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Research Article

Predictive profiling of gram-negative antibiotics in CagA oncoprotein inactivation: a molecular dynamics simulation approach

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Pages 501-521 | Received 20 Apr 2023, Accepted 24 Jun 2023, Published online: 18 Jul 2023

References

  • H. Zubair and A. Ahmad, Cancer metastasis: An introduction, in Introduction to Cancer Metastasis, A. Ahmed, ed., Academic Press, Cambridge, 2017, pp. 3–12.
  • H. Sung, J. Ferlay, R.L. Siegel, M. Laversanne, I. Soerjomataram, A. Jemal, and F. Bray, Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries, CA Cancer J. Clin. 71 (2021), pp. 209–249. doi:10.3322/caac.21660.
  • A. Ferro, B. Peleteiro, M. Malvezzi, C. Bosetti, P. Bertuccio, F. Levi, E. Negri, C.L. Vecchia, and N. Lunet, Worldwide trends in gastric cancer mortality (1980–2011), with predictions to 2015, and incidence by subtype, Eur. J. Cancer 50 (2014), pp. 1330–1344. doi:10.1016/j.ejca.2014.01.029.
  • C. de Martel, J. Ferlay, S. Franceschi, J. Vignat, F. Bray, D. Forman, and M. Plummer, Global burden of cancers attributable to infections in 2008: A review and synthetic analysis, Lancet Oncol. 13 (2012), pp. 607–615. doi:10.1016/S1470-2045(12)70137-7.
  • Y. Zhao, J. Zhang, A.S.L. Cheng, J. Yu, K.F. To, and W. Kang, Gastric cancer: Genome damaged by bugs, Oncogene 39 (2020), pp. 3427–3442. doi:10.1038/s41388-020-1241-4.
  • C. Sonkar, T. Verma, D. Chatterji, A.K. Jain, and H.C. Jha, Status of kinases in Epstein-Barr virus and Helicobacter pylori coinfection in gastric cancer cells, BMC Cancer 20 (2020), pp. 925. doi:10.1186/s12885-020-07377-0.
  • S. Pandey, H.C. Jha, S.K. Shukla, M.K. Shirley, and E.S. Robertson, Epigenetic regulation of tumor suppressors by Helicobacter pylori enhances EBV-induced proliferation of gastric epithelial cells, MBio 9 (2018), pp. e00649–18. doi:10.1128/mBio.00649-18.
  • C. Sonkar, N. Varshney, S. Koganti, and H.C. Jha, Kinases and therapeutics in pathogen mediated gastric cancer, Mol. Biol. Rep. 49 (2022), pp. 2519–2530. doi:10.1007/s11033-021-07063-9.
  • M. Kandpal, O. Indari, B. Baral, S. Jakhmola, D. Tiwari, V. Bhandari, R.K. Pandey, K. Bala, A. Sonawane, and H.C. Jha, Dysbiosis of gut microbiota from the perspective of the gut–brain axis: Role in the provocation of neurological disorders, Metabolites 12 (2022), pp. 1064. doi:10.3390/metabo12111064.
  • K. Suganya and B.-S. Koo, Gut–brain axis: Role of gut microbiota on neurological disorders and how probiotics/prebiotics beneficially modulate microbial and immune pathways to improve brain functions, Int. J. Mol. Sci. 21 (2020), pp. 7551. doi:10.3390/ijms21207551.
  • J. Watari, Helicobacter pylori associated chronic gastritis, clinical syndromes, precancerous lesions, and pathogenesis of gastric cancer development, World J. Gastroenterol. 20 (2014), pp. 5461–5473. doi:10.3748/wjg.v20.i18.5461.
  • D. Kashyap, N. Varshney, H.S. Parmar, and H.C. Jha, Gankyrin: At the crossroads of cancer diagnosis, disease prognosis, and development of efficient cancer therapeutics, Adv.Cancer Biol. Metastasis 4 (2022), pp. 100023. doi:10.1016/j.adcanc.2021.100023.
