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All Journal Narra J
Iskandar, Israini W.
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Biochemistry, Genetics & Molecular Biology Health Professions Immunology & microbiology Medicine & Pharmacology Public Health

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Green algae Caulerpa racemosa compounds as antiviral candidates for SARS-CoV-2: In silico study Tassakka, Asmi CMAR.; Iskandar, Israini W.; Juniyazaki, Andi BA.; Zaenab, St; Alam, Jamaluddin F.; Rasyid, Haerani; Kasmiati, Kasmiati; Sinurat, Ellya; Dwiany, Fenny M.; Martien, Ronni; Moore, Abigail M.
Narra J Vol. 3 No. 2 (2023): August 2023
Publisher : Narra Sains Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52225/narra.v3i2.179

Abstract

Green algae (Caulerpa racemosa) are known to contain bioactive compounds which are hypothesized to have antiviral activities against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19) pandemic. The aim of this study was to analyze the anti-SARS-CoV-2 potential of compounds extracted from the green alga Caulerpa racemosa using in silico analysis. The extract was obtained through maceration with 96% ethanol and the compounds present in the extract were identified through gas chromatography-mass spectroscopy (GC-MS). The binding affinities were analyzed in silico using the PyRx application and visualized in the PyMOL software. GC-MS analysis of Caulerpa racemosa extract showed 92 spectral peaks, each of which was assigned to a bioactive compound. Of the six compounds with a strong binding affinity, n-[1-(1-adamantan-1-yl-propyl)-2,5-dioxo-4-trifluoromethyl-imidazo lidin-4-yl] 4-methoxy-benzamide had the lowest score (-8.1 kcal/mol) against the SARS-CoV-2 3C-like protease binding site, similar with that of remdesivir. The molecular dynamics calculations demonstrated that root means square deviation values of the selected inhibitors remained stable throughout a 15-nanosecond simulation. In conclusion, the in silico analysis suggests that Caulerpa racemosa extract is a potential antiviral candidate against SARS-CoV-2.
Association between vitamin D levels with IL-6 and IL-10 in umbilical cord blood of infants Massi, Muhammad N.; Fikri, Bahrul; Putera, Azwin M.; Alfian, Sofa D.; Ridha, Nadira R.; Putri, Sri H.; Chaera, Ummi; Iskandar, Israini W.; Shimojo, Naoki
Narra J Vol. 4 No. 3 (2024): December 2024
Publisher : Narra Sains Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52225/narra.v4i3.889

Abstract

A worldwide issue, vitamin D deficiency affects pregnant mothers and babies everywhere, including Indonesia. It involves the adaptive immune system by controlling the production of pro- and anti-inflammatory cytokines and the balance between humoral (Th2) and cell-mediated (Th1) immunity. The aim of this study was to investigate the relationship between vitamin D and the cytokines IL-6 and IL-10 in infants. It also examined the relationship between ferritin and IL-6/IL-10 in newborns. The study collected 114 umbilical cord blood samples from term-born mothers without clinical symptoms. IL-6 and IL-10 were among the cytokine profiles measured by the enzyme-linked immunosorbent assay (ELISA). SPSS was used for statistical analysis, and an in-silico investigation was carried out to examine the molecular relationships between vitamin D and IL-6/IL-10. Using the 20 ng/mL as the cut-off for vitamin D insufficiency suggested the insignificant association of vitamin D with IL-6 (p=0.42), IL-10 (p=0.76), and ferritin (p=0.47). When the umbilical cord vitamin D level was categorized into four quartiles, the association with the highest statistical significance (quartile 4 versus quartile 2) was observed for IL-6 (p<0.001), IL-10 (p<0.001), and ferritin (p<0.001). However, the linear regression did not suggest the significant correlations of vitamin D with IL-6 (p=0.40) and IL-10 (p=0.45). A significant correlation based on the linear regression was found between ferritin and IL-10 (p=0.03). Molecular docking studies demonstrated binding affinities of -8.04 kcal/mol for IL-6-vitamin D and -8.53 kcal/mol for IL-10-vitamin D complexes, with stable root mean square deviation throughout the simulations. This study contributes valuable insights into the clinical and computational analysis of the relationship of vitamin D with IL-6 or IL-10.
Computational drug repurposing for tuberculosis by inhibiting Ag85 complex proteins Iskandar, Israini W.; Nurhasanah, Astutiati; Hatta, Mohammad; Hamid, Firdaus; Handayani, Irda; Chaera, Ummi; Yusriyyah, Andi A.; Jamaluddin, Balqis D.; Zaenab, St; Hidayah, Najdah; Karimah, Nihayatul; Permana, Andi D.; Massi, Muhammad N.
Narra J Vol. 5 No. 1 (2025): April 2025
Publisher : Narra Sains Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52225/narra.v5i1.1130

Abstract

Tuberculosis (TB) remains a significant and deadly infection among pulmonary diseases caused by Mycobacterium tuberculosis, a highly adaptive bacterium. The ability of M. tuberculosis to evade certain drugs has been linked to its unique structure, particularly in the cell envelope, where the Ag85 complex proteins play an essential role in this part.  The aim of this study was to utilize a drug repurposing strategy targeting the Ag85 complex proteins. This study utilized a computational approach with 120 selected drugs experimentally identified to inhibit Tuberculosis. A virtual screening molecular docking with Autodock Vina was used to filter the compounds and identify the strong binders to the Ag85 Complex. Molecular dynamics simulations employed the Gromacs Packages to evaluate the stability of each complex, including root mean square deviation (RMSD), root mean square fluctuation (RMSF), and radius of gyration (RoG). Additionally, absorption, distribution, metabolism, excretion, and toxicity (ADMET) assessments were conducted to gather more information about the drug-likeness of each hit compound. Three compounds, selamectin, imatinib, and eltrombopag were selected as potential drugs repurposed to inhibit the activity of the Ag85 complex enzyme, with binding affinities ranging between -10.560 kcal/mol and -11.422 kcal/mol. The MD simulation within 100 ns (3 replicas) showed that the average RMSD of each Ag85A complex was 0.15 nm–0.16 nm, RMSF was 0.09 nm–0.10 nm, and RoG was 1.80 nm–1.81 nm. For Ag85B, the average RMSD was 1.79 nm–1.80 nm, RMSF was 0.08 nm–0.09 nm, and RoG was 1.79 nm – 1.80 nm. Then, for Ag85C, the mean RMSD was 0.16 nm–0.18 nm, RMSF was 0.09, and RoG was 1.77 nm. The study highlights that these promising results demonstrate the potential of some repurposed drugs in combating the Ag85 complex.
Co-Authors Alam, Jamaluddin F. ASTUTIATI NURHASANAH Chaera, Ummi Dwiany, Fenny M. Fikri, Bahrul Haerani Rasyid, Haerani Hamid, Firdaus Handayani, Irda Hatta, Mohammad Hidayah, Najdah Jamaluddin, Balqis D. Juniyazaki, Andi BA. Karimah, Nihayatul Kasmiati Kasmiati Martien, Ronni Massi, Muhammad N. Moore, Abigail M. Permana, Andi D. Putera, Azwin M. Putri, Sri H. Ridha, Nadira R. Shimojo, Naoki Sinurat, Ellya Sofa D. Alfian, Sofa D. Tassakka, Asmi CMAR. Yusriyyah, Andi A. Zaenab, St