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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 : ALCHEMY Jurnal Penelitian Kimia

 1 
Identifikasi Mekanisme Molekuler Senyawa Ftalosianina sebagai Kandidat Photosensitizer pada Terapi Fotodinamika secara In Silico Taufik Muhammad Fakih; Anggi Arumsari; Mentari Luthfika Dewi; Nurfadillah Hazar; Tanisa Maghfira Syarza
ALCHEMY Jurnal Penelitian Kimia Vol 17, No 1 (2021): March
Publisher : UNIVERSITAS SEBELAS MARET (UNS)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20961/alchemy.17.1.41184.37-42

Abstract

Bakteri patogen seperti Pseudomonas aeruginosa membutuhkan zat besi untuk dapat mempertahankan kelangsungan hidupnya. HasAp merupakan suatu protein yang dihasilkan oleh bakteri patogen sebagai sumber zat besi tersebut. Protein HasAp selanjutnya akan berikatan dengan protein membran luar yaitu HasR untuk dapat meneruskan sinyal pada sel bakteri. Penyerapan zat besi pada bakteri patogen ini dapat menjadi strategi pengembangan metode terapi dalam mengendalikan dan mencegah penyakit infeksi yang disebabkan oleh bakteri patogen Pseudomonas aeruginosa, salah satunya dengan memanfaatkan ftalosianina sebagai photosensitizer pada terapi fotodinamika. Penelitian ini bertujuan untuk mengidentifikasi, mengevaluasi, dan mengeksplorasi mekanisme aksi senyawa ftalosianina terhadap protein HasAp, serta pengaruhnya pada bagian sisi aktif HasR dengan menggunakan studi in silico. Studi ligan-protein docking dilakukan dengan menggunakan perangkat lunak MGLTools 1.5.6 yang dilengkapi dengan AutoDock 4.2 untuk mengamati afinitas dan interaksi molekuler antara molekul senyawa Fe-ftalosianina (Fe-Pc) dan Ga-ftalosianina (Ga-Pc) terhadap makromolekul protein HasAp. Selanjutnya, studi protein-protein docking dilakukan terhadap sistem kompleks ligan-protein untuk mengamati pengaruhnya terhadap area pengikatan dari makromolekul protein HasR dengan menggunakan perangkat lunak PatchDock. Berdasarkan hasil ligan-protein docking, senyawa Fe-ftalosianina (Fe-Pc) memiliki afinitas paling baik terhadap kedua protein HasAp, yaitu dengan nilai masing-masing -68,45 kJ/mol dan -69,16 kJ/mol. Kemudian, hasil studi protein-protein docking antara kompleks senyawa Fe-ftalosianina (Fe-Pc) dan protein HasAp terhadap protein HasR memiliki nilai Atomic Contact Energy (ACE) positif, yaitu 556,56 kJ/mol. Perbedaan struktur molekul senyawa ftalosianina terbukti mampu mempengaruhi mekanisme aksi terhadap protein target, sehingga hasil studi ini dapat menjadi acuan dalam mendesain struktur senyawa ftalosianina sebagai kandidat photosensitizer dalam terapi fotodinamika.Identification of the Molecular Mechanism of Phthalocyanine Compounds as Photosensitizer Candidates in Photodynamic Therapy by In Silico. Pathogenic bacteria including Pseudomonas aeruginosa need iron elements to be able to maintain their survival. HasAp is a protein produced by pathogenic bacteria as a source of iron. The HasAp protein will then bind to the outer membrane protein, namely HasR, to be able to forward signals in bacterial cells. Absorption of iron in these pathogenic bacteria can be a strategy for developing therapeutic methods in controlling and preventing infectious diseases caused by pathogenic bacteria Pseudomonas aeruginosa, one of which is by using phthalocyanine as a photosensitizer in photodynamic therapy. This study aims to identify, evaluate, and explore the mechanism of action of phthalocyanine compounds against HasAp proteins, and their effects on the active site of HasR through in silico studies. Ligand-protein docking studies were performed using MGLTools 1.5.6 with AutoDock 4.2 to observe the affinity and molecular interactions between molecules of Fe-phthalocyanine (Fe-Pc) and Ga-phthalocyanine (Ga-Pc) against HasAp protein macromolecules. Furthermore, a protein-protein docking study of the ligand-protein complexes system was simulated to observe its effect on the binding area of the HasR protein macromolecules using PatchDock. Based on the ligand-protein docking results, Fe-phthalocyanine (Fe-Pc) compounds have the best affinity for both HasAp proteins, with a binding energy value of -68.45 kJ/mol and -69.16 kJ/mol, respectively. The protein-protein docking study results between the complex compound Fe-phthalocyanine (Fe-Pc) and HasAp protein against HasR protein have a positive Atomic Contact Energy (ACE) value, with an ACE value of 556.56 kJ/mol. Differences in the molecular structure of phthalocyanine compounds are proven to be able to influence the mechanism of action against the target protein. Therefore, the results of this study can be a reference in designing the structure of phthalocyanine compounds as photosensitizer candidates in photodynamic therapy.
Identifikasi Aktivitas Inhibitor Enzim Tirosinase Senyawa Turunan Flavonoid pada Kulit Buah Cokelat (Theobroma cacao L) secara In Silico Sani Ega Priani; Taufik Muhammad Fakih
ALCHEMY Jurnal Penelitian Kimia Vol 17, No 2 (2021): September
Publisher : UNIVERSITAS SEBELAS MARET (UNS)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20961/alchemy.17.2.45317.168-176

