Insilico screening to identify novel inhibitors targeting 30S ribosomal protein S12 in meningitis-causing organism ‘Elizabethkingia meningoseptica’

References

• Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High-performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
   Google Scholar
• Baker, N. A., Sept, D., Joseph, S., Holst, M. J., & McCammon, J. A. (2001). Electrostatics of nanosystems: Application to microtubules and the ribosome. Proceedings of the National Academy of Sciences of the United States of America, 98(18), 10037–10041. https://doi.org/10.1073/pnas.181342398
   PubMed Web of Science ®Google Scholar
• Beceiro, A., Tomás, M., & Bou, G. (2013). Antimicrobial resistance and virulence: A successful or deleterious association in the bacterial world? Clinical Microbiology Reviews, 26(2), 185–230. https://doi.org/10.1128/CMR.00059-12
   PubMed Web of Science ®Google Scholar
• Beloor, S. A., Rosani, A., Patel, P. & Wadhwa, R. (2022, January). Rifampin. In StatPearls. StatPearls Publishing.
   Google Scholar
• Bloch, K. C., Nadarajah, R., & Jacobs, R. (1997). Chryseobacterium meningosepticum: An emerging pathogen among immunocompromised adults. Medicine, 76(1), 30–41. https://doi.org/10.1099/00207713-44-4-827
   PubMed Web of Science ®Google Scholar
• Bowers, K. C., Edmond, X., Huafeng, D., Ron, E., Michael, G., Brent, K., John, K., István, M., Mark, S., Federico, S., John, S., & Shaw, D. E, Yibing. (2006). Molecular dynamics-scalable algorithms for molecular dynamics simulations on commodity clusters. Supercomputing, 2006. SC'06. Proceedings of the ACM/ IEEE (vol. 84).
   Google Scholar
• Brandi, L., Maffioli, S., Donadio, S., Quaglia, F., Sette, M., Milón, P., Gualerzi, C. O., & Fabbretti, A. (2012). Structural and functional characterization of the bacterial translocation inhibitor GE82832. FEBS Letters, 586(19), 3373–3378. https://doi.org/10.1016/j.febslet.2012.07.040
   PubMed Web of Science ®Google Scholar
• Bulkley, D., Brandi, L., Polikanov, Y. S., Fabbretti, A., O’Connor, M., Gualerzi, C. O., & Steitz, T. A. (2014, January 30). The antibiotics dityromycin and GE82832 bind protein S12 and block EF-G-catalyzed translocation. Cell Reports, 6(2), 357–365. https://doi.org/10.1016/j.celrep.2013.12.024
   PubMed Web of Science ®Google Scholar
• Carter, A. P., Clemons, W. M., Brodersen, D. E., Morgan-Warren, R. J., Wimberly, B. T., & Ramakrishnan, V. (2000). Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature, 407(6802), 340–348. https://doi.org/10.1038/35030019
   PubMed Web of Science ®Google Scholar
• Castro-Alvarez, A., Costa, A. M., & Vilarrasa, J. (2017). The performance of several docking programs at reproducing protein–macrolide-like crystal structures. Molecules, 22(1), 136. https://doi.org/10.3390/molecules22010136]
   PubMed Web of Science ®Google Scholar
• Ceyhan, M., & Celik, M. (2011). Elizabethkingia meningosepticum (Chryseobacterium meningosepticum) infections in children. International Journal of Pediatrics, 2011, 215237. https://doi.org/10.1155/2011/215237
   PubMedGoogle Scholar
• Chatrchai, W. (1984). Mode of action and in-vitro activity of vancomycin. Journal of Antimicrobial Chemotherapy, 14(D), 7–18. https://doi.org/10.1093/jac/14.suppl_D.7
   Google Scholar
• Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S., & Richardson, D. C. (2010). MolProbity: All-atom structure validation for macromolecular crystallography. Acta Crystallographica-Section D, Biological Crystallography, 66(Pt 1), 12–21. https://doi.org/10.1107/S0907444909042073
   PubMed Web of Science ®Google Scholar
• Colovos, C., & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science, 2(9), 1511–1519. https://doi.org/10.1002/pro.5560020916
