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1.
Virologie (Montrouge) ; 28(3): 187-197, 2024 Jun 01.
Artículo en Francés | MEDLINE | ID: mdl-38970340

RESUMEN

Orthoflaviviruses are enveloped positive-sense RNA viruses comprising numerous human pathogens transmitted by hematophagous arthropods. This includes viruses such as dengue virus, Zika virus, and yellow fever virus. The viral nonstructural protein NS1 plays a central role in the pathogenesis and cycle of these viruses by acting in two different forms: associated with the plasma membrane (NS1m) or secreted outside the cell (NS1s). The versatility of NS1 is evident in its ability to modulate various aspects of the infectious process, from immune evasion to pathogenesis. As an intracellular protein, it disrupts many processes, interfering with signaling pathways and facilitating viral replication in concert with other viral proteins. As a secreted protein, NS1 actively participates in immune evasion, interfering with the host immune system, inhibiting the complement system, facilitating viral dissemination, and disrupting the integrity of endothelial barriers. This review primarily aims to address the role of NS1 in viral pathogenesis associated with orthoflaviviruses.


Asunto(s)
Proteínas no Estructurales Virales , Replicación Viral , Proteínas no Estructurales Virales/metabolismo , Proteínas no Estructurales Virales/fisiología , Humanos , Animales , Infecciones por Flavivirus/virología , Evasión Inmune , Flavivirus/fisiología , Flavivirus/patogenicidad , Virus Zika/fisiología , Virus Zika/patogenicidad , Virus del Dengue/fisiología
3.
Methods Mol Biol ; 2824: 105-120, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-39039409

RESUMEN

The Rift Valley fever virus is one of the bunyaviruses on the WHO's priority list of pathogens that may cause future pandemics. A better understanding of disease progression and viral pathogenesis is urgently needed to develop treatments. The non-structural proteins NSs and NSm of human pathogenic bunyaviruses represent promising therapeutic targets, as they are often key virulence factors. However, their function is still poorly understood, and their structure is yet unknown, mainly because no successful production of these highly complex proteins has been reported. Here we propose a powerful combination of wheat germ cell-free protein synthesis and NMR to study the structure of these proteins and in particular detail cell-free synthesis and lipid reconstitution methods that can be applied to complex membrane proteins.


Asunto(s)
Sistema Libre de Células , Humanos , Espectroscopía de Resonancia Magnética/métodos , Proteínas no Estructurales Virales/metabolismo , Proteínas no Estructurales Virales/química , Triticum/metabolismo , Resonancia Magnética Nuclear Biomolecular/métodos , Biosíntesis de Proteínas , Virus de la Fiebre del Valle del Rift , Proteínas Virales/metabolismo , Proteínas Virales/química
4.
Methods Mol Biol ; 2824: 147-164, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-39039412

RESUMEN

Single-domain antibodies, referred to as VHH (variable heavy chains of heavy chain-only antibodies) or in their commercial name as nanobodies, are potent tools for the detection of target proteins in biological samples. They have the advantage of being highly stable, specific, and sensitive, with affinities reaching the nanomolar range. We utilized this tool to develop a rapid detection method that discriminates cells infected with Rift Valley fever virus (RVFV), based on the intracellular detection of the viral nonstructural NSm protein localized on the outer membrane of mitochondria. Here we describe how NSm-specific VHHs have been produced, cloned, and characterized, highlighting their value in RVFV research and diagnosis. This work may also raise interest in other potential applications such as antiviral therapy.


Asunto(s)
Fiebre del Valle del Rift , Virus de la Fiebre del Valle del Rift , Anticuerpos de Dominio Único , Proteínas no Estructurales Virales , Virus de la Fiebre del Valle del Rift/inmunología , Anticuerpos de Dominio Único/inmunología , Humanos , Fiebre del Valle del Rift/inmunología , Fiebre del Valle del Rift/diagnóstico , Fiebre del Valle del Rift/virología , Proteínas no Estructurales Virales/inmunología , Animales , Anticuerpos Antivirales/inmunología
5.
Methods Mol Biol ; 2824: 397-408, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-39039426

RESUMEN

The NSs protein is a major virulence factor in bunyaviruses, crucial for viral pathogenesis. However, assessing NSs protein function can be challenging due to its inhibition of cellular RNA polymerase II, impacting NSs protein expression from plasmid DNA. The recombinant Rift Valley fever virus (RVFV) MP-12 strain (rMP-12), a highly attenuated vaccine strain, can be safely manipulated under biosafety level 2 conditions. Leveraging a reverse genetics system, we can engineer rMP-12 variants expressing heterologous NSs genes, enabling functional testing in cultured cells. Human macrophages hold a central role in viral pathogenesis, making them an ideal model for assessing NSs protein functions. Consequently, we can comprehensively compare and analyze the functional significance of various NSs proteins in human macrophages using rMP-12 NSs variants. In this chapter, we provide a detailed overview of the preparation process for rMP-12 NSs variants and introduce two distinct human macrophage models: THP-1 cells and primary macrophages. This research framework promises valuable insights into the virulence mechanisms of RVFV and other bunyaviruses and the potential for vaccine development.