Abstract

Limbah kulit buah cokelat diketahui mengandung berbagai senyawa aktif, termasuk di antaranya adalah golongan flavonoid. Senyawa flavonoid diketahui berpotensi memiliki aktivitas inhibitor enzim tirosinase, suatu enzim yang menstimulasi proses pembentukan melanin. Penelitian ini bertujuan untuk mengevaluasi interaksi antara senyawa flavonoid dari kulit buah cokelat dengan enzim tirosinase menggunakan metode penambatan molekuler secara in silico. Pengujian dilakukan dengan beberapa tahapan yakni preparasi makromolekul enzim, pemodelan molekul senyawa uji, identifikasi sisi aktif molekul enzim, identifikasi dan evaluasi penambatan molekuler, serta simulasi dinamika molekuler senyawa uji dengan molekul enzim. Hasil simulasi penambatan molekuler antara molekul enzim dengan ligan alaminya yakni tirosin memberikan energi ikatan sebesar -4,91 kkal/mol. Senyawa flavonoid dari kulit buah cokelat yakni apigenin, epikatekin, katekin, kaemferol, kuersetin, dan kuersitrin  diketahui memiliki afinitas pada sisi aktif enzim tirosinase dengan energi ikatan berturut turut -6,14; -6,17; -6,01; -5,89; -6,13; -6,81 kkal/mol. Hasil simulasi dinamika molekuler menunjukkan kuersitrin memiliki stabilitas yang baik dengan nilai RMSD rata-rata dan nilai energi bebas ikatan MM/PBSA masing-masing sebesar ±1,73 Å dan -80,12 kJ/mol. Hasil penelitian menunjukkan bahwa senyawa turunan flavonoid tersebut mampu berikatan dengan sisi aktif enzim tirosinase dengan afinitas yang lebih baik dibandingkan dengan ligan alaminya diamati dari nilai energi ikatannya. Senyawa turunan flavonoid yang terkandung dalam kulit buah cokelat berpotensi menjadi inhibitor kompetitif dari enzim tirosinase.Identification of In Silico Tyrosinase Inhibitory Activity of Flavonoid Derivative Compounds in Cocoa Pod Husk (Theobroma cacao L.). Cocoa pod husk was known to contain several active compounds, such as flavonoids. Flavonoid compounds are known to potentially have inhibitory activity of the tyrosinase, the enzyme which stimulates melanin synthesis.This study was conducted to evaluate the molecular interaction between flavonoids from cocoa pod husk with tyrosinase enzyme using in silico molecular docking method. The study was carried out through several stages, including preparation of enzyme macromolecules, modeling the molecule of the test compound, identifying the active site of the enzyme molecule, identifying and evaluating molecular docking, and molecular dynamics simulations of the test compound with the enzyme molecule. Molecular docking simulation between the enzyme and its natural ligand (tyrosine) produces binding energy of -4.91 kcal/mol. Flavonoid compounds from cocoa pod husk, including apigenin, epicatechin, catechin, kaempferol, quercetin, dan quercitrin, have an affinity on the active site of the enzyme with binding energy were -6.14; -6.17; -6.01; -5.89; -6.13; -6.81 kcal/mol, respectively. Then the molecular dynamics simulation shows quercitrin has good stability interaction with the average RMSD value and the MM/PBSA binding-free energy values of ±1.73 Å and -80.12 kJ/mol, respectively. The results showed that flavonoids of cocoa pod husc extract have an affinity to the active site of the enzyme, with a stronger binding energy than the original ligand. The flavonoid compounds of cocoa pod husk potential as a competitive inhibitor of the tyrosinase enzyme.
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 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