J. Pharm. Pharmacogn. Res., vol. 10, no. 6, pp. 1126-1138, November-December 2022.
DOI: https://doi.org/10.56499/jppres22.1489_10.6.1126
Original Article
Molecular simulation of compounds from n-hexane fraction of Sonchus arvensis L. leaves as SARS-CoV-2 antiviral through inhibitor activity targeting strategic viral protein
[Simulación molecular de compuestos de la fracción de n-hexano de las hojas de Sonchus arvensis L. como antivirales del SARS-CoV-2 a través de la actividad inhibidora dirigida a la proteína viral estratégica]
Dwi Kusuma Wahyuni1,2*, Sumrit Wacharasindhu3, Wichanee Bankeeree2, Hunsa Punnapayak2, Hery Purnobasuki1, Junairiah1, Arif NM Ansori4, Viol Dhea Kharisma1,5, Arli Aditya Parikesit6, Listyani Suhargo1*, Sehanat Prasongsuk1,2*
1Department of Biology, Faculty of Science and Technology, Universitas Airlangga Surabaya, East Java, 60115, Indonesia.
2Plant Biomass Utilization Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
3Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok,10330, Thailand.
4Professor Nidom Foundation, Surabaya, East Java, 60115, Indonesia.
5Computational Virology Research Unit, Division of Molecular Biology and Genetics, Generasi Biologi Indonesia Foundation, Gresik, East Java, 61171, Indonesia.
6Department of Bioinformatics, School of Life Science, Indonesia International Institute for Life Sciences, Jakarta, 13210, Indonesia.
*E-mail: dwi-k-w@fst.unair.ac.id (DKW), listyani-s@fst.unair.ac.id (LS), sehanat.p@chula.ac.th (SP)
Abstract
Context: COVID-19 was caused by the spread and transmission of SARS-CoV-2 at the end of 2019 until now. The problem comes when antiviral drugs have not yet been found and patients infected with SARS-CoV-2 can trigger a cytokine storm condition due to the effects of viral replication. Indonesia has various kinds of medicinal plants, such as Sonchus arvensis L., which are used as medicinal plants.
Aims: To analyze the activity of the inhibitor as SARS-CoV-2 antiviral agents from n-hexane fractions of S. arvensis leaves.
Methods: The sample was collected from GC-MS analysis, PubChem, and Protein Databank database, then drug-likeness identification using Lipinski Rule of Five server and bioactive prediction of bioactive compounds as inhibitor activity was conducted by Molinspiration server. Furthermore, the docking simulation was performed using PyRx 0.9.9 software to determine the binding activity, molecular interaction by Discovery Studio software to identify position and interaction type, 3D molecular visualization by PyMol 2.5. software, and dynamic by CABS-flex 2.0 server to predict interaction stability.
Results: α-Amyrin and β-amyrin from n-hexane fractions of S. arvensis leaves had activity as SARS-CoV-2 inhibitors through interactions on helicase, RdRp, Mpro, and RBD-Spike, both compounds had more negative binding affinity than control drug and can produce stable chemical bond interactions in the ligand-protein complexes. However, the results were merely computational, so they must be validated through an in vivo and in vitro research approach.
Conclusions: Sonchus arvensis L. leaves were predicted to have SARS-CoV-2 antiviral through inhibitor activity by α-amyrin and β-amyrin.
Keywords: antiviral; bioinformatics; SARS-CoV-2; Sonchus arvensis L.

Resumen
Contexto: La propagación y la transmisión del SARS-CoV-2 han sido causadas por el COVID-19 desde finales de 2019 hasta ahora. El problema surge cuando aún no se han encontrado medicamentos antivirales y los pacientes infectados por el SARS-CoV-2 pueden desencadenar una condición de tormenta de citocinas debido a los efectos de la replicación viral. Indonesia tiene varios tipos de plantas medicinales, como Sonchus arvensis L., que se utilizan como plantas medicinales.
Objetivos: Analizar la actividad inhibidora de SARS-CoV-2 de fracciones de n-hexano de las hojas de S. arvensis.
Métodos: La muestra se recogió del análisis GC-MS, PubChem y la base de datos Protein Databank, luego se identificó la similitud de los fármacos utilizando el servidor Lipinski Rule of Five y se realizó la predicción de los compuestos bioactivos como actividad inhibidora mediante el servidor Molinspiration. Además, se realizó la simulación de acoplamiento mediante el software PyRx 0.9.9 para determinar la actividad de unión, la interacción molecular mediante el software Discovery Studio para identificar la posición y el tipo de interacción, la visualización molecular 3D mediante el software PyMol 2.5. y la dinámica mediante el servidor CABS-flex 2.0 para predecir la estabilidad de la interacción.