Asunto(s)
Macrófagos , Virus de la Fiebre del Valle del Rift , Proteínas no Estructurales Virales , Humanos , Macrófagos/virología , Macrófagos/inmunología , Virus de la Fiebre del Valle del Rift/genética , Virus de la Fiebre del Valle del Rift/patogenicidad , Proteínas no Estructurales Virales/genética , Proteínas no Estructurales Virales/metabolismo , Células THP-1
6.
BMC Infect Dis ; 24(1): 688, 2024 Jul 10.
Artículo en Inglés | MEDLINE | ID: mdl-38987682

RESUMEN

BACKGROUND: Dengue fever has become a significant worldwide health concern, because of its high morbidity rate and the potential for an increase in mortality rates due to lack of adequate treatment. There is an immediate need for the development of effective medication for dengue fever. METHODS: Homology modeling of dengue virus (DENV) non-structural 4B (NS4B) protein was performed by SWISS-MODEL to predict the 3D structure of the protein. Structure validation was conducted using PROSA, PROCHECK, Ramachandran plot, and VERIFY-3D. MOE software was used to find out the in-Silico inhibitory potential of the five triterpenoids against the DENV-NS4B protein. RESULTS: The SWISS-MODEL was employed to predict the three-dimensional protein structure of the NS4B protein. Through molecular docking, it was found that the chosen triterpenoid NS4B protein had a high binding affinity interaction. It was observed that the NS4B protein binding energy for 15-oxoursolic acid, betulinic acid, ursolic acid, lupeol, and 3-o-acetylursolic acid were - 7.18, - 7.02, - 5.71, - 6.67 and - 8.00 kcal/mol, respectively. CONCLUSIONS: NS4B protein could be a promising target which showed good interaction with tested triterpenoids which can be developed as a potential antiviral drug for controlling dengue virus pathogenesis by inhibiting viral replication. However, further investigations are necessary to validate and confirm their efficacy.


Asunto(s)
Antivirales , Virus del Dengue , Simulación del Acoplamiento Molecular , Triterpenos , Proteínas no Estructurales Virales , Proteínas no Estructurales Virales/química , Proteínas no Estructurales Virales/metabolismo , Triterpenos/farmacología , Triterpenos/química , Virus del Dengue/efectos de los fármacos , Virus del Dengue/química , Antivirales/farmacología , Antivirales/química , Unión Proteica , Humanos , Dengue/virología , Dengue/tratamiento farmacológico , Conformación Proteica , Proteínas de la Membrana
7.
ACS Chem Biol ; 19(7): 1648-1660, 2024 Jul 19.
Artículo en Inglés | MEDLINE | ID: mdl-38954741

RESUMEN

Hepatitis C virus (HCV) is a positive-stranded RNA virus that mainly causes chronic hepatitis, cirrhosis and hepatocellular carcinoma. Recently we confirmed m5C modifications within NS5A gene of HCV RNA genome. However, the roles of the m5C modification and its interaction with host proteins in regulating HCV's life cycle, remain unexplored. Here, we demonstrate that HCV infection enhances the expression of the host m5C reader YBX1 through the transcription factor MAX. YBX1 acts as an m5C reader, recognizing the m5C-modified NS5A C7525 site in the HCV RNA genome and significantly enhancing HCV RNA stability. This m5C-modification is also required for YBX1 colocalization with lipid droplets and HCV Core protein. Moreover, YBX1 facilitates HCV RNA replication, as well as viral assembly/budding. The tryptophan residue at position 65 (W65) of YBX1 is critical for these functions. Knockout of YBX1 or the application of YBX1 inhibitor SU056 suppresses HCV RNA replication and viral protein translation. To our knowledge, this is the first report demonstrating that the interaction between host m5C reader YBX1 and HCV RNA m5C methylation facilitates viral replication. Therefore, hepatic-YBX1 knockdown holds promise as a potential host-directed strategy for HCV therapy.


