A novel antiviral candidate from Moringa oleifera through dual targeting mechanism of SARS-CoV-2 protease: Computational Sscreening
Abstract
COVID-19 is triggered by SARS-CoV-2 which is related in a similar way to SARS-CoV and MERS-CoV. RdRp is an essential component of the virus in replication and transcription. RdRp triggers polymerase activity through binding to cofactors such as nsp7 and nsp8. Mpro plays an important role in viral protease activity for the assembly process. RdRp and Mpro can be used as targets to inhibit the replicative activity of SARS-CoV-2. Moringa oleifera is used by people around the world as a traditional medicine because it has antioxidant, anti-inflammatory, and antiviral properties. This study reveals the molecular mechanism of Moringa oleifera as an inhibitor of key proteins in SARS-CoV-2 replication through a computational approach. Additionally, the in silico method in this study consists of sample preparation in the database, druglikeness prediction, antiviral probability, virtual screening, chemical bond interaction, and 3D visualization. Moringa oleifera may have potential as an antiviral candidate through Ellagic Acid activity as a dual inhibitor through inhibition of SARS-CoV-2 replication and assembly. The candidate compound can generate weak bonding interactions such as hydrogen and hydrophobic to trigger binding stability at specific domains.
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Hu B, Guo H, Zhou P, Shi ZL. Characteristics of SARS-CoV-2 and COVID-19. Nat Rev Microbiol. 2021;19(3):141-154. doi: 10.1038/s41579-020-00459-7. Epub 2020 Oct 6.
Holmes EC, Goldstein SA, Rasmussen AL, Robertson DL, Crits-Christoph A, Wertheim JO, Anthony SJ, Barclay WS, Boni MF, Doherty PC, Farrar J, Geoghegan JL, Jiang X, Leibowitz JL, Neil SJD, Skern T, Weiss SR, Worobey M, Andersen KG, Garry RF, Rambaut A. The origins of SARS-CoV-2: A critical review. Cell. 2021;184(19):4848-4856. doi: 10.1016/j.cell.2021.08.017.
Jin Z, Wang H, Duan Y, Yang H. The main protease and RNA-dependent RNA polymerase are two prime targets for SARS-CoV-2. Biochem Biophys Res Commun. 2021;538:63-71. doi: 10.1016/j.bbrc.2020.10.091.
Pathania S, Rawal RK, Singh PK. RdRp (RNA-dependent RNA polymerase): A key target providing anti-virals for the management of various viral diseases. J Mol Struct. 2022;1250:131756. doi: 10.1016/j.molstruc.2021.131756.
Uengwetwanit T, Chutiwitoonchai N, Wichapong K, Karoonuthaisiri N. Identification of novel SARS-CoV-2 RNA dependent RNA polymerase (RdRp) inhibitors: From in silico screening to experimentally validated inhibitory activity. Comput Struct Biotechnol J. 2022;20:882-890. doi: 10.1016/j.csbj.2022.02.001.
Biswas SK, Mudi SR. Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. Genomics Inform. 2020;18(4):e44. doi: 10.5808/GI.2020.18.4.e44.
Mishra A, Rathore AS. RNA dependent RNA polymerase (RdRp) as a drug target for SARS-CoV2. J Biomol Struct Dyn. 2022;40(13):6039-6051. doi: 10.1080/07391102.2021.1875886.
Fan Q, Zhang B, Ma J, Zhang S. Safety profile of the antiviral drug remdesivir: An update. Biomed Pharmacother. 2020;130:110532. doi: 10.1016/j.biopha.2020.110532.
Goyal B, Goyal D. Targeting the Dimerization of the Main Protease of Coronaviruses: A Potential Broad-Spectrum Therapeutic Strategy. ACS Comb Sci. 2020;22(6):297-305. doi: 10.1021/acscombsci.0c00058.
Rossetti GG, Ossorio MA, Rempel S, Kratzel A, Dionellis VS, Barriot S, Tropia L, Gorgulla C, Arthanari H, Thiel V, Mohr P, Gamboni R, Halazonetis TD. Non-covalent SARS-CoV-2 Mpro inhibitors developed from in silico screen hits. Sci Rep. 2022;12(1):2505. doi: 10.1038/s41598-022-06306-4.
Xiong Y, Rajoka MSR, Mehwish HM, Zhang M, Liang N, Li C, He Z. Virucidal activity of Moringa A from Moringa oleifera seeds against Influenza A Viruses by regulating TFEB. Int Immunopharmacol. 2021;95:107561.
