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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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The Stability Study of Electrochemical Aptasensor to Detect SARS-CoV-2 Spike Protein and Its Application for Clinical Samples of Nasopharyngeal Swab Arum Kurnia Sari; Ghina Nur Fadhilah; Irkham Irkham; Muhammad Yusuf; Shabarni Gaffar; Yeni Wahyuni Hartati
Indonesian Journal of Chemistry Vol 23, No 2 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.77887

Abstract

The stability characteristics associated with the shelf life of a biosensor are rarely investigated, however, they are important factors for real applications. Stability is the variation in the detection signal over a long period of storage. This study aims to determine the effect of storage time on the stability of SARS-CoV-2 receptor binding domain (RBD) spike protein aptamers related to shelf life and the performance of an electrochemical aptasensor on clinical samples. The research method includes a stability study conducted using the accelerated stability method based on the Arrhenius equation at three variations of temperature and storage time. The electrochemical aptasensor's performance was evaluated on clinical samples of 32 nasopharyngeal swabs at biosafety level 3 and its potential on clinical saliva samples. The results indicated that the developed electrochemical aptasensor was stable for ± 15 days with a shelf life of 18, 17 and 16 days, respectively, at 25, 40 and 50 °C. This electrochemical aptasensor has the potential to be a Point of Care (POC) device for the clinical detection of SARS-CoV-2 because it can be tested on clinical samples of nasopharyngeal swabs and the results show its potential application to detect in clinical saliva samples.
Modifikasi Screen Printed Carbon Electrode Menggunakan Cerium dan Optimasi Kondisi Percobaan Biosensor Elektrokimia untuk Deteksi DNA Mitokondria Sus Scrofa Fajriyah, Maulida; Hartati, Yenni Wahyuni; Anggraeni, Anni; Gaffar, Shabarni
JC-T (Journal Cis-Trans): Jurnal Kimia dan Terapannya Vol 6, No 1 (2022)
Publisher : State University of Malang or Universitas Negeri Malang (UM)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (314.918 KB) | DOI: 10.17977/um0260v6i12022p032

Abstract

Penggunaan cerium dalam aplikasi sensor telah banyak dikembangkan. Dalam penelitian ini, biosensor elektrokimia telah dikembangkan untuk mendeteksi DNA mitokondria Sus scrofa menggunakan screen printed carbon elektrode-cerium (SPCE-Ce). Permukaan elektrode SPCE sebelum dan sesudah dimodifikasi dengan cerium dikarakterisasi menggunakan Scanning Electron Microscopy (SEM) dan voltammetri siklik (CV). Desain urutan nukleotida babi sebagai DNA probe, ditentukan dengan menggunakan program NCBI blast dan T-Coffee. DNA probe diamobilisasikan pada SPCE-Ce melalui interaksi elektrostatik antara permukaan cerium dengan tulang punggung fosfat dari DNA. Selanjutnya proses hibridisasi DNA probe - target dikarakterisasi menggunakan voltammetri diferensiasi pulsa (DPV). Permukaan SPCE dan SPCE-Ce secara SEM menunjukkan perbedaan morfologi yaitu permukaan yang lebih halus dan rata setelah permukaan karbon tertutupi cerium. Voltammogram siklik menunjukkan adanya kenaikan puncak arus redoks dari spesi elektroaktif ferisianida pada SPCE-Ce. Urutan DNA probe adalah 5’-TATTIATACCAATCACTAIC-3’ yang memiliki homologi 100% dengan DNA babi dan homologi 0% dengan DNA ayam dan sapi. Persamaan linier konsentrasi target terhadap arus menghasilkan persamaan I = 0,0303 [target] + 3,947 untuk rentang konsentrasi DNA target 5,0 sampai 30,0 µg/mL, dan nilai LoD adalah 1,44 µg/mL. Biosensor ini selanjutnya dapat digunakan untuk penentuan konsentrasi mtDNA babi dalam sampel.
Dysobinol Extracted from Chisocheton Macrophyllus Triggers Proliferation Inhibition, Potential Apoptosis, and Cell Cycle Arrest of He La Cancer Cell Lines Gaffar, Shabarni; Hafiz, Ersanda; Wiraswati, Hesti Lina; Ishmayana, Safri; Nurlelasari, Nurlelasari
Majalah Kedokteran Bandung Vol 56, No 1 (2024)
Publisher : Faculty of Medicine, Universitas Padjadjaran

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15395/mkb.v56.3249

Abstract

Dysobinol is a new limonoid from C. macrophyllus seeds reported to have an anticancer activity. This study aimed to determine the cytotoxic activity of Dysobinol against HeLa cancer cell lines and evaluate its mechanism of action by determining the expression level of several carcinogenesis genes related to apoptosis and cell cycle. In this experimental study, the cytotoxic activity was determined using the MTS assay and gene expression by real-time reverse transcriptase PCR. The result shows that Dysobinol has an anticancer activity in a dose and time-dependent manner against HeLa cells and was categorized as toxic with IC50 values of 52.92, 52.70, and 14.96 μg/ml for 24, 48, and 72 hours, respectively. Dysobinol significantly increased the expression of Bax, Cas-8, and Cas-3 and decreased the expression of Cyc D1 at both doses (IC50 and 2x IC50) but only high doses (2x IC50) could affect Cas9 and NF-κB expressions, indicating that Dysobinol can induce apoptosis via the extrinsic pathway and inhibits the cell cycle through the Cyc D1 regulator. Dysobinol has the potential to be developed as a chemotherapy drug or an adjuvant agent for cervical cancer treatment.
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.
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 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