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All Journal Jurnal Ilmiah Farmasi JURNAL KIMIA SAINS DAN APLIKASI Pharmaciana: Jurnal Kefarmasian Media Farmasi : Jurnal Ilmu Farmasi (Journal Of Pharmaceutical Science) Biogenesis: Jurnal Ilmiah Biologi Journal of Biomedicine and Translational Research The Journal of Pure and Applied Chemistry Research Jurnal Riset Kimia Global Medical and Health Communication Pharmacon JURNAL FARMASI DAN ILMU KEFARMASIAN INDONESIA Jurnal Farmasi Galenika (Galenika Journal of Pharmacy) Jurnal Biodjati ALCHEMY Jurnal Penelitian Kimia BIOEDUSCIENCE Majalah Farmasi dan Farmakologi (Trends in Pharmacy and Pharmaceutical Sciences) Pharmacology and Clinical Pharmacy Research JSFK (Jurnal Sains Farmasi & Klinis) Jurnal Inovasi Hasil Pengabdian Masyarakat (JIPEMAS) Molekul: Jurnal Ilmiah Kimia Jurnal Mandala Pharmacon Indonesia Jurnal Ilmiah Farmasi Farmasyifa Jurnal Ilmiah Farmako Bahari Poltekita: Jurnal Pengabdian Masyarakat Pharmaceutical Sciences and Research (PSR) Makara Journal of Science Bandung Conference Series: Pharmacy Borneo Journal of Pharmacy al Kimiya : Jurnal Ilmu Kimia dan Terapan Indonesian Journal of Chemical Science Journal of Tropical Pharmacy and Chemistry Jurnal Sains dan Kesehatan Jurnal Info Kesehatan

Taufik Muhammad Fakih

Universitas Islam Bandung

Author-ID : 1562230

Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Dentistry Earth & Planetary Sciences Education Energy Engineering Environmental Science Health Professions Immunology & microbiology Materials Science & Nanotechnology Medicine & Pharmacology Nursing Physics Public Health Other

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Identifikasi Peptida Bioaktif dari Protein Kedelai sebagai Inhibitor Enzim Î±-glukosidase untuk Kandidat Antidiabetes Fakih, Taufik Muhammad; Dewi, Mentari Luthfika
Pharmacon: Jurnal Farmasi Indonesia Vol 17, No 2 (2020)
Publisher : Universitas Muhammadiyah Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23917/pharmacon.v17i2.10635

Diabetes mellitus is one of the endocrine metabolic disorders that has caused morbidity and mortality worldwide. Î‘-glucosidase inhibitor which plays an important role in carbohydrate metabolism is needed to avoid postprandial hyperglycemia. A bioactive peptide derived from soy protein was chosen as an alternative treatment for diabetes because of its therapeutic potential. Several bioactive peptides have been shown to inhibit the Î±-glucosidase enzyme, such as the bioactive peptide LLPLPVLK, SWLRL, and WLRL. This study aims to identify and evaluate molecular interactions that occur between bioactive peptide molecules and Î±-glucosidase enzyme macromolecules using protein-peptide docking methods through in silico. Bioactive peptide sequencing was first modeled using the PEP-FOLD software. The best conformation was chosen for an interaction study of the Î±-glucosidase enzyme macromolecule using HPEPDock software. Further exploration was carried out on the molecular interactions formed using BIOVIA Discovery Studio 2020 software. Based on the results of molecular docking, the WLRL bioactive peptide has the best affinity against the Î±-glucosidase enzyme, with a binding free energy value of âˆ’748.12 kJ/mol. Therefore, the bioactive peptide is predicted to be a suitable candidate for the Î±-glucosidase enzyme inhibitor.

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.

