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All Journal HAYATI Journal of Biosciences VALENSI Bionatura Microbiology Indonesia Majalah Kedokteran Bandung Jurnal Riset Kimia Indonesian Journal of Pharmaceutical Science and Technology JC-T (Journal Cis-Trans): Jurnal Kimia dan Terapannya Health Notions Chimica et Natura Acta ALCHEMY Jurnal Penelitian Kimia Jurnal Kimia Terapan Indonesia Jurnal Pendidikan Kimia (JPKim) Indonesian Journal of Chemistry PENDIPA Journal of Science Education Molekul: Jurnal Ilmiah Kimia Jurnal Ilmiah Farmako Bahari
Shabarni Gaffar
Departemen Kimia, Fakultas Matematika Dan Ilmu Pengetahuan Alam, Universitas Padjadjaran
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Computer Science & IT Dentistry Earth & Planetary Sciences Education Energy Environmental Science Health Professions Immunology & microbiology Materials Science & Nanotechnology Mathematics Medicine & Pharmacology Nursing Public Health

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Exploration of Anti-FABP3 Aptamer Conformation Using Coarse-Grained Molecular Dynamics Simulation Aathirah, A Sayyidatina; Hardianto, Ari; Gaffar, Shabarni
Indonesian Journal of Pharmaceutical Science and Technology Vol 12 (2025): Vol. 12 Suppl. 2 (2025)
Publisher : Indonesian Journal of Pharmaceutical Science and Technology

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24198/ijpst.v12s2.58912

Abstract

Aptamers have been extensively utilized in the development of diagnostic and therapeutic methodologies for a variety of diseases. Aptamer N13, obtained through the SELEX process in previous research, has been identified as an anti-FABP3 ssDNA aptamer to enhance diagnostic techniques for myocardial infarction. This study provides an in-depth examination of the conformation and structural dynamics of aptamer N13 using in-silico methods. These include secondary structure prediction via DNA-fold, 3D structures modeling through RNA-Composer, and coarse-grained molecular dynamics (MD) simulations with SIRAH AMBER. The 83 μs MD simulation results reveal that the predicted conformation generally struggles to maintain stability, as indicated by the RMSD values and their fluctuations. However, residues 1-50 demonstrate relatively stable conformations, particularly beyond the 40 μs point in the simulation. In contrast, residues 51-90, constituting the free end, exhibit persistent conformational instability. This instability is likely attributable to their single-stranded and free nature compared to the other regions characterized by loops that confer greater stability. Our findings suggest that the predicted conformation from existing tools does not yet provide the most stable reference structure, necessitating further exploration through extended molecular dynamics simulations. While current simulations offer a relatively stable conformational reference, additional simulations are warranted to determine the most stable configuration of the free-end region, thereby elucidating its role in the aptamer’s affinity and specificity
New Custom Primers for the Detection of SARS-CoV-2 using the Singleplex rRT‒PCR SYBR Green-Based Method with the NSP10 and N genes as Targets Gaffar, Shabarni; Shabrinna, Hanif; Putri, Rafika; Wiraswati, Hesti Lina; Hartati, Yeni Wahyuni; Ishmayana, Safri; Faridah, Lia; Ekawardhani, Savira
Chimica et Natura Acta Vol 13, No 1 (2025)
Publisher : Departemen Kimia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24198/cna.v13.n1.53493

