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All Journal HAYATI Journal of Biosciences Jurnal Teknologi Industri Pertanian Indonesian Journal of Biotechnology Journal of Agromedicine and Medical Sciences Journal of Tropical Biodiversity and Biotechnology Manajemen Pendidikan BERITA BIOLOGI JURNAL BIOLOGI INDONESIA Jurnal Teknologi Laboratorium Jurnal RESTI (Rekayasa Sistem dan Teknologi Informasi) Chimica et Natura Acta Indonesian Journal of Chemistry Jurnal Sinergitas PkM & CSR FaST : Jurnal Sains dan Teknologi Walisongo Journal of Chemistry Menara Perkebunan Jurnal Teknik Informatika (JUTIF) Bioinformatics and Biomedical Research Journal Cermin Dunia Kedokteran Indonesian Journal of Life Sciences Makara Journal of Science Makara Journal of Technology Biosaintifika: Journal of Biology & Biology Education Jurnal Bioteknologi & Biosains Indonesia (JBBI) Cermin Dunia Kedokteran Kesmas: Jurnal Kesehatan Masyarakat Nasional (National Public Health Journal) Jurnal Bioteknologi & Biosains Indonesia Berita Biologi
Arli Aditya Parikesit
Department Of Bioinformatics, School Of Life Sciences, Indonesia International Institute For Life Sciences (i3l), Jakarta, Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Civil Engineering, Building, Construction & Architecture Computer Science & IT Earth & Planetary Sciences Economics, Econometrics & Finance Education Electrical & Electronics Engineering Engineering Environmental Science Health Professions Immunology & microbiology Industrial & Manufacturing Engineering Materials Science & Nanotechnology Mechanical Engineering Medicine & Pharmacology Public Health Social Sciences Other

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Kajian Prediksi 3-Dimensi Biomarker Kanker Payudara Dari Jalur Ekspresi LincRNA-ROR/MIR-145/ARF6 [3D Prediction of Breast Cancer Biomarker from The Expression Pathway of LincRNA-ROR/MIR-145/ARF6] Arli Aditya Parikesit; Dito Anurogo
FaST : Jurnal Sains dan Teknologi Vol. 2 No. 1 (2018): MAY
Publisher : Universitas Pelita Harapan

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

Abstract

According to WHO, breast cancer is one of the main causes of mortality in women. To overcome this malady, molecular biomedical research is carried out intensively. Anomalies in the lincRNA-RoR/miR-145/ARF6 expression pathway were found to play a very important role in breast cancer, especially in the type of Triple-Negative Breast Cancer (TNBC), which is the most dangerous variant of the deadly disease. Bioinformatics research has found the existence of non-coding RNA (ncRNA) in these expression pathways, whose interactions are worth studying with 3-dimensional prediction methods. The 3-D prediction method for biomolecules has been widely developed and has been successfully applied to DNA and protein. However, for the structure of RNA, it has just been developed, due to its low stability and very high dynamics on the biomolecule. Our aim is to apply the latest computational method for predicting the 3-dimensional structure of ncRNA, which can be applied as key information in biomedical application research. Extrapolation of kinetics and thermodynamic indicators of ncRNA ultimately yields the siRNA Linc-ROR 3-Dimensional structure and siRNA mRNA-ARF6, each having 13 and 8 hydrogen bonds. The existence of these hydrogen bonds is very important in maintaining the stability of the compounds and shows its efficacy as drug candidates. It is expected that preliminary information from the predicted 3-dimensional structure of ncRNA is useful for optimization of laboratory experiments in the field of crystallographic biomolecules.
Computational Design of siRNA Targeting Homo sapiens HER2 Splice Variant mRNA: A Potential Strategy for Breast Cancer Intervention Arli Aditya Parikesit; Arif Nur Muhammad Ansori; Viol Dhea Kharisma
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 Albert Widjaja Aldino Hafidzhah, Muhammad Alhussain, Shaheer Alyaa Farrah Dibha Angelique, Priscilla Arif Nur Muhammad Ansori Arif Nur Muhammad Ansori Bernard, Stefanus Bhat, Nausheen Burkov, Pavel Chandra, Nelson David Agustriawan Dedy Sugiono Deidre Valeska, Margareta Derkho, Marina Dian, Farida Aryani Didik Huswo Utomo Dito Anurogo Dito Anurogo Dito Anurogo Dito Anurogo Dito ANUROGO Dito Anurogo Dito Anurogo, Dito Ema Utami Ezra Bernandus Wijaya Fugaha, Daniel Ryan Gabriela, Vania Gabriele Mustika Kresnia Gabriella Patricia Adisurja Hafidzhah, Muhammad Aldino Heerlie, Devita Mayanda Herdiansyah, Mochammad Aqilah Hutapea, Hotma Martogi Lorensi Imron Imron Jakhmola, Vikash Jeremias Ivan Josephine, Evalina Junaida Astina Karimah, Nihayatul Karimah, Nihayatul Kharisma, Viol Dhea Kusrini Maksim Rebezov Margareta Deidre Valeska Margaretha, Febrina Maria Kiseleva Maulani Wijaya, Renadya Miko Wahyono, Tri Yunis Muhammad Aldino Hafidzhah Muhammad Aldino Handzhah Muhammad Hermawan Widyananda Murtadlo, Ahmad Affan Ali Nadezhda Kenijz Natalia Satya, Putri Gabriella Angel Nelda Aprilia Salim Nihayatul Karimah Patricia Adisurja, Gabriella Patricia, Gabriella Posa, Gabrielle Ann Villar Prakoso, Muhammad Ja'far Pratama, Rico Alexander Putri Gabriella Angel Natalia Satya Rahadian Zainul Ramanto, Kevin Nathanael Ratnasari, Nanda Risqia Pradana Renadya Maulani Wijaya Ridarto, Afif Maulana Yusuf Riza A PUTRANTO Rizky Nurdiansyah Rizky, Wahyu Choirur Ryan Fugaha, Daniel Ryan Wijaya Ryan Wijaya, Ryan Satrio Wibowo Scherbakov, Pavel Sepiashvili, Ekaterina Shemuel, Josia Sofy Permana Sri Wahyuningsih Stefanus Bernard Sudaryo, Mondastri Korib Sugiono, Dedy Svetlana Artyukhova Tambunan, Usman Sumo Friend Teguh Hari Sucipto, Teguh Hari Theo A Tochary Tochary, Theo A. Usman Sumo Friend Tambunan Utomo, Didik Huswo Utomo, Didik Huswo Vikash Jakhmola Viol Dhea Kharisma Viol Dhea Kharisma Wicaksono, Adhityo Wijaya, Renadya Maulani Yanuargi, Bayu Yulia Matrosova