Advertisement

Inhibitor discovery for the E. coli meningitis virulence factor IbeA from homology modeling and virtual screening

  • Xiaoqian XuEmail author
  • Li Zhang
  • Ying Cai
  • Dongxin Liu
  • Zhengwen Shang
  • Qiuhong Ren
  • Qiong Li
  • Weidong Zhao
  • Yuhua ChenEmail author
Article
  • 49 Downloads

Abstract

Escherichia coli (E. coli) K1 is the most common Gram-negative bacteria cause of neonatal meningitis. The penetration of E. coli through the blood–brain barrier is a key step of the meningitis pathogenesis. A host receptor protein, Caspr1, interacts with the E. coli virulence factor IbeA and thus facilitates bacterial penetration through the blood–brain barrier. Based on this result, we have now predicted the binding pattern between Caspr1 and IbeA by an integrated computational protocol. Based on the predicted model, we have identified a putative molecular binding pocket in IbeA, that directly bind with Caspr1. This evidence indicates that the IbeA (229–343aa) region might play a key role in mediating the bacteria invasion. Virtual screening with the molecular model was conducted to search for potential inhibitors from 213,279 commercially available chemical compounds. From the top 50 identified compounds, 9 demonstrated a direct binding ability to the residues within the Caspr1 binding site on IbeA. By using human brain microvascular endothelial cells (hBMEC) with E. coli strain RS218, four molecules were characterized that significantly attenuated the bacteria invasions at concentrations devoid of cell toxicity. Our study provides useful structural information for understanding the pathogenesis of neonatal meningitis, and have identified drug-like compounds that could be used to develop effective anti-meningitis agents.

Keywords

Protein structure Binding ability Virtual screening Bacterial meningitis inhibitor Bacteria invasion 

Notes

Acknowledgements

The authors thank Professor Cameron Mackereth from European institute of Chemistry and Biology, Professor Yuxing Chen and Congzhao Zhou from University of Science and Technology of China for their suggestions and polishing the manuscript.

Author contributions

X.Q.X. and L.Z. conducted the computational experiments and analysis; Y.C., Z.W.S. and Q.H.R. carried out the cellular and bacterial assays; Q.L. performed the SPR binding ability tests; D.X.L. and W.D.Z. contributed in the experimental data arrangement and summary; X.Q.X and Y.H.C. designed the experiments and wrote the manuscript.

Funding

This research was supported by grants from the National Natural Science Foundation of China (No. 31600611) and the Department of Education of Liaoning province (No. L2015594).

Compliance with ethical standards

Conflict of interest

The authors declare that there is no conflict of interest.

Supplementary material

10822_2019_250_MOESM1_ESM.docx (1.8 mb)
Supplementary file1 (DOCX 1860 kb)
10822_2019_250_MOESM2_ESM.zip (2904.9 mb)
Supplementary file2—Trajectory files (ZIP 2974645 kb)