Kharisma VD, Kharisma SD, Ansori ANM, Kurniawan HP, Witaningrum AM, Fadholly A, Tacharina MR. Antiretroviral Effect Simulation from Black Tea (Camellia sinensis) via Dual Inhibitors Mechanism in HIV-1 and its Social Perspective in Indonesia. Res J Pharm Technol. 2021;14(1): 455-460. doi: 10.5958/0974-360X.2021.00083.4
Fadholly A, Ansori ANM, Kharisma VD, Rahmahani J, Tacharina MR. Immunobioinformatics of Rabies Virus in Various Countries of Asia: Glycoprotein Gene. Res J Pharm Technol. 2021; 14(2): 883-886. doi: 10.5958/0974-360X.2021.00157.8
Ansori ANM, Fadholly A, Proboningrat A, Hayaza S, Susilo RJK, Naw SW, Posa GAV, Yusrizal YF, Sibero MT, Sucipto TH, Soegijanto S. In vitro antiviral activity of Pinus merkusii (Pinaceae) stem bark and cone against dengue virus type-2 (DENV-2). Res J Pharm Technol. 2021;14(7):3705-8. doi: 10.52711/0974-360X.2021.00641
Ansori ANM, Kharisma VD, Fadholly A, Tacharina MR, Antonius Y, Parikesit AA. Severe Acute Respiratory Syndrome Coronavirus-2 Emergence and Its Treatment with Alternative Medicines: A Review. Res J Pharm Technol. 2021;14(10):5551-7. doi: 10.52711/0974-360X.2021.00967
Ansori ANM, Kharisma VD, Solikhah TI. Medicinal properties of Muntingia calabura L.: A Review. Res J Pharm Technol. 2021;14(8):4509-2. doi: 10.52711/0974-360X.2021.00784
Proboningrat A, Kharisma VD, Ansori ANM, Rahmawati R, Fadholly A, Posa GAV, Sudjarwo SA, Rantam FA, Achmad AB. In silico Study of Natural inhibitors for Human papillomavirus-18 E6 protein. Res J Pharm Technol. 2022; 15(3):1251-6. doi: 10.52711/0974-360X.2022.00209
Kharisma VD, Ansori ANM, Jakhmola V, Rizky WC, Widyananda MH, Probojati RT, Murtadlo AAA, Rebezov M, Scherbakov P, Burkov P, Matrosova Y, Romanov A, Sihombing MAEM, Antonius Y, Zainul R. Multi-strain human papillomavirus (HPV) vaccine innovation via computational study: A mini review. Res J Pharm Technol. 2022; 15(8):3802-7. doi: 10.52711/0974-360X.2022.00638
Fahmi M, Kharisma VD, Ansori ANM, Ito M. Retrieval and Investigation of Data on SARS-CoV-2 and COVID-19 Using Bioinformatics Approach. Adv Exp Med Biol. 2021; 1318:839-857. doi: 10.1007/978-3-030-63761-3_47
Kharisma VD, Probojati RT, Murtadlo AAA, Ansori ANM, Antonius Y, Tamam MB. Revealing Potency of Bioactive Compounds as Inhibitor of Dengue Virus (DENV) NS2B/NS3 Protease from Sweet Potato (Ipomoea batatas L.) Leaves. Indian J Forensic Med Toxicol. 2020; 15(1): 1627–1632. doi: 10.37506/ijfmt.v15i1.13644
Turista DDR, Islamy A, Kharisma VD, Ansori ANM. Distribution of COVID-19 and Phylogenetic Tree Construction of SARS-CoV-2 in Indonesia. J Pure Appl Microbiol. 2020; 14: 1035-1042. doi: 10.22207/JPAM.14.SPL1.42
Kharisma VD, Widyananda MH, Ansori ANM, Nege AS, Naw SW, Nugraha AP Tea catechin as antiviral agent via apoptosis agonist and triple inhibitor mechanism against HIV-1 infection: A bioinformatics approach. J Pharm Pharmacogn Res. 9(4):435-445.
Kharisma VD, Ansori ANM, Nugraha AP. Computational study of ginger (Zingiber Officinale) as E6 inhibitor in human papillomavirus type 16 (Hpv-16) infection. Biochemical and Cellular Archives. 2020; 20:3155-3159. doi: 10.35124/bca.2020.20.S1.3155
Ansori ANM, Kharishma VD, Muttaqin SS, Antonius Y, Parikesit AA. Genetic Variant of SARS-CoV-2 Isolates in Indonesia: Spike Glycoprotein Gene. J Pure Appl Microbiol. 2020;14: 971-978. doi: 10.22207/JPAM.14.SPL1.35
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 Pharmacogn Res. 9(4):484–496.
