eprintid: 21886 rev_number: 8 eprint_status: archive userid: 3858 dir: disk0/00/02/18/86 datestamp: 2023-04-02 10:42:02 lastmod: 2023-04-02 10:42:02 status_changed: 2023-04-02 10:42:02 type: thesis metadata_visibility: show creators_name: Halimah, Latifah Nur creators_name: Rachmania, Rizky Arcinthya creators_name: Hariyanti, Hariyanti title: KAJIAN SENYAWA BIOAKTIF SEBAGAI ANTI COVID TERHADAP PENGHAMBATAN ENZIM MAIN PROTEASE (Mpro) SECARA VIRTUAL SCREENING ispublished: pub subjects: R subjects: RS divisions: 48201 abstract: COVID-19 adalah penyakit pernapasan akibat virus yang menyebabkan keadaan darurat kesehatan global dan diumumkan sebagai penyakit pandemi oleh Organisasi Kesehatan Dunia. Main protease (Mpro) merupakan reseptor penting dalam memediasi replikasi dan transkripsi pada SARS-CoV-2, dan menjadi target penting dalam penghambatan COVID-19. Tujuan penelitian ini adalah untuk mengumpulkan dan mengkaji senyawa bioaktif dari tanaman herbal terhadap reseptor main protease (Mpro) untuk mendapatkan hasil energi bebas ikatan yang terbaik melalui virtual screening. Berdasarkan hasil studi literatur dapat disimpulkan bahwa software yang paling baik adalah Autodock. Software ini digunakan untuk mencari senyawa bioaktif yang memiliki potensi sebagai anti covid dengan menggunakan enzim main protease (Mpro). Berdasarkan hasil molecular docking diperoleh senyawa Theaflavin-3-3’-digallate dari golongan fenol memiliki energi bebas ikatan terendah dengan nilai sebesar -12,41 kkal/mol dibandingkan dengan senyawa pembanding yaitu lopinavir (-5,4 kkal/mol sampai - 9,70 kkal/mol) Kata kunci : main protease, SARS-CoV-2, senyawa bioaktif, molecular docking, kajian literatur date: 2022 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: Abdelmohsen UR, Albohy A, Abdulrazik, B. S, Bayoumi SA. L, Malak LG, Khallaf ISA, Bringmann G & Farag SF. 2021. Natural coumarins as potential antiSARS-CoV-2 agents supported by docking analysis. RSC Advances, 11(28) : 16970–16979. Agarwal S. 2014. Writing a Review Article: For the Beginners in Research. International Journal of Science and Research (IJSR), 3(10) : 813-815 Al-Karmalawy AA, Farid MM, Mostafa A, Ragheb AY, Mahmoud SH, Shehata M, Abo Shama NM, Gaballah M, Mostafa-Hedeab G & Marzouk MM. 2021. Naturally available flavonoid aglycones as potential antiviral drug candidates against SARS-CoV-2. Molecules, 26(21) : 1–11. Arba, M. 2019. Buku Ajar Farmasi Komputasi.Penerbit Deepublish. Yogyakarta. 127-128. Arwansyah A, Ambarsari L & Sumaryada T I. 2014. Simulasi Docking Senyawa Kurkumin dan Analognya Sebagai Inhibitor Reseptor Androgen pada Kanker Prostat. Current Biochemistry, 1(1) : 11–19. Bramantoro P. 2018. Pengantar Metodologi Penelitian Bidang Kesehatan. Penerbit Airlangga University Press. Surabaya. 46 Cahyono EA. 2019. Literatur Review Panduan Penulisan dan Penyusunan. Jurnal Keperawatan, 1(10) : 1-12. Chaturvedi M, Nagre K & Yadav J P. 2021. In silico approach for identification of natural compounds as potential COVID 19 main protease (Mpro) inhibitors. VirusDisease, 32(2) : 325–329. Cherrak SA, Merzouk H, & Mokhtari-Soulimane N. 2020. Potential bioactive glycosylated flavonoids as SARS-CoV-2 main protease inhibitors: A molecular docking and simulation studies. PLoS ONE, 15(10) : 2-11. El Gizawy HA, Boshra SA, Mostafa A, Mahmoud SH, Ismail MI, Alsfouk AA, Taher AT & Al-Karmalawy AA. 2021. Pimenta dioica (L.) merr. bioactive constituents exert anti-sars-cov-2 and anti-inflammatory activities: Molecular docking and dynamics, in vitro, and in vivo studies. Molecules, 26(19) : 5884 Fakih TM & Dewi ML. 2020. Identifikasi Protease Utama (Mpro) Sebagai Makromolekul Target Inhibitor Novel Coronavirus 2019 ( SARS-SoV-2) Secara In Silico. Jurnal Ilmiah Farmasi Farmasyifa. 