{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,29]],"date-time":"2026-10-29T17:59:38Z","timestamp":1793296778216,"version":"4.5.0"},"reference-count":34,"publisher":"Springer Science and Business Media LLC","issue":"11","license":[{"start":{"date-parts":[[2023,3,13]],"date-time":"2023-03-13T00:00:00Z","timestamp":1678665600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2023,3,13]],"date-time":"2023-03-13T00:00:00Z","timestamp":1678665600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Appl Biochem Biotechnol"],"published-print":{"date-parts":[[2023,11]]},"DOI":"10.1007\/s12010-023-04413-0","type":"journal-article","created":{"date-parts":[[2023,3,13]],"date-time":"2023-03-13T08:03:42Z","timestamp":1678694622000},"page":"6675-6693","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Computational Modelling, Functional Characterization and Molecular Docking to Lead Compounds of Bordetella pertussis Diaminopimelate Epimerase"],"prefix":"10.1007","volume":"195","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2274-9090","authenticated-orcid":false,"given":"Shilpy","family":"Singh","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5868-5079","authenticated-orcid":false,"given":"Afsana","family":"Praveen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7891-8159","authenticated-orcid":false,"given":"Suruchi M.","family":"Khanna","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2023,3,13]]},"reference":[{"key":"4413_CR1","doi-asserted-by":"publisher","first-page":"9238","DOI":"10.1074\/jbc.M113.450148","volume":"288","author":"L Hor","year":"2013","unstructured":"Hor, L., Dobson, R. C. J., Downton, M. T., Wagner, J., Hutton, C. A., & Perugini, M. A. (2013). Dimerization of bacterial diaminopimelate epimerase is essential for catalysis. Journal of Biological Chemistry, 288, 9238\u20139248.","journal-title":"Journal of Biological Chemistry"},{"key":"4413_CR2","doi-asserted-by":"publisher","first-page":"115","DOI":"10.2174\/1389557033405359","volume":"3","author":"C Hutton","year":"2003","unstructured":"Hutton, C., Southwood, T., & Turner, J. (2003). Inhibitors of lysine biosynthesis as antibacterial agents. Mini-Reviews in Medicinal Chemistry, 3, 115\u2013127.","journal-title":"Mini-Reviews in Medicinal Chemistry"},{"key":"4413_CR3","doi-asserted-by":"publisher","first-page":"458","DOI":"10.1039\/b705624a","volume":"3","author":"CA Hutton","year":"2007","unstructured":"Hutton, C. A., Perugini, M. A., & Gerrard, J. A. (2007). Inhibition of lysine biosynthesis: an evolving antibiotic strategy. Molecular Biosystems, 3, 458\u2013465.","journal-title":"Molecular Biosystems"},{"key":"4413_CR4","doi-asserted-by":"publisher","first-page":"397","DOI":"10.1107\/S0907444903027999","volume":"60","author":"AJ Lloyd","year":"2004","unstructured":"Lloyd, A. J., Huyton, T., Turkenburg, J., & Roper, D. I. (2004). Refinement of Haemophilus influenzae diaminopimelic acid epimerase (DapF) at 1.75 \u00c5 resolution suggests a mechanism for stereocontrol during catalysis. Acta Crystallographica. Section D, Biological Crystallography, 60, 397\u2013400.","journal-title":"Acta Crystallographica. Section D, Biological Crystallography"},{"key":"4413_CR5","doi-asserted-by":"publisher","first-page":"42318","DOI":"10.1038\/srep42318","volume":"7","author":"HY Sagong","year":"2017","unstructured":"Sagong, H. Y., & Kim, K. J. (2017). Structural basis for redox sensitivity in Corynebacterium glutamicum diaminopimelate epimerase: an enzyme involved in llysine biosynthesis. Scientific Reports, 7, 42318.","journal-title":"Scientific Reports"},{"key":"4413_CR6","doi-asserted-by":"publisher","first-page":"383","DOI":"10.1107\/S0907444909002522","volume":"65","author":"V Usha","year":"2009","unstructured":"Usha, V., Dover, L. G., Roper, D. I., F\u00fctterer, K., & Besra. (2009). Structure of the diaminopimelate epimerase DapF from Mycobacterium tuberculosis. Acta Crystallographica. Section D, Biological Crystallography, 65, 383\u2013387.","journal-title":"Acta Crystallographica. Section D, Biological