Resultados: La α-amirina y la β-amirina de las fracciones de n-hexano de las hojas de S. arvensis tuvieron actividad como inhibidores del SARS-CoV-2 a través de las interacciones en la helicasa, RdRp, Mpro y RBD-Spike, ambos compuestos tuvieron más afinidad de unión negativa que el fármaco de control y pueden producir interacciones de enlace químico estables en los complejos ligando-proteína. Sin embargo, los resultados fueron meramente computacionales, por lo que deben ser validados mediante un enfoque de investigación in vivo e in vitro.
Conclusiones: Se predijo que las hojas de S. arvensis tienen actividad antiviral contra el SARS-CoV-2 a través de la actividad inhibidora de la α-amirina y la β-amirina.
Palabras Clave: antiviral; bioinformática; SARS-CoV-2; Sonchus arvensis L.

Citation Format: Wahyuni DK, Wacharasindhu S, Bankeeree W, Punnapayak H, Parikesit AA, Kharisma VD, Ansori ANM, Suhargo L, Prasongsuk S (2022) Molecular simulation of compounds from n-hexane fraction of Sonchus arvensis L. leaves as SARS-CoV-2 antiviral through inhibitor activity targeting strategic viral protein. J Pharm Pharmacogn Res 10(6): 1126–1138. https://doi.org/10.56499/jppres22.1489_10.6.1126
References
Ahamed T, Rahman SKM, Shohae AM (2017) Thin layer chromatographic profiling and phytochemical screening of six medicinal plants in Bangladesh. Int J Biosci 11(1): 131-140. https://doi.org/10.12692/ijb/11.1.131-140
Ahmad B, Batool M, Ain QU, Kim MS, Choi S (2021) Exploring the binding mechanism of PF-07321332 SARS-CoV-2 protease inhibitor through molecular dynamics and binding free energy simulations. Int J Mol Sci 22(17): 9124. https://doi.org/10.3390/ijms22179124
Aldakheel RK, Rehman S, Almessiere MA, Khan FA, Gondal MA, Mostafa A, Baykal A (2020) Bactericidal and in vitro cytotoxicity of Moringa oleifera seed extract and its elemental analysis using laser-induced breakdown spectroscopy. Pharmaceuticals 13(8): 193. https://doi.org/10.1101/2020.04.15.042663
Ali KS, Mohammed ASA, Munayem RT (2017) Phytochemical screening and thin layer chromatography of Acacia etbaica ssp. uncinata leaves. World J Pharm Res 6(12): 1278-1283. https://doi.org/10.20959/wjpr201712-9772
Ansori ANM, Fadholly A, Proboningrat A, Hayaza S, Susilo RJK, Naw SW, Posa GAV, Yusrizal YF, Sibero MT, Sucipto TH, Soegijanto S (2021a) In vitro antiviral activity of Pinus merkusii (Pinaceae) stem bark and cone against dengue virus type-2 (DENV-2). Res J Pharm Technol 14(7): 3705-3708. http://dx.doi.org/10.52711/0974-360X.2021.00641
Ansori ANM, Kharisma VD, Fadholly A, Tacharina MR, Antonius Y, Parikesit AA (2021b) Severe acute respiratory syndrome coronavirus-2 emergence and its treatment with alternative medicines: A review. Res J Pharm Technol 14(10): 5551-5557. https://doi.org/10.52711/0974-360X.2021.00967
Ansori ANM, Susilo RJK, Hayaza S (2021c) Biological activity investigation of phytocomponents in mangosteen (Garcinia mangostana L.): in silico study. Indian J Forensic Med Toxicol 15(1): 847-851. https://doi.org/10.37506/ijfmt.v15i1.13522
Benet LZ, Hosey CM, Ursu O, Oprea TI (2016) BDDCS, the rule of 5 and drugability. Adv Drug Deliv Rev 101:89-98. https://doi.org/10.1016/j.addr.2016.05.007
Biskup E, Golebiowski R, Stepnowski P, Lojkowska E (2012) Triterpenoid α-amyrin stimulates proliferation of human keratinocytes but does not protect them against UVB damage. Acta Biochim Pol 59(2): 255–260.
