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All Journal HAYATI Journal of Biosciences Biotropika Indonesian Journal of Biotechnology BERITA BIOLOGI Jurnal Sinergitas PkM & CSR Walisongo Journal of Chemistry Acta Biochimica Indonesiana TIERS Information Technology Journal Cermin Dunia Kedokteran Indonesian Journal of Life Sciences Makara Journal of Science Cermin Dunia Kedokteran
Rizky Nurdiansyah
Indonesia International Institute For Life Sciences
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Computer Science & IT Earth & Planetary Sciences Economics, Econometrics & Finance Education Environmental Science Health Professions Immunology & microbiology Materials Science & Nanotechnology Medicine & Pharmacology Public Health Social Sciences

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Drug Repurposing Option for COVID-19 with Structural Bioinformatics of Chemical Interactions Approach Arli Aditya Parikesit; Rizky Nurdiansyah
Cermin Dunia Kedokteran Vol 47, No 3 (2020): Dermatologi
Publisher : PT. Kalbe Farma Tbk.

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55175/cdk.v47i3.376

Abstract

The SARS-CoV-2 virus is the pathogenic agent that caused the COVID-19 disease. The epicenter of this disease is the city of Wuhan, China. It is already categorized as “pandemic” by WHO, as many countries already affected with the infections, including recently Indonesia. Although the standard RT-PCR and DNA sequencing protocols has already developed for diagnostic, no drugs are available to cure this disease until today. The anti-malaria drug of chloroquine phosphate was repurposed, as well as other anti-viral drugs. In this regard, a structural bioinformatics pipeline was utilized to validate the claim in the computational realm. Within the sphere of the online molecular docking method, it was found that all the tested repurposed drugs attached accordingly with the SARS-CoV-2 protease enzyme that plays a role in viral replication. The repurposed drugs could be proposed as drug candidates for COVID-19, after clinical trials or further laboratory testing.Virus SARS-CoV-2 adalah patogen penyebab penyakit COVID-19. Episentrum penyakit ini adalah kota Wuhan, Tiongkok. WHO mengeluarkan peringatan ‘pandemi’ karena banyak negara sudah terkena infeksi, termasuk Indonesia. Meskipun protokol RT-PCR dan sekuensing DNA standar telah dikembangkan untuk tujuan diagnostik, hingga saat ini tidak ada obat untuk menyembuhkan penyakit ini. Obat anti-malaria chloroquine phosphate dicoba, bersama dengan beberapa obat anti-virus. Alur analisis bioinformatika struktural digunakan untuk validasi di ranah komputasi. Dalam lingkup metode molecular docking secara daring, ditemukan bahwa obat tersebut tertambat dengan enzim protease SARS-CoV-2 yang berperan dalam replikasi virus. Obat ini dapat diusulkan sebagai kandidat obat untuk COVID-19, setelah pengujian laboratorium dan uji klinis lebih lanjut.
Protein Annotation of Breast-cancer-related Proteins with Machine-learning Tools Parikesit, Arli Aditya; Agustriawan, David; Nurdiansyah, Rizky
Makara Journal of Science Vol. 24, No. 2
Publisher : UI Scholars Hub

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

Abstract

One of the primary contributors to the mortality of women is breast cancer. Several approaches are used to cure it, but recurrence occurs in 79% of the cases because the underlying mechanism of the protein molecules is not carefully ex-amined. The goal of this research was to use machine-learning tools is to elucidate conserved regions and to obtain functional annotations of breast-cancer-related proteins. The sequences of five breast-cancer-related proteins (BRCA2, BCAR1, BCAR3, BCAR4, and BRMS1) and their annotations were retrieved from the UniProt and TCGA databases, respectively. Conserved regions were extracted using CLUSTALX. We constructed a phylogenetic tree using the MEGA 7.0. SUPERFAMILY database to obtain fine-grained domain annotation. The tree revealed that the BRCA2 and BCAR4 protein sequences are located in a clade, which indicates that they have overlapping functions. Several protein domains were identified, including the SH2 and Ras GEF domains in BCAR3, the SH3 domain in BCAR1, and the BRCA2 helical domain, the nucleic-acid-binding protein, and tower domain. We found that no protein domains could be annotated for BCAR4 or BRMS1, which may indicate the presence of a disordered protein state. We suggest that each protein has distinct functionalities that are complementary in regulating the progression of breast cancer, although further study is necessary for confirmation. This protein-domain annotation project could be leveraged by the complete integration of mapping with respect to gene and disease ontology. This type of leverage is vital for obtaining biochemical insights regarding breast cancer.
Drug Repurposing Option for COVID-19 with Structural Bioinformatics of Chemical Interactions Approach Arli Aditya Parikesit; Rizky Nurdiansyah
Cermin Dunia Kedokteran Vol. 47 No. 3 (2020): Dermatologi
Publisher : PT Kalbe Farma Tbk.

