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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

Abstract

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

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.
Simulasi Penambatan Molekuler Senyawa Kompleks Besi Terhadap Protein Hemofor sebagai Kandidat Fotosensitizer pada Terapi Fotodinamika Taufik Muhammad Fakih; Anggi Arumsari; Mentari Luthfika Dewi; Nurfadillah Hazar; Tanisa Maghfira Syarza
al Kimiya: Jurnal Ilmu Kimia dan Terapan Vol 8, No 1 (2021): al Kimiya: Jurnal Ilmu Kimia dan Terapan
Publisher : Department of Chemistry, Faculty of Science and Technology, UIN Sunan Gunung Djati Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15575/ak.v8i1.8502

Abstract

Resistensi antibiotika muncul sebagai polemik yang dapat mempengaruhi kesehatan manusia. Kemajuan teknologi membuka peluang dalam penemuan molekul senyawa baru yang mampu mencegah perkembangan mikroba patogen, seperti Pseudomonas aeruginosa yang resisten terhadap beberapa jenis antibiotika. Terapi fotodinamika dengan memanfaatkan penggunaan fotosensitizer yang berasal dari senyawa yang membentuk kompleks dengan besi merupakan salah satu pendekatan alternatif untuk mengatasi penyakit infeksi dengan risiko resistensi mikroba yang lebih rendah. Penelitian yang dilakukan secara in silico ini bertujuan untuk mengamati, mengeksplorasi, dan mengevaluasi mekanisme aksi berbasis struktural dari molekul senyawa yang membentuk kompleks dengan besi, yaitu besi-ftalosianina dan besi-salofen terhadap protein hemofor HasAp serta pengaruh molekularnya terhadap bagian situs aktif pengikatan dari protein hemofor HasR. Identifikasi interaksi molekuler dan afinitas antara molekul senyawa besi-ftalosianina dan besi-salofen terhadap protein hemofor HasAp dilakukan dengan simulasi ligan-protein docking mempergunakan software MGLTools 1.5.6 yang dilengkapi dengan AutoDock 4.2. Di samping itu, dilakukan juga simulasi protein-protein docking terhadap sistem kompleks ligan-protein untuk memastikan pengaruh molekularnya terhadap bagian situs aktif pengikatan dari protein hemofor HasR dengan mempergunakan software PatchDock. Berdasarkan simulasi ligan-protein docking diperoleh hasil bahwa senyawa besi-ftalosianina memiliki afinitas paling baik terhadap kedua protein hemofor HasAp, dengan nilai energi bebas pengikatan masing-masing sebesar −68,45 kJ/mol dan −65,23 kJ/mol. Menariknya, hasil simulasi protein-protein docking antara kompleks molekul senyawa besi-ftalosianina dan protein hemofor HasAp-besi-ftalosianina terhadap protein hemofor HasR memiliki nilai energi kontak atom yang positif sebesar 556,56 kJ/mol. Dari penelitian ini dapat diprediksikan bahwa perbedaan struktur molekul senyawa yang membentuk kompleks dengan besi mampu mempengaruhi mekanisme aksi berbasis structural terhadap protein hemofor target.
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

Abstract

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.
INTERAKSI MOLEKULER INHIBITOR DIPEPTIDYL PEPTIDASE-IV (DPP-IV) DARI PROTEIN SUSU KAMBING SECARA IN SILICO SEBAGAI KANDIDAT ANTIDIABETES Taufik Muhammad Fakih; Mentari Luthfika Dewi
Media Farmasi: Jurnal Ilmu Farmasi Vol 17, No 1: Maret 2020
Publisher : Universitas Ahmad Dahlan

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (315.784 KB) | DOI: 10.12928/mf.v17i1.16249

Abstract

Dipeptidyl peptidase-IV (DPP-IV) merupakan salah satu target dalam pengobatan diabetes tipe-2. Beberapa obat golongan gliptin yang tersedia secara komersial seperti sitagliptin, anagliptin, linagliptin, saxagliptin, dan alogliptin secara khusus digunakan sebagai inhibitor DPP-IV untuk pasien diabetes. Saat ini, penggunaan peptida pada protein susu kambing untuk mengobati diabetes telah dilaporkan dalam berbagai percobaan in vitro. Namun, pemahaman tentang interaksi molekuler penghambatan peptida tersebut terhadap DPP-IV masih kurang. Penelitian ini bertujuan untuk melakukan identifikasi, evaluasi, dan eksplorasi mengenai afinitas beberapa molekul peptida tersebut, yaitu MHQPPQPL, SPTVMFPPQSVL, VMFPPQSVL, INNQFLPYPY, dan AWPQYL terhadap makromolekul DPP-IV dengan menggunakan simulasi penambatan molekuler berbasis protein-peptida. Sekuensing peptida terlebih dahulu dilakukan pemodelan dengan menggunakan server PEP-FOLD. Konformasi terbaik dipilih untuk dilakukan studi interaksi terhadap makromolekul DPP-IV dengan menggunakan software HPEPDock. Identifikasi lebih lanjut dilakukan terhadap interaksi molekuler yang terbentuk dengan menggunakan software BIOVIA Discovery Studio 2020.  Berdasarkan hasil dari penambatan molekuler berbasis protein-peptida diperoleh bahwa molekul peptida INNQFLPYPY memiliki afinitas yang paling baik terhadap makromolekul DPP-IV, yaitu dengan nilai energi bebas ikatan 923,46 kJ/mol. Dengan demikian, peptida tersebut diprediksi dapat digunakan sebagai kandidat inhibitor DPP-IV.
Identifikasi Peptida Bioaktif dari Protein Kedelai sebagai Inhibitor Enzim α-glukosidase untuk Kandidat Antidiabetes Taufik Muhammad Fakih; Mentari Luthfika Dewi
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

