ORCID Profile
0000-0001-6065-5437
Current Organisation
Universitas Padjadjaran
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Publisher: Maad Rayan Publishing Company
Date: 02-10-2020
DOI: 10.34172/PS.2020.63
Abstract: Background: Epithelial sodium channel (ENaC) is a transmembrane protein involved in maintaining sodium levels in blood plasma. It is also a potential biomarker for the early detection of hypertension since the amount of ENaC is related to the familial history of hypertension. ENaC can be detected by an aptamer, a single-stranded DNA (ssDNA) or RNA which offers advantages over an antibody. This study aimed to obtain an ssDNA aptamer specific to ENaC through virtual screening. Methods: Forty-one aptamers were retrieved from the Protein Data Bank (PDB) and the RNA was converted to ssDNA aptamers. The X-ray crystallographic structure of ENaC protein was remodelled using Modeller 9.20 to resolve missing residues. Molecular docking of aptamers against ENaC was performed using Patchdock and Firedock, then the selected aptamer was subjected to molecular docking against other ion channel proteins to assess its selectivity to ENaC. A molecular dynamics (MD) simulation was also conducted using Amber16 to acquire an in-depth understanding of the interaction within the aptamer-ENaC complex. Results: The virtual screening suggested that the ssDNA of iSpinach aptamer (PDB: 5OB3) displayed the strongest binding to ENaC (-49.46 kcal/mol) and was selective for ENaC over the other ion protein channels. An MMGBSA calculation on the complex of aptamer-ENaC revealed binding energy of -42,12 kcal/mol. Conclusion: The iSpinach-based aptamer is a potential probe for detecting ENaC or iDE and may be useful for the development of hypertension early detection systems.
Publisher: Universitas Gadjah Mada
Date: 31-08-2021
DOI: 10.22146/IJC.65951
Abstract: Coronavirus disease (COVID-19) is a pandemic burdening the global economy. It is caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Black cumin (Nigella sativa) seed may contain antivirals for the disease since it was reported to inhibit the human immunodeficiency virus (HIV) and hepatitis C virus (HCV). Main protease (Mpro) is a vital protein for viral replication and a promising target for COVID-19 drug development. Hence, in this study, we intended to uncover the potency of N. sativa seed as the natural source of inhibitors for SARS-CoV-2 Mpro. We collected secondary metabolites in N. sativa seed through a literature search and employed Lipinski’s rule of five as the initial filter. Subsequently, virtual screening c aigns using a molecular docking method were performed, with N3 inhibitor and leupeptin as reference ligands. The top hits were analyzed further using a molecular dynamics simulation approach. Molecular dynamics simulations showed that binding affinities of nigellamine A2 and A3 to Mpro are comparable to that of leupeptin, with median values of -43.9 and -36.2 kcal mol–1, respectively. Ultimately, this study provides scientific information regarding N. sativa seeds’ potency against COVID-19 and helps direct further wet experiments.
Publisher: Public Library of Science (PLoS)
Date: 05-10-2023
Publisher: American Chemical Society (ACS)
Date: 04-08-2023
Publisher: Asian Journal of Chemistry
Date: 2021
DOI: 10.14233/AJCHEM.2021.23076
Abstract: Gadolinium is a potential T1 contrast agent because it provides a better image for magnetic resonance imaging (MRI). However, as toxic gadolinium ions can be released from the coordination compounds, it is often encapsulated using silica. Silica-encapsulated gadolinium citrate is a colloid, therefore, encapsulation efficiency should be determined by the standard addition method, not the external standard, to minimize errors in the matrix. Silica-encapsulated gadolinium citrate (Gd-C6H5O7@SiO2) was prepared via the Stöber sol-gel method by mixing gadolinium citrate, ethanol, aqua proinjection, tetraethylorthosilicate (TEOS) and ammonia, then the encapsulation efficiency was determined using the standard addition method. Particle size analysis revealed that the average size of Gd-C6H5O7@SiO2 particles was 1.53 μm having a encapsulation efficiency of 90.44%.
Publisher: Elsevier
Date: 2018
Publisher: Royal Society of Chemistry (RSC)
Date: 2017
DOI: 10.1039/C7OB00129K
Abstract: Enhanced selectivity for homologous ATP sites by composite chemical and conformational perturbation by stereospecific fluorination.
Publisher: MDPI AG
Date: 25-07-2023
DOI: 10.3390/MOLECULES28155625
Abstract: Marennine, a blue pigment produced by the blue diatom Haslea ostrearia, is known to have some biological activities. This pigment is responsible for the greening of oysters on the West Coast of France. Other new species of blue diatom, H. karadagensis, H. silbo sp. inedit., H. provincialis sp. inedit, and H. nusantara, also produce marennine-like pigments with similar biological activities. Aside from being a potential source of natural blue pigments, H. ostrearia-like diatoms present a commercial potential for the aquaculture, food, cosmetics, and health industries. Unfortunately, for a hundred years, the exact molecular structure of this bioactive compound has remained a mystery. A lot of hypotheses regarding the chemical structure of marennine have been proposed. The recent discovery of this structure revealed that it is a macromolecule, mainly carbohydrates, with a complex composition. In this study, some glycoside hydrolases were used to digest marennine, and the products were further analyzed using nuclear magnetic resonance (NMR) and mass spectroscopy (MS). The reducing sugar assay showed that marennine was hydrolyzed only by endo-1,3-β-glucanase. Further insight into the structure of marennine was provided by the spectrum of 1H NMR, MS, a colorimetric assay, and a computational study, which suggest that the chemical structure of marennine contains 1,3-β-glucan.
