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Biology, Medicine, & Natural Product Chemistry
Published by Universitas Islam Negeri Sunan Kalijaga Yogyakarta
ISSN : -     EISSN : -     DOI : -
Core Subject : Health, Science,
Biochemistry, Genetics & Molecular Biology Medicine & Pharmacology Public Health
BIOLOGY, MEDICINE, & NATURAL PRODUCT CHEMISTRY, this journal is published to attract and disseminate innovative and expert findings in the fields of plant, animal, and microorganism secondary metabolite, and also the effect of natural product on biological system as a reference source for researchers in these fields, and with the aim to set international standards in their methodology.
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Articles 485 Documents
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Predicting the Anti-Pulmonary Fibrosis Potential of Physalis angulata Compounds A Computational Study Farid, Muhammad; Kirana, Assa Aulia; Oktaviana, Nandita Diah; Rasyda, Sofia; Anggraini, Dwi; Ramadhania, Widya Aryana
Biology, Medicine, & Natural Product Chemistry Vol 14, No 2 (2025)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14421/biomedich.2025.142.817-824

Abstract

Pulmonary fibrosis is a progressive lung disease characterized by tissue scarring and respiratory decline. Existing treatments have limited efficacy and significant side effects. Physalis angulata, a traditional medicinal plant, shows promise for antifibrotic therapy due to its bioactive compounds potentially targeting key fibrotic pathways. This study aims to predict the potential of Physalis angulata compounds to PI3K/AKT protein as candidates for antifibrotic therapy. Ten active compounds from P. angulata were docked against the PI3K/AKT protein (PDB ID: 2UZT) using AutoDock Vina. Docking was validated by redocking the native ligand. Binding affinities and molecular interactions were analyzed. ADMET properties were predicted via the pkCSM platform to assess pharmacokinetics and toxicity. Myricetrin exhibited the strongest binding affinity (-9.6 kcal/mol), surpassing the native ligand (-9.1 kcal/mol). Other flavonoids, including eriodictyol (-8.9 kcal/mol), naringin (-8.8 kcal/mol), and apigenin (-8.5 kcal/mol), also showed favorable affinities. Critical amino acids involved were Asp184 and Glu121. The redocking RMSD value of 0.893 Ã confirmed methodological accuracy. ADMET predictions revealed high intestinal absorption for tangeretin and apigenin, with no mutagenic or hepatotoxic risks, indicating good pharmacokinetic profiles. Physalis angulata flavonoids exhibit strong PI3K/AKT binding and favorable pharmacokinetics, supporting their potential as antifibrotic agents.
Isolation, Morphological Characterization, Biochemistry, and Antagonistic Activity of Endophytic Bacteria from Rice Against Xanthomonas oryzae pv. Oryzae Sihotang, Saipul; Butar-Butar, Alfons Dwi Putra; Nasution, Lita; Rahma, Haliatur; Trizelia, Trizelia; Saragih, Magdalena; Kuswardani, Retna Astuti; Listiana, Ika; Napitupulu, Beatrix Sofranes
Biology, Medicine, & Natural Product Chemistry Vol 14, No 2 (2025)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14421/biomedich.2025.142.825-829

Abstract

Endophytic bacteria have the potential as environmentally friendly biocontrol agents in controlling bacterial leaf blight (BLB) in rice caused by Xanthomonas oryzae pv. oryzae (Xoo). This study aims to isolate, characterize morphology and biochemical tests, and test the antagonistic activity of endophytic bacteria from rice against Xoo. Isolation was carried out from healthy rice root tissue using a surface sterilization method. Morphological characterization included colony shape, color, edge, elevation, and Gram properties, while biochemical characterization included catalase, oxidase, motility, starch hydrolysis, and sugar fermentation tests. The antagonistic test used a dual culture assay method on NA (nutrient agar) media. The isolation results obtained six endophytic bacterial isolates (BETP 01–06) identified as the genus Pseudomonas and Bacillus with varying colony morphological characters. Antimicrobial activity test showed two potential isolates, BETP 03 (Pseudomonas) and BETP 05 (Bacillus), with an average inhibitory diameter of 16.3 mm and 16.5 mm against Xoo, respectively. Biochemical characterization showed that BETP 03 was bacillus, Gram-negative, citrate-negative, motile, gelatin hydrolysis positive, starch hydrolysis positive, and catalase positive; while BETP 05 was bacillus, Gram-positive, citrate-positive, motile, gelatin hydrolysis negative, starch hydrolysis positive, and catalase positive. These results indicate that both isolates have high potential as biological biocontrol agents in controlling bacterial leaf blight disease in rice.
Analysis of Nutritional Composition and Antioxidant Activity of Yogurt Enriched with Butterfly Pea (Clitoria ternatea L.) Extract Windarsih, Yulia; Budiarsa, I Made; Trianto, Manap; Akram, Akram; Ashari, Abdul
Biology, Medicine, & Natural Product Chemistry Vol 14, No 2 (2025)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14421/biomedich.2025.142.831-841

