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Identifikasi Aktivitas Biologis, Prediksi Toksisitas, dan Molecular Docking Senyawa Jubanine dari Tanaman Bidara Arab sebagai Kandidat Antivirus SARS-CoV-2 Fakih, Taufik Muhammad; Putri, Nawang Wulan Rachmatillah Prastowo; Marillia, Viola; Ramadhan, Dwi Syah Fitra; Darusman, Fitrianti
Jurnal Riset Kimia Vol 13, No 1 (2022): March
Publisher : Universitas Andalas

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.25077/jrk.v13i1.437

Coronavirus disease (COVID-19) is a disease of the respiratory tract caused by the coronavirus (SARS-CoV-2). Jubanine A, jubanine B, jubanine C, jubanine G, and jubanine H compounds in the arabian bidara plant (Ziziphus spina-christi L.) are known to treat viral and bacterial infections. The purpose of this study was to test the affinity of the compounds jubanine A, jubanine B, jubanine C, jubanine G, and jubanine H in the arabian bidara plant to the non-structural protein 15 (Nsp15) receptor. This research was carried out by identifying the physicochemical properties of the test compounds using the swissADME server. After that, geometry optimization was performed using the Quantum ESPRESSO 6.6 software, then macromolecule preparation was accomplished using the BIOVIA Discovery Studio 2020 software. Furthermore, method validation and molecular docking simulations were demonstrated using MGLTools 1.5.6 software with AutoDock Tools 4.2. Then the analysis of the molecular docking results was carried out using the BIOVIA Discovery Studio 2020 software. Finally, the toxicity of the test compound was predicted using the Toxtree 3.1.0 software. Based on the results of free binding energy (âˆ†G), jubanine H has the best affinity among the other five compounds with the lowest binding energy value of âˆ’6.51 kcal/mol.

In Silico Activity Identification of Cyclo Peptide Alkaloids from Zizyphus Spina-Christi Species Against Sars-Cov-2 Main Protease Taufik Muhammad Fakih; Dwi Syah Fitra Ramadhan; Fitrianti Darusman
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

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.

Biological activity, molecular docking, and ADME predictions of amphibine analogues of Ziziphus spina-christi towards SARS-CoV-2 Mpro Taufik Muhammad Fakih; Dwi Syah Fitra Ramadhan; Fitrianti Darusman
Biogenesis: Jurnal Ilmiah Biologi Vol 9 No 1 (2021)
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.v9i1.21335

The main protease of the SARS-CoV-2 virus, SARS-CoV-2 Mpro, can be discovered as a promising target to treat the COVID-19 pandemic. The peptide-based inhibitors may present better options than small molecules to inhibit SARS-CoV-2 Mpro. Ziziphus spina-christi species reported have a peptide-based of alkaloids group, i.e., amphibine whose analogues can be identified the potential as an inhibitor of SARS-CoV-2 Mpro. The compound structure was drawn and optimized using semi-empirical AM-1 method using Quantum ESPRESSO v.6.6, while the biological activity using PASS. Prediction server and molecular docking simulation using MGLTools 1.5.6 with AutoDock 4.2 were performed. Afterward, the ADME profiles were predicted using the SWISS-ADME server. PASS server was predicting amphibine B-F and H showed potency both as antiviral and as a protease inhibitor. The molecular docking simulation of amphibine analogues showed lower binding energy than the native ligand. The binding energy of the native ligand was −7.69 Kcal/mol compared to the lowest binding energy of amphibine analogues was −10.10 Kcal/mol (amphibine-F). The ADME prediction showed that amphibine-F has the best bioavailability as an oral drug, amphibine-B, C, and D have good bioavailability, and amphibian-E and H have poor bioavailability. Concluded, amphibine B-F and H of amphibine analogues showed potency as COVID-19 treatment targeting SARS-CoV-2 Mpro.

