Author(s):
Hendra Dian Adhita Dharsono, Mumu Mujahid, Eti Apriyanti, Rahmi Alma Farah Adang, Salsabila Aqila Putri, Mieke Hemiawati Satari, Dikdik Kurnia
Email(s):
adhita@fkg.unpad.ac.id
DOI:
10.52711/0974-360X.2023.00744 
Address:
Hendra Dian Adhita Dharsono1, Mumu Mujahid2, Eti Apriyanti3, Rahmi Alma Farah Adang4, Salsabila Aqila Putri5, Mieke Hemiawati Satari6, Dikdik Kurnia7
1Department of Conservative Dentistry, Faculty of Dentistry, Universitas Padjadjaran, Jl. Sekeloa Selatan 1, Bandung, 40132, Indonesia.
2Department of Conservative Dentistry, Faculty of Dentistry, Universitas Padjadjaran, Jl. Sekeloa Selatan 1, Bandung, 40132, Indonesia.
3Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Jl. Raya Bandung-Sumedang, Km.21, Jatinangor 45363 Indonesia.
4Department of Conservative Dentistry, Faculty of Dentistry, Universitas Padjadjaran, Jl. Sekeloa Selatan 1, Bandung, 40132, Indonesia.
5Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Jl. Raya Bandung-Sumedang, Km.21, Jatinangor 45363 Indonesia.
6Department of Oral Biology, Faculty of Dentistry, Universitas Padjadjaran, l. Sekeloa Selatan 1, Bandung, 40132, In
Published In:
Volume - 16,
Issue - 10,
Year - 2023
ABSTRACT:
The high prevalence of pulp and periapical disease is an important problem for dental and oral health in dentistry. Treatment of pulp and periapical disease is generally carried out utilizing root canal treatment, but the results of the treatment are often not as expected. Enterococcus faecalis is a bacterium that plays a role in the failure of root canal treatment. E. faecalis are Gram-positive bacteria that use the Muramidase B (MurB) enzyme in the biosynthesis of peptidoglycan, which will build bacteria cell walls and play an important role in protecting bacteria. Gambir (Uncaria gambir Roxb.) is an herbal plant that is used in the field of medicine and contains tannin compounds that have antibacterial activity. The purpose of this study was to predict the antibacterial activity of Gambir extracts against the MurB enzyme compared with chlorhexidine through in silico approach. The Mur B enzyme was obtained from the Protein Data Bank (PDB), and the structure of the compound (tannins and chlorhexidine) was obtained from Pubchem. Using Auto dock tools from Pyrx software for docking between the two compounds (tannin and chlorhexidine) with the MurB enzyme, and visualize using Pymol and 3D analysis using Biovia. The results showed that tannins had a binding affinity of more than -7.4 kcal.mol-1 to the MurB enzyme and chlorhexidine had a higher binding affinity than tannins. Both tannins and chlorhexidine have hydrogen bonds with the same three amino acids, that is ARG 159, GLY 123, and ASN 233. The results showed that tannins interacted with the MurB enzyme and could inhibit the action of the MurB enzyme.
Cite this article:
Hendra Dian Adhita Dharsono, Mumu Mujahid, Eti Apriyanti, Rahmi Alma Farah Adang, Salsabila Aqila Putri, Mieke Hemiawati Satari, Dikdik Kurnia. Tannin derived from Uncaria gambir Roxb. as potential Enterococcus faecalis UDP-N-Acetylenolpyruvoyl-Glucosamine Reductase (Mur Benzyme) inhibitor: In-silico antibacterial study. Research Journal of Pharmacy and Technology 2023; 16(10):.4568-4 doi: 10.52711/0974-360X.2023.00744
Cite(Electronic):
Hendra Dian Adhita Dharsono, Mumu Mujahid, Eti Apriyanti, Rahmi Alma Farah Adang, Salsabila Aqila Putri, Mieke Hemiawati Satari, Dikdik Kurnia. Tannin derived from Uncaria gambir Roxb. as potential Enterococcus faecalis UDP-N-Acetylenolpyruvoyl-Glucosamine Reductase (Mur Benzyme) inhibitor: In-silico antibacterial study. Research Journal of Pharmacy and Technology 2023; 16(10):.4568-4 doi: 10.52711/0974-360X.2023.00744 Available on: https://rjptonline.org/AbstractView.aspx?PID=2023-16-10-14
REFERENCES:
1. American Association of Endodontists. Glossary of Endodontic Terms 2015; 9:43. http://www.nxtbook.com/nxtbooks/aae/endodonticglossary2016/#/0.
