Jurnal Kimia Valensi
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Indonesian Black Tea (Camellia sinensis) as a Potential Acetylcholinesterase Inhibitor Against Alzheimer’s Disease: Docking, DFT, and In Vitro Evidence
Full text linkAlzheimer’s disease (AD) is a progressive neurodegenerative disorder predominantly affecting the elderly and characterized by dementia. AD pathology involves impaired cholinergic neurotransmission, largely due to β-amyloid (Aβ) plaque accumulation, which inhibits choline acetyltransferase (ChAT) and reduces acetylcholine (ACh) levels. Acetylcholinesterase (AChE) contributes to AD progression by hydrolyzing ACh and promoting Aβ plaque formation, making it a key therapeutic target. This study investigated natural compounds from black tea (Camellia sinensis) as potential AChE inhibitors. Molecular docking analyses assessed interactions between bioactive compounds from aqueous black tea extracts and AChE, followed by evaluation of bioavailability, biological activity, toxicity, stability, and reactivity. Epigallocatechin gallate exhibited the strongest binding affinity (∆Gbind = –12.2740 kcal/mol), forming extensive interactions with the catalytic active site located at the bottom of a deep and narrow gorge (~20 Å). Density Functional Theory (DFT) analysis confirmed its high stability and favorable reactivity in complex with AChE. In vitro validation using black tea extracts from Bogor, Indonesia, showed significant AChE inhibition with an IC50 value of 44.85 ± 1.48 µg/mL. These findings highlight the promising potential of Indonesian black tea as a natural alternative for Alzheimer’s disease therapy
Discriminating Green Beans of Puntang Arabica Coffees with 1H NMR Based-Metabolomics
Full text linkPuntang Arabica Coffee is one of the famous Indonesian coffees from West Java. This coffee is cultivated in the area of Mount Puntang, Bandung Regency. This study evaluated green beans of Puntang Arabica coffee obtained from different cultivating locations, including Cimulek, Cimenong, Ganda Paraja, and Nameur, with 1H NMR-based metabolomics. The green coffee bean samples were ground, extracted with D2O, and then measured with NMR spectroscopy. The obtained 1H NMR spectra were processed and evaluated by multivariate data analysis techniques using Orthogonal Partial Least Square Discriminant Analysis (OPLSDA) as the main model. In total, 20 metabolites were successfully identified in the 1H NMR spectra of Puntang coffees. Based on multivariate analysis, Cimulek and Cimenong coffee regions possessed similar metabolite profiles possibly due to being in proximity. Trigonelline, 5-chlorogenic acid, and citric acid were detected as the discriminant compounds for Cimulek and Cimenong coffees, whereas lactic acid, lipids, and stearic acid were associated with Ganda Paraja coffee. Meanwhile, GABA was detected constantly as the characteristic compound of Nameur coffee. This report revealed the metabolite profile of Puntang Arabica coffees for the first time and provided scientific information for the development of coffee plantations
Papain-like Protease Peptides as Construction Material for the SARS-CoV-2 Vaccine Design Candidate: In-silico Study
Full text linkCOVID-19 remains a major global health threat. In addition to implementing health protocols and consuming supplements, proactive prevention strategies are essential to limit the spread of the virus. One of the most promising approaches is the use of vaccines, particularly peptide-based vaccines, which are under active development. This study aimed to design a peptide vaccine derived from the SARS-CoV-2 papain-like protease (PLpro) and evaluate its interaction with key components of the human immune system, namely Toll-like receptor 3 (TLR3), major histocompatibility complex class I (MHC-I), and class II (MHC-II). The research employed an immunoinformatics approach utilizing NetCTL, IEDB Tepitool, PEP-FOLD3, trRosetta, HDOCK, GalaxyRefine2, and other molecular modeling tools. The designed vaccine construct was visualized in 3D using trRosetta and validated through ERRAT2, achieving a 100% quality score, indicating excellent structural integrity. The docking simulations demonstrated stable interactions between the vaccine and the immune receptors, suggesting strong immunogenic potential. In conclusion, the in silico-designed peptide vaccine based on SARS-CoV-2 PLpro shows promise in triggering immune responses through stable binding with TLR3, MHC-I, and MHC-II, highlighting its potential as a candidate for further experimental validation in COVID-19 vaccine development
Efficacy Test of Prototype Kit for Detection Bacillus cereus and Listeria monocytogenes in Processed Meat using Real-time PCR Method