The design of bioactive marine peptides as a HIV-1 protease inhibitor Taufik Muhammad Fakih; Mentari Luthfika Dewi
Jurnal Ilmiah Farmasi Vol. 17 No. 2 (2021): Jurnal Ilmiah Farmasi
Publisher : Universitas Islam Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20885/jif.vol17.iss2.art6

AbstractBackground: Human immunodeficiency virus/acquired immunodeficiency syndrome (HIV or AIDS) is a disease related to the human immune system. Given its important role in viral replication, HIV1 protease (HIV1 PR) becomes the major therapeutic target in the treatment of AIDS. In this case, we need a dynamic aspect of molecular interactions that can demonstrate the important role of conformational variability in the design of HIV1 PR inhibitors. There are several inhibitor candidates from marine organisms, such as the LLEYSL and LLEYSI bioactive peptides produced by oysters (Crassostrea gigas).Objective: Proteinpeptide docking method was used in silico to identify, evaluate, and explore the molecular interactions between bioactive peptide molecules and HIV-1 protease macromolecules.Methods: The sequencing of bioactive peptide molecules was modeled into 3D conformation using the PEPFOLD software. The best conformation was chosen for the study of molecular interactions against HIV1 protease macromolecules using the PatchDock software. The molecular interactions formed were further observed using the BIOVIA Discovery Studio 2020 software.Results: The results of this study indicated that the LLEYSL bioactive peptide had the best affinity with an ACE score of minus 1284.70 kJ per mol.Conclusion: Bioactive peptide molecule is predicted to be a candidate for HIV1 protease inhibitor.Keywords: AIDS, HIV1 protease, bioactive peptides, protein-peptide docking, in silico Intisari Latar belakang: Infeksi human immunodeficiencyvirus/acquired immunodeficiency syndrome (HIVor AIDS) adalah penyakit yang berkaitan dengan sistem kekebalan tubuh pada manusia. Mengingat perannya yang penting dalam replikasi virus, HIV1 protease (HIV1 PR) merupakan target terapi utama dalam pengobatan AIDS. Dalam hal ini, maka diperlukan aspek dinamis dari interaksi molekuler yang dapat menunjukkan peran penting dari variabilitas konformasi dalam desain inhibitor HIV-1 PR. Terdapat beberapa kandidat inhibitor yang berasal dari organisme laut, seperti peptida bioaktif LLEYSL dan LLEYSI yang dihasilkan oleh tiram (Crassostrea gigas). Tujuan: Metode penambatan molekuler berbasis protein-peptida dilakukan untuk mengdentifikasi, mengevaluasi, dan mengeksplorasi interaksi molekuler antara molekul peptida bioaktif dengan makromolekul HIV1 protease secara in silico.Metode: Sekuensing molekul peptida bioaktif terlebih dahulu dimodelkan menjadi konformasi 3D dengan menggunakan software PEPFOLD. Konformasi terbaik dipilih untuk kemudian dilakukan studi interaksi molekuler terhadap makromolekul HIV1 protease dengan menggunakan software PatchDock. Interaksi molekuler yang terbentuk diamati lebih lanjut dengan menggunakan software BIOVIA Discovery Studio 2020.Hasil: Hasil dari penelitian ini menunjukkan bahwa peptida bioaktif LLEYSL memiliki afinitaspaling baik dengan ACE score sebesar minus 1284,70 kJ per mol.Kesimpulan:Dengan demikian, molekul peptida bioaktif tersebut diprediksi dapat dijadikan sebagai kandidat inhibitor HIV1 protease.Kata kunci : AIDS, HIV1 protease, peptida bioaktif, penambatan molekuler berbasis protein-peptida, in silico.

Magainin as an Antiviral Peptide of SARS-CoV-2 Main Protease for Potential Inhibitor: An In Silico Approach Taufik Muhammad Fakih; Mentari Luthfika Dewi; Eky Syahroni
Biogenesis: Jurnal Ilmiah Biologi Vol 8 No 1 (2020)
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.v8i1.13871