Asunto(s)
Hepacivirus , ARN Viral , Replicación Viral , Proteína 1 de Unión a la Caja Y , Hepacivirus/fisiología , Hepacivirus/efectos de los fármacos , Proteína 1 de Unión a la Caja Y/metabolismo , Humanos , Replicación Viral/efectos de los fármacos , ARN Viral/metabolismo , ARN Viral/genética , Proteínas no Estructurales Virales/metabolismo , Proteínas no Estructurales Virales/genética , Replicación de ARN , ARN Polimerasa Dependiente del ARN
8.
ACS Chem Biol ; 19(7): 1593-1603, 2024 Jul 19.
Artículo en Inglés | MEDLINE | ID: mdl-38980755

RESUMEN

The recent pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) highlighted a critical need to discover more effective antivirals. While therapeutics for SARS-CoV-2 exist, its nonstructural protein 13 (Nsp13) remains a clinically untapped target. Nsp13 is a helicase responsible for unwinding double-stranded RNA during viral replication and is essential for propagation. Like other helicases, Nsp13 has two active sites: a nucleotide binding site that hydrolyzes nucleoside triphosphates (NTPs) and a nucleic acid binding channel that unwinds double-stranded RNA or DNA. Targeting viral helicases with small molecules, as well as the identification of ligand binding pockets, have been ongoing challenges, partly due to the flexible nature of these proteins. Here, we use a virtual screen to identify ligands of Nsp13 from a collection of clinically used drugs. We find that a known ion channel inhibitor, IOWH-032, inhibits the dual ATPase and helicase activities of SARS-CoV-2 Nsp13 at low micromolar concentrations. Kinetic and binding assays, along with computational and mutational analyses, indicate that IOWH-032 interacts with the RNA binding interface, leading to displacement of nucleic acid substrate, but not bound ATP. Evaluation of IOWH-032 with microbial helicases from other superfamilies reveals that it is selective for coronavirus Nsp13. Furthermore, it remains active against mutants representative of observed SARS-CoV-2 variants. Overall, this work provides a new inhibitor for Nsp13 and provides a rationale for a recent observation that IOWH-032 lowers SARS-CoV-2 viral loads in human cells, setting the stage for the discovery of other potent viral helicase modulators.


Asunto(s)
Antivirales , Reposicionamiento de Medicamentos , SARS-CoV-2 , Proteínas no Estructurales Virales , SARS-CoV-2/efectos de los fármacos , Proteínas no Estructurales Virales/metabolismo , Proteínas no Estructurales Virales/antagonistas & inhibidores , Antivirales/farmacología , Antivirales/química , Humanos , ARN Helicasas/metabolismo , ARN Helicasas/antagonistas & inhibidores , COVID-19/virología , Ácidos Nucleicos/metabolismo , Ácidos Nucleicos/química , Betacoronavirus/efectos de los fármacos , Tratamiento Farmacológico de COVID-19 , Adenosina Trifosfatasas/metabolismo , Adenosina Trifosfatasas/antagonistas & inhibidores , Metiltransferasas
9.
Proc Natl Acad Sci U S A ; 121(29): e2317977121, 2024 Jul 16.
Artículo en Inglés | MEDLINE | ID: mdl-38990941

RESUMEN

In a recent characterization of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variability present in 30 diagnostic samples from patients of the first COVID-19 pandemic wave, 41 amino acid substitutions were documented in the RNA-dependent RNA polymerase (RdRp) nsp12. Eight substitutions were selected in this work to determine whether they had an impact on the RdRp activity of the SARS-CoV-2 nsp12-nsp8-nsp7 replication complex. Three of these substitutions were found around the polymerase central cavity, in the template entry channel (D499G and M668V), and within the motif B (V560A), and they showed polymerization rates similar to the wild type RdRp. The remaining five mutations (P323L, L372F, L372P, V373A, and L527H) were placed near the nsp12-nsp8F contact surface; residues L372, V373, and L527 participated in a large hydrophobic cluster involving contacts between two helices in the nsp12 fingers and the long α-helix of nsp8F. The presence of any of these five amino acid substitutions resulted in important alterations in the RNA polymerization activity. Comparative primer elongation assays showed different behavior depending on the hydrophobicity of their side chains. The substitution of L by the bulkier F side chain at position 372 slightly promoted RdRp activity. However, this activity was dramatically reduced with the L372P, and L527H mutations, and to a lesser extent with V373A, all of which weaken the hydrophobic interactions within the cluster. Additional mutations, specifically designed to disrupt the nsp12-nsp8F interactions (nsp12-V330S, nsp12-V341S, and nsp8-R111A/D112A), also resulted in an impaired RdRp activity, further illustrating the importance of this contact interface in the regulation of RNA synthesis.


