COMPUTATIONAL ANALYSIS, IN SILICO TOXICITY PREDICTION AND IN VITRO ANTIMICROBIAL EFFICACY OF ZINGIBER OFFICINALE ROSC. EXTRACT AGAINST PORPHYROMONAS GINGIVALIS

MINASARI; FILIA DANA TYASINGSIH; RINI OKTAVIA NASUTION; FIDELIA NAVA SHAKIRA

doi:10.22159/ijap.2024v16i6.51740

Authors

MINASARI Department of Oral Biology, and Department of Periodontics, Faculty of Dentistry, Universitas Sumatera Utara, Medan, Indonesia
FILIA DANA TYASINGSIH Department of Oral Biology, and Department of Periodontics, Faculty of Dentistry, Universitas Sumatera Utara, Medan, Indonesia
RINI OKTAVIA NASUTION Department of Oral Biology, and Department of Periodontics, Faculty of Dentistry, Universitas Sumatera Utara, Medan, Indonesia
FIDELIA NAVA SHAKIRA Department of Oral Biology, and Department of Periodontics, Faculty of Dentistry, Universitas Sumatera Utara, Medan, Indonesia

DOI:

https://doi.org/10.22159/ijap.2024v16i6.51740

Keywords:

In silico, In vitro, Ginger extract, Porphyromonas gingivalis, Physicochemical parameters, MIC, MBC

Abstract

Objective: This study aimed to determine the molecular activity, toxicity prediction and in vitro antimicrobial efficacy of Zingiber officinale Rosc Extract.

Methods: The molecular docking method was used to evaluate the antibacterial activity of the main compounds in Zingiber officinale by examining their interaction with DNA Gyrase IIb and Topoisomerase II. Chemical toxicity analysis was conducted using pK-CSM, SwissADME, and Pro-Tox II methodologies. Zingiber officinale rhizome was extracted via maceration, and its phytochemical content was determined. An in vitro antibacterial study against P. gingivalis was performed by measuring the inhibition zone using digital slide calipers and the disk diffusion method.

Results: The in silico toxicity test of the main components from Zingiber officinale revealed that gingerol, shogaols, and paradols have predicted LD50 values of 250 mg/kg, 687 mg/kg, and 2580 mg/kg, respectively, placing them in toxicity classes 3, 4, and 5. Their average similarity is 100% for gingerol and shogaols, and 87.52% for paradols, with prediction accuracies of 100% and 70.97%. Molecular docking indicated that gingerol, shogaols, and paradols inhibit DNA gyrase B and Topoisomerase II, which are involved in bacterial regeneration. The inhibition zones for concentrations of 60%, 40%, 20%, and 10% averaged 22.87 mm, 18.5 mm, 14.5 mm, and 11.31 mm, respectively, with Minimum Inhibitory Concentration (MIC) values of 10% and Minimum Bactericidal Concentration (MBC) values of 40%, showing the highest inhibition zone at 60%.

Conclusion: Zingiber officinale rhizome extract showed growth inhibition activity of Porphyromonas gingivalis ATCC®33277™.

Downloads

Download data is not yet available.

References

Mysak J, Podzimek S, Sommerova P, Lyuya-Mi Y, Bartova J, Janatova T. Porphyromonas gingivalis: major periodontopathic pathogen overview. J Immunol Res. 2014;2014(1):476068. doi: 10.1155/2014/476068, PMID 24741603.

Rashmi KJ, Tiwari R. Pharmacotherapeutic properties of ginger and its use in diseases of the oral cavity: a narrative review. Journal of Advanced Oral Research. 2016 May;7(2):1-6. doi: 10.1177/2229411220160201.

Supu RD, Diantini A, Levita J. Red ginger (Zingiber officinale var. rubrum): its chemical constituents pharmacological activities and safety. Fitofarmaka Jurnal Ilmiah Farmasi. 2019 May;8(1):23-9. doi: 10.33751/jf.v8i1.1168.

Baskaran Subramani, Baradwaj RG. Antibacterial anti-oxidant and in vitro anticancer analysis of Zingiber officinale (L.) Rosc. JOAASR. 2016;1(6):33-49. doi: 10.46947/joaasr16201635.