The new coronavirus (SARS-CoV-2), which caused the global pandemic Coronavirus Disease-2019 (COVID-2019), has infected nearly 206 countries. There is still little information about molecular compounds that can inhibit the development of infections caused by this disease. It is crucial to discover competent natural inhibitor candidates, such as antiviral peptides, because they have a variety of biological activities and have evolved to target biochemical machinery from different pathogens or host cell structures. In silico studies will be carried out, including protein-peptide docking and protein-protein docking, to identify, evaluate, and explore the affinity and molecular interactions of the Magainin-1 and Magainin-2 peptide molecules derived from frog skin (Xenopus laevis) to the main protease macromolecule (Mpro) SARS-CoV-2, and its effect on the ACE-2 receptor (Angiotensin Converting Enzyme-2 Receptor). Protein-peptide docking simulations show that both peptide molecules have a good affinity for the active site area of the SARS-CoV-2 Mpro macromolecule. These results were then confirmed using protein-protein docking simulations to observe the ability of the peptide molecule in preventing attachment to the ACE-2 receptor surface area. In silico studies show that Magainin-2 has the best affinity, with a bond free energy value of −3054.53 kJ/mol. Then the protein-protein docking simulation provided by Magainin-2 prevented the attachment of ACE-2 receptors, with an ACE score of 1697.99 kJ/mol. Thus, through in silico research, the Magainin peptide molecule can be further investigated in the development of new antiviral peptides for the treatment of infectious diseases of COVID-19.

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.

The Discovery of Tyrosinase Enzyme Inhibitors Activity from Polyphenolic Compounds in Red Grape Seeds through In Silico Study Mentari Luthfika Dewi; Taufik Muhammad Fakih; Resty Imfyani Sofyan
The Journal of Pure and Applied Chemistry Research Vol 10, No 2 (2021): Edition May-August 2021
Publisher : Chemistry Department, The University of Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jpacr.2021.010.02.551

Tyrosinases are essential metal-containing enzymes in the biosynthesis of melanin, therefore responsible for pigmentation of the skin. The upregulation of tyrosinase enzyme activities leads to hyperpigmentation that will become a health problems and interfere psychosocially. Inhibition of tyrosinase enzyme activity, both competitive and non-competitive become widely developed for most anti hyperpigmentation agent. Natural antioxidants are one of the potential compounds for this purpose. Red grape seeds contain high levels of antioxidant compounds, such as procyanidin, prodelphinidin, and propelargonidin. In this research in silico studies, including molecular docking, molecular dynamics simulations, and toxicity predictions, were used to assess the activity of the three molecules of polyphenolic compounds on macromolecules of the tyrosinase enzyme. Molecular docking studies show that the compound propelargonidin has the highest affinity against the macromolecule of the tyrosinase enzyme, with a binding free energy value of −32.87 kJ/mol. These results were confirmed in molecular dynamics simulations that show strong interactions at the macromolecular active site of the tyrosinase enzyme. Toxicity prediction results show that the three polyphenolic compound molecules were classified in the High-Class Category, which shows that safety is not guaranteed, but is likely, not carcinogenic and nongenotoxic. Therefore, the compound propelargonidin is predicted to be able to interact strongly with the tyrosinase enzyme. The results in this research are useful for further study in the development of tyrosinase enzyme inhibitors.

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

Identification of the molecular mechanism of christinin compounds from Arabian bidara leaves (Ziziphus spina-christi L.) on microorganisms that cause female genital problems through computational approaches Fitrianti Darusman; Taufik Muhammad Fakih
Pharmaciana Vol 10, No 3 (2020): Pharmaciana
Publisher : Universitas Ahmad Dahlan

