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All Journal JURNAL BIOLOGI INDONESIA Narra J DEIKTIS: Jurnal Pendidikan Bahasa dan Sastra
Karimah, Nihayatul
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Humanities Biochemistry, Genetics & Molecular Biology Education Health Professions Immunology & microbiology Languange, Linguistic, Communication & Media Medicine & Pharmacology Public Health Other

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PROTEIN DOMAIN ANNOTATION OF PLASMODIUM SPP. CIRCUMSPOROZOITE PROTEIN (CSP) USING HIDDEN MARKOV MODEL-BASED TOOLS Parikesit, Arli Aditya; Utomo, Didik Huswo; Karimah, Nihayatul
JURNAL BIOLOGI INDONESIA Vol 14, No 2 (2018): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/jbi.v14i2.3737

Abstract

ABSTRACTPlasmodium sp. Circumsporozoite Protein (CSP) has a crucial role in sporozoite function and hepatocyte invasion. The basic understanding of this protein can reveal the mechanism of action. Protein domain annotation could determine the functional region of the specific protein. This study aimed is to identify the conserved and functional region of circumsporozoite protein using Hidden Markov Model approach. Three samples of CSP was retrieved from UniProt database; Circumsporozoite protein from Plasmodium vivax (P08677), Circumsporozoite protein from Plasmodium malariae (P13815), and Circumsporozoite protein from Plasmodium knowlesi (P02894). All sequenced was reviewed and could be used for further analysis. Multiple Sequences alignment (MSA) was used for analyzing the conserved region. CLUSTAL X software employed to run the MSA of circumsporozoite protein. Protein homology was clustered using MEGA 7.0, and domain annotation was done by the SUPERFAMILY hidden Markov models. The result showed that Circumsporozoite Protein has two specific conserved regions among species. This conserved region indicates the similar function and takes a vital role in their life cycle. Plasmodium  knowlesi and Plasmodium vivax had more similar sequence than Plasmodium malariae. The clustering result based on Circumsporozoite Protein indicates that Plasmodium malariae may have distinct infection mode to the host. The CSP was identified has one domain in C-terminus. Domain family of  CSP was TSP-1 type 1 repeat with high reliability. It can be concluded that conserved domain of Circumsporozoite Protein could reveal its critical role in Malaria Disease. To this end, CSP could be a potential candidate for vaccine development. Keywords: Circumsporozoite, conserved domain, Plasmodium spp, TSP-1 type 1 repeat.  
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.
Penerapan Model Kooperatif Tipe Jigsaw Dalam Pembelajaran Teks Artikel Ilmiah Populer Kelas VIII-C SMP IT Al-Fateeh Semarang Karimah, Nihayatul; Azizah, Aida
DEIKTIS: Jurnal Pendidikan Bahasa dan Sastra Vol. 5 No. 3 (2025)
Publisher : Perkumpulan Dosen Muslim Indonesia - Sulawesi Selatan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.53769/deiktis.v5i3.1472

Abstract

Penelitian ini bertujuan untuk mendeskripsikan model kooperatif tipe jigsaw dalam pembelajaran teks artikel ilmiah populer kelas VIII C SMP IT Al-Fateeh Semarang. Jenis penelitian ini adalah mix method yang menggabungkan metode penelitian kualitatif dan metode penelitian kuantitatif. Analisis data dilakukan dengan teknik tes dan nontes. Analisis data tes diperoleh melalui hasil tes yang diberikan kepada peserta didik, sedangkan data nontes diperoleh melalui hasil observasi dan dokumentasi yang dilakukan selama kegiatan pembelajaran. Penelitian ini menujukkan hasil bahwa model kooperatif tipe jigsaw dapat meningkatkan hasil belajar peserta didik secara signifikan.
Co-Authors Aida Azizah, Aida Arli Aditya Parikesit ASTUTIATI NURHASANAH Chaera, Ummi Hamid, Firdaus Handayani, Irda Hatta, Mohammad Hidayah, Najdah Iskandar, Israini W. Jamaluddin, Balqis D. Massi, Muhammad N. Permana, Andi D. Utomo, Didik Huswo Yusriyyah, Andi A. Zaenab, St