   PubMed Web of Science ®Google Scholar
• Da Silva, P. S. L., & Pereira, G. H. (2013). Elizabethkingia meningoseptica: Emergent bacteria causing pneumonia in a critically ill child. Pediatrics International, 55(2), 231–234. https://doi.org/10.1111/j.1442-200X.2012.03650.x
   PubMed Web of Science ®Google Scholar
• De Castro, E., Sigrist, C. J. A., Gattiker, A., Bulliard, V., Langendijk-Genevaux, P. S., Gasteiger, E., Bairoch, A., & Hulo, N. (2006). ScanProsite: Detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Research, 34(Web Server issue), W362–5. https://doi.org/10.1093/nar/gkl124
   PubMed Web of Science ®Google Scholar
• Demirci, H., Wang, L., Murphy, F. V., Murphy, E. L., Carr, J. F., Blanchard, S. C., Jogl, G., Dahlberg, A. E., & Gregory, S. T. (2013, December). The central role of protein S12 is in organizing the structure of the decoding site of the ribosome. RNA, 19(12), 1791–1801. https://doi.org/10.1261/rna.040030.113
   PubMed Web of Science ®Google Scholar
• De Oliveira, D. M. P., Forde, B. M., Kidd, T. J., Harris, P. N. A., Schembri, M. A., Beatson, S. A., Paterson, D. L., & Walker, M. J. (2020). Antimicrobial resistance in ESKAPE pathogens. Clinical Microbiology Reviews, 33(3), e00181-19. https://doi.org/10.1128/CMR.00181-19
   PubMed Web of Science ®Google Scholar
• Eisenberg, D., Lüthy, R., & Bowie, J. U. (1997). VERIFY3D: Assessment of protein models with three-dimensional profiles. Methods in Enzymology, 277, 396–404. https://doi.org/10.1016/s0076-6879(97)77022-8
   PubMed Web of Science ®Google Scholar
• Ferreira de Freitas, R., & Schapira, M. (2017). A systematic analysis of atomic protein-ligand interactions in the PDB. MedChemComm, 8(10), 1970–1981. https://doi.org/10.1039/c7md00381a
   PubMed Web of Science ®Google Scholar
• Fragkou, P. C., Poulakou, G., Blizou, A., Blizou, M., Rapti, V., Karageorgopoulos, D. E., Koulenti, D., Papadopoulos, A., Matthaiou, D. K., & Tsiodras, S. (2019). The role of minocycline in the treatment of nosocomial infections caused by multidrug, extensively drug, and pandrug resistant Acinetobacter baumannii: A systematic review of clinical evidence. Microorganisms, 7(6), 159. https://doi.org/10.3390/microorganisms7060159
   PubMed Web of Science ®Google Scholar
• Garrido-Mesa, N., Zarzuelo, A., & Gálvez, J. (2013). Minocycline: Far beyond an antibiotic. British Journal of Pharmacology, 169(2), 337–352. https://doi.org/10.1111/bph.12139
   PubMed Web of Science ®Google Scholar
• Girdhar, N., Kumari, N., & Krishnamachari, A. (2022). Computational characterization and analysis of molecular sequence data of Elizabethkingia meningoseptica. BMC Research Notes, 15(1), 133. https://doi.org/10.1186/s13104-022-06011-5
   PubMed Web of Science ®Google Scholar
• Giuliodori, A. M., Spurio, R., Milón, P., & Fabbretti, A. (2018). Antibiotics targeting the 30S ribosomal subunit: A lesson from nature to find and develop new drugs. Current Topics in Medicinal Chemistry, 18(24), 2080–2096. https://doi.org/10.2174/1568026618666181025092546
   PubMed Web of Science ®Google Scholar
• Hoque, S. N., Graham, J., Kaufmann, M. E., & Tabaqchali, S. (2001). Chryseobacterium (Flavobacterium) meningosepticum outbreak associated with colonization of water taps in a neonatal intensive care unit. The Journal of Hospital Infection, 47(3), 188–192. https://doi.org/10.1053/jhin.2000.0908
   PubMed Web of Science ®Google Scholar
• Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., & Simmerling, C. (2006). Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins, 65(3), 712–725. https://doi.org/10.1002/prot.21123 16981200
