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All Journal Jurnal Teknologi Laboratorium Jurnal Kesehatan Bioinformatics and Biomedical Research Journal Makara Journal of Science Borneo Journal of Pharmacy Biosaintifika: Journal of Biology & Biology Education Genbinesia Journal of Biology
Kharisma, Viol Dhea
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Education Engineering Health Professions Immunology & microbiology Medicine & Pharmacology Public Health Other

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Journal : Makara Journal of Science

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COVID-19 In Silico Drug with Zingiber officinale Natural Product Compound Library Targeting the Mpro Protein Wijaya, Renadya Maulani; Hafidzhah, Muhammad Aldino; Kharisma, Viol Dhea; Ansori, Arif Nur Muhammad; Parikesit, Arli Aditya
Makara Journal of Science Vol. 25, No. 3
Publisher : UI Scholars Hub

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Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a worldwide pandemic. Ginger (Zingiber officinale) is a rhizome, which is commonly used for culinary and medicinal purposes. In Indonesia, ginger is taken as traditional medicine by processing it into a drink known as jamu. The present study aimed to assess and evaluate the bioactive compounds in ginger that can be used in drug design for treating COVID-19. The crystal structure of the SARS-CoV-2 main protease (Mpro) was generated from a protein sequence database, i.e., Protein Data Bank, and the bioactive compounds in ginger were derived from the existing compounds library. Mpro is involved in polyprotein synthesis, including viral maturation and nonstructural protein gluing, making it a potential antiviral target. Furthermore, the bioactive compounds in ginger were analyzed using Lipinski’s rule of five to determine their drug-like molecular properties. Moreover, molecular docking analysis was conducted using the Python Prescription 0.8 (Virtual Screening Tool) software, and the interaction between SARS-CoV-2 Mpro and the bioactive compounds in ginger was extensively examined using the PyMOL software. Out all of the 16 bioactive compounds that were docked successfully, 4-gingerol, which has the lowest binding energy against SARS-CoV-2 Mpro, as per the virtual screening results, was proven to have the most potential as a viral inhibitor of SARS-CoV-2
Molecular Simulation of B-Cell Epitope Mapping from Nipah Virus Attachment Protein to Construct Peptide-Based Vaccine Candidate: A Reverse Vaccinology Approach Kharisma, Viol Dhea; Dian, Farida Aryani; Burkov, Pavel; Scherbakov, Pavel; Derkho, Marina; Sepiashvili, Ekaterina; Sucipto, Teguh Hari; Parikesit, Arli Aditya; Murtadlo, Ahmad Affan Ali; Jakhmola, Vikash; Zainul, Rahadian
Makara Journal of Science Vol. 27, No. 2
Publisher : UI Scholars Hub

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There are no specific drugs or vaccines for Nipah virus (NiV), which is a new Paramyxovirus that infects swine and humans. This study was conducted to investigate B-cell epitope mapping of the NiV attachment glycoprotein and to construct peptide-based vaccine candidates using the reverse vaccinology approach. To generate the linear B-cell epitope, the NiV isolates were extractad from GenBank, NCBI, using the IEDB web server; peptide modeling was conducted using PEP-FOLD3; docking was conducted using PatchDock and FireDock; and in silico cloning was designed using SnapGene. Various peptides were successfully identified from the NiV attachment glycoprotein based on B-cell epitope prediction, allergenicity prediction, similarity prediction, and toxicity prediction. An in silico cloning design of the pET plasmic was also developed. The peptide “RFENTTSDKGKIPSKVIKSYYGTMDIKKINEGLLD” (1G peptide) is predicted to be a potential candidate for the NiV vaccine as it has several good vaccine characteristics. It increases the immune response of B cells through activation, differentiation into plasma cells, the formation of memory cells, and it may increase IgM/IgG antibody titres for viral neutralization. However, the results of this study should be further verified through in vivo and in vitro analyses
Development of a Multi-Epitope Peptide Vaccine Against Monkeypox Virus: Immunoinformatics Analysis for South East Asian HLA Alleles Chandra, Nelson; Herdiansyah, Mochammad Aqilah; Kharisma, Viol Dhea; Ansori, Arif Nur Muhammad; Parikesit, Arli Aditya
Makara Journal of Science Vol. 29, No. 1
Publisher : UI Scholars Hub

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The monkeypox virus (MPXV), a DNA virus causing zoonotic disease, poses major global public health challenges, with mortality rates between 3%–6%. Although smallpox vaccines provide partial cross-protection, there is a critical need for a dedicated, effective monkeypox (mpox) vaccine. This study aimed to design a multi-epitope peptide-based vaccine specifically adapted to the HLA allele profiles common in Southeast Asian populations, where MPXV cases are rising. Using immunoinformatics, we screened for and detected B and T cell epitopes from the MPXV cell surface antigen and IFN-alpha/beta receptor proteins. The vaccine design was validated through a rigorous evaluation of its antigenicity, immunogenicity, allergenicity, and toxicity to ensure both safety and efficacy. Key epitopes were mapped to HLA alleles including HLA-A*11:01, HLA-A*24:02, and HLA-B*15:02, which are highly prevalent in Southeast Asia populations. Molecular docking analyses demonstrated stable interactions between the vaccine construct and TLR3/TLR4 immune receptors, suggesting a robust immune response activation. Additionally, molecular dynamics simulations confirmed the structural stability of the vaccine-receptor complex. This immunoinformatics-driven multi-epitope vaccine design offers a promising candidate for combating MPXV, with high projected coverage and immuno-genic potential for Southeast Asian populations. Validation in laboratory and clinical settings is recommended to con-firm these findings.
Co-Authors Adi Sofyan Ansori, Muhammad Aini, Nur Sofiatul Alfaruqi, Nuri Thobibatus Shofia Alifiansyah, Mochamad Radika Tory Anggraini, Dhea Arif Nur Muhammad Ansori Arli Aditya Parikesit Bezhinar, Tatyana Burkov, Pavel Chandra, Nelson Derkho, Marina Dharmawan, Muhammad Alsyifaa Dian, Farida Aryani Didik Wahyudi Fedik Abdul Rantam Fetty, Amelia Julia Tria Gudz, Petr Hafidzhah, Muhammad Aldino Hebert Adrianto Herdiansyah, Mochammad Aqilah Hery Purnobasuki Hikam, Agus Mohammad Jakhmola, Vikash Khairullah, Aswin Rafif Kolesnik, Evgeniy Maksimiuk, Nikolai Munawir Sazali Murtadlo, Ahmad Affan Ali Novian Budi Santoso Nurul Jadid Mubarokati Posa, Gabrielle Ann Villar Priyono, Qiara Amelia Putri Rahadian Zainul Rasyadan Taufiq Probojati Rebezov, Maksim Rizky, Wahyu Choirur Rollando, Rollando Scherbakov, Pavel Sepiashvili, Ekaterina Septiadi, Luhur Sofy Permana Susanto Susanto Syafrudin Syafrudin Tacharina, Martia Rani Tamam, Muhammad Badrut Teguh Hari Sucipto, Teguh Hari Turista, Dora Dayu Rahma Ullah, Md. Emdad Wicaksono, Adhityo Widyananda, Muhammad Hermawan Wijaya, Renadya Maulani Yulanda Antonius Yusniasari, Putri Antika