Evaluation of antibacterial potential of oxazole derivative compounds against Mirolysin toxin of Tannerella forsythia using In silico molecular docking and Admet prediction

Main Article Content

S. Vidyashri
Parkavi Arumugam
Rajalakshmanan Eswaramoorthy

Keywords

In silico analysis, Molecular Docking, Periodontitis, Drug designing, Mirolysin, Tanerella Forsythia

Abstract

Introduction: mirolysin is a metalloproteinase secreted by Tannerella forsythia which is associated with periodontitis. Mirolysin inhibits the classical and lectin complement pathways. contribute to excessive and sustained inflammation at the site of infection. In this study we are analyzing the antimicrobial potential of oxazole compounds against the Mirolysin toxin of T. forsythia via insilico targeting.
Materials and Methods: 7 oxazole ligands were fabricated using Chem-Draw and Chem-3D software. The structure of the receptor molecule Mirolysin was downloaded from the protein databank. The preparation of the Mirolysin protein of T. forsythia was done using Biovia discovery studio. The ligand-protein interaction was assessed via Auto-Doc Vina. The data was the input into SwissADME and PROTOX softwares to assess their efficiency, potential side effects and toxicity.
Results: The docking score of all 7 prepared drugs shows better affinity than the control groups indicating increased efficacy of the drugs. VD2, VD4, VD5, VD6, VD7 show good GI absorption. The toxicity class of all drugs were 4 and based on the hepatotoxicity, carcinogenicity, immunotoxicity, mutagenicity and cytotoxicity, it can be seen that VD2, VD5 and VD7 are relatively safer groups of drugs.


Conclusion: Based on the toxicity levels and properties of the drugs VD2, VD5 and VD7 are potential drug candidates for further development. The prepared drugs showed better properties when compared to the clinically available compounds. Thus, further development of the lead molecules will aid in better treatment regimen.