Arabian bidara leaves (Ziziphus spina-christi, L.) are known to have strong antimicrobial activity against microorganisms that cause infection in the female genital area, namely Staphylococcus aureus bacteria and Candida albicans fungi. They contain main secondary metabolites such as flavonoids, alkaloids, and saponins. Christinin is a saponin glycoside derivative compound which consists of four types, namely christinin-A, B, C, and D. The role of computational studies in the discovery of new drugs is crucial and interesting nowadays because it is relatively cheap, effective, fast, and precise with a reliable level of accuracy. This computational study result will later be used to confirm in vitro test results which are carried out using experimental microbiological testing methods in the laboratory. This study identified, evaluated, and explored the interactions between christinin-A, B, C, and D compounds with Penicillin Binding Protein (PBP) from Staphylococcus aureus and Dihydrofolate Reductase from the fungus Candida albicans using computational study were carried out using the molecular docking. The christinin-A, B, C, and D compounds were modeled into 3D conformation using GaussView 5.0.8 and Gaussian09 software. The best conformation was selected for molecular interaction studies on Penicillin Binding Protein (PBP) from Staphylococcus aureus bacteria and Dihydrofolate Reductase from Candida albicans using MGLTools 1.5.6 software with AutoDock 4.2. The molecular interactions that occurred were further observed using the BIOVIA Discovery Studio 2020 software. Based on the molecular docking results, the christinin-B compound had the highest affinity for Penicillin Binding Protein (PBP) from Staphylococcus aureus bacteria, with a binding-free energy value of âˆ’7.67 kcal/mol. Meanwhile, the christinin-A compound has the highest affinity for Dihydrofolate Reductase from the fungus Candida albicans, with a binding-free energy value of âˆ’8.38 kcal/mol. Thus, it is predicted that christinin compounds can be chosen as the main component in feminine hygiene preparations to maintain the female genital area's health.Â

Co-Authors Adryan Fristiohady Akmal Syihabuddin Aksar, M Aldhiya Nurshafa Huwaida Alivia Dyanira Anggi Arumsari Annisa Fitriyani Suryana Annisa Meilani Annisa Meilani Annisa Rahmah Furqaani Arfan Arfan Arini Nabila Putri Asikin, Asyhari Aulia Fikri Hidayat Az-zahra, Dhea Khairunnisa Budi P Soewondo Budiana, Wempi Candra Hermawan Choesrina, Ratu Dewi, Mentari Luthfika Dewi, Mentari Luthfika Diar Herawati Dina Mulyanti Dina Mulyanti Dwi Syah Fitra Ramadhan Eky Syahroni Fajarwati, Kania Faqih Radina Farendina Suarantika Firda Aulia Jannati Firliani Dwiputri Fitrianti Darusman Gina Fuji Nurfarida Gita Cahya Eka Darma Hakim, Supartina Hilda Aprilia, Hilda Indraswari, Ni Luh Astri Ismet Muchtar Nur Jilan Salsabila Auliya Putri Julia Hartati Latifa Hana Silfadani Lina Jamilah Liza Dzulhijjah Mardiana, Neng Dian Marillia, Viola Meike Rachmawati Mentari Luthfika Dewi Mentari Luthfika Dewi Meta Maulida Damayanti Muhammad Fillah Nabila Shofura Mahardhika Nadhifah Mauludia Rinaldie Nandhy Agustian Luca Pratama Nawang Wulan Rachmatillah Prastowo Putri Nurfadillah Hazar Nurisyah, Nurisyah Nuzulfikri, Rizki Prayitno, Robby Putri, Nawang Wulan Rachmatillah Prastowo R. Rusli Radina, Faqih Resty Imfyani Sofyan Ridwan Wijaya Rizki Nuzulfikri rizkita, aden Rizkita, Aden Dhana Robby Prayitno Robby Prayitno Rohayah Rohayah Rusli Rusli Salsabilla Wijaya Sani Ega Priani Sari, Ajeng Kartika Sellygani Budi Vaelani Siddiq, Tita Barriah Sintia Ayu Dewi Sintya Suherlan Siti Ainun Rohaniah Siti Hardianti Siti Nurlita Permana Soewondo, Budi Prabowo Sonia alivia putri Syahrizal Nazala Syahroni, Eky Sylvie Kurniasih Tanisa Maghfira Syarza Teti Sofia Yanti Trully Nouval Larasati Vinda Maharani Patricia Viola Marillia Vivi Amalia Dwi Pratiwi Wijaya, Salsabilla Wisnuwardhani, Hilda Aprilia

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