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All Journal Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences Bioscience El-Hayah : Jurnal Biologi Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati Biosfer: Jurnal Tadris Biologi Biogenesis: Jurnal Ilmiah Biologi Prosiding Seminar Biologi Jurnal Florea Al-Kimia Jurnal BIOEDUIN : Program Studi Pendidikan Biologi Jurnal Penelitian dan Pengkajian Ilmu Pendidikan: e-Saintika Jurnal Jejaring Matematika dan Sains JSMARTech : Journal of Smart Bioprospecting and Technology Spizaetus: Jurnal Biologi dan Pendidikan Biologi Jurnal Ilmiah Medicamento Jurnal Biosense Jurnal Farmasi Tinctura Jurnal Penelitian Sains dan Pendidikan (JPSP) As-Sidanah : Jurnal Pengabdian Masyarakat Medical Sains : Jurnal Ilmiah Kefarmasian Jurnal Sylva Lestari Makara Journal of Science Journal of Life Science and Technology Jurnal Farmasi Ma Chung: Sains, Teknologi, dan Klinis Komunitas Medical Sains : Jurnal Ilmiah Kefarmasian Alamtana

Sari, Dewi Ratih Tirto

Unknown Affiliation

Author-ID : 1137081

Religion Agriculture, Biological Sciences & Forestry Humanities Biochemistry, Genetics & Molecular Biology Chemistry Computer Science & IT Decision Sciences, Operations Research & Management Earth & Planetary Sciences Economics, Econometrics & Finance Education Energy Environmental Science Health Professions Immunology & microbiology Languange, Linguistic, Communication & Media Materials Science & Nanotechnology Mathematics Medicine & Pharmacology Neuroscience Physics Public Health Social Sciences Other

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In Silico Insight the Prediction of Chlorogenic Acid in Coffee through Cyclooxygenase-2 (COX2) Interaction Yohanes Bare; Dewi Ratih Tirto Sari; Yoga Tribakti Rachmad; Gabriella Candrakirana Krisnamurti; Agustina Elizabeth; Andri Maulidi
Biogenesis: Jurnal Ilmiah Biologi Vol 7 No 2 (2019)
Publisher : Department of Biology, Faculty of Sci and Tech, Universitas Islam Negeri Alauddin Makassar

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24252/bio.v7i2.9847

Inflammation was signs of pathological or abnormality in tissue to give an alert as a trouble signal to the system. Therapeutic using NSAIDs has some side effects. This research explored the potential role of chlorogenic acid as natural therapeutic compound to inhibit the inflammation target such as COX-2 by interaction model. The research method used in this study was the molecular docking approach, which binds ligand and protein. Protein data provided by Protein Data Bank (ID: 6cox) while, chlorogenic acid obtain from PubChem (CID: 1794427). We docked COX-2 and chlorogenic acid using Hex 8.0.0. Visualization and analysis of the molecular interactions of chlorogenic acid and COX-2 conducted by the Discovery Studio Client 4.1 software. Chlorogenic acid has a high permeability and is easily absorbed based on five Lipinski Rule. Interestingly, we found Fifteen amino acid was binding with chlorogenic acid that formed by hydrogen bond and van der Waals.The interaction between ligand-protein results in energy binding -327.59cal/mol. Chlorogenic acid has a potential role to inhibit inflammation pathway by inhibiting COX-2. We predicted chlorogenic acid has a potential as therapy anti-inflammatory to suppress COX-2 as mediator inflammation.

