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All Journal Pharmaciana: Jurnal Kefarmasian Biogenesis: Jurnal Ilmiah Biologi Jurnal Riset Kimia Jurnal Biodjati ALCHEMY Jurnal Penelitian Kimia JSFK (Jurnal Sains Farmasi & Klinis) Jurnal Mandala Pharmacon Indonesia Jurnal Abdimas Ilmiah Citra Bakti (JAICB) Jurnal Mandala Pengabdian Masyarakat Bandung Conference Series: Pharmacy FASKES : Jurnal Farmasi, Kesehatan, dan Sains Media Kesehatan Politeknik Kesehatan Makassar Jurnal Pharmacia Mandala Waluya Borneo Journal of Pharmacy Jurnal Sains dan Kesehatan
Dwi Syah Fitra Ramadhan
Department Of Pharmacy, Poltekkes Kemenkes Makassar, Indonesia
Agriculture, Biological Sciences & Forestry Arts Humanities Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Computer Science & IT Dentistry Earth & Planetary Sciences Energy Environmental Science Health Professions Immunology & microbiology Languange, Linguistic, Communication & Media Law, Crime, Criminology & Criminal Justice Materials Science & Nanotechnology Mathematics Medicine & Pharmacology Nursing Physics Public Health Social Sciences

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Studi Molecular Docking Senyawa Ircinianin Terhadap Reseptor Sodium-Glukose Co-Transporter 2 (SGLT-2) ramadhan, dwi syah fitra; Dewi, Ratnasari; Ibrahim, Ismail; Rachmawati Daswi, Dwi; Nurisyah, Nurisyah; Asyikin, Asyhari; Abdullah, Tajuddin
FASKES : Jurnal Farmasi, Kesehatan, dan Sains Vol. 2 No. 2 (2024): Bulan November 2024 Faskes : Jurnal Farmasi, Kesehatan, dan Sains
Publisher : Program Studi Farmasi

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.32665/faskes.v2i2.3514

Abstract

Latar Belakang: Sodium-glucose cotransporter 2 (SGLT-2) merupakan target potensial dalam pengobatan diabetes tipe 2, dengan inhibitor SGLT-2 yang bekerja menghambat reabsorpsi glukosa di ginjal. Penelitian ini bertujuan untuk mengevaluasi potensi ircinianin, senyawa alami yang diisolasi dari spons Ircinia sp., sebagai inhibitor SGLT-2 menggunakan pendekatan molecular docking. Tujuan: Penelitian ini bertujuan untuk menganalisis interaksi antara ircinianin dan protein SGLT-2 serta mengevaluasi potensi penghambatan ircinianin terhadap reseptor SGLT-2. Metode: Metode yang digunakan adalah molecular docking dengan perangkat lunak AutoDock4. Prosedur dilakukan dengan docking ligan pada situs aktif SGLT-2. Ligan didocking dengan 100 iterasi untuk memperoleh konformasi ikatan yang optimal. Interaksi dianalisis berdasarkan energi ikatan dan visualisasi dilakukan menggunakan Discovery Studio. Hasil: Ircinianin menunjukkan energi ikatan sebesar -10,76 kcal/mol, sedikit lebih tinggi dibandingkan native ligand (-11,46 kcal/mol). Ircinianin membentuk dua ikatan hidrogen dengan residu PHE:98 dan TRP:291. Kesimpulan dan Saran: Ircinianin memiliki potensi sebagai inhibitor SGLT-2, meskipun ikatan hidrogennya lebih sedikit dibandingkan ligan asli. Penelitian lebih lanjut diperlukan untuk mengeksplorasi potensi terapeutik ircinianin dalam pengobatan diabetes tipe 2.
Identifikasi Metabolit Bioaktif pada Asam Jawa (Tamarindus indica L.) menggunakan Komputasi Dinamika Molekuler untuk Penargetan HER-2 Kanker Payudara Ramadhan, Dwi Syah Fitra; Indraswari, Ni Luh Astri; Hakim, Supartina; Rusli, Rusli; Nurisyah, Nurisyah; Asikin, Asyhari; Fakih, Taufik Muhammad; Aksar, M
Jurnal Mandala Pharmacon Indonesia Vol. 10 No. 1 (2024): Jurnal Mandala Pharmacon Indonesia
Publisher : Program Studi Farmasi Universitas Mandala Waluya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.35311/jmpi.v10i1.520