Publisher: Asian Journal of Chemistry
Date: 2023
DOI: 10.14233/AJCHEM.2023.26924
Abstract: Gadolinium is one of the rare earth elements, which plays an essential role in modern industry. Its separation from mixtures of other rare earth elements is challenging due to similar physical and chemical properties. The extraction method using an emulsion liquid membrane is an effective and simple method for separating low concentration gadolinium from other rare earth elements mixtures. It is more eco-friendly than the liquid-liquid extraction process and also has various advantages. This study aims to determine the effectiveness, permeability and optimum formulation conditions for the separation of gadolinium and samarium using synergistic ligands tributyl phosphate and di-(2-ethylhexyl)phosphoric acid. The results showed a quantitative extraction (87.40%) of gadolinium ion at the optimum conditions of 0.025 M tributyl phosphate + 0.075 M di-(2-ethylhexyl phosphate), 4% span 80 as surfactant, 9000 rpm emulsification stirring speed and 0.5 M nitric acid as stripping phase, for a feed containing 1.5 mg/L gadolinium ion and 3 mg/L samarium ion at 5 M HNO3.
Publisher: The Royal Society
Date: 02-2021
DOI: 10.1098/RSOS.202040
Abstract: Epithelial sodium channel (ENaC) is a transmembrane protein that has an essential role in maintaining the levels of sodium in blood plasma. A person with a family history of hypertension has a high enough amount of ENaC protein in the kidneys or other organs, so that the ENaC protein acts as a marker that a person is susceptible to hypertension. An aptasensor involves aptamers, which are oligonucleotides that function similar to antibodies, as sensing elements. An electrochemical aptasensor for the detection of ENaC was developed using a screen-printed carbon electrode (SPCE) which was modified by electrodeposition of cerium oxide (CeO 2 ). The aptamer immobilization was via the streptavidin–biotin system. The measurement of changes in current of the active redox [Fe(CN) 6 ] 3−/4− was carried out by differential pulse voltammetry. The surfaces of SPCE and SPCE/CeO 2 were characterized using scanning electron microscopy, voltammetry and electrochemical impedance spectroscopy. The Box–Behnken experimental optimization design revealed the streptavidin incubation time, aptamer incubation time and streptavidin concentrations were 30 min, 30 min and 10.8 µg ml −1 , respectively. Various concentrations of ENaC were used to obtain the linearity range of 0.05–3.0 ng ml −1 , and the limits of detection and quantification were 0.012 ng ml −1 and 0.038 ng ml −1 , respectively. This aptasensor method has the potential to measure the ENaC protein levels in urine s les as well as to be a point-of-care device.
Publisher: Springer Science and Business Media LLC
Date: 12-2017
Publisher: MDPI AG
Date: 15-09-2022
DOI: 10.3390/MOLECULES27186018
Abstract: Flavonoids are a secondary metabolite group with various bioactivities, such as antioxidants. They are rich in the genus Erythrina, such as Erythrina crista-galli. This research aims to isolate and characterize flavonoids from the twigs of E. crista-galli and determine their antioxidant properties through in silico and in vitro assays. The ethyl acetate extract of E. crista-galli twigs were separated by column chromatography and characterized using spectroscopic methods. Density functional theory (DFT) calculations were performed on the isolated flavonoids and the reference compounds (ascorbic acid and quercetin) to obtain global descriptive parameters and a donor–acceptor map (DAM). We successfully isolated lupinifolin (1) and citflavanone (2) for the first time from E. crista-galli, along with lonchocarpol A (3), which has been discovered previously. The DAM suggests that these flavanones are good antiradicals with effective electron donors. However, they tend to be electron acceptors in methanol. The frontier molecular orbital analysis implies that lupinifolin (1) is a better antiradical than the other flavanones. The DPPH assays show that lupinifolin (1) has the highest antioxidant (antiradical) activity, with an IC50 value of 128.64 ppm. The in silico studies showed similar trends to the in vitro assays using the DPPH method.