Abstract

Although COVID-19 is no longer a global health emergency, rapid, sensitive, and specific detection tests are still needed. In this study, we developed a cost-effective test, the SYBR Green-based rRT‒PCR kit, using new custom primers targeting the N and NSP10 genes of the SARS-CoV-2 virus. The specificity of the designed primers was determined through agarose gel electrophoresis. A standard curve generated from a ten-fold dilution of SARS-CoV-2 RNA was used to determine the efficiency and sensitivity of the kit. Validation of this protocol was carried out on ten clinical specimens. As expected, the results showed that the N and NSP10 gene primers produced 134 and 161 bp products, respectively. The limits of detection and limit of quantification with N gene primers were 7.74 and 23.46 copies/μL, respectively, and those with the NSP10 gene primers were 4.69 and 14.21 copies/μL, with a PCR efficiency of 102.5% and 110.6%, respectively. The validation results with clinical specimens revealed that seven samples were true-positive for COVID-19 (Ct range 15.09–21.33), and three were confirmed to be true-negative. Costs associated with COVID-19 patient testing can be anticipated to decrease with the use of custom primers for the detection of SARS-CoV-2 via the use of the singleplex rRT‒PCR mix SYBR Green.
Determination of Apoptosis Level of Hela Cells Treated with Disobinol Compound from Chisocheton Macrophyllus Plant Hafiz, Ersanda; Albayyinah, Dyandra Hera; Melati, Rima; Herlina, Tati; Permadi, Nandang; Amalia, Riezki; Nurlelasari, Nurlelasari; Gaffar, Shabarni
Jurnal Riset Kimia Vol. 16 No. 1 (2025): March
Publisher : Universitas Andalas

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.25077/jrk.v16i1.772

Abstract

Disobinol is a limonoid compound from the seeds of the Chisocheton macrophyllus plant that has been reported to have anticancer activity against cervical cancer cell lines. Cervical cancer is a type of cancer caused by infection with Human papillomavirus (HPV) types 16 and 18, leading to the transformation of normal cervical epithelial cells into cancerous cells. Previous studies show that Disobinol has a cytotoxic effect on HeLa cells with the IC50 value 52,92 μg/mL (24 hours’ incubation). This study aims to determine the level of apoptosis in HeLa cells treated with Disobinol and observe the DNA fragmentation in HeLa cells undergoing apoptosis. The HeLa cells were treated with Disobinol at concentrations of 26,5 μg/mL (1/2 IC50), 52,3 μg/mL (IC50), and 104,6 μg/mL (2x IC50) and incubated for 24 hours. The level of apoptosis was analyzed by using flow cytometry, and the DNA fragmentation pattern was analyzed by agarose gel electrophoresis. The results showed that Disobinol induces early apoptosis in HeLa cells, although the difference in the percentage of cell death is not very significant, which were 37.05%, 37.7%, and 41.60%, respectively. The DNA fragmentation pattern in HeLa cells treated with various concentrations of Disobinol was also observed on agarose gel. Therefore, Disobinol has the potential to be used as a chemotherapeutic drug or as a lead compound for the treatment of cervical cancer.
In-house Multiplex rRT-PCR Assay for Sars-Cov2 Detection in Indonesia using a new primer design Gaffar, Shabarni; Putri, Rafika Nanda; Shabrinna, Hanif; Supriyadi, Isma Yustifania; Wiraswati, Hesti Lina; Ekawardani, Savira; Ishmayana, Safri; Hartati, Yeni Wahyuni; Faridah, Lia
Jurnal Riset Kimia Vol. 16 No. 1 (2025): March
Publisher : Universitas Andalas