Asunto(s)
Mutación Puntual , ARN Viral , SARS-CoV-2 , Proteínas no Estructurales Virales , SARS-CoV-2/genética , SARS-CoV-2/metabolismo , Proteínas no Estructurales Virales/genética , Proteínas no Estructurales Virales/metabolismo , Proteínas no Estructurales Virales/química , ARN Viral/genética , ARN Viral/metabolismo , Humanos , ARN Polimerasa Dependiente de ARN de Coronavirus/genética , ARN Polimerasa Dependiente de ARN de Coronavirus/metabolismo , Polimerizacion , COVID-19/virología , Sustitución de Aminoácidos , ARN Polimerasa Dependiente del ARN/genética , ARN Polimerasa Dependiente del ARN/metabolismo , Modelos Moleculares
10.
Sci Rep ; 14(1): 16363, 2024 Jul 16.
Artículo en Inglés | MEDLINE | ID: mdl-39013947

RESUMEN

Resistance-associated substitutions (RASs) of hepatitis C virus (HCV) affect the efficacy of direct-acting antivirals (DAAs). In this study, we aimed to clarify the susceptibility of the coexistence of nonstructural (NS) 5A Q24K/L28M/R30Q (or R30E)/A92K RASs, which were observed in patients with DAAs re-treatment failure and to consider new therapeutic agents. We used a subgenomic replicon system in which HCV genotype 1B strain 1B-4 was electroporated into OR6c cells derived from HuH-7 cells (Wild-type [WT]). We converted WT genes to NS5A Q24K/L28M/R30Q/A92K or Q24/L28K/R30E/A92K. Compared with the WT, the Q24K/L28M/R30Q/A92K RASs was 36,000-fold resistant to daclatasvir, 440,000-fold resistant to ledipasvir, 6300-fold resistant to velpatasvir, 3100-fold resistant to elbasvir, and 1.8-fold resistant to pibrentasvir. Compared with the WT, the Q24K/L28M/R30E/A92K RASs was 640,000-fold resistant to daclatasvir and ledipasvir, 150,000-fold resistant to velpatasvir, 44,000-fold resistant to elbasvir, and 1500-fold resistant to pibrentasvir. The Q24K/L28M/R30E/A92K RASs was 816.3 times more resistant to pibrentasvir than the Q24K/L28M/R30Q/A92K RASs. Furthermore, a combination of pibrentasvir and sofosbuvir showed therapeutic efficacy against these RASs. Combination regimens may eradicate HCV with NS5A Q24K/L28M/R30E/A92K RASs.


Asunto(s)
Antivirales , Bencimidazoles , Farmacorresistencia Viral , Hepacivirus , Imidazoles , Proteínas no Estructurales Virales , Hepacivirus/efectos de los fármacos , Hepacivirus/genética , Proteínas no Estructurales Virales/genética , Proteínas no Estructurales Virales/antagonistas & inhibidores , Humanos , Antivirales/farmacología , Antivirales/uso terapéutico , Farmacorresistencia Viral/genética , Farmacorresistencia Viral/efectos de los fármacos , Bencimidazoles/farmacología , Imidazoles/farmacología , Carbamatos/farmacología , Fluorenos/farmacología , Sofosbuvir/farmacología , Pirrolidinas/farmacología , Compuestos Heterocíclicos de 4 o más Anillos/farmacología , Valina/análogos & derivados , Valina/farmacología , Genotipo , Replicón/efectos de los fármacos , Replicón/genética , Sulfonamidas/farmacología , Benzofuranos/farmacología , Pirazinas/farmacología , Benzopiranos , ARN Polimerasa Dependiente del ARN
11.
Nat Commun ; 15(1): 6080, 2024 Jul 19.
Artículo en Inglés | MEDLINE | ID: mdl-39030239

RESUMEN

Dengue fever represents a significant medical and socio-economic burden in (sub)tropical regions, yet antivirals for treatment or prophylaxis are lacking. JNJ-A07 was described as highly active against the different genotypes within each serotype of the disease-causing dengue virus (DENV). Based on clustering of resistance mutations it has been assumed to target DENV non-structural protein 4B (NS4B). Using a photoaffinity labeling compound with high structural similarity to JNJ-A07, here we demonstrate binding to NS4B and its precursor NS4A-2K-NS4B. Consistently, we report recruitment of the compound to intracellular sites enriched for these proteins. We further specify the mechanism-of-action of JNJ-A07, which has virtually no effect on viral polyprotein cleavage, but targets the interaction between the NS2B/NS3 protease/helicase complex and the NS4A-2K-NS4B cleavage intermediate. This interaction is functionally linked to de novo formation of vesicle packets (VPs), the sites of DENV RNA replication. JNJ-A07 blocks VPs biogenesis with little effect on established ones. A similar mechanism-of-action was found for another NS4B inhibitor, NITD-688. In summary, we unravel the antiviral mechanism of these NS4B-targeting molecules and show how DENV employs a short-lived cleavage intermediate to carry out an early step of the viral life cycle.


