Triple Inhibitor Mechanism of Antiretroviral from Sambucus nigra Phytochemical through Screening Docking
Keywords:
Antiviral, Computational Screening, Bioactivity, Green Tea, PhytochemicalAbstract
Human immunodeficiency virus type 1 (HIV-1) has a higher infectious nature than HIV-2 because of the genetic drift mechanism. Several HIV-1 strains such as A, B, C, D, E, F, G, H, & J were obtained from Africa, Asia, Europe, Australia, and America. Endemic cases of HIV-1 are often found and HIV-2 is very rare, therefore the development of antiretroviral drugs is currently focused on treating HIV-1 infection5. Research on HIV-1 vaccines is still in the research phase and some patients are only taking antiretrovirals to survive. Sambucus nigra L. is used by the community for traditional medicine such as influenza A, B, C and SARS-CoV-2 infectious diseases. There are no research reports related to the potential of Sambucus nigra L. as an antiretroviral in the treatment of HIV-1 infection and the specific molecular mechanisms that explain it, therefore this research is important for the discovery of alternative antiretroviral drugs from natural materials. The in silico method used in this study consists of Sambucus nigra L. compounds retrieval, HIV-1 protein preparation, molecular docking, and 3D visualization. Sambucus nigra L. can have inhibitory activity on three enzymes of HIV-1 such as protease (PR), reverse transcriptase (RT), integrase (INT) through naringenin and Cyanidin-3,5-diglucoside compounds. Both compounds have more negative binding energy, form stable binding interactions in the target domain, and trigger inhibitory activity.
References
Huerta L. Editorial: Anti-infective 2020: HIV-From pathogenesis to treatment. Curr Opin Pharmacol. 2020; 54: x-xii. DOI: 10.1016/j.coph.2020.
Porter RS, Bode RF. A Review of the Antiviral Properties of Black Elder (Sambucus nigra L.) Products. Phytother Res. 2017; 31(4): 533-554. DOI: 10.1002/ptr.5782.
Mahboubi M. Sambucus nigra (black elder) as alternative treatment for cold and flu. ADV TRADIT MED (ADTM). 2021;21(3):405–14. DOI: 10.1007/s13596-020-00469-z.
Asgary S, Pouramini A. The Pros and Cons of Using Elderberry (Sambucus nigra) for Prevention and Treatment of COVID-19. Adv Biomed Res. 2022; 11: 96. DOI: 10.4103/abr.abr_146_21.
Ramadhani NF, Nugraha AP, Ihsan IS, Agung YA, Rantam FA, Ernawati DS et al. Gingival medicinal signaling cells conditioned medium effect on the osteoclast and osteoblast number in lipopolysaccharide-induced calvaria bone resorption in wistar rats’ (Rattus novergicus). Research Journal of Pharmacy and Technology. 2021; 14(10): 5232-5237. DOI: 10.52711/0974-360X.2021.00911
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
Husen SA, Winarni D, Salamun, Ansori ANM, Susilo RJK, Hayaza S. Hepatoprotective Effect of Gamma-mangostin for Amelioration of Impaired Liver Structure and Function in Streptozotocin-induced Diabetic Mice. IOP Conference Series: Earth and Environmental Science. 2019; 217(1): 012031. DOI: 10.1088/1755-1315/217/1/012031
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.
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. 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. 2021; 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. Biochemical and Cellular Archives. 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. Biochemical and Cellular Archives. 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. Journal of Pharmacy and Pharmacognosy Research. 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 Journal of Forensic Medicine and Toxicology. 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. Biochemical and Cellular Archives. 2020;20:2785-2793. DOI: 10.35124/bca.2020.20.S1.2785
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. Journal of Pure and Applied Microbiology. 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. Pharmacognosy Journal. 2022; 14(3): 536-543. DOI: 10.5530/pj.2022.14.68
Młynarczyk K, Walkowiak-Tomczak D, Łysiak GP. Bioactive properties of Sambucus nigra L. as a functional ingredient for food and pharmaceutical industry. J Funct Foods. 2018; 40: 377-390. DOI: 10.1016/j.jff.2017.11.025.
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. Pharmacognosy Journal. 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. Pharmacognosy Journal. 2022; 14(3): 604-609. DOI: 10.5530/pj.2022.14.78
Aini NS, Kharisma VD, Widyananda MH, Murtadlo AA, Probojati RT, Turista DD, et al. In Silico Screening of Bioactive Compounds from Syzygium cumini L. and Moringa oleifera L. Against SARS-CoV-2 via Tetra Inhibitors. Pharmacognosy Journal. 2022;14(4):267-272. DOI: 10.5530/pj.2022.14.95
Aini NS, Kharisma VD, Widyananda MH, Murtadlo AA, Probojati RT, Turista DD, et al. Bioactive Compounds from Purslane (Portulaca oleracea L.) and Star Anise (Illicium verum Hook) as SARS-CoV-2 Antiviral Agent via Dual Inhibitor Mechanism: In Silico Approach. Pharmacognosy Journal. 2022;14(4):352-357. DOI: 10.5530/pj.2022.14.106
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
Wicaksono A, Kharisma VD, Parikesit AA. New Perspectives on Reverse Translation: Brief History and Updates. Universitas Scientiarum. 2023; 28(1): 1-20.
Ningrum SG, R Sasmita, Kharisma VD. Edible Bird’s Nest as Potential Food with Anti-Viral and Anti-Inflammatory Properties Against Covid-19: an in Silico Study. 2023; 11(1): 43-50
