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Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences
Published by Universitas Brawijaya
ISSN : 20875517     EISSN : 25274376     DOI : -
Core Subject : Agriculture, Social,
Agriculture, Biological Sciences & Forestry Environmental Science
The Journal of Tropical Life Science (JTLS) provides publication of full-length papers, short communication and review articles describing of new finding or theory in living system, cells and molecular level in tropical life science and related areas. The journal publishes articles that report novel findings of wide Tropical Life system phenomenon in the areas of biodiversity, agriculture, fisheries, health, husbandry, forestry and environmental technology. JTLS has 1 volume with 3 issues per year.
Arjuna Subject : -
Articles 995 Documents
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In silico analysis of myricetin and fisetin as potential B-cell lymphoma extra-large (Bcl-xL) inhibitors in cancer therapy: Myricetin and fisetin as potential Bcl-xL inhibitors Nordin, Noraziah; Abd Ghani, Mohd Faiz; Roslan, Nuruliza; Riandini Aisyah; Sri Wahyuni; Peni Indrayudha; Em Sutrisna
Journal of Tropical Life Science Vol. 15 No. 3
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.15.03.02

Abstract

B-cell lymphoma extra-large (Bcl-xL) is an anti-apoptotic protein that is crucial for cancer cell survival and resistance to chemotherapy. Flavonoids have shown potential as anticancer agents through various pathways, including apoptosis. However, molecular interactions of flavonoids with Bcl-xL remain unknown. This study aims to evaluate the binding affinity and stability of myricetin and fisetin as Bcl-xL inhibitors using in silico approaches, including molecular docking and molecular dynamics (MD) simulations. Molecular docking was performed by AutoDock Vina software to evaluate the binding affinity of myricetin and fisetin to the Bcl-xL protein. MD simulations were conducted using the AMBER 2022.1 package to analyze the stability and dynamic behavior of the flavonoids-Bcl-xL complexes over a 100 ns trajectory. Docking analysis revealed strong binding affinities for both flavonoids, with fisetin exhibiting a slightly higher affinity (-7.6 kcal/mol) compared to myricetin (-7.2 kcal/mol). MD simulations confirmed the stability of both complexes, with myricetin forming a more extensive hydrogen bonding due to its additional hydroxyl groups, contributing to lower RMSD fluctuations and higher structural stability. Binding free energy calculations further supported the favorable interaction of myricetin with Bcl-xL (-61.542 kJ/mol), suggesting its potential as a potent inhibitor. In silico analysis indicates that both myricetin and fisetin have promising inhibitory potential against Bcl-xL, with myricetin demonstrating better stability and binding efficiency. These findings provide a basis for further experimental validation and the potential development of flavonoid-based Bcl-xL inhibitors for targeted cancer therapy.
Integrated In Silico Approach Discovery of β-Caryophyllene from Piper crocatum Ruiz & Pav. as an Antidiabetic Candidate: β-Caryophyllene from Piper crocatum Ruiz & Pav. as an Antidiabetic Candidate Febyaningrum, Vitasigi Dwi; Putri Kharisma Novita Sari; Hadi , Saptono
Journal of Tropical Life Science Vol. 15 No. 3
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.15.03.05

Abstract

Type 2 diabetes mellitus (T2DM) remains a significant global health challenge, responsible for more than 90% of all diagnosed diabetes cases worldwide. The progression of T2DM is primarily driven by insulin resistance and progressive pancreatic β-cell dysfunction, both of which contribute to various metabolic complications. Metformin is widely used as a first-line antidiabetic drug. However, its long-term use is associated with gastrointestinal disturbances, lactic acidosis, and vitamin B12 deficiency. These limitations highlight the need for safer and more effective therapeutic alternatives. β-caryophyllene, a sesquiterpene compound derived from the stem extract of Piper crocatum Ruiz & Pav., has demonstrated antioxidant, anti-inflammatory, and antilipidemic properties that may support its potential as an antidiabetic agent. This study evaluated the pharmacological potential of β-caryophyllene as an antidiabetic agent through an in silico approach. The analysis included drug-likeness assessment via Lipinski’s Rule of Five, ADMET profiles, network pharmacology, such as KEGG pathway and GO, inhibitory activity prediction using SVM regression in DataWarrior, and molecular docking through AutoDockTools and BIOVIA Discovery Studio, with metformin used as a reference standard. β-caryophyllene fully complies with Lipinski’s Rule of Five, indicating good drug-likeness and potential for oral bioavailability. The IC50 prediction results indicated that β-caryophyllene exhibited stronger inhibitory potential than metformin against several key T2DM-related proteins, including IL6, HSP90AA1, NOS3, TLR4, KRAS, and NFKB1. Consistently, molecular docking analysis demonstrated that β-caryophyllene also had stronger interactions with these targets, exhibiting higher binding affinities compared to metformin. These proteins are implicated in insulin resistance, inflammation, and vascular dysfunction. Additionally, pharmacokinetic data demonstrated high intestinal absorption (94.8%), extensive distribution (VDss ≈ 4.49 L/kg), minimal CYP450 inhibition, and limited toxicity risks. Collectively, β-caryophyllene exhibits good pharmacological properties and multitarget activity, supporting its candidacy for further in vitro and in vivo studies as a potential therapeutic agent for T2DM.
Quercetin Inhibits the Progression of Atherosclerosis by Enhancing the Activity of M2 Macrophages in Wistar Rats Ermawan, Romi; Pikir, Budi Susetyo; Mulyanto, Mulyanto
Journal of Tropical Life Science Vol. 15 No. 3
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/pfc2jx21