3(2) : 84–91. Purwaniati & Asnawi A. 2020. Target Kerja Obat COVID-19 : Review. Jurnal Farmagazine. 7(2) : 30–42. Firdayani F & Winarni Agustini T. 2019. Ekstraksi Senyawa Bioaktif sebagai Antioksidan Alami Spirulina Platensis Segar dengan Pelarut yang Berbeda. Jurnal Pengolahan Hasil Perikanan Indonesia. 18(1) : 28–37. Garg S, Anand A, Lamba Y & Roy A. 2020. Molecular docking analysis of selected phytochemicals against SARS-CoV-2 Mpro receptor. Vegetos, 33(4) : 766–781. Gembloux D & Biophysique CD. 2020. The hydrophobic effect in protein folding. Review Literature And Arts Of The Americas. 9(4) : 535–540. Ghosh R, Chakraborty A, Biswas A & Chowdhuri, S. 2021. Evaluation of green tea polyphenols as novel corona virus (SARS CoV-2) main protease (Mpro) inhibitors–an in silico docking and molecular dynamics simulation study. Journal of Biomolecular Structure and Dynamics. 39(12) : 4362–4374. Giofr SV, Napoli E, Iraci N, Speciale A, Cimino F, Muscar C, Sofia M, Ruberto G & Saija A. 2020. Interaction of selected terpenoids with two SARS-CoV-2 key therapeutic targets: An in silico study through molecular docking and dynamics simulations. Computers in Biology and Medicine. 134(3) : 1-11. Głowacki ED, Irimia-Vladu M, Bauer S & Sariciftci NS. 2013. Hydrogen-bonds in molecular solids-from biological systems to organic electronics. Journal of Materials Chemistry B, 1(31) : 3742–3753. Gulpinar O & Guclu AG. 2013. How to write a review article . Turkish Journal Of Urologi. 39 (1) : 44–48. Gupta S, Singh AK, Kushwaha PP, Prajapati KS, Shuaib M, Senapati S & Kumar S. 2021. Identification of potential natural inhibitors of SARS-CoV2 main protease by molecular docking and simulation studies. Journal of Biomolecular Structure and Dynamics. 39(12) : 4334–4345. Halder P, Pal U, Paladhi P, Dutta S, Paul P, Pal S, Das D, Ganguly A, Dutta I, Mandal S, Ray A & Ghosh S. 2022. Evaluation of potency of the selected bioactive molecules from Indian medicinal plants with MPro of SARS-CoV2 through in silico analysis. Journal of Ayurveda and Integrative Medicine. 3(2) : 1-14. Halgren TA, Murphy RB, Friesner RA, Beard HS, Frye LL, Pollard WT & Banks JL. 2004. Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening. Journal of Medicinal Chemistry. 47(7) : 1750–1759. Ibrahim MA, Abdelrahman AH, Hussien TA & Badr EAA. 2020. In silico drug discovery of major metabolites from spices as SARS-CoV-2 main protease inhibitors. Computers in Biology and Medicine. 126 (8) : 1-11. Imran M, Iqbal S, Hussain A, Uddin J, Shahzad M, Khaliq T, Ahmed AR, Mushtaq L, Muhammad Kashif & Mahmood K. 202. In silico screening, SAR and kinetic studies of naturally occurring flavonoids against SARS CoV-2 main protease. Ann Oncol. 3(10) : 19–21. Jamiu AT, Aruwa CE, Abdulakeem IA, Ajao AA & Sabiu, S. 2020. Phytotherapeutic evidence against coronaviruses and prospects for COVID19. Pharmacognosy Journal. 12(6) : 1252–1267. Joshi T, Joshi T, Pundir H, Sharma P, Mathpal S & Chandra S. 2021. Predictive modeling by deep learning, virtual screening and molecular dynamics study of natural compounds against SARS-CoV-2 main protease. Journal of Biomolecular Structure and Dynamics. 