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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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Immunobioinformatics analysis and phylogenetic tree construction of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Indonesia: spike glycoprotein gene Ansori, Arif Nur Muhammad; Kharisma, Viol Dhea; Antonius, Yulanda; Tacharina, Martia Rani; Rantam, Fedik Abdul
Jurnal Teknologi Laboratorium Vol 9 No 1 (2020): 2020 (1): Special Edition "COVID-19"
Publisher : POLTEKKES KEMENKES YOGYAKARTA

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (986.383 KB) | DOI: 10.29238/teknolabjournal.v9i1.221

Abstract

The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), has spread worldwide and as a result, the World Health Organization (WHO) declared it a pandemic. At present, there are no approved vaccines against SARS-CoV-2. Therefore, the aim of this study was to predict epitope-based vaccines using bioinformatics approaches and phylogenetic tree construction of SARS-CoV-2 against the backdrop of the COVID-19 pandemic. In this study, we employed 27 isolates of SARS-CoV-2 spike glycoprotein genes retrieved from GenBank® (National Center for Biotechnology Information, USA) and the GISAID EpiCoV™ Database (Germany). We analyzed the candidate epitopes using the Immune Epitope Database and Analysis Resource. Furthermore, we performed a protective antigen prediction with VaxiJen 2.0. Data for B-cell epitope prediction, protective antigen prediction, and the underlying phylogenetic tree of SARS-CoV-2 were obtained in this research. Therefore, these data could be used to design an epitope-based vaccine against SARS-CoV-2. However, the advanced study is recommended for confirmation (in vitro and in vivo).
The In Silico Analysis and Identification of Possible Inhibitor of H5N1 Virus: Compounds Analysis and Identification of Possible Neuraminidase Inhibitors Syafrudin, Syafrudin; Septiadi, Luhur; Alfaruqi, Nuri Thobibatus Shofia; Wahyudi, Didik; Kharisma, Viol Dhea
Bioinformatics and Biomedical Research Journal Vol. 1 No. 2 (2018): Volume 1 Issue 2
Publisher : Future Science

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Abstract

Fingerroot (Boesenbergia pandurata (Roxb.)) belongs to the family Zingiberaceae (Ginger). B. pandurata has pharmacological benefits such as neuroprotective, chemoprotective, anti-inflammatory, anti-angiogenic, antioxidant, an inhibitor of protease enzyme NS2B/NS3 dengue virus, Japanese encephalitis virus and swine flu virus (H1N1). This study aims to determine the most effective compounds from B. pandurata as neuraminidase inhibitors of H5N1 virus. The amino acid sequence for neuraminidase of avian influenza A virus subtype H5N1 of A/China/GD02/2006 was retrieved from protein sequence database at NCBI. Then, modeled by Swiss Model. Analyse of molecular docking was performed using PyRx and the interactions between neuraminidase inhibitors of H5N1 and B. pandurata active compound was analyzed by PyMol software and LigPlot+ software. From the 30 active compounds which have been docked, 4-hydroxypanduratin A, rubranine, boesenbergin B, boesenbergin A, 5,7-dimethoxyflavone, and tectochrysin had an equal or smaller free binding energy than control compound. 4-hydroxypanduratin A proved to be the most potent active compound as a neuraminidase inhibitor (NA 1) because it has the most negative binding energy and the same amino acid binding residue with the control compound. Therefore, 4-hydroxypanduratin A is predicted to be used as inhibitors of neuraminidase in the H5N1 virus.
Prediction of Novel Bioactive Compound from Zingiber officinale as Non-nucleoside Reverse Transcriptase Inhibitors (NNRTIs) of HIV-1 through Computational Study Kharisma, Viol Dhea; Septiadi, Luhur; Syafrudin, Syafrudin
Bioinformatics and Biomedical Research Journal Vol. 1 No. 2 (2018): Volume 1 Issue 2
Publisher : Future Science