In silico study of columbin from Tinospora crispa L as dihydrofolate reductase-thymidylate synthase (DHFR-TS) inhibitor Yohanes Bare; Dewi Ratih Tirto Sari; Lydia Efliani Coriessa Meak; Marsiana Coo Mogi
Bioscience Vol 6, No 1 (2022): Biology
Publisher : UNIVERSITAS NEGERI PADANG

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/0202261116090-0-00

The Brotowali plant is used to treat malaria. Tinospora crispa L contains active compounds that are good for health and has been widely used for medicine. Crude extract from Tinospora crispa L can be used as target dihydrofolate reductase-thymidylate synthase (DHFR-TS). This research study was to analyse the potential chemical content of Tinospora crispa L in the form of columbine compounds as a focus of malaria therapy through inhibition of dihydrofolate reductase-thymidylate synthase (DHFR-TS). In silico research method, columbine (CID: 188289) ligand was obtained from Pubchem while DHFR-TS (PDB ID 2bl9) protein was obtained from Protein Data Bank, ligands and proteins were interacted using HEX 8.0.0.0 and visualised using discovery studio. The results obtained are six amino acid residues that bind to the DHFR-TS protein. This binding has an impact on the work function of the DHFR-TS protein. Physicochemical analysis shows that the ligand acts as a donor and acceptor so that the protein is formed and the ligand becomes very strong. This interaction is also supported by amino acid residues that act as supports by forming Van der Waals forces outside of the Van hydrogen bonding forces, pi-Alkyl and Pi also provide support in order to increase the strength and stabilisation of the. Based on the discussion, it can be concluded that the columbine content in Tinospora crispa L has potential as a therapy and treatment for malaria through inhibition of DHFR-TS.Tanaman Brotowali digunakan untuk mengobati penyakit malaria. Tinospora crispa L mengandung senyawa aktif yang baik untuk kesehatan dan telah banyak digunakan untuk pengobatan. Ekstrak kasar dari Tinospora crispa L dapat digunakan sebagai target dihydrofolate reductase-thymidylate synthase (DHFR-TS). Penelitian ini bertujuan untuk menganalisis potensi kandungan kimia Tinospora crispa L berupa senyawa kolumbin sebagai fokus terapi malaria melalui penghambatan dihydrofolate reductase-thymidylate synthase (DHFR-TS). Metode penelitian in silico diperoleh ligan kolumbin (CID: 188289) dari Pubchem sedangkan protein DHFR-TS (PDB ID 2bl9) diperoleh dari Protein Data Bank, ligan dan protein diinteraksikan menggunakan HEX 8.0.0.0 dan divisualisasikan menggunakan discovery studio. Hasil yang diperoleh adalah enam residu asam amino yang berikatan dengan protein DHFR-TS. Pengikatan ini berdampak pada fungsi kerja protein DHFR-TS. Analisis fisikokimia menunjukkan bahwa ligan berperan sebagai donor dan akseptor sehingga protein yang terbentuk dan ligan menjadi sangat kuat. Interaksi ini juga didukung oleh residu asam amino yang bertindak sebagai pendukung dengan membentuk gaya Van der Waals di luar gaya ikatan hidrogen Van, pi-Alkil dan Pi juga memberikan dukungan dalam rangka meningkatkan kekuatan dan stabilisasi. Berdasarkan pembahasan dapat disimpulkan bahwa kandungan kolumbin pada Tinospora crispa L berpotensi sebagai terapi dan pengobatan malaria melalui penghambatan DHFR-TS.

Prediction Potential Chlorogenic Acid As Inhibitor Ace (In Silico Study) Yohanes Bare; Dewi Ratih Tirto Sari; Yoga Tribakti Rachmad; Sri Sulistyaningsih Natalia Daeng Tiring; Apriani Herni Rophi; Fitra Arya Dwi Nugraha
Bioscience Vol 3, No 2 (2019): Biology
Publisher : UNIVERSITAS NEGERI PADANG

One of the derivatives of flavonoid explored is chlorogenic acid. Chlorogenic acid has antioxidant and anti-inflammatory activity. Hypertension has support for Angiotensin converting enzyme (ACE) which has a role in regulating the renin-angiotensin system. Hypertension therapy is carried out in inhibit ACE pathway. This study aims to analyze and assess the potential of chlorogenic acid as an anti-hypertensive material by inhibiting the work of ACE. The method used is in silico. Chlorogenic acid ligand was obtained from PubChem while ACE was obtained from RCSB. Interaction of ligand and protein using HEX 8.0.0. Analysis and visualization of the results of interactions using Discovery Study Version 4.1. The results showed an interaction between ligand and protein, namely interactions that occur between chlorogenic acid and sixteen amino acid residues. This interaction produces energy of -292.5cal / mol. This interaction approved the ACE block in the AT-I transformation towards AT-II. Chlorogenic acid has potential as an anti-hypertension material.

