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All Journal Indonesian Journal of Chemistry Jurnal Sains dan Teknologi Farmasi Indonesia
Umi Baroroh
Department Of Biotechnology, Sekolah Tinggi Farmasi Indonesia, Jl. Soekarno Hatta No. 354, Bandung 40266, Indonesia
Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Immunology & microbiology Medicine & Pharmacology Public Health

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Protein Modelling Insight to the Poor Sensitivity of Chikungunya Diagnostics on Indonesia’s Chikungunya Virus Bevi Lidya; Muhammad Yusuf; Umi Baroroh; Korry Novitriani; Bachti Alisjahbana; Iman Rahayu; Toto Subroto
Indonesian Journal of Chemistry Vol 23, No 5 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.79301

Abstract

Sensitive detection of infectious diseases is crucial for effective clinical care. However, commercial rapid tests may be limited in their ability to detect pathogen variants across different countries. It was found that the sensitivity of a chikungunya rapid test on local strain was only 20.5% as compared to the East, Central, and South Africa (ECSA) phylogroup. Therefore, the development of geographically specific diagnostics is essential. Investigating the distinctive structural properties of a locally sourced antigenic protein is an important initiative for the development of a specific antibody. This study utilized structural bioinformatics and molecular dynamics simulations to investigate the differences between the E1-E2 antigenic proteins of the Indonesian chikungunya virus (Ind-CHIKV) and that of ECSA. The results showed that some of the mutation points are located at the antibody binding sites of Ind-CHIKV. G194S and V318R mutations were proposed as distinctive features of Ind-CHIKV, leading to weaker antibody binding compared to ECSA. It suggests that modifying the antibody to accommodate bulkier side chains at positions 194 and 318 could improve its effectiveness against Ind-CHIKV. These insights are valuable for developing a highly sensitive immunoassay for Ind-CHIKV and other regional pathogens, ultimately enhancing diagnostic capabilities in Indonesia.
PENAMBATAN MOLEKUL MUTAN TOKSIN DIFTERI TERHADAP SENYAWA NAD+ SEBAGAI ALTERNATIF CRM197 PADA VAKSIN KONJUGAT Baroroh, Umi; Fauziyah, Hanifa; Astriany, Dewi; Yusuf, Muhammad; Novianti, Mia Tria
JURNAL SAINS DAN TEKNOLOGI FARMASI INDONESIA Vol 9, No 2 (2020)
Publisher : Sekolah Tinggi Farmasi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (668.996 KB) | DOI: 10.58327/jstfi.v9i2.148

Abstract

Difteri merupakan penyakit pernapasan menular yang menjadi salah satu penyebab utama kematianpada anak-anak. Penggunaan formaldehid pada pembuatan toksoid difteri dinilai merusak sejumlahsitus antigenik penting pada toksoid. CRM197 merupakan komponen vaksin yang mengalami mutasiasam amino pada toksin difteri. Adanya efek sitotoksisitas CRM197 terhadap sel mamalia dan sel ragimenandakan bahwa mutasi yang terjadi belum menurunkan toksisitas secara optimal, sehinggadiperlukan studi lebih lanjut untuk pengembangan mutan toksin difteri baru. Penelitian ini bertujuanuntuk memodelkan mutan tersebut dan menguji afinitasnya terhadap ligan NAD+. Pendekatanbioinformatika dilakukan dengan penambatan molekul menggunakan program AutoDock 4.2.Diperoleh energi bebas ikatan terendah pada natif sebesar -7,62 kcal/mol. Asam amino Ile31 dan Tyr65dirancang dengan mensubstitusi menjadi Lys31 dan Gln65 (I31K/Y65Q). Hasil penambatan molekulmutan uji menunjukkan nilai energi ikatan meningkat menjadi -5,91 kcal/mol, menandakan adanyapenurunan afinitas NAD+. Titik mutasi ini dapat diusulkan untuk pengembangan mutan toksin difteridengan afinitas rendah terhadap NAD+ sebagai kandidat vaksin difteri.Kata kunci: toksin difteri, CRM197, penambatan molekul, vaksin, bioinformatika
EXPLORATION OF POTENTIAL NATURAL COMPOUNDS THROUGH IN SILICO APPROACH: A CASE STUDY ON TOKARAMID COMPOUNDS Baroroh, Umi; Sin, Cindy Wan Yik; Riasari, Hesti
JURNAL SAINS DAN TEKNOLOGI FARMASI INDONESIA Vol 12, No 2 (2023)
Publisher : Sekolah Tinggi Farmasi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.58327/jstfi.v12i2.225

Abstract

Indonesia, renowned for its rich biodiversity, boasts diverse marine ecosystems that have long remained untapped in the quest for novel therapeutic compounds. This shows the great potential of Indonesia's biodiversity, particularly within its marine habitats, as a treasure trove for exploring bioactive compounds for disease treatment. These compounds can be explored using in silico analyses, including activity prediction, ADME (absorption, distribution, metabolism, and excretion) prediction, toxicity prediction, and molecular docking, to accelerate the discovery of promising drug candidates. The compound TG-0205221, modified Tokaramide A from the sponge Theonella mirabilis, is reported to have potential as an anti-3CLPro from SARS-CoV-1, which is genomically similar to SARS-CoV-2 by 96%. 3CLPro is the most prospective working target of anti-COVID-19. In this study, the exploration of TG-0205221 and Tokaramide A as anti-3CLPro was conducted using in silico approach. It is shown that based on ADMET prediction, all compounds are anticipated to be suitable for oral consumption and exhibit a non-toxic profile. TG-0205221 is predicted to have activity as a 3CLPro inhibitor higher than others. Furthermore, the potential anti-3CLPro SARS-CoV-2 activity of all ligands in molecular docking is envisaged to be considerably high. The binding energy of Tokaramide A and TG-0205221 is relatively similar, -9.16 and -8.39 kcal/mol, respectively. Both Tokaramide A and TG-0205221 show potential as anti-SARS-CoV-2 agents and may aid in the exploration of natural compounds for drug discovery.
Co-Authors Bachti Alisjahbana Bevi Lidya Dewi Astriany Fauziyah, Hanifa Iman Rahayu Korry Novitriani Muhammad Yusuf Novianti, Mia Tria Riasari, Hesti Sin, Cindy Wan Yik Toto Subroto