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All Journal Farmasains : Jurnal Farmasi dan Ilmu Kesehatan 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 MPI (Media Pharmaceutica Indonesiana) JURNAL FARMASI DAN ILMU KEFARMASIAN INDONESIA Jurnal Farmasi Galenika (Galenika Journal of Pharmacy) Jurnal Biodjati ALCHEMY Jurnal Penelitian Kimia BIOEDUSCIENCE JRST (Jurnal Riset Sains dan Teknologi) 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 Jurnal Riset Farmasi Pharmaceutical Sciences and Research (PSR) Makara Journal of Science Bandung Conference Series: Pharmacy Media Kesehatan Politeknik Kesehatan Makassar 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 Indonesian Journal of Jamu Jurnal Info Kesehatan Journal of Pharmascience
Taufik Muhammad Fakih
Prodi Farmasi, Fakultas Matematika Dan Ilmu Pengetahuan Alam, Universitas Islam Bandung
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Civil Engineering, Building, Construction & Architecture Computer Science & IT 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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Structure-Based Virtual Screening and Molecular Docking of Dual Inhibitors of Plasmodium Falciparum Prolyl-tRNA Synthetase Achsendo Yuniarta, Tegar; Arief, Imtiyaz Izdihar; Syabihah, Haura; Fakih, Taufik Muhammad
Farmasains : Jurnal Farmasi dan Ilmu Kesehatan Vol. 11 No. 1 (2026)
Publisher : Universitas Muhammadiyah Malang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22219/farmasains.v11i1.44203

Abstract

Malaria is a disease caused by Plasmodium parasites, which remains a global problem including in Indonesia. One of the main types of parasites that cause malaria is Plasmodium falciparum which currently shows a tendency to be resistant to artemisinin-based combination therapy (ACT). This highlights the need to discover of more effective new drugs. This study aims to discover new drug candidates capable of overcoming ACT resistance using a computational approach. The methods used include structure-based pharmacophore modeling using the Pharmit webserver, virtual screening using the ChemDiv database, molecule docking using AutoDock Vina, and evaluation of ADME parameters using the SwissADME webserver. The molecular target used was the prolyl-tRNA synthetase enzyme (PDB ID: 4YDQ) with halofuginone as the reference compound. The pharmacophore screening successfully identified 312 hit compounds. Molecular docking using AutoDock Vina showed that 164 compounds had better binding affinity than halofuginone. Evaluation of ADME parameters showed that 11 compounds met the pharmacokinetic and toxicity criteria. Among them, ChemDiv-1481-0030 compound showed a binding affinity value of -10.6 kcal/mol with an 80% similarity in residue interactions compared to halofuginone. These results show that ChemDiv-1481-0030 has potential as an antimalarial drug candidate that works through the mechanism of inhibiting the PfPRS enzyme.
Molecular Docking Analysis Of Phenolic and Flavonoid Compounds from Eichhornia Crassipes for Antidiabetic Activity Through Interaction with PPAR- γ (5Y2O) and A-Glucosidase (3TOP) Khoirunnisa Muslimawati; Taufik Muhammad Fakih; Nabila Hadiah Akbar; Aditya Maulana Perdana Putra; Nazhipah Isnani
Journal of Pharmascience Vol. 12 No. 2 (2025): Jurnal Pharmascience
Publisher : Universitas Lambung Mangkurat

