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Comparative genomics study of Salmonella Typhimurium LT2 for the identification of putative therapeutic candidates. (English) Zbl 1406.92210
Summary: A computational, comparative genomics workflow was defined for the identification of novel therapeutic candidates against Salmonella Typhimurium LT2, with the aim that the selected targets should be essential to the pathogen, and have no homology with the human host. Bioinformatics analysis identified 43 proteins as non-host essential, which could serve as potential drug and vaccine targets. Additional prioritization parameters characterized 13 proteins as vaccine candidates while druggability of each of the identified proteins was evaluated by the Drug Bank database prioritized same number proteins suitable for drug targets. As a case study we built a homology model of one of the potential drug targets MurD ligase using MODELLER (9v12) software. The model has been further explored for in silico docking study with the inhibitors having druggability potential from the Drug Bank database. Results from this study could facilitate selective S. Typhimurium LT2 proteins for drug design and vaccine production pipelines.
92C40 Biochemistry, molecular biology
92C50 Medical applications (general)
92D10 Genetics and epigenetics
Full Text: DOI
[1] Aguero, F.; Al-Lazikani, B.; Aslett, M.; Berriman, M.; Buckner, F. S.; Campbell, R. K.; Carmona, S.; Carruthers, I. M.; Chan, A. W.; Crowther, F., Genomic scale prioritization of drug targets: the TDR targets database, Nat. Rev. Drug Discov., 7, 900-907, (2008)
[2] Altschul, S. F.; Madden, T. L.; Schaffer, A. A.; Zhang, J.; Zhang, Z.; Miller, W.; Lipman, D. J., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 25, 3389-3402, (1997)
[3] Anderson, M. S.; Bull, H. G.; Galloway, S. M., UDP-N acetyl glucosamine acyltransferase of Escherichia coli. the first step of endotoxin biosynthesis is thermodynamically unfavorable, J. Biol. Chem., 268, 19858-19865, (1993)
[4] Anishetty, S.; Pulimi, M.; Pennathur, G., Potential drug targets in mycobacterium tuberculosis through metabolic pathway analysis, Comput. Biol. Chem., 29, 368-378, (2005) · Zbl 1088.92013
[5] Beaver, J. E.; Bourne, P. E.; Ponomarenko, J. V., Epitopeviewer: a Java application for the visualization and analysis of immune epitopes in the immune epitope database and analysis resource (IEDB), Immunome Res., 3, 3, (2007)
[6] Bernstein, F. C.; Koetzle, T. F.; Williams, G. J.; Meyer, E. F.; Brice, M. D.; Rodgers, J. R.; Kennard, O.; Shimanouchi, T.; Tasumi, M., The protein data bank. A computer-based archival file for macromolecular structures, Eur. J. Biochem., 80, 319-324, (1977)
[7] Bjorkman, J.; Hughes, D.; Andersson, D. I., Virulence of antibiotic-resistant salmonella typhimurium, Proc. Natl. Acad. Sci. USA, 95, 3949-3953, (1998)
[8] Boeckmann, B.; Bairoch, A.; Apweiler, R.; Blatter, M. C.; Estreicher, A.; Gasteiger, E.; Martin, M. J.; Michoud, K.; Donovan, C. O.; Phan, I.; Pilbout, I. S.; Schneider, M., The SWISS-PROT protein knowledgebase and its supplement trembl in 2003, Nucleic Acids Res., 31, 365-370, (2003)
[9] Bouhss, A.; Trunkfield, A. E.; Bugg, T. D.; Mengin-Lecreulx, D., The biosynthesis of peptidoglycan lipid-linked intermediates, FEMS Microbiol. Rev., 32, 208-233, (2008)
[10] Cano, D. A.; Mouslim, C.; Ayala, J. A.; García-del Portillo, F.; Casadesús, J., Cell division inhibition in salmonella typhimurium histidine-constitutive strains: an ftsi-like defect in the presence of wild-type penicillin-binding protein 3 levels, J. Bacteriol., 180, 5231-5234, (1998)