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Abstract

Human immunodeficiency virus 1 (HIV-1) is one of the viruses of that causes AIDS in humans and disease outbreaks in this modern era. Reverse transcriptase (RT) enzyme though to be the functional enzyme that play a role on the HIV-1 virus replication. Bioactive compounds contained on Ginger (Zingiber officinale) is known to inhibit viral replication. This study aims to determine the alternative bioactive compounds contained on Ginger (Zingiber officinale) as as a non-nucleoside reverse transcriptase (NNRTIs) HIV-1 inhibitors through computational study. The reverse transcriptase (RT) enzyme model was retrieved from protein sequence database (PDB) and validated with Ramachandran Plot and the compound contained on Ginger was retrieved from database. Analysis of molecular docking, performed using PyRx and the interactions between Reverse Transcriptase (RT) enzyme of HIV-1 virus and Zingiber officinale active compound was analyzed by PyMol and LigPlot+, also the drug-likeness molecule properties with The Lipinski Rule’s of Five. From 24 active compound which have been docked, ?-sitosterol proven to be the most potential bioactive compound as inhibitors of Reverse Transcriptase (RT) enzyme because it has more negative binding energy and the same amino acid residue with the control. Therefore, ?-sitosterol is predicted to be used as non-nucleoside reverse transcriptase (NNRTIs) HIV-1 inhibitors.
Conserved B-cell epitope identification of envelope glycoprotein (GP120) HIV-1 to develop multi-strain vaccine candidate through bioinformatics approach Kharisma, Viol Dhea; Ansori, Arif Nur Muhammad; Posa, Gabrielle Ann Villar; Rizky, Wahyu Choirur; Permana, Sofy; Parikesit, Arli Aditya
Jurnal Teknologi Laboratorium Vol 10 No 1 (2021): inpress
Publisher : POLTEKKES KEMENKES YOGYAKARTA

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29238/teknolabjournal.v10i1.274

Abstract

Acquired immune deficiency syndrome (AIDS) has been identified from US patients since 1981. AIDS is caused by infection with the human immunodeficiency virus type 1 (HIV-1) which is a retrovirus. HIV-1 gp120 can be recognized by the immune system because it is located outside the virion. The conserved region is identified in gp120, and it is recognized by an immune cell which then initiates specific immune responses, viral mutation escape, and increase vaccine protection coverage, a benefit derived from the conserved region-based vaccine design. However, previous researchers have little knowledge on this conserved region as a target for vaccine design. This paper explains how the conserved region of gp120 HIV-1 is a major target for vaccine design through a bioinformatics approach. The conserved region from gp120 was explored as a vaccine design target with a bioinformatics tool that consists of B-cell epitope mapping, vaccine properties, molecular docking, and dynamic simulation. The peptide vaccine candidate of B5 with the gp120 HIV-1 conserved region was found to provoke B-cell activation through a direct pathway, produce specific antibody, and increase protection from multi-strain viral infection.
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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Abstract

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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Abstract

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
Penghambatan Senyawa di dalam Kopi terhadap Protein Fibronektin dan Protein Shroom: Kajian Gangguan Neurulasi Primer Secara in Silico Santoso, Novian Budi; Susanto, Susanto; Adrianto, Hebert; Kharisma, Viol Dhea
Jurnal Kesehatan Vol 13 No 2 (2022): Jurnal Kesehatan
Publisher : Poltekkes Kemenkes Tanjung Karang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.26630/jk.v13i2.2641

