eprintid: 18843 rev_number: 14 eprint_status: archive userid: 3858 dir: disk0/00/01/88/43 datestamp: 2023-02-01 09:42:50 lastmod: 2023-02-01 09:42:50 status_changed: 2023-02-01 09:42:50 type: thesis metadata_visibility: show creators_name: Lidia Putri, Rizki creators_name: Hariyanti, Hariyanti creators_name: Rachmania, Rizky Arcinthya title: SIMULASI PENAMBATAN MOLEKUL DAN DINAMIKA MOLEKUL SENYAWA PADA DAUN SALAM (Syzygium polyanthum) SEBAGAI ANTIINFLAMASI TERHADAP ENZIM SIKLOOKSIGENASE-2 ispublished: pub subjects: R subjects: RS divisions: 48201 abstract: Daun salam sering dipercaya masyarakat dapat digunakan sebagai terapi hipertensi, diabetes, asam urat, diare, hiperlipidemia dan antiinflamasi. Penelitian ini bertujuan untuk menguji efektivitas senyawa pada daun salam terhadap enzim siklooksigenase-2 sebagai antiinflamasi dan untuk menganalisis stabilitasnya dengan dinamika molekul. Penambatan molekul dilakukan dengan aplikasi PLANTS dan dinamika molekular dengan aplikasi GROMACS. Senyawa αHumulene menghasilkan skor ChemPLP –20 kkal/mol berdasarkan metode penambatan molekul, senyawa tesebut mengasilkan interaksi dan jarak yang baik, toksisitas senyawa α-Humulene termasuk kedalam kelas V dan celecoxib kelas IV sehingga tingkat toksisitasnya lebih rendah dibandingkan dengan celecoxib. Stabilitas senyawa α-Humulene yang diuji melalui dinamika molekular berdasarkan parameter RMSD, RMSF, energi potensial, ikatan hidrogen dan MMPBSA memiliki stabilitasnya tidak baik jika dibandingkan dengan celecoxib. Senyawa pada daun salam yang memiliki aktifitas antiinflamasi yaitu α-Humulene tetapi tidak stabil jika dibandingkan dengan celecoxib. Kata Kunci: Daun salam, penambatan molekul, dinamika molekul. date: 2020 date_type: completed full_text_status: public institution: Universitas Muhammadiyah Prof. DR. HAMKA department: Fakultas Farmasi dan Sains thesis_type: bachelor thesis_name: bphil referencetext: Abraham MJ, Murtolad T, Schulzb R, Palla S, Smithb JC, Hessa B, Lindahla E. 2015. GROMACS: High Performance Molecular Simulations Through Multi level Parallelism from Laptops to Supercomputers. SoftwareX. 1(2):19-25. Agustina R, Indrawati DTMM. 2015. Aktivitas Ekstrak Daun Salam. Journal of Tropical Pharmacy and Chemistr. 3(2):120–123. Allena MP. 2004. Introduction to Molecular Dynemic Simulation. Neumann Institute for Computing. 23(1):1-28. Alonso H, Bliznyuk AA, Gredy EJ. 2006. Combining Docking and Molecular Dynamic Simulations in Drug Design. Medicinal Research Reviews. 26(5): 531–568. Anna L, Blobaum, Lawrence J, Manett. 2007. Structural and Functional Basis of Cyclooxygenase Inhibition. Journal of Medicinal Chemistry. 50(7):1425–1441. Banerjee P, Eckert OA, Schrey AK, Preissner R. 2018. ProTox-II: A Webserver for The Prediction of Toxicity of Chemicals. Nucleic Acids Research. 46(1):257– 263. Bortolat A, Moro S. 2008. Designing a ligand for pharmaceutical purposes. Expert Opinion on Drug Discovery. 3(5):579-590. Dermawan D, Sumirtanurdin R, Dewantisari D. 2019. Molecular Dynamics Simulation of Estrogen Receptor Alpha Against Andrografolid as Anti Breast Cancer. Indonesian Journal of Pharmaceutical Science and Technology. 