Full text linkAccording to the World Health Organization (WHO), harmful agents such as Bacillus cereus and Listeria monocytogenes are responsible for 600 million cases of disease and 420,000 deaths annually. This research aims to test the effectiveness of the real-time PCR method for developing a prototype kit to detect pathogenic bacteria in processed meat. As a comparison, the and conventional PCR methods were used to obtain the accuracy, specificity, sensitivity, and effectiveness of the real-time PCR method. All the samples were cultured in solid media agar, performed amplification using specific primers cyt-K 2 and hly using PCR and real-time PCR. Meatballs, nuggets, and sausages, five samples each, were found to be positive positively contaminated with all targeted bacteria. However, they did not provide specific results using solid media culture and the PCR method. In addition, the real-time PCR method using prototype kit formulas accomplished that all contaminated samples had a Ct value smaller than the negative control, NTC (No Template Control), and had a similar melting curve to the positive control. This establishes that the real-time PCR method clarifies that all samples were contaminated with target bacteria. A formula was developed in the prototype kit with real-time PCR methods that can be used and applied on a commercial scale efficiently and precisely
Eudesman-Type Sesquiterpenoids from Stem Bark Dysoxylum gaudichaudianum and Cytotoxic Evaluation Against Human HeLa Cervical Cancer
Full text linkTwo eudesmane-type sesquiterpenoids were isolated from the stem bark of Dysoxylum gaudichaudianum: 6α-hydroxy-eudesm-4(15)-en-1-one (1) and eudesm-4(15),7-dien-1β-ol (2). This study represents the first report of these compounds not only from D. gaudichaudianum but also from the genus Dysoxylum. The cytotoxic potential of two sesquiterpenoids was assessed against human cervical carcinoma (HeLa) cells employing the Resazurin-based PrestoBlue assay. Using cisplatin as a positive control, compound 1 exhibited moderate cytotoxicity with an IC₅₀ of 28.04 µM, whereas compound 2 showed comparatively weaker activity, with an IC₅₀ of 58.37 µM. Their structures were elucidated through comprehensive spectroscopic analyses, including HR-ESI-MS, ¹H NMR, and ¹³C NMR. Structure–activity relationship analysis indicates that hydroxylation at C-6 enhances cytotoxic activity, whereas the C-6/C-7 olefinic moiety reduces potency, likely due to increased molecular rigidity, highlighting key structural features for activity modulation in the eudesmane scaffold
Decolorization of Reactive Black 5 by Myceliophthora thermophila KLUM1
Full text linkThis research aimed to ascertain the impact of alkaline lignin of teak sawdust on the synthesis of ligninase and decolorization of Reactive Black 5 (RB5) by M. thermophilia KLUM1, also to elucidate the mechanism of mycoremediation. This research was conducted within the cultivation of the spore suspension in a co-culture setting. The RB5 dye percentage decolorization and ligninase activity were produced by varying the addition of alkaline lignin. The results show that the addition of 0.5% alkaline lignin accelerates the production of ligninase in the Kirk medium. However, adding more than 0.5% alkaline lignin does not affect the highest amount of ligninase produced. The increase in RB5 dye decolorization by M. thermophila KLUM1 is proportional to the increase in alkaline lignin in the medium. The percentage of wood-rot fungi decolorization in Kirk medium with and without lignin with the addition of 0.5%, 1%, and 2% lignin on the 10th day was 26.29%, 29.51%, 34.74%, and 40.43%, respectively. The decolorization process of RB5 by M. thermophilia KLUM1 in Kirk medium with alkaline lignin occurs through several mechanisms, i.e., enzymatic degradation, adsorption by the growing mycelia, and alkaline lignin present in the medium
Exploring Brazilin as a Potential Breast Cancer Therapy via Molecular Dynamics Simulation Targeting ERα, 17β-HSD1, and NUDT5 Receptors
Full text linkBreast cancer remains one of the leading causes of cancer-related mortality worldwide, suggesting the need for novel therapeutic agents with greater efficacy and fewer side effects. Brazilin, a natural flavonoid compound isolated from Caesalpinia sappan L., has shown promising anticancer activity, particularly against breast cancer cells. This study explores the therapeutic potential of brazilin by evaluating its interactions with three key molecular targets: estrogen receptor alpha (ERα), 17β-hydroxysteroid dehydrogenase 1 (17β-HSD1), and Nudix hydrolase 5 (NUDT5). Using molecular dynamics (MD) simulations, the study assesses the stability and binding interactions of complex systems. The results indicate that brazilin forms a stable complex with ERα, demonstrated by a low RMSD (2.6 Å) and strong hydrogen bonding with Glu353, occupancies of 97.8%, and minimal flexibility at the binding site (average RMSF < 2.5 Å). The binding free energy (ΔG Total) for the ERα–brazilin complex was -54.28 kcal/mol, indicating a stronger affinity than the reference ligand 4-hydroxytamoxifen. Brazilin also showed favorable binding with 17β-HSD1 and NUDT5, with binding energies of -39.71 kcal/mol and -23.23 kcal/mol, respectively. These findings suggest that brazilin may modulate critical targets involved in breast cancer progression, particularly in hormone receptor-positive subtypes. Further experimental validation is necessary to confirm its efficacy and optimize its therapeutic potential