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20527/jps.v12i2.23583

Abstract

Diabetes Mellitus Tipe 2 (DMT2), ditandai dengan resistensi insulin dan hiperglikemia. Penelitian ini mengevaluasi potensi 30 senyawa golongan fenolik dan flavonoid dari Eichhornia crassipes sebagai agen antidiabetes melalui studi in silico, meliputi uji toksisitas (ToxTree 3.1.0, ProTox 3), analisis ADME (SwissADME), dan molecular docking (AutoDock 4.2.6). Struktur ligan uji diperoleh dari PubChem, sedangkan reseptor PPAR-γ (PDB ID: 5Y2O) dan α-Glukosidase (PDB ID: 3TOP) diunduh dari RCSB Protein Data Bank. Sebelum docking, analisis toksisitas dan ADME dilakukan. Hasil docking menunjukkan Tricin (flavonoid) berinteraksi baik dengan kedua reseptor dan memiliki nilai energi Gibbs -7.53 kcal/mol untuk PPAR-γ dan -5.19 kcal/mol untuk α-Glukosidase, mendekati ligan asli Pioglitazone (-10.03 kcal/mol) dan Acarbose (-6.86 kcal/mol). Interaksi ligan-reseptor Tricin melibatkan ikatan hidrogen dan kontak hidrofobik dengan residu kunci (misalnya, ARG288 dan TYR pada PPAR- γ, residu GLN1561 dan GLN1372 pada α-Glukosidase), mencerminkan interaksi ligan asli. Prediksi toksisitas mengklasifikasikan Tricin sebagai senyawa dengan risiko toksisitas rendah (Cramer Rules Kelas I, Kroes TTC). Selanjutnya, evaluasi ADME menunjukkan bahwa Tricin memenuhi Lipinski's Rule of Five, yang mengindikasikan penyerapan dan bioavailabilitas oral yang baik. Secara keseluruhan, senyawa Tricin dari E. crassipes menunjukkan potensi signifikan sebagai kandidat agen antidiabetes melalui penghambatan PPAR-γ dan α-Glukosidase yang selanjutnya memerlukan validasi dnegan pengujian in vitro dan in vivo. Kata Kunci: Eichhornia crassipes, Molecular Docking, Antidiabetic, PPAR-γ, α-Glucosidase Type 2 Diabetes Mellitus (T2DM), is characterized by insulin resistance and persistent hyperglycemia. This study investigated the antidiabetic potential of 30 phenolic and flavonoid compounds derived from Eichhornia crassipes using in silico approaches, including toxicity assessments (ToxTree 3.1.0, ProTox 3), ADME analysis (SwissADME), and molecular docking (AutoDock 4.2.6). Ligand structures were retrieved from PubChem, while PPAR-γ (5Y2O) and α-Glucosidase (3TOP) receptors were obtained from the RCSB Protein Data Bank. Toxicity and ADME analyses were conducted prior to molecular docking, which employed the Genetic Algorithm with 50 conformations. Docking results revealed that Tricin (a flavonoid) exhibited strong interactions with both receptors, with Gibbs free energy values of -7.53 kcal/mol for PPAR-γ and -5.19 kcal/mol for α-Glucosidase. These values are comparable to those of the native ligands Pioglitazone (-10.03 kcal/mol) and Acarbose (-6.86 kcal/mol). Tricin formed hydrogen bonds and hydrophobic contacts with key active site residues including, ARG288 and TYR327 in PPAR-γ, GLN1561 and GLN1372 in α-Glucosidase), mirroring the interactions of the native ligands. Toxicity predictions classified Tricin as low risk (Class I Cramer Rules, Kroes TTC). Furthermore, ADME evaluation showed that Tricin (aglycone) is fully compliant with Lipinski's Rule of Five, suggesting favorable properties for oral absorption and bioavailability. In conclusion, Tricin from E. crassipes demonstrates significant potential as an antidiabetic candidate and warrants further in vitro and in vivo validation.
In silico Evaluation of Quercetin and Apigenin from Litsea angulata as Potential Dual Binders of DPP-4 and SUR1 Aulia Rhamadani Arfan; Nabila Hadiah Akbar; Taufik Muhammad Fakih; Tegar Asandra Ghifari; Sulthan Waliid Anggara Wisesa
Journal of Pharmascience Vol. 13 No. 1 (2026): Jurnal Pharmascience
Publisher : Universitas Lambung Mangkurat

