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All Journal PROSIDING SEMINAR NASIONAL Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences JURNAL KIMIA SAINS DAN APLIKASI The Journal of Experimental Life Sciences (JELS) Abdimas Sainteknol : Jurnal Sains dan Teknologi Bioeksperimen: Jurnal Penelitian Biologi Journal of Biology Education Unnes Science Education Journal Jurnal Penelitian Pendidikan IPA (JPPIPA) Biosaintifika: Journal of Biology & Biology Education Journal of Creativity Student Biopendix: Jurnal Biologi, Pendidikan dan Terapan Best Journal (Biology Education, Sains and Technology) Abdimasku : Jurnal Pengabdian Masyarakat Buletin Peternakan Tropis (Bulletin of Tropical Animal Science) Berkala Penelitian Hayati Unram Journal of Community Service (UJCS) Life Science Proceeding Seminar Nasional IPA Prosiding Seminar Nasional Biologi Unnes Science Education Journal Bioteach : Biology and Biology Education Journal Jurnal Ilmu Kesehatan Masyarakat (The Public Health Science Journal) Jurnal Abdimas Sainteknol : Jurnal Sains dan Teknologi Life Science
Dewi Mustikaningtyas
Fakultas MIPA, Universitas Negeri Semarang Semarang
Agriculture, Biological Sciences & Forestry Arts Humanities Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Computer Science & IT Decision Sciences, Operations Research & Management Economics, Econometrics & Finance Education Engineering Environmental Science Health Professions Immunology & microbiology Industrial & Manufacturing Engineering Law, Crime, Criminology & Criminal Justice Materials Science & Nanotechnology Medicine & Pharmacology Neuroscience Physics Public Health Social Sciences Other

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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.
Co-Authors Achmadi, Taofan Ali Afiddah, Tawallani Andin Irsadi Andiniyati, Fitri Anggyi Trisnawan Putra Anisa Dewi Sri Puspitasari Annis Aulia Hastuti, Annis Aulia Apriansyah Wibowo Aprilia Indra Kartika, Aprilia Indra Ari Yuniastuti Arif Widiyatmoko, Arif Arvidhea Safira Gunawan Astrid Farmayati Atunnisa, Rifa' Aulia Nur Lita, Aulia Nur Azkiyah, Nimas Catur B., F. Putut Martin H. Bambang Priyono Budi Astuti Burhan, Ilham Damar Galih Darmawan, Melissa Salma Dewi, Novi Ratna Didik Ariwibowo Dinia Rizqi Dwijayanti Elissa, Intan Ayu Ely Rudyatmi, Ely Endah Peniati Fahmi Arifan Faj'ria, Nur Fajriyanti, Lisa Amelia Fatimah Azzahra Febriyanto, Hendra Fidia Fibriana Fitri Arum Sasi, Fitri Arum Fitriyah, Nanda Delva Grahadi, Rahmat Gunawan, Arvidhea Safira Hadikawuryan, Danang Subarkah Hafil Kusuma, Kavana Haris, Amnan Hasyim Abdurrasyid Heriyanti, Andhina Putri Hery Sutarto Hisan, Aisyah Khoirotun Hisan, Aisyah Khoirotun Ibnul Mubarok Ibnul Mubarok Ika Christina, Yuyun Indah Hartati Indriani, Betty Irawati Irawati Isnaeni Karunia Annisa Kaisar Akhmad Khan Kartika Widyaningrum Kholil, Putri Alifa Krispinus Kedati Pukan Kusuma, Kavana Hafil Listiaji, Prasetyo Maftuhah, Anis Maharani, Ria Ika Marlita Marlita, Marlita Martien Herna Susanti Milah, Nihayatul Moch Sasmito Djati Mohamad Endy Yulianto Muhammad Abdullah Na:am, Muh Fakhrihun Nafisah, Wirdatun Nashi Widodo Natalia, Lidya Ayu Nicky, Dhea Nikmatul Hidayah Noor Aini Habibah Nugrahaningsih Nugrahaningsih Nugrahaningsih WH, Nugrahaningsih Nugraini, Anisa Ratna Nur Rahayu Utami Nurul Fadhilah Nurussalma, Syafina Parmin - Pramesti Dewi Priyantini Widiyaningrum Purwadi, Cintiya Egi Purwaningsih, Indri R Susanti R. Adi Susanti, R. Adi R. Susanti, R. Susanti Rahmawati, Maya Putri Rakainsa, Senda Kartika Ramadani, Mutiara Bintang Retno Sri Iswari Ria Ika Maharani Ria Ika Maharani Rizki Oktavia, Rizki Rizky Ajie Aprilianto Rizqi Dwijayanti, Dinia Rohmah, Ilmiana Nurur Romadhon, Vhaviriele Abel Salsabilla, Nur Hayati Afrilda Sasabila Mumtaz Sekar Jatiningrum Parnonansia Sekar Jatiningrum Parnonansia Sigit Saptono Siti Alimah Siti Harnina Bintari Siti Nur Chasanah, Siti Nur Sofiyani, Rakhma Dita Solichin Solichin Solikin, Ahmad Solikin, Ahmad Sri Sukaesih Sudarmin Sudarmin Sunarsih, Sarly Sutiyani, Iis Sutiyani, Iis Talitha Widiatningrum Trida Ridho Fariz Tuti Widianti Ufi Saraswati, Ufi Ulfa, Berlina Maika Ulung Anggraito , Yustinus Walandipa, Ghani Wara, Adisti Danis Wardana, Irfan Ihza Weni Ratna Nurlita Hening, Weni Ratna Nurlita Wicaksono, Maulana Malik Widyananda, Muhammad Hermawan Winanti, Ruri Wiwi Isnaeni Wiyanto - Wiyanto Wiyanto Wulan Christijanti Wulansari Prasetyaningtyas, Wulansari Yustinus Ulung Anggraito Yuyun Ika Christina Zaenafree, Intan