2. Olcay K, Ataoglu H, Belli S. Evaluation of Related Factors in the Failure of Endodontically Treated Teeth: A Cross-sectional Study. Journal of Endodontics. 2018; 44(1):38-45. doi:10.1016/j.joen.2017.08.029
3. Setzer FC, Boyer KR, Jeppson JR, Karabucak B, Kim S. Long-term prognosis of endodontically treated teeth: A retrospective analysis of preoperative factors in molars. Journal of Endodontics. 2011;37(1):21-25. doi:10.1016/j.joen.2010.10.005
4. Hargreaves KM. Epidemiological evaluation of the outcomes of nonsurgical root canal treatment in a large cohort of insured dental patients. Journal of Endodontics. 200;27(12):791-796. doi:10.1097/00004770-200112000-00021
5. Chen SC, Chueh LH, Kate Hsiao C, Tsai MY, Ho SC, Chiang CP. An Epidemiologic Study of Tooth Retention After Nonsurgical Endodontic Treatment in a Large Population in Taiwan. Journal of Endodontics. 2007;33(3):226-229. doi:10.1016/j.joen.2006.11.022
6. Al-Timan JAA, Al-Huwaizi HF, Abed HH. Evaluating the effect of adding chitosan nanoparticles on the disinfection properties of Glyde material: An in vitro study. Research Journal of Pharmacy and Technology. 2020;13(1):255-8, doi: 10.5958/0974-360X.2020.00051.7
7. Anjana S, Beena P, Shahana S, Navas N, Mathew SC, Salim S, et al. Formulation and evaluation of intrapacket dental film of antibacterial agent for periodontitis. Research Journal of Pharmacy and Technology. 2021;14(5):2750-6, doi: 10.52711/0974-360X.2021.00485
8. Stuart CH, Schwartz SA, Beeson TJ, Owatz CB. Enterococcus faecalis: Its role in root canal treatment failure and current concepts in retreatment. Journal of Endodontics. 2006;32(2):93-98. doi:10.1016/j.joen.2005.10.049
9. Darrag AM. Antimicrobial efficacy of endodontic irrigation solutions against planktonic microorganisms and dual-species biofilm. Tanta Dental Journal. 2013;10(3):129-137. doi:10.1016/j.tdj.2013.11.005
10. Soraya C, Dharsono HDA, Aripin D, Satari MH, Kurnia D, Hilmanto D. Effects of sarang semut (Myrmecodia Pendens Merr. & Perry) extracts on Enterococcus faecalis sensitivity. Dental Journal. 2016; 49(4):175. doi:10.20473/j.djmkg.v49.i4.p175-180
11. Molander A, Reit C, Dahlén G, Kvist T. Microbiological status of root-filled teeth with apical periodontitis. International Endodontic Journal. 1998; 31(1): 1-7. doi:10.1046/j.1365-2591.1998.t01-1-00111.x
12. Alghamdi F, Shakir M. The influence of Enterococcus faecalis as a dental root canal pathogen on endodontic treatment: A systematic review. Cureus. 2020; 12(3). 10.7759/cureus.7257
13. Alghamdi F, Shakir M. The Influence of Enterococcus faecalis as a Dental Root Canal Pathogen on Endodontic Treatment : A Systematic Review Material and methods. Cureus. 2020;12(3):1-10. doi:10.7759/cureus.7257
14. Baccouri O, Boukerb AM, Farhat L Ben, et al. Probiotic Potential and Safety Evaluation of Enterococcus faecalis OB14 and OB15, Isolated from Traditional Tunisian Testouri Cheese and Rigouta, Using Physiological and Genomic Analysis. Frontiers in Microbiology. 2019; 10(APR):1-15. doi:10.3389/fmicb.2019.00881
15. Wang T, Ding J, Zhang Y, Wang DC, Liu W. Complex structure of type VI peptidoglycan muramidase effector and a cognate immunity protein. Acta Crystallography D Biological Crystallography. 2013 ;69(10): 1889-1900. doi:10.1107/S090744491301576X
16. Apriyanti E, Satari MH, Kurnia D. Potential of MurA Enzyme and GBAP in Fsr Quorum Sensing System as Antibacterial Drugs Target: In vitro and In silico Study of Antibacterial Compounds from Myrmecodia pendans. Combinatorial Chemistry and High Throughput Screening. 2020:1-10. doi:10.2174/1386207323666200628111348
17. Benson TE, Filman DJ, Walsh C, Hogle JM. An enzyme-substrate complex involved in bacterial cell wall biosynthesisNatural Structural Biology. 1995;2(8):663-673. doi:10.1038/nsb0895-644
18. El Zoeiby A, Sanschagrin F, Levesque RC. Structure and function of the Mur enzymes: Development of novel inhibitors. Molecular Microbiology. 2003;47(1):1-12. doi:10.1046/j.1365-2958.2003.03289.x
19. Mihalovits LM, FerenczyGrG, Keserű GrM. Catalytic Mechanism and Covalent Inhibition of UDP-N-Acetylglucosamine Enolpyruvyl Transferase (MurA): Implications to The Design of Novel Antibacterials. Journal of Chemical Information and Modeling. 2019; 59(12):5161-73.doi.org/10.1021/acs.jcim.9b00691
