In Silico Study of Mutational Stability of SARS-CoV-2 Proteins

Chaudhuri, Dwaipayan; Majumder, Satyabrata; Datta, Joyeeta; Giri, Kalyan

doi:10.1007/s10930-021-09988-3

Cited by 8 publications

(7 citation statements)

References 28 publications

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“…The Q57H and T151I mutations identified in ORF3a were also observed by another study utilizing a different bioinformatic approach 35 . Additionally, the Q57H mutation in ORF3a is also consistently observed in a mutational analysis done using sequences obtained from the early part of the COVID‐19 pandemic 36 …”

Section: Discussionsupporting

confidence: 59%

“…35 Additionally, the Q57H mutation in ORF3a is also consistently observed in a mutational analysis done using sequences obtained from the early part of the COVID-19 pandemic. 36 Despite the numerous findings on accessory protein mutations in this study, interpretation of these data should be done with caution due to some limitations. proteins.…”

Section: Discussionmentioning

confidence: 77%

“… 35 Additionally, the Q57H mutation in ORF3a is also consistently observed in a mutational analysis done using sequences obtained from the early part of the COVID‐19 pandemic. 36 …”

Section: Discussionmentioning

confidence: 99%

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Temporal changes in the accessory protein mutations of SARS‐CoV‐2 variants and their predicted structural and functional effects

Cruz

Medina

2022

Journal of Medical Virology

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Emerging variants enable the continuous spread of SARS‐CoV‐2 in humans. The factors contributing to behavioral differences in variants remain elusive despite associations with several Spike protein mutations. Exploring accessory proteins may provide a wider understanding of these differences since these proteins may affect viral processes that occur beyond infection. Various bioinformatics tools were utilized to identify significant accessory protein mutations and determine their structural and functional effects over time. The ViruClust web application was used to retrieve accessory protein amino acid sequences and determine mutation frequencies in these sequences across time. The structural and functional effects of the mutations were determined using Missense3D and PROVEAN, respectively. The accessory and Spike protein mutations were compared using mutation densities. Q57H and T151I of ORF3a; T21I and W27L of ORF6; G38V, V82A, and T120I of ORF7a; S31P and T40I of ORF7b; and R52I, C61F, and I121L of ORF8 were highly frequent in most variants of concern and were within known functional domains. Thus, these are good candidates for further experimental evaluation. Among the accessory proteins, ORF6 and ORF8 were highlighted because of their strong and weak correlation with Spike protein mutations, respectively.

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Section: Discussionsupporting

confidence: 59%

Section: Discussionmentioning

confidence: 77%

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Temporal changes in the accessory protein mutations of SARS‐CoV‐2 variants and their predicted structural and functional effects

Cruz

Medina

2022

Journal of Medical Virology

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“…Conversely, we chose as targets the five nsps including Mpro, PLpro, RdRp, Helicase and 2'-O-MTase of SARS-CoV-2 (Table 1). These nsps are very important in the replication of SARS-CoV-2 and are also highly conserved in these viruses [8,9,39,40]. In addition, they are constantly targeted in the search for drugs against COVID-19 [41][42][43][44][45][46].…”

Section: Discussionmentioning

confidence: 99%

Molecular docking study of seventy-six phytomolecules from sixteen aromatics medicinal plants as promising inhibitors of five non-structural proteins of SARS-CoV-2

RANDRIAMAMISOLONIRINA¹,

MAMINIAINA²

2022

GSC Biol. Pharm. Sci.

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Since the identification of COVID-19 in China in December 2019, scientists and researchers have been continuously discovering and proposing drugs for this disease. Many efforts have been made to examine medicinal plants known for their benefits in treating infectious diseases and for their actions in boosting of the immune system. Repurposing of FDA-approved antiviral drugs has also been advanced. However, no effective antiviral drug specific to COVID-19 is currently available. To contribute in the search for drugs against this disease, the present study aims to identify secondary metabolites (or phytomolecules) possessing an inhibitory effect on the replication of SARS-CoV-2, the etiological agent of COVID-19. 76 secondary metabolites from 16 aromatics medicinal plants from Madagascar were uploaded to the PubChem server. Then, they were docked with 5 non-structural proteins (nsps) of SARS-CoV-2, including the main protease, the papain-type protease, the RNA-dependent RNA polymerase, the helicase and the 2'-O-methyltransferase, using the Autodock Vina program integrated in the PYRIX 0.8 software. The results show that 5 secondary metabolites of Cinnamosma fragrans (Capsicodendrin, Ugandensolide, Cinnamolide, Tocotrienol and Pereniporin B) have good affinity with the 5 nsps of SARS-CoV-2 and can inhibit its functions in viral replication. Therefore, these phytomolecules could be used in the development of antiviral drugs against SARS-CoV-2 and COVID-19. Nevertheless, further in vitro and in vivo studies should be performed to valorize these results obtained by the in silico method.

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“…For this reason, we used the bioinformatics or in silico method, which is not expensive but allows to obtain faster and exploitable results [28,29]. Some researchers have already used it for the characterization of mutations in structural proteins of the Severe Acute Respiratory Syndrome Coronavirus 2 or SARS Cov2 [30,31].…”

Section: Discussionmentioning

confidence: 99%

Analysis of mutations in the fusion protein and hemagglutinin-neuraminidase in twelve strains of NDV isolated in Madagascar by bioinformatics methods

RANDRIAMAMISOLONIRINA¹,

ANDRIANTSIMAHAVANDY²,

MAMINIAINA³

2022

Int. J. Sci. Res. Arch.

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Many researchers have made efforts to generate genotype-matched and subunit vaccines for Newcastle disease (ND). During the design process, we found that they only considered certain characteristics of the virulent strains. As a result, the resulting vaccines are still poorly effective against new emerging strains of ND virus (NDV). This analysis suggests that consideration of various characteristics of virulent strains in the design is necessary to increase the efficacy of these new vaccines. Thus, analysis of mutations in viral proteins targeted in the design such as fusion proteins (F) and hemagglutinin-neuraminidase (HN) is essential. For this reason, the present study aims to analyze mutations in these two proteins in twelve NDV strains isolated in Madagascar. To achieve this, we employed bioinformatics methods such as sequence alignment, molecular modeling, 3D structure comparison and mutation impact prediction via bioinformatics software and servers. As results, we identified respectively 26 and 41 mutations in the F and HN proteins of the Madagascar isolates. All these mutations have an impact on the stability of the protein. However, only 6 mutations (D344N, G303V, P315S, E347K, P391S and E495S) have an impact on their 3D structures. Finally, the 3 mutations (A477T, G303V and P315S) also affect the functions of these two proteins. In conclusion, we have identified 67 mutations that may affect the stability, structures, and functions of NDV F and HN proteins. Further studies are needed to know their effects on the antigenicity and immunogenicity of these two proteins.

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In Silico Study of Mutational Stability of SARS-CoV-2 Proteins

Cited by 8 publications

References 28 publications

Temporal changes in the accessory protein mutations of SARS‐CoV‐2 variants and their predicted structural and functional effects

Temporal changes in the accessory protein mutations of SARS‐CoV‐2 variants and their predicted structural and functional effects

Molecular docking study of seventy-six phytomolecules from sixteen aromatics medicinal plants as promising inhibitors of five non-structural proteins of SARS-CoV-2

Analysis of mutations in the fusion protein and hemagglutinin-neuraminidase in twelve strains of NDV isolated in Madagascar by bioinformatics methods

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