In silico strategies for identifying therapeutic candidates against Acinetobacter baumannii: spotlight on the UDP-N-acetylmuramoyl-L-alanine-D-glutamate:meso-diaminopimelate ligase (MurE)

References

• Antunes, L. C., Visca, P., & Towner, K. J. (2014). Acinetobacter baumannii: Evolution of a global pathogen. Pathogens and Disease, 71(3), 292–301. https://doi.org/10.1111/2049-632X.12125
   PubMed Web of Science ®Google Scholar
• Berman, H., Henrick, K., & Nakamura, H. (2003). Announcing the worldwide Protein Data Bank. Nature Structural Biology, 10(12), 980–980. https://doi.org/10.1038/nsb1203-980
   PubMedGoogle 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
• David, C. C., & Jacobs, D. J. (2014). Principal component analysis: A method for determining the essential dynamics of proteins. Methods in Molecular Biology, 1084, 193–226.
   PubMedGoogle Scholar
• De Oliveira, D. M. P., Forde, B. M., Kidd, T. J., Harris, P. N. , 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
• Dijkshoorn, L., Nemec, A., & Seifert, H. (2007). An increasing threat in hospitals: Multidrug-resistant Acinetobacter baumannii. Nature Reviews. Microbiology, 5(12), 939–951. https://doi.org/10.1038/nrmicro1789
   PubMed Web of Science ®Google Scholar
• Egan, A. J. F., Errington, J., & Vollmer, W. (2020). Regulation of peptidoglycan synthesis and remodelling. Nature Reviews. Microbiology, 18(8), 446–460. https://doi.org/10.1038/s41579-020-0366-3
   PubMed Web of Science ®Google Scholar
• Gan, J. H., Liu, J. X., Liu, Y., Chen, S. W., Dai, W. T., Xiao, Z. X., & Cao, Y. (2023). DrugRep: An automatic virtual screening server for drug repurposing. Acta Pharmacologica Sinica, 44(4), 888–896. https://doi.org/10.1038/s41401-022-00996-2
   PubMed Web of Science ®Google Scholar
• Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), 449–461. https://doi.org/10.1517/17460441.2015.1032936
   PubMed Web of Science ®Google Scholar
• Gordon, E., Flouret, B., Chantalat, L., van Heijenoort, J., Mengin-Lecreulx, D., & Dideberg, O. (2001). Crystal structure of UDP-N-acetylmuramoyl-L-alanyl-D-glutamate: Meso-diaminopimelate ligase from Escherichia coli. The Journal of Biological Chemistry, 276(14), 10999–11006. https://doi.org/10.1074/jbc.M009835200
   PubMed Web of Science ®Google Scholar
• Huang, W., Lin, Z., & van Gunsteren, W. F. (2011). Validation of the GROMOS 54A7 force field with respect to beta-peptide folding. Journal of Chemical Theory and Computation, 7(5), 1237–1243. https://doi.org/10.1021/ct100747y
   PubMed Web of Science ®Google Scholar
• Jha, R. K., Jabeer Khan, R., Singh, E., Kumar, A., Jain, M., Muthukumaran, J., & Singh, A. K. (2022). An extensive computational study to identify potential inhibitors of acyl-homoserine-lactone synthase from Acinetobacter baumannii (strain AYE). Journal of Molecular Graphics & Modelling, 114, 108168. https://doi.org/10.1016/j.jmgm.2022.108168
   PubMed Web of Science ®Google Scholar
• Jha, R. K., Khan, R. J., Amera, G. M., Singh, E., Pathak, A., Jain, M., Muthukumaran, J., & Singh, A. K. (2020). Identification of promising molecules against MurD ligase from Acinetobacter baumannii: Insights from comparative protein modelling, virtual screening, molecular dynamics simulations and MM/PBSA analysis. Journal of Molecular Modeling, 26(11), 304. https://doi.org/10.1007/s00894-020-04557-4
   PubMed Web of Science ®Google Scholar
• Jung, K. H., Kim, Y. G., Kim, C. M., Ha, H. J., Lee, C. S., Lee, J. H., & Park, H. H. (2021). Wide-open conformation of UDP-MurNc-tripeptide ligase revealed by the substrate-free structure of MurE from Acinetobacter baumannii. FEBS Letters, 595(2), 275–283. https://doi.org/10.1002/1873-3468.14007
   PubMed Web of Science ®Google Scholar
• Jurrus, E., Engel, D., Star, K., Monson, K., Brandi, J., Felberg, L. E., Brookes, D. H., Wilson, L., Chen, J., Liles, K., Chun, M., Li, P., Gohara, D. W., Dolinsky, T., Konecny, R., Koes, D. R., Nielsen, J. E., Head-Gordon, T., Geng, W., … Baker, N. A. (2018). Improvements to the APBS biomolecular solvation software suite. Protein Science, 27(1), 112–128. https://doi.org/10.1002/pro.3280
   PubMed Web of Science ®Google Scholar
• Kanehisa, M., Furumichi, M., Tanabe, M., Sato, Y., & Morishima, K. (2017). KEGG: New perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Research, 45(D1), D353–D361. https://doi.org/10.1093/nar/gkw1092
   PubMed Web of Science ®Google Scholar
• Khan, R. J., Singh, E., Jha, R. K., Kumar, A., Bhati, S. K., Zia, M. P., Jain, M., Singh, R. P., Muthukumaran, J., & Singh, A. K. (2023). Identification and prioritization of potential therapeutic molecules against LpxA from Acinetobacter baumannii – A computational study. Current Research in Structural Biology, 5, 100096. https://doi.org/10.1016/j.crstbi.2023.100096
   PubMedGoogle Scholar
• Land, H., & Humble, M. S. (2018). YASARA: A tool to obtain structural guidance in biocatalytic investigations. Methods in Molecular Biology, 685, 43–67.