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55175/cdk.v47i3.359

Abstract

The SARS-CoV-2 virus is the pathogenic agent that caused the COVID-19 disease. The epicenter of this disease is the city of Wuhan, China. It is already categorized as “pandemic” by WHO, as many countries already affected with the infections, including recently Indonesia. Although the standard RT-PCR and DNA sequencing protocols has already developed for diagnostic, no drugs are available to cure this disease until today. The anti-malaria drug of chloroquine phosphate was repurposed, as well as other anti-viral drugs. In this regard, a structural bioinformatics pipeline was utilized to validate the claim in the computational realm. Within the sphere of the online molecular docking method, it was found that all the tested repurposed drugs attached accordingly with the SARS-CoV-2 protease enzyme that plays a role in viral replication. The repurposed drugs could be proposed as drug candidates for COVID-19, after clinical trials or further laboratory testing. Virus SARS-CoV-2 adalah patogen penyebab penyakit COVID-19. Episentrum penyakit ini adalah kota Wuhan, Tiongkok. WHO mengeluarkan peringatan ‘pandemi’ karena banyak negara sudah terkena infeksi, termasuk Indonesia. Meskipun protokol RT-PCR dan sekuensing DNA standar telah dikembangkan untuk tujuan diagnostik, hingga saat ini tidak ada obat untuk menyembuhkan penyakit ini. Obat anti-malaria chloroquine phosphate dicoba, bersama dengan beberapa obat anti-virus. Alur analisis bioinformatika struktural digunakan untuk validasi di ranah komputasi. Dalam lingkup metode molecular docking secara online, ditemukan bahwa obat tersebut tertambat dengan enzim protease SARS-CoV-2 yang berperan dalam replikasi virus. Obat ini dapat diusulkan sebagai kandidat obat untuk COVID-19, setelah pengujian laboratorium dan uji klinis lebih lanjut.
In silico investigation of bioactive compounds from Ginkgo biloba as alternatives to non-steroidal anti-inflammatory drugs Jai, Jyotsna; Yosiano, Stephanie Angela; Trisna, Tifara Elaine; Rosaceae, Agnes Maria; Kurniawan, Laurentius Hardy; Nurdiansyah, Rizky
Indonesian Journal of Life Sciences 2022: IJLS Vol 04 No .02
Publisher : Indonesia International Institute for Life Sciences

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.54250/ijls.v4i2.147

Abstract

Non-steroidal Anti-inflammatory Drugs (NSAIDs) are common over-the-counter drugs that are used for numerous inflammation-associated ailments. Despite their widespread consumption, these synthetic drugs are not without side effects. Adversities caused by NSAIDs range from simple nausea and vomiting to fatal conditions such as hypertension, gastrointestinal bleeding and diminished renal function. There is thus a need to develop novel alternatives to these drugs which possess comparable efficacies. Phytocompounds are attractive alternatives for a plethora of medicines used for various disorders and diseases as they are readily available in nature and have negligible side effects. In an attempt to identify safe alternatives to NSAIDs, we tested six bioactive compounds from Ginkgo biloba (Ginkgolide A, Amentoflavone, Bilobetin, Ginkgetin, Quercetin, and Bilobalide) for their abilities to inhibit Cyclooxygenase-1, Cyclooxygenase-2 and 5-Lipoxygenase which are inflammation-causing enzymes. Molecular docking experiments using Autodock Vina resulted in binding energy values between -6.6 and -11.9 kcal/mol, comparable to that of control drugs, which indicated that the tested phytocompounds were able to bind strongly to the active sites of the three proteins. Analyses of receptor-ligand interactions using Discovery Studio Visualizer revealed that all the tested compounds formed numerous non-covalent interactions with the surrounding amino acid residues, which confirmed their binding stabilities. Finally, evaluation of their drug likeness based on Lipinski’s rule of five showed that the tested G. biloba compounds possess the potential to be taken as oral drugs to replace conventional NSAIDs.
Forward Chaining Method for Diagnosing Diseases and Pests in Melon Plants Dapiokta, Jum; Nurdiansyah, Rizky; Muris, Anggeraeni Agustin; Kuswanto, Joko
TIERS Information Technology Journal Vol. 5 No. 2 (2024)
Publisher : Universitas Pendidikan Nasional

