In Silico Analysis of Active Compounds from Allium tuberosum as Drug Candidate for Inhibitor DENV-3 Envelope Protein
Abstract
Dengue fever has become a global health issue, the development of dengue vaccine has not yet been established. Medicinal plants are an ideal alternative for DENV infection drugs. The purpose of this study was to determine in silico the potential of active compounds from Allium tuberosum as envelope protein inhibitors of DENV-3. The method of this research is to do docking analysis of compounds with DENV-3 envelope protein and analysis of amino acid residues using MVD, pharmacokinetic analysis using SwissADME, toxicity analysis using ProTox-II. The best docking value for the potential activity to inhibit the receptor DENV-3 is the thymidine compound (RS: -81.1245 kcal/mol). The highest activity of thymidine is the most promising as a drug candidate, as evidenced by the toxicity analysis which is predicted to have non-carcinogenic, non-mutagenic, inactive properties against hepatotoxicity, cytotoxicity and immunotoxicity parameters, as well as pharmacokinetic analysis that fulfills 6 parameters of lipopolicity, molecular weight, polarity. , insolubility, insaturation, and flexibility which indicate the drug candidate of thymidine is safe for its bioavailability. The conclusion from the results of this study is that one compound has the ability as an antiviral, binding score with DENV-3 is good, and is safe in terms of pharmacokinetics and toxicity, namely thymidine compound.
References
CLCbio. 2013. Molegro Virtual Docker User Manual, MVD 2013 6.0 for Windows, Linux, and Mac OS X. A CLC Bio Company.
Costa RL, Voloch CM & Schrago CG. 2012. Comparative Evolutionary Epidemiology of Dengue Virus Serotypes. Infection, Genetics and Evolution. 12(2): 309-314.
Daina A, Michielin O & Zoete V. 2017. SwissADME: A Free Web Tool To Evaluate Pharmacokinetics, Drug-Likeness and Medicinal Chemistry Friendliness of Small Molecules. Scientific Reports. 7(March): 1-13.
Hadi D & Hamzah N. 2013. Studi Hubungan Kuantitatif Struktur-Aktivitas, Fitur Farmakofor, dan Docking Molekuler Senyawa Turunan Pirazolo-[3,4-d]-pirimidin sebagai Inhibitor Mer Tirosin Kinase. Acta Pharmaceutica Indonesia. 38(1): 1-10.
Hardjono S. 2017. Prediksi Sifat Farmakokinetik, Toksisitas dan Aktivitas Sitotoksik Turunan N-Benzoil-N’-(4-fluorofenil)tiourea sebagai Calon Obat Antikanker melalui Pemodelan Molekul. Jurnal Ilmu Kefarmasian Indonesia. 14(2): 246-255.
Haryanto S, Hayati RF, Yohan B, Sijabat L, Sihite IF, Fahri S, Meutiawati F, Halim JAN, Halim SN, Soebandrio A & Sasmono RT. 2016. The molecular and clinical features of dengue during outbreak in Jambi, Indonesia in 2015. Pathogens and Global Health. 110(3): 119-129.
Jannat, K., Rahman, T., & Rahmatullah, M. 2019. Traditional uses, phytochemicals and pharmacological properties of Allium tuberosum Rottler ex spreng. J Med Plants Stud. 7: 214-220.
Lohidashan K, Rajan M, Ganesh A, Paul M & Jerin J. 2018. Pass and Swiss ADME Collaborated in Silico Docking Approach to The Synthesis Of Certain Pyrazoline Spacer Compounds for Dihydrofolate Reductase Inhibition and Antimalarial Activity. Bangladesh Journal of Pharmacology. 13(1): 23-29.
Martin YC. 2005. A Bioavailability Score. Journal of Medicinal Chemistry. 48(9): 3164-3170.
Messina JP, Brady OJ, Scott TW, Zou C, Pigott DM, Duda KA, Bhatt S, Katzelnick L, Howes RE & Battle KE. 2014. Global Spread of Dengue Virus Types: Mapping The 70 Year History. Trends in Microbiology. 22(3): 138-146.
Nhut PT, An TNT, Minh LV, Truc TT & Anh NHT. 2020. Phytochemical screening of Allium Tuberosum Rottler. ex Spreng as food spice. IOP Conference Series: Materials Science and Engineering. 991(1): 12021.
Nursanti O, Aziz A & Hadisoebroto G. 2022. Docking dan Uji Toksisitas Secara Insilico untuk Mendapatkan Kandidat Obat Analgesik. INPHARNMED Journal. 6(1): 35-46.
Pratoko DK. 2012. Molecular Docking Senyawa Fitokimia Piper Longum (L.) Terhadap Reseptor Siklooksigenase-2 (Cox-2) Sebagai Antiinflamasi. Chemistry Progress. 5(1): 31-36.
Puspaningtyas A. 2013. Docking Molekul dengan Metoda Molegro Virtual Docker dari Ekstrak Air Psidium Gujava, Linn dan Citrus Sinensus, Peels Sebagai Inhibitor Pada Tirosinase Untuk Pemutih Kulit. Jurnal Kimia Terapan Indonesia. 15(1): 31-39.
Routhu NK, Lehoux SD, Rouse EA, Bidokhti MRM, Giron LB, Anzurez A, Reid SP, Abdel-Mohsen M, Cummings RD & Byrareddy SN. 2019. Glycosylation of Zika Virus is Important in Host–Virus Interaction and Pathogenic Potential. International Journal of Molecular Sciences. 20(20): 5206.
Sasmono RT, Kalalo LP, Trismiasih S, Denis D, Yohan B, Hayati RF & Haryanto S. 2019. Multiple Introductions of Dengue Virus Strains Contribute to Dengue Outbreaks in East Kalimantan, Indonesia, in 2015-2016. Virology Journal. 16(1): 93.
Schaeffer L. 2008. The Role of Functional Groups in Drug-Receptor Interactions. The Practice of Medicinal Chemistry. 464-480.
Sqra CD. 2022. Komparasi Penilaian Risiko Kesehatan Bahan Kimia : Metode CHRA dan SQRA. IAKMI Jurnal Kesehatan Masyarakat Indonesia. 3(1): 1-12.
Sukohar A. 2014. Demam Berdarah Dengue (DBD). Jurnal Medula. 2(02): 1-15.
Syahputra G, Ambarsari L & Sumaryada T. 2014. Simulasi Docking Kurkumin Enol, Bisdemetoksikurkumin dan Analognya Sebagai Inhibitor enzim12-lipoksigenase. Biofisika. 10(1): 55-67.
Umboro RO, Bimmaharyanto E, Yanti NKW & Kesehatan F. 2020. Uji efektivitas antioksidan (IC50) dan toksisitas akut (LD50) fraksi etanol daun nangka (Artocarpus Heterophyllus Lam.). JUPE (Jurnal Pendidikan Mandala), 5(6): 187-196.
Wei H & Cai RG. 2008. Cosmological Constraints on New Agegraphic Dark Energy. Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics. 663(1-2): 1-6.
Zaidan S, Rahmat D, Djamil R & Mumpuni E. 2019. Activity of Compounds in Sargassum sp. as Anti-atherosclerosis with Ligand-Receptor Comparison HMG-CoA Reductase- Simvastatin (1HW9) and In-Silico Toxicity Test. Ilmu Kefarmasian Indonesia. 17(1): 120-125.
![Creative Commons License](http://i.creativecommons.org/l/by-sa/4.0/88x31.png)
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.