  • F.-W. Tsay and P.-I. Hsu, H. pylori infection and extra-gastroduodenal diseases, J. Biomed. Sci. 25 (2018), pp. 65. doi:10.1186/s12929-018-0469-6.
  • C.-Y. Kao, B.-S. Sheu, and -J.-J. Wu, Helicobacter pylori infection: An overview of bacterial virulence factors and pathogenesis, Biomed. J. 39 (2016), pp. 14–23. doi:10.1016/j.bj.2015.06.002.
  • L.E. Wroblewski, R.M. Peek, and K.T. Wilson, Helicobacter pylori and gastric cancer: Factors that modulate disease risk, Clin. Microbiol. Rev. 23 (2010), pp. 713–739. doi:10.1128/CMR.00011-10.
  • N. Ohnishi, H. Yuasa, S. Tanaka, H. Sawa, M. Miura, A. Matsui, H. Higashi, M. Musashi, K. Iwabuchi, M. Suzuki, G. Yamada, T. Azuma, and M. Hatakeyama, Transgenic expression of Helicobacter pylori CagA induces gastrointestinal and hematopoietic neoplasms in mouse, Proc. Natl. Acad. Sci. U.S.A. 105 (2008), pp. 1003–1008. doi:10.1073/pnas.0711183105.
  • K.M. Kampa, J.D. Acoba, D. Chen, J. Gay, H. Lee, K. Beemer, E. Padiernos, N. Boonmark, Z. Zhu, A.C. Fan, A.S. Bailey, W.H. Fleming, C. Corless, D.W. Felsher, L. Naumovski, and C.D. Lopez, Apoptosis-stimulating protein of p53 (ASPP2) heterozygous mice are tumor-prone and have attenuated cellular damage–response thresholds, Proc. Natl. Acad. Sci. U.S.A. 106 (2009), pp. 4390–4395. doi:10.1073/pnas.0809080106.
  • B.M. Roesler, S.C.B. Costa, and J.M.R. Zeitune, Eradication treatment of Helicobacter pylori infection: Its importance and possible relationship in preventing the development of gastric cancer, ISRN Gastroenterol. 2012 (2012), pp. 1–9. doi:10.5402/2012/935410.
  • A.K. Nanayakkara, H.W. Boucher, V.G. Fowler, A. Jezek, K. Outterson, and D.E. Greenberg, Antibiotic resistance in the patient with cancer: Escalating challenges and paths forward, CA Cancer J. Clin. 71 (2021), pp. 488–504. doi:10.3322/caac.21697.
  • K.V.I. Rolston, Infections in cancer patients with solid tumors: A review, Infect. Dis. Ther. 6 (2017), pp. 69–83. doi:10.1007/s40121-017-0146-1.
  • G. Shrestha, X. Wei, K. Hann, K.T. Soe, S. Satyanarayana, B. Siwakoti, S. Bastakoti, R. Mulmi, K. Rana, and N. Lamichhane, Bacterial profile and antibiotic resistance among cancer patients with urinary tract infection in a national tertiary cancer hospital of Nepal, Trop. Med. Infect. Dis. 6 (2021), pp. 49. doi:10.3390/tropicalmed6020049.
  • G.T. Garcia, K.R.S. Aranda, M.E.P. Gonçalves, S.R. Cardoso, K. Iriya, N.P. Silva, and I.C.A. Scaletsky, High prevalence of clarithromycin resistance and caga, vaca, icea2, and baba2 genotypes of Helicobacter pylori in Brazilian children, J. Clin. Microbiol. 48 (2010), pp. 4266–4268. doi:10.1128/JCM.01034-10.
  • A. Khan, A. Farooqui, and S. Kazmi, CagA gene carriage impact on intrahost dynamics of antimicrobial resistance to Helicobacter pylori, Int. J. Inf. Dis. 73 (2018), pp. 127. doi:10.1016/j.ijid.2018.04.3703.