Asunto(s)
Antivirales , Virus del Dengue , Dengue , Proteínas no Estructurales Virales , Replicación Viral , Virus del Dengue/efectos de los fármacos , Virus del Dengue/genética , Virus del Dengue/fisiología , Proteínas no Estructurales Virales/metabolismo , Proteínas no Estructurales Virales/genética , Proteínas no Estructurales Virales/antagonistas & inhibidores , Replicación Viral/efectos de los fármacos , Antivirales/farmacología , Humanos , Dengue/virología , Dengue/tratamiento farmacológico , Serogrupo , ARN Helicasas/metabolismo , ARN Helicasas/antagonistas & inhibidores , ARN Helicasas/genética , Serina Endopeptidasas/metabolismo , Serina Endopeptidasas/genética , Unión Proteica , Animales , Orgánulos/metabolismo , Orgánulos/efectos de los fármacos , Proteasas Virales , Aminofenoles , Proteínas de la Membrana , Indoles , ARN Helicasas DEAD-box , Nucleósido-Trifosfatasa , Butiratos
12.
PLoS Pathog ; 20(7): e1011909, 2024 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-38976719

RESUMEN

Viruses are obligate intracellular parasites that rely on host cell metabolism for successful replication. Thus, viruses rewire host cell pathways involved in central carbon metabolism to increase the availability of building blocks for successful propagation. However, the underlying mechanisms of virus-induced alterations to host metabolism are largely unknown. Noroviruses (NoVs) are highly prevalent pathogens that cause sporadic and epidemic viral gastroenteritis. In the present study, we uncovered several strain-specific and shared host cell metabolic requirements of three murine norovirus (MNV) strains, MNV-1, CR3, and CR6. While all three strains required glycolysis, glutaminolysis, and the pentose phosphate pathway for optimal infection of macrophages, only MNV-1 relied on host oxidative phosphorylation. Furthermore, the first metabolic flux analysis of NoV-infected cells revealed that both glycolysis and glutaminolysis are upregulated during MNV-1 infection of macrophages. Glutamine deprivation affected the viral lifecycle at the stage of genome replication, resulting in decreased non-structural and structural protein synthesis, viral assembly, and egress. Mechanistic studies further showed that MNV infection and overexpression of the non-structural protein NS1/2 increased the enzymatic activity of the rate-limiting enzyme glutaminase. In conclusion, the inaugural investigation of NoV-induced alterations to host glutaminolysis identified NS1/2 as the first viral molecule for RNA viruses that regulates glutaminolysis either directly or indirectly. This increases our fundamental understanding of virus-induced metabolic alterations and may lead to improvements in the cultivation of human NoVs.


Asunto(s)
Infecciones por Caliciviridae , Glutamina , Norovirus , Proteínas no Estructurales Virales , Replicación Viral , Norovirus/fisiología , Replicación Viral/fisiología , Ratones , Animales , Proteínas no Estructurales Virales/metabolismo , Proteínas no Estructurales Virales/genética , Glutamina/metabolismo , Infecciones por Caliciviridae/virología , Infecciones por Caliciviridae/metabolismo , Macrófagos/virología , Macrófagos/metabolismo , Humanos , Glutaminasa/metabolismo , Glucólisis/fisiología , Células RAW 264.7
13.
Virulence ; 15(1): 2379371, 2024 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-39014540

RESUMEN

The economic losses caused by high pathogenicity (HP) avian influenza viruses (AIV) in the poultry industry worldwide are enormous. Although chickens and turkeys are closely related Galliformes, turkeys are thought to be a bridging host for the adaptation of AIV from wild birds to poultry because of their high susceptibility to AIV infections. HPAIV evolve from low pathogenicity (LP) AIV after circulation in poultry through mutations in different viral proteins, including the non-structural protein (NS1), a major interferon (IFN) antagonist of AIV. At present, it is largely unknown whether the virulence determinants of HPAIV are the same in turkeys and chickens. Previously, we showed that mutations in the NS1 of HPAIV H7N1 significantly reduced viral replication in chickens in vitro and in vivo. Here, we investigated the effect of NS1 on the replication and virulence of HPAIV H7N1 in turkeys after inoculation with recombinant H7N1 carrying a naturally truncated wild-type NS1 (with 224 amino-acid "aa" in length) or an extended NS1 with 230-aa similar to the LP H7N1 ancestor. There were no significant differences in multiple-cycle viral replication or in the efficiency of NS1 in blocking IFN induction in the cell culture. Similarly, all viruses were highly virulent in turkeys and replicated at similar levels in various organs and swabs collected from the inoculated turkeys. These results suggest that NS1 does not play a role in the virulence or replication of HPAIV H7N1 in turkeys and further indicate that the genetic determinants of HPAIV differ in these two closely related galliform species.


