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All Journal VALENSI Jurnal Penelitian Pendidikan Jurnal Pendidikan Ekonomi & Bisnis DIJB (Diponegoro International Journal of Business) Jurnal Medik Veteriner Journal of Applied Veterinary Science and Technology Makara Journal of Science Borneo Journal of Pharmacy Svāsthya: Trends in General Medicine and Public Health Genbinesia Journal of Biology
Adi Sofyan Ansori, Muhammad
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Decision Sciences, Operations Research & Management Economics, Econometrics & Finance Education Health Professions Immunology & microbiology Medicine & Pharmacology Public Health Veterinary

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A bioinformatics approach to design a novel epitope-based vaccine against Simian Immunodeficiency Virus (Retroviridae: Lentivirus) Dhea Kharisma, Viol; Ansori, Arif Nur Muhammad; Ullah, Md. Emdad; Dings, Tim Godefridus Antonius; Probojati, Rasyadan Taufiq; Fadholly, Amaq; Turista, Dora Dayu Rahma; Tacharina, Martia Rani; Zainul, Rahadian
Genbinesia Journal of Biology Vol. 2 No. 1 (2022): November 2022
Publisher : Generasi Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55655/genbinesia.v2i1.26

Abstract

Simian Immunodeficiency Viruses (SIV) have been found to naturally infect African nonhuman primates (NHP). This causative agents are important and one of the special interest as the root cause of the HIV/AIDS pandemic, one of the most threatening infectious diseases worldwide. The aim of this study was to design an epitope-based vaccine using bioinformatics approaches of the circulating SIV in Kenya, Africa. In this study, we used 17 partial SIV envelope glycoprotein genes retrieved from GenBank® (National Center for Biotechnology Information, USA). We analysed the candidate epitopes using the Immune Epitope Database and Analysis Resource. Then, we performed the protective antigens prediction usingVaxiJen. Interestingly, this study revealed the data of B cell epitope prediction, protective antigens prediction, and molecular phylogenetic of circulating SIV in Kenya, Africa. In sum, this study can be used to design a novel epitope-based vaccine against SIV. We suggest further studies to conduct confirmatory experiments (in vitro and in vivo).
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.
Health Impacts of Yoga: A Brief Review Ansori, Arif Nur Muhammad
Genbinesia Journal of Biology Vol. 2 No. 2 (2023): March 2023
Publisher : Generasi Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55655/genbinesia.v2i2.36

Abstract

Yoga is a holistic practice that has been used for thousands of years to promote health and well-being. The physical postures, breath control, and meditation techniques used in yoga have been found to have numerous health benefits, including improving flexibility, strength, balance, and cardiovascular health, reducing stress and anxiety, and improving mental clarity and focus. Recent research has shown that yoga can also be an effective complementary therapy for a variety of health conditions, such as chronic pain, depression, anxiety, and insomnia. Yoga has been found to be particularly effective in reducing stress and anxiety, which are common risk factors for many chronic diseases. Yoga is a non-competitive practice that can be adapted to suit the needs and abilities of individuals of all ages and fitness levels. It is a safe and effective way to improve overall health and well-being, and can be easily integrated into a daily routine. Therefore, yoga is a valuable tool for promoting health and well-being on all levels - physical, mental, emotional, and spiritual. It has become increasingly popular around the world, and is now widely recognized as a valuable complementary therapy for a variety of health conditions.
Isolation and Molecular Identification of Endophytic Fungi Associated with Brown Algae for Inhibiting Escherichia coli ESBL Wiradana, Putu Angga; Permatasari , Anak Agung Ayu Putri; Sari, Ni Kadek Yunita; Widhiantara, I Gede; Sandhika, I Made Gde Sudyadnyana; Waruwu, Ernawati; Fimaputra, Jatu Maranatha; Panjaitan, Novaria Sari Dewi; Putri, Fadillaisyia Riandani; Ansori, Arif Nur Muhammad

