Navegar

Colección

Datos Estadísticas

Artículo

Jamal, S.B.; Hassan, S.S.; Tiwari, S.; Viana, M.V.; De Jesus Benevides, L.; Ullah, A.; Turjanski, A.G.; Barh, D.; Ghosh, P.; Costa, D.A.; Silva, A.; Röttger, R.; Baumbach, J.; Azevedo, V.A.C. "An integrative in-silico approach for therapeutic target identification in the human pathogen Corynebacterium diphtheriae" (2017) PLoS ONE. 12(10)
Estamos trabajando para incorporar este artículo al repositorio
Consulte el artículo en la página del editor
Consulte la política de Acceso Abierto del editor

Abstract:

Corynebacterium diphtheriae (Cd) is a Gram-positive human pathogen responsible for diphtheria infection and once regarded for high mortalities worldwide. The fatality gradually decreased with improved living standards and further alleviated when many immunization programs were introduced. However, numerous drug-resistant strains emerged recently that consequently decreased the efficacy of current therapeutics and vaccines, thereby obliging the scientific community to start investigating new therapeutic targets in pathogenic microorganisms. In this study, our contributions include the prediction of modelome of 13 C. diphtheriae strains, using the MHOLline workflow. A set of 463 conserved proteins were identified by combining the results of pangenomics based core-genome and core-modelome analyses. Further, using subtractive proteomics and modelomics approaches for target identification, a set of 23 proteins was selected as essential for the bacteria. Considering human as a host, eight of these proteins (glpX, nusB, rpsH, hisE, smpB, bioB, DIP1084, and DIP0983) were considered as essential and non-host homologs, and have been subjected to virtual screening using four different compound libraries (extracted from the ZINC database, plant-derived natural compounds and Di-terpenoid Iso-steviol derivatives). The proposed ligand molecules showed favorable interactions, lowered energy values and high complementarity with the predicted targets. Our proposed approach expedites the selection of C. diphtheriae putative proteins for broad-spectrum development of novel drugs and vaccines, owing to the fact that some of these targets have already been identified and validated in other organisms. © 2017, Public Library of Science. All rights reserved. This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

Registro:

Documento: Artículo
Título:An integrative in-silico approach for therapeutic target identification in the human pathogen Corynebacterium diphtheriae
Autor:Jamal, S.B.; Hassan, S.S.; Tiwari, S.; Viana, M.V.; De Jesus Benevides, L.; Ullah, A.; Turjanski, A.G.; Barh, D.; Ghosh, P.; Costa, D.A.; Silva, A.; Röttger, R.; Baumbach, J.; Azevedo, V.A.C.
Filiación:PG Program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
Department of Chemistry, Islamia College University Peshawar, KPK, Pakistan
Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón II, Buenos Aires, Argentina
Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Nonakuri, Purba Medinipur, West Bengal, India
Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States
Institute of Biologic Sciences, Federal University of Para, Belém, PA, Brazil
Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
Department of General Biology (LGCM), Institute of Biologic Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
Palabras clave:bacterial protein; protein bioB; protein DIP0983; protein DIP1084; protein glpX; protein hisE; protein nusB; protein rpsH; protein smpB; unclassified drug; antiinfective agent; bacterial protein; bacterial vaccine; ligand; Article; bacterial genome; bacterial strain; bacterium identification; computer model; controlled study; Corynebacterium diphtheriae; gene identification; molecular docking; nonhuman; protein analysis; protein function; protein protein interaction; protein structure; proteomics; biological model; computer simulation; Corynebacterium diphtheriae; drug effects; genetics; human; metabolism; pathogenicity; validation study; Anti-Bacterial Agents; Bacterial Proteins; Bacterial Vaccines; Computer Simulation; Corynebacterium diphtheriae; Genome, Bacterial; Humans; Ligands; Models, Biological; Molecular Docking Simulation
Año:2017
Volumen:12
Número:10
DOI: http://dx.doi.org/10.1371/journal.pone.0186401
Título revista:PLoS ONE
Título revista abreviado:PLoS ONE
ISSN:19326203
CODEN:POLNC
CAS:Anti-Bacterial Agents; Bacterial Proteins; Bacterial Vaccines; Ligands
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_19326203_v12_n10_p_Jamal

Referencias:

