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Abstract
Background: Many natural and synthetic treatments are used to help the COVID-19 (Coronavirus Disease 2019) patient's recovery, but the effectiveness of inhibiting this virus still needs to be studied further.
Objective: To predict whether chondroitin sulfate compounds in sea cucumbers have antiviral activity in COVID-19.
Methods: The antiviral activity of chondroitin sulfate was tested on COVID-19 based on its interaction with the 6LU7 and 2GTB proteins, which are the main proteases (M pro) found in COVID-19, using the molecular docking method in silico. The research stages were the preparation of the 6LU7 and 2GTB protein structure databases, the preparation and optimization of the 3D chondroitin sulfate structure using the Biovia Discovery Studio application, and the validation of the molecular docking and chondroitin sulfate docking methods on the 6LU7 and 2GTB proteins using the Autodock 4.2 application.
Results: Chondroitin sulfate has a higher affinity and forms hydrogen bonds with 6LU7 protein with an affinity value for the 6LU7 receptor (-9.5 kcal/mol) with RMSD I.b. (0.000) and RMSD u.b. (0.000) compared to 2GTB protein, which has a lower affinity, namely the affinity value of the 2GTB receptor (-7.7 kcal/mol) with RMSD I.b. (0.000) and RMSD u.b. (0.000).
Conclusion: Based on the results of molecular docking studies, chondroitin sulfate has potential as an antiviral activity because it has affinity with 6LU7 and 2GTB proteins, which can inhibit the infection pathway of the COVID-19 virus.
Keywords: COVID-19, chondroitin sulfate, 6LU7 and 2GTB receptors, molecular docking
Intisari
Latar belakang: Banyak pengobatan secara alami atau pun sintetik yang digunakan untuk membantu kesembuhan pasien COVID-19 (Coronavirus Disease 2019) tetapi efektifitas dalam menghambat virus ini masih perlu untuk dikaji lebih dalam lagi.
Tujuan: Untuk memprediksi suatu hubungan aktivitas senyawa kondroitin sulfat pada teripang pasir sebagai antivirus pada COVID-19.
Metode: Dilakukan uji aktivitas kondroitin sulfat sebagai antivirus pada COVID-19 berdasarkan interaksinya pada protein 6LU7 dan 2GTB yang merupakan protease utama (M pro) yang ditemukan pada COVID-19, menggunakan metode molecular docking secara in silico. Tahapan penelitian yang dilakukan adalah penyiapan database struktur protein 6LU7 dan 2GTB, preparasi dan optimasi struktur 3D kondroitin sulfat menggunakan aplikasi Biovia Discovery Studio, serta validasi metode molecular docking dan docking kondroitin sulfat pada protein 6LU7 dan 2GTB menggunakan aplikasi Autodock 4.2.
Hasil: Kondroitin sulfat memiliki afinitas yang lebih tinggi dan membentuk ikatan hidrogen dengan protein 6LU7 dengan nilai afinitas untuk reseptor 6LU7 (-9.5 kcal/mol) dengan RMSD I.b. (0.000) dan RMSD u.b. (0.000) dibandingkan dengan protein 2GTB yang memiliki afinitas yang lebih rendah yaitu dengan nilai afinitas reseptor 2GTB (-7.7 kcal/mol) dengan RMSD I.b. (0.000) dan RMSD u.b. (0.000).
Kesimpulan: Berdasarkan hasil penelitian molecular docking, kondroitin sulfat memiliki potensi aktivitas sebagai antivirus karena memiliki afinitas dengan protein 6LU7 dan 2GTB yang mampu menghambat jalur infeksi virus COVID-19.
Kata kunci: COVID-19, kondroitin sulfat, reseptor 6LU7 dan 2GTB , molecular docking
Keywords
Article Details
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References
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References
Agistia D.D., Purnomo H., Tegar M., & Nugroho A.E. (2013). Interaksi Senyawa Aktif Dari Aegle Marmelos Correa Sebagai Anti Inflamasi Dengan Reseptor Cox-1 dan Cox-2. Traditional Medicine Journal, 18(2), 80–87.
Burhan E. (2020). Coronavirus yang Meresahkan Dunia. Journal Of The Indonesian Medical Association, 70(2), 1–3. https://doi.org/10.47830/jinma-vol.70.2-2020-170
Darmananda S. (2002). Sea Cucumber. Portland Oregeon. URL http://www.itmonline.org/arts/seacuke.htm
Girija C.R., Karunakar P., Poojari C.S., Begum N.S., & Syed A.A. (2010). Molecular Docking Studies of Curcumin Derivatives with Multiple Protein Targets for Procarcinogen Activating Enzyme Inhibition. Journal of Proteomics & Bioinformatics, 3(6), 200–203. https://doi.org/10.4172/jpb.1000140
Jain A.N., & Nicholls A. (2008). Recommendations for Evaluation of Computational Methods. Journal of Computer-Aided Molecular Design, 22, 133–139. https://doi.org/10.1007/s10822-008-9196-5
Kementerian Kesehatan RI. (2020). Situasi Terkini Perkembangan Novel Coronavirus (COVID-19). https://covid19.kemkes.go.id/situasi-infeksi-emerging/info-corona-virus/situasi-terkini-perkembangan-coronavirus-disease-covid-19-15-juli-2020/#.XxEzR2YRWMo (diakses 15 Juli 2020).
Lai C., Shih T., Ko W., Tang H., & Hsueh P. (2020). Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Coronavirus Disease-2019 (COVID-19): The Epidemic and The Challenges. International Journal of Antimicrobial Agents, 55, 105924. https://doi.org/10.1016/j.ijantimicag.2020.105924
Laksmiani N.P.L., Paramita N.L.P.V., & Wirasuta I.M.A.G. (2016). In Vitro and In Silico Antioxidant Activity of Purified Fractions From Purple Sweet Potato Ethanolic Extract. International Journal of Pharmacy and Pharmaceutical Sciences, 8(8), 177–181.
Lestari T. (2015). Studi Interaksi Senyawa Turunan 1 , 3-Dibenzoiltiourea sebagai Ribonukleotida Reduktase Inhibitor. Jurnal Farmasi Indonesia, 7(3), 163–169.
Li C., Zhao W., He C., Wu D., Yue Y., & Chen Y. (2020). COVID-19 Prevention and Control Strategies for Psychiatric Hospitals. Psychiatry Research. 289, 112935. https://doi.org/10.1016/j.psychres.2020.112935
Shereen MA, Khan S, Kazmi A, Bashir N, Siddique R. (2020). COVID-19 infection: Origin, transmission, and characteristics of human coronaviruses. J Adv Res. 24:91-98.
Stahel, P.F. (2020). How to Risk-stratify Elective Surgery During The COVID-19 Pandemic?. Patient Safety in Surgery. 14(8) :1-4.
Xu Y.(2020). Unveiling the origin and transmission of 2019-nCoV. Trends Microbiol. 28(4):239–240