Targeting the YXXΦ Motifs of the SARS Coronaviruses 1 and 2 ORF3a Peptides by In Silico Analysis to Predict Novel Virus—Host Interactions

Kakkanas, Athanassios; Karamichali, Eirini; Koufogeorgou, Efthymia Ioanna; Kotsakis, Stathis D.; Georgopoulou, Urania; Foka, Pelagia

doi:10.3390/biom12081052

Cited by 5 publications

(7 citation statements)

References 138 publications

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“…The reason for the dCR3:∆aa215-234 mutant’s retention in the ER remains unclear. However, an in silico analysis of the ORF3a structure suggests that the Y233 residue might constitute another potential YXXΦ motif (aa233-236: YNKI) ( 54 ). It is also interesting to note that the dCR3:∆aa215-234 mutant encompasses a region that includes naturally occurring mutations such as Y233N and T223I, with the latter being identified in the Omicron variants ( 1 ).…”

Section: Discussionmentioning

confidence: 99%

Endoplasmic reticulum-associated SARS-CoV-2 ORF3a elicits heightened cytopathic effects despite robust ER-associated degradation

Zhang,

Cruz-Cosme,

Zhang

et al. 2024

mBio

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ORF3a protein plays a vital role in viral pathogenesis and coronavirus disease 2019 (COVID-19). Like the spike protein, ORF3a mutates frequently, and certain variants are associated with the severity of COVID-19. Given the clinical significance and functional implications of ORF3a mutations, we conducted a comprehensive mutagenesis study targeting various known functional elements and revealed two distinctive types of ORF3a proteins based on their subcellular localizations: ORF3a proteins primarily localize on the lysosomal membrane (L-ORF3a) and those present in the endoplasmic reticulum (E-ORF3a). The objective of this study was to contrast the functional and mechanistic distinctions between these two types of ORF3a proteins. We examined six distinct ORF3a mutants and assessed their effects on cellular oxidative stress, nuclear factor kappa B-induced cytokine production, and cell death. Mechanistically, we explored ORF3a-induced ER stress, autophagy, and interactions with relevant cellular proteins. Our findings indicate that ORF3a proteins induce cytopathic effects through a similar mechanism, irrespective of their subcellular location. However, E-ORF3a proteins elicit more pronounced cytopathic effects despite their lower abundance and minimal impact on ER stress and autophagy when compared to L-ORF3a proteins. This discrepancy is attributed to ER-associated degradation since ORF3a proteins bind to a ubiquitin E3 ligase TRIM59. Inhibition of the 26S proteasome partially restores the protein levels of E-ORF3a and cellular ER stress response. This suggests that even a small quantity of ORF3a can lead to significant cytopathic effects due to the delicate nature of ER. Our study underscores the intricate interplay of dynamic cellular signaling within these two subcellular compartments in response to ORF3a. IMPORTANCE The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has tragically claimed millions of lives through coronavirus disease 2019 (COVID-19), and there remains a critical gap in our understanding of the precise molecular mechanisms responsible for the associated fatality. One key viral factor of interest is the SARS-CoV-2 ORF3a protein, which has been identified as a potent inducer of host cellular proinflammatory responses capable of triggering the catastrophic cytokine storm, a primary contributor to COVID-19-related deaths. Moreover, ORF3a, much like the spike protein, exhibits a propensity for frequent mutations, with certain variants linked to the severity of COVID-19. Our previous research unveiled two distinct types of ORF3a mutant proteins, categorized by their subcellular localizations, setting the stage for a comparative investigation into the functional and mechanistic disparities between these two types of ORF3a variants. Given the clinical significance and functional implications of the natural ORF3a mutations, the findings of this study promise to provide invaluable insights into the potential roles undertaken by these mutant ORF3a proteins in the pathogenesis of COVID-19.

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Section: Discussionmentioning

confidence: 99%

Endoplasmic reticulum-associated SARS-CoV-2 ORF3a elicits heightened cytopathic effects despite robust ER-associated degradation

Zhang,

Cruz-Cosme,

Zhang

et al. 2024

mBio

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“…Further, Kakkanas et al. ( 29 ) used the same methodology and identified YXXΦ Motifs of the SARS Coronaviruses 1 and 2 ORF3a Peptides and proposed that targeting these YXXΦ Motifs might help in the prediction of by novel Host-virus interactions. This study revolves around the identification of tyrosine-based motif (YXXΦ[I/L/M/F/V]) and YXXΦ-like tetrapeptides within nucleoprotein sequences of PUUV, SEOV, DOBV, and HTNV to identify novel anti-viral targets.…”

Section: Discussionmentioning

confidence: 99%

“…YXXΦ[I/L/M/F/V] motif has a significant role in the internalization process and is typically found in the cytoplasmic domains of various transmembrane receptors, including the transferrin and asialoglycoprotein receptors ( 28 ). In the secretory and endosomal pathways, YXXΦ[I/L/M/F/V] signal motifs have dual specificity in the form of an endocytotic functional motif and a trafficking signal ( 29 ). Some viruses have incorporated these signaling motifs into their proteins and then utilize it to regulate the immune system ( 30 – 32 ).…”