  • S. Jakhmola, N.A. Jonniya, M.F. Sk, A. Rani, P. Kar, and H.C. Jha, Identification of potential inhibitors against Epstein–Barr Virus nuclear antigen 1 (EBNA1): An insight from docking and molecular dynamic simulations, ACS Chem. Neurosci. 12 (2021), pp. 3060–3072. doi:10.1021/acschemneuro.1c00350.
  • S. Jakhmola, Z. Hazarika, A.N. Jha, and H.C. Jha, In silico analysis of antiviral phytochemicals efficacy against Epstein–Barr virus glycoprotein H, J. Biomol. Struct. Dyn. 40 (2022), pp. 5372–5385. doi:10.1080/07391102.2020.1871074.
  • D. Tiwari, S. Murmu, O. Indari, H.C. Jha, and S. Kumar, Targeting Epstein‐Barr virus dUTPase, an immunomodulatory protein using antiviral, anti‐inflammatory, and neuroprotective phytochemicals, Chem. Biodivers. 19 (2022), pp. e202200527. doi:10.1002/cbdv.202200527.
  • S. Kim, P.A. Thiessen, E.E. Bolton, J. Chen, G. Fu, A. Gindulyte, L. Han, J. He, S. He, B.A. Shoemaker, J. Wang, B. Yu, J. Zhang, and S.H. Bryant, PubChem substance and compound databases, Nucleic Acids Res. 44 (2016), pp. D1202–D1213. doi:10.1093/nar/gkv951.
  • D. Kashyap, S. Jakhmola, D. Tiwari, R. Kumar, N.S.H.N. Moorthy, M. Elangovan, N.F. Brás, and H.C. Jha, Plant derived active compounds as potential anti SARS-CoV-2 agents: An in-silico study, J. Biomol. Struct. Dyn. 40 (2022), pp. 10629–10650. doi:10.1080/07391102.2021.1947384.
  • G.M. Morris, R. Huey, W. Lindstrom, M.F. Sanner, R.K. Belew, D.S. Goodsell, and A.J. Olson, AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility, J. Comput. Chem. 30 (2009), pp. 2785–2791. doi:10.1002/jcc.21256.
  • S.K. Behera, A.K. Panda, R. Mishra, A. Mahanty, and S.S. Bisht, Structure based virtual screening and molecular dynamics of natural anti-biofilm compounds against SagS response regulator/sensor kinase in Pseudomonas aeruginosa, J. Biomol. Struct. Dyn. (2022), pp. 1–16.
  • S. Mahata, S.K. Behera, S. Kumar, P.K. Sahoo, S. Sarkar, M.H.U.T. Fazil, and V.D. Nasare, In-silico and in-vitro investigation of STAT3-PIM1 heterodimeric complex: Its mechanism and inhibition by curcumin for cancer therapeutics, Int. J. Biol. Macromol. 208 (2022), pp. 356–366. doi:10.1016/j.ijbiomac.2022.03.137.
  • S. Kumar, K. Ahmad, S.K. Behera, D.T. Nagrale, A. Chaurasia, M.K. Yadav, S. Murmu, Y. Jha, M.V.S. Rajawat, D. Malviya, U.B. Singh, R. Shankar, M. Tripathy, and H.V. Singh, Biocomputational assessment of natural compounds as a potent inhibitor to quorum sensors in Ralstonia Solanacearum, Molecules 27 (2022), pp. 3034. doi:10.3390/molecules27093034.
  • O. Trott and A.J. Olson, AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading, J. Comput. Chem. 31 (2009), pp. 455–461.
  • N. Schmid, A.P. Eichenberger, A. Choutko, S. Riniker, M. Winger, A.E. Mark, and W.F. van Gunsteren, Definition and testing of the GROMOS force-field versions 54A7 and 54B7, Eur. Biophys. J. 40 (2011), pp. 843–856. doi:10.1007/s00249-011-0700-9.
