Inhibitor discovery for the E. coli meningitis virulence factor IbeA from homology modeling and virtual screening
- 49 Downloads
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.
KeywordsProtein structure Binding ability Virtual screening Bacterial meningitis inhibitor Bacteria invasion
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.
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.
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.
- 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
- 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
- 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
- 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
- 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.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
- 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