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All Journal Pharmacy Reports Biodiversitas Journal of Biological Diversity
ENDANG RAHMAT
Department of Biotechnology, Faculty of Engineering, Universitas Bina Nusantara. Jl. Jalur Sutera Barat Kav. 21, Alam Sutera, Tangerang 15143, Banten, Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemistry Health Professions Immunology & microbiology Medicine & Pharmacology

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Exploring antioxidant potential of thiazole derivatives through functional group engineering: a molecular docking and molecular dynamics approach Haura Habiba; Hendrik Manullang; Putri Sekar Kristiany; Zahra Wahdini; Yuni Marhayuni; Citra Deliana Dewi Sundari; Atthar Luqman Ivansyah; Endang Rahmat; Refsya Azanti Putri; Sarmoko; Muhammad Yogi Saputra
Pharmacy Reports Vol. 6 No. 2 (2026): Pharmacy Reports
Publisher : Indonesian Young Scientist Group and UPN Veteran Jakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.51511/pr.150

Abstract

Thiazole derivatives are promising antioxidant candidates due to their tunable structures and diverse biological activities. This study investigated the effect of functional group engineering on the antioxidant potential of thiazole derivatives using molecular docking and 100 ns molecular dynamics simulations against the antioxidant-related target protein 1U7F. Five substituents, namely amide, hydroxyl, catechol, imidazole, and thiol groups, were introduced into the thiazole scaffold. Docking results showed that the amide-substituted derivative exhibited the strongest binding affinity, with a binding energy of −186.364 kJ/mol, followed by catechol, hydroxyl, imidazole, and thiol derivatives. Interaction analysis indicated that amide and hydroxyl-containing ligands formed more extensive hydrogen-bonding interactions with key active-site residues, contributing to stronger protein–ligand stabilization. Molecular dynamics analyses based on RMSD, RMSF, radius of gyration, solvent-accessible surface area, and hydrogen bonding confirmed that all complexes remained structurally stable throughout the simulation. The thiol-substituted derivative showed the highest dynamic structural stability, whereas MM-PBSA analysis revealed that the amide-substituted derivative had the most favorable binding free energy. Overall, these findings demonstrate that functional group modification significantly influences the binding affinity and dynamic stability of thiazole derivatives. The amide group is the most promising substituent for enhancing antioxidant potential through stronger protein binding, while the thiol group contributes to superior structural stability during simulation.
Chloroplast genome variation and phylogeny of mutant Typhonium flagelliforme (Araceae) from Indonesia NESTI FRONIKA SIANIPAR; ZIDNI MUFLIKHATI; ENDANG RAHMAT; REFLINUR REFLINUR; KHOIRUNNISA ASSIDQI; DWIYANTARI WIDYANINGRUM
Biodiversitas Journal of Biological Diversity Vol. 26 No. 11 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d261129

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Abstract. Sianipar NF, Muflikhati Z, Rahmat E, Reflinur, Assidqi K, Widyaningrum D. 2025. Chloroplast genome variation and phylogeny of mutant Typhonium flagelliforme (Araceae) from Indonesia. Biodiversitas 26: 5703-5713. Typhonium flagelliforme (rodent tuber) is an indigenous Indonesian medicinal plant valued for its anticancer properties. Mutation induced by gamma irradiation have produced mutant accessions with enhanced bioactivity, yet the underlying genetic basis remains poorly understood. To address this gap, we conducted a comparative analysis of complete chloroplast genomes from wild-type and mutant T. flagelliforme. Both genomes displayed a typical quadripartite structure, with lengths of 167,195 bp (wild-type) and 167,204 bp (mutant). Gene annotation revealed 118 genes in the wild-type, but only 116 in the mutant, with the absence of psaL and petN, genes related to photosystem I and the cytochrome b6f complex. In addition to both accessions preferring A/U-ending codons, simple sequence repeat (SSR) profiling identified 131 motifs in the wild type and 132 in the mutant. Divergent hotspot analysis detected high nucleotide diversity in loci, such as ndhE and ccsA. Phylogenetic reconstruction confirmed that both accessions form a monophyletic clade closely related to T. blumei, reinforcing their genetic proximity within the genus. These findings demonstrate that induced mutation results in localized plastome alterations without disrupting overall structural stability, thereby providing valuable genomic resources for phylogenetic inference, biodiversity conservation, and marker-assisted breeding in Typhonium and related Araceae taxa.
Revealing genetic markers and evolutionary insights within Piperaceae in chloroplast genome architecture of Indonesian Piper betle ENDANG RAHMAT; LAURA ANINDITA; NESTI FRONIKA SIANIPAR; KHOIRUNISSA ASSIDQI; YOUNGMIN KANG; KENNETH HAPPY; ADHITYO WICAKSONO
Biodiversitas Journal of Biological Diversity Vol. 26 No. 11 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d261146

Abstract

Abstract. Rahmat E, Anindita L, Sianipar NF, Assidqi K, Kang Y, Happy K, Wicaksono A. 2025. Revealing genetic markers and evolutionary insights within Piperaceae in chloroplast genome architecture of Indonesian Piper betle. Biodiversitas 26: 5906-5919. Piper betle is one of the most significant medicinal plants in Southeast Asian tradition, yet its genomic resources remain limited compared to other members of the genus. In this study, we report the first complete chloroplast genome of an Indonesian isolate of P. betle, providing a much-needed reference for future molecular work. The genome was assembled into 161,313 bp with a typical quadripartite structure consisting of an LSC (88,995 bp), an SSC (18,201 bp), and two nearly identical IRs (27,057 and 27,060 bp). A total of 113 genes were annotated, including 79 protein-coding, 30 tRNA, and 4 rRNA genes. Repeat analysis revealed 70 cpSSRs, markedly fewer than those described in other Piper species, along with 104 long repeats dominated by palindromic types. Sliding-window analysis detected variable regions in ndhG and ndhI in addition to the well-known hotspots ycf1 and rpl32-ndhF, two novel loci that may serve as species-specific markers. Phylogenetic reconstruction clustered the Indonesian isolate with P. hancei, P. nigrum, and P. kadsura, yet comparison with a Chinese isolate indicated paraphyletic placement across two clades which may indicate a role of geographic divergence in shaping plastome evolution. The results of these genomic resources reveal reduced SSR content, novel divergence hotspots in ndhG and ndhI, and the paraphyletic relationship with the Chinese isolate: creating potential in marker development and evolutionary studies, while also laying the groundwork for future applications in conservation and biotechnology.
Co-Authors ADHITYO WICAKSONO Atthar Luqman Ivansyah Citra Deliana Dewi Sundari DWIYANTARI WIDYANINGRUM Haura Habiba Hendrik Manullang KENNETH HAPPY KHOIRUNISSA ASSIDQI KHOIRUNNISA ASSIDQI LAURA ANINDITA Muhammad Yogi Saputra Putri Sekar Kristiany REFLINUR REFLINUR Refsya Azanti Putri Sarmoko Sianipar, Nesti Fronika YOUNGMIN KANG Yuni Marhayuni Zahra Wahdini ZIDNI MUFLIKHATI