  • Funke, G., Von Graevenitz, A., Clarridge, J.E., 3rd, Bernard, K.A., Clinical microbiology of coryneform bacteria (1997) Clin Microbiol Rev, 10 (1), pp. 125-159. , PMID: 8993861; PubMed Central PMCID: PMCPMC172946
  • Goodfellow, M., Kämpfer, P., Busse, H.J., Trujillo, M., Suzuki, K.I., Ludwig, W., (2012) Whitman Bergey’s Manual of Systematic Bacteriology, , Springer
  • Hodes, H.L., Diphtheria (1979) Pediatr Clin North Am, 26 (2), pp. 445-459. , PMID: 379784
  • Hart, P.E., Lee, P.Y., Macallan, D.C., Wansbrough-Jones, M.H., Cutaneous and pharyngeal diphtheria imported from the Indian subcontinent (1996) Postgrad Med J, 72 (852), pp. 619-620. , PMID: 8977947; PubMed Central PMCID: PMCPMC2398589
  • Wagner, K.S., White, J.M., Crowcroft, N.S., De Martin, S., Mann, G., Efstratiou, A., Diphtheria in the United Kingdom, 1986–2008: The increasing role of Corynebacterium ulcerans (2010) Epidemiol Infect, 138 (11), pp. 1519-1530. , https://doi.org/10.1017/S0950268810001895, PMID: 20696088
  • Barh, D., Gupta, K., Jain, N., Khatri, G., Leon-Sicairos, N., Canizalez-Roman, A., Conserved host-pathogen PPIs. Globally conserved inter-species bacterial PPIs based conserved host-pathogen interactome derived novel target in C. Pseudotuberculosis, C. Diphtheriae, M. Tuberculosis, C. Ulcerans, Y. Pestis, and E. Coli targeted by Piper betel compounds (2013) Integr Biol, 5 (3), pp. 495-509. , https://doi.org/10.1039/c2ib20206a, (Camb). PMID: 23288366
  • Perumal, D., Lim, C.S., Sakharkar, K.R., Sakharkar, M.K., Differential genome analyses of metabolic enzymes in Pseudomonas aeruginosa for drug target identification (2007) Silico Biol, 7 (4-5), pp. 453-465. , PMID: 18391237
  • Pizza, M., Scarlato, V., Masignani, V., Giuliani, M.M., Arico, B., Comanducci, M., Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing (2000) Science, 287 (5459), pp. 1816-1820. , PMID: 10710308
  • Asif, S.M., Asad, A., Faizan, A., Anjali, M.S., Arvind, A., Neelesh, K., Dataset of potential targets for Mycobacterium tuberculosis H37Rv through comparative genome analysis (2009) Bioinformation, 4 (6), pp. 245-248. , PMID: 20975918; PubMed Central PMCID: PMCPMC2951718
  • Chong, C.E., Lim, B.S., Nathan, S., Mohamed, R., In silico analysis of Burkholderia pseudomallei genome sequence for potential drug targets (2006) Silico Biol, 6 (4), pp. 341-346. , PMID: 16922696
  • Dutta, A., Singh, S.K., Ghosh, P., Mukherjee, R., Mitter, S., Bandyopadhyay, D., In silico identification of potential therapeutic targets in the human pathogen Helicobacter pylori (2006) Silico Biol, 6 (1-2), pp. 43-47. , PMID: 16789912
  • Sakharkar, K.R., Sakharkar, M.K., Chow, V.T., A novel genomics approach for the identification of drug targets in pathogens, with special reference to Pseudomonas aeruginosa (2004) Silico Biol, 4 (3), pp. 355-360. , PMID: 15724285
  • Barh, D., Kumar, A., In silico identification of candidate drug and vaccine targets from various pathways in Neisseria gonorrhoeae (2009) Silico Biol, 9 (4), pp. 225-231. , PMID: 20109152
  • Rathi, B., Sarangi, A.N., Trivedi, N., Genome subtraction for novel target definition in Salmonella typhi (2009) Bioinformation, 4 (4), pp. 143-150. , PMID: 20198190; PubMed Central PMCID: PMCPMC2825597
  • Barh, D., Jain, N., Tiwari, S., Parida, B.P., D’Afonseca, V., Li, L., A novel comparative genomics analysis for common drug and vaccine targets in Corynebacterium pseudotuberculosis and other CMN group of human pathogens (2011) Chem Biol Drug Des, 78 (1), pp. 73-84. , https://doi.org/10.1111/j.1747-0285.2011.01118.x, PMID: 21443692