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.38043/tiers.v5i2.6018

Abstract

There are many problems encountered in the field of agriculture, for example problems about diseases and pests in melon plants. Experts or experts in the field of agriculture rarely need to build a system that is able to adopt human processes and ways of thinking in the form of an expert system. The purpose of this study is to build an expert system to diagnose diseases and pests in melon plants using the forward chaining method. A reasoning that starts from facts first to test the correctness of a hypothesis. The system was tested using the black box testing method which was tested on experts and melon farmers. Based on the results of testing using the black box testing method tested on experts and farmers, the results of the assessment were obtained that the expert system for diagnosing diseases in melon plants was proven to run well as expected with 100% validation. The end result of this expert system is to make it easier for users to carry out the consultation process by providing a list of indication of diseases and pests experienced. Then the control of the type of disease and pest will be displayed according to the selected indication. In addition, this expert system also makes it easier for admins to update data such as disease data, indication and control. This expert system application program is also not only beneficial for experts but can also be useful for farmers that ordinary people who do not understand a little about melon plant diseases and pests.
Drug Repurposing Option for COVID-19 with Structural Bioinformatics of Chemical Interactions Approach Arli Aditya Parikesit; Rizky Nurdiansyah
Cermin Dunia Kedokteran Vol 47 No 3 (2020): Dermatologi
Publisher : PT Kalbe Farma Tbk.

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55175/cdk.v47i3.359

Abstract

The SARS-CoV-2 virus is the pathogenic agent that caused the COVID-19 disease. The epicenter of this disease is the city of Wuhan, China. It is already categorized as “pandemic” by WHO, as many countries already affected with the infections, including recently Indonesia. Although the standard RT-PCR and DNA sequencing protocols has already developed for diagnostic, no drugs are available to cure this disease until today. The anti-malaria drug of chloroquine phosphate was repurposed, as well as other anti-viral drugs. In this regard, a structural bioinformatics pipeline was utilized to validate the claim in the computational realm. Within the sphere of the online molecular docking method, it was found that all the tested repurposed drugs attached accordingly with the SARS-CoV-2 protease enzyme that plays a role in viral replication. The repurposed drugs could be proposed as drug candidates for COVID-19, after clinical trials or further laboratory testing. Virus SARS-CoV-2 adalah patogen penyebab penyakit COVID-19. Episentrum penyakit ini adalah kota Wuhan, Tiongkok. WHO mengeluarkan peringatan ‘pandemi’ karena banyak negara sudah terkena infeksi, termasuk Indonesia. Meskipun protokol RT-PCR dan sekuensing DNA standar telah dikembangkan untuk tujuan diagnostik, hingga saat ini tidak ada obat untuk menyembuhkan penyakit ini. Obat anti-malaria chloroquine phosphate dicoba, bersama dengan beberapa obat anti-virus. Alur analisis bioinformatika struktural digunakan untuk validasi di ranah komputasi. Dalam lingkup metode molecular docking secara online, ditemukan bahwa obat tersebut tertambat dengan enzim protease SARS-CoV-2 yang berperan dalam replikasi virus. Obat ini dapat diusulkan sebagai kandidat obat untuk COVID-19, setelah pengujian laboratorium dan uji klinis lebih lanjut.
Co-Authors Arli Aditya Parikesit Dapiokta, Jum David Agustriawan fatchiyah . Fatchiyah Fatchiyah Imron Imron Jai, Jyotsna Jeremias Ivan Joko Kuswanto Kurniawan, Laurentius Hardy Muris, Anggeraeni Agustin Rahmat Azhari Kemal Rosaceae, Agnes Maria Ryan Wijaya Ryan Wijaya, Ryan Sri Rahayu Lestari Trisna, Tifara Elaine Yosiano, Stephanie Angela