Borg J, Toazara J, Hietter H, Henry M, Schmitt G, Luu B (1987) Neurotrophic effect of naturally occurring long-chain fatty alcohols on cultured CNS. Neurons 213(2): 406-410. https://doi.org/10.1016/0014-5793(87)81531-4
Bourgonje AR, Abdulle AE, Timens W, Hillebrands JL, Navis GJ, Gordijn SJ, Bolling MC, Dijkstra G, Voors AA, Osterhaus AD, van der Voort PH, Mulder DJ, van Goor H (2020) Angiotensin-converting enzyme 2 (ACE2), SARS-CoV-2 and the pathophysiology of coronavirus disease 2019 (COVID-19). J Pathol 251(3): 228-248. https://doi.org/10.1002/path.5471
Delyan E (2016) Analysis of composition of volatile compounds of field sow thistle (Sonchus arvensis L.) leaves using the method of gas chromatography with mass-detection. J Pharm Innov 5: 118-121.
Dhama K, Khan S, Tiwari R, Sircar S, Bhat S, Malik YS, Singh KP, Chaicumpa W, Bonilla-Aldana DK, Rodriguez-Morales AJ (2020) Coronavirus disease 2019-COVID-19. Clin Microbiol Rev 33(4): e00028-20. https://doi.org/10.1128/CMR.00028-20
Dibha AF, Wahyuningsih S, Ansori ANM, Kharisma VD, Widyananda MH, Parikesit AA, Sibero MT, Probojati RT, Murtadlo AAA, Trinugroho JP, Sucipto TH, Turista DDR, Rosadi I, Ullah ME, Jakhmola V, Zainul R (2022) Utilization of secondary metabolites in algae Kappaphycus alvarezii as a breast cancer drug with a computational method. Pharmacog J 14(3): 536-543. https://doi.org/10.5530/pj.2022.14.68
Du X, Li Y, Xia YL, Ai SM, Liang J, Sang P, Ji XL, Liu SQ (2016). Insights into protein-ligand interactions: mechanisms, models, and methods. Int J Mol Sci 17(2): 144. https://doi.org/10.3390/ijms17020144
Duke JA (1992) Handbook of phytochemical constituents of GRAS herbs and other economic plants, CRC Press, Boca Raton, FL, USA.
Ekalu A, Ayo RGO, Habila JD, Hamisu (2019) Bioactivities of phaeophytin a, α-amyrin, and lupeol from Brachystelma togoense Schltr. J Turk Chem Soc 6(3): 411-418. https://doi.org/10.18596/jotcsa.571770
Elnakady YA, Rushdi AI, Franke R, Abutaha N, Ebaid H, Baabbad M, Omar MOM, Al Ghamdi AA (2017) Characteristics, chemical compositions and biological activities of propolis from Al-Bahah, Saudi Arabia. Sci Rep 7: 41453. https://doi.org/10.1038/srep41453
Gade S, Rajamanikyam M, Vadlapudi V, Nukala MK, Aluvala R, Giddigari C, Karanam NJ, Barua NC, Pandey R, Upadhayayula VSV, Srpadi P, Amanchy R, Upadhyayula SM (2017) Acetylcholinesterase inhibitory activity of stigmasterol & hexacosanol is responsible for larvicidal and repellent properties of Chromolaena odorata. Biochim Biophys Acta 1861(3): 541-550. https://doi.org/10.1016/j.bbagen.2016.11.044
Hassan NM, Alhossary AA, Mu Y, Kwoh CK (2017) Protein-ligand blind docking using QuickVina-W with inter-process spatio-temporal integration. Scie Rep 7(1): 15451. https://doi.org/10.1038/s41598-017-15571-7
Hendriani R, Sukandar EY, Anggadiredja K. Sukrasno (2015) In vitro evaluation of xanthine oxidase inhibitory activity of selected medicinal plants. Int J Pharm Clin 8: 235-238.