Publisher: American Chemical Society (ACS)
Date: 27-01-2018
Abstract: (-)-Balanol is an adenosine triphosphate mimic that inhibits protein kinase C (PKC) isozymes and cAMP-dependent protein kinase (PKA) with limited selectivity. While PKA is known as a tumor promoter, PKC isozymes can be tumor promoters or suppressors. In particular, PKCε is frequently involved in tumorigenesis and a potential target for anticancer drugs. We recently reported that stereospecific fluorination of balanol yielded a balanoid with enhanced selectivity for PKCε over other PKC isozymes and PKA, although the global fluorine effect behind the selectivity enhancement is not fully understood. Interestingly, in contrast to PKA, PKCε is more sensitive to this fluorine effect. Here we investigate the global fluorine effect on the different binding responses of PKCε and PKA to balanoids using molecular dynamics (MD) simulations. For the first time to the best of our knowledge, we found that a structurally equivalent residue in each kinase, Thr184 in PKA and Ala549 in PKCε, is essential for the different binding responses. Furthermore, the study revealed that the invariant Lys, Lys73 in PKA and Lys437 in PKCε, already known to have a crucial role in the catalytic activity of kinases, serves as the main anchor for balanol binding. Overall, while Thr184 in PKA attenuates the effect of fluorination, Ala549 permits remote response of PKCε to fluorine substitution, with implications for rational design of future balanol-based PKCε inhibitors.
Publisher: Bentham Science Publishers Ltd.
Date: 03-2024
DOI: 10.2174/1570180820666221025120744
Abstract: The most significant antioxidant enzymes are glutathione peroxidase (GSHPx), catalase (CAT), and superoxide dismutase (SOD) have a significant role in the scavenging of free radicals but overexpressing of these enzymes can have deleterious effects. Therefore, compounds from outside the body are needed that can suppress the growth rate of this enzyme. Several previous studies have stated that Piper betle L. has high antioxidant and inhibits enzyme activity including of allypyrocatechol. The current study aimed to evaluate the molecular mechanism of allylpyrocatecachol with SOD, CAT, GSHPx and find out its potential of the lead compounds against some antioxidant enzyme by an in silico approach. Allylpyrocatechol were docked to SOD, CAT, and GSHPx enzyme using Autodock4 tools. Evaluation of receptor-ligand interactions based on comparison of binding affinity, accuracy of involved amino acid residues, and compare with gallic acid as a positive control ligand. By in silico analysis showed that the binding affinity between the ligand and the three receptors were -4.3, -6.8, -4.5 kcal/mol for the SOD, CAT, and GHSPx receptors, respectively. This finding indicates that Allylpyrocatechol have a promising candidate as a compound to inhibits antioxidant enzyme activity. It can be seen from the accuracy of the amino acids residue involved and value of the binding affinity compared to positive control ligand
Publisher: MDPI AG
Date: 09-10-2023
Publisher: MDPI AG
Date: 23-11-2020
DOI: 10.20944/PREPRINTS202011.0586.V1
Abstract: Citrus essential oils (EOs) have various bioactivities like antioxidants, with many applications. Antioxidant activities depend on the chemical compositions of the EOs, which are affected by climate, soil, and geographical region. Thus, investigations on chemical compositions and antioxidant activities of Citrus EOs in different countries are valuable. In this study, we distilled EOs from peels of Indonesian-grown Citrus, including C. nobilis, C. limon, C. aurantifolia, C. amblycarpa, and Citrus spp.Chemical compositions of EOs were analyzed using Gas Chromatography-Mass Spectrometer (GC-MS), whereas the antioxidant activities were determined by employing 2,2-diphenyl-2-picrylhydrazyl (DPPH) method. Furthermore, principal component analysis (PCA) was applied to elucidate the main contributing compounds for antioxidant activity. The results show that all EOs possess unique chemical characteristics, with limonene as the majority constituent. For antioxidant activities, C. limon and C. amblycarpa EOs are the two strongest, IC50 values below 7.00 & mu L/mL. PCA approach suggests that -terpinene mainly contributes to the high antioxidant activities of C. limon and C. amblycarpa. Moreover, o-cymene, thymol, p-cymene, and & alpha -pharnesene may also be responsible for the antioxidant activity of C. limon EO. These results are valuable information for the applications of Citrus EOs as antioxidant sources.
Publisher: MDPI AG
Date: 17-06-2023
DOI: 10.3390/MOLECULES28124836
Abstract: Lipid nanoparticles (LNPs) have emerged as a promising delivery system, particularly for genetic therapies and vaccines. LNP formation requires a specific mixture of nucleic acid in a buffered solution and lipid components in ethanol. Ethanol acts as a lipid solvent, aiding the formation of the nanoparticle’s core, but its presence can also affect LNP stability. In this study, we used molecular dynamics (MD) simulations to investigate the physicochemical effect of ethanol on LNPs and gain a dynamic understanding of its impact on the overall structure and stability of LNPs. Our results demonstrate that ethanol destabilizes LNP structure over time, indicated by increased root mean square deviation (RMSD) values. Changes in the solvent-accessible surface area (SASA), electron density, and radial distribution function (RDF) also suggest that ethanol affects LNP stability. Furthermore, our H-bond profile analysis shows that ethanol penetrates the LNP earlier than water. These findings emphasize the importance of immediate ethanol removal in lipid-based systems during LNP production to ensure stability.
Publisher: Springer Science and Business Media LLC
Date: 02-2019
Publisher: Elsevier
Date: 2018
No related grants have been discovered for ARI HARDIANTO.