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20527/jps.v13i1.24835

Abstract

Litsea angulata leaves have traditionally been used for diabetes management; however, the molecular mechanisms underlying their antidiabetic activity remain poorly understood. This study aimed to evaluate the interaction potential of two major flavonoids from L. angulata, quercetin and apigenin, against two protein targets associated with type 2 diabetes mellitus: dipeptidyl peptidase-4 (DPP-4, PDB ID: 1X70) and sulfonylurea receptor 1 (SUR1, PDB ID: 5YKG). Ligand structures were optimized using density functional theory at the B3LYP/6-31G level, followed by molecular docking simulations using AutoDock Vina. Sitagliptin and glibenclamide were used as reference ligands for DPP-4 and SUR1, respectively. The docking results showed that quercetin and apigenin exhibited moderate binding affinities toward DPP-4 (–8.0 and –7.5 kcal/mol), interacting with key residues including Arg125 and Tyr547. In contrast, both flavonoids demonstrated stronger predicted binding energies toward SUR1 (–9.1 and –9.0 kcal/mol) compared with glibenclamide (–8.8 kcal/mol), although the interactions occurred at residues different from the primary functional binding site. The protein–ligand interactions were mainly stabilized by π–π stacking and van der Waals interactions rather than strong hydrogen bonds. Additional in silico analysis indicated that both compounds possess favorable physicochemical and pharmacokinetic properties based on ADME prediction, while toxicity assessment suggested relatively acceptable safety profiles. These findings indicate that quercetin and apigenin may serve as promising flavonoid scaffolds for the development of antidiabetic agents targeting multiple proteins involved in glucose regulation. Further experimental studies are required to validate their pharmacological activity and clarify their mechanisms of action.
Molecular Docking Senyawa Kuersetin sebagai Kandidat Antikanker Paru terhadap Target EGFR Imtiyaz Izdihar Arief; Taufik Muhammad Fakih; Tegar Achsendo Yuniarta
Jurnal Riset Farmasi Volume 5, No. 2, Desember 2025, Jurnal Riset Farmasi (JRF)
Publisher : UPT Publikasi Ilmiah Unisba

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29313/jrf.v5i2.8275

Abstract

Abstract. Lung cancer remains the leading cause of cancer-related deaths worldwide. One promising therapeutic target in non-small cell lung cancer (NSCLC) is the Epidermal Growth Factor Receptor (EGFR). Quercetin, a flavonoid compound naturally found in various plants, is known for its potential anticancer activity. This study aimed to evaluate the potential of quercetin as an EGFR inhibitor using a molecular docking approach. The EGFR protein structure (PDB ID: 4I23) was obtained from the Protein Data Bank and prepared using BIOVIA Discovery Studio Visualizer. Docking validation was performed through redocking, resulting in an RMSD value of 1.012 Å, indicating a valid docking protocol. The docking results showed a binding affinity of –7.45 kcal/mol and an inhibition constant (Ki) of 3.46 µM. Quercetin formed hydrogen bonds with residues THR790, GLN791, MET793, and GLU762, as well as hydrophobic interactions with LEU718, ALA743, VAL726, LYS745, and LEU844. These findings indicate that quercetin exhibits favorable binding affinity and complex stability with EGFR, supporting its potential as a molecular inhibitor. This study provides a scientific basis for further development of quercetin as a natural anticancer agent. Abstrak. Kanker paru masih menjadi penyebab utama kematian akibat kanker secara global. Salah satu target terapi yang menjanjikan dalam kanker paru non-sel kecil (NSCLC) adalah Epidermal Growth Factor Receptor (EGFR). Kuersetin, senyawa flavonoid yang ditemukan secara alami dalam berbagai tanaman, diketahui memiliki aktivitas antikanker yang potensial. Penelitian ini bertujuan untuk mengevaluasi potensi kuersetin sebagai inhibitor EGFR melalui pendekatan molecular docking. Struktur protein EGFR (PDB ID: 4I23) diperoleh dari Protein Data Bank dan dipreparasi menggunakan BIOVIA Discovery Studio Visualizer. Validasi metode docking dilakukan melalui proses redocking, menghasilkan nilai RMSD sebesar 1,012 Å yang menunjukkan bahwa metode yang digunakan valid. Hasil docking menunjukkan nilai binding affinity sebesar –7,45 kcal/mol dan konstanta inhibisi (Ki) sebesar 3,46 µM. Kuersetin membentuk ikatan hidrogen dengan residu THR790, GLN791, MET793, dan GLU762, serta interaksi hidrofobik dengan LEU718, ALA743, VAL726, LYS745, dan LEU844. Temuan ini menunjukkan bahwa kuersetin memiliki afinitas pengikatan dan stabilitas kompleks yang baik terhadap EGFR, mendukung potensinya sebagai kandidat inhibitor molekuler. Penelitian ini memberikan dasar ilmiah untuk pengembangan lanjutan kuersetin sebagai agen antikanker berbasis bahan alam.
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.
Network Pharmacology-Guided Identification of Antiaging Targets of Lavandula Flower Bioactives Using LC–MS/MS and Molecular Simulation Approaches Syafnir, Livia; Fajarwati, Kania; Faizal, Ibnu Dharsono; Fakih, Taufik Muhammad
MPI (Media Pharmaceutica Indonesiana) Vol. 8 No. 1 (2026): JUNE
Publisher : Fakultas Farmasi, Universitas Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24123/mpi.v8i1.8597