39(17) : 6728–6746. Kar P, Sharma NR, Singh B, Sen A & Roy A. 2021. Natural compounds from Clerodendrum spp. as possible therapeutic candidates against SARS-CoV-2: An in silico investigation. Journal of Biomolecular Structure and Dynamics. 39(13) : 4774–4785. Kemenkes RI. 2020. Kesiapan Kementrian Kesehatan RI Dalam Menghadapi Outbreak Novel Coronavirus. Kemenkes RI. 29(1) : 1–26. Khan J, Sakib SA, Mahmud S, Khan Z, Islam MN, Sakib MA, Emran T Bin & Simal-Gandara J. 2021. Identification of potential phytochemicals from Citrus Limon against main protease of SARS-CoV-2: molecular docking, molecular dynamic simulations and quantum computations. Journal of Biomolecular Structure and Dynamics. 19(7) : 1–12. Khatami, F. 2020. Studi Molecular Docking Senyawa Diterpenoid Abieten Terhadap Enzim Protease Utama (Mpro) Virus Corona. Natural Sciences. 20 (8) : 1–12. Korb O, Stutzle T & Exner TE. 2009. Empirical scoring functions for advanced Protein-Ligand docking with PLANTS. Journal of Chemical Information and Modeling. 49(1) : 84–96. Kramer B, Rarey M & Lengauer T .1999. Evaluation of the FlexX incremental construction algorithm for protein- ligand docking. Proteins: Structure, Function and Genetics. 37(2) : 228–241. Kumar A, Mishra DC, Angadi UB, Yadav R, Rai A & Kumar D. 2021. Inhibition Potencies of Phytochemicals Derived from Sesame Against SARS-CoV-2 Main Protease: A Molecular Docking and Simulation Study. Frontiers in Chemistry. 9(10) : 1–16. Kumar SB, Krishna S, Pradeep S, Mathews DE, Pattabiraman R, Murahari M & Murthy TPK. 2021. Screening of natural compounds from Cyperus rotundus Linn against SARS-CoV-2 main protease (Mpro): An integrated computational approach. Computers in Biology and Medicine. 134(5) : 2-9. Kushwaha PP, Singh AK, Prajapati KS, Shuaib M, Gupta S & Kumar S. 2021. Phytochemicals present in Indian ginseng possess potential to inhibit SARSCoV-2 virulence: A molecular docking and MD simulation study. Microbial Pathogenesis. 157(3) : 1-11. Kusuma AT & Hadi D. 2019. Virtual screening natural compounds from plants as inhibitor of estrogen receptor alpha I ( ESR1 ) skrining virtual senyawa bahan alam sebagai inhibitor sstrogen receptor alpha I ( ESR1 ). Ijpst-Supp. 1(1) : 30–41. Li Y, Xie Z, Lin W, Cai W, Wen C, Guan Y, Mo X, Wang J, Wang Y, Peng P, Chen X, Hong W, Xiao G, Liu J, Zhang L, Hu F, Li F, Zhang F, Deng X & Li L. 2020. Efficacy and Safety of Lopinavir/Ritonavir or Arbidol in Adult Patients with Mild/Moderate COVID-19: An Exploratory Randomized Controlled Trial. Med Clinical Advances, 1(1) : 105-113. Liliwana EA. 2021. Analisis in-silico penghambatan main protease (Mpro) Pada SARS-CoV-2 Oleh Senyawa Aktif The Hijau (Camelia sinensis). Jurnal Farmagazine. 7(2) : 1–7. Lokhande K, Nawani NK, Venkateswara S & Pawar S. 2020. Biflavonoids from Rhus succedanea as probable natural inhibitors against SARS-CoV-2: a molecular docking and molecular dynamics approach. Journal of Biomolecular Structure and Dynamics. 30(11) : 1-13. Luan B, Huynh T, Cheng X, Lan G & Wang HR. 2020. Targeting Proteases for Treating COVID-19. Journal of Proteome Research. 19(11) : 4316–4326. Marzali A. 2016. Menulis Kajian Literatur . Jurnal Etnosia. 1(2) : 27-36. Maulydia NB, Tallei TE, Ginting B, Idroes R, Illian DN & Faradilla M. 2022. Analysis of flavonoid compounds of Orange (Citrus sp.) peel as anti-main protease of SARS-CoV-2: A molecular docking study. IOP Conference Series: Earth and Environmental Science. 