Aghazadeh M, Zahedi Bialvaei A, Aghazadeh M, Kabiri F, Saliani N, Yousefi M. Survey of the antibiofilm and antimicrobial effects of Zingiber officinale (in vitro study). Jundishapur J Microbiol. 2016 Feb;9(2):e30167. doi: 10.5812/jjm.30167, PMID 27127591.

Murugesan S, Venkateswaran MR, Jayabal S, Periyasamy S. Evaluation of the antioxidant and anti-arthritic potential of Zingiber officinale Rosc. by in vitro and in silico analysis. S Afr J Bot. 2020 May 1;130:45-53. doi: 10.1016/j.sajb.2019.12.019.

Kaushik S, Jangra G, Kundu V, Yadav JP, Kaushik S. Anti-viral activity of Zingiber officinale (Ginger) ingredients against the chikungunya virus. Virus Disease. 2020 Sep;31(3):270-6. doi: 10.1007/s13337-020-00584-0, PMID 32420412.

Al-khazraji SM, Hossain MH, Hassoon AS. Estimation of some bioactive substances and antibacterial activity of Zingiber officinale (Ginger) extract. JBB. 2022 Aug 1;1(2):29-33. doi: 10.57238/jbb.2022.5544.1017.

Yuandani JI, Jantan I, Haque MA, Rohani AS, Nugraha SE, Salim E. Immunomodulatory effects and mechanisms of the extracts and secondary compounds of Zingiber and Alpinia species: a review. Front Pharmacol. 2023 Jul 18;14:1222195. doi: 10.3389/fphar.2023.1222195, PMID 37533631.

Marianne M, Mariadi M, Nugraha SE, Nasution R, Syuhada PN, Pandiangan S. Characteristics and hepatoprotective activity of the Curcuma heyneana rhizome extract toward wistar rats induced by ethanol. Jundishapur J Nat Pharm Prod. 2021 Nov 30;16(4). doi: 10.5812/jjnpp.112653.

Banu KS, Cathrine L. General techniques involved in phytochemical analysis. Intr J Adv Res Chem Sci. 2015;2(4):25-32. doi: 10.20431/2349-0403.0204005.

Roney M, Issahaku AR, Forid MS, Huq AK, Soliman ME, Mohd Aluwi MF. In silico evaluation of usnic acid derivatives to discover potential antibacterial drugs against DNA gyrase B and DNA topoisomerase IV. J Biomol Struct Dyn. 2023;41(24):14904-13. doi: 10.1080/07391102.2023.2193996, PMID 36995164.

Dighe SN, Collet TA. Recent advances in DNA gyrase targeted antimicrobial agents. Eur J Med Chem. 2020 Aug 1;199:112326. doi: 10.1016/j.ejmech.2020.112326, PMID 32460040.

Martins DA Silva AY, Arouche TS, Siqueira MR, Ramalho TC, DE Faria LJ, Gester RM. SARS-CoV-2 external structures interacting with nanospheres using docking and molecular dynamics. J Biomol Struct Dyn. 2023 Sep 1:1-16. doi: 10.1080/07391102.2023.2252930.

Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC. UCSF Chimera a visualization system for exploratory research and analysis. J Comput Chem. 2004 Oct;25(13):1605-12. doi: 10.1002/jcc.20084, PMID 15264254.

Gluge J, McNeill K, Scheringer M. Getting the smiles right: identifying inconsistent chemical identities in the ECHA database pubchem and the comptox chemicals dashboard. Environ Sci Adv. 2023;2(4):612-21. doi: 10.1039/D2VA00225F.

Ayipo YO, Ahmad I, Najib YS, Sheu SK, Patel H, Mordi MN. Molecular modelling and structure-activity relationship of a natural derivative of o-hydroxybenzoate as a potent inhibitor of dual NSP3 and NSP12 of SARS-CoV-2: in silico study. J Biomol Struct Dyn. 2023;41(5):1959-77. doi: 10.1080/07391102.2022.2026818, PMID 35037841.

Mallikarjunayya Mathapati, Akash More, Ujwal Gajbe, Deepti Shrivastava. Comparative study of effect of GnRH protocols on the quality and the quantity of oocytes retrieved and embryos form. Journal of Pharmaceutical Negative Results. 2022 Oct 7;13(3):1081-4. doi: 10.47750/pnr.2022.13.03.175.