Asunto(s)
Pollos , Subtipo H7N1 del Virus de la Influenza A , Gripe Aviar , Pavos , Proteínas no Estructurales Virales , Tropismo Viral , Replicación Viral , Animales , Pavos/virología , Proteínas no Estructurales Virales/genética , Proteínas no Estructurales Virales/metabolismo , Gripe Aviar/virología , Subtipo H7N1 del Virus de la Influenza A/genética , Subtipo H7N1 del Virus de la Influenza A/patogenicidad , Pollos/virología , Virulencia , Enfermedades de las Aves de Corral/virología
14.
Front Immunol ; 15: 1424307, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-39011043

RESUMEN

Introduction: Bluetongue (BT) poses a significant threat to the livestock industry, affecting various animal species and resulting in substantial economic losses. The existence of numerous BT virus (BTV) serotypes has hindered control efforts, highlighting the need for broad-spectrum vaccines. Methodology: In this study, we evaluated the conserved amino acid sequences within key non-structural (NS) proteins of BTV and identified numerous highly conserved murine- and bovine-specific MHC class I-restricted (MHC-I) CD8+ and MHC-II-restricted CD4+ epitopes. We then screened these conserved epitopes for antigenicity, allergenicity, toxicity, and solubility. Using these epitopes, we developed in silico-based broad-spectrum multiepitope vaccines with Toll-like receptor (TLR-4) agonists. The predicted proinflammatory cytokine response was assessed in silico using the C-IMMSIM server. Structural modeling and refinement were achieved using Robetta and GalaxyWEB servers. Finally, we assessed the stability of the docking complexes through extensive 100-nanosecond molecular dynamics simulations before considering the vaccines for codon optimization and in silico cloning. Results: We found many epitopes that meet these criteria within NS1 and NS2 proteins and developed in silico broad-spectrum vaccines. The immune simulation studies revealed that these vaccines induce high levels of IFN-γ and IL-2 in the vaccinated groups. Protein-protein docking analysis demonstrated promising epitopes with strong binding affinities to TLR-4. The docked complexes were stable, with minimal Root Mean Square Deviation and Root Mean Square Fluctuation values. Finally, the in silico-cloned plasmids have high % of GC content with > 0.8 codon adaptation index, suggesting they are suitable for expressing the protein vaccines in prokaryotic system. Discussion: These next-generation vaccine designs are promising and warrant further investigation in wet lab experiments to assess their immunogenicity, safety, and efficacy for practical application in livestock. Our findings offer a robust framework for developing a comprehensive, broad-spectrum vaccine, potentially revolutionizing BT control and prevention strategies in the livestock industry.


Asunto(s)
Virus de la Lengua Azul , Biología Computacional , Epítopos de Linfocito T , Proteínas no Estructurales Virales , Vacunas Virales , Animales , Virus de la Lengua Azul/inmunología , Epítopos de Linfocito T/inmunología , Vacunas Virales/inmunología , Proteínas no Estructurales Virales/inmunología , Proteínas no Estructurales Virales/genética , Ratones , Biología Computacional/métodos , Serogrupo , Bovinos , Lengua Azul/prevención & control , Lengua Azul/inmunología , Lengua Azul/virología , Secuencia Conservada
15.
PLoS Biol ; 22(7): e3002709, 2024 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-39012844

RESUMEN

RNA viruses have notoriously high mutation rates due to error-prone replication by their RNA polymerase. However, natural selection concentrates variability in a few key viral proteins. To test whether this stems from different mutation tolerance profiles among viral proteins, we measured the effect of >40,000 non-synonymous mutations across the full proteome of coxsackievirus B3 as well as >97% of all possible codon deletions in the nonstructural proteins. We find significant variation in mutational tolerance within and between individual viral proteins, which correlated with both general and protein-specific structural and functional attributes. Furthermore, mutational fitness effects remained stable across cell lines, suggesting selection pressures are mostly conserved across environments. In addition to providing a rich dataset for understanding virus biology and evolution, our results illustrate that incorporation of mutational tolerance data into druggable pocket discovery can aid in selecting targets with high barriers to drug resistance.


Asunto(s)
Enterovirus Humano B , Mutación , Proteoma , Enterovirus Humano B/genética , Proteoma/metabolismo , Humanos , Proteínas Virales/genética , Proteínas Virales/metabolismo , Aptitud Genética , Replicación Viral/genética , Proteínas no Estructurales Virales/genética , Proteínas no Estructurales Virales/metabolismo
16.
Math Biosci Eng ; 21(5): 5996-6018, 2024 May 20.
Artículo en Inglés | MEDLINE | ID: mdl-38872567

RESUMEN

Severe acute respiratory syndrome coronavirus 2 (SARS­CoV­2) has been evolving rapidly after causing havoc worldwide in 2020. Since then, it has been very hard to contain the virus owing to its frequently mutating nature. Changes in its genome lead to viral evolution, rendering it more resistant to existing vaccines and drugs. Predicting viral mutations beforehand will help in gearing up against more infectious and virulent versions of the virus in turn decreasing the damage caused by them. In this paper, we have proposed different NMT (neural machine translation) architectures based on RNNs (recurrent neural networks) to predict mutations in the SARS-CoV-2-selected non-structural proteins (NSP), i.e., NSP1, NSP3, NSP5, NSP8, NSP9, NSP13, and NSP15. First, we created and pre-processed the pairs of sequences from two languages using k-means clustering and nearest neighbors for training a neural translation machine. We also provided insights for training NMTs on long biological sequences. In addition, we evaluated and benchmarked our models to demonstrate their efficiency and reliability.