Kharisma VD, Ansori ANM. Construction of Epitope-Based Peptide Vaccine Against SARS-CoV-2: Immunoinformatics Study. J Pure Appl Microbiol. 2020;14:999-1005. doi: 10.22207/JPAM.14.SPL1.38
Kharisma VD, Ansori ANM, Widyananda MH, Utami SL, Nugraha AP. Molecular simulation: The potency of conserved region on E6 HPV-16 as a binding target of black tea compounds against cervical cancer. Biochem Cell Arch. 2020;20: 2795-2802. doi: 10.35124/bca.2020.20.S1.2795
Kharisma VD, Agatha A, Ansori ANM, Widyananda MH, Rizky WC, Dings TGA, Derkho M, Lykasova I, Antonius Y, Rosadi I, Zainul R. 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. 2022;10(1):138-146.doi: 10.56499/jppres21.1174_10.1.138
Wijaya RM, Hafidzhah MA, Kharisma VD, Ansori ANM, Parikesit AP. COVID-19 In Silico Drug with Zingiber officinale Natural Product Compound Library Targeting the Mpro Protein. Makara J Sci. 2021;25(3):5. doi: 10.7454/mss.v25i3.1244
Ansori ANM, Fadholly A, Kharisma VD, Nugraha AP. Therapeutic potential of avian paramyxovirus serotype 1 for cancer therapy. Biochem Cell Arch. 2020;20:2827-2832. DOI: 10.35124/bca.2020.20.S1.2827
Prahasanti C, Nugraha AP, Kharisma VD, Ansori ANM, Ridwan RD, Putri TPS et al. Un enfoque bioinformático de la exploración con compuestos de hidroxiapatita y polimetilmetacrilato como biomaterial de implantes dentales. J Pharm Pharmacog Res. 2021;9(5):746-754.
Kharisma VD, Ansori ANM, Fadholly A, Sucipto TH. Molecular mechanism of caffeine-aspirin interaction in kopi balur 1 as anti-inflammatory agent: A computational study. Indian J Forensic Med Toxicol. 2020;14(4):4040-4046. doi: 10.37506/ijfmt.v14i4.12274
Kharisma VD, Widodo N, Ansori ANM, Nugraha AP. A vaccine candidate of zika virus (ZIKV) from polyvalent conserved b-cell epitope on viral glycoprotein: In silico approach. Biochem Cell Arch. 2020;20:2785-2793. doi: 10.35124/bca.2020.20.S1.2785
Ansori ANM, Kharisma VD, Nugraha AP. Phylogenetic and pathotypic characterization of avian paramyxovirus serotype 1 (APMV-1) in Indonesia. Biochem Cell Arch. 2020;20:3023-3027. doi: 10.35124/bca.2020.20.S1.3023
Padmi H, Kharisma VD, Ansori ANM, Sibero MT, Widyananda MH, Ullah E, Gumenyuk O, Chylichcova S, Bratishko N, Prasedya ES, Sucipto TH, Zainul R. Macroalgae Bioactive Compounds for the Potential Antiviral of SARS-CoV-2: An In Silico Study. J Pure App Microbiol. 2022;16(2):1018-1027. doi: 10.22207/JPAM.16.2.26
Antonius Y, Kharisma VD, Widyananda MH, Ansori ANM, Trinugroho JP, Ullah ME, Naw SW, Jakhmola V, Wahjudi M. Prediction of Aflatoxin-B1 (AFB1) Molecular Mechanism Network and Interaction to Oncoproteins Growth Factor in Hepatocellular Carcinoma. J Pure Appl Microbiol. 2022;16(3):1844-1854. doi: 10.22207/JPAM.16.3.29
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. Utilization of Secondary Metabolites in Algae Kappaphycus alvarezii as a Breast Cancer Drug with a Computational Method. Pharmacog J. 2022;14(3):536-543. doi: 10.5530/pj.2022.14.68
Aini NS, Ansori ANM, Kharisma VD, Syadzha MF, Widyananda MH, Murtadlo AA, et al. Potential Roles of Purslane (Portulaca oleracea L.) as Antimetabolic Syndrome: A Review. Pharmacog J. 2022;14(3):710-714. doi: 10.5530/pj.2022.14.90
Listiyani P, Kharisma VD, Ansori AN, Widyananda MH, Probojati RT, Murtadlo AA, et al. In Silico Phytochemical Compounds Screening of Allium sativum Targeting the Mpro of SARS-CoV-2. Pharmacog J. 2022;14(3):604-609. doi: 10.5530/pj.2022.14.78
Ansori AN, Kharisma VD, Parikesit AA, Dian FA, Probojati RT, Rebezov M, Scherbakov P, Burkov P, Zhdanova G, Mikhalev A, Antonius Y, Pratama MRF, Sumantri NI, Sucipto TH, Zainul R. Bioactive Compounds from Mangosteen (Garcinia mangostana L.) as an Antiviral Agent via Dual Inhibitor Mechanism against SARS-CoV- 2: An In Silico Approach. Phcog J. 2022;14(1):85-90. doi: 10.5530/pj.2022.14.12
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