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All Journal Biosaintifika: Journal of Biology & Biology Education
Arif Nur Muhammad Ansori
Postgraduate School, Universitas Airlangga, Surabaya, Indonesia.
Agriculture, Biological Sciences & Forestry

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In Silico Study of Cladosporol and Its Acyl Derivatives as Anti-Breast Cancer Against Alpha-Estrogen Receptor Mochammad Aqilah Herdiansyah; Arif Nur Muhammad Ansori; Viol Dhea Kharisma; Mochamad Radika Tory Alifiansyah; Dhea Anggraini; Qiara Amelia Putri Priyono; Putri Antika Yusniasari; Amelia Julia Tria Fetty; Rahadian Zainul; Maksim Rebezov; Evgeniy Kolesnik; Nikolai Maksimiuk
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.
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 Amelia Julia Tria Fetty Arli Aditya Parikesit Dhea Anggraini Evgeniy Kolesnik Maksim Rebezov Mochamad Radika Tory Alifiansyah Mochammad Aqilah Herdiansyah Nikolai Maksimiuk Putri Antika Yusniasari Qiara Amelia Putri Priyono Rahadian Zainul Viol Dhea Kharisma Viol Dhea Kharisma