References

  1. 1.
    Chandran A, Herbert H, Misurski D, Santosham M (2011) Long-term sequelae of childhood bacterial meningitis: an underappreciated problem. Pediatr Infect Dis J 30:3–6.  https://doi.org/10.1097/INF.0b013e3181ef25f7 CrossRefPubMedGoogle Scholar
  2. 2.
    Theodoridou K, Vasilopoulou VA, Katsiaflaka A, Theodoridou MN, Roka V, Rachiotis G, Hadjichristodoulou CS (2013) Association of treatment for bacterial meningitis with the development of sequelae. Int J Infect Dis 17:707–713.  https://doi.org/10.1016/j.ijid.2011.12.019 CrossRefGoogle Scholar
  3. 3.
    Kim KS (2010) Acute bacterial meningitis in infants and children. Lancet Infect Dis 10:32–42.  https://doi.org/10.1016/S1473-3099(09)70306-8 CrossRefPubMedGoogle Scholar
  4. 4.
    Fauci AS (2001) Infectious diseases: considerations for the 21st century. IDSA Lecture Clin Infect Dis 32:675–685.  https://doi.org/10.1086/3192355 CrossRefGoogle Scholar
  5. 5.
    Kim KS, Itabashi H, Gemski P, Warren RL, Cross AS (1992) The K1 capsule is the critical determinant in the development of Escherichia coli meningitis in the rat. J Clin Invest 90:897–905.  https://doi.org/10.1172/JCI115965 CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Sarff LD, McCracken GH, Schiffer MS et al (1975) Epidemiology of Escherichia coli K1 in healthy and diseased newborns. Lancet 1:1099–1104.  https://doi.org/10.1016/S0140-6736(75)92496-4 CrossRefPubMedGoogle Scholar
  7. 7.
    Pietzak MM, Badger J, Huang SH, Thomas DW, Shimada H, Kim KS (2001) Escherichia coli K1 IbeA is required for efficient intestinal epithelial invasion in vitro and in vivo in neonatal rats. J Pediatr Gastroenterol Nutr 33:400.  https://doi.org/10.1097/MPG.0b013e31812e0149 CrossRefGoogle Scholar
  8. 8.
    Huang SH, Wan Z, Chen Y, Jong AY, Kim KS (2001) Further Characterization of Escherichia coli brain microvascular endothelial cell invasion gene ibeA by deletion, complementation, and protein expression. J Infect Dis 183(7):1071–1078.  https://doi.org/10.1086/319290 CrossRefPubMedGoogle Scholar
  9. 9.
    Zou Y, He L, Huang SH (2006) Identification of a surface protein on human brain microvascular endothelial cells as vimentin interacting with Escherichia coli invasion protein IbeA. Biochem Biophys Res Commun 351(3):625–630.  https://doi.org/10.1016/j.bbrc.2006.10.091 CrossRefPubMedGoogle Scholar
  10. 10.
    Zou Y, He L, Wu CH, Cao H, Xie ZH, Ouyang Y, Huang SH (2007) PSF is an IbeA-binding protein contributing to meningitic Escherichia coli K1 invasion of human brain microvascular endothelial cells. Med Microbiol Immunol 196(3):135–143.  https://doi.org/10.1007/s00430-006-0034-x CrossRefPubMedGoogle Scholar
  11. 11.
    Zhao WD, Liu DX, Wei JY, Miao ZW, Zhang K, Su ZK, Chen YH (2018) Caspr1 is a host receptor for meningitis-causing Escherichia coli. Nat Commun 9:2296.  https://doi.org/10.1038/s41467-018-04637-3 CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Tan YC, Gill AK, Kim KS (2015) Treatment strategies for central nervous system infections: an update. Expert Opin Pharmacother 16:187–203.  https://doi.org/10.1517/14656566.2015.1092520 CrossRefPubMedGoogle Scholar
  13. 13.
    Clatworthy AE, Pierson E, Hung DT (2007) Targeting virulence: a new paradigm for antimicrobial therapy. Nat Chem Biol 3:541–548.  https://doi.org/10.1038/nchembio.2007.24 CrossRefPubMedGoogle Scholar
  14. 14.
    Ghai R, Mobli M, Norwood SJ, Bugarcic A, Teasdale RD, King GF, Collins BM (2011) Phox homology band 4.1/ezrin/radixin/moesin-like proteins function as molecular scaffolds that interact with cargo receptors and Ras GTPases. Proc Natl Acad Sci 108(19):7763–7768.  https://doi.org/10.1073/pnas.1017110108 CrossRefPubMedGoogle Scholar
  15. 15.
