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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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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

Abstract

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

Abstract

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.
DNA damage, inflammation, and cellular senescence investigation in SARS-CoV-2 infection: A short review Kharisma, Viol Dhea; Ansori, Arif Nur Muhammad; Murtadlo, Ahmad Affan Ali; Turista, Dora Dayu Rahma; Tamam, Muhammad Badrut; Ullah, Md. Emdad; Jakhmola, Vikash
Genbinesia Journal of Biology Vol. 2 No. 3 (2023): July 2023
Publisher : Generasi Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55655/genbinesia.v2i3.35

Abstract

SARS-2 infection is predicted to trigger DNA damage due to excessive inflammatory responses from the immune system such as cytokine storms. The cytokine storm leads to an increase in oxidative stress in cells, possibly triggering senescence through activation of the DNA damage response (DDR) signaling pathway. Alterations in the DDR pathway that induce cellular senescence have been identified due to the regulation of viral proteins that lead to impaired DNA repair. However, previous studies have not examined the relationship between DNA damage, inflammation, and cellular senescence. In this short review, we will discuss with a simple perspective why SARS-CoV-2 infection can accelerate the cellular senescence process and its relationship with the inflammatory response.
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

Show Abstract | Download Original | Original Source | Check in Google Scholar

Abstract

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.
Computational Design of siRNA Targeting Homo sapiens HER2 Splice Variant mRNA: A Potential Strategy for Breast Cancer Intervention Parikesit, Arli Aditya; Ansori, Arif Nur Muhammad; Kharisma, Viol Dhea
Biosaintifika: Journal of Biology & Biology Education Vol. 16 No. 3 (2024): December 2024
Publisher : Universitas Negeri Semarang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v16i3.3685

Abstract

This research focuses on an innovative approach utilizing in silico methods to design small interfering RNA (siRNA) targeting the HER2 splice variant mRNA in Homo sapiens. HER2 is known to be overexpressed in certain types of breast cancer, contributing to tumor progression and poor prognosis. By designing siRNA molecules that can specifically bind to and degrade HER2 mRNA, this study aims to reduce HER2 protein levels, thereby hindering the growth and spread of breast cancer cells. The in-silico design process involves identifying optimal siRNA sequences that maximize target specificity and minimize off-target effects, which is crucial for potential therapeutic applications. This approach represents a promising step towards personalized medicine in the treatment of breast cancer, offering a targeted strategy to combat this variant associated with aggressive disease. The methodology comprises the RNA computational tools used for the design, the selection criteria for siRNA candidates, and the potential implications of this research in a clinical setting. The resulting outcomes are 2D and 3D siRNA designs that could potentially silence HER2 mRNA through an in-silico approach. The leads were generated using a de novo modeling approach, with no existing template available in GenBank. Moreover, it is concluded that computational tools can generate sufficiently stable 2D and 3D RNA models that could be advanced for further molecular simulation studies. The benefit of this outcome is that it facilitates better preparation for wet laboratory experiments in siRNA assays, with future implementation in vivo and clinical trial settings.
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