1-dehydrogingerdione, Senyawa volatil jahe sebagai agen sedatif subtitutif γ-aminobutyrate (GABA); Kajian biokomputasi Dewi Ratih Tirto Sari; Gabriella Chandrakirana Krisnamurti
Prosiding Seminar Biologi Vol 7 No 1 (2021): PROSIDING BIOLOGI ACHIEVING THE SUSTAINABLE DEVELOPMENT GOALS WITH BIODIVERSITY I
Publisher : Jurusan Biologi, Fakultas Sains dan Teknologi, Universitas Islam Negeri Alauddin Makassar

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24252/psb.v7i1.24709

Gamma aminobutyrate (GABA) merupakan molekul penting dalam sistem saraf pusat. Ekspresi GABA yang tinggi menyebabkan abnormalitas sel saraf dan mengakibatkan beberapa penyakit termasuk penyakit mental. Penelitian ini bertujuan untuk menganalisis potensi tiga senyawa volatil yang terkandung di dalam jahe sebagai penenang melalui kajian biokomutasi. Pendekatan in silico digunakan dalam penelitian ini. Struktur senyawa volatil jahe didapatkan dari database PubChem dan struktur protein diperoleh dari database Protein Data Bank. Senyawa jahe, GABA diinteraksikan dengan protein target aminobutyrate aminotransferase dengan program Molegro virtual Docker 5 dan dianalisis menggunakan Discovery Studio ver 21.1.1. Senyawa 6-paradol, 6- gingerdione, dan 1-dehydrogingerdione berinteraksi dengan aminobutyrate aminotransferase pada beberapa sisi aktif, residu Phe217 teridentifikasi pada ketiga interaksi dan menunjukkan energi ikatan lebih rendah dari interaksi GABA dengan protein target. Jenis ikatan antara senyawa volatil jahe dan protein aminobutyrate aminotransferase yaitu ikatan hidrogen dan interaksi hidrofobik. Penelitian ini disimpulkan bahwa senyawa 1-dehydrogingerdione merupakan inhibitor aminobutyrate aminotransferase yang paling baik dan menunjukkan ikatan yang lebih kuat dari kompleks GABA-aminobutyrate aminotransferase. Kajian in vitro dan in vivo perlu dilakukan untuk analisis lebih lanjut.

Senyawa Fucodiphlorethol Dan Phloroglucinol Alga Coklat Sebagai Inhibitor Lipase Secara In Silico Yohanes Bare; Dewi Ratih Tirto Sari; Marsiana Coo Mogi; Maria Marcelina Dua Nurak
Florea : Jurnal Biologi dan Pembelajarannya Vol 9, No 1 (2022)
Publisher : UNIVERSITAS PGRI MADIUN