Abstract

Diabetes mellitus is one of the endocrine metabolic disorders that has caused morbidity and mortality worldwide. Α-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 α-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 α-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 α-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 α-glucosidase enzyme, with a binding free energy value of −748.12 kJ/mol. Therefore, the bioactive peptide is predicted to be a suitable candidate for the α-glucosidase enzyme inhibitor.
Studi Interaksi Molekuler Aktivitas Antimikroba Peptida Bioaktif terhadap Staphylococcus aureus Secara In silico Taufik Muhammad Fakih; Mentari Luthfika Dewi
JURNAL FARMASI DAN ILMU KEFARMASIAN INDONESIA Vol. 7 No. 2 (2020): JURNAL FARMASI DAN ILMU KEFARMASIAN INDONESIA
Publisher : Universitas Airlangga

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/jfiki.v7i22020.93-99

Abstract

Pendahuluan: Lendir kulit ikan lele kuning (Pelteobagrus fulvidraco), mengandung peptida bioaktif dan banyak dimanfaatkan dalam pengobatan berbagai penyakit karena memiliki aktivitas biologis, diantaranya sebagai antimikroba. Beberapa peptida bioaktif tersebut, antara lain pelteobagrin, myxinidin, pleurocidin, dan pardaxin-P1 dan telah terbukti mampu menghambat Penicillin-Binding Protein 3 (PBP3) dari Staphylococcus aureus. Tujuan: Penelitian ini bertujuan untuk mengidentifikasi aktivitas antimikroba molekul peptida bioaktif secara in silico terhadap makromolekul Penicillin-Binding Protein 3 (PBP3) dari Staphylococcus aureus dan interaksi peptida bioaktif tersebut yang terlibat dalam mekanisme aksi antimikroba. Metode: Sekuensing peptida bioaktif terlebih dahulu dilakukan pemodelan ke dalam bentuk konformasi 3D menggunakan software PEP-FOLD. Konformasi terbaik hasil pemodelan dipilih untuk kemudian dilakukan studi penambatan molekuler terhadap makromolekul dari Staphylococcus aureus menggunakan software PatchDock. Interaksi molekuler yang terbentuk selanjutnya diidentifikasi lebih lanjut menggunakan software BIOVIA Discovery Studio 2020. Hasil: Berdasarkan hasil penambatan molekuler menunjukkan bahwa peptida bioaktif myxinidin memiliki afinitas paling baik dengan ACE score −2497,26 kJ/mol. Kesimpulan: Peptida bioaktif lendir kulit ikan lele kuning (Pelteobagrus fulvidraco) dapat dipertimbangkan sebagai kandidat antimikroba alami.
In silico Identification of Characteristics Spike Glycoprotein of SARS-CoV-2 in the Development Novel Candidates for COVID-19 Infectious Diseases Taufik Muhammad Fakih; Mentari Luthfika Dewi
Journal of Biomedicine and Translational Research Vol 6, No 2 (2020): Augusts 2020
Publisher : Faculty of Medicine, Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jbtr.v6i2.7590

Abstract

Background: The emergence of infectious diseases caused by SARS-CoV-2 has resulted in more than 90,000 infections and 3,000 deaths. The coronavirus spike glycoprotein encourages the entry of SARS-CoV-2 into cells and is the main target of antivirals. SARS-CoV-2 uses ACE2 to enter cells with an affinity similar to SARS-CoV, correlated with the efficient spread of SARS-CoV-2 among humans.Objective: In the research, identification, evaluation, and exploration of the structure of SARS-CoV and SARS-CoV-2 spike glycoprotein macromolecules and their effects on Angiotensin-Converting Enzyme 2 (ACE-2) using in silico studies.Methods: The spike glycoproteins of the two coronaviruses were prepared using the BIOVIA Discovery Studio 2020. Further identification of the three-dimensional structure and sequencing of the macromolecular spike glycoprotein structure using Chimera 1.14 and Notepad++. To ensure the affinity and molecular interactions between the SARS-CoV and SARS-CoV-2 spike glycoproteins against ACE-2 protein-protein docking simulations using PatchDock was accomplished. The results of the simulations were verified using the BIOVIA Discovery Studio 2020.Results: Based on the results of the identification of the macromolecular structure of the spike glycoprotein, it was found that there are some similarities in characteristics between SARS-CoV and SARS-CoV-2. Protein-protein docking simulations resulted that SARS-COV-2 spike glycoprotein has the strongest bond with ACE-2, with an ACE score of −1509.13 kJ/mol.Conclusion: Therefore, some information obtained from the results of this research can be used as a reference in the development of SARS-CoV-2 spike glycoprotein inhibitor candidates for the treatment of infectious diseases of COVID-19.
Pemodelan Molekuler Peptida Bioaktif Laut sebagai Antikoagulan Alami terhadap Enzim Sitokrom P450 (CYP) 2C9: Molecular Modelling of Marine Bioactive Peptides as Natural Anticoagulants against Cytochrome P450 (CYP) 2C9 Enzymes Taufik Muhammad Fakih; Mentari Luthfika Dewi
Jurnal Farmasi Galenika (Galenika Journal of Pharmacy) (e-Journal) Vol. 6 No. 2 (2020): (October 2020)
Publisher : Universitas Tadulako