Crystallography"},{"key":"4413_CR7","doi-asserted-by":"publisher","first-page":"580","DOI":"10.1016\/j.jmb.2008.10.072","volume":"385","author":"B Pillai","year":"2009","unstructured":"Pillai, B., Moorthie, V. A., van Belkum, M. J., et al. (2009). Crystal structure of Diaminopimelate Epimerase from Arabidopsis thaliana, an amino acid racemase critical for l-lysine biosynthesis. Journal of Molecular Biology, 385, 580\u2013594.","journal-title":"Journal of Molecular Biology"},{"key":"4413_CR8","doi-asserted-by":"publisher","first-page":"16452","DOI":"10.1021\/bi982138o","volume":"37","author":"M Cirilli","year":"1998","unstructured":"Cirilli, M., Zheng, R., Scapin, G., & Blanchard, J. S. (1998). Structural symmetry: the three-dimensional structure of Haemophilus influenzae diaminopimelate epimerase. Biochemistry, 37, 16452\u201316458.","journal-title":"Biochemistry"},{"key":"4413_CR9","doi-asserted-by":"crossref","unstructured":"Pillai, B., Cherney, M. M., Diaper, C. M. (2006). Structural insights into stereochemical inversion by diaminopimelate epimerase: an antibacterial drug target.\u00a0Proceedings of the National Academy of Sciences of the United States of America, 103, 8668\u20138673.","DOI":"10.1073\/pnas.0602537103"},{"key":"4413_CR10","doi-asserted-by":"crossref","unstructured":"Gasteiger, E., Hoogland, C., Gattiker, A., Wilkins, M. R., Appel, R. D., & Bairoch, A. (2005). In J. M. Walker (Ed.), The Proteomics Protocols Handbook, Identification and analysis tools on the ExPASy server (pp. 571\u2013607). Humana Press.","DOI":"10.1385\/1-59259-890-0:571"},{"key":"4413_CR11","doi-asserted-by":"publisher","first-page":"1511","DOI":"10.1038\/nprot.2012.085","volume":"7","author":"M K\u00e4llberg","year":"2012","unstructured":"K\u00e4llberg, M., Wang, H., Wang, S., Peng, J., Wang, Z., Lu, H., et al. (2012). Template-based protein structure modeling using the RaptorX web server. Nature Protocols, 7, 1511\u20131522.","journal-title":"Nature Protocols"},{"key":"4413_CR12","unstructured":"Hall, T. A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95\/98\/NT. Nucleic Acids Symposium Series, 41, 95\u201398."},{"key":"4413_CR13","doi-asserted-by":"publisher","first-page":"845","DOI":"10.1038\/nprot.2015.053","volume":"10","author":"LA Kelley","year":"2015","unstructured":"Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N., & Sternberg, M. J. (2015). The Phyre2 web portal for protein modeling, prediction and analysis. Nature Protocols, 10, 845\u2013858.","journal-title":"Nature Protocols"},{"key":"4413_CR14","unstructured":"Schr\u00f6dinger, L., & DeLano, W. (2020). PyMOL. Retrieved from http:\/\/www.pymol.org\/pymol"},{"key":"4413_CR15","doi-asserted-by":"publisher","unstructured":"Laskowski, R. A. (2009). PDBsum new things. Nucleic Acids Research, 37, D355\u2013D359. Retrieved from:\u00a0https:\/\/doi.org\/10.1093\/nar\/gkn860","DOI":"10.1093\/nar\/gkn860"},{"key":"4413_CR16","doi-asserted-by":"publisher","first-page":"1511","DOI":"10.1002\/pro.5560020916","volume":"2","author":"C Colovos","year":"1993","unstructured":"Colovos, C., & Yeates, T. O. (1993). Verification of protein structures: patterns of nonbonded atomic interactions. Protein Science, 2, 1511\u20131519.","journal-title":"Protein Science"},{"key":"4413_CR17","doi-asserted-by":"crossref","unstructured":"Eisenberg, D., L\u00fcthy, R., & Bowie, J. U. (1997). VERIFY3D: Assessment of protein models with three-dimensional profiles.\u00a0Methods in Enzymology, 277, 396\u2013404.","DOI":"10.1016\/S0076-6879(97)77022-8"},{"key":"4413_CR18","doi-asserted-by":"publisher","first-page":"W407","DOI":"10.1093\/nar\/gkm290","volume":"35","author":"M Wiederstein","year":"2007","unstructured":"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, W407\u2013W410.","journal-title":"Nucleic Acids Research"},{"key":"4413_CR19","doi-asserted-by":"publisher","first-page":"D447","DOI":"10.1093\/nar\/gku1003","volume":"43","author":"D Szklarczyk","year":"2015","unstructured":"Szklarczyk, D., Franceschini, A., Wyder, S., Forslund, K., Heller, D., Huerta-Cepas, J., Simonovic, M., Roth, A., Santos, A., Tsafou, K. P., & Kuhn, M. (2015). STRING