Abstract

Quercetin, widely acknowledged as an exceptionally potent antioxidant, is known for its diverse array of bioactive properties that confer numerous health benefits. However, the specific effect of quercetin on atherosclerosis progression remains unclear and warrants further investigation. This experimental study used Wistar rats with a post-test-only control-group design. It aimed to analyze the effect of quercetin in inhibiting the progression of atherosclerosis. Twelve adult male rats were selected and used to construct an experimental model that mimics atherosclerotic plaque formation. The model was achieved by administering a high-fat diet with a caloric value of 414 kcal per 100 grams and performing an endothelial injury procedure during the second week of the study. After six weeks, the rats were divided into two groups of six: the control group continued on the high-fat diet, while the quercetin group maintained the same diet and received 10 mg/kg of quercetin via gavage. At the end of week eight, the progression of atherosclerotic plaques was evaluated by measuring the activity of M1 and M2 macrophages, as well as the carotid artery intima-media thickness and the degree of carotid arterial stenosis. Quercetin administration significantly increased the activity of M2 macrophages (p=0.002, mean difference 10.66, 95% CI 5.90 - 15.41); in contrast, no significant effect was found on the activity of M1 macrophages (p=0.562), carotid artery intima-media thickness (p=0.407), and the degree of carotid arterial stenosis (p=0.734). This study emphasizes quercetin's role in inhibiting atherosclerosis progression by enhancing the activity of M2 macrophages. Additional studies are necessary to explore various quercetin doses involving more atherosclerosis parameters.
Codon Optimization and Epitope Identification of L1 Protein Human Papillomavirus Type 52 for Expression in Lactococcus lactis: Codon Optimization and Epitope Identification L1 Protein HPV52 Prastyowati, Anika; Hakim, Mohamad Saifudin; Wijayanti, Nastiti; Wibawa, Tri
Journal of Tropical Life Science Vol. 15 No. 3
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.15.03.03

Abstract

Human papillomavirus (HPV) type 52 is among the top three high-risk oncogenic types that are associated with cervical cancer worldwide, especially in Indonesia. Designing a vaccine against HPV using an Lactococcus lactis expression system is a promising strategy, as this bacterium is well-known for its probiotic properties and can be safely utilized as a delivery carrier for oral vaccines. This study aimed to optimize the codon usage of the L1 protein of HPV type 52 for expression in L. lactis expression system and to identify potential epitopes using bioinformatics tools. To determine the codon optimization, the L1 protein sequence of HPV type 52 was retrieved from the National Center for Biotechnology Information (NCBI) database. Furthermore, codon optimization was conducted once the model had been established using OPTIMIZER, Clustal Omega, Restriction Mapper, and the ExPASy tool, based on L. lactis. The final construct was predicted to have a B-cell epitope by Ellipro tools, antigenicity by VaxiJen v.2.0, allergenicity by AllerTOP v.2.0, and toxicity by ToxIBTL. This resulted in a potential vaccine candidate with a Codon Adaptation Index (CAI) of 0.754 and GC content of 39.0%. Identification of epitopes from the optimized gene resulted in two peptide sequences, WRPSEATVYLPPVPVSKVVS and GTLGDPVPGDLYIKGSNSGNTATVQ, as components of the vaccine candidate.
In silico Analysis of Phospholipase C Proteins Revealed Role During the Growth and Development of Peanut (Arachis hypogaea): Genome-wide analysis of the phospholipase C genes in peanut Chu, Ha Duc; Tran, Huyen Thi Thanh; Le, Quynh Thi Ngoc; La, Hong Viet; Le, Thuy Thi; Cao, Phi Bang
Journal of Tropical Life Science Vol. 15 No. 3
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.15.03.06

Abstract

Phospholipase C (PLC) enzymes, including phosphatidylinositol-specific PLC (PI-PLC) and non-specific PLC (NPC), play central roles in plant lipid signalling, although their genomic features and expression patterns in peanut (Arachis hypogaea) are still insufficiently characterized. This study aimed to identify all PLC family members in the peanut genome and to analyze their structural properties, phylogenetic relationships, and expression profiles across major tissues. Through homology-based searches and domain validation, we identified a total of 10 and 16 ArahyNPC and ArahyPI-PLC genes within the peanut genome, respectively. Phylogenetic analysis classified these PLC proteins into two distinct clades, including NPC and PI-PLC. Gene structure and physicochemical assessment indicated conserved organization and similar protein characteristics within each subfamily. Re-analysis of publicly available RNA-Seq datasets revealed clear tissue-specific expression patterns. Interestingly, ArahyNPC-02 and ArahyNPC-09 showed predominant expression in nodules, while ArahyPI-PLC-15 was expressed mainly in roots. These findings indicate functional diversification among PLC genes in peanut and highlight several candidates that may regulate key developmental processes. The results provide a comprehensive genomic resource that supports future functional studies on PLC-mediated signalling and contributes to breeding strategies aimed at enhancing stress resilience in peanut cultivars. This genome-wide characterization, combined with transcriptomic re-analysis, provides a systematic resource for understanding PLC-mediated lipid signalling in peanut. The identified tissue-preferential PLC candidates offer promising targets for future functional studies aimed at elucidating their roles in development and stress-responsive pathways.

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