Abstract

The growing demand for functional foods has encouraged the development of dairy products enriched with natural bioactive ingredients to improve nutritional value and health benefits. This study aimed to analyze the nutritional composition and antioxidant activity of yogurt enriched with butterfly pea (Clitoria ternatea L.) extract. Yogurt was prepared from fresh goat milk with varying concentrations of butterfly pea extract and evaluated for protein, fat, carbohydrate, moisture, ash, vitamin C contents, antioxidant activity, and sensory acceptance. Proximate analysis, UV–Vis spectrophotometry, and the DPPH method were used for chemical determinations, while a hedonic test assessed color, taste, aroma, and texture. Results showed that increasing butterfly pea extract significantly decreased protein and fat contents but increased vitamin C and antioxidant activity, with the highest values observed in yogurt containing 60% extract and 4% formulation (N60K2). Moisture and ash contents were not significantly affected. Sensory evaluation indicated that yogurt with 60% extract and 2% formulation (N60K1) was preferred regarding color, taste, aroma, and texture. Considering compliance with the Indonesian National Standard (SNI) and consumer acceptance, N60K1 was the optimal formulation. The findings suggest that butterfly pea extract can enhance the functional properties of yogurt, particularly its antioxidant potential, while maintaining acceptable sensory quality. This provides insights for developing functional dairy products with natural plant-based bioactives.
DFT Study and ADMET Investigation of Bioactive 2-Phenoxyquinolines Aina, Oluwafemi S.; Rofiu, Mujeeb O.; Adams, Luqman A.; Familoni, Oluwole B.
Biology, Medicine, & Natural Product Chemistry Vol 14, No 2 (2025)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14421/biomedich.2025.142.843-856

Abstract

Pharmacologically active quinoline compounds show interesting functionalities. However, there is still a dearth of information on the potential wide applications of the quinoline scaffolds especially when the substituents on the rings or functionalities are modified. In this study 2-phenoxyquinoline-3-carbaldehyde derivatives were synthesized and investigated using DFT to determine the molecular parameters, electronic and chemical reactivity descriptors including their possible application as drug candidates. Geometry optimisations were carried out using Becke three-parameter hybrid functional combined with Lee-Yang-Parr correlation functionals and augmented basis set with added sets of diffuse s- and p-functions: BL3YP /6-311++G(d,p). Drug-likeness scores and bioactivity prediction were carried out using the webserver programs ADMET Sar 2. Our results showed slightly lower energy values in water than in ethanol depicting high reactiveness of the 2-phenoxyquinolines in water especially compounds with fluoro- and methoxy substituted having the lowest Egap of 3.79 eV and 3.381 eV respectively. The methoxy substitution confers higher susceptibility to electron transfer and chemical reactive in aqeous medium. The ionization potential energies were lower in water and ethanol when compared to the other gas states calculated values. The MEP surfaces of all the compounds investigated reveals the ether oxygen atoms and carbonyl groups as necessities for effective antioxidant properties. It is noteworthy that five of the compounds investigated have high activity values above 3.0 octanol–water partition coefficient value indicating an excellent inhibitory activity and strong chemical reactivity. Good oral bioavailability was shown by the compounds depicting their excellent activity as kinase inhibitors, nuclear receptor compounds and enzyme inhibitors. It is noteworthy that cytochromes CYP2C19, CYP2C29, CYP2D6 and CYP3A4 are not inhibited and therefore do not pose potential adverse drug reactions or toxicity. Interestingly, only one compound showed one violation. Consequently, such scaffolds are potential drug candidates.
Antibacterial Activity of Bacteriocin from Pediococcus pentosaceus Against Propionibacterium acnes: Molecular Docking, In Vitro, and 16S rRNA Genetic Identification Pribadhi, Adhitya Naufal; Herlambang, Penggalih Mahardika; Purwaningrum, Ellyka
Biology, Medicine, & Natural Product Chemistry Vol 14, No 2 (2025)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14421/biomedich.2025.142.943-949