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.25273/florea.v9i1.11743

Brown algae is a marine functional food that high fibers, vitamins, and bioactive compounds. Brown algae improved blood glucose and lipid profile. This study investigated the potential activity of two bioactive compounds from brown algae, as anti-obesity through pancreatic lipase inhibition. Molecular docking was conducted for investigating the lipase inhibition of bioactive compounds. Lipase structure (PDB ID 1ETH) was obtained from protein data bank and docked with fucodiphlorethol and phloroglucinol in specific position. Then, the complex was analyzed by PyMol following by Discovery Studio version 21.1.1. Phloroglucinol - pancreatic lipase showed five amino acid residues by hydrogen bonds, hydrophobic and electrostatic. Â Fucodiphlorethol - pancreatic lipase generated binding energy -392 kJ/mol and consisted of eight hydrogen bonds, three electrostatic, and 4 hydrophobic interactions. The active sites of fucodiphlorethol and phloroglucinol with lipase were not considered as active sites or catalytic sites. Therefore, we predicted that both of fucodiphlorethol and phloroglucinol inhibit lipase allosterically by altering the protein structure conformations. molecular docking analysis suggested that fucodiphlorethol and phloroglucinol have potential antiobesity effect by inhibiting lipase. Molecular dynamic are needed for further investigation.

KAJIAN IN SILICO 6-PARADOL SEBAGAI HERBAL ALTERNATIF PENGOBATAN PENYAKIT ALZHEIMER: IN SILICO REPURPOSING OF 6-PARADOL AS AN ALTERNATIVE HERBAL MEDICINE FOR ALZHEIMER DISEASE Yohanes Bare; Dewi Ratih Tirto Sari; Wa Ode Ujiana; Paula Yunita Seku Ra'o; Krisna Pada
Medical Sains : Jurnal Ilmiah Kefarmasian Vol 7 No 2 (2022)
Publisher : Sekolah Tinggi Farmasi Muhammadiyah Cirebon

Jahe mengandung beberapa senyawa volatil dan non-volatil yaitu 6-paradol yang memiliki manfaat kesehatan dan kinerja nutrisi dan antioksidan yang tinggi. Penelitian ini mengeksplorasi dan menyelidiki potensi senyawa bioaktif dari jahe sebagai anti-alzheimer. Aplikasi In silico dilakukan dalam penelitian, beberapa senyawa bioaktif disaring dan senyawa terpilih dari jahe digunakan 6-paradol (CID 94378), diperoleh struktur 3D dari Database PubChem. Choline acetyltransferase (PDB ID 2FY3) dipilih sebagai protein alzheimer dan berinteraksi dengan senyawa jahe. Kolin sebagai ligan asli untuk Choline acetyltransferase digunakan sebagai kontrol. Struktur tiga dimensi senyawa jahe dengan Choline acetyltransferase menunjukkan interaksi yang tepat, menunjukkan semua senyawa terpilih menurunkan aktivitas Choline acetyltransferase Menariknya, 6-paradol berinteraksi dengan Choline acetyltransferase di situs choline yang berarti menghambat interaksi kolin- Kolin asetiltransferase. Kesimpulan, senyawa 6-paradol memiliki aktivitas potensial untuk mengurangi Choline acetyltransferase Dinamika molekuler lebih lanjut, penelitian in vitro dan in vivo diperlukan

Virtual Screening: Prediksi potensi 8-shogaol terhadap c-Jun N-Terminal Kinase (JNK) Yohanes Bare; Mansur S; Sri Sulystyaningsih Natalia Daeng Tiring; Dewi Ratih Tirto Sari; Andri Maulidi
Jurnal Penelitian dan Pengkajian Ilmu Pendidikan: e-Saintika Vol. 4 No. 1: March 2020
Publisher : Lembaga Penelitian dan Pemberdayaan Masyarakat (LITPAM)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.36312/e-saintika.v4i1.157