[11] Chawley, P.; Samal, H. B.; Prava, J.; Suar, M.; Mahapatra, R. K., Comparative genomics study for identification of drug and vaccine targets in vibrio cholerae: mura ligase as a case study, Genomics, 103, 83-93, (2014)
[12] Chen, J.; Liu, H.; Yang, J., Prediction of linear B-cell epitopes using amino acid pair antigenicity scale, Amino Acids, 33, 423-428, (2007)
[13] Cheng, A. C.; Coleman, R. G.; Smyth, K. T.; Cao, Q.; Soulard, P.; Caffrey, D. R.; Salzberg, A. C.; Huang, E. S., Structure-based maximal affinity model predicts small molecule druggability, Nat. Biotechnol., 25, 71-75, (2007)
[14] Chou, K. C., The biological functions of low-frequency phonons: 6. A possible dynamic mechanism of allosteric transition in antibody molecules, Biopolymers, 26, 285-295, (1987)
[15] Chou, K. C., Low-frequency resonance and cooperatively of hemoglobin, Trends Biochem. Sci., 14, 212-213, (1989)
[16] Chou, K. C., Review: low-frequency collective motion in bio macromolecules and its biological functions, Biophys. Chem., 30, 3-48, (1988)
[17] Chou, K. C.; Mao, B., Collective motion in DNA and its role in drug intercalation, Biopolymers, 27, 1795-1815, (1988)
[18] Chou, K. C.; Watenpaugh, K. D.; Heinrikson, R. L., A model of the complex between cyclin-dependent kinase 5 (cdk5) and the activation domain of neuronal cdk5 activator, Biochemical & Biophysical Research Communications (BBRC), 259, 420-428, (1999)
[19] Chou, K. C., Review: structural bioinformatics and its impact to biomedical science, Curr. Med. Chem., 11, 2105-2134, (2004)
[20] Chou, K. C.; Wei, D. Q.; Zhong, W. Z., Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS, Biochem. Biophys. Res. Commun. (BBRC), 308, 148-151, (2003)
[21] Chou, K. C.; Shen, H. B., Memtype-2L: A web server for predicting membrane proteins and their types by incorporating evolution information through pse-PSSM, Biochem. Biophys. Res. Comm. (BBRC), 360, 339-345, (2007)
[22] Colovos, C.; Yeates, T. O., Verification of protein structures: patterns of non-bonded atomic interactions, Protein Sci., 2, 9, 1511-1519, (1993)
[23] Corpet, F., Multiple sequence alignment with hierarchical clustering, Nucleic Acids Res., 16, 10881-10890, (1988)
[24] Du, Q. S.; Wang, S.; Wei, D. Q.; Sirois, S., Molecular modeling and chemical modification for finding peptide inhibitor against SARS cov mpro, Anal. Biochem., 337, 262-270, (2005)
[25] Du, Q. S.; Wei, Y. T.; Pang, Z. W., Predicting the affinity of epitope-peptides with class I MHC molecule HLA-A*0201: an application of amino acid-based peptide prediction, Protein Eng. Des. Sel., 20, 417-423, (2007)
[26] Du, Q. S.; Huang, R. B.; Wang, C. H., Energetic analysis of the two controversial drug binding sites of the M2 proton channel in influenza A virus, J. Theor. Biol., 259, 159-164, (2009)
[27] Eisenberg, D.; Luthy, R.; Bowie, J. U., VERIFY3D: assessment of protein models with three-dimensional profiles, Methods Enzymol., 277, 396-404, (1997)
[28] Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shelley, M.; Perry, J. K.; Shaw, D. E.; Francis, P.; Shenkin, P. S., Glide: a new approach for rapid, accurate docking and scoring. 1. method and assessment of docking accuracy, J. Med. Chem., 47, 1739-1749, (2004)
[29] Gao, F.; Zhang, C. T., Ori-finder: a web-based system for finding orics in unannotated bacterial genomes, BMC Bioinf., 9, 79, (2008)
[30] Gao, F.; Zhang, R. R., Enzymes are enriched in bacterial essential genes, PLoS One, 6, e21683, (2011)
[31] Holman, A. G.; Davis, P. J.; Foster, J. M.; Carlow, C. K.; Kumar, S., Computational prediction of essential genes in an unculturable endosymbiotic bacterium, wolbachia of brugia malayi, BMC Microbiol., 9, 243, (2009)