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.25077/jrk.v16i1.781

Abstract

During the COVID-19 pandemic, we attempted to develop an in-house rRT-PCR kit, utilizing custom primers targeting NSP14 and RdRp, with the RPP30 gene as an internal control. This kit will support Indonesian independence in enhancing COVID-19 diagnostics. The primer and probe were designed by a bioinformatics tool, determining primer specificity and sensitivity, optimizing probe concentrations, establishing LoD (Limit of Detection), LoQ (Limit of Quantification), and rRT-PCR efficiency, multiplex testing of the rRT-PCR kit on clinical samples, and testing the kit's stability. The in-house rRT-PCR kit can detect NSP14, RdRp, and RPP30 genes. The optimal concentrations for the NSP14, RdRp, and RPP30 probes are 1 μM, 1.5 μM, and 1.5 μM, respectively. The LoD and LoQ for the NSP14 are 0.22 ng/μL and 0.67 ng/μL, and for the RdRp are 1.08 ng/μL and 3.28 ng/μL. The rRT-PCR efficiencies for the NSP14, RdRp, and RPP30 are 80.3%, 100.6%, and 106%, respectively. Detection of ten clinical samples, comprising seven true positive and three true negative samples, showed Ct (Cycle threshold) values of 28–31 for the RPP30 gene, Ct 21–27 for the RdRp gene, and Ct 30–34 for the NSP14 gene. Stability testing of the rRT-PCR kit demonstrated promising results, where the kit stored at -20°C for seven days showed almost no difference in Ct values. This in-house multiplex rRT-PCR will support Indonesian independence in enhancing COVID-19 diagnostics, providing a dependable method for detecting SARS-CoV-2 in clinical samples.
Dysobinol from Chisocheton macrophyllus Selectively Induces G1 Cell Cycle Arrest in MCF-7 Breast Cancer Cells Gaffar, Shabarni; Tambunan, Ghina Uli Felicia; Hafiz, Ersanda; Herlina, Tati; Wiraswati, Hesti Lina; Nurlelasari, Nurlelasari; Ma'ruf, Ilma Fauziah
Indonesian Journal of Chemistry Vol 26, No 1 (2026)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.100479

Abstract

Chisocheton macrophyllus is a medicinal plant that contains sesquiterpenoids, triterpenoids, limonoids, steroids, and phenolic compounds. This research aimed to assess the effect of Dysobinol, a limonoid compound from the seed of C. macrophyllus, on MCF-7 cell growth. Cell viability was evaluated using the MTS colorimetric assay, DNA fragmentation was assessed by agarose electrophoresis, apoptosis and cell cycle arrest were determined by flow cytometry, and gene expression levels were evaluated using qRT-PCR. Dysobinol was also analyzed in silico using drug-likeness, pharmacokinetic, and molecular docking analysis. Dysobinol demonstrated moderate cytotoxicity against MCF-7 cells, with an IC50 of 148.20 μg/mL. Dysobinol induced G1 phase cell cycle arrest that was not accompanied by the induction of apoptosis in MCF-7 cells. In silico studies showed that the EGFR/AKT/cyclin D1 proteins were affected by Dysobinol. Furthermore, drug-likeness and pharmacokinetics analysis showed that Dysobinol is bioavailable orally and has high gastrointestinal absorption and low penetration into the blood-brain barrier. Together, these results indicate that Dysobinol can regulate breast cancer cell proliferation through cell cycle arrest rather than apoptosis, and its pharmacological profile highlights its potential as a promising lead compound for anticancer drug development.
Aktivitas Sitotoksik Ekstrak Etanol, Fraksi Etil Asetat dan n-heksana Daun Kelor (Moringa oleifera) Terhadap Sel Kanker Payudara T47D Shabarni Gaffar; Riza Apriani; Tati Herlina
ALCHEMY Jurnal Penelitian Kimia Vol 14, No 2 (2018): September
Publisher : UNIVERSITAS SEBELAS MARET (UNS)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20961/alchemy.14.2.17298.303-313