Prediction of SARS-CoV-2 3C-like protease (3CLpro) crystal structure to provide COVID-19 inhibitor design through computational studies Taufik Muhammad Fakih; Dwi Syah Fitra Ramadhan
Biogenesis: Jurnal Ilmiah Biologi Vol 9 No 2 (2021)
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.v9i2.24520

Infectious diseases have lately become pandemic, posing a threat to global public health with the introduction of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), previously provisionally named 2019 novel coronavirus or 2019-nCoV). Technological advancements have increased the possibility of discovering natural inhibitor candidates capable of preventing and controlling COVID-19 infections. The SARS-CoV-2 3C-like protease (3CLpro) is critical for SARS-CoV-2 replication and is a prospective therapeutic target. This study aims to identify, evaluate, and explore the 3CLpro macromolecular structures from SARS-CoV and SARS-CoV-2, as well as their impact on angiotensin-converting enzyme 2 (ACE-2). The discovery of the two 3CLpro macromolecules revealed structural similarities in several regions. These findings were subsequently confirmed by performing protein-protein docking simulations to observe the interaction of 3CLpro with the active site ACE-2. With an ACE score of 701.41 kJ/mol, SARS-COV-2 3CLpro forms the strongest binding with ACE-2. As a result, the findings of this research can be used to guide the development of potential SARS-CoV-2 3CLpro inhibitors for the treatment of COVID-19 infectious diseases.

Identifikasi Aktivitas Biologis, Prediksi Toksisitas, dan Molecular Docking Senyawa Jubanine dari Tanaman Bidara Arab sebagai Kandidat Antivirus SARS-CoV-2 Taufik Muhammad Fakih; Nawang Wulan Rachmatillah Prastowo Putri; Viola Marillia; Dwi Syah Fitra Ramadhan; Fitrianti Darusman
Jurnal Riset Kimia Vol. 13 No. 1 (2022): March
Publisher : Universitas Andalas

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.25077/jrk.v13i1.437

Coronavirus disease (COVID-19) is a disease of the respiratory tract caused by the coronavirus (SARS-CoV-2). Jubanine A, jubanine B, jubanine C, jubanine G, and jubanine H compounds in the arabian bidara plant (Ziziphus spina-christi L.) are known to treat viral and bacterial infections. The purpose of this study was to test the affinity of the compounds jubanine A, jubanine B, jubanine C, jubanine G, and jubanine H in the arabian bidara plant to the non-structural protein 15 (Nsp15) receptor. This research was carried out by identifying the physicochemical properties of the test compounds using the swissADME server. After that, geometry optimization was performed using the Quantum ESPRESSO 6.6 software, then macromolecule preparation was accomplished using the BIOVIA Discovery Studio 2020 software. Furthermore, method validation and molecular docking simulations were demonstrated using MGLTools 1.5.6 software with AutoDock Tools 4.2. Then the analysis of the molecular docking results was carried out using the BIOVIA Discovery Studio 2020 software. Finally, the toxicity of the test compound was predicted using the Toxtree 3.1.0 software. Based on the results of free binding energy (âˆ†G), jubanine H has the best affinity among the other five compounds with the lowest binding energy value of âˆ’6.51 kcal/mol.

Simulasi Dinamika Molekuler Senyawa Asam Ferulat dan Turunannya dari Kulit Buah Nanas (Ananas comosus) sebagai Inhibitor Enzim Tirosinase Taufik Muhammad Fakih; Hilda Aprilia Wisnuwardhani; Mentari Luthfika Dewi; Dwi Syah Fitra Ramadhan; Aulia Fikri Hidayat; Robby Prayitno
Jurnal Sains Farmasi & Klinis Vol 8, No 2 (2021): J Sains Farm Klin 8(2), Agustus 2021
Publisher : Fakultas Farmasi Universitas Andalas