Abstract

This study aimed to evaluate the antibacterial potential of bacteriocin produced by lactic acid bacteria against Propionibacterium acnes through an integrative approach involving molecular docking, in vitro assays, and genetic identification using 16S rRNA sequencing. The target protein PDB 7LBU, representing the cell wall of P. acnes, was docked with Small Bacteriocin obtained from PubChem. The best binding affinity was recorded at –7.5 kcal/mol, indicating a stable interaction, supported by cavity analysis and ligand–protein interaction mapping using PyMOL. The results of the in vitro study, as determined by antibacterial activity testing against P. acnes, showed an average inhibition zone of 20.6 mm. In addition, genetic identification through BLAST confirmed the isolate as Pediococcus pentosaceus strain DSM 20336 with a similarity of 99.64%. These findings indicate that the bacteriocin derived from P. pentosaceus has promising potential as a natural agent in the development of alternative therapies for acne.
Synthesis, Characterization, and Micellar Behavior of Amphiphilic Chitosan Bearing Sulfate and Anisaldehyde Imine Groups Herayati, Herayati; Wahyuningrum, Deana; Bima, Damar Nurwahyu; Sari, Indah Puspita
Biology, Medicine, & Natural Product Chemistry Vol 14, No 2 (2025)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14421/biomedich.2025.142.905-909

Abstract

Amphiphilic chitosan derivatives bearing sulfate and anisaldehyde imine (anisimine) groups were successfully synthesized and characterized for potential applications as functional biomaterials. The synthesis involved two key steps: (1) sulfation of chitosan using chlorosulfonic acid to introduce O-sulfate groups, and (2) Schiff base formation via reaction with p-anisaldehyde to generate N-anisimine functionalities. Structural modifications were confirmed by Fourier-transform infrared (FTIR) spectroscopy, which showed characteristic absorption bands at ~1250 cm-¹ and ~820 cm-¹ corresponding to O=S=O stretching of sulfate, and a C=N stretch at ~1640 cm-¹ indicating imine formation. Proton nuclear magnetic resonance (1H-NMR) spectra further verified the successful attachment of aromatic protons from p-anisaldehyde and the disappearance of primary amine peaks, confirming imination. The amphiphilic behavior and micelle-forming ability of the N-anisimine-O-sulfated (NAOS) chitosan were evaluated using pyrene as a hydrophobic fluorescent probe for determining the critical micelle concentration (CMC), which was found to be 0.012 mg/mL. The observed low CMC value indicates strong self-assembly capability in aqueous media. These results suggest that NAOS chitosan possesses promising structural and surface-active properties suitable for advanced applications in drug delivery and cosmetic formulations.
Optimization of Arabica Coffee (Coffea arabica L.) Shoot Cutting Growth Using Plastic Bottle Covers and Goat Urine Treatments Safinah, Safinah; Darmanti, Sri; Nurchayati, Yulita
Biology, Medicine, & Natural Product Chemistry Vol 14, No 2 (2025)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14421/biomedich.2025.142.867-872

Abstract

Arabica coffee (Coffea arabica L.) is a high-value commodity, yet its productivity in Indonesia remains low due to suboptimal cultivation techniques. One of the main constraints is the limited availability of quality seedlings, which is influenced by propagation methods. Vegetative propagation through shoot cuttings is widely used, but often constrained by low survival and root formation rates. The application of plastic bottle covers and goat urine has the potential to improve propagation success by creating a favorable microclimate and supplying growth regulators and essential nutrients. This study examined the effects of plastic bottle cover types and goat urine concentrations on the growth of C. arabica shoot cuttings. The experiment was arranged in a 3×3 factorial Completely Randomized Design (CRD), with two factors: plastic bottle cover types (no cover, open-cap cover, and closed cover) and goat urine concentrations (0, 100, and 180 mL/L). Observed parameters included shoot length, shoot number, leaf length, leaf number, root length, root number, and root diameter. Data were analyzed using analysis of variance (ANOVA) followed by Tukey’s Honestly Significant Difference (HSD) test at a 5% significance level. The results showed a significant interaction between cover type and goat urine concentration. Combining a closed cover with 100 mL/L goat urine produced the highest shoot growth, cutting survival rate, and rooting percentage, while optimal root development was obtained with the closed cover and 180 mL/L goat urine. The most effective treatment was the closed cover combined with 100 mL/L goat urine.
Molecular Identification of Lepidopteran Predators of Coccidae on Coffee Plants (Coffea canephora) in Sigi Regency Budiarsa, I Made; Trianto, Manap; Adnan, Bahana Aditya
Biology, Medicine, & Natural Product Chemistry Vol 14, No 2 (2025)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14421/biomedich.2025.142.983-992