Abstract

Lavandula flowers are widely used in cosmetic and dermatological formulations, yet the molecular basis of their antiaging activity remains incompletely understood. This study aimed to elucidate the antiaging potential of lavandula flower bioactives through LC–MS/MS-based metabolite profiling integrated with network pharmacology and molecular docking analysis. Metabolites were characterized using LC–MS/MS and annotated based on accurate mass and fragmentation patterns. Predicted targets of selected metabolites were obtained using in silico target prediction and intersected with antiaging-related genes to construct protein–protein interaction networks and identify key regulatory pathways. Molecular docking was performed to evaluate binding affinity and interaction modes between prioritized metabolites against JAK2. LC–MS/MS analysis revealed a diverse chemical profile dominated by carveol (16.12%), methylumbelliferone (8.77%), camphor (3.97%), and two late-eluting high-molecular-weight metabolites contributing 29.86% and 35.36% of the total peak area. Network pharmacology highlighted convergence on kinase-driven signaling, extracellular matrix regulation, inflammatory response, and oxidative stress pathways relevant to skin aging. The docking results against JAK2 showed that the substituted pyridin-4-ol derivative exhibited the strongest affinity among Lavandula metabolites (ΔG = −8.81 kcal/mol), followed by the piperidinyl-substituted trienone (ΔG = −7.92 kcal/mol), while methylumbelliferone (ΔG = −5.93 kcal/ mol) and ferulic acid (ΔG = −5.53 kcal/mol) displayed moderate binding. Lavandula flower bioactives exhibit antiaging potential through multitarget modulation of signaling and matrix-associated proteins, supported by quantitative metabolite profiling and docking-validated target engagement.
Formulation and In Vitro Evaluation of Fig Leaf (Ficus carica L.) Ethyl Acetate Extract Transdermal Patch as a Candidate for Wound Healing Application Ratih Aryani; Safira Qamarani; Hanifa Rahma; Taufik Muhammad Fakih
Media Kesehatan Politeknik Kesehatan Makassar Vol 21 No 1 (2026): Media Kesehatan
Publisher : Direktorat Politeknik Kesehatan Makassar

