Pangenome profiling of novel drug target against vancomycin-resistant Enterococcus faecium

References

• Alcock, B. P., Raphenya, A. R., Lau, T. T. Y., Tsang, K. K., Bouchard, M., Edalatmand, A., Huynh, W., Nguyen, A.-L V., Cheng, A. A., Liu, S., Min, S. Y., Miroshnichenko, A., Tran, H.-K., Werfalli, R. E., Nasir, J. A., Oloni, M., Speicher, D. J., Florescu, A., Singh, B., … McArthur, A. G. (2020). CARD 2020: Antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Research, 48(D1), D517–D525. https://doi.org/10.1093/nar/gkz935
   PubMed Web of Science ®Google Scholar
• Arias, C. A., Contreras, G. A., & Murray, B. E, J. C. M., & Infection. (2010). Management of multidrug-resistant enterococcal infections. Clinical Microbiology Infection, 16(6), 555–562.
   PubMed Web of Science ®Google Scholar
• Arias, C. A., & Murray, B. E. (2009). Antibiotic-resistant bugs in the 21st century—A clinical super-challenge. The New England Journal of Medicine, 360(5), 439–443.
   PubMed Web of Science ®Google Scholar
• Basharat, Z., Jahanzaib, M., & Rahman, N. (2021). Therapeutic target identification via differential genome analysis of antibiotic resistant Shigella sonneii and inhibitor evaluation against a selected drug target. Infection, Genetics, Evolution, 94, 105004.
   PubMed Web of Science ®Google Scholar
• Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., … Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research, 28(1), 235–242.
   PubMed Web of Science ®Google Scholar
• Bharti, A. K., Farooq, U., Singh, S., Kaur, N., Ahmed, R., & Singh, K. (2016). Incidence of enterococcal urinary tract infection and it’s sensitivity pattern among patients attending Teerthanker Mahaveer Medical College and Research Centre, Moradabad, India. International Journal of Scientific Study, 3(12), 115–119.
   Google Scholar
• Bonten, M. J., Willems, R., & Weinstein, R. A. (2001). Vancomycin-resistant enterococci: why are they here, and where do they come from? The Lancet Infectious Diseases, 1(5), 314–325.
   PubMedGoogle Scholar
• Boyer, E., Leroyer, P., Malherbe, L., Fong, S. B., Loréal, O., Bonnaure Mallet, M., & Meuric, V. (2020). Oral dysbiosis induced by Porphyromonas gingivalis is strain-dependent in mice. Journal of Oral Microbiology, 12(1), 1832837. https://doi.org/10.1080/20002297.2020.1832837
   PubMed Web of Science ®Google Scholar
• Brilisauer, K., Rapp, J., Rath, P., Schöllhorn, A., Bleul, L., Weiß, E., … Forchhammer, K. (2019). Cyanobacterial antimetabolite 7-deoxy-sedoheptulose blocks the shikimate pathway to inhibit the growth of prototrophic organisms. Nature Communications, 10(1), 1–11.
   PubMedGoogle Scholar
• Cacaci, M., Giraud, C., Leger, L., Torelli, R., Martini, C., Posteraro, B., … Hartke, A. (2018). Expression profiling in a mammalian host reveals the strong induction of genes encoding LysM domain-containing proteins in Enterococcus faecium. Scientific Reports, 8(1), 1–11.
   PubMedGoogle Scholar
• Chaudhari, N. M., Gupta, V. K., & Dutta, C. (2016). BPGA: An ultra-fast pan-genome analysis pipeline. Scientific Reports, 6(1), 1–10.
   PubMedGoogle Scholar
• Cox, G., & Wright, G. D. (2013). Intrinsic antibiotic resistance: Mechanisms, origins, challenges and solutions. International Journal of Medical Microbiology, 303(6–7), 287–292.
   PubMed Web of Science ®Google Scholar
• Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7(1), 1–13.
   PubMed Web of Science ®Google Scholar
• Dubin, K., & Pamer, E. (2014). Enterococci and their interactions with the intestinal microbiome. Microbiology Spectrum, 5(6), 5–6.
   Google Scholar
• Dym, O., Eisenberg, D., & Yeates, T. (2012). ERRAT. Crystallography of Biological Macromolecules, ch. 21.3 (Vol. F. , pp. 678-679).
   Google Scholar
• Edgar, R. C. (2004). MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32(5), 1792–1797.
   PubMed Web of Science ®Google Scholar
• Edgar, R. C. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26(19), 2460–2461.
   PubMed Web of Science ®Google Scholar
• Eltigani, S. A., Eltayeb, M. M., Bito, T., Ichiyanagi, T., Ishihara, A., & Arima, J. (2020). Argeloside I inhibits the pathogenicity of Porphyromonas gingivalis TDC60. Journal of Bioscience & Bioengineering, 130(6), 644–649. https://doi.org/10.1016/j.jbiosc.2020.07.016
   PubMed Web of Science ®Google Scholar
• Gallagher, L. A., Lee, S. A., & Manoil, C. (2017). Importance of core genome functions for an extreme antibiotic resistance trait. MBio, 8(6), e01655-01617.