   Google Scholar
• Ma, Y. X., Wang, C. Y., Li, Y. Y., Li, J., Wan, Q. Q., Chen, J. H., Tay, F. R., & Niu, L. N. (2020). Considerations and caveats in combating ESKAPE pathogens against nosocomial infections. Advanced Science, 7(1), 1901872.
   Web of Science ®Google Scholar
• Maisuradze, G. G., Liwo, A., & Scheraga, H. A. (2009). Principal component analysis for protein folding dynamics. Journal of Molecular Biology, 385(1), 312–329. https://doi.org/10.1016/j.jmb.2008.10.018
   PubMed Web of Science ®Google Scholar
• Maragakis, L. L., & Perl, T. M. (2008). Acinetobacter baumannii: Epidemiology, antimicrobial resistance, and treatment options. Clinical Infectious Diseases, 46(8), 1254–1263. https://doi.org/10.1086/529198
   PubMed Web of Science ®Google Scholar
• Marturano, J. E., & Lowery, T. J. (2019). ESKAPE pathogens in bloodstream infections are associated with higher cost and mortality but can be predicted using diagnoses upon admission. Open Forum Infectious Diseases, 6(12), ofz503.
   PubMed Web of Science ®Google Scholar
• Morris, A. L., MacArthur, M. W., Hutchinson, E. G., & Thornton, J. M. (1992). Stereochemical quality of protein structure coordinates. Proteins, 12(4), 345–364. https://doi.org/10.1002/prot.340120407
   PubMed Web of Science ®Google Scholar
• Needleman, S. B., & Wunsch, C. D. (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology, 48(3), 443–453. https://doi.org/10.1016/0022-2836(70)90057-4
   PubMed Web of Science ®Google Scholar
• Pendleton, J. N., Gorman, S. P., & Gilmore, B. F. (2013). Clinical relevance of the ESKAPE pathogens. Expert Review of Anti-Infective Therapy, 11(3), 297–308. https://doi.org/10.1586/eri.13.12
   PubMed Web of Science ®Google Scholar
• Rose, P. W., Prlic, A., Altunkaya, A., Bi, C., Bradley, A. R., Christie, C. H., Costanzo, L. D., Duarte, J. M., Dutta, S., Feng, Z., Green, R. K., Goodsell, D. S., Hudson, B., Kalro, T., Lowe, R., Peisach, E., Randle, C., Rose, A. S., Shao, C., … Burley, S. K. (2017). The RCSB protein data bank: Integrative view of protein, gene and 3D structural information. Nucleic Acids Research, 45(D1), D271–D281.
   PubMed Web of Science ®Google Scholar
• Schüttelkopf, A. W., & van Aalten, D. M. F. (2004). PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica. Section D, Biological Crystallography, 60(Pt 8), 1355–1363. https://doi.org/10.1107/S0907444904011679
   PubMedGoogle Scholar
• Skjærven, L., Jariwala, S., Yao, X.-Q., & Grant, B. J. (2016). Online interactive analysis of protein structure ensembles with Bio3D-web. Bioinformatics, 32(22), 3510–3512. https://doi.org/10.1093/bioinformatics/btw482
   PubMed Web of Science ®Google Scholar
• Smith, C. A. (2006). Structure, function and dynamics in the Mur family of bacterial cell wall ligases. Journal of Molecular Biology, 362(4), 640–655. https://doi.org/10.1016/j.jmb.2006.07.066
   PubMed Web of Science ®Google Scholar
• Tomašić, T., Sink, R., Zidar, N., Fic, A., Contreras-Martel, C., Dessen, A., Patin, D., Blanot, D., Müller-Premru, M., Gobec, S., Zega, A., Kikelj, D., & Mašič, L. P. (2012). Dual inhibitor of MurD and MurE ligases from Escherichia coli and Staphylococcus aureus. ACS Medicinal Chemistry Letters, 3(8), 626–630. https://doi.org/10.1021/ml300047h
   PubMed Web of Science ®Google Scholar
• Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/10.1002/jcc.21334
   PubMed Web of Science ®Google Scholar
• Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. https://doi.org/10.1002/jcc.20291
   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
   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
• Wishart, D. S., Feunang, Y. D., Guo, A. C., Lo, E. J., Marcu, A., Grant, J. R., Sajed, T., Johnson, D., Li, C., Sayeeda, Z., Assempour, N., Iynkkaran, I., Liu, Y., Maciejewski, A., Gale, N., Wilson, A., Chin, L., Cummings, R., Le, D., … Wilson, M. (2018). DrugBank 5.0: A major update to the DrugBank database for 2018. Nucleic Acids Research, 46(D1), D1074–D1082. https://doi.org/10.1093/nar/gkx1037
   PubMed Web of Science ®Google Scholar
• Zielkiewicz, J. (2005). Structural properties of water: Comparison of the SPC, SPCE, TIP4P, and TIP5P models of water. Journal of Chemical Physics, 123(10), 104501.
   PubMed Web of Science ®Google Scholar