Asunto(s)
COVID-19 , Genoma Viral , Mutación , Redes Neurales de la Computación , SARS-CoV-2 , Proteínas no Estructurales Virales , SARS-CoV-2/genética , Humanos , COVID-19/virología , COVID-19/transmisión , Proteínas no Estructurales Virales/genética , Algoritmos
17.
Front Immunol ; 15: 1395809, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38938568

RESUMEN

Human respiratory viruses are the most prevalent cause of disease in humans, with the highly infectious RSV being the leading cause of infant bronchiolitis and viral pneumonia. Responses to type I IFNs are the primary defense against viral infection. However, RSV proteins have been shown to antagonize type I IFN-mediated antiviral innate immunity, specifically dampening intracellular IFN signaling. Respiratory epithelial cells are the main target for RSV infection. In this study, we found RSV-NS1 interfered with the IFN-α JAK/STAT signaling pathway of epithelial cells. RSV-NS1 expression significantly enhanced IFN-α-mediated phosphorylation of STAT1, but not pSTAT2; and neither STAT1 nor STAT2 total protein levels were affected by RSV-NS1. However, expression of RSV-NS1 significantly reduced ISRE and GAS promoter activity and anti-viral IRG expression. Further mechanistic studies demonstrated RSV-NS1 bound STAT1, with protein modeling indicating a possible interaction site between STAT1 and RSV-NS1. Nuclear translocation of STAT1 was reduced in the presence of RSV-NS1. Additionally, STAT1's interaction with the nuclear transport adapter protein, KPNA1, was also reduced, suggesting a mechanism by which RSV blocks STAT1 nuclear translocation. Indeed, reducing STAT1's access to the nucleus may explain RSV's suppression of IFN JAK/STAT promoter activation and antiviral gene induction. Taken together these results describe a novel mechanism by which RSV controls antiviral IFN-α JAK/STAT responses, which enhances our understanding of RSV's respiratory disease progression.


Asunto(s)
Interferón-alfa , Infecciones por Virus Sincitial Respiratorio , Virus Sincitial Respiratorio Humano , Factor de Transcripción STAT1 , Transducción de Señal , Proteínas no Estructurales Virales , Factor de Transcripción STAT1/metabolismo , Humanos , Interferón-alfa/metabolismo , Interferón-alfa/farmacología , Interferón-alfa/inmunología , Virus Sincitial Respiratorio Humano/inmunología , Virus Sincitial Respiratorio Humano/fisiología , Proteínas no Estructurales Virales/metabolismo , Infecciones por Virus Sincitial Respiratorio/inmunología , Infecciones por Virus Sincitial Respiratorio/metabolismo , Infecciones por Virus Sincitial Respiratorio/virología , Quinasas Janus/metabolismo , Núcleo Celular/metabolismo , Fosforilación , Transporte Activo de Núcleo Celular , Línea Celular
18.
Vet Res ; 55(1): 79, 2024 Jun 17.
Artículo en Inglés | MEDLINE | ID: mdl-38886840

RESUMEN

Porcine deltacoronavirus (PDCoV) is an enteropathogenic coronavirus that has been reported to use various strategies to counter the host antiviral innate immune response. The cGAS-STING signalling pathway plays an important role in antiviral innate immunity. However, it remains unclear whether PDCoV achieves immune evasion by regulating the cGAS-STING pathway. Here, we demonstrated that the nonstructural protein 2 (nsp2) encoded by PDCoV inhibits cGAS-STING-mediated type I and III interferon (IFN) responses via the regulation of porcine STING (pSTING) stability. Mechanistically, ectopically expressed PDCoV nsp2 was found to interact with the N-terminal region of pSTING. Consequently, pSTING was degraded through K48-linked ubiquitination and the proteasomal pathway, leading to the disruption of cGAS-STING signalling. Furthermore, K150 and K236 of pSTING were identified as crucial residues for nsp2-mediated ubiquitination and degradation. In summary, our findings provide a basis for elucidating the immune evasion mechanism of PDCoV and will contribute to the development of targets for anti-coronavirus drugs.