6(2): 65-76. Ferreira LH, Santos RND, Oliva G, Andricopulo A. 2015. Molecular Docking and Structure Based Drug Design Strategies. Molecules. 20(1):13384-13421. Garret A, Fitzferald MD, Carlo PM. 2001. The Coxib Selective Inhibitor of Cyclooxcugenase-2. The New England Journal of Medicine. 345(6):433–442. Hasanah F, Hidayah N. 2018. Uji Aktivitas Antiinflamsi Ekstrak Air Daun Salam (Sygyzium polyanthum Wight.) Terhadap Tikus Wistar Jantan Yang Diinduksi Karagenan 1%. Journal of Pharmaceutical and Science. 1(1):16-22. Harirforoosh S, Asghar W, Amali F. 2013. Adverse Effects of Nonsteroidal Antiinflammatory Drugs: An Update of Gastrointestinal, Cardiovascular and Renal Complications. Journal of Pharmacy and Pharmaceutical Sciences. 16(5):821–847. Korb O, Stutzel T, Exner TE. 2009. Empirical Scoring Functions for Advanced Protein-Senyawa d Docking with PLANTS. American Chemical Societ. 49(1): 84-96. Kumari R, Kumar R, Lynn A. 2014. g_mmpbsa—A GROMACS Tool for HighThroughput MM-PBSA Calculations. Journal of Chemical Information and Modeling. 54(7):1951–1962. Leach AR, Shoichet BK, Peishoff CE. 2006. Prediction of Protein-Ligand Interactions: Docking and Scoring. Journal of Medicinal Chemistry. 49(20): 5851-5855. Lipinski CA, Lombardo F, Dominy BWFP. 2002. Experimental and Computational Approaches to Estimate Solubility and Permeability in Drug Discovery and Development Settings. Advanced Drug Delivery Reviews Experimental. 23(3): 1–12. Manna A, Laksitorini MD, Hudiyanti D, Siahaan P. 2017. Molecular Docking of Interaction Between E-Cadherin Protein and Conformational Structure of Cyclic Peptide ADTC3 (Ac-CADTPCNH2) Simulated on 20 ns. Journal of Scientific and Applied Chemistry. 20(1):30–36. Meng XY, Zhang HX, Mezei M, Cui M. 2012. Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery. Current ComputerAided-Drug Design. 7(2):146–157. Moodley I. 2008. Review of The Cardiovascular Safety of Coxibs Compared to NSAIDS. Cardiovascular Journal of Africa. 19(2):102–107. Mukesh B, Kumar R. 2011. Molecular Docking: A Rwview. International Journal of Recent Advances in Physics. 2(6):1746-1751. Mycek MJ, Haevery RA, Champe PC. 2001. Farmakologi: Ulasan Bergambar Edisi II. Terjemah: Agoes A. Widya Medika. Jakarta. Hlm. 405 Nandave M, Ojha S, Arya D. 2009. Should Selective Cox-2 Inhibitors Be Used More. Indian Journal of Pharmaceutical Sciences. 68(3):235-347. Pollastri MP. 2010. Overview on the Rule of Five. Drug Discovery Technologies. 1(1):1-8. Praja RA, Pratiwi D, Nuraini. 2018. Studi Penambatan Molekuler Ligan Scopoletin dari Buah Mengkudu (Morinda Citrifolia L.) Pada Enzim ACE Sebagai Antihipertensi. Farmagazine. 5(1):40-47. Priyanto. 2015. Toksikologi Mekanisme, Terapi Antidotum, dan Penilaian Resiko. Lembaga Studi dan Konsultasi Farmakologi. Leskonfi. Depok. Hlm. 7-8. Purnomo H. 2011. Kimia Komputasi: Molecular Docking PLANTS (Protein Ligan Ant Sistem). Pustaka Pelajar. Yogyakarta. Hlm. 1-2. Purnomo H, Tegar M. 2013. Tea Leaves Extracted as Anti-malaria Based on Molecular Docking PLANTS. Procedia Environmental Sciences. 17(1):188- 194. Rahim ENAA, Ismail A, Omar MN, Ahmad WANW. 2018. GC-MS Analysis of Phytochemical Compounds in Syzygium polyanthum Leaves Extracted using Ultrasound-Assisted Method. Pharmacognosy Journal. 