    Dong C, Beis K, Nesper J, Brunkan LaMontagne AL, Clarke BR, Whitfield C, Naismith JH (2006) Wza the translocon for E. coli capsular polysaccharides defines a new class of membrane protein. Nature 444(7116):226–229.  https://doi.org/10.1038/nature05267 CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Bhatt TK, Khan S, Dwivedi VP, Banday MM, Sharma A, Chandele A, Sharma A (2011) Malaria parasite tyrosyl-tRNA synthetase secretion triggers pro-inflammatory responses. Nat Commun 2(1):530.  https://doi.org/10.1038/ncomms1522 CrossRefPubMedGoogle Scholar
  17. 17.
    Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE, DeBolt S, Kollman P (1995) AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. J Comput Chem 91(1–3):1–41.  https://doi.org/10.1016/0010-4655(95)00041-d CrossRefGoogle Scholar
  18. 18.
    Berman HM, Westbrook J, Feng ZK, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28(1):235–242.  https://doi.org/10.1093/nar/28.1.235 CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Altschul S (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389–3402.  https://doi.org/10.1093/nar/25.17.3389 CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Chen F, Venugopal V, Murray B, Rudenko G (2011) The structure of neurexin 1α reveals features promoting a role as synaptic organizer. Structure 19:779–789.  https://doi.org/10.1016/j.str.2011.03.012 CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Tisi D, Talts JF, Timpl R, Hohenester E (2000) Structure of the C-terminal laminin G-like domain pair of the laminin alpha 2 chain harbouring binding sites for alpha-dystroglycan and heparin. Embo J 19:1432.  https://doi.org/10.1093/emboj/19.7.1432 CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen M, Sali A (2007) Comparative protein structure modeling using MODELLER. Curr Protoc Protein Sci 50(1):2.9.1–2.9.31.  https://doi.org/10.1002/0471140864.ps0209s50 CrossRefGoogle Scholar
  23. 23.
    Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Richardson DC (2009) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66(1):12–21.  https://doi.org/10.1107/s0907444909042073 CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Chen R, Li L, Weng ZP (2003) ZDOCK: an initial-stage protein-docking algorithm. Proteins Struct Funct Bioinf.  https://doi.org/10.1002/prot.10389 CrossRefGoogle Scholar
  25. 25.
    Chaudhury S, Berrond M, Weitzner BD, Muthu P, Bergman H, Gray JJ (2011) Benchmarking and analysis of protein docking performance in Rosetta v32. PLoS ONE 6(8):e22477.  https://doi.org/10.1371/journal.pone.0022477 CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Hwang H, Vreven T, Pierce B, Hung JH (2010) Performance of ZDOCK and ZRANK in CAPRI rounds 13–19. Proteins Struct Funct Bioinf.  https://doi.org/10.1002/prot.22764 CrossRefGoogle Scholar
  27. 27.
    Lyskov S, Gray JJ (2008) The RosettaDock server for local protein-protein docking. Nucleic Acids Res 36:W233–W238.  https://doi.org/10.1093/nar/gkn216 CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577–8593.  https://doi.org/10.1063/1.470117 CrossRefGoogle Scholar
  29. 29.
    Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684–3690.  https://doi.org/10.1063/1.448118 CrossRefGoogle Scholar
  30. 30.
    Ryckaert JP, Ciccotti G, Berendsen HJC (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comp Chem 23:327–341.  https://doi.org/10.1016/0021-9991(77)90098-5 CrossRefGoogle Scholar
  31. 31.
    Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM, Woods RJ (2005) The Amber biomolecular simulation programs. J Comput Chem 26(16):1668–1688.  https://doi.org/10.1002/jcc.20290 CrossRefPubMedPubMedCentralGoogle Scholar
  32. 32.
    Gohlke H, Case DA (2003) Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. J Comput Chem 25(2):238–250.  https://doi.org/10.1002/jcc.10379 CrossRefGoogle Scholar
  33. 33.