[32] Huang, R. B.; Du, Q. S.; Wang, C. H., An in-depth analysis of the biological functional studies based on the NMR M2 channel structure of influenza A virus, Biochem. Biophys. Res. Commun. (BBRC), 377, 1243-1247, (2008)
[33] Hughes, J. M., Preserving the life saving power of antimicrobial agents, J. Am. Med. Assoc., 305, 1027-1028, (2011)
[34] Izumiya, H.; Sekizuka, T.; Nakaya, H.; Taguchi, M.; Oguchi, A.; Ichikawa, N.; Nishiko, R.; Yamazaki, S.; Fujita, N.; Watanabe, H.; Ohnishi, M.; Kuroda, M., Whole-genome analysis of salmonella enterica serovar typhimurium T000240 reveals the acquisition of a genomic island involved in multidrug resistance via IS1 derivatives on the chromosome, Antimicrob. Agents Chemother., 55, 623-630, (2011)
[35] Kanehisa, M.; Goto, S.; Furumichi, M.; Tanabe, M.; Hirakawa, M., KEGG for representation and analysis of molecular networks involving diseases and drugs, Nucleic Acids Res., 38, D355-D360, (2010)
[36] Keller, T. H.; Pichota, A.; Yin, Z., A practical view of ‘druggability’, Curr. Opin. Chem. Biol., 10, 357-361, (2006)
[37] Krogh, A.; Larssonvon, B.; Heijne, G.; Sonnhammer, E. L., Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes, J. Mol. Biol., 305, 567-580, (2001)
[38] Laskowski, R. A.; MacArthur, M. N.; Moss, D. S.; Thorton, J. M., PROCHECK—a program to check the steriochemical quality of protein structures, J. Appl. Crystallogr., 26, 283-291, (1993)
[39] Lee, C. R.; Lee, J. H.; Jeong, B. C.; Lee, S. H., Lipid a biosynthesis of multidrug-resistant pathogens—a novel drug target, Curr. Pharm. Des., 19, 6534-6550, (2013)
[40] Li, X. B.; Wang, S. Q.; Xu, W. R., Novel inhibitor design for hemagglutinin against H1N1 influenza virus by core hopping method, PLoS One, 6, e28111, (2011)
[41] Lin, S. X.; Lapointe, J., Theoretical and experimental biology in one, J. Biomedical Science and Engineering (JBiSE), 6, 435-442, (2013)
[42] Lovering, A. L.; Safadi, S. S.; Strynadka, N. C., Structural perspective of peptidoglycan biosynthesis and assembly, Annu. Rev. Biochem., 81, 451-478, (2012)
[43] Maclachlan, P. N.; Kadam, S. K.; Sanderson, K. E., Cloning, characterization and DNA sequence of the rfalk region for lipopolysaccharide synthesis in salmonella typhimurium LT2, J. Bacteriol., 22, 7151-7163, (1991)
[44] McClelland, M.; Sanderson, K. E.; Spieth, J.; Clifton, S. W.; Courtney, L.; Porwollik, S., Complete genome sequence of salmonella enterica serovar typhimurium LT2, Nature, 413, 852-856, (2001)
[45] McLean, S.; Bowman, L. A.; Poole, R. K., Katg from salmonella typhimurium is a peroxynitritase, FEBS Lett., 584, 1628-1632, (2010)
[46] Mohammadi, F.; Richards, N. G.J.; Guida, W. C.; Liskamp, R.; Lipton, M.; Caufield, C.; Chang, G.; Hendrickson, T.; Still, W. C., Macromodel - an integrated software system for modeling organic and bioorganic molecules using molecular mechanics, J. Comput.Chem., 11, 440-467, (1990)
[47] Norrby, S. R.; Nord, C. E.; Finch, R., Lack of development of new antimicrobial drugs: a potential serious threat to public health, Lancet Infect. Dis., 5, 115-119, (2005)
[48] Onishi, H. R.; Pelak, B. A.; Gerckens, L. S., Antibacterial agents that inhibit lipid A biosynthesis, Science, 274, 980-982, (1996)
[49] Opella, S. J.; Marassi, F. M., Structure determination of membrane proteins by NMR spectroscopy, Chem. Rev., 104, 3587-3606, (2004)
[50] Pielak, R. M.; Jason R. Schnell, J. R., Mechanism of drug inhibition and drug resistance of influenza A M2 channel, Proc. Natl. Acad. Sci. USA, 106, 7379-7384, (2009)
[51] Pieper, U.; Webb, B. M.; Barkan, D. T.; Schneidman-Duhovny, D., Modbase, a database of annotated comparative protein structure models, and associated resources, Nucleic Acids Res., 39, D465-D474, (2011)
