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All Journal Biotropika Tropical Genetics
Prabasari, Kartika
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Immunology & microbiology

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In silico Exploration of Bioactive Compounds from Withania somnifera as Inhibitor for Alpha Delta Bungarotoxin of Bungarus candidus Venom Prabasari, Kartika; Kurnianingsih, Nia; Kurniawan, Nia
Biotropika: Journal of Tropical Biology Vol. 11 No. 2 (2023)
Publisher : Universitas Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.biotropika.2023.011.02.01

Abstract

The antivenom for Malayan krait (Bungarus candidus) venom has not yet been available in Indonesia, leading to many fatal snakebite cases. Alternative treatment approaches using medicinal plants are needed to be explored. This study investigated the potential of medicinal plants’ natural bioactive compounds as toxic alpha-delta bungarotoxin protein inhibitors in B. candidus venom. The approach taken is using the 3D structure of the alpha-delta protein of bungarotoxin B. candidus predicted by SWISS-MODEL. Knapsack Family Database and PubChem were used for bioactive compounds datamining. ADME analysis and drug-likeness of the compounds were carried out with SWISS-ADME. Docking between alpha-delta-Bungarotoxin protein and bioactive compounds was carried out with Pyrx 0.9.5. Visualization of docking results was performed with PyMOL and Discovery Studio 2016 was used to evaluate docking interactions. The docking results showed that a compound with the potential inhibitor of alpha-delta bungarotoxin came from Ashwagandha (Withania somnifera) with a binding energy ranging from -6.6 to -6.9. The compound with the best inhibitor potential, namely withanolide D, was seen from the stability of the interaction based on hydrogen bonding at three amino acid residues: THR59, SER62, and THR63. The evaluation is supported by the results of molecular dynamics simulations which show stability in almost all aspects. Our results suggest the potential for exploratory research in the field of bioinformatics related to bioactive compounds from herbal plants as an alternative to antivenom.
Phylogenetic and Genetic Distance Analysis of the Mangrove Worm (Namalycastis) Based on the 18S rRNA Gene Using in Silico Methods Aditya, Arielda Putri; Aditya, Junardi; Candramila, Wolly; Prabasari, Kartika
Tropical Genetics Vol. 5 No. 2 (2025): Genetics
Publisher : Genetikawan Muda Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/tg.v5i2.100

Abstract

Namalycastis is a polychaete worm that inhabits dynamic aquatic environments and exhibits high genetic and morphological variability. This study investigates the phylogeny of the genus Namalycastis through an in silico analysis using the 18S ribosomal RNA (rRNA) gene. This genetic marker is considered ideal as it combines conserved and variable regions, both essential for taxonomic and evolutionary analyses. The objective of this research was to examine the phylogenetic relationships and genetic distances among 12 species of the genus Namalycastis based on their 18S rRNA gene sequences. DNA sequences were obtained from the NCBI database and aligned using Clustal-W in MEGA XI software. Phylogenetic reconstruction was performed using the Neighbor-Joining method with 1000 bootstrap replications, applying the Kimura 2-Parameter (K2P) model. The results revealed that Namalycastis jaya shares a very close evolutionary relationship with Namalycastis abiuma, forming a monophyletic clade that is distinct from Namalycastis hawaiiensis. The genetic distances among N. jaya, N. abiuma, and N. abiuma group sp. indicate a close evolutionary affinity, whereas N. hawaiiensis displays greater genetic divergence from the other two species. Overall, this study demonstrates that the 18S rRNA gene is an effective molecular marker for identifying phylogenetic relationships among Namalycastis species. The findings also highlight the potential of in silico methods in elucidating evolutionary patterns within the genus Namalycastis.
Co-Authors Aditya, Arielda Putri Aditya, Junardi Kurnianingsih, Nia Nia Kurniawan WOLLY CANDRAMILA