    Hou T, Wang J, Li Y, Wang W (2011) Assessing the performance of the MM/PBSA and MM/GBSA methods 1 The accuracy of binding free energy calculations based on molecular dynamics simulations. J Chem Inf Model 51(1):69–82.  https://doi.org/10.1021/ci100275a CrossRefPubMedGoogle Scholar
  34. 34.
    Chen F, Liu H, Sun H, Pan P, Li Y, Li D, Hou T (2016) Assessing the performance of the MM/PBSA and MM/GBSA methods 6 Capability to predict protein–protein binding free energies and re-rank binding poses generated by protein–protein docking. Phys Chem Chem Phys 18(32):22129–22139.  https://doi.org/10.1039/c6cp03670h CrossRefPubMedGoogle Scholar
  35. 35.
    Still WC, Tempczyk A, Hawley RC, Hendrickson T (1990) Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc 112(16):6127–6129.  https://doi.org/10.1021/ja00172a038 CrossRefGoogle Scholar
  36. 36.
    Zoete V, Meuwly M, Karplus M (2005) Study of the insulin dimerization: binding free energy calculations and per-residue free energy decomposition. Proteins 61(1):79–93.  https://doi.org/10.1002/prot.20528 CrossRefPubMedGoogle Scholar
  37. 37.
    O'Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR (2011) Open Babel: an open chemical toolbox. J Cheminform 5:33.  https://doi.org/10.1186/1758-2946-3-33 CrossRefGoogle Scholar
  38. 38.
    Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 30:2785–2791.  https://doi.org/10.1002/jcc.21256 CrossRefPubMedPubMedCentralGoogle Scholar
  39. 39.
    Trott O, Olson AJ (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31:455–461.  https://doi.org/10.1002/jcc.21334 CrossRefPubMedPubMedCentralGoogle Scholar
  40. 40.
    Huang SH, Chen YH, Fu Q, Monique S, Wang Y, Carol W, Kwang SK (1999) Identification and characterization of an Escherichia coli invasion gene locus, ibeB, required for penetration of brain microvascular endothelial cells. Infect Immun 67:2103–2109PubMedPubMedCentralGoogle Scholar
  41. 41.
    Komatsuzawa H, Ohtaa K, Sugaia M, Fujiwaraa T, Glanzmannb P, Berger-Bächib B, Suginaka H (2000) Tn551-mediated insertional inactivation of the fmtB gene encoding a cell wall-associated protein abolishes methicillin resistance in Staphylococcus aureus. J Antimicrob Chemother 45:421–431.  https://doi.org/10.1093/jac/45.4.421 CrossRefPubMedGoogle Scholar
  42. 42.
    Ouhara K, Komatsuzawa K, Kawai T, Nishi H, Fujiwara T, Fujiue Y, Kuwabara M, Sayama K, Hashimoto K, Sugai M (2008) Increased resistance to cationic antimicrobial peptide LL-37 in methicillin-resistant strains of Staphylococcus aureus. J Antimicrob Chemother 61:1266–1269.  https://doi.org/10.1093/jac/dkn106 CrossRefPubMedPubMedCentralGoogle Scholar
  43. 43.
    Wu XS, Zhang Z, Zhao WD, Wang D, Luo F, Wu LG (2014) Calcineurin is universally involved in vesicle endocytosis at neuronal and nonneuronal secretory cells. Cell Rep 7:982–988.  https://doi.org/10.1016/j.celrep.2014.02.030 CrossRefPubMedPubMedCentralGoogle Scholar
  44. 44.
    Huang SH, Wass C, Fu Q, Prasadarao NV, Stins M, Kim KS (1995) Escherichia coli invasion of brain microvascular endothelial cells in vitro and in vivo: molecular cloning and characterization of invasion gene ibe10. Infect Immun 63:4470–4475PubMedPubMedCentralGoogle Scholar
  45. 45.
    Zhao WD, Liu W, Fang WG, Kim KS, Chen YH (2010) Vascular endothelial growth factor receptor 1 contributes to Escherichia coli K1 invasion of human brain microvascular endothelial cells through the phosphatidylinositol 3-kinase/Akt signaling pathway. Infect Immun 78:4809–4816.  https://doi.org/10.1128/IAI.00377-10 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Department of Developmental Biology, Key Laboratory of Cell Biology, Ministry of Public Health and Key Laboratory of Medical Cell Biology, Ministry of EducationChina Medical UniversityShenyangChina
  2. 2.Department of Life ScienceLiaoning UniversityShenyangChina
  3. 3.Department of Life ScienceUniversity of Science and Technology of ChinaHefeiChina

Personalised recommendations