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All Journal Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences Biotropika
Nafisah, Wirdatun
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Environmental Science Immunology & microbiology

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Design of Epitope-Based Vaccine Against SARS-CoV-2: An Immuno-Informatics Study: Epitope-Based Vaccine Against SARS-CoV-2 Kusuma, Kavana Hafil; Widyananda, Muhammad Hermawan; Nafisah, Wirdatun; Grahadi, Rahmat; Christina, Yuyun Ika; Dwijayanti, Dinia Rizqi; Mustikaningtyas, Dewi; Widodo, Nashi; Djati, Muhammad Sasmito
Journal of Tropical Life Science Vol. 14 No. 3 (2024): In Press
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.03.07

Abstract

This study aimed to develop an epitope-based vaccine of SARS-CoV-2 S protein through an immuno-informatics study. The whole genome of SARS-CoV-2 sequences was obtained from the GISAID database and then trimmed to obtain the S protein sequences. The alignment was done by Clustal-W of MEGA software. Epitope prediction and modeling were performed by Discotope BepiPred and the PepFold3 web server. The allergic responses and physicochemical characteristics of predicted epitopes were analyzed using the AlgPred and ProtParam from ExPASy. Molecular docking and dynamic stimulation were performed using AutoDock Vina and YASARA. Biovia Discovery Studio 2019 was used to visualize the molecular docking results. The study predicted 3 potential epitopes, including ‘GDEVRQIAPGQTGKIADYNYKLP’ (epitope 1), ‘YTMSLGAENSVAYSNN’ (epitope 2), and ‘VNNSYECDIPI’ (epitope 3) located in the spike head specifically RBD region. The epitopes did not show an allergen reaction based on IgE epitope mapping. The suitable overexpression for the host of epitopes was mammalian cells. Only epitopes 1 and 2 were stable (instability index above 40). Epitopes 1, 2, and 3 interacted with BCR with binding affinity values -6.6, -7.8, and -7.5 kcal/mol. Epitope 2 wasere stable when interacting with the BCR. Therefore, three epitopes were predicted to have high potency as the SARS-CoV-2 epitope-based vaccine.
Design of Epitope-Based Vaccine Against SARS-CoV-2: An Immuno-Informatics Study: Epitope-Based Vaccine Against SARS-CoV-2 Kusuma, Kavana Hafil; Widyananda, Muhammad Hermawan; Nafisah, Wirdatun; Grahadi, Rahmat; Christina, Yuyun Ika; Dwijayanti, Dinia Rizqi; Mustikaningtyas, Dewi; Widodo, Nashi; Djati, Muhammad Sasmito
Journal of Tropical Life Science Vol. 14 No. 3 (2024)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.03.07

Abstract

This study aimed to develop an epitope-based vaccine of SARS-CoV-2 S protein through an immuno-informatics study. The whole genome of SARS-CoV-2 sequences was obtained from the GISAID database and then trimmed to obtain the S protein sequences. The alignment was done by Clustal-W of MEGA software. Epitope prediction and modeling were performed by Discotope BepiPred and the PepFold3 web server. The allergic responses and physicochemical characteristics of predicted epitopes were analyzed using the AlgPred and ProtParam from ExPASy. Molecular docking and dynamic stimulation were performed using AutoDock Vina and YASARA. Biovia Discovery Studio 2019 was used to visualize the molecular docking results. The study predicted 3 potential epitopes, including ‘GDEVRQIAPGQTGKIADYNYKLP’ (epitope 1), ‘YTMSLGAENSVAYSNN’ (epitope 2), and ‘VNNSYECDIPI’ (epitope 3) located in the spike head specifically RBD region. The epitopes did not show an allergen reaction based on IgE epitope mapping. The suitable overexpression for the host of epitopes was mammalian cells. Only epitopes 1 and 2 were stable (instability index above 40). Epitopes 1, 2, and 3 interacted with BCR with binding affinity values -6.6, -7.8, and -7.5 kcal/mol. Epitope 2 wasere stable when interacting with the BCR. Therefore, three epitopes were predicted to have high potency as the SARS-CoV-2 epitope-based vaccine.
Virtual Based Screening of Rosmaniric Acid and Its Derivatives as Potential Anticancer Approach Targeting HIF-1a Naufal, Achmad Hanif; Wachid, Nisa Nabila Aufa; Kamila, Fairuz Sarah; Wahyuningsih, Nadia; Ilmiyah, Silvi Zakiyatul; Nafisah, Wirdatun; Fatchiyah, Fatchiyah
Biotropika: Journal of Tropical Biology Vol. 13 No. 1 (2025)
Publisher : Universitas Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.biotropika.2025.013.01.03

Abstract

Cancer is one of the leading causes of death in the world. Rosmarinic acid becomes one of the important polyphenolic compounds. It includes derivatives of two amino acids, caffeic acid from phenylalanine and 3,4-dihydroxyphenyl-lactic acid from tyrosine, secondary metabolites found in many herbal plants from the subfamily Lamiaceae and Boraginaceae. Rosmarinic acid works in inhibiting the occurrence of metastases and tumor formation. In this study, we evaluated rosmarinic acid and its derivatives through study literature. The compounds were downloaded from the PubChem database, while the three-dimensional structure of HIF-1a was retrieved from RCSB PDB. The biological activity was analyzed using the PASS server, and the cytotoxic effect was predicted using CLC-Pred., The pharmacological properties of bioactive compounds were analyzed using SwissADME. The compounds and HIF-1a were prepared using PyRx 0.8 version and Discovery Studio software, docked specifically using Autodock Vina, visualized using Discovery Studio software, and molecular dynamic simulation using CABS-flex 2.0. Rosmarinic acid and its derivative showed an inhibition with the highest affinity value of compound against HIF-1a are control (-6.9 kcal/mol), Rosmarinic acid (-6.4 kcal /mol), and Methyl rosmarinate (-6.3 kcal/mol). Rosmarinic acid could be expected to have activity as an inhibitor modulated at the post-translational level. Comprehensive and further analysis is required in future research based in vivo and in vitro for the development of cancer treatments.
Co-Authors Dewi Mustikaningtyas Dinia Rizqi Dwijayanti fatchiyah . Grahadi, Rahmat Ilmiyah, Silvi Zakiyatul Kamila, Fairuz Sarah Kusuma, Kavana Hafil Moch Sasmito Djati Nashi Widodo Naufal, Achmad Hanif Wachid, Nisa Nabila Aufa Wahyuningsih, Nadia Widyananda, Muhammad Hermawan Yuyun Ika Christina