Enzim tirosinase merupakan enzim utama pada proses pembentukan pigmen melanin. Penghambatan aktivitas enzim tirosinase secara kompetitif maupun non-kompetitif menjadi kunci utama pengembangan agen pencerah kulit. Asam ferulat merupakan salah satu senyawa antioksidan yang kuat dan mampu melindungi kulit dari dampak buruk sinar UV yang menginduksi stress oksidatif. Penelitian ini bertujuan untuk mengidentifikasi interaksi molekuler antara senyawa asam ferulat dari kulit buah nanas (Ananas comosus) dan turunannya dengan enzim tirosinase menggunakan motode dinamika molekuler. Molekul senyawa uji dimodelkan menggunakan perangkat lunak Quantum ESPRESSO v.6.6. Model terbaik dipilih untuk dilakukan studi interaksi menggunakan perangkat lunak MGLTools 1.5.6 yang dilengkapi dengan AutoDock 4.2. Konformasi terbaik hasil penambatan molekuler kemudian dikonfirmasi stabilitasnya dengan simulasi dinamika molekuler menggunakan perangkat lunak Gromacs 2016.3. Berdasarkan hasil dari penambatan molekuler, senyawa asam iso-ferulat memiliki afinitas yang paling baik, yaitu dengan nilai energi bebas ikatan −25,06 kJ/mol dan memilki ikatan dengan logam seng (Zn) pada sisi aktif enzim tirosinase. Kemudian senyawa tersebut memiki stabilitas interaksi yang baik berdasarkan grafik RMSD, RMSF, Rg, SASA, RDF, dan H-Bond. Dengan demikian, senyawa asam iso-ferulat diprediksi dapat digunakan sebagai kandidat inhibitor kompetitif dan non-kompetitif enzim tirosinase

PELATIHAN PEMBUATAN PRODUK HERBAL INSTAN UNTUK PENINGKATAN POLA HIDUP SEHAT Nike Herpianti Lolok; Bai Athur Ridwan; Dwi Syahfitra Ramadhan; Wa Ode Yuliastri
Jurnal Abdimas Ilmiah Citra Bakti Vol 2 No 1 (2021)
Publisher : STKIP Citra Bakti

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.38048/jailcb.v2i1.185

Warisan budaya bangsa Indonesia yang masih digunakan hingga saat ini khususnya dalam pemeliharaan dan peningkatan kesehatan serta pencegahan dan pengobatan penyakit adalah penggunaan obat tradisional. Salah satu tanaman yang dapat dimanfaatkan adalah temulawak (Curcuma Xanthorrhiza) yang dapat diolah sebagai minuman instan dalam bentukserbuk yang mudah dan praktis dalam penyajiannya serta dapat memperpanjang umur simpan. Namun sebagian besar masyarakat belum pernah memperoleh pelatihan tentang pemanfaatan produk herbal untuk peningkatan pola hidup sehat. Untuk mengatasi masalah tersebut maka perlu dilakukan suatu kegiatan dengan tujuan untuk meningkatkan keterampilan masyarakat dalam memanfaatkan tanaman obat secara praktis dan mudah sebagai bagian dalam peningkatan hidup sehat. Kegiatan ini dilaksanakan di Desa Boro-Boro Lameuru Kecamatan Ranomeeto Barat Kabupaten Konawe Selatan, Sulawesi Tenggara dengan melibatkan masyarakat dengan menggunakan metode pelatihan dengan cara mendemonstrasikan pembuatan minuman instan. Hasil kegiatan pelatihan diperoleh produk herbal berbentuk serbuk temulawak berwarna kuning, aroma khas temulawak dan tekstur yang sedikit kasar dengan ukuran yang homogen serta masyarakat suka terhadap produk yang dihasilkan. Temulawak juga diketahui memiliki khasiat meningkatkan sistem imun, menyegarkan tubuh, memperlancar metabolisme, menyehatkan fungsi hati, menambah nafsu makan, sebagai imunomodulator, hepatoprotektor, dan dapat meningkatkan daya tahan dan stamina tubuh. Kegiatan ini dapat meningkatkan keterampilan masyakat dalam memanfaatkan bahan alam yang tersedia untuk meningkatkan kesehatan atau mencegah paparan dari penyakit terutama dimasa pandemi seperti saat ini.

Pengembangan Obat Baru dari Senyawa Curcumin, Genistein, Lactacystin, Phloretin, Quercetin sebagai Inhibitor RNA Polimerase MTB dengan Menggunakan Metode In Silico Akmal Syihabuddin; Taufik Muhammad Fakih; Dwi Syah Fitra Ramadhan
Bandung Conference Series: Pharmacy Vol. 2 No. 2 (2022): Bandung Conference Series: Pharmacy
Publisher : UNISBA Press