Abstract

This study aimed to identify the species of Lepidopteran predators that prey on soft scale insects (Coccidae) found on coffee plants in Sigi Regency using molecular techniques. DNA was extracted using the modified CTAB method (Doyle & Doyle, 1990). PCR amplification targeted the COI gene using universal primers LCO1490 and HCO2198 with a GeneAmp PCR System 9700. Visualization was done using 1% agarose gel and UV-transilluminator. Sequencing was conducted externally. Data were analyzed using BioEdit 7.2.5, BLAST, BOLD Systems, and MEGA11 software. The DNA sequence of the predator sample showed 97.91% similarity to Autoba rubra based on GenBank and 97.59% in BOLD Systems. Phylogenetic analysis confirmed a close genetic relationship with A. rubra, distinct from Eublemma. Morphological similarities with Eublemma were misleading, highlighting the accuracy of molecular identification. This study is the first to confirm the identity of a Lepidopteran predator of coffee scale insects in Indonesia using molecular techniques, revealing its close relation to Autoba rubra. The results correct previous morphological misidentifications and contribute new data on predator diversity in biological control contexts.
Evaluation of Forest Honey on the Proliferation and Migration of Dermal Fibroblasts under Hyperglycemic Conditions: An In Vitro Study Rizqi, Januar; Agustiningsih, Denny; Nugrahaningsih, Dwi Aris Agung
Biology, Medicine, & Natural Product Chemistry Vol 14, No 2 (2025)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14421/biomedich.2025.142.951-955

Abstract

This study aims to evaluate the effect of forest honey on fibroblast proliferation and migration under hyperglycemic conditions in vitro. The research method involved culturing primary fibroblasts in high-glucose DMEM (25 mM) and dividing them into five groups: standard control (standard medium), hyperglycemia control (high-glucose medium without treatment), 3% honey, 1.5% honey, and 0.75% honey. Proliferation was assessed by counting live cells (Trypan Blue staining/hemocytometer) at 24, 48, and 72 hours. Migration was measured using a scratch assay (0, 24, 48, 72 hours) and analyzed with ImageJ. The Shapiro–Wilk test was used for normality; data were analyzed with ANOVA followed by LSD or Kruskal–Wallis (p<0.05). Results showed that hyperglycemia decreased proliferation compared to the standard control. Treatment with 1.5% honey and 0.75% honey consistently increased proliferation compared to the hyperglycemic control at all time points (p<0.05), while 3% honey showed a relatively lower increase. The standard control group achieved 100% closure at 72 hours in the migration variable. The honey groups (0.75–3%) showed an increase compared to the hyperglycemic control, but the difference was not significant at 24–48 hours and approached significance at 72 hours (p=0.057). In conclusion, forest honey at a concentration of 1.5% can increase fibroblast proliferation in a hyperglycemic environment. The effect on migration requires confirmation with osmolality controls and more sensitive endpoints. These findings provide a biological basis for developing honey-based diabetic wound care adjuvants focusing on dose optimization and formulation standardization.
Formulation Of Instant Functional Collagen Drink With Date Seeds Coffee (Phoenix dactylifera) And Spices (Ginger, Cinnamon, Cardamom, Clove) Using The D-Optimal Mixture Design Method Hanifa, Mutia
Biology, Medicine, & Natural Product Chemistry Vol 14, No 2 (2025)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14421/biomedich.2025.142.911-919

Abstract

The functional food trend has grown rapidly since the Covid-19 pandemic, including products made from natural ingredients like herbal collagen drinks. This research aims to develop an optimal collagen drink formulation by adding date seed coffee with ginger, cinnamon, cardamom, and cloves as antioxidants to optimize collagen function.Optimization was carried out using the Design Expert-13 device with the optimization response of antioxidant activity (mg TE/100g) and water content (%). The results showed that the optimal formulation consisted ofdate seed coffee 35.57%; hydrolyzed collagen 25%; and spice mixture (ginger, cinnamon, cardamom, cloves) of 39.432% with a desirability value of 0.741.The optimal product was then instantiated using the spray drying method and compared with commercial products without instantiation and collagen addition.The optimal product has an IC50 antioxidant activity of 743.86 ppm and total phenols of 187.23 mg GAE/100g), with a water content of 3.35%, hygroscopicity of 7.76%, bulk density of 0.488 g/mL, and a dissolution time of 23.32 seconds. The results of the hedonic test on the optimal sample as a whole from 100 panelists were “rather like” to “like” with an average value of 3.17 with the most preferred attributes being the consistency and aroma of spices.

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