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All Journal Jurnal Penelitian Pendidikan IPA (JPPIPA) Tropical Genetics
Yulianto Ade Prasetya
Universitas Anwar Medika
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Education Materials Science & Nanotechnology Physics

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Exploring Oxygenated Sesquiterpenes from Merauke Agarwood as PBP1a and PBP3 Inhibitors in Acinetobacter baumanii: An In-Silico Approach Yulianto Ade Prasetya; Triono Bagus Saputro; Yohanes Ardian Kapri Negara; Arif Luqman
Jurnal Penelitian Pendidikan IPA Vol 12 No 3 (2026): In Progress
Publisher : Postgraduate, University of Mataram

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29303/jppipa.v12i3.14627

Abstract

Acinetobacter baumannii is a multidrug-resistant pathogen causing severe nosocomial infections, primarily associated with alterations in penicillin-binding proteins (PBPs) that reduce the effectiveness of β- lactam antibiotics. Despite increasing interest in plant-derived bioactive compounds, the potential of oxygenated sesquiterpenes from Aquilaria malaccensis as inhibitors of PBPs remains underexplored, indicating a clear research gap. This study aimed to evaluate the antibacterial potential of three oxygenated sesquiterpenes—Agaruspirol, Eudesmol, and Sinenofuranol—against PBP1a (3UE3) and PBP3 (3UDF). A systematic literature review (SLR) integrated with an in silico approach was conducted, including ligand retrieval from PubChem, ADMET prediction using ADMETlab 3.0, molecular docking using CB-Dock2, interaction analysis with UCSF ChimeraX and PLIP, and antibacterial activity prediction using PASS Online. The results showed that all compounds satisfied Lipinski’s rule of five and exhibited favorable ADMET profiles. Molecular docking demonstrated stable interactions with both PBPs, dominated by hydrogen bonding and hydrophobic interactions. Agaruspirol exhibited the strongest binding affinity toward PBP3 (–6.9 kcal/mol) and PBP1a (–6.5 kcal/mol), along with the highest predicted antibacterial activity (Pa = 0.364; Pi = 0.039). These findings suggest that oxygenated sesquiterpenes, particularly agaruspirol, have potential as lead compounds for the development of antibacterial agents targeting PBP-mediated resistance in A. baumannii, and provide a scientific basis for further in vitro and in vivo validation.
In Silico Analysis of Non-synonymous Mutations in the durA Gene and Their Effects on the Stability and Physicochemical Properties of Duramycin Yulianto Ade Prasetya; Tjie Kok; Mariana Wahjudi
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.v5i2.84

Abstract

Duramycin is a lantibiotic peptide encoded by the durA gene, known for its antimicrobial activity against Gram-positive bacteria. This study aimed to evaluate the effects of single-point mutations on the stability and structural integrity of duramycin using a comprehensive in silico approach. Five variants—C1S, F7A, T11Y, D15E, and K19V—were designed and assessed using I-Mutant2.0 to predict their impact on protein stability. ProtParam analysis was conducted to determine molecular weight, isoelectric point (pI), net charge at pH 7, instability index, aliphatic index, and hydropathicity (GRAVY). In addition, PEP-FOLD3 was employed to model the 3D conformations of each mutant peptide. Results showed that K19V improved peptide stability and increased aliphatic index and GRAVY score, indicating enhanced hydrophobicity and potential thermal stability. In contrast, F7A led to a major structural shift marked by an α-helical conformation and reduced stability. C1S and T11Y induced minor destabilizing effects, while D15E offered a moderately stabilizing substitution with minimal structural deviation. Overall, this study highlights the functional relevance of C-terminal and hydrophobic residues in maintaining duramycin’s structural compactness and provides a framework for future design of optimized antimicrobial peptides through rational mutation
Co-Authors Arif Luqman Mariana Wahjudi Triono Bagus Saputro, Triono Bagus Yohanes Ardian Kapri Negara