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All Journal Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences Medical Journal of Indonesia Biosaintifika: Journal of Biology & Biology Education
Huyop, Fahrul
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Agriculture, Biological Sciences & Forestry Environmental Science Medicine & Pharmacology

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Structural Comparison of α-agarase (α-AgaD) from Thalassomonas sp. LD5: An in-silico study: Structural Comparison of α-agarase (α-AgaD) from Thalassomonas sp. LD5 Oyewusi, Habeebat Adekilekun; Oladipo, Oluwatosin; Abdul Wahab, Roswanira; Adekilekun , Habeebulahi Ajibola; Wayan Gunam, Ida Bagus; Huyop, Fahrul
Journal of Tropical Life Science Vol. 15 No. 2 (2025): In Press
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/

Abstract

The significance of agarase enzymes spans various high-value industries, including food, cosmetics, and medicine. These enzymes play a crucial role in the hydrolysis of agar to produce bioactive oligosaccharides, enabling wide-ranging applications across multiple fields. Among them, α-AgaD is a novel α-agarase enzyme produced by the Thalassomonas sp. LD5 strain. However, the structural and functional characteristics of α-AgaD within biological systems remain largely unexplored. This study therefore aims to provide a comprehensive in silico analysis of α-AgaD, focusing on its physicochemical properties, phylogenetic relationships, secondary structure composition, and 3D homology modelling. A range of computational tools was employed to validate the findings and enhance the structural understanding of this newly identified α-AgaD enzyme. The α-AgaD protein consists of 1,466 amino acids with a molecular weight of 158,787.82 Da. It has a theoretical isoelectric point (pI) of 4.14, indicating an overall acidic nature. Structural analysis revealed that alpha helices and random coils are the predominant secondary structures. Hydrophobic amino acids were more abundant than hydrophilic ones, with glycine accounting for approximately 10.4% of the total residues. The protein's aliphatic index was 72.05, and the instability index was 28.28, suggesting that α-AgaD is stable and likely to maintain its structure across a wide temperature range. Three-dimensional models of α-AgaD were constructed using I-TASSER, NCBI-PDB, SWISS-MODEL, and AlphaFold2, and subsequently validated using ERRAT, Verify3D, and PROCHECK. Among the models generated, AlphaFold2 produced the most accurate prediction, with nearly all amino acid residues located in the preferred regions of the Ramachandran plot. This further confirmed the reliability and quality of the refined models. The in silico structural analysis of α-AgaD offers valuable insights into the enzyme’s primary sequence, functional domains, and overall structural architecture, enhancing our understanding of α-agarase from Thalassomonas sp. LD5.
Medicines in medicines: Challenges and Prospects in Drug Discovery from Fungal Endophytes of Medicinal Plants in Southeast Asia: Challenges and Prospects in Drug Discovery from Fungal Endophytes of Medicinal Plants Guerrero, Jonathan Jaime G.; General, Mheljor; Balendres, Mark Angelo; Tan, Mario; Buiza, Marielle; Huyop, Fahrul
Journal of Tropical Life Science Vol. 15 No. 2 (2025): In Press
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/xvfdnn97

Abstract

Fungal endophytes engage in a balanced symbiotic continuum with their host plants, from mutualism to commensalism and parasitism. These host-endophyte interactions play a pivotal role in shaping the biosynthetic and chemical space of the host plants and their associated mycobiomes, resulting in a wealth of biologically active natural products that are attractive for drug discovery. Endophytic fungi in medicinal plants continue to attract attention, highlighting a holistic view of plant-based therapeutics that considers the plant and its endophytic partners as sources of medicinal compounds. In this review, we assembled recent Southeast Asian studies related to fungal endophytes from plants with traditional medicinal uses and their potential biomedical applications. Here, we present a comprehensive analysis of the interactions within the region, identifying prolific fungal classes that produce compounds of biomedical significance. This analysis is based on a consolidated dataset of over 1,300 interactions. We noted an association between plant-endophyte-synthesized compounds and their related chemistry. However, the majority are preliminary and lack comprehensive follow-through research. While fungal endophytes in the region produce important compounds, their applicability in drug discovery necessitates extensive long-term studies.
Co-Authors Ab Wahabb, Roswanira Abdul Hamid, Azzmer Azzar Abdul Wahab, Roswanira Abdul Wahhab, Batool Hazim Adekilekun , Habeebulahi Ajibola Adekilekun Oyewusi, Habeebat Al Nimer, Marwan S.M. Al-Thuwaini, Tahreer Mohammed Balendres, Mark Angelo Bradosty, Sarwan Wasman Buiza, Marielle Damuri, Nur Wahida Edbeib, Mohamed Edbeib, Mohamed Faraj General, Mheljor Guerrero, Jonathan Jaime G. Harisun Yaakub Huda , Nurul Ida Bagus Wayan Gunam Izzah Ismail, Norjihada Kaya, Yilmaz Khairul Anuar, Nurul Fatin Syamimi Mohammed, Amera Kamal Mohd Rozdhi, Amira Azawani Mohd Shariff , Amir Husni Muhammad Muhammad Musafer, Karar Nadhum Jawad Nafea, Juman Notarte, Kin Israel R. Oladipo, Oluwatosin Oyewusi, Habeebat Adekilekun Rajindran, Nanthini Samsulrizal, Nurul HIdayah Tan, Mario Tirmizhi Abubakar, Munkaila Wahab, Roswanira Abdul Zaidi, Zatty Zawani Zakary, sefatullah