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Due to the uprising resistance towards H. pylori infection through the present and\ncommon proton pump inhibitors regimens, the investigation of novel candidates is the inevitable\nissue. Medicinal plants have always been a source of lead compounds for drug discovery. The research\nof the related effective enzymes linked with this gram-negative bacterium is critical for the\ndiscovery of novel drug targets.<\/jats:p>\n<\/jats:sec>\n<jats:sec>\n<jats:title>Objective:<\/jats:title>\n<jats:p>The aim of the study is to identify the best candidate to evaluate the inhibitory effect of\nthymoquinone and thymol against H. pylori oncoproteins, Cag A and Vac A in comparison to the\nstandard drug, metronidazole by using a computational approach.<\/jats:p>\n<\/jats:sec>\n<jats:sec>\n<jats:title>Materials and Methods:<\/jats:title>\n<jats:p>The targeted oncoproteins, Cag A and Vac A were retrieved from RCSB\nPDB. Lipinski\u2019s rule and ADMET toxicity profiling were carried out on the phytoconstituents of the\nN. sativa. The two compounds of N. sativa were further analyzed by molecular docking and MD\nsimulation studies. The reported phytoconstituents, thymoquinone and thymol present in N. sativa\nwere docked with H. pylori Cag A and Vac A oncoproteins. Structures of ligands were prepared\nusing ChemDraw Ultra 10 software and then changed into their 3D PDB structures using Molinspiration\nfollowed by energy minimization by using software Discovery Studio client 2.5.<\/jats:p>\n<\/jats:sec>\n<jats:sec>\n<jats:title>Results:<\/jats:title>\n<jats:p>The docking results revealed the promising inhibitory potential of thymoquinone against\nCag A and Vac A with docking energy of -5.81 kcal\/mole and -3.61kcal\/mole, respectively. On the\ncontrary, the inhibitory potential of thymol against Cag A and Vac A in terms of docking energy\nwas -5.37 kcal\/mole and -3.94kcal\/mole as compared to the standard drug, metronidazole having\ndocking energy of -4.87 kcal\/mole and -3.20 kcal\/mole, respectively. Further, molecular dynamic\nsimulations were conducted for 5ns for optimization, flexibility prediction, and determination of\nfolded Cag A and Vac A oncoproteins stability. The Cag A and Vac A oncoproteins-TQ complexes\nwere found to be quite stable with the root mean square deviation value of 0.2nm.<\/jats:p>\n<\/jats:sec>\n<jats:sec>\n<jats:title>Conclusion:<\/jats:title>\n<jats:p>The computational approaches suggested that thymoquinone and thymol may play an\neffective pharmacological role to treat H. pylori infection. Hence, it could be summarized that the\nligands thymoquinone and thymol bound and interacted well with the proteins Cag A and Vac A as\ncompared to the ligand MTZ. Our study showed that all lead compounds had good interaction with\nCag A and Vac A proteins and suggested them to be a useful target to inhibit H. pylori infection.<\/jats:p>\n<\/jats:sec>","DOI":"10.2174\/1573406416666200302113729","type":"journal-article","created":{"date-parts":[[2020,3,2]],"date-time":"2020-03-02T12:54:25Z","timestamp":1583153665000},"page":"146-157","update-policy":"https:\/\/doi.org\/10.2174\/bsp_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Molecular Docking and Dynamics Simulation Analysis of Thymoquinone and Thymol Compounds from Nigella sativa L. that Inhibit Cag A and Vac A Oncoprotein of Helicobacter pylori: Probable Treatment of H. pylori Infections"],"prefix":"10.2174","volume":"17","author":[{"given":"Heena","family":"Tabassum","sequence":"first","affiliation":[{"name":"Natural Products Laboratory, Department of Bioengineering, Integral University, Dasauli, Kursi Road, Lucknow- 226026, Uttar Pradesh, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2583-1794","authenticated-orcid":true,"given":"Iffat Zareen","family":"Ahmad","sequence":"additional","affiliation":[{"name":"Natural Products Laboratory, Department of Bioengineering, Integral University, Dasauli, Kursi Road, Lucknow- 226026, Uttar Pradesh, India"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"965","reference":[{"key":"ref=1","doi-asserted-by":"publisher","DOI":"10.5812\/ircmj.12581","volume":"16","author":"Sayehmiri F.","year":"2014","unstructured":"Sayehmiri F.; Darvishi Z.; Sayehmiri K.; Soroush S.; Emaneini M.; Zarrilli R.; Taherikalani M.; A systematic review and meta-analysis study to investigate the prevalence of Helicobacter pylori and the sensitivity of its diagnostic methods in Iran. 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