Parvekar P, Palaskar J, Metgud S, Maria R, Dutta S. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of silver nanoparticles against staphylococcus aureus. Biomater Investig Dent. 2020;7(1):105-9. doi: 10.1080/26415275.2020.1796674, PMID 32939454.

Sukandar EY, Fidrianny IR, Susanto ER, Safitri DE. The study of antifungal activity from indigenous plants from Indonesia: an in vitro study. Asian J Pharm Clin Res. 2017;10(1):196-201. doi: 10.22159/ajpcr.2017.v10i1.14838.

Yit KH, Zainal Abidin Z. Antimicrobial potential of natural compounds of Zingiberaceae plants and their synthetic analogues: a scoping review of in vitro and in silico approaches. Curr Top Med Chem. 2024 May 1;24(13):1158-84. doi: 10.2174/0115680266294573240328050629, PMID 38584545.

Rigane G, Mnif S, Ben Salem R. One-step purification of 6-shogaol from Zingiber officinale rosco a phenolic compound having a high effectiveness against bacterial strains. Rev Roum Chim. 2018;63(1):5-10.

Lorna Hamman L, Hyedima Garba S, Watson Jacks T, Vandi Zirahei J, Isaac Dibal N, Orendu Oche Attah M. Acute toxicity and effect of prolonged oral administration of Zingiber officinale ethanol extract on liver and kidney histology in rats. AJBAR. 2022 Jun 29;17-23. doi: 10.55639/607fedc.

Mohammed SA, Aliyu AY. Comparative phytochemical screening and acute toxicity study of two varieties of ginger Zingiber officinale. USci. 2022 Sep 29;1(1):6-11. doi: 10.56919/usci.1122.002.

Okediran BS, Suleiman KY, Adah AS, Sanusi F. Mitigation of lead acetate induced toxicity by ginger (Zingiber officinale). Ann Clin Toxicol. 2019;2(2):1020. doi: 10.4038/cjs.v47i2.7512.

Okesola MA, Ajiboye BO, Oyinloye BE, Ojo OA. Effect of Zingiber officinale on some biochemical parameters and cytogenic analysis in lead-induced toxicity in experimental rats. Toxicol Mech Methods. 2019 May 4;29(4):255-62. doi: 10.1080/15376516.2018.1558321, PMID 30585515.

Plengsuriyakarn T, NA Bangchang K. Preclinical toxicology and anti cholangiocarcinoma activity of oral formulation of standardized extract of Zingiber officinale. Planta Med. 2020 Jan;86(2):104-12. doi: 10.1055/a-1037-4081, PMID 31777055.

Kwon JH, Chang MJ, Seo HW, Lee JH, Min BS, NA M. Triterpenoids and a sterol from the stem bark of Styrax japonica and their protein tyrosine phosphatase 1B inhibitory activities. Phytother Res. 2008;22(10):1303-6. doi: 10.1002/ptr.2484, PMID 18693295.

Giriraju A, Yunus GY. Assessment of antimicrobial potential of 10% ginger extract against streptococcus mutans Candida albicans and enterococcus faecalis: an: in vitro study. Indian J Dent Res. 2013 Jul 1;24(4):397-400. doi: 10.4103/0970-9290.118017.

Khan I, Khan A. Medicinal plants as alternative treatments for oral health problems. Asian J Pharm Clin Res. 2018;11(9):58-64. doi: 10.22159/ajpcr.2018.v11i9.24918.

Ahmed N, Karobari MI, Yousaf A, Mohamed RN, Arshad S, Basheer SN. The antimicrobial efficacy against selective oral microbes antioxidant activity and preliminary phytochemical screening of Zingiber officinale. Infect Drug Resist. 2022 Jan 1;15:2773-85. doi: 10.2147/IDR.S364175, PMID 35668854.

Abouelsoued D, Shaapan R, Elkhateeb RM, Elnattat W, Abd elhameed mohamed, Hammam AM. Therapeutic efficacy of ginger (zingiber officinale), ginseng (panax ginseng) and sage (salvia officinalis) against cryptosporidium parvum in experimentally infected mice. Nidoc-Asrt. 2020;51(2):241-51. doi: 10.21608/ejvs.2020.24183.1152.