Now any DNA made in your lab can be recorded in an electronic file and shared worldwide with the free software SnapGene Viewer. Palabras Clave: COVID-19 SARS-CoV-2 vaccine design viroinformatics.SnapGene is a product of GSL Biotech, the first molecular biology software that is easier to use than pen and paper. Sin embargo, para la validación se requieren más ensayos in vitro e in vivo. Además, se logró con éxito el desarrollo de la clonación in silico utilizando el plásmido pET.Ĭonclusiones: Este estudio exhibe las transformaciones de aminoácidos en aislados B.1.1.7 de Indonesiay propone cuatro péptidos (“LTPGDSSSGWTAG”, “VRQIAPGQTGKIAD”, “ILPDPSKPSKRS” y “KNHTSPDVDLG”) de la proteína S como candidato para una vacuna basada en péptidos. Además, se identificaron varios péptidos basados en la predicción del epítopo de células B, la predicción de la alergenicidad, la predicción de la toxicidad de la proteína S para generar una vacuna contraria al SARS-CoV-2. Resultados: En este estudio, se descubrieron los cambios de aminoácidos en los siete aislamientos de B.1.1.7 de Indonesia. Además, la clonación in silico se desarrolló utilizando el software SnapGene v.3.2.1. Además, se utilizó el servidor web PEP-FOLD3 para realizar el modelado de péptidos, mientras que el acoplamiento se realizó mediante PatchDock, FireDock y el software PyMOL. El IEDB se implementó para revelar los epítopos de células B lineales. Se empleó MEGA X para comprender las transformaciones de aminoácidos en la proteína S y para desarrollar un árbol filogenético molecular. Métodos: Las secuencias de siete aislamientos B.1.1.7 indonesios, el aislado Wuhan-Hu-1 y el aislado WIV04 se extrajeron de GISAID EpiCoV y GenBank, NCBI.
Objetivos: Analizar la región conservada del epítopo de células B y el estudio basado en viroinformática del linaje SARS-CoV-2 de los aislados B.1.1.7 de Indonesia para inventar una vacuna candidata para superar COVID-19. ResumenĬontexto: SARS-CoV-2, un miembro de la familia Coronaviridae y el agente causante de COVID-19, es un virus que se transmite a humanos y otros mamíferos. Keywords: COVID-19 SARS-CoV-2 vaccine design viroinformatics. However, further advance trials such as in vitro and in vivo testing are involved for validation. Furthermore, the development of in silico cloning using pET plasmid was successfully achieved.Ĭonclusions: This study exhibits the transformations of amino acid in Indonesian B.1.1.7 isolates, and proposes four peptides (“LTPGDSSSGWTAG”, “VRQIAPGQTGKIAD”, “ILPDPSKPSKRS”, and “KNHTSPDVDLG”) from S protein as the candidate for a peptide-based vaccine. Furthermore, various peptides based on the B-cell epitope prediction, allergenicity prediction, toxicity prediction from S protein to generate a vaccine contrary to SARS-CoV-2 were identified. Results: In this study, the changes of amino acid in all seven Indonesian B.1.1.7 isolates were uncovered. Moreover, in silico cloning was developed by using SnapGene v.3.2.1 software. In addition, PEP-FOLD3 web server was utilized to perform peptide modeling, while docking was performed using PatchDock, FireDock, and the PyMOL software. The IEDB was implemented to reveal the linear B-cell epitopes.
MEGA X was employed to understand the transformations of amino acid in the S protein and to develop a molecular phylogenetic tree. Methods: The sequences of seven Indonesian B.1.1.7 isolates, Wuhan-Hu-1 isolate, and WIV04 isolate were extracted from the GISAID EpiCoV and GenBank, NCBI. Nidom 1,2,3*ġCoronavirus and Vaccine Formulation Research Group, Professor Nidom Foundation, Surabaya, Indonesia.ĢFaculty of Veterinary Medicine, Universitas Airlangga, Surabaya, Indonesia.ģRiset AIRC Indonesia, Surabaya, Indonesia.ĤFaculty of Medicine, Universitas Airlangga, Surabaya, Indonesia.ĥFaculty of Science and Data Analytics, Institut Teknologi Sepuluh Nopember, Surabaya, Indonesia.ĦFaculty of Veterinary Medicine, IPB University, Bogor, Indonesia.Ĭontext: SARS-CoV-2, a member of family Coronaviridae and the causative agent of COVID-19, is a virus which is transmitted to human and other mammals.Īims: To analyze the B-cell epitope conserved region and viroinformatics-based study of the SARS-CoV-2 lineage from Indonesian B.1.1.7 isolates to invent a vaccine nominee for overcoming COVID-19. Alamudi 1,3, Umi Cahyaningsih 6, Kuncoro P. Kusala 1,2, Setyarina Indrasari 1,3, Irine Normalina 1,4, Astria N. Original article 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 Arif N.
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