Abstract

Coffee drinking habits exist in Indonesian culture. Coffee as the primary source of caffeine is here the effect of embryotoxicity on paralysis, wrong brain. The brain is going on so that the body is a curiosity. Fibronectin and shroom proteins play in the primary stacking cage, which is the seasoning of the nerve roof. This study aimed to predict molecular inhibition of compounds in coffee in fibronectin protein and shroom protein in silica. The research method used samples of ligands and target proteins from the PubChem database and protein databank, then analyzed using PyRx, Discovery Studio, and PyMol software. The results of the study of literature there are five compounds in coffee. As a result of molecular docking simulation analysis, caffeine compounds (CID 2519) had lower total binding energy (-9.9 kcal/mol) in other combinations in fibronectin and shroom proteins. There are six residues of the amino acid fibronectin and 5 in shroom with caffeine. There are chemical bonds provided for caffeine compounds consisting of hydrophobic, alkyl, Van der Waals, and electrostatic. Caffeine can inhibit fibronectin and shroom protein activity and in vitro and in vivo tests to validate bioinformatics results.
In Silico Study of Cladosporol and Its Acyl Derivatives as Anti-Breast Cancer Against Alpha-Estrogen Receptor Herdiansyah, Mochammad Aqilah; Ansori, Arif Nur Muhammad; Kharisma, Viol Dhea; Alifiansyah, Mochamad Radika Tory; Anggraini, Dhea; Priyono, Qiara Amelia Putri; Yusniasari, Putri Antika; Fetty, Amelia Julia Tria; Zainul, Rahadian; Rebezov, Maksim; Kolesnik, Evgeniy; Maksimiuk, Nikolai
Biosaintifika: Journal of Biology & Biology Education Vol. 16 No. 1 (2024): April 2024
Publisher : Universitas Negeri Semarang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v15i1.949

Abstract

Breast cancer is a chronic health problem that causes 690,000 deaths worldwide. The development of secondary metabolite compounds from natural preparations through an in silico approach is needed as a predictive tool to prevent breast cancer, one of them is cladosporol from Cladosporium spp. This study aims to utilize an in silico approach to predict the potential of cladosporol against alpha-estrogen receptors. The alpha-estrogen receptor with code 6CBZ was selected based on group function as pharmacophore in ligand-receptor interaction. The methods used in this study are by using an in silico approach with Molegro Virtual Docker (MVD) Ver 5.5 for the docking process and CABS-flex 2.0 for identifying the stability of the complexes. ADMET properties analysis was also performed to know the pharmacokinetics attributes of cladosporol. Based on research conducted, stated that cladosporol octanoate has the lowest rerank score with a -84.3593 value and the RMSD value is 1.195 Å so it’s valid for molecular docking. Exploration of cladosporol for anti-breast cancer from Cladosporium spp fungi can be a novelty for the development of future pharmaceutical research. Thus, the development of anti-cancer drugs for early prevention can be carried out to reduce the number of breast cancer cases worldwide.
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

Abstract

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.
Vaccine construction for human papilloma virus (HPV) type 16 and 18 Infection using in silico approach to combat cervical cancer Dharmawan, Muhammad Alsyifaa; Ansori, Arif Nur Muhammad; Dian, Farida Aryani; Probojati, Rasyadan Taufiq; Tamam, Muhammad Badrut; Kharisma, Viol Dhea
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.v1i1.3

Abstract

Human papillomavirus (HPV) is a virus that causes infection on the surface of the skin and has the potential to cause cervical cancer. This viral infection is characterized by the growth of warts on the skin in various areas of the body, such as the arms, legs, mouth, and genital area. Because the virus can endanger health, it is necessary to design an HPV vaccine to overcome this problem. In this study, we performed a study characterization of HPV types 16 and 18 sequences to obtain immunogenic epitopes retrieved from the National Center for Biotechnology Information (NCBI) web server. Then, epitope prediction was performed using the immune epitope database (IEDB) web server and selected to get the best vaccine candidate for HPV types 16 and 18. We recommend 16P1 as an epitope-based peptide vaccine candidate for HPV type 16 and 18P4 for type 18. Both vaccine candidates are antigenic, non-allergenic, and non-toxic. The 16P1 and 18P4 have the lowest global energy values ​​among the other candidates. However, further research is needed to be able to develop the best vaccine (in vitro and in vivo experiments).
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 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