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22487/j24428744.2020.v6.i2.15041

Abstract

Anticoagulants are very important for the treatment and prevention of thrombotic disorders. The use of conventional anticoagulants like heparin and warfarin can cause bleeding complications. To find safer anticoagulant therapy agents, the development of isolation of new anticoagulant compounds has shifted towards natural sources. Bioactive peptides can be considered a better alternative because of their therapeutic potential in the treatment of various diseases. Several peptide molecules have been shown to inhibit the cytochrome P450 (CYP) 2C9 enzyme as a natural anticoagulant, such as bioactive peptides produced by yellowfin sole (Limanda aspera) and bioactive peptides in blue mussel (Mytilus edulis). This study aims to identify and evaluate the interactions that occur between peptide molecules with the cytochrome P450 (CYP) 2C9 enzyme using protein-peptide docking methods. Bioactive peptide sequencing was modeled using the PEP-FOLD software. The best conformation was chosen for an interaction study against the macromolecule of cytochrome P450 (CYP) 2C9 enzyme using PatchDock software. Further observations were made of interactions formed using BIOVIA Discovery Studio 2020 software. Based on the results of protein-peptide docking, the yellowfin sole peptide molecule has a good affinity against the macromolecule of cytochrome P450 (CYP) 2C9 enzyme, with an ACE score of −2527.01 kJ / mol. Therefore, the bioactive peptide is predicted to be used as a candidate for the cytochrome P450 (CYP) 2C9 enzyme inhibitor.
STUDI IN SILICO MEKANISME AKSI SENYAWA FTALOSIANINA SEBAGAI KANDIDAT FOTOSENSITIZER DALAM TERAPI COVID-19 BERBASIS FOTODINAMIKA Taufik Muhammad Fakih; Nurfadillah Hazar; Mentari Luthfika Dewi; Tanisa Maghfira Syarza; Anggi Arumsari
Jurnal Ilmiah Farmasi Farmasyifa Vol 4, No 1 (2021)
Publisher : Universitas Islam Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29313/jiff.v4i1.6784

Abstract

Sindrom pernapasan akut parah coronavirus-2 (SARS-CoV-2) yang menyebabkan pandemi penyakit infeksi COVID-19 menggunakan protein spike untuk dapat berikatan dengan reseptor angiotensin-converting enzyme 2 (ACE2) dalam sel inang. Beberapa kandidat obat yang diprediksi dapat digunakan dalam terapi COVID-19 seperti, tegobuvir, sonidegib, siramesine, antrafenine, bemcentinib, itacitinib, dan ftalosianina secara farmakologis mampu menghambat penempelan SARS-CoV-2 pada reseptor ACE2. Akan tetapi menariknya terapi fotodinamika dengan memanfaatkan senyawa ftalosianina berlabel logam saat ini dapat menjadi pilihan alternatif untuk terapi COVID-19 karena lebih efektif dan spesifik terhadap target.Melalui penelitian ini akan dilakukan identifikasi, evaluasi, dan eksplorasi afinitas serta interaksi molekular yang mampu menggambarkan mekanisme aksi dari struktur senyawa turunan ftalosianina berlabel logam secara in silico. Simulasi penambatan molekular ligan-protein antara besi ftalosianina (Fe-Pc) dan galium ftalosianina (Ga-Pc) terhadap protein spike SARS-CoV-2 dilakukan dengan menggunakan perangkat lunak PatchDock. Berdasarkan simulasi penambatan molekular ligan-protein diperoleh hasil bahwa senyawa galium ftalosianina (Ga-Pc) memiliki afinitas yang lebih baik dibandingkan besi ftalosianina (Fe-Pc) terhadap protein spike SARS-CoV-2, dengan nilai masing-masing sebesar −2366,68 kJ/mol dan −2225,55 kJ/mol. Dari hasil tersebut dapat diprediksi perbedaan struktur molekul senyawa turunan ftalosianina berlabel logam terbukti mampu mempengaruhi mekanisme aksi terhadap protein target. Dengan demikian, hasil penelitian ini diharapkan dapat menjadi referensi dalam mendesain struktur senyawa turunan ftalosianina berlabel logam sebagai kandidat fotosensitizer dalam terapi fotodinamika untuk penyakit infeksi COVID-19.