   PubMed Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Kirby, J. T., Sader, H. S., Walsh, T. R., & Jones, R. N. (2004). Antimicrobial susceptibility and epidemiology of a worldwide collection of Chryseobacterium spp.: Report from the SENTRY antimicrobial surveillance program (1997–2001). Journal of Clinical Microbiology, 42(1), 445–448. https://doi.org/10.1128/JCM.42.1.445-448.2004
   PubMed Web of Science ®Google Scholar
• Kollman, P. A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., Lee, M., Lee, T., Duan, Y., Wang, W., Donini, O., Cieplak, P., Srinivasan, J., Case, D. A., & Cheatham, T. E. (2000). Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Accounts of Chemical Research, 33(12), 889–897. https://doi.org/10.1021/ar000033j
   PubMed Web of Science ®Google Scholar
• Kumari, R., Kumar, R., Lynn, A., & Lynn, A, Open Source Drug Discovery Consortium. (2014). g_mmpbsa a GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Le Guilloux, V., Schmidtke, P., & Tuffery, P. (2009). Fpocket: An open-source platform for ligand pocket detection. BMC Bioinformatics, 10(1), 168. https://doi.org/10.1186/1471-2105-10-168
   PubMedGoogle Scholar
• Lin, J., Zhou, D., Steitz, T. A., Polikanov, Y. S., & Gagnon, M. G. (2018). Ribosome-targeting antibiotics: Modes of action, mechanisms of resistance, and implications for drug design. Annual Review of Biochemistry, 87(1)20, 451–478. https://doi.org/10.1146/annurev-biochem-062917-011942
   PubMedGoogle Scholar
• Lin, P. Y., Chu, C., Su, L. H., Huang, C. T., Chang, W. Y., & Chiu, C. H. (2004). Clinical and microbiological analysis of bloodstream infections caused by Chryseobacterium meningosepticum in nonneonatal patients. Journal of Clinical Microbiology, 42(7), 3353–3355. https://doi.org/10.1128/JCM.42.7.3353-3355.2004
   PubMed Web of Science ®Google Scholar
• Lin, Y. T., Chiu, C. H., Chan, Y. J., Lin, M. L., Yu, K. W., Wang, F. D., & Liu, C. Y. (2009). Clinical and microbiological analysis of Elizabethkingia meningoseptica bacteremia in adult patients in Taiwan. Scandinavian Journal of Infectious Diseases, 41(9), 628–634. https://doi.org/10.1080/00365540903089476
   PubMed Web of Science ®Google Scholar
• Lobanov, M. Y., Bogatyreva, N. S., & Galzitskaya, O. V. (2008). Radius of gyration as an indicator of protein structure compactness. Molecular Biology, 42(4), 623–628. https://doi.org/10.1134/S0026893308040195
   Web of Science ®Google Scholar
• Lohning, A. E., Levonis, S. M., Williams-Noonan, B., & Schweiker, S. S. (2017). A practical guide to molecular docking and homology modelling for medicinal chemists. Current Topics in Medicinal Chemistry. 17(18), 2023–2040. https://doi.org/10.2174/15680266176661701301108
   PubMed Web of Science ®Google Scholar
• Mahfuz, A. M. U. B., Iqbal, M. N., Opazo, F. S., & Zubair-Bin-Mahfuj, A. M. (2022). Characterization of ribonucleotide reductases of emerging pathogens Elizabethkingia anophelis and Elizabethkingia meningoseptica and streptonigrin as their inhibitor: A computational study. Journal of Biomolecular Structure & Dynamics, 40(19), 9509–9521. https://doi.org/10.1080/07391102.2021.1930166
   PubMed Web of Science ®Google Scholar
• Mahoney, M. W., & Jorgensen, W. L. (2000). A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions. The Journal of Chemical Physics, 112(20), 8910–8922. https://doi.org/10.1063/1.481505
   Web of Science ®Google Scholar
• Mark, P., & Nilsson, L, P. M. (2001). Structure and dynamics of the tip3p, spc, and spc/e water models at 298 k. The Journal of Physical Chemistry A, 105(43), 9954–9960. https://doi.org/10.1021/jp003020w
   Web of Science ®Google Scholar
• Moore, L. S., Owens, D. S., Jepson, A., Turton, J. F., Ashworth, S., Donaldson, H., & Holmes, A. H. (2016). Waterborne Elizabethkingia meningoseptica in adult critical care. Emerging Infectious Diseases, 22(1), 9–17. https://doi.org/10.3201/eid2201.150139