Abstract

The HER-2 (Human EGF Receptor-2) receptor is a receptor known to be strongly correlated with carcinogenesis and a worse prognosis in breast cancer patients. One of the native Indonesian plants that has been reported to inhibit breast cancer growth is tamarind (Tamarindus indica L.) which is known to contain various active metabolites. However, until now, the molecular activity of each of these metabolites has not been known. and one of the highly accurate simulation methods commonly used is molecular dynamics simulation. This study aims to understand the binding stability of active metabolites in tamarind computationally using molecular dynamics. The simulation begins with the preparation of 3D structures of ligands and receptors. The ligand of active metabolite from tamarind tree was obtained from KnapSack natural compound database, and the 3D structure of HER-2 receptor was obtained from PDB site with code 3PP0 and resolution of 2.25 Å. Furthermore, molecular tethering was performed using Autodock4 software. A high-performance computer was used for molecular dynamics simulation with Gromacs 2016 software for 100 nanoseconds (ns). Afterwards, molecular affinity analysis was performed, including RMSD (Root Mean Square Deviation) and RMSF (Root Mean Square Fluctuation). The analysis results showed that of the 6 compounds found in tamarind plants, the orientin compound showed the most favorable molecular Tethering activity with a value of -8.41 Kcal/mol. Although still higher than the natural ligand, the value is close to the value of the natural ligand with a difference of 1.8 Kcal/mol, which is -10.21 Kcal/mol. Furthermore, orientin showed very similar stability to the native ligand, as observed from the RMSD and RMSF analysis. In conclusion, the compound orientin found in tamarind has the potential to be a lead compound for inhibiting HER-2 in breast cancer.
In Silico Activity Identification of Cyclo Peptide Alkaloids from Zizyphus Spina-Christi Species Against Sars-Cov-2 Main Protease Fakih, Taufik Muhammad; Ramadhan, Dwi Syah Fitra; Darusman, Fitrianti
Jurnal Biodjati Vol 6 No 1 (2021): May
Publisher : UIN Sunan Gunung Djati Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15575/biodjati.v6i1.10603

Abstract

The COVID-19 has spread worldwide and become an international pandemic. The promising target for drug discovery of COVID-19 was SARS-CoV-2 Main Protease (Mpro), that has been successfully crystallized along with its inhibitor. The discovery of peptide-based inhibitors may present better options than small molecules for inhibitor SARS-CoV-2 Mpro. Natural compounds have such a wide potential and still few explored, Zizyphus spina-christi is one of the medicinal plants that have many pharmacological activities and contains a peptide compound from alkaloids class, i.e. cyclopeptide alkaloids, that is interesting to explore as SARS-CoV-2 Mpro inhibitor. The compound structure was drawn and optimized using density functional theory 3-21G method. The protein chosen was the high resolution of SARS-CoV-2 MPro receptor (1.45 Å) with PDB ID: 6WNP, in complex with boceprevir. Molecular docking simulation was performed using Autodock4 with 100 numbers of GA run, the validation methods assessed by RMSD calculation. Furthermore, the prediction of pharmacological activity spectra was carried out using the PASS Prediction server. The results showed RMSD value was 1.98 Å, this docking method was valid. The binding energy of all compounds showed better results than the native ligand (Boceprevir). The in silico PASS prediction results indicated that all compounds showed antiviral activity. Some compounds showed protease inhibitory activity, i.e Ambiphibine-H, Franganine, and Mauritine-A, and the highest Pa (Predicted activity) value showed by Mauritine-A compounds. It can be concluded that the cyclopeptide compounds of Zizyphus spina-christi were indicated to have a potential as COVID-19 therapy targeting SARS-CoV-2 Mpro.
Studi In Silico Aktivitas Analog Senyawa Zizyphine dari Bidara Arab (Zizyphus spina-christi) sebagai Antivirus SARS-CoV-2 terhadap Reseptor 3CLpro Taufik Muhammad Fakih; Firda Aulia Jannati; Annisa Meilani; Dwi Syah Fitra Ramadhan; Fitrianti Darusman
ALCHEMY Jurnal Penelitian Kimia Vol 18, No 1 (2022): March
Publisher : UNIVERSITAS SEBELAS MARET (UNS)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20961/alchemy.18.1.52188.70-79