Abstract. The discovery and development of new drugs begins with detecting the target of action of the drug which is then continued with the discovery of compounds and prediction of performance based on their chemical structure using the in silico method. The purpose of this study was to determine whether curcumin, genistein, lactacystin, phloretin, and quercetin compounds have the potential to be developed into medicinal compounds that have activity as RNA polymerase inhibitors. The research method used was to determine the physicochemical properties of the test compounds, then predict pharmacological activity using the way2drug.com server, then prepare macromolecular structures using the BIOVIA Discovery Study Visualizer 2021 software. Then validate and simulate the docking method using MGL Tools 1.5.7 software. which is equipped with Autodock Tools 4.4. Then proceed with toxicity prediction using the PreAdmet server. The results obtained from this study are that the compound quercetin has the potential to be developed into a drug as an RNA polymerase inhibitor with a bond free energy value (ΔG) of -5.62 kcal/mol and an inhibition constant (Ki) of 76.40 M. This value is still higher than the natural ligand (rifampicin) with the value of free bond energy (ΔG) in the natural ligand of -10.33 kcal/mol and the value of the inhibition constant (Ki) of 26.63 nM. However, this value is good enough to bind to the receptor and this value has a fairly good inhibitory activity as an MTB RNA Polymerase inhibitor. Abstrak. Penemuan dan pengembangan obat baru dimulai dengan mendeteksi target kerja dari obat yang kemudian dialnjutkan dengan penemuan senyawa dan prediksi kinerja berdasarkan struktur kimianya menggunakan metode in silico. Tujuan dari penelitian ini yaitu untuk mengetahui apakah senyawa curcumin, genistein, lactacystin, phloretin, dan quercetin berpotensi untuk dikembangkan menjadi senyawa obat yang memliki aktivitas sebagai inhibitor RNA Polimerase. Metode penelitian yang dilakukan yaitu penentuan sifat fisikokimia senyawa uji, kemudian prediksi aktivitas farmakologi menggunakan server way2drug.com, selanjutnya dilakukan preparasi struktur makromolekul menggunakan perangkat lunak BIOVIA Discovery Studi Visualizer 2021. Kemudian dilakukan validasi dan simulasi metode docking menggunakan perangkat lunak MGL Tools 1.5.7 yang dilengkapi dengan Autodock Tools 4.4. Kemudian dilanjutkan dengan prediksi toksisitas menggunakan server PreAdmet. Hasil yang diperoleh dari penelitian ini yaitu senyawa quercetin memiliki potensi untuk dikembangkan menjadi obat sebagai inhibitor RNA Polimerase dengan nilai energi bebas ikatan (ΔG) sebesar -5.62 kcal/mol dan nilai konstanta inhibisi (Ki) sebesar 76.40 µM. Nilai tersebut masih lebih tinggi dibandingkan dengan ligan alami (rifampisin) dengan nilai energi bebas ikatan (ΔG) pada ligan alami sebesar -10.33 kcal/mol dan nilai konstanta inhibisi (Ki) sebesar 26,63 nM. Tetapi nilai tersebut sudah cukup baik untuk berikatan dengan reseptor dan nilai tersebut memiliki aktivitas penghambatan yang cukup baik sebagai inhibitor RNA Polimerase MTB.

Comparative analysis of the stability features of human alpha-defensins as candidates for the future COVID-19 therapy through molecular dynamics Taufik Muhammad Fakih; Dwi Syah Fitra Ramadhan; Arfan Arfan
Pharmaciana Vol 12, No 3 (2022): Pharmaciana
Publisher : Universitas Ahmad Dahlan

Coronavirus 19 (COVID-19) is still a global health issue to date, SARS-CoV-2 is a novel coronavirus that is responsible for this sickness. The receptor-binding domain of the SARS-CoV-2 virus associates with angiotensin-converting enzyme 2 (ACE-2) and allows the virus to enter human cells. Natural peptides such alpha-defensin are thought to attach to the SARS-CoV-2 RBD and prohibit it from engaging with ACE-2. Molecular dynamics simulations using a computational approach are utilized to understand the stability of six alpha-defensin macromolecules using the Gromacs 2016 software. The trajectories formed are then analyzed using VMD 1.9.4 and BIOVIA Discovery Studio 2020 software. Finally, the free energy is estimated using the MM/PBSA method. The alpha-defensins 2 macromolecules were found to have the best stability based on numerous study results (trajectory visualization, RMSD, RMSF, and free energy calculations). As a result, these macromolecules could be used to build new antiviral treatments for COVID-19 infectious disease candidates.

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

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.

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