JNK adalah gen yang berperan dalam metabolisme DMT2. Dalam pengobatan T2DM digunakan JNK sebagai potensi terapi dengan menggunakan bahan alam. 8-shogaol adalah komponen kimia yang terkandung dalam jahe yang memiliki aktivitas antioksidan. Tujuan dari penelitina ini adalah menginversitagasi dan menganalisis peran 8-shogaol terhadap JNK. Protein JNK (ID: 464Y) diperoleh dari Protein Data Bank dan ligan 8-shogaol (CID:6442560 ) didapat dari pubchem. Ligan dan protein didocking menggunakan Hex 8.0.0. File dalam bentuk pdb divisualtisasi dan analisis menggunakan Discovery Studio Client 4.1 software. Interaksi ligan-protein menunjukan ikatan hidrogen pada residu asam amino LYS93 dan van der Waals pada 18 residu asam amino dengan energi ikatan-289.68cal/mol. Interkasi ini berpotensi sebagai penghambat kerja JNK dan dapat digunakan dalam terapi DMT2.Virtual screening: potential prediction of 8-shogaol againts c-Jun N-Terminal Kinase (JNK)AbstractJNK is one of gene that has a role in T2DM condition. To curve T2DM use JNK as potential healing using natural compounds. Eight-shogaol which found in ginger has function as a antioxidant.. The aim of the research is to investigate and analyze role 8-shogaol againts JNK. Protein JNK (ID: 464Y) was taken from Protein Data Bank and ligand 8-shogaol (CID:6442560 ) acquired from pubchem. Ligand and protein model were docked using Hex 8.0.0 software. Visualization and analysis molecular interactions by the Discovery Studio Client 4.1 software. Interaction ligand-protein showed one hydrogen bond in amino acid residue LYS93 and formed van der Waals in eighteen amino acid residues which energy binding -289.68cal/mol. This interaction has a potential to inhibit JNK role and lead to therapy T2DM.

PENGEMBANGAN LEMBAR KERJA MAHASISWA (LKM) BERBASIS INKUIRI PADA MATERI INTERAKSI MOLEKULER Yohanes Bare; Dewi Ratih Tirto Sari
Jurnal BIOEDUIN : Program Studi Pendidikan Biologi Vol 11, No 1 (2021): Bioeduin Februari
Publisher : Department of Biology Education UIN Sunan Gunung Djati Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15575/bioeduin.v11i1.12077

KAJIAN SENYAWA HEXOSE DAN MALIC ACID SEBAGAI INHIBITOR PAPAIN LIKE PROTEASE (PLPro) CORONA VIRUS Yohanes Bare; Frederiksen Novenrius Sini Timba; Sukarman Hadi Jaya Putra; M A Yohanita Nirmalasari; Dewi Ratih Tirto Sari; Maximus M Taek
JURNAL BIOSENSE Vol 5 No 01 (2022): Edisi Juni 2022
Publisher : Program Studi Biologi, Fakultas Matematika dan Ilmu Pengetahuan Alam, Universitas PGRI Banyuwangi, Jalan Ikan Tongkol No 01, Telp (0333) 421593, 428592 Banyuwangi 68416

Papain-like protease is a SARSCOV-2 protease that functions for ubiquitination in host cells. Caffeine compounds have been widely reported to have antioxidant, anti-inflammatory, antidiabetic, and antiobesity activities. However, hexose and malic acid compounds in coffee rind as potential inhibitors of the papain-like protease SARSCOV2 have not been reported. This study investigated the potential of malic acid and hexose compounds as PLPro inhibitor agents in inhibiting SARSCOV2 ubiquitination. In silico studies were used to identify the potential of the two compounds by interacting hexose and malic acid compounds with papain-like protease (PLPro) proteins with the Molegro virtual Docker 5 program. Next, the ligand-protein complex visualization was done with discovery studio version 5.0. hexose and malic acid compounds showed interactions with papain-like protease proteins on several active site residues. The interactions showed inhibition of ubiquitination and stimulation of interferon in host cells. The two compound complexes – PLPro protein showed hydrophobic interactions, hydrogen bonds, and van der Waals forces, which contributed to the formation of bond energy and strong bonds between compounds and proteins. In this study, it was concluded that hexose and malic acid compounds have the potential to act as inhibitors of papain-like protease (PLPro) protein.