  • M.J. Abraham, T. Murtola, R. Schulz, S. Páll, J.C. Smith, B. Hess, and E. Lindahl, GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers, SoftwareX. 1–2 (2015), pp. 19–25. doi:10.1016/j.softx.2015.06.001.
  • S.K. Behera, N. Vhora, D. Contractor, A. Shard, D. Kumar, K. Kalia, and A. Jain, Computational drug repurposing study elucidating simultaneous inhibition of entry and replication of novel corona virus by grazoprevir, Sci. Rep. 11 (2021), pp. 7307. doi:10.1038/s41598-021-86712-2.
  • O. Indari, M.F. Sk, S. Jakhmola, N.A. Jonniya, H.C. Jha, and P. Kar, Decoding the host–parasite protein interactions involved in cerebral malaria through glares of molecular dynamics simulations, J. Phys. Chem. B 126 (2022), pp. 387–402. doi:10.1021/acs.jpcb.1c07850.
  • J.D. Durrant and J.A. McCammon, Molecular dynamics simulations and drug discovery, BMC Biol. 9 (2011), pp. 71. doi:10.1186/1741-7007-9-71.
  • T. Hayashi, M. Senda, H. Morohashi, H. Higashi, M. Horio, Y. Kashiba, L. Nagase, D. Sasaya, T. Shimizu, N. Venugopalan, H. Kumeta, N.N. Noda, F. Inagaki, T. Senda, and M. Hatakeyama, Tertiary structure-function analysis reveals the pathogenic signaling potentiation mechanism of Helicobacter pylori oncogenic effector CagA, Cell Host Microbe 12 (2012), pp. 20–33. doi:10.1016/j.chom.2012.05.010.
  • M. Hatakeyama, Structure and function of Helicobacter pylori CagA, the first-identified bacterial protein involved in human cancer, Proc. Jpn. Acad. Ser. B. Phys. Biol. Sci. 93 (2017), pp. 196–219. doi:10.2183/pjab.93.013.
  • F. Bagnoli, L. Buti, L. Tompkins, A. Covacci, and M.R. Amieva, Helicobacter pylori CagA induces a transition from polarized to invasive phenotypes in MDCK cells, Proc. Natl. Acad. Sci. U.S.A. 102 (2005), pp. 16339–16344. doi:10.1073/pnas.0502598102.
  • N. Murata-Kamiya, K. Kikuchi, T. Hayashi, H. Higashi, and M. Hatakeyama, Helicobacter pylori exploits host membrane phosphatidylserine for delivery, localization, and pathophysiological action of the CagA oncoprotein, Cell Host Microbe 7 (2010), pp. 399–411. doi:10.1016/j.chom.2010.04.005.
  • M.R. Jouimyi, G. Bounder, I. Essaidi, H. Boura, K. Zerouali, H. Lebrazi, A. Kettani, and F. Maachi, Molecular docking of a set of flavonoid compounds with Helicobacter pylori virulence factors CagA and VacA, J. Herbmed Pharmacol. 9 (2020), pp. 412–419. doi:10.34172/jhp.2020.52.
  • I.H. Eissa, M.S. Alesawy, A.M. Saleh, E.B. Elkaeed, B.A. Alsfouk, A.-A.M.M. El-Attar, and A.M. Metwaly, Ligand and structure-based in silico determination of the most promising sars-cov-2 nsp16-nsp10 2′-o-methyltransferase complex inhibitors among 3009 FDA approved drugs, Molecules 27 (2022), pp. 2287. doi:10.3390/molecules27072287.
  • Y.H. Tsang, A. Lamb, J. Romero-Gallo, B. Huang, K. Ito, R.M. Peek, Y. Ito, and L.F. Chen, Helicobacter pylori CagA targets gastric tumor suppressor RUNX3 for proteasome-mediated degradation, Oncogene 29 (2010), pp. 5643–5650. doi:10.1038/onc.2010.304.

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