Asunto(s)
Deltacoronavirus , Proteínas no Estructurales Virales , Animales , Porcinos , Proteínas no Estructurales Virales/metabolismo , Proteínas no Estructurales Virales/genética , Deltacoronavirus/genética , Deltacoronavirus/fisiología , Enfermedades de los Porcinos/virología , Enfermedades de los Porcinos/inmunología , Proteínas de la Membrana/metabolismo , Proteínas de la Membrana/genética , Infecciones por Coronavirus/veterinaria , Infecciones por Coronavirus/virología , Infecciones por Coronavirus/inmunología , Infecciones por Coronavirus/metabolismo , Interferón Tipo I/metabolismo , Interferón Tipo I/genética , Inmunidad Innata , Células HEK293 , Evasión Inmune , Ubiquitinación
19.
Int J Mol Sci ; 25(12)2024 Jun 10.
Artículo en Inglés | MEDLINE | ID: mdl-38928101

RESUMEN

In our prior investigations, we elucidated the role of the tryptophan-to-tyrosine substitution at the 61st position in the nonstructural protein NSsW61Y in diminishing the interaction between nonstructural proteins (NSs) and nucleoprotein (NP), impeding viral replication. In this study, we focused on the involvement of NSs in replication via the modulation of autophagosomes. Initially, we examined the impact of NP expression levels, a marker for replication, upon the infection of HeLa cells with severe fever thrombocytopenia syndrome virus (SFTSV), with or without the inhibition of NP binding. Western blot analysis revealed a reduction in NP levels in NSsW61Y-expressing conditions. Furthermore, the expression levels of the canonical autophagosome markers p62 and LC3 decreased in HeLa cells expressing NSsW61Y, revealing the involvement of individual viral proteins on autophagy. Subsequent experiments confirmed that NSsW61Y perturbs autophagy flux, as evidenced by reduced levels of LC3B and p62 upon treatment with chloroquine, an inhibitor of autophagosome-lysosome fusion. LysoTracker staining demonstrated a decrease in lysosomes in cells expressing the NS mutant compared to those expressing wild-type NS. We further explored the mTOR-associated regulatory pathway, a key regulator affected by NS mutant expression. The observed inhibition of replication could be linked to conformational changes in the NSs, impairing their binding to NP and altering mTOR regulation, a crucial upstream signaling component in autophagy. These findings illuminate the intricate interplay between NSsW61Y and the suppression of host autophagy machinery, which is crucial for the generation of autophagosomes to facilitate viral replication.


Asunto(s)
Autofagosomas , Autofagia , Phlebovirus , Triptófano , Tirosina , Proteínas no Estructurales Virales , Replicación Viral , Humanos , Proteínas no Estructurales Virales/metabolismo , Proteínas no Estructurales Virales/genética , Replicación Viral/genética , Autofagosomas/metabolismo , Células HeLa , Phlebovirus/genética , Phlebovirus/fisiología , Phlebovirus/metabolismo , Autofagia/genética , Tirosina/metabolismo , Triptófano/metabolismo , Serina-Treonina Quinasas TOR/metabolismo , Mutación , Sustitución de Aminoácidos , Síndrome de Trombocitopenia Febril Grave/metabolismo , Síndrome de Trombocitopenia Febril Grave/virología , Síndrome de Trombocitopenia Febril Grave/genética , Lisosomas/metabolismo , Nucleoproteínas/metabolismo , Nucleoproteínas/genética
20.
Viruses ; 16(6)2024 May 21.
Artículo en Inglés | MEDLINE | ID: mdl-38932107

RESUMEN

Rotaviruses (RVs) are 11-segmented, double-stranded (ds) RNA viruses and important causes of acute gastroenteritis in humans and other animal species. Early RV particle assembly is a multi-step process that includes the assortment, packaging and replication of the 11 genome segments in close connection with capsid morphogenesis. This process occurs inside virally induced, cytosolic, membrane-less organelles called viroplasms. While many viral and cellular proteins play roles during early RV assembly, the octameric nonstructural protein 2 (NSP2) has emerged as a master orchestrator of this key stage of the viral replication cycle. NSP2 is critical for viroplasm biogenesis as well as for the selective RNA-RNA interactions that underpin the assortment of 11 viral genome segments. Moreover, NSP2's associated enzymatic activities might serve to maintain nucleotide pools for use during viral genome replication, a process that is concurrent with early particle assembly. The goal of this review article is to summarize the available data about the structures, functions and interactions of RV NSP2 while also drawing attention to important unanswered questions in the field.


Asunto(s)
Genoma Viral , Rotavirus , Proteínas no Estructurales Virales , Ensamble de Virus , Replicación Viral , Rotavirus/genética , Rotavirus/fisiología , Proteínas no Estructurales Virales/metabolismo , Proteínas no Estructurales Virales/genética , Humanos , Animales , ARN Viral/genética , ARN Viral/metabolismo , Cápside/metabolismo , Proteínas de Unión al ARN
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