20. Gomes BPFA, Vianna ME, Zaia AA, Almeida JFA, Souza-Filho FJ, Ferraz CCR. Chlorhexidine in endodontics. Brazilian Dental Journal. 2013;24(2):89-102. doi:10.1590/0103-6440201302188
21. Gomes BPFA, et.al. Effectiveness of 2% chlorhexidine gel and calcium hydroxide against Enterococcus faecalis in bovine root dentine in vitro.International Journal of Endodontic. 2003 36(4):267-275.doi: 10.1046/j.1365-2591.2003.00634.x
22. Mohammadi Z, Abbott P V. The properties and applications of chlorhexidine in endodontics. International Endodontic Journal 2009 ;42(4):288-302. doi:10.1111/j.1365-2591.2008.01540.x
23. Madden GR, Sifri CD. Antimicrobial resistance to agents used for Staphylococcus aureus decolonization: is there a reason for concern? Current Infectious Disease Reports. 2018;20(8):1-11. doi.org/10.1007/s11908-018-0630-0
24. Pai NR, Dubhashi DS. Pharmacological evaluation of substituted benzeneacetic acid ester derivatives for their sedative, antibacterial and antifungal potential. Research Journal of Pharmacognosy and Phytochemistry. 2010;3(2):570-7, doi: 10.5958/0974-360X
25. Cieplik F, Jakubovics NS, Buchalla W, Maisch T, Hellwig E, Al-Ahmad A. Resistance toward chlorhexidine in oral bacteria-is there cause for concern? Frontiers in Microbiology. 2019; 22;10(MAR). doi:10.3389/fmicb.2019.00587
26. Bernardi A, Teixeira CS. The properties of chlorhexidine and undesired effects of its use in endodontics. Quintessence International. 2015;46(7):575-57582. doi:10.3290/j.qi.a33934
27. Chang YC, Huang FM, Tai KW, Chou MY. The effect of sodium hypochlorite and chlorhexidine on cultured human periodontal ligament cells. Oral Surgery Oral Medicine Oral Pathology Oral Radiology Endododontic. 2001;92(4):446-450. doi:10.1067/moe.2001.116812
28. Simanjuntak PA, Djauharie N, Nursasongko B. Antibacterial effectiveness of 2% chitosan and 2% chlorhexidine against Enterococcus faecalis in biofilm (Laboratory experiment). International Journal of Applied Pharmaceutics. 2019;11(1):44-48. doi:10.22159/ijap.2019.v11s1.163
29. Zeroual S, Daoud I, Gaouaoui R, Ghalem S. In vitro and molecular docking studies of DPPH with Phoenix dactylifera L.(Deglet-Nour) crude fruits extracts and evaluation of their antioxidant activity. Asian Journal of Research in Chemistry. 2020;13(1):52-9, doi: 10.5958/0974-4150.2020.00012.7
30. Lakshmanan K, Balasubramanian HB, Aiyalu R, Ramasamy A. Molecular docking studies of flavones in Gentianaceae family against liver corrective targets. Research Journal of Pharmacognosy and Phytochemistry. 2019;11(2):49-53, doi: 10.5958/0975-4385.2019.00010.4
31. Carvalho RS, Carollo CA, de Magalhães JC, et al. Antibacterial and antifungal activities of phenolic compound-enriched ethyl acetate fraction from Cochlospermum regium (mart. Et. Schr.) Pilger roots: Mechanisms of action and synergism with tannin and gallic acid. South African Journal of Botany. 2018; 114:181-187. doi:10.1016/j.sajb.2017.11.010
32. Katu H, Kirana Mattulada I, Samad R, Hatta M, As S. Inhibitory Concentration and Minimum Contact Time Gambir Extract (Uncaria gambier Roxb) Against Bacterial Growth Enterococcus faecalis. International Jurnal of Sciences: Basic Applied Research. 2016;27(3):239-246. https://www.researchgate.net/deref/http%3A%2F%2Fgssrr.org%2Findex.php%3Fjournal%3DJournalOfBasicAndApplied
33. Girard M, Bee G. Invited review: Tannins as a potential alternative to antibiotics to prevent coliform diarrhea in weaned pigs. Animal. 2020;14(1):95-107. doi:10.1017/S1751731119002143
34. Maisetta G, Batoni G, Caboni P, Esin S, Rinaldi AC, Zucca P. Tannin profile, antioxidant properties, and antimicrobial activity of extracts from two Mediterranean species of parasitic plant Cytinus. BMC Complementary and Alternative Medicine. 2019;19(1):1-11. doi:10.1186/s12906-019-2487-7
35. Omojate GC, Enwa FO, Jewo AO, Eze CO. Mechanisms of Antimicrobial Actions of Phytochemicals against Enteric Pathogens – A Review. Journal of Pharmaceutical, Chemical, and Biological Sciences. 2014;2(2):77-85.