v10: protein\u2013protein interaction networks, integrated over the tree of life. Nucleic Acids Research, 43, D447\u2013D452.","journal-title":"Nucleic Acids Research"},{"key":"4413_CR20","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1002\/jcc.21334","volume":"31","author":"O Trott","year":"2010","unstructured":"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, 455\u2013461.","journal-title":"Journal of Computational Chemistry"},{"key":"4413_CR21","doi-asserted-by":"publisher","first-page":"1293","DOI":"10.1002\/pmic.200300720","volume":"4","author":"O Drews","year":"2004","unstructured":"Drews, O., Reil, G., Parlar, H., & Gorg, A. (2004). Setting up standards and a reference map for the alkaline proteome of the gram-positive bacterium Lactococcus lactis Proteomics, 4, 1293\u20131304.","journal-title":"Proteomics"},{"issue":"5","key":"4413_CR22","doi-asserted-by":"crossref","first-page":"553","DOI":"10.4103\/0973-1296.301874","volume":"16","author":"H Singh","year":"2020","unstructured":"Singh, H., Das, S., Gupta, P. P., Batra, S., Prakash, R., Srivastava, V. K., Jyoti, A., Gupta, V., Kothari, S. L., & Kaushik, S. (2020). Binding of metronidazole to Enterococcus faecalis homoserine kinase: binding studies, docking studies, and molecular dynamics simulation studies. Pharmacognosy Magazine, 16(5), 553.","journal-title":"Pharmacognosy Magazine"},{"key":"4413_CR23","doi-asserted-by":"publisher","first-page":"2157","DOI":"10.1021\/jm00170a018","volume":"33","author":"F Gerhart","year":"1990","unstructured":"Gerhart, F., Higgins, W., Tardif, C., & Ducep, J. B. (1990). 2-(4-Amino-4-carboxybutyl) aziridine-2-carboxylic acid-A potent irreversible inhibitor of diaminopimelic acid epimerase. Spontaneous formation from \u03b1-(Halomethy 1) diaminopimelic acids. Journal of Medicinal Chemistry, 33, 2157\u20132162.","journal-title":"Journal of Medicinal Chemistry"},{"key":"4413_CR24","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1016\/j.jtbi.2009.09.029","volume":"262","author":"SK Kushwaha","year":"2010","unstructured":"Kushwaha, S. K., & Shakya, M. (2010). Protein interaction network analysis\u2014approach for potential drug target identification in Mycobacterium tuberculosis. Journal of Theoretical Biology, 262, 284\u2013294.","journal-title":"Journal of Theoretical Biology"},{"key":"4413_CR25","doi-asserted-by":"publisher","first-page":"D459","DOI":"10.1093\/nar\/gkt1103","volume":"42","author":"R Caspi","year":"2014","unstructured":"Caspi, R., Altman, T., Billington, R., Dreher, K., Foerster, H., Fulcher, C. A., Holland, T. A., Keseler, I. M., Kothari, A., Kubo, A., & Krummenacker, M. (2014). The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway\/Genome databases. Nucleic Acids Research, 42, D459\u2013D471.","journal-title":"Nucleic Acids Research"},{"key":"4413_CR26","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1111\/j.1574-6968.2012.02527.x","volume":"330","author":"V Usha","year":"2012","unstructured":"Usha, V., Lloyd, A. J., Lovering, A. L., & Besra, G. S. (2012). Structure and function of Mycobacterium tuberculosis meso-diaminopimelic acid (DAP) biosynthetic enzymes. FEMS Microbiology Letters, 330, 10\u201316.","journal-title":"FEMS Microbiology Letters"},{"key":"4413_CR27","doi-asserted-by":"publisher","first-page":"1119","DOI":"10.1128\/AAC.32.8.1119","volume":"32","author":"RJ Baumann","year":"1988","unstructured":"Baumann, R. J., Bohme, E. H., Wiseman, J. S., Vaal, M., & Nichols, J. S. (1988). Inhibition of Escherichia coli growth and diaminopimelic acid epimerase by 3-chlorodiaminopimelic acid. Antimicrobial Agents and Chemotherapy, 32, 1119\u20131123.","journal-title":"Antimicrobial Agents and Chemotherapy"},{"key":"4413_CR28","doi-asserted-by":"publisher","first-page":"1441","DOI":"10.1002\/JPER.18-0673","volume":"90","author":"PJ Vijayashree","year":"2019","unstructured":"Vijayashree, P. J. (2019). In silico validation of the non-antibiotic drugs acetaminophen and ibuprofen as antibacterial agents against red complex pathogens. Journal of Periodontology, 90, 1441\u20131448.","journal-title":"Journal