and critical site targets for future therapeutic research.

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Geneticin shows selective antiviral activity against SARS-CoV-2 by interfering with programmed −1 ribosomal frameshifting

Cited by 13 publications

References 53 publications

Structure of the SARS-CoV-2 Frameshift Stimulatory Element with an Upstream Multibranch Loop

Structure of the SARS-CoV-2 Frameshift Stimulatory Element with an Upstream Multibranch Loop

Alpha and Omicron SARS-CoV-2 Adaptation in an Upper Respiratory Tract Model

Tying the Knot: Unraveling the Intricacies of the Coronavirus Frameshift Pseudoknot

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