Modeling of Aqueous Root Extract Compounds of Ruellia tuberosa L. for Alpha-Glucosidase Inhibition Through in Silico Study Safitri, Anna; Sari, Dewi Ratih Tirto; Fatchiyah, Fatchiyah; Roosdiana, Anna
Makara Journal of Science Vol. 25, No. 1
Publisher : UI Scholars Hub

Show Abstract | Download Original | Original Source | Check in Google Scholar

This study aims to analyze the inhibitory activities of aqueous root extract compounds of Ruellia tuberosa L. toward alpha-glucosidase protein by computational docking analysis. Three major compounds contained in the extracts (i.e., betaine, daidzein, and hispidulin) were selected as ligands; quercetin and acarbose were used as the reference. Computational docking analysis was performed using the HEX 8.0.0 program and visualized using the Discovery Studio Visualizer v19.1.0.18287 (2019 version) on the basis of the scoring functions. The interactions between ligands and alpha-glucosidase protein showed different binding patterns. The types of bonds involved in the interaction between the enzyme and these ligands were hydrogen and hydrophobic bonds. Energy generated from docking of betaine, daidzein, hispidulin, quercetin, and acarbose to alpha-glucosidase protein were −167.6, −249.5, −251.2, −241.5, and −322.1 cal/mol, respectively. Acarbose had the lowest energy, indicating that it has the strongest interaction with alpha-glucosidase, followed by hispidulin, daidzein, quercetin, and betaine. Amino acid residues that interacted with the ligands were His717, Met363, Arg608, Pro361, Phe362, Leu865, Glu869, Arg594, andAsp356. The current research shows that R. tuberosa L. aqueous root extracts have the potential to be used as an inhibitor for the alpha-glucosidase protein and as an antidiabetic agent. Nonetheless, further studies are needed to support this modeling study.

Co-Authors Afza, Hadfina Agustina Elizabeth Aini, Fadilatul Ana Maria Ulfa Andri Maulidi Andri Maulidi Angeliana Desimaris Nita Anna Roosdiana Apriani Herni Rophi Arofah, Siti Dina Mega Bare, Yohanes Cairns, James Robert Ketudat Catur Retnaningdyah Dadang Suherman Daeng Tiring, Sri Sulistyaningsih Natalia Devi Rahmawati, Devi Eliyawati Eliyawati Estri Laras Arumingtyas fatchiyah . Fitra Arya Dwi Nugraha Fitraya, Riyatul Frederiksen Novenrius Sini Timba Gabriella Candrakirana Krisnamurti Gabriella Chandrakirana Krisnamurti Handayani, Aisyah Heny Yusuf Ihwan Ihwan Indahsari, Lilin Ika Nur Krisna Pada Krisnamurti, Gabriella Candrakirana Krisnamurti, Gabriella Chandrakirana Kuki, Agustina Dua Lailaty, Intani Quarta Laily Sifaiyah Laily, Siti Lorenza, Margaretha Rika Wahyu Gabrella Luchman Hakim Lydia Efliani Coriessa Meak M A Yohanita Nirmalasari Mansur S Maria Marcelina Dua Nurak Maria Marcelina Dua Nurak Marsiana Coo Mogi Marsiana Coo Mogi Maximus M Taek Nanang Yunarto Nisa, Mujiatun Nita, Angeliana Desimaris Nur Dina Camelia Nurak, Maria Marcelina Dua Oktavius Yoseph Tuta Mago Pahirah, Pahirah Paula Yunita Seku Ra'o Pranoto, M. Eko Pratiwi, Maulidia Riska Raodatul Jannah Rosyidah, A'liyatur S, Mansur Safitri, Anna Sarifah, Lailatus Siti Zamilatul Azkiyah Sri Sulistyaningsih Natalia Daeng Tiring Sri Sulystyaningsih Natalia Daeng Tiring Taek, Maximus M Theopilus W Watuguly Udrika Lailatul Qodri Wa Ode Ujiana Yoga Tribakti Rachmad Yoga Tribakti Rachmad Yusuf, Heny

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