of Periodontology"},{"key":"4413_CR29","doi-asserted-by":"publisher","first-page":"02268","DOI":"10.1128\/AAC.02268-16","volume":"61","author":"P Zimmermann","year":"2017","unstructured":"Zimmermann, P., & Curtis, N. (2017). Antimicrobial effects of antipyretics. Antimicrobial Agents and Chemotherapy, 61, 02268\u201302216.","journal-title":"Antimicrobial Agents and Chemotherapy"},{"key":"4413_CR30","first-page":"351","volume":"4","author":"ZR Abdul-Hussein","year":"2014","unstructured":"Abdul-Hussein, Z. R. (2014). Acetaminophen as antibacterial agent and its effect on antibiotic susceptibilities of some pathogenic bacteria. European Journal of Experimental Biology, 4, 351\u2013356.","journal-title":"European Journal of Experimental Biology"},{"key":"4413_CR31","doi-asserted-by":"publisher","first-page":"615","DOI":"10.1001\/archotol.134.6.615","volume":"134","author":"A Neher","year":"2008","unstructured":"Neher, A., Arnitz, R., Gst\u00f6ttner, M., Sch\u00e4, D., Kr\u00f6ss, E. M., & Nagl, M. (2008). Antimicrobial activity of dexamethasone and its combination with N-chlorotaurine. Archives of Otolaryngology - Head and Neck Surgery, 134, 615\u2013620.","journal-title":"Archives of Otolaryngology - Head and Neck Surgery"},{"key":"4413_CR32","doi-asserted-by":"publisher","first-page":"1146","DOI":"10.1080\/07391102.2018.1451387","volume":"37","author":"S Skariyachan","year":"2019","unstructured":"Skariyachan, S., Manjunath, M., & Bachappanavar, N. (2019). Screening of potential lead molecules against prioritised targets of multi-drug-resistant-Acinetobacter baumannii\u2013insights from molecular docking, molecular dynamic simulations and in vitro assays. Journal of Biomolecular Structure & Dynamics, 37, 1146\u20131169.","journal-title":"Journal of Biomolecular Structure & Dynamics"},{"key":"4413_CR33","doi-asserted-by":"crossref","unstructured":"Singh, H., Das, S., Yadav, J., Srivastava, V. K., Jyoti, A., & Kaushik, S. (2021). In silico prediction, molecular docking and binding studies of acetaminophen and dexamethasone to Enterococcus faecalis diaminopimelate epimerase.\u00a0Journal of Molecular Recognition, 34, e2894.","DOI":"10.1002\/jmr.2894"},{"key":"4413_CR34","doi-asserted-by":"publisher","first-page":"3626","DOI":"10.1128\/JB.182.13.3626-3631.2000","volume":"182","author":"TM Fuchs","year":"2000","unstructured":"Fuchs, T. M., Schneider, B., Krumbach, K., Eggeling, L., & Gross, R. (2000). Characterization of a Bordetella pertussis diaminopimelate (DAP) biosynthesis locus identifies dapC, a novel gene coding for an N-succinyl-L, L-DAP aminotransferase. Journal of Bacteriology, 182, 3626\u20133631.","journal-title":"Journal of Bacteriology"}],"container-title":["Applied Biochemistry and Biotechnology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s12010-023-04413-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s12010-023-04413-0\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s12010-023-04413-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,14]],"date-time":"2023-11-14T13:10:55Z","timestamp":1699967455000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s12010-023-04413-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,3,13]]},"references-count":34,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2023,11]]}},"alternative-id":["4413"],"URL":"https:\/\/doi.org\/10.1007\/s12010-023-04413-0","relation":{},"ISSN":["0273-2289","1559-0291"],"issn-type":[{"value":"0273-2289","type":"print"},{"value":"1559-0291","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,3,13]]},"assertion":[{"value":"17 February 2023","order":1,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 March 2023","order":2,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics Approval"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent to Participate"}},{"value":"Not applicable.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent to Publish"}},{"value":"The authors have no relevant financial or non-financial interests to disclose.","order":5,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing Interests"}}]}}