Abstract

Daun Kelor (Moringa oleifera) merupakan salah satu tanaman yang berpotensi memiliki aktivitas antikanker. Beberapa penelitian telah melaporkan bahwa daun M. oleifera mengandung sejumlah senyawa bioaktif yang memiliki potensi sebagai antikanker. Penelitian ini bertujuan untuk mengetahui aktivitas sitotoksik esktrak etanol, fraksi etil asetat dan fraksi n-heksana daun M. oleifera terhadap sel kanker payudara T47D. Daun M. oleifera dimaserasi dengan pelarut etanol 90%. Ekstrak yang diperoleh dipartisi dengan menggunakan pelarut n-heksana dan etil asetat. Masing-masing ekstrak etanol, fraksi etil asetat dan fraksi n-heksana diuji aktivitas sitotoksiknya terhadap sel kanker payudara T47D menggunakan metode MTS (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium). Konsentrasi ekstrak dan fraksi yang digunakan adalah berturut-turut: 1500, 750, 375, 187, 93, 46, 50 dan 23 μg/mL dengan waktu inkubasi selama 48 jam. Nilai IC50 ekstrak etanol, fraksi etil asetat dan fraksi n-heksana daun M. oleifera berturut-turut yaitu sebesar 51,31; 20,17; 223,67 μg/mL. Berdasarkan hasil tersebut, terlihat bahwa fraksi etil asetat daun M. oleifera memiliki aktivitas sitotoksik yang paling tinggi terhadap sel kanker payudara T47D.Cytotoxic Activity of the Ethanol Extract, Ethyl Acetate and n-hexane Fractions of Kelor Leaves (Moringa oleifera) against Breast Cancer Cell T74D. Moringa oleifera is one plant that has the potential anticancer activity. Several studies have been reported that M. oleifera leaves contain bioactives compounds that are potential as anticancer. This study was aimed to determine the cytotoxic activity of the ethanol extract, ethyl acetate and n-hexane fraction of M. oleifera leaf against breast cancer cell T47D. M. oleifera leaves were extracted by maceration with ethanol solvent. The extracts that have been obtained were partitioned by using n-hexane and ethyl acetate solvents. Each ethanol extract, ethyl acetate fraction and n-hexane fraction were tested for their cytotoxic activity against T47D breast cancer cells using MTS (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium) method. The applied concentration of extract and fraction were 1500, 750, 375, 187, 93, 46, 50 and 23 μg/mL with an incubation time of 48 hours. IC50 value of ethanol extract, ethyl acetate and n-hexane fractions of M. oleifera leaves were 51.31; 20.17; 223.67 μg/mL. Based on these results, it shows that the ethyl acetate fractions of M. oleiferaleaves are highly toxic against T47D breast cancer cells. 
Senyawa Golongan Limonoid dari Tanaman Genus Chisocheton dan Aktivitas Antikankernya Ghina Uli Felicia Tambunan; Nurlelasari Nurlelasari; Shabarni Gaffar
ALCHEMY Jurnal Penelitian Kimia Vol 17, No 1 (2021): March
Publisher : UNIVERSITAS SEBELAS MARET (UNS)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20961/alchemy.17.1.41279.10-26