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Abstract

Background: The marine environment is the main source of research on natural products in the future. In addition, marine microorganisms have been identified as a natural source capable of developing new antibiotic compounds, including controlling urinary tract infections caused by Escherichia coli ESBL. Purpose: This study aims to isolate, select, and test the potential of brown macroalgae endophytic fungi (Phaeophyceae) collected from the coastal waters of Sanur, Bali Province. Methods: Three types of brown algae were collected from Sanur Beach and their endophytic fungi were isolated using PDA media. Antibacterial activ
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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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.
Exploring Brazilin as a Potential Breast Cancer Therapy via Molecular Dynamics Simulation Targeting ERα, 17β-HSD1, and NUDT5 Receptors Baroroh, Umi; Dasilva, Jasmine Aulia; Sundalian, Melvia; Astriany, Dewi; Ansori, Arif Nur Muhammad; Yee, Jonie C.
Jurnal Kimia Valensi Jurnal Kimia VALENSI, Volume 11, No. 2, November 2025
Publisher : Department of Chemistry, Faculty of Science and Technology Syarif Hidayatullah Jakarta State Islamic University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15408/jkv.v11i2.46465

Abstract

Breast cancer remains one of the leading causes of cancer-related mortality worldwide, suggesting the need for novel therapeutic agents with greater efficacy and fewer side effects. Brazilin, a natural flavonoid compound isolated from Caesalpinia sappan L., has shown promising anticancer activity, particularly against breast cancer cells. This study explores the therapeutic potential of brazilin by evaluating its interactions with three key molecular targets: estrogen receptor alpha (ERα), 17β-hydroxysteroid dehydrogenase 1 (17β-HSD1), and Nudix hydrolase 5 (NUDT5). Using molecular dynamics (MD) simulations, the study assesses the stability and binding interactions of complex systems. The results indicate that brazilin forms a stable complex with ERα, demonstrated by a low RMSD (2.6 Å) and strong hydrogen bonding with Glu353, occupancies of 97.8%, and minimal flexibility at the binding site (average RMSF < 2.5 Å). The binding free energy (ΔG Total) for the ERα–brazilin complex was -54.28 kcal/mol, indicating a stronger affinity than the reference ligand 4-hydroxytamoxifen. Brazilin also showed favorable binding with 17β-HSD1 and NUDT5, with binding energies of -39.71 kcal/mol and -23.23 kcal/mol, respectively. These findings suggest that brazilin may modulate critical targets involved in breast cancer progression, particularly in hormone receptor-positive subtypes. Further experimental validation is necessary to confirm its efficacy and optimize its therapeutic potential.
Co-Authors Aini, Nur Sofiatul Amaq Fadholly Arli Aditya Parikesit Asih Kuswardinah Bezhinar, Tatyana Burkov, Pavel Chandra, Nelson Dasilva, Jasmine Aulia Deky Aji Suseno, Deky Aji Derkho, Marina Dewi Astriany Dharmawan, Muhammad Alsyifaa Dhea Kharisma, Viol Dian, Farida Aryani Dings, Tim Godefridus Antonius Endang Suprihati Fimaputra, Jatu Maranatha Gudz, Petr Herdiansyah, Mochammad Aqilah Hery Purnobasuki Hikam, Agus Mohammad I Gede Widhiantara I Made Gde Sudyadnyana Sandhika Jakhmola, Vikash Khairullah, Aswin Rafif Kharisma, Viol Dhea Kurniawan, Muhammad 'Ahdi Kusnoto Kusnoto, Kusnoto Lucia Tri Suwanti, Lucia Tri Maksimiuk, Nikolai Melvia Sundalian Moses, Ikechukwu Benjamin Mufasirin Munawir Sazali Murtadlo, Ahmad Affan Ali Nastiti Wijayanti NI KADEK YUNITA SARI Nurul Jadid Mubarokati Nury Ariani Wulansari Panjaitan, Novaria Sari Dewi Permatasari , Anak Agung Ayu Putri Poedji Hastutiek Pratama, Bima Putra Putri, Fadillaisyia Riandani Putu Angga Wiradana R.C. Hidayat Soesilohadi Rahadian Zainul Rasyadan Taufiq Probojati Rebezov, Maksim Riwu, Katty Hendriana Priscilia Rollando, Rollando Rosidah Rosidah Sandy Arief Sukirno Sukirno Tacharina, Martia Rani Tamam, Muhammad Badrut Teguh Hari Sucipto, Teguh Hari Tri Wibawa Turista, Dora Dayu Rahma Ullah, Md. Emdad Umi Baroroh, Umi Waruwu, Ernawati Wicaksono, Adhityo Widyananda, Muhammad Hermawan Yee, Jonie C. Yulianna Puspitasari