10(1):110–119. Russell RI. 2014. Non-steroid Anti-inflammatory Drugs and Gastrointesinal Damage-Problem an Solutions. Postgraduet Medicine. 6 (1):1-8. Ruswanto. 2015. Docking Empat Turunan Isonicotinohydrazide Pada Mycobacterium Tuberculosis Enoyl-Acyl carrier Protein Reductase ASE (InhA). Jurnal Kesehatan.13 (1):135-141. Ruswanto, Mardiana M. 2019. Simulasi Dinamika Molekular Senyawa Pyridin Pada Protein 2XNB Sebagai Antikanker Menggunakan Aplikasi Gomacs. Jurnal Kesehatan. 1(1):1-15. Sabri MZ, Hamid AAA, Sharifah, Hitam SMS, Rahim MZA. 2019. In Silico Screening of Aptamers Configuration against Hepatitis B Surface Antigen. Advances in Bioinformatics. 1(1):1-12. Sam H, Waheed A. 2013. Adverse Effects of Nonsteroidal Antiinflammatory Drugs: An Update of Gastrointestinal, Cardiovascular and Renal Complications. Journal of Pharmacy and Pharmaceutical Sciences. 16(5):821–847. Simanjuntak RM. 2015. Analisis Dinamika Molekuler Hasil Penambatan Molekuler Kompleks α-Glukosidase dengan Sepuluh Senyawa Kimia Tanaman Hasil Virtual Screening dari Basis Data Herbal. Universitas Indonesia. Jakarta. Hlm. 3-5. Siswodihardjo S. 2016. Kimia Medisinal Edisi Kedua. Airlangga. Surabaya. Hlm. 202-205. Soekardjo SB. 2000. Kimia Medicinal. Airlangga. Surabaya. Hlm. 125-126. Tegar M, Purnomo H. 2013. Tea Leaves Extracted as Anti-malaria Based on Molecular Docking PLANTS. Procedia Environmental Sciences. 17(1):188– 194. Theoduloz C, Alzate MJ, Jiménez-Aspee F, Isla MI, Alberto MR, Pertino MW, Schmeda-Hirschmann G. 2018. Inhibition of Key Enzymes in The Inflammatory Pathway by Hybrid Molecules of Terpenes and Synthetic Drugs: In Vitro and In Silico Studies. Chemical Biology and Drug Design. 2(1):2-18. Tjitrosoepomo G. 2005. Morfologi Tumbuhan. Gajah Mada University Press. Yogyakarta. Hlm. 5. Tomić M, Micov A, Pecikoza U, Stepanović-Petrović R. 2017. Clinical Uses of Nonsteroidal Anti-Inflammatory Drugs (NSAIDs) and Potential Benefits of NSAIDs Modified-Release Preparations. Pharmachology medicine. 1(1):1–29. Touw WG, Baakman C, Black J, Beek TAH, Krieger E, Joosten RP, Vriend G. 2014. A Series of PDB-related Databanks for Everyday Needs. Nucleic Acids Research. 43(1):364–368. Utami P. 2013. The Miracle of Herbs. Agromedia Pustaka. Jakarta. Hlm. 8. Yanur, A. 2012. Penambatan Molekul. Fakultas Farmasi Universitas. Depok. Hlm. 3-5. Wang C, Greene D, Xiao LQR, Luo R. 2018. Recent Developments and Applications of the MMPBSA Method. Frontiers in Molecular Biosciences. 4(87): 1-18. Zhan JH, Zhao X, Huang RI, Sun CC. 2009. Molecular Dynamics and Free Energy Analyses of ERK2–Pyrazolyloyrrole Inhibitors Interactions: Insight into Structure-Based Ligand Design. Journal of Theoretical and Computational Chemistry. 8(5):887–908. citation: Lidia Putri, Rizki dan Hariyanti, Hariyanti dan Rachmania, Rizky Arcinthya (2020) SIMULASI PENAMBATAN MOLEKUL DAN DINAMIKA MOLEKUL SENYAWA PADA DAUN SALAM (Syzygium polyanthum) SEBAGAI ANTIINFLAMASI TERHADAP ENZIM SIKLOOKSIGENASE-2. Bachelor thesis, Universitas Muhammadiyah Prof. DR. HAMKA. document_url: http://repository.uhamka.ac.id/id/eprint/18843/1/S03-200218.pdf