Isolation of Endophytic Pseudomonas Strains from Papaya Leaves and Their Extracellular Enzyme Production and Antioxidant Profile
Full text linkEndophytic bacteria, symbiotic microorganisms residing in plant tissues, produce bioactive compounds similar to host plants, such as antioxidants. These antioxidants are crucial in combating free radicals linked to degenerative diseases. This study isolates and characterizes two endophytic bacterial strains from papaya leaves, exploring their enzymatic and antioxidant activities. Two isolates of endophytic bacteria from papaya leaves were obtained, F1-A and F1-B. F1-A endophytic bacteria are types of monobacilli, Gram-positive bacteria. F1-B endophytic bacteria are types of Bacilli. Using 16S rRNA analysis, both isolates were predicted to belong to the Pseudomonas bacterial strain. Research on optimizing their growth under various temperatures and pH conditions showed that both isolates grow best at 37°C. F1-B provides a better opportunity as a source of industrial enzymes because it can excrete amylase, urease, cellulose, and protease enzymes compared to F1-A, which can only produce amylase and protease enzymes. Nevertheless, F1-A can act as a potent antioxidant with an IC50 of 34.18 ppm compared to F1-B, which has an IC50 value of 292.31 ppm. The IC50 value of the F1-A isolate was not much different from the IC50 of quercetin, which was 12.50 ppm. The ability of F1-A as an antioxidant is also influenced by the results of phytochemical screening, which can contain more secondary metabolites than F1-B. These results highlight the potential of Pseudomonas strains as sources of industrial enzymes and natural antioxidants, warranting further investigation
In Vitro and In Silico Study of Antibacterial Activity of Sirih Merah Leaf Extract (Piper crocatum Ruiz & Pav.) Against Streptococcus mutans
Full text linkSirih merah leaf (Piper crocatum Ruiz & Pav) is a natural material that has the potential to be used as a natural antibacterial agent in treating dental caries caused by Streptococcus mutans because it is known to contain secondary metabolite compounds that have antibacterial properties that can inhibit the activity of glucosyltransferase and glucan-binding protein (Gbp) enzymes produced by S. mutans. This study was conducted to determine the antibacterial activity of Sirih merah leaf extract against S. mutans using the Kirby-Bauer method and to predict the potential molecular activity of antibacterial compounds contained in Sirih merah leaves in inhibiting the growth of S. mutans bacteria in silico using the molecular docking method. Antibacterial activity testing of Sirih merah leaf extract fractions obtained from methanol extract showed that fractions 7 and 10 are active fractions because they can inhibit the growth of S. mutans at the highest concentration of 10% with a strong inhibition zone category. The active fractions were then analyzed by the LC-HRMS method to obtain active compounds. The results of the in silico molecular docking test showed that the active compounds of Sirih merah leaves have the potential to interact with the GtfB and GbpC enzymes of S. mutans, where the best binding energy in the interaction of cafedrine compounds is -8.75 kcal/mol and -9.27 kcal/mol. The docking results were validated through a molecular docking process using native ligands with RMSD values of 1,861 Å and 3,170 Å
Fabrication and Synthesis of Fluorescent Carbon Nanodots from Black Sticky Rice as Probes for detection Mg2+ ions
No full textHerein, fluorescent carbon nanodots (C-dots) with average diameter of 5.51 nm were fabricated from black sticky rice by using carbonization method. These C-dots have been synthesized with magnesium (Mg2+) ions to investigate their potential application as probes for detection Mg2+ ions. The as-obtained C-dots were measured their absorption (Abs), photoluminescence (PL), and FTIR spectra, X-ray diffraction (XRD) patterns and transmission electron microscopy (TEM) image. According to their Abs spectrum, the Abs peak at 276 nm confirmed the presence of C-dots in ethanol solution. Fortunately, the PL peak at 427 nm corresponded to their blue emission color. The XRD patterns and the TEM image confirmed also the formation of amorphous state and monodispersed spherical C-dots, respectively. When the as-prepared C-dots were synthesized with Mg2+ ions, the PL intensities of C-dots quenched as increasing the concentration of Mg2+ ions. A characteristic PL quenching of the C-dots through Mg2+ chelation demonstrated the sensing system up to the detection limit of 2.98 µM. This is the first reporting the application of C-dots as sensors for detection Mg2+ ions. These findings can pave the large opportunity for application of these C-dots in sensing, bioimaging, drug delivery, and so on