36. Akiyama H, Fujii K, Yamasaki O, Oono T, Iwatsuki K. Antibacterial action of several tannins against Staphylococcus aureus. Journal of Antimicrobial Chemotherapy. 2001; 48(4):487-491. doi:10.1093/jac/48.4.487
37. Dharsono HDA, Wibisono L, Apriyanti E, Hayati AT, Satari MH, Kurnia D. Mode action prediction of catechin from Uncariagambir Roxb. against UDP-N-acetylenolpyruvyl-glucosamine reductase (MurB enzyme) of Streptococcus mutans: In silico study. Journal of Advanced Pharmaceutical Technology and Research. 2022; 13(3): 197-201.doi: 10.4103/japtr.japtr_313_21
38. Ferreira LG, Dos Santos RN, Oliva G, Andricopulo AD. Molecular Docking and Structure-Based Drug Design Strategies. Molecules. 2015;20(7):13384-421. 10.3390/molecules200713384
39. Boittier ED, Tang YY, Buckley ME, Schuurs ZP, Richard DJ, Gandhi NS. Assessing Molecular Docking Tools to Guide Targeted Drug Discovery of CD38 Inhibitors. International Journal of Molecular Sciences. 2020;21(15):5183. doi.org/10.3390/ijms21155183
40. Geldenhuys WJ, Gaasch KE, Watson M, Allen DD, Van Der Schyf CJ. Optimizing the use of open-source software applications in drug discovery. Drug Discovery Today. 2006;11(3-4):127-132. doi:10.1016/S1359-6446(05)03692-5
41. Pawar RP, Rohane SH. Role of autodock vina in PyRx molecular docking. Asian Journal of Research in Chemistry. 2021 Nov;14(2):132-4, doi: 10.5958/0974-4150.2021.00024.9
42. Sindhu T, Akhilesh K, Jose A, Binsiya K, Thomas B, Wilson E. Antibacterial screening of Clerodendrum infortunatum leaves: experimental and molecular docking studies. Asian Journal of Research in Chemistry. 2020;13(2):128-32, doi: 10.5958/0974-4150.2020.00026.7
43. Padmini R, Sitrarasi R, Razia M. Molecular docking studies of bioactive compounds from Allium sativum against EML4-ALK receptor. Research Journal of Pharmacy and Technology. 2017; 10(11):3741-7, doi:10.5958/0974-360X.2017.00679.5
44. Kumar MS, Aanandhi MV. An insight into the therapeutic potential of pyridopyrimidines as anticancer agents. Research Journal of Pharmacy and Technology. 2018;11(3):1259-69, doi: 10.5958/0974-360X.2018.00235.4
45. Bagal A, Borkar T, Ghige T, Kulkarni A, Kumbhar A, Devane G, et al. Molecular docking–useful tool in drug discovery. Asian Journal of Research in Chemistry. 2022;15(2):129-32, doi: 10.52711/0974-4150.2022.00020
46. Rodrigues CG, et.al. Antibacterial activity of tannins from Psidium guineenseSw. (Myrtaceae). Journal of Medicinal Plant Research. 2014; 8(35):1095-1100, doi: 10.5897/JMPR2014.5500
47. Agostini-Costa TS, et.al. Total phenolics, flavonoids, tannins and antioxidant activity of lima beans conserved in a Brazilian Genebank; Ciênca Rural. 2015; 45(2):335-341.doi: 10.1590/0103-8478cr20140030
48. Cavalcanti-Dantas VM, et.al. Taninos: principal componente do extratoPiptadeniastipulacea(Benth) Duckeinibe o crescimento de cepasclínicas de Staphylococcus aureusde origem bovina. Biotemas. 2016; 29 (1): 109-114. doi: 10.5007/2175-7925.2016v29n1p109
49. Pereira AV, Góis MB, Azevêdo TKB, et al. Effects of associations of tannins from Anacardium occidentale and Anadenanthera colubrina with cephalosporin against bovine Staphylococcus aureusisolates. Arquivos de Instituto Biológica (Sao Paulo). 2018; 85(0): 1-8. doi:10.1590/1808-1657000582016
50. Smith AH, Zoetendal E, Mackie RI. Bacterial mechanisms to overcome inhibitory effects of dietary tannins. Microbial Ecology. 2005; 50(2): 80-x197-205.doi:10.1007/s00248-004-0180-x