951(1) : 1-9. Meng XY. 2011. Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery. Current Computer-Aided Drug Design. Curr. Comput. Aid. Dru. Des. 7(2) : 146–157. Naiola E, Widhyastuti N. Semi Purifikasi Karakteristik Enzim Protease Bacillus sp. Berk Penel Hayati. 13(5) : 51-56. Noviardi Harry F. 2015.Potensi Senyawa Bullatalisin Sebagai Inhibitor Protein Nukleotrien A4 Hidrolase Pada Kanker Kolon Secara In Silico. Fitofarmaka. 5(2) : 65–73. Olson OT & AJ. 2013. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading. NIH Public Access. 23(1) : 1–7. Owis AI, El-Hawary MS, El Amir D, Aly OM, Abdelmohsen UR & Kamel MS. 2020. Molecular docking reveals the potential of Salvadora persica flavonoids to inhibit COVID-19 virus main protease. RSC Advances. 10(33) : 19570– 19575. Panikar S, Shoba G & Arun M. 2020. Essential oils as an effective alternative for the treatment of COVID-19: Molecular interaction analysis of protease (Mpro) with pharmacokinetics and toxicological properties. Journal of Infection and Public Health. 14(12) : 1-11. Perdana AT & Permana AA. 2021. Molecular Docking Senyawa Potensial Anticovid-19 . Jurnal Informatika. 6(30) : 159–166. Prabowo AY, Teti E & Indria P. 2014. Umbi gembili ( Dioscorea esculenta L .) sebagai bahan pangan mengandung senyawa bioaktif : kajian pustaka. Jurnal Pangan Dan Agroindustri. 2(3) : 129–135. Pratoko DK. 2012. Molecular Docking Senyawa Fitokimia Piper Longum (L.) Terhadap Reseptor Siklooksigenase-2 (Cox-2) Sebagai Antiinflamasi. Chemistry Progress. 5(1) : 31–36. Purwaniati P. 2020. Molecular Docking Study on COVID-19 Drug Activity of N- (2-phenylethyl)methanesulfonamide Derivatives as Main Protease Inhibitor. Ad-Dawaa’ Journal of Pharmaceutical Sciences. 3(1) : 1–11. Ramadhan DSF, Fakih TM & Arfan A. 2020. Activity Prediction of Bioactive Compounds Contained in Etlingera elatior Against the SARS-CoV-2 Main Protease: An In Silico Approach. Borneo Journal of Pharmacy. 3(4) : 235– 242. Rollando. (2017). Pengantar Kimia Medisinal. Penerbit CV. Seribu Bintang. Malang. 12-22. Rusdi MS. 2021. Farmakologi pada Corona Virus Disease (Covid-19). Lumbung Farmasi: Jurnal Ilmu Kefarmasian. 103(2) : 54–61. Seyed E, Riahi N & Nikzad H. 2020. The novel coronavirus Disease-2019 (COVID-19): Mechanism of action, detection and recent therapeutic strategies. Virology. 551(9) : 2-9. Shah S, Chaple D, Arora S, Yende S, Mehta C & Nayak U. 2021. Prospecting for Cressa cretica to treat COVID-19 via in silico molecular docking models of the SARS-CoV-2. Journal of Biomolecular Structure and Dynamics. 29(5) : 1–10. Shivanika C, Deepak Kumar S, Ragunathan V, Tiwari P, Sumitha A & Brindha Devi P. 2022. Molecular docking, validation, dynamics simulations, and pharmacokinetic prediction of natural compounds against the SARS-CoV-2 main-protease. Journal of Biomolecular Structure and Dynamics. 40(2) : 585– 611. Shree P, Mishra P, Selvaraj C, Singh SK, Chaube R, Garg N & Tripathi YB. 2022. Targeting COVID-19 (SARS-CoV-2) main protease through active phytochemicals of ayurvedic medicinal plants–Withania somnifera (Ashwagandha), Tinospora cordifolia (Giloy) and Ocimum sanctum (Tulsi)– a molecular docking study. Journal of Biomolecular Structure and Dynamics. 