Abstract

Indonesia merupakan negara yang kaya akan keanekaragaman hayati. Terdapat banyak tanaman yang mengandung senyawa metabolit sekunder yang memiliki aktivitas biologi sehingga berpotensi untuk digunakan sebagai obat, salah satunya adalah genus Chisocheton. Tanaman genus Chisocheton sudah banyak dilaporkan mengandung senyawa triterpenoid, seskuiterpenoid, limonoid, steroid, dan fenol. Limonoid merupakan turunan triterpenoid yang paling banyak ditemukan pada tanaman genus Chisocheton. Lebih dari tiga puluh senyawa golongan limonoid telah diuji aktivitas antikankernya terhadap beberapa jenis sel kanker manusia, seperti sel kanker payudara, mulut, paru-paru, leukimia, serviks, dan hati. Beberapa senyawa limonid tersebut diketahui memiliki aktivitas sitotoksik yang tinggi dengan kisaran nilai IC50 1,67 − 50,27 µg/mL. Review ini memaparkan beberapa senyawa limonoid yang diisolasi dari genus Chisocheton, aktivitas sitotoksiknya terhadap sel-sel kanker manusia, serta hubungan struktur dan aktifitas biologisnya (SAR = Structure Activity Relationship). Selain itu beberapa penelitian juga sudah melakukan penelitian lebih lanjut seperti pengujian induksi apoptosis dan penentuan tingkat ekspresi gen-gen yang berhubungan dengan apoptosis. Penelitian-penelitian yang dilakukan ini mengarah pada pencarian senyawa baru yang dapat digunakan sebagai lead compound untuk mendapatkan obat antikanker yang efektif.Limonoid Compounds from Genus Chisocheton Plant and Its Anticancer Activity. Indonesia is a country with a large biodiversity. There are many plants contain secondary metabolite compounds with biological activity, such as Chisocheton genus. The Chisocheton is reported as plant with triterpenoids, sesquiterpenoids, limonoids, steroids and phenols content. Limonoids arethe derivative of triterpenoid which mostly found in Chisocheton genus. More than thirty limonoids have been studied for their anticancer activity against several types of human cancer cells, such as breast, mouth, lung, leukemia, cervical, and liver cancer cells. Some of these limonoids are known to have high cytotoxic activity with the IC50 values of 1.67 − 50.27 µg/mL. This review discuss many kind of limonoid compounds isolated from Chisocheton, their cytotoxic activity against human cancer cells, and their structural activity relationship (SAR) study. This review also discusses some research result for further studies of Chisocheton wether in the mechanism of apoptosis induction and also the determination genes level expression or proteins associated with the apoptosis. This review reveals the important of the study to find a new compounds for an effective anticancer drug.
Co-Authors Aathirah, A Sayyidatina Abu Bakar M.I. Syihab Ade Rizki Ridwan Firdaus Aga Adi Masyhuri Agus Safari Al Arofatus Naini Albayyinah, Dyandra Hera Amalia, Riezki Anni Anggraeni, Anni Annisa Ilma Naviardianti Ari Hardianto Arum Kurnia Sari Bacthi Alisjahbana Bayu Shiddiq Widhi Pratama Dani Permana Darwati Darwati Desi Harneti Putri Huspa DESSY NATALIA Diana P Rahmawati Egista Istioka Fazrin Ekawardani, Savira Endang Srieatimah - Erina Hilmayanti Ersanda Hafiz Euis Julaeha Euis Julaeha Fajriyah, Maulida Ghina Nur Fadhilah Ghina Uli Felicia Tambunan Hafiz, Ersanda Hesti Lina Wiraswati Iman Permana Maksum Iqbal Wahyu Mustaqim Irkham Irkham KHOMAINI HASAN Kindi Farabi Korry Novitriani, Korry Lia Faridah LINAWATI HARDJITO Lubis, Rubianto A. M. Lutfi Firdaus Ma'ruf, Ilma Fauziah Masyhuri, Aga Adi Mohamad Nurul Azmi Muhammad Hilman Daniswara Muhammad Yudha Nugraha Muhammad Yusuf Murniaty Simorangkir Nayla Haraswati Nurlelasari Nurlelasari Nurmalasari, Ratna Nurul Auliany O Suprijana Oo Suprijana Permadi, Nandang Pertiwi, Wulan Purba Upay Purnama Purnama PUTRI, RAFIKA Putri, Rafika Nanda R. Ukun M.S. Soedjanaatmadja Rani Maharani Rima Melati Rini Surbakti Riza Apriani Riza Apriani Riza Apriani Rubianto A. Lubis Rudi Hartono Rustaman Rustaman Saadah D. Rachman Safri Ishmayana Safrl Ismayana Santhy Wyantuti Sari Syahruni SARONOM SILABAN Saronom Silaban Savira Ekawardhani Shabrinna, Hanif Soetijoso Soemitro Soetijoso Soemitro SOETIJOSO SOEMITRO Sofa Fajriah Sofyan Multazam N Aji Supriyadi, Isma Yustifania Sutarya Enus SUTARYA ENUS Syifa Al Fauziah Rahmani Tambunan, Ghina Uli Felicia Tati Herlina Tati Herlina Toto Subroto Tri Mayanti Triana N Meirina Umi Baroroh Unang Supratman Upay, Purba Vicki Nishinarizki Wulan Pertiwi Yeni W Hartati Yeni Wahyuni Hartati Yenni Wahyuni Hartati, Yenni Wahyuni Yohan Yohan Yohan Yohan Yoshihito Shiono