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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.

Daruju (Acanthus ilicifolius L.) May Exhibit Anti-Breast Cancer Activity Through Inhibition of Proliferation Regulators: A Computational Study: Daruju (Acanthus ilicifolius L.) as Anti-Breast Cancer Agent Rosyadah, Nuraini; Kamila, Fairuz Sarah; Hermanto, Feri Eko; Widyananda, Muhammad Hermawan; Grahadi, Rahmat; Dwijayanti, Dinia Rizqi; Widodo, Nashi; Ulfa, Siti Mariyah
Journal of Tropical Life Science Vol. 15 No. 1 (2025)
Publisher : Journal of Tropical Life Science

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

Breast cancer's increasing prevalence globally underscores the urgent need for effective and gentle therapies, positioning the exploration of herbal remedies as a critical pursuit. Daruju (Acanthus ilicifolius L.) emerges as a compelling candidate due to its inherent bioactive components. This research pioneers the application of advanced computational techniques to unveil the latent anti-breast cancer potential within A. ilicifolius. Our in-silico investigation commenced by cataloging A. ilicifolius compounds using the KNApSAcK database and existing literature. These compounds underwent rigorous screening for drug-like characteristics via SWISS-ADME and potential biological activity using PASS ONLINE. Protein targets relevant to breast cancer were predicted through SWISS Target and the STRING database, integrated with Cytoscape for network visualization. Molecular docking, performed with PyRx 0.8, assessed the binding strength between the identified compounds and target proteins, with the most promising interactions selected for further scrutiny. The stability of these crucial interactions was then evaluated through molecular dynamics simulations using YASARA. This comprehensive computational strategy aims to pinpoint potential anti-breast cancer agents derived from A. ilicifolius. Initial analysis of 17 compounds from A. ilicifolius, based on chromatography, databases, and prior studies, narrowed down to five that adhered to Lipinski’s Rule of Five for drug-likeness: 4-O-beta-D-glucosyl-4-coumaric acid, (-)-lyoniresinol, α-amyrin, adenosine, and p-coumaric acid. These compounds were predicted to directly interact with key breast cancer-related proteins across pathways like estrogen signaling, JAK/STAT, and PI3K/AKT. Notably, molecular docking revealed strong binding affinities for α-amyrin with CDK4, ER, and EGFR (-7.5 kcal/mol, -9.5 kcal/mol, and -8.7 kcal/mol, respectively), comparable to known inhibitors. Molecular dynamics simulations further corroborated the stability of these complexes, analyzing RMSD and binding affinity parameters. Consequently, α-amyrin stands out as a promising anti-breast cancer agent within A. ilicifolius, exhibiting potential to inhibit proteins crucial for breast cancer cell proliferation and survival, including CDK4, ER, and EGFR.

Molecular Docking Analysis of Flavonoids from Syzygium cumini (L.) Skeels: Proapoptotic Potential as an Anticancer Mechanism Aini, Nur Sofiatul; Ansori, Arif Nur Muhammad; Widyananda, Muhammad Hermawan; Kharisma, Viol Dhea; Murtadlo, Ahmad Affan Ali; Herdiansyah, Mochammad Aqilah; Rebezov, Maksim; Burkov, Pavel; Gudz, Petr; Derkho, Marina; Bezhinar, Tatyana; Maksimiuk, Nikolai; Sazali, Munawir; Purnobasuki, Hery; Rollando, Rollando; Khairullah, Aswin Rafif; Sucipto, Teguh Hari
Borneo Journal of Pharmacy Vol. 8 No. 3 (2025): Borneo Journal of Pharmacy
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33084/bjop.v8i3.9843

Non-small cell lung cancer (NSCLC) presents a significant global health challenge, with its prevalence and mortality rates rising steadily. In Indonesia, Syzygium cumini (L.) Skeels, known for its flavonoid richness, has a long history in traditional medicine. However, its specific mechanisms of action against cancer, particularly in inducing apoptosis in NSCLC, have not been fully elucidated. This study utilized an in silico approach to evaluate the pro-apoptotic potential of S. cumini flavonoids against NSCLC by targeting key proteins: Bcl-2, Bax, and Caspase-3. We retrieved flavonoid structures from PubChem and protein data from the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB). The drug-likeness of these compounds was assessed using Swiss ADME, adhering to Lipinski's rule of five, while their anti-NSCLC probability was predicted using PASS Online. Molecular docking and screening were performed with PyRx, and the results were visualized using Discovery Studio. Our findings identified epigallocatechin 3-O-gallate and ellagic acid as the most promising anti-NSCLC candidates. Ellagic acid demonstrated the strongest binding affinity to Caspase-3, suggesting a potent pro-apoptotic effect. Epigallocatechin 3-O-gallate, on the other hand, exhibited the lowest binding energy across multiple target proteins, particularly Bcl-2 and Bax, indicating its broad pro-apoptotic potential. These results collectively suggest that flavonoids from S. cumini may hold significant promise as a source of novel anti-NSCLC agents, warranting further in vitro and in vivo investigations.