40(1) : 190–203. Susilo A, Rumende CM, Pitoyo CW, Santoso WD, Yulianti M, Sinto R, Singh G, Nainggolan L, Nelwan EJ, Khie L, Widhani A, Wijaya E, Wicaksana B, Maksum M, Annisa F, Jasirwan OM, Yunihastuti E, Penanganan T, New Cipto R. 2020. Coronavirus Disease 2019 : Tinjauan Literatur Terkini Coronavirus Disease 2019 : Review of Current Literatures. Jurnal Penyakit Dalam Indonesia. 7(1) : 45–67. Tallei TE, Tumilaar SG, Niode NJ, Fatimawali Kepel BJ, Idroes R, Effendi Y, Sakib SA & Emran TBin. 2020. Potential of Plant Bioactive Compounds as SARSCoV-2 Main Protease (Mpro) and Spike (S) Glycoprotein Inhibitors: A Molecular Docking Study. Scientifica. 23(12) : 1-18. Tambunan USF & Alamudi S. 2010. Designing cyclic peptide inhibitor of dengue virus NS3-NS2B protease by using molecular docking approach. Bioinformation. 5(6) : 250–254. Tjahyanto Teddy, Eldy Clarissa & Jesica Karmenia LO. 2022. Aktivitas Antivirus Polifenol Sebagai Profilaksis Dan Terapi Potensial Dalam Penanganan Covid19 . Jurnal Health Sains. 3(2) : 311- 330. Vargas M, Servillo G & Einav S. 2020. Lopinavir/ritonavir for the treatment of SARS, MERS and COVID-19: a systematic review. European Review for Medical and Pharmacological Sciences. 24(16) : 8592–8605. Verma D, Mitra D, Paul M, Chaudhary P, Kamboj A, Thatoi H, Janmeda P, Jain D, Panneerselvam P, Shrivastav R, Pant K & Das Mohapatra PK. 2021. Potential inhibitors of SARS-CoV-2 (COVID 19) proteases PLpro and Mpro/ 3CLpro: molecular docking and simulation studies of three pertinent medicinal plant natural components. Current Research in Pharmacology and Drug Discovery 2(4) : 1-23. Verma S, Patel CN & Chandra M. 2021. Identification of novel inhibitors of SARSCoV-2 main protease (Mpro) from Withania sp. by molecular docking and molecular dynamics simulation. Journal of Computational Chemistry. 42(26) : 1861–1872. Vijayakumar M, Janani B, Kannappan P, Renganathan S, Al-Ghamdi S, Alsaidan M, Abdelaziz MA, Peer Mohideen A, Shahid M & Ramesh T. 2022. In silico identification of potential inhibitors against main protease of SARS-CoV-2 6LU7 from Andrographis panniculata via molecular docking, binding energy calculations and molecular dynamics simulation studies. Saudi Journal of Biological Sciences. 29(1) : 18–29. Wahidah I, Athallah R, Hartono NFS, Rafqie MCA & Septiadi MA. 2020. Pandemik COVID-19: Analisis Perencanaan Pemerintah dan Masyarakat dalam Berbagai Upaya Pencegahan. Jurnal Manajemen Dan Organisasi. 11(3) : 179–188. Wijaya RM, Hafidzhah MA, Kharisma VD, Ansori ANM & Parikesit AA. 2021. Covid-19 in silico drug with zingiber officinale natural product compound library targeting the mpro protein. Makara Journal of Science. 25(3) : 162– 171. Zackria AA, Pattabiraman R, Murthy TPK, Kumar SB, Mathew BB & Biju VG. 2021. Computational screening of natural compounds from Salvia plebeia R. Br. for inhibition of SARS-CoV-2 main protease. Vegetos. 17(9) : 1-15. Zaki AA, Ashour A, Elhady SS, Darwish KM & Al-Karmalawy AA. 2021. Calendulaglycoside A showing potential activity against SARS-CoV-2 main protease: Molecular docking, molecular dynamics, and SAR studies. Journal of Traditional and Complementary Medicine. 11(3) : 1-19. citation: Halimah, Latifah Nur dan Rachmania, Rizky Arcinthya dan Hariyanti, Hariyanti (2022) KAJIAN SENYAWA BIOAKTIF SEBAGAI ANTI COVID TERHADAP PENGHAMBATAN ENZIM MAIN PROTEASE (Mpro) SECARA VIRTUAL SCREENING. Bachelor thesis, Universitas Muhammadiyah Prof. DR. HAMKA. document_url: http://repository.uhamka.ac.id/id/eprint/21886/1/FS03-220259.pdf