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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 al-Kimiya Journal of Biomedicine and Translational Research The Journal of Pure and Applied Chemistry Research Jurnal Riset Kimia 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) JSFK (Jurnal Sains Farmasi & Klinis) Jurnal Inovasi Hasil Pengabdian Masyarakat (JIPEMAS) Journal of Tropical Pharmacy and Chemistry Molekul: Jurnal Ilmiah Kimia Jurnal Ilmiah Farmasi Farmasyifa Poltekita: Jurnal Pengabdian Masyarakat Pharmaceutical Sciences and Research (PSR) Makara Journal of Science Bandung Conference Series: Pharmacy Borneo Journal of Pharmacy
Taufik Muhammad Fakih
Department Of Pharmacy, Faculty Of Mathematics And Natural Sciences, Universitas Islam Bandung, Bandung, 40116|Universitas Islam Bandung|Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Earth & Planetary Sciences Education Energy Engineering Environmental Science Health Professions Immunology & microbiology Materials Science & Nanotechnology Medicine & Pharmacology Nursing Public Health Other

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Journal : Biogenesis: Jurnal Ilmiah Biologi

 1 
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

Abstract

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

Abstract

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

Abstract

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.
Co-Authors Adryan Fristiohady Akmal Syihabuddin Aldhiya Nurshafa Huwaida Alivia Dyanira Anggi Arumsari Annisa Fitriyani Suryana Annisa Meilani Annisa Meilani Arfan Arfan Arini Nabila Putri Aulia Fikri Hidayat Budi Prabowo Soewondo Dewi, Mentari Luthfika Dewi, Mentari Luthfika Diar Herawati Dina Mulyanti Dina Mulyanti Dwi Syah Fitra Ramadhan Eky Syahroni Faqih Radina Faqih Radina Farendina Suarantika Farendina Suarantika Firda Aulia Jannati Firliani Dwiputri Fitrianti Darusman Gina Fuji Nurfarida Gita Cahya Eka Darma Hilda Aprilia, Hilda Latifa Hana Silfadani Lina Jamilah Liza Dzulhijjah Marillia, Viola Mentari Luthfika Dewi Muhammad Fillah Nabila Shofura Mahardhika Nadhifah Mauludia Rinaldie Nandhy Agustian Luca Pratama Nawang Wulan Rachmatillah Prastowo Putri Nurfadillah Hazar Putri, Nawang Wulan Rachmatillah Prastowo Resty Imfyani Sofyan Ridwan Wijaya Rizki Nuzulfikri Rizki Nuzulfikri Robby Prayitno Robby Prayitno Robby Prayitno Rohayah Rohayah Salsabilla Wijaya Sani Ega Priani Sellygani Budi Vaelani Sintya Suherlan Siti Ainun Rohaniah Siti Hardianti Syahrizal Nazala Sylvie Kurniasih Tanisa Maghfira Syarza Teti Sofia Yanti Trully Nouval Larasati Viola Marillia