Viroinformatics study: polytope mapping of envelope glycoprotein to tackle HIV-2 infection and develop vaccine candidate Kharisma, Viol Dhea; Widyananda, Muhammad Hermawan; Probojati, Rasyadan Taufiq; Ansori, Arif Nur Muhammad; Murtadlo, Ahmad Affan Ali; Tamam, Muhammad Badrut; Wicaksono, Adhityo; Turista, Dora Dayu Rahma
Genbinesia Journal of Biology Vol. 1 No. 1 (2021): November 2021
Publisher : Generasi Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55655/genbinesia.v1i1.6

Human Immunodeficiency Virus type 2 (HIV-2) has been identified to exhibit an ability to resist antiretroviral administration and many scientists has predicted increases in the pathogenicity of HIV-2. The development of a vaccine against the type 1 virus (HIV-1) infection has reached the phase 3 clinical trial stage, but currently there is no information on the development of a vaccine against HIV-2. Vaccine development to trigger an increase in the coverage of the expansion of protection can be done through B cell polytope. This study aims to provide an important preliminary for the construction of vaccine candidates by identifying the peptides that make up the B cell polytope in the HIV-2 envelope glycoprotein region. The HIV-2 sequence was obtained from the database. The study followed by 3D modelling, prediction of linear B-cell epitope mapping, antigenicity, allergenicity, peptide properties, and immune simulation was carried out via a webserver. The 3D structure of the peptide was displayed through molecular visualization software. The results showed that the 23-mer peptides E1 'HPRYTGVKNIRDITLTEPGRGSD', F1 'NFIENRKGTQHN' 12-mer, M1 'YLKDQARLNS' 10-mer, N1 'PWVNDSIQPNWNNMTWQQWELQVRD' 25-mer, and O1 'KLQNSWNMGVQTO' can be used as a candidate polytope HIV-2 vaccine because it is recognized by B cells is an antigenic peptide with stable molecule, non-allergenic. The peptides trigger proliferation and activation of B cells to produces a humoral response and work as functionally protective antibody for neutralization of HIV-2. Key words: Acquired Immune Deficiency Syndrome, B-cell, Bioinformatics, Human Immunodeficiency Virus, Retrovirus

Exploring active compounds of kelor (Moringa oleifera Lam.) leaves as an alternative medicine to improve immunity in facing COVID-19 via in silico study Hikam, Agus Mohammad; Mubarakati, Nurul Jadid; Probojati, Rasyadan Taufiq; Widyananda, Muhammad Hermawan; Kharisma, Viol Dhea; Ansori, Arif Nur Muhammad
Genbinesia Journal of Biology Vol. 1 No. 1 (2021): November 2021
Publisher : Generasi Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55655/genbinesia.v1i1.7

SARS-CoV-2 is a new strain of coronavirus (CoV) that was identified in Wuhan in 2019. This virus is known to have the ability to reduce human immunity. Kelor (Moringa oleifera) is a potential natural resource in Indonesia, which is very abundant and contains several metabolic compounds such as phenolics, flavonoids, saponins, cytokines, and caffeoylquinic acid, which was reported to show antioxidants, antibacterial and antiviral. This study aims to predict the biological activity, physicochemical properties, toxicity, and affinity-interactions of the active compounds of M. oleifera leave. The active compounds of M. oleifera were obtained from the KNApSAcK and PubChem. Analysis of the bioactivity of the compounds using the Way2Drug Pass Online. Analysis of drug-likeness and toxicity using the Lipinski web server and pkCSM. Docking is done using Autodock vina software to analyze the interaction of the compounds with Mpro. The results indicate that the compound astragalin is the compound with the highest affinity value, namely -8.7 (kcal/mol), compared to lopinavir as a control compound with an affinity value -6.6 (kcal/mol). The types of bonds in astragalin compounds are hydrogen bonds with amino acids Glutamine 127 and Arginine 298. From these results, it is predicted that astragalin compounds have the highest potential as alternative drugs to increase body immunity against the COVID-19.

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