Imelda I, Azaria C, Lucretia T (2017) Protective effect of ethanol extract tempuyung leaf (Sonchus arvensis L.) against gentamicin induced renal injury viewed from blood ureum level. Med Health 1: 575-82. https://doi.org/10.28932/jmh.v1i6.555
Kabinger F, Stiller C, Schmitzová J, Dienemann C, Kokic G, Hillen HS, Höbartner C, Cramer P (2021) Mechanism of molnupiravir-induced SARS-CoV-2 mutagenesis. Nat Struct Mol Biol 28(9): 740-746. https://doi.org/10.1038/s41594-021-00651-0
Khan RA (2012) Evaluation of flavonoids and diverse antioxidant activities of Sonchus arvensis. Chem Cent J6(1): 126. https://doi.org/10.1186/1752-153X-6-126
Kharisma VD, Agatha A, Ansori ANM, Widyananda MH, Rizky WC, Dings TGA, Derkho M, Lykasova I, Antonius Y, Rosadi I, Zainul R (2022) Herbal combination from Moringa oleifera Lam. and Curcuma longa L. as SARS-CoV-2 antiviral via dual inhibitor pathway: A viroinformatics approach. J Pharm Pharmacogn Res 10(1): 138–146. https://doi.org/10.56499/jppres21.1174_10.1.138
Kharisma VD, Ansori ANM, Nugraha AP (2020) Computational study of ginger (Zingiber officinale) as E6 inhibitor in human papillomavirus type 16 (HPV-16) infection. Biochem Cell Arch 20 (Suppl 1): 3155-3159. https://doi.org/10.35124/bca.2020.20.S1.3155
Listiyani P, Kharisma VD, Ansori AN, Widyananda MH, Probojati RT, Murtadlo AA (2022) In silico phytochemical compounds screening of Allium sativum targeting the Mpro of SARS-CoV-2. Pharmacog J 14(3): 604-609. https://10.5530/pj.2022.14.78
Maio N, Lafont BAP, Sil D, Li Y, Bollinger JM Jr, Krebs C, Pierson TC, Linehan WM, Rouault TA (2021) Fe-S cofactors in the SARS-CoV-2 RNA-dependent RNA polymerase are potential antiviral targets. Science 373(6551): 236-241. https://doi.org/10.1126/science.abi5224
Murgolo N, Therien AG, Howell B, Klein D, Koeplinger K, Lieberman LA, Adam GC, Flynn J, McKenna P, Swaminathan G, Hazuda DJ, Olsen DB (2021) SARS-CoV-2 tropism, entry, replication, and propagation: considerations for drug discovery and development. PLoS Pathog 17(2): e1009225. https://doi.org/10.1371/journal.ppat.1009225
Niewolik D, Bednarczyk-Cwynar B, Ruszkowsk P, Sosnowski TR, Jaszcz K (2021) Bioactive betulin and PEG based polyanhydrides for use in drug delivery systems. Int J Mol Sci 22(3): 1090. https://doi.org/10.3390/ijms22031090
Ogwuche CE, Amupitan JO, Ayo RG (2014) Isolation and biological activity of the triterpene ß-amyrin from the aerial plant parts of Maesobotrya barteri (Baill). Med Chem 4: 729–733. https://doi.org/10.4172/2161-0444.1000221
Okoye NN, Ajaghaku DL, Okeke HN, Ilodigwe EE, Nworu CS, Okoye FBC (2014) Beta-amyrin and alpha-amyrin acetate isolated from the stem bark of Alstonia boonei display profound anti-inflammatory activity. Pharm Biol 52: 1478–1486. https://doi.org/10.3109/13880209.2014.898078
Prahasanti C, Nugraha AP, Kharisma VD, Ansori ANM, Devijanti R, Ridwan TPSP, Ramadhani NF, Narmada IB, Ardani IGAW, Noor TNEBA (2021) A bioinformatic approach of hydroxyapatite and polymethylmethacrylate composite exploration as dental implant biomaterial. J Pharm Pharmacog Res 9(5): 746-754. https://doi.org/10.56499/jppres21.1078_9.5.746
Proboningrat A, Kharisma VD, Ansori ANM, Rahmawati R, Fadholly A, Posa GAV, Sudjarwo SA, Rantam FA, Achmad AB (2022) In silico study of natural inhibitors for human papillomavirus-18 E6 protein. Res J Pharm Technol 15(3): 1251-1256. https://doi.org/10.52711/0974-360X.2022.00209
Putra WE, Kharisma VD, Susanto H (2020) Potential of Zingiber officinale bioactive compounds as inhibitory agent against the IKK-B. AIP Conf Proc 2231(1): 040048. https://doi.org/10.1063/5.0002478
Ramos RS, Borges RS, de Souza JSN, Araujo IF, Chaves MH, Santos CBR (2022) Identification of potential antiviral inhibitors from hydroxychloroquine and 1,2,4,5-tetraoxanes analogues and investigation of the mechanism of action in SARS-CoV-2. Int J Mol Sci 23(3): 1781. https://doi.org/10.3390/ijms23031781
Rumondang M, Kusrini D, Fachriyah E (2013) Isolation, identification and antibacterial test of triterpenoid compounds from n-hexane extract of tempuyung leaves (Sonchus arvensis L.). Pharm Sci 05: 506-507.