   Web of Science ®Google Scholar
• George, P. E., Celin, J. A., Antonysamy, A., & Ambrose, D. (2005). UPGMA cluster analysis as a tool in the biosystematics of Reduviidae (Insecta: Hemiptera). Shashpa, 12(2), 73–78.
   Google Scholar
• Gordon, S. P., Contreras-Moreira, B., Levy, J. J., Djamei, A., Czedik-Eysenberg, A., Tartaglio, V. S., … Katz, A. (2020). Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors. Nature Communications, 11(1), 1–16.
   PubMed Web of Science ®Google Scholar
• Gouliouris, T., Coll, F., Ludden, C., Blane, B., Raven, K. E., Naydenova, P., … Brown, N. M. (2021). Quantifying acquisition and transmission of Enterococcus faecium using genomic surveillance. Nature Microbiology, 6(1), 103–111.
   PubMed Web of Science ®Google Scholar
• Herrmann, K. M. (1995). The shikimate pathway as an entry to aromatic secondary metabolism. Plant Physiology, 107(1), 7.
   PubMed Web of Science ®Google Scholar
• Higuita, N. I. A., & Huycke, M. M. (2014). Enterococcal disease, epidemiology, and implications for treatment. Enterococci: From commensals to leading causes of drug resistant infection.
   Google Scholar
• Huey, R., Morris, G. M., & Forli, S. (2012). Using AutoDock 4 and AutoDock vina with AutoDockTools: A tutorial. The Scripps Research Institute Molecular Graphics Laboratory, 10550, 92037.
   Google Scholar
• Isa, M. A., & Ibrahim, M. M. (2020). In silico docking and molecular dynamic simulation of 3-dehydroquinate dehydratase from Mycobacterium tuberculosis through virtual screening and pharmacokinetics studies. Biological & Medicinal Chemistry.
   Google Scholar
• Johnson, M., Zaretskaya, I., Raytselis, Y., Merezhuk, Y., McGinnis, S., & Madden, T. L. (2008). NCBI BLAST: A better web interface. Nucleic Acids Research, 36(suppl_2), W5–W9.
   PubMedGoogle Scholar
• Judzentiene, A., Budiene, J., Nedveckyte, I., & Garjonyte, R. (2022). Antioxidant and toxic activity of Helichrysum arenarium (L.) Moench and Helichrysum italicum (Roth) G. Don essential oils and extracts. Molecules, 27(4), 1311.
   PubMed Web of Science ®Google Scholar
• Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., … Potapenko, A. J. N. (2021). Highly accurate protein structure prediction with AlphaFold, 596(7873), 583–589.
   Google Scholar
• Laskowski, R., MacArthur, M., & Thornton, J. (2006). PROCHECK: Validation of protein–structure coordinates. Crystallography of Biological Macromolecules.
   Google Scholar
• Malde, A. K., Zuo, L., Breeze, M., Stroet, M., Poger, D., Nair, P. C., … Mark, A. E. (2011). An automated force field topology builder (ATB) and repository: Version 1.0. Journal of Chemical Theory Computation, 7(12), 4026–4037.
   PubMed Web of Science ®Google Scholar
• Marra, A., Dib-Hajj, F., Lamb, L., Kaczmarek, F., Shang, W., Beckius, G., … Gootz, T. D. (2007). Enterococcal virulence determinants may be involved in resistance to clinical therapy. Diagnostic Microbiology Infectious Disease, 58(1), 59–65.
   PubMed Web of Science ®Google Scholar
• Munita, J., & Arias, C. (2016). Mechanisms of antibiotic resistance. Microbiology Spectrum, 4(2), 4–2.
   Web of Science ®Google Scholar
• Murray, B. E. (2000). Vancomycin-resistant enterococcal infections. New England Journal of Medicine, 342(10), 710–721.
   PubMed Web of Science ®Google Scholar
• Muzzi, A., Masignani, V., & Rappuoli, R. (2007). The pan-genome: towards a knowledge-based discovery of novel targets for vaccines and antibacterials. Drug Discovery Today, 12(11–12), 429–439.
   PubMed Web of Science ®Google Scholar
• Nishida, S., & Ono, Y. (2020). Genomic analysis of a pan-resistant Klebsiella pneumoniae sequence type 11 identified in Japan in 2016. International Journal of Antimicrobial Agents, 55(4), 105854.
   PubMed Web of Science ®Google Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF chimera—A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612.
   PubMed Web of Science ®Google Scholar
• Pronk, S., Páll, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., … Van Der Spoel, D. (2013). GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics, 29(7), 845–854.
   PubMed Web of Science ®Google Scholar
• Pruitt, K. D., Tatusova, T., & Maglott, D. R. (2005). NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Research, 33(suppl_1), D501–D504.
   PubMedGoogle Scholar
• Rasheed, M. A., Iqbal, M. N., Saddick, S., Ali, I., Khan, F. S., Kanwal, S., … Awais, M. (2021). Identification of lead compounds against Scm (fms10) in Enterococcus faecium using computer aided drug designing. Life, 11(2), 77.