   PubMed Web of Science ®Google Scholar
• NCBI genome. https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=238
   Google Scholar
• Nicholson, A. C., Gulvik, C. A., Whitney, A. M., Humrighouse, B. W., Graziano, J., Emery, B., Bell, M., Loparev, V., Juieng, P., Gartin, J., Bizet, C., Clermont, D., Criscuolo, A., Brisse, S., & McQuiston, J. R. (2018). Revisiting the taxonomy of the genus Elizabethkingia using whole-genome sequencing, optical mapping, and MALDI-TOF, along with the proposal of three novel Elizabethkingia species: Elizabethkingia bruuniana sp. nov., Elizabethkingia ursingii sp. nov., and Elizabethkingia occulta sp. nov. Antonie Van Leeuwenhoek, 111(1), 55–72. https://doi.org/10.1007/s10482-017-0926-3
   PubMed Web of Science ®Google Scholar
• O'Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3(1), 33. https://doi.org/10.1186/1758-2946-3-33)
   PubMed Web of Science ®Google Scholar
• Ogle, J. M., Brodersen, D. E., Clemons, W. M., Tarry, M. J., Carter, A. P., & Ramakrishnan, V. (2001). Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science, 292(5518), 897–902. https://doi.org/10.1126/science.1060612
   PubMed Web of Science ®Google Scholar
• Raturi, A., Yadav, V., Hoda, N., Subbarao, N., & Chaudhry, S. A. (2023). In silico identification of colchicine derivatives as novel and potential inhibitors based on molecular docking and dynamic simulations targeting multifactorial drug targets involved in Alzheimer’s disease. Journal of Biomolecular Structure & Dynamics, 1–19. https://doi.org/10.1080/07391102.2023.2263586
   PubMedGoogle Scholar
• Richmond, T. J. (1984). Solvent accessible surface area and excluded volume in proteins: Analytical equations for overlapping spheres and implications for the hydrophobic effect. Journal of Molecular Biology, 178(1), 63–89. https://doi.org/10.1016/0022-2836(84)90231-6
   PubMed Web of Science ®Google Scholar
• Roman, A., & Mark, B, Laskowski. Swindells. (2011). LigPlot+: Multiple ligand–protein interaction diagrams for drug discovery. Journal of Chemical Information and Modeling, 51(10), 2778–2786. https://doi.org/10.1021/ci200227u
   PubMed Web of Science ®Google Scholar
• Sahu, M. K., Balasubramaniam, U., C, B., Singh, S. P., & Talwar, S. (2019). Elizabethkingia Meningoseptica: An emerging nosocomial pathogen causing septicemia in critically ill patients. Indian Journal of Critical Care Medicine, 23(2), 104–105. https://doi.org/10.5005/jp-journals-10071-23127
   PubMed Web of Science ®Google Scholar
• Sarker, P., Mitro, A., Hoque, H., Hasan, M. N., Nurnabi, A., & Jewel, G. M. (2023). Identification of potential novel therapeutic drug target against Elizabethkingia anophelis by integrative pan and subtractive genomic analysis: An in silico approach. Computers in Biology and Medicine, 165, 107436. https://doi.org/10.1016/j.compbiomed.2023.107436
   PubMed Web of Science ®Google Scholar
• Schwab, C. H. (2010). Conformations and 3D pharmacophore searching. Drug Discovery Today: Technologies, 7(4), e245–e253. www.molecular-networks.com/online_demos/corina_demo) https://doi.org/10.1016/j.ddtec.2010.10.003
   Google Scholar
• Soto, S. M. (2013). Role of efflux pumps in the antibiotic resistance of bacteria embedded in a biofilm. Virulence, 4(3), 223–229. https://doi.org/10.4161/viru.23724
   PubMed Web of Science ®Google Scholar
• Sousa da Silva, A. W., & Vranken, W. F. (2012). ACPYPE-antechamber python parser interface. BMC Research Notes, 5(1), 367. https://doi.org/10.1186/1756-0500-5-367
   PubMedGoogle Scholar
• Schrödinger, L.& DeLano, W. (2020) .PyMOL. Retrieved from http://www.pymol.org/pymol.