  • Aronov, A.M., Verlinde, C.L., Hol, W.G., Gelb, M.H., Selective tight binding inhibitors of trypanosomal glyceral-dehyde-3-phosphate dehydrogenase via structure-based drug design (1998) J Med Chem, 41 (24), pp. 4790-4799. , https://doi.org/10.1021/jm9802620, PMID: 9822549
  • Singh, S., Malik, B.K., Sharma, D.K., Molecular modeling and docking analysis of Entamoeba histolytica glyceraldehyde-3 phosphate dehydrogenase, a potential target enzyme for anti-protozoal drug development (2008) Chem Biol Drug Des, 71 (6), pp. 554-562. , https://doi.org/10.1111/j.1747-0285.2008.00666.x, PMID: 18489439
  • Hassan, S.S., Tiwari, S., Guimaraes, L.C., Jamal, S.B., Folador, E., Sharma, N.B., Proteome scale comparative modeling for conserved drug and vaccine targets identification in Corynebacterium pseudotuberculosis (2014) BMC Genomics, 15, p. S3. , https://doi.org/10.1186/1471-2164-15-S7-S3, PMID: 25573232; PubMed Central PMCID: PMCPMC4243142
  • Eswar, N., Webb, B., Marti-Renom, M.A., Madhusudhan, M.S., Eramian, D., Shen, M.Y., Comparative protein structure modeling using MODELLER (2007) Curr Protoc Protein Sci, , https://doi.org/10.1002/0471140864.ps0209s50, Chapter 2:Unit 2 9. PMID: 18429317
  • Mount, D.W., Using the Basic Local Alignment Search Tool (BLAST) (2007) CSH Protoc, 2007, p. pdbtop17. , https://doi.org/10.1101/pdb.top17, PMID: 21357135
  • Tusnady, G.E., Simon, I., The HMMTOP transmembrane topology prediction server (2001) Bioinformatics, 17 (9), pp. 849-850. , PMID: 11590105
  • Laskowski, R.A., MacArthur, M.W., Moss, D.S., Thornton, J.M., PROCHECK: A program to check the ste-reochemical quality of protein structures (1993) Journal of Applied Crystallography, 26. , https://doi.org/10.1107/S0021889892009944, Epub 291
  • Blom, J., Albaum, S.P., Doppmeier, D., Puhler, A., Vorholter, F.J., Zakrzewski, M., EDGAR: A software framework for the comparative analysis of prokaryotic genomes (2009) BMC Bioinformatics, 10, p. 154. , https://doi.org/10.1186/1471-2105-10-154, PMID: 19457249; PubMed Central PMCID: PMCPMC2696450
  • Abadio, A.K., Kioshima, E.S., Teixeira, M.M., Martins, N.F., Maigret, B., Felipe, M.S., Comparative genomics allowed the identification of drug targets against human fungal pathogens (2011) BMC Genomics, 12, p. 75. , https://doi.org/10.1186/1471-2164-12-75, PMID: 21272313; PubMed Central PMCID: PMCPMC3042012
  • Zhang, R., Ou, H.Y., Zhang, C.T., DEG: A database of essential genes (2004) Nucleic Acids Res, 32, pp. D271-D272. , https://doi.org/10.1093/nar/gkh024, (Database issue): PMID: 14681410; PubMed Central PMCID: PMCPMC308758
  • Kanehisa, M., Goto, S., KEGG: Kyoto encyclopedia of genes and genomes (2000) Nucleic Acids Res, 28 (1), pp. 27-30. , PMID: 10592173; PubMed Central PMCID: PMCPMC102409
  • Magrane, M., Consortium, U., UniProt Knowledgebase: A hub of integrated protein data (2011) Database, 2011, p. bar009. , https://doi.org/10.1093/database/bar009, (Oxford). PMID: 21447597; PubMed Central PMCID: PMCPMC3070428
  • Yoon, S.H., Park, Y.K., Lee, S., Choi, D., Oh, T.K., Hur, C.G., Towards pathogenomics: A web-based resource for pathogenicity islands (2007) Nucleic Acids Res, 35, pp. D395-D400. , https://doi.org/10.1093/nar/gkl790, (Database issue): PMID: 17090594; PubMed Central PMCID: PMCPMC1669727
  • Yu, C.S., Lin, C.J., Hwang, J.K., Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions (2004) Protein Sci, 13 (5), pp. 1402-1406. , https://doi.org/10.1110/ps.03479604, PMID: 15096640; PubMed Central PMCID: PMCPMC2286765