Abstract

COVID-19 merupakan penyakit yang penularannya human to human yang pertama kali ditemukan di China (Kota Wuhan). Tanaman bidara arab mengandung banyak metabolit sekunder yang bermanfaat, hasil fraksinasi dari buah bidara memiliki aktivitas sebagai antivirus yang signifikan terhadap virus herpes simpleks tipe 1. Tujuan penelitian ini adalah untuk mengetahui afinitas dan interaksi antara senyawa uji Zizyphine dengan reseptor 3CLpro secara in silico. Pada penelitian ini dilakukan identifikasi aktivitas biologis menggunakan PASS prediction dan sifat fisikokimia pada senyawa uji Zizyphine menggunakan webserver Swiss-ADME. Senyawa uji Zizyphine dioptimasi secara geometris menggunakan software Quantum ESPRESSO versi 6.6. Konformasi senyawa uji Zizyphine terbaik dilanjutkan ke tahap simulasi docking terhadap reseptor 3CLpro yang telah dipisahkan dengan ligan alaminya dan telah divalidasi menggunakan software MGL Tools versi 1.5.6 yang telah dilengkapi dengan Autodock Tools versi 4.2. Berdasarkan penelitian yang telah dilakukan dapat disimpulkan bahwa senyawa uji Zizyphine C memiliki afinitas yang lebih baik dibandingkan senyawa Zizyphine A, Zizyphine F, dan Zizyphine I dengan nilai energi bebas ikatan sebesar -9,32 kcal/mol dan konstanta inhibisi 146,89 nM, sehingga senyawa Zizyphine C berpotensi sebagai agen terapi COVID-19 yang bekerja terhadap reseptor 3CLpro. Selanjutnya dari hasil analisis aktivitas biologis, keseluruhan senyawa analog Zizyphine menunjukkan potensi sebagai antivirus. Akan tetapi dari prediksi ADME, senyawa-senyawa tersebut tidak menunjukkan profil yang baik sebagai obat oral.In Silico Study of Zizyphine Analog Compound Activity of Christ's Thorn Jujube (Zizyphus spina-christi) as SARS-CoV-2 Antivirus against 3CLpro Receptors. COVID-19 is a disease with human-to-human transmission that was first discovered in China (Wuhan City). The arabian bidara plant (Christ's Thorn Jujube) contains many useful secondary metabolites, fractionated from bidara fruit has significant antivirus activity against herpes simplex virus type 1. The purpose of this study was to determine the affinity and interaction between the Zizyphine test compound and the 3CLpro receptor through in silico. In this study, the identification of biological activity using PASS prediction and physicochemical properties of Zizyphine test compounds using the Swiss-ADME webserver. The Zizyphine test compound was optimized for geometry using Quantum ESPRESSO version 6.6 software. The conformation of the best Zizyphine test compound was continued to the docking simulation stage for the 3CLpro receptor which has been separated from its natural ligand and has been validated using MGL Tools version 1.5.6 with Autodock Tools version 4.2 software. Based on the results, it can be concluded that the test compound Zizyphine C has a better affinity than Zizyphine A, Zizyphine F, and Zizyphine I with a binding free energy value of -9.32 kcal/mol and inhibition constant of 146.89 nM. Therefore, the compound Zizyphine C has potential as a COVID-19 therapeutic agent that acts against the 3CLpro receptor. Furthermore, from the results of the analysis of biological activity, all Zizyphine analog compounds showed potential as antiviruses. However according to ADME predictions, these compounds did not show a good profile as oral drugs.
Co-Authors Abdullah, Tajuddin Akmal Syihabuddin Aksar, M Anggraeni, Ni Kadek Dwi Annisa Meilani Arfan Arfan Arisanty, Arisanty Asikin, Asyhari Asyikin, Asyhari Aulia Fikri Hidayat Bahar, Frida Bai Athur Ridwan Budi Prabowo Soewondo Citra Dewi Daryono H. Tjahjono Dewi Ratnasari Dewi, Mentari Luthfika Dewi, Mentari Luthfika Firda Aulia Jannati Fitrianti Darusman Hakim, Supartina Handayani, Rizky Dwi Hilda Aprilia, Hilda Indraswari, Ni Luh Astri Ismail Ibrahim Kamaliah, Naila Bintan Latifah, Siti Diwani Lolok, Nikeherpianti Marillia, Viola Muhammad Isrul Nawang Wulan Rachmatillah Prastowo Putri Nike Herpianti Lolok Nurisyah, Nurisyah Prayitno, Robby Putri, Eka Ruliyati Putri, Nawang Wulan Rachmatillah Prastowo R. Rusli Rachmawati Daswi, Dwi Ramadani, Suci Riski Vitasari Rizkita, Aden Dhana Robby Prayitno Rusli Rusli Taufik Muhammad Fakih Teti Sofia Yanti Trisnaputri, Dian Rahmaniar Viola Marillia Wa Ode Yuliastri Wisnuwardhani, Hilda Aprilia