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.32382/medkes.v21i1.2198

Abstract

Wound healing can be enhanced through both non-pharmacological and pharmacological approaches. Non-pharmacological methods include proper wound cleaning and dressing, while pharmacological strategies utilize antiseptics and synthetic antibiotics to prevent infection. Recently, natural compounds such as Ficus carica L. leaves, rich in flavonoids, have gained attention for their wound-healing potential. Flavonoids play a crucial role in accelerating wound contraction, enhancing collagen deposition, and promoting granulation tissue formation. This study aimed to formulate and evaluate a wound-healing patch incorporating the ethyl acetate extract of Ficus carica L. leaves, obtained via multistep maceration. The total flavonoid content (TFC) of the extract was 89.299 ± 0.14 mgQE/g. The patch was developed using the solvent casting method with HPMC K100M as the polymer matrix and propylene glycol as a plasticizer. The optimized formulation, containing 5.6% ethyl acetate extract (equivalent to 50 mg quercetin), met key evaluation criteria, exhibiting a uniform structure without wrinkling, a thickness of 1.0 ± 0.2 mm, a pH of 5, and a folding endurance of >200 cycles. In vitro permeation studies demonstrated effective active compound penetration, with a cumulative quercetin permeation of 21.76% within 180 minutes. The flux profile revealed an initial burst release followed by a transition toward controlled diffusion behavior, which is characteristic of HPMC-based monolithic matrices.
Molecular Docking and In Silico Evaluation of Beluntas (Pluchea indica) Phytochemicals as Potential Angiotensin-Converting Enzyme Inhibitors for Hypertension Treatment Achmad Ramadhanna’il Rasjava; Nabila Hadiah Akbar; Aulia Rhamdani Arfan; Dyah Ayu Pramoda Wardani; Aditya Maulana Perdana Putra; Khoirunnisa Muslimawati; Putri Helena Junjung Buih; Taufik Muhammad Fakih
Borneo Journal of Pharmacy Vol. 9 No. 1 (2026): Borneo Journal of Pharmacy
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33084/bjop.v9i1.9706

Abstract

Hypertension remains a major global health concern due to its high prevalence and strong association with cardiovascular diseases and kidney failure. A key component of blood pressure regulation is the Angiotensin-Converting Enzyme (ACE), which catalyzes the conversion of Angiotensin I into the vasoconstrictor Angiotensin II, making it a primary target for antihypertensive drugs. Although synthetic ACE inhibitors such as ramiprilat are effective, their use is often associated with adverse effects, highlighting the need for safer alternatives. This study employs molecular docking and in silico analysis to evaluate the potential of phytochemicals from beluntas (Pluchea indica) as natural ACE inhibitors. A total of 110 phytoconstituents were screened for pharmacokinetic properties using ADMET analysis, leading to the selection of 20 ligands for docking simulations. Among these, 4,5-di-O-caffeoylquinic acid exhibited the highest binding affinity (-9.409 kcal/mol), followed by di-O-caffeoylquinic acid (-8.984 kcal/mol) and quercetin-3-O-β-D-galactopyranoside (-8.372 kcal/mol). These compounds demonstrated stronger binding affinities than the ACE natural substrate, Angiotensin I (-7.133 kcal/mol), and the ACE inhibitor, ramiprilat (-8.717 kcal/mol), suggesting their potential as competitive ACE inhibitors. The binding interactions of these compounds were characterized by hydrogen bonding with key catalytic residues (HIS368, GLU368), electrostatic stabilization, and hydrophobic interactions within the enzyme active site. Notably, caffeoylquinic acid derivatives closely mimicked the binding mode of ramiprilat, whereas quercetin glycosides exhibited a distinct interaction pattern, indicating a possible alternative inhibitory mechanism. These findings provide evidence supporting the potential of P. indica phytochemicals as natural ACE inhibitors and warrant further investigation into their therapeutic applications in hypertension management.
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