   Google Scholar
• Vandamme, P., Bernardet, J. F., Segers, P., Kersters, K., & Holmes, B. (1994). New perspectives in the classification of the flavobacteria: Description of Chryseobacterium gen. nov., Bergeyella gen. nov., and Empedobacter nom. rev. International Journal of Systematic Bacteriology, 44(4), 827–831. https://doi.org/10.1099/00207713-44-4-827
   Google Scholar
• Verdonk, M. L., Cole, J. C., Hartshorn, M. J., Murray, C. W., & Taylor, R. D. (2003). Improved protein-ligand docking using GOLD. Proteins, 52(4), 609–623. https://doi.org/10.1002/prot.10465
   PubMed Web of Science ®Google Scholar
• Verma, J., & Subbarao, N. (2022). In silico identification of small molecule protein-protein interaction inhibitors: Targeting hotspot regions at the interface of MXRA8 and CHIKV envelope protein. Journal of Biomolecular Structure & Dynamics, 41(8), 3349–3367. https://doi.org/10.1080/07391102.2022.2048080
   PubMed Web of Science ®Google Scholar
• Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25(9), 1157–1174. https://doi.org/10.1002/jcc.20035
   PubMed Web of Science ®Google Scholar
• Wang, R., Lai, L., & Wang, S. (2002). Further development and validation of empirical scoring functions for structure-based binding affinity prediction. Journal of Computer-Aided Molecular Design, 16(1), 11–26. https://doi.org/10.1023/a:1016357811882
   PubMed Web of Science ®Google Scholar
• Waseem, M., Thakur, J. K., & Subbarao, N. (2023). Prediction of novel and potent inhibitors of lanosterol 14-a demethylase. Journal of Biomolecular Structure & Dynamics, 41(12), 5744–5756. https://doi.org/10.1080/07391102.2022.2096116
   PubMed Web of Science ®Google Scholar
• Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F. T., De Beer, T. A. P., Rempfer, C., Bordoli, L., Lepore, R., & Schwede, T. (2018). SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Research, 46(W1), W296–W303. https://doi.org/10.1093/nar/gky427 29788355
   PubMed Web of Science ®Google Scholar
• Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35(Web Server issue), W407–W410. https://doi.org/10.1093/nar/gkm290
   PubMed Web of Science ®Google Scholar
• Wimberly, B. T., Brodersen, D. E., Clemons, W. M., Jr, Morgan-Warren, R. J., Carter, A. P., Vonrhein, C., Hartsch, T., & Ramakrishnan, V. (2000). Structure of the 30S ribosomal subunit. Nature, 407(6802), 327–339. https://www.ebi.ac.uk/chembl/ https://doi.org/10.1038/35030006
   PubMed Web of Science ®Google Scholar
• Woods, C. J., Malaisree, M., Michel, J., Long, B., McIntosh-Smith, S., & Mulholland, A. J. (2014). Rapid decomposition and visualization of protein-ligand binding free energies by residue and by water. Faraday Discussions, 169, 477–499. https://doi.org/10.1039/c3fd00125c
   PubMed Web of Science ®Google Scholar