Section: Introductionmentioning

confidence: 99%

Comprehensive computational analysis reveals YXXΦ[I/L/M/F/V] motif and YXXΦ-like tetrapeptides across HFRS causing Hantaviruses and their association with viral pathogenesis and host immune regulation

et al. 2022

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Hemorrhagic fever with renal syndrome (HFRS) is an acute zoonotic disease transmitted through aerosolized excrement of rodents. The etiology of HFRS is complex due to the involvement of viral factors and host immune and genetic factors. The viral species that dominantly cause HFRS are Puumala virus (PUUV), Seoul virus (SEOV), Dobrava-Belgrade virus (DOBV), and Hantaan virus (HTNV). Despite continuous prevention and control measures, HFRS remains a significant public health problem worldwide. The nucleocapsid protein of PUUV, SEOV, DOBV, and HTNV is a multifunctional viral protein involved in various stages of the viral replication cycle. However, the exact role of nucleoproteins in viral pathogenesis is yet to be discovered. Targeting a universal host protein exploited by most viruses would be a game-changing strategy that offers broad-spectrum solutions and rapid epidemic control. The objective of this study is to understand the replication and pathogenesis of PUUV, SEOV, DOBV, and HTNV by targeting tyrosine-based motif (YXXΦ[I/L/M/F/V]) and YXXΦ-like tetrapeptides. In the light of the current study, in silico analysis uncovered many different YXXΦ[I/L/M/F/V] motifs and YXXΦ-like tetrapeptides within nucleoproteins of PUUV, SEOV, DOBV, and HTNV. Following that, the 3D structures of nucleoproteins were predicted using AlphaFold2 to map the location of YXXΦ[I/L/M/F/V] motif and YXXΦ-like tetrapeptides in a 3D environment. Further, in silico analysis and characterization of Post Translational Modifications (PTMs) revealed multiple PTMs sites within YXXΦ[I/L/M/F/V] motif and YXXΦ-like tetrapeptides, which contribute to virulence and host immune regulation. Our study proposed that the predicted YXXΦ[I/L/M/F/V] motif and YXXΦ-like tetrapeptides may confer specific functions such as virulence, host immune regulation, and pathogenesis to nucleoproteins of PUUV, SEOV, DOBV, and HTNV. However, in vivo and in vitro studies on YXXΦ[I/L/M/F/V] motif and YXXΦ-like tetrapeptides will assign new biological roles to these antiviral targets.

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“…aa107-114 and aa141-149) [32]; a YXXΦ motif (aa160-163) and a diG motif (aa177-178) [31,33,34 and a PBM (aa272-275) [18,35]. A putative YXXΦ motif (aa233-236) is also indicated [36]. (B) Ce lular pathways of ORF3a-mediated effects that lead to the NLRP3 inflammasome activation an cytokine storm (a) [37][38][39], NF-κB-mediated cytokine production, apoptosis and necrosis leadin to kidney injury (b) [40], and disruption of autophagy-lysosomal pathway by ORF3a that caus reactive microglia and astrocyte activation leading to neuroinflammation and brain damage (c) [41 Elevation of kidney injury molecule 1 (KIM-1) is a specific biomarker for kidney injury [42]; elev tion of glial fibrillary acidic protein (GFAP) is a well-accepted biomarker for brain damage [43,44 [18,28]).…”

Section: Structure and Unique Features Of Orf3a Proteinmentioning

confidence: 99%

SARS-CoV-2 ORF3a Protein as a Therapeutic Target against COVID-19 and Long-Term Post-Infection Effects

Zhang,

Hom,

Zhang

et al. 2024

Pathogens

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The COVID-19 pandemic caused by SARS-CoV-2 has posed unparalleled challenges due to its rapid transmission, ability to mutate, high mortality and morbidity, and enduring health complications. Vaccines have exhibited effectiveness, but their efficacy diminishes over time while new variants continue to emerge. Antiviral medications offer a viable alternative, but their success has been inconsistent. Therefore, there remains an ongoing need to identify innovative antiviral drugs for treating COVID-19 and its post-infection complications. The ORF3a (open reading frame 3a) protein found in SARS-CoV-2, represents a promising target for antiviral treatment due to its multifaceted role in viral pathogenesis, cytokine storms, disease severity, and mortality. ORF3a contributes significantly to viral pathogenesis by facilitating viral assembly and release, essential processes in the viral life cycle, while also suppressing the body’s antiviral responses, thus aiding viral replication. ORF3a also has been implicated in triggering excessive inflammation, characterized by NF-κB-mediated cytokine production, ultimately leading to apoptotic cell death and tissue damage in the lungs, kidneys, and the central nervous system. Additionally, ORF3a triggers the activation of the NLRP3 inflammasome, inciting a cytokine storm, which is a major contributor to the severity of the disease and subsequent mortality. As with the spike protein, ORF3a also undergoes mutations, and certain mutant variants correlate with heightened disease severity in COVID-19. These mutations may influence viral replication and host cellular inflammatory responses. While establishing a direct link between ORF3a and mortality is difficult, its involvement in promoting inflammation and exacerbating disease severity likely contributes to higher mortality rates in severe COVID-19 cases. This review offers a comprehensive and detailed exploration of ORF3a’s potential as an innovative antiviral drug target. Additionally, we outline potential strategies for discovering and developing ORF3a inhibitor drugs to counteract its harmful effects, alleviate tissue damage, and reduce the severity of COVID-19 and its lingering complications.

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Targeting the YXXΦ Motifs of the SARS Coronaviruses 1 and 2 ORF3a Peptides by In Silico Analysis to Predict Novel Virus—Host Interactions

Cited by 5 publications

References 138 publications

Endoplasmic reticulum-associated SARS-CoV-2 ORF3a elicits heightened cytopathic effects despite robust ER-associated degradation

Endoplasmic reticulum-associated SARS-CoV-2 ORF3a elicits heightened cytopathic effects despite robust ER-associated degradation

Comprehensive computational analysis reveals YXXΦ[I/L/M/F/V] motif and YXXΦ-like tetrapeptides across HFRS causing Hantaviruses and their association with viral pathogenesis and host immune regulation

SARS-CoV-2 ORF3a Protein as a Therapeutic Target against COVID-19 and Long-Term Post-Infection Effects

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