Viroinformatics investigation of B-cell epitope conserved region in SARS-CoV-2 lineage B.1.1.7 isolates originated from Indonesia to develop vaccine candidate against COVID-19

Ansori, Arif Nur Muhammad; Nidom, Reviany V.; Kusala, Muhammad K. J.; Indrasari, Setyarina; Normalina, Irine; Nidom, Astria N; Afifah, Balqis; Sari, Kartika Buana; Ramadhaniyah, N. L.; Alamudi, Mohammad Yusuf; Cahyaningsih, U.; Santoso, Kuncoro Puguh; Kuswanto, H.; Nidom, Chairul A.

doi:10.56499/jppres21.1101_9.6.766

Cited by 10 publications

(3 citation statements)

References 38 publications

(52 reference statements)

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“…The predicted epitopes KLNDLCFTNV and ITLCFTLKRK ( Can et al, 2020 ) were ideal antigens for the development of an epitope-based peptide, and GGDGKMKD ( Can et al, 2020 ) was ideal for a serodiagnostic assay. However, the significant predicted epitopes should be further examined in wet lab studies ( Can et al, 2020 ; Ansori et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

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VOE: automated analysis of variant epitopes of SARS-CoV-2 for the development of diagnostic tests or vaccines for COVID-19

Lee,

Sangket

2024

PeerJ

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Background The development of serodiagnostic tests and vaccines for COVID-19 depends on the identification of epitopes from the SARS-CoV-2 genome. An epitope is the specific part of an antigen that is recognized by the immune system and can elicit an immune response. However, when the genetic variants contained in epitopes are used to develop rapid antigen tests (Ag-RDTs) and DNA or RNA vaccines, test sensitivity and vaccine efficacy can be low. Methods Here, we developed a “variant on epitope (VOE)” software, a new Python script for identifying variants located on an epitope. Variant analysis and sensitivity calculation for seven recommended epitopes were processed by VOE. Variants in 1,011 Omicron SRA reads from two variant databases (BCFtools and SARS-CoV-2-Freebayes) were processed by VOE. Results A variant with HIGH or MODERATE impact was found on all epitopes from both variant databases except the epitopes KLNDLCFTNV, RVQPTES, LKPFERD, and ITLCFTLKRK on the S gene and ORF7a gene. All epitope variants from the BCFtools and SARS-CoV-2 Freebayes variant databases showed about 100% sensitivity except epitopes APGQTGK and DSKVGGNYN on the S gene, which showed respective sensitivities of 28.4866% and 6.8249%, and 87.7349% and 71.1177%. Conclusions Therefore, the epitopes KLNDLCFTNV, RVQPTES, LKPFERD, and ITLCFTLKRK may be useful for the development of an epitope-based peptide vaccine and GGDGKMKD on the N gene may be useful for the development of serodiagnostic tests. Moreover, VOE can also be used to analyze other epitopes, and a new variant database for VOE may be further established when a new variant of SARS-CoV-2 emerges.

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Section: Introductionmentioning

confidence: 99%

“…The previous studies ( Can et al, 2020 ; Lu et al, 2021b ; Ansori et al, 2021 ) used predicted epitopes to design epitope-based vaccines and a serodiagnosis assay. Essential useful bioinformatics entities were also reported to solve the SARS-CoV-2 conundrum ( Fahmi et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

VOE: automated analysis of variant epitopes of SARS-CoV-2 for the development of diagnostic tests or vaccines for COVID-19

Lee,

Sangket

2024

PeerJ

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“…Older people and people with underlying medical conditions, such as cancer, diabetes, cardiovascular disease, or chronic respiratory disorders, are more prone to have severe illness. Anyone can get COVID-19 and become seriously ill or die at any age [1][2][3][4][5][6][7] .…”

Section: Introductionmentioning

confidence: 99%

Curcumin from Curcuma longa L. as Dual Inhibitors Against Indonesian SARS-CoV-2 Isolates: A Molecular Docking Study

Nidom¹,

Ansori²,

Nidom³

et al. 2023

Pharmacogn J.

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Using Lipinski's rule of five on the SCFBIO web server (http://www.scfbio-iitd. res.in/software/ drugdesign/lipinski.jsp), curcumin was utilized for further drug-likeness analysis. It was regarded as a successful forecast when two minimal guidelines ABSTRACT COVID-19 has become a global pandemic since 2020. The search for promising drugs based on the abundant herbal ingredients in Indonesia is one of the breakthroughs. Curcumin is a chemical compound with various potentials such as antioxidant, anti-inflammatory and antiviral. We conducted a molecular docking analysis to determine the potential of curcumin against SARS-CoV-2 non-structural and structural proteins, such as the main protease and spike protein. This study used the compound of curcumin (PubChem CID: 969516) from Curcuma longa L. or turmeric and two Indonesian SARS-CoV-2 isolates that have been deposited in the GISAID database (hCoV-19/Indonesia/JI-PNF-217315/2021 -EPI_ ISL_12777089 or lineage B.1.617.2 and hCoV-19/Indonesia/JI-PNF-211373/2021 -EPI_ISL_6425649 or lineage B.1.470). In addition, we used molnupiravir (PubChem CID: 145996610) as a drug control. We performed molecular docking analysis with PyRx software 0.9.9 (academic license) and visualization of molecular docking results with PyMOL software 2.5.4 (academic license). The results of this study found that curcumin had good potential against main protease and spike protein compared to the drug (control). In summary, we suggested that curcumin is a potential drug candidate against SARS-CoV-2. However, there is a need for future wet laboratory-based pre-clinical research such as in vitro and in vivo.

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An overview on medicinal plants used for combating coronavirus: Current potentials and challenges

Baker

Hassan

Gengaihi

2023

Journal of Agriculture and Food Research

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Viroinformatics investigation of B-cell epitope conserved region in SARS-CoV-2 lineage B.1.1.7 isolates originated from Indonesia to develop vaccine candidate against COVID-19

Cited by 10 publications

References 38 publications

VOE: automated analysis of variant epitopes of SARS-CoV-2 for the development of diagnostic tests or vaccines for COVID-19

VOE: automated analysis of variant epitopes of SARS-CoV-2 for the development of diagnostic tests or vaccines for COVID-19

Curcumin from Curcuma longa L. as Dual Inhibitors Against Indonesian SARS-CoV-2 Isolates: A Molecular Docking Study

An overview on medicinal plants used for combating coronavirus: Current potentials and challenges

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