   PubMedGoogle Scholar
• Sievert, D. M., Ricks, P., Edwards, J. R., Schneider, A., Patel, J., Srinivasan, A., … Fridkin, S. (2013). Antimicrobial-resistant pathogens associated with healthcare-associated infections summary of data reported to the National Healthcare Safety Network at the Centers for Disease Control and Prevention, 2009–2010. Infection Control Hospital Epidemiology, 34(1), 1–14.
   PubMed Web of Science ®Google Scholar
• Tacconelli, E., Carrara, E., Savoldi, A., Harbarth, S., Mendelson, M., Monnet, D. L., … Carmeli, Y. (2018). Discovery, research, and development of new antibiotics: The WHO priority list of antibiotic-resistant bacteria and tuberculosis. The Lancet Infectious Diseases, 18(3), 318–327.
   PubMed Web of Science ®Google Scholar
• Tan, S.-A., Yam, H. C., Cheong, S. L., Chow, Y. C., Bok, C. Y., Ho, J. M., Lee, P. Y., & Gunasekaran, B. (2022). Inhibition of Porphyromonas gingivalis peptidyl arginine deiminase, a virulence factor, by antioxidant-rich Cratoxylum cochinchinense: In vitro and in silico evaluation. Saudi Journal of Biological Sciences, 29(4), 2573–2581. https://doi.org/10.1016/j.sjbs.2021.12.037
   PubMed Web of Science ®Google Scholar
• Tatusov, R. L., Galperin, M. Y., Natale, D. A., & Koonin, E. V. (2000). The COG database: A tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Research, 28(1), 33–36.
   PubMed Web of Science ®Google Scholar
• Top, J., Willems, R., van der Velden, S., Asbroek, M., & Bonten, M. (2008). Emergence of clonal complex 17 Enterococcus faecium in The Netherlands. Journal of Clinical Microbiology, 46(1), 214–219.
   PubMed Web of Science ®Google Scholar
• Trendafilova, A., Kutova, N., Ozek, G., Todorova, M., Yur, S., Ozek, T., & Dimitrov, D. (2020). Phenolic profile and antioxidant, acetylcholinesterase, and tyrosinase inhibitor activities of Jurinea tzar-ferdinandii Davidov, an endemic plant of the Balkans. Boletín Latinoamericano y Del Caribe de Plantas Medicinales y Aromáticas, 19(2), 161–166.
   Web of Science ®Google Scholar
• UniProt: The Universal Protein Knowledgebase. (2017). Nucleic Acids Research, 45(D1), D158–D169.
   PubMed Web of Science ®Google Scholar
• Vankerckhoven, V., Van Autgaerden, T., Vael, C., Lammens, C., Chapelle, S., Rossi, R., … Goossens, H. (2004). Development of a multiplex PCR for the detection of asa1, gelE, cylA, esp, and hyl genes in enterococci and survey for virulence determinants among European hospital isolates of Enterococcus faecium. Journal of Clinical Microbiology, 42(10), 4473–4479.
   PubMed Web of Science ®Google Scholar
• Varadi, M., Anyango, S., Deshpande, M., Nair, S., Natassia, C., Yordanova, G., Yuan, D., Stroe, O., Wood, G., Laydon, A., Žídek, A., Green, T., Tunyasuvunakool, K., Petersen, S., Jumper, J., Clancy, E., Green, R., Vora, A., Lutfi, M., … Velankar, S. (2022). AlphaFold Protein Structure Database: Massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Research, 50(D1), D439–D444. https://doi.org/10.1093/nar/gkab1061
   PubMed Web of Science ®Google Scholar
• Webb, B., & Sali, A. (2016). Comparative protein structure modeling using MODELLER. Current Protocols in Bioinformatics, 54(1), 5.6.1–5.6.37.
   PubMedGoogle Scholar
• Wishart, D. S., Knox, C., Guo, A. C., Cheng, D., Shrivastava, S., Tzur, D., Gautam, B., & Hassanali, M. (2008). DrugBank: A knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Research, 36(Database issue), D901–D906.
   PubMed Web of Science ®Google Scholar
• Zarb, P., Coignard, B., Griskeviciene, J., Muller, A., Vankerckhoven, V., Weist, K., … Catry, B. (2012). The European Centre for Disease Prevention and Control (ECDC) pilot point prevalence survey of healthcare-associated infections and antimicrobial use. Eurosurveillance, 17(46), 20316.
   Web of Science ®Google Scholar
• Zhang, R., & Lin, Y. (2009). DEG 5.0: A database of essential genes in both prokaryotes and eukaryotes. Nucleic Acids Research, 37(suppl_1), D455–D458.
   PubMedGoogle Scholar
• Zhou, X., Willems, R. J., Friedrich, A. W., Rossen, J. W., & Bathoorn, E. (2020). Enterococcus faecium: From microbiological insights to practical recommendations for infection control and diagnostics. Antimicrobial Resistance Infection Control, 9(1), 1–13.
   PubMed Web of Science ®Google Scholar