Abstract

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.
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 Abriel shafar Faiza Achmad Ramadhanna’il Rasjava Achsendo Yuniarta, Tegar Adryan Fristiohady Aghnia Fuadatul Inayah Aisya Rahma Fatimah Akbar, Nabila Hadiah Akmal Syihabuddin Aksar, M Aldhiya Nurshafa Huwaida Alivia Dyanira Anggi Arumsari Annisa Fitriyani Suryana Annisa Meilani Annisa Meilani Annisa Rahmah Furqaani Arfan Arfan Arief, Imtiyaz Izdihar Arini Nabila Putri Asikin, Asyhari Aulia Fikri Hidayat Aulia Rhamadani Arfan Aulia Rhamdani Arfan Aura Lintang Ayu Cahyani Az-zahra, Dhea Khairunnisa Bambang Tri Laksono Bertha Rusdi Budi P Soewondo Budi Prabowo Soewondo Budiana, Wempi Buih, Putri Helena Junjung Candra Hermawan Choesrina, Ratu Dadang Juanda Dewi, Mentari Luthfika Dewi, Mentari Luthfika Diar Herawati Dina Mulyanti Dina Mulyanti Dita Anggun Novianta Dwi Syah Fitra Ramadhan Dyah Ayu Pramoda Wardani Eky Syahroni Engrid Juni Astuti Entris Sutrisno Erlin Julian Navisyah Faisal Anwar Faizal, Ibnu Dharsono Fajarwati, Kania Faqih Radina Farendina Suarantika Felia Rahma Cahya Andita Fetri Lestari Fetri Lestari Firda Aulia Jannati Firliani Dwiputri Fitrianti Darusman Galand Febrial Akbar Gina Fuji Nurfarida Gita Cahya Eka Darma Hakim, Supartina Hamdan Ramdani Hanifa Rahma Hilal Faturohman Hilda Aprilia, Hilda Ibnu Dharsono Faizal Imtiyaz Izdihar Arief Indraswari, Ni Luh Astri Ingka Mardiana Putri Ismet Muchtar Nur Ismi Relivtintaeni Jajang Japar Sodik Jilan Salsabila Auliya Putri Julia Hartati Khansha Putri Amaturrofy Khoirunnisa Muslimawati Khoirunnisa Muslimawati Latifa Hana Silfadani Lina Jamilah Liza Dzulhijjah Luthfi Maulana Firmasnyah M. Artabah Muchlisin Mardiana, Neng Dian Marillia, Viola Meike Rachmawati Mentari Luthfika Dewi Mentari Luthfika Dewi Meta Maulida Damayanti Muhamad Akbar Dirgana Muhamad Inzaghi Divi Wijaya Muhammad Algif Qolbun Salim Muhammad Fikri Hakiki Muhammad Fillah Nabila Hadiah Akbar Nabila Shofura Mahardhika Nadhifah Mauludia Rinaldie Nandhy Agustian Luca Pratama Nawang Wulan Rachmatillah Prastowo Putri Nazhipah Isnani Nisa Neli Aunillah Nisa Qotrunida Afwa Nur Islami Vikri Abdillah Nurfadillah Hazar Nurisyah, Nurisyah Nuzulfikri, Rizki Prayitno, Robby Putra, Aditya Maulana Perdana Putri, Nawang Wulan Rachmatillah Prastowo R. Rusli Radina, Faqih Ratih Aryani, Ratih Ratu Choesrina Resty Imfyani Sofyan Ridwan Wijaya RISA NURRAHWANI Rizki Nuzulfikri rizkita, aden Rizkita, Aden Dhana Robby Prayitno Robby Prayitno Rohayah Rohayah Rusli Rusli Safira Qamarani Salsabilla Wijaya Sani Ega Priani Sari, Ajeng Kartika Sellygani Budi Vaelani Sintia Ayu Dewi Sintya Suherlan Siti Ainun Rohaniah Siti Hardianti Siti Nurlita Permana Sonia alivia putri Sulthan Waliid Anggara Wisesa Syabihah, Haura Syafnir, Livia Syahrizal Nazala Syahroni, Eky Sylvie Kurniasih Tanisa Maghfira Syarza Tegar Achsendo Yuniarta Tegar Achsendo Yuniarta Tegar Achsendo Yuniarta Tegar Achsendo Yuniarta Tegar Asandra Ghifari Teti Sofia Yanti Thias Najminuri Tita Barriah Siddiq Trully Nouval Larasati Vinda Maharani Patricia Viola Marillia Vivi Amalia Dwi Pratiwi Wijaya, Salsabilla Wisnuwardhani, Hilda Aprilia