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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

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

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.

CaCO3-Reformulated Interlocking Bricks: Physical Characterization and Their Antibacterial and Anti-Inflammatory Potential for Healthy Housing Djati, Muhammad Sasmito; Rachmawati, Turniningtyas Ayu; Anggraini, Retno; Zacoeb, Achfas; Rifa`i, Muhaimin; Minang, Bony Zulkarnaen; Kusuma, Kavana Hafil; Prima, Alex; Christina, Yuyun Ika
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.2025.013.01.01

Calcium carbonate (CaCO3) has many benefits for medicine, manufacturing, and nanotechnology due to its antibacterial and anti-inflammatory properties. Interlocking bricks (i-bricks) are widely used in sustainable housing for efficient air circulation and reducing humidity inside the house. If CaCO3 is mixed with interlocking brick, it can inhibit bacterial growth, leading to a healthier indoor environment. Therefore, this study aimed to investigate the physical characterization and antibacterial activity of CaCO3-reformulated i-brick, and its anti-inflammatory potential in mice infected with Salmonella typhimurium. The physical characterization of CaCO3-reformulated i-brick (F1-F10 formulas), including its density, compression, and absorption, was analyzed. The inhibitory activity of CaCO3-reformulated i-brick on S. typhimurium growth was determined using a linear regression equation between culture age and cell density values. BALB/c male mice were randomly divided into four groups (n=4): healthy mice (N), S. typhimurium-infected mice (S), S. typhimurium-infected mice treated with F6 formula (F6) and F7 formula (F7) for 7 days. After 7 days of treatment, lymphocytes were isolated to determine the relative number of TGF-beta, interleukin (IL)-10, and TNF-alpha using flow cytometry analysis. The results showed that formulas 6 and 7 of CaCO3-reformulated i-bricks exhibited optimal physical properties, including density, compression, and water absorption. These formulas also inhibited the growth of S. typhimurium. Furthermore, formulas 6 and 7 possessed anti-inflammatory effects in S. typhimurium-infected mice indicated by the high increase in IL-10 and TGF-beta production and low levels of TNF-alpha. In conclusion, CaCO3 brick formulation can inhibit the growth of S. typhimurium and exert an anti-inflammatory effect. Further investigation is needed to reveal the effect of CaCO3-reformulated i-bricks on another inflammatory marker to further elucidate its anti-inflammatory mechanism.

Antioxidant Properties and Quantification of Phenolic and Flavonoid Compounds in Alpinia purpurata (Viell.) K. Schum Ethanol Extract Djati, Muhammad Sasmito; Azerlyn, Defiona Rensia Naomi; Kusuma, Kavana Hafil; Rosyadah, Nuraini; Kamila, Fairuz Sarah; Annisa, Yuslinda; Christina, Yuyun Ika; Dwijayanti, Dinia Rizqi; Widodo, Nashi
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.2025.013.01.02

Phenolic and flavonoid compounds have been found to have positive benefits due to their antioxidant activity. Alpinia purpurata (Viell.) K. Schum, or lengkuas merah, is known to have aromatic rhizomes and is rich in active compounds such as flavonoids and phenolics. This research aimed to investigate the total phenolic and flavonoid content of A. purpurata ethanol extract and its antioxidant activity. A. purpurata was extracted using Microwave-Assisted Extraction (MAE) with 97% ethanol solvent. The ethanol extract of A. purpurata was then analyzed for the total phenolic and flavonoid content. The antioxidant activity and nitric oxide (NO) levels were determined by DPPH and NO scavenging assay, respectively. The results showed that A. purpurata ethanol extract had a high phenolic content (148.76 ± 1.03 mg GAE.g-1extract) but weak DPPH scavenging activity (IC50 of 219.06 ± 8.15 µg.mL-1), indicating that high phenolic content does not necessarily correlate with strong antioxidant properties. In contrast, the extract exhibited strong NO scavenging activity with an IC50 of 22.73 ± 7.57 µg.mL-1. Despite its high phenolic content, the weak DPPH activity indicates that total phenolic concentration alone is not always a reliable indicator of antioxidant strength. Further studies should include additional antioxidant assays to comprehensively evaluate the extract’s antioxidant potential.

Corrigendum: Evaluating SARS-CoV-2 Spike Protein Transfection in HEK-293T Cells for VLP Applications Rohmah, Ilmiana Nurur; Marlita, Marlita; Kusuma, Kavana Hafil; Christina, Yuyun Ika; Dwijayanti, Dinia Rizqi; Mustikaningtyas, Dewi; Widodo, Nashi; Djati, M. Sasmito
The Journal of Experimental Life Science Vol. 15 No. 2 (2025)
Publisher : Graduate School, Universitas Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jels.2025.015.02.01

The spike protein of SARS-CoV-2 is crucial for initiating infections by binding to host cells and mediating membrane fusion. In this study, HEK-293T cells were transfected with plasmids encoding three structural proteins of SARS-CoV-2, i.e., Spike (S), Membrane (M), and Envelope (E). This transfection enabled the formation of SARS-CoV-2 Virus-Like Particles (VLPs), which allows for safer studies of the virus and its proteins. To serve as a marker for expression, an enhanced green fluorescent protein (EGFP) was fused to the spike protein, resulting in a Spike-EGFP (S-EGFP) fusion protein. The characteristics of SARS-CoV-2 spike protein expression in the transfected HEK-293T cells were then investigated using polymerase chain reaction (PCR) and flow cytometry. The PCR analysis revealed non-specific DNA band smearing, which did not provide conclusive confirmation of spike protein expression. However, flow cytometry analysis demonstrated that approximately 30% of the transfected cells exhibited green fluorescence, indicating the expression of the Spike-EGFP fusion protein. These findings, obtained through flow cytometry, confirmed the successful spike protein expression in transfected HEK-293T cells.

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