Saito M, Kinoshita Y, Satoh I, Bex A, Bertaccini A (2006) Ability of cyclohexenonic long-chain fatty alcohol to reverse diabetes-induced cystopathy in the rat. Eur Urol 51(2): 479-488. https://doi.org/10.1016/j.eururo.2006.06.024
Shaheen U, Akka J, Hinore JS, Girdhar A, Bandaru S, Sumithnath TG, Nayarisseri A, Munshi A (2015) Computer aided identification of sodium channel blockers in the clinical treatment of epilepsy using molecular docking tools. Bioinformation 11(3): 131-137. https://doi.org/10.6026/97320630011131
Shamsi A, Mohammad T, Anwar S, Amani S, Khan MS, Husain FM, Rehman MT, Islam A, Hassan MI (2021) Potential drug targets of SARS-CoV-2: From genomics to therapeutics. Int J Biol Macromol 177: 1-9. https://doi.org/10.1016/j.ijbiomac.2021.02.071
Sharma K, Zafar R (2015) Occurrence of taraxerol and taraxasterol in medicinal plants. Pharmacog Rev 9(17): 19-23. https://doi.org/10.4103/0973-7847.156317
Shivanika C, Deepak KS, Venkataraghavan R, Pawan T, Sumitha A, Brindha DP (2022) Molecular docking, validation, dynamics simulations, and pharmacokinetic prediction of natural compounds against the SARS-CoV-2 main-protease. J Biomol Struct Dyn 40(2): 585-611. https://doi.org/10.1080/07391102.2020.1815584
Singh AK, Singh A, Singh R, Misra A (2021) Molnupiravir in COVID-19: A systematic review of literature. Diabetes Metab Syndr 15(6): 102329. https://doi.org/10.1016/j.dsx.2021.102329
Sunil C, Irudayaraj SS, Duraipandiyan V, AlDhabi NA, Agastian P, Ignacimuthu S (2014) Antioxidant and free radical scavenging effects of ß-amyrin isolated from S. cochinchinensis Moore. leaves. Ind Crops Prod 61: 510–516. https://doi.org/10.1016/j.indcrop.2014.07.005
Tolstikov GA, Flekhter OB, Shultz EE, Baltina LA, Tolstikov AG (2005) Betulin and its derivatives. Chemistry and biological activity. Chem Sustainable Dev 13: 1-29.
Wahyuni DK, Lestari S, Kuncoro EP, Purnobasuki H (2020b) Callus induction and its metabolite profiles of Sonchus arvensis L. under temperature treatment. Ann Biol 36(2): 299–303.
Wahyuni DK, Purnobasuki H, Kuncoro EP, Ekasari W (2020a) Callus induction of Sonchus arvensis L. and its antiplasmodial activity. Afr J Infect 14: 1-7. https://doi.org/10.21010/ajid.v14i1.1
Wahyuni DK, Rahayu S, Purnama PR, Saputro TB, Suharyanto, Wijayanti N (2019) Morpho-anatomical structure and DNA barcode of Sonchus arvensis L. Biodiversitas 20(24): 17-26. https://doi.org/10.13057/biodiv/d200841
Wahyuni DK, Rahayu S, Zaidan AH, Ekasari W, Prasongsuk S, Purnobasuki H (2021) Growth, secondary metabolite production, and in vitro antiplasmodial activity of Sonchus arvensis L. callus under dolomite [CaMg(CO3)2] treatment. PLoS One 16: e0254804. https://doi.org/10.1371/journal.pone.0254804
Widyananda MH, Pratama SK, Samoedra RS, Sari FN, Kharisma VD, Ansori ANM, Antonius Y (2021) Molecular docking study of sea urchin (Arbacia lixula) peptides as multi-target inhibitor for non-small cell lung cancer (NSCLC) associated proteins. J Pharm Pharmacog Res 9(4): 484-496. https://doi.org/10.56499/jppres21.1047_9.4.484
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 J Sci 25(3): 162-171. https://doi.org/10.7454/mss.v25i3.1244
© 2022 Journal of Pharmacy & Pharmacognosy Research (JPPRes)