Abstract 114 | pdf Downloads 90

References

1. Cavasotto CN. In Silico Drug Discovery and Design: Theory, Methods, Challenges, and Applications. CRC Press; 2015. 558 p.
2. Roy K. In Silico Drug Design: Repurposing Techniques and Methodologies. Academic Press; 2019. 886 p.
3. Brogi S, Castro Ramalho T, Medina-Franco JL, Kuca K, Valko M. In Silico Methods for Drug Design and Discovery. Frontiers Media SA; 2020.
504 p.
4. Leon D, Markel S. In Silico Technologies in Drug Target Identification and Validation. CRC Press; 2006. 504 p.
5. Brown N. In Silico Medicinal Chemistry: Computational Methods to Support Drug Design. Royal Society of Chemistry; 2015. 232 p.
6. Rudrapal M, Egbuna C. Computer Aided Drug Design (CADD): From Ligand-Based Methods to Structure-Based Approaches. Elsevier; 2022. 322 p.
7. Sahilu R, Eswaramoorthy R, Mulugeta E, Dekebo A. Synthesis, DFT analysis, dyeing potential and evaluation of antibacterial activities of azo dye derivatives combined with in-silico molecular docking and ADMET predictions [Internet]. Vol. 1265, Journal of Molecular Structure. 2022. p. 133279. Available from: http://dx.doi.org/10.1016/j.molstruc.2022.133279
8. Speck-Planche A. Multi-Scale Approaches in Drug Discovery: From Empirical Knowledge to In silico Experiments and Back. Elsevier; 2017. 238 p.
9. Onishi H, Shin K. Involvement of Tannerella forsythia virulence factor Forsythia detaching factor in periodontitis [Internet]. Vol. 55, Nihon
Shishubyo Gakkai Kaishi (Journal of the Japanese Society of Periodontology). 2013. p. 249–55. Available from: http://dx.doi.org/10.2329/perio.55.249
10. Antonyuk SV, Strange RW. Crystal structure of Tannerella forsythia Apo HmuY analog (TFO) [Internet]. 2018. Available from: http://dx.doi.org/10.2210/pdb6eu8/pdb
11. Onishi S. The Role of Tannerella Forsythia BspA Protein in Host-cell Interactions. 2009. 89 p.
12. Sharma A. Virulence mechanisms of Tannerella forsythia [Internet]. Vol. 54, Periodontology 2000. 2010. p. 106–16. Available from: http://dx.doi.org/10.1111/j.1600-0757.2009.00332.x
13. Choi YJ, Jung YJ, An SJ, Choi BK. Bone resorption by Tannerella forsythia GroEL [Internet]. Bone Abstracts. 2016. Available from:
http://dx.doi.org/10.1530/boneabs.5.p173
14. Rodriguez-Banqueri A, Guevara T, Ksiazek M, Potempa J, Gomis-Ruth FX. Tannerella forsythia promirolysin mutant E225A [Internet]. 2019.
Available from: http://dx.doi.org/10.2210/pdb6r7v/pdb
15. Rodriguez-Banqueri A, Guevara T, Ksiazek M, Potempa J, Gomis-Ruth FX. Tannerella forsythia mature mirolysin in complex with a cleaved
peptide [Internet]. 2019. Available from: http://dx.doi.org/10.2210/pdb6r7w/pdb
16. Landau M, Engelberg Y. Crystal structure of the human LL37(17-29) antimicrobial peptide [Internet]. 2020. Available from:
http://dx.doi.org/10.2210/pdb6s6m/pdb
17. Koneru L, Ksiazek M, Waligorska I, Straczek A, Lukasik M, Madej M, et al. Mirolysin, a LysargiNase from Tannerella forsythia,
proteolytically inactivates the human cathelicidin, LL-37 [Internet]. Vol. 398, Biological Chemistry. 2017. p. 395–409. Available from: http://dx.doi.org/10.1515/hsz-2016-0267
18. Zak KM, Bostock MJ, Ksiazek M. Mirolysin in complex with compound 9 [Internet]. 2021. Available from: http://dx.doi.org/10.2210/pdb7od0/pdb
19. Rauf A, Farshori NN. Oxazoles [Internet]. SpringerBriefs in Molecular Science. 2012. p. 9–14. Available from: http://dx.doi.org/10.1007/978-94-007-1485-4_2
20. Johnson TO, Adeyemi OE, Adegboyega AE, Olomu SA, Enokela F, Ibrahim S, et al. Elucidation of the anti-plasmodial activity of
novel imidazole and oxazole compounds through computational and experimental approaches. J Biomol Struct Dyn. 2022 Oct 30;1–9.
21. Neelakantan P, Grotra D, Sharma S. Retreatability of 2 mineral trioxide aggregatebased root canal sealers: a cone-beam computed
tomography analysis. J Endod. 2013 Jul;39(7):893–6.
22. Aldhuwayhi S, Mallineni SK, Sakhamuri S, Thakare AA, Mallineni S, Sajja R, et al. Covid-19 Knowledge and Perceptions Among Dental
Specialists: A Cross-Sectional Online Questionnaire Survey. Risk Manag Healthc Policy. 2021 Jul 7;14:2851–61.
23. Sheriff KAH, Ahmed Hilal Sheriff K, Santhanam A. Knowledge and Awareness towards Oral Biopsy among Students of Saveetha Dental College [Internet]. Vol. 11, Research Journal of Pharmacy and Technology. 2018. p. 543. Available from: http://dx.doi.org/10.5958/0974-360x.2018.00101.4
24. Markov A, Thangavelu L, Aravindhan S, Zekiy AO, Jarahian M, Chartrand MS, et al. Mesenchymal stem/stromal cells as a valuable
source for the treatment of immune-mediated disorders. Stem Cell Res Ther. 2021 Mar 18;12(1):192.
25. Jayaraj G, Ramani P, Herald J. Sherlin, Premkumar P, Anuja N. Inter-observer agreement in grading oral epithelial dysplasia – A systematic review [Internet]. Vol. 27, Journal of Oral and Maxillofacial Surgery, Medicine, and Pathology. 2015. p. 112–6. Available from: http://dx.doi.org/10.1016/j.ajoms.2014.01.006
26. Paramasivam A, Priyadharsini JV, Raghunandhakumar S, Elumalai P. A novel COVID-19 and its effects on cardiovascular disease. Hypertens Res. 2020 Jul;43(7):729–30.
27. Li Z, Veeraraghavan VP, Mohan SK, Bolla SR, Lakshmanan H, Kumaran S, et al. Apoptotic induction and anti-metastatic activity of eugenol
encapsulated chitosan nanopolymer on rat glioma C6 cells via alleviating the MMP signaling pathway [Internet]. Vol. 203, Journal of Photochemistry and Photobiology B: Biology. 2020. p. 111773. Available from: http://dx.doi.org/10.1016/j.jphotobiol.2019.111773
28. Gan H, Zhang Y, Zhou Q, Zheng L, Xie X, Veeraraghavan VP, et al. Zingerone induced caspase-dependent apoptosis in MCF-7 cells and prevents 7,12-dimethylbenz(a)anthraceneinduced mammary carcinogenesis in experimental rats. J Biochem Mol Toxicol. 2019
Oct;33(10):e22387.
29. Dua K, Wadhwa R, Singhvi G, Rapalli V, Shukla SD, Shastri MD, et al. The potential of siRNA based drug delivery in respiratory disorders:
Recent advances and progress. Drug Dev Res. 2019 Sep;80(6):714–30.
30. Mohan M, Jagannathan N. Oral field cancerization: an update on current concepts. Oncol Rev. 2014 Mar 17;8(1):244.