[52] Ruiz, N., Bioinformatics identification of murj (mvin) as the peptidoglycan lipid II flippase in Escherichia coli, Proc. Natl. Acad. Sci. USA, 105, 15553-15557, (2008)
[53] Sagara, K.; Matsuyama, S.; Mizushima, S., Secf stabilizes secd and secy, components of the protein translocation machinery of the Escherichia coli cytoplasmic membrane, J. Bacteriol., 176, 4111-4116, (1994)
[54] Sali, A.; Blundell, T. L., Comparative protein modeling by satisfaction of spatial restraints, J. Mol. Biol., 5, 779-815, (1993)
[55] Sandy, J.; Holton, S.; Fullam, E.; Sim, E.; Noble, M., Binding of the anti-tubercular drug isoniazid to the arylamine N-acetyltransferase protein from mycobacterium smegmatis, Protein Sci., 14, 775-782, (2005)
[56] Schnell, J. R.; Chou, J. J., Structure and mechanism of the M2 proton channel of influenza A virus, Nature, 451, 591-595, (2008)
[57] Seringhaus, M.; Paccanaro, A.; Borneman, A.; Snyder, M.; Gerstein, M., Predicting essential genes in fungal genomes, Genome Res., 16, 1126-1135, (2006)
[58] Sharp, P. M.; Li, W. H., The codon adaptation index—a measure of directional synonymous codon usage bias, and its potential applications, Nucleic Acids Res., 15, 1281-1295, (1987)
[59] Smith, C. S., Structure, function and dynamics in the mur family of bacterial cell wall ligases, J. Mol. Biol., 362, 640, (2006)
[60] Vetrivel, U.; Arunkumar, V.; Dorairaj, S., ACUA: a software tool for automated codon usage analysis, Bioinformation, 2, 62-63, (2007)
[61] Wang, J. F., Insights into the mutation-induced HHH syndrome from modeling human mitochondrial ornithine transporter-1, PLoS One, 7, e31048, (2012)
[62] Wang, J. F., Insights from studying the mutation-induced allostery in the M2 proton channel by molecular dynamics, Protein Eng. Des. Sel. (PEDS), 23, 663-666, (2010)
[63] Wang, J. F., Insights from modeling the 3D structure of New Delhi metallo-beta-lactamase and its binding interactions with antibiotic drugs, PLoS One, 6, e18414, (2011)
[64] Wang, J. F.; Gong, K.; Wei, D. Q., Molecular dynamics studies on the interactions of PTP1B with inhibitors: from the first phosphate-binding site to the second one, Protein Eng. Des. Sel. (PEDS), 22, 349-355, (2009)
[65] Wang, S. Q.; Du, Q. S., Study of drug resistance of chicken influenza A virus (H5N1) from homology-modeled 3D structures of neuraminidases, Biochem. Biophys. Res. Commun. (BBRC), 354, 634-640, (2007)
[66] Wang, J. F., Insight into the molecular switch mechanism of human rab5a from molecular dynamics simulations, Biochem. Biophys. Res. Commun. (BBRC), 390, 608-612, (2009)
[67] Wei, D. Q.; Du, Q. S.; Sun, H., Insights from modelling the 3D structure of H5N1 influenza virus neuraminidase and its binding interactions with ligands, Biochem. Biophys. Res. Commun. (BBRC), 344, 1048-1055, (2006)
[68] Yu, C. S.; Chen, Y. C.; Lu, C. H.; Hwang, J. K., Prediction of protein sub-cellular localization, Proteins, 64, 643-651, (2006)
[69] Yu, N. Y.; Wagner, J. R.; Laird, M. R.; Melli, G.; Rey, S.; Lo Dao, R. P.; Sahinalp, S. C.; Ester, M.; Foster, L. J.; Brinkman, F. S., Psortb 3.0: improved protein sub-cellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes, Bioinformatics, 26, 1608-1615, (2010)
[70] Zhang, J.; Luan, C. H.; Johnson, G. V.W.,, Identification of the N-terminal functional domains of cdk5 by molecular truncation and computer modeling, Proteins: Struct., Funct., Genet., 48, 447-453, (2002)
[71] Zhang, R.; Ou, H. Y.; Zhang, C. T., DEG: a database of essential genes, Nucleic Acids Res., 32, D271-D272, (2004)
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