  • Aguero, F., Al-Lazikani, B., Aslett, M., Berriman, M., Buckner, F.S., Campbell, R.K., Genomic-scale prioritization of drug targets: The TDR Targets database (2008) Nat Rev Drug Discov, 7 (11), pp. 900-907. , https://doi.org/10.1038/nrd2684, PMID: 18927591; PubMed Central PMCID: PMCPMC3184002
  • Butt, A.M., Nasrullah, I., Tahir, S., Tong, Y., Comparative genomics analysis of Mycobacterium ulcerans for the identification of putative essential genes and therapeutic candidates (2012) Plos One, 7 (8). , https://doi.org/10.1371/journal.pone.0043080, PMID: 22912793; PubMed Central PMCID: PMCPMC3418265
  • Volkamer, A., Kuhn, D., Rippmann, F., Rarey, M., DoGSiteScorer: A web server for automatic binding site prediction, analysis and druggability assessment (2012) Bioinformatics, 28 (15), pp. 2074-2075. , https://doi.org/10.1093/bioinformatics/bts310, PMID: 22628523
  • Tiwari, S., Da Costa, M.P., Almeida, S., Hassan, S.S., Jamal, S.B., Oliveira, A., C. Pseudotuberculosis Phop confers virulence and may be targeted by natural compounds (2014) Integr Biol, 6 (11), pp. 1088-1099. , https://doi.org/10.1039/c4ib00140k, (Camb). PMID: 25212181
  • Voigt, J.H., Bienfait, B., Wang, S., Nicklaus, M.C., Comparison of the NCI open database with seven large chemical structural databases (2001) J Chem Inf Comput Sci, 41 (3), pp. 702-712. , PMID: 11410049
  • Wadood, A., Jamal, S.B., Riaz, M., Mir, A., Computational analysis of benzofuran-2-carboxlic acids as potent Pim-1 kinase inhibitors (2014) Pharm Biol, 52 (9), pp. 1170-1178. , https://doi.org/10.3109/13880209.2014.880488, PMID: 24766364
  • Thomsen, R., Christensen, M.H., MolDock: A new technique for high-accuracy molecular docking (2006) J Med Chem, 49 (11), pp. 3315-3321. , https://doi.org/10.1021/jm051197e, PMID: 16722650
  • Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., UCSF Chimera—a visualization system for exploratory research and analysis (2004) J Comput Chem, 25 (13), pp. 1605-1612. , https://doi.org/10.1002/jcc.20084, PMID: 15264254
  • Caffrey, C.R., Rohwer, A., Oellien, F., Marhofer, R.J., Braschi, S., Oliveira, G., A comparative chemoge-nomics strategy to predict potential drug targets in the metazoan pathogen, Schistosoma mansoni (2009) Plos One, 4 (2). , https://doi.org/10.1371/journal.pone.0004413, PMID: 19198654; PubMed Central PMCID: PMCPMC2635471
  • Crowther, G.J., Shanmugam, D., Carmona, S.J., Doyle, M.A., Hertz-Fowler, C., Berriman, M., Identification of attractive drug targets in neglected-disease pathogens using an in silico approach (2010) Plos Negl Trop Dis, 4 (8). , https://doi.org/10.1371/journal.pntd.0000804, PMID: 20808766; PubMed Central PMCID: PMCPMC2927427
  • Shanmugham, B., Pan, A., Identification and characterization of potential therapeutic candidates in emerging human pathogen Mycobacterium abscessus: A novel hierarchical in silico approach (2013) Plos One, 8 (3). , https://doi.org/10.1371/journal.pone.0059126, PMID: 23527108; PubMed Central PMCID: PMCPMC3602546
  • Folador, E.L., De Carvalho, P.V., Silva, W.M., Ferreira, R.S., Silva, A., Gromiha, M., In silico identification of essential proteins in Corynebacterium pseudotuberculosis based on protein-protein interaction networks (2016) BMC Syst Biol, 10 (1), p. 103. , https://doi.org/10.1186/s12918-016-0346-4, PMID: 27814699; PubMed Central PMCID: PMCPMC5097352
  • Wadood, A., Riaz, M., Jamal, S.B., Shah, M., Interactions of ketoamide inhibitors on HCV NS3/4A protease target: Molecular docking studies (2014) Mol Biol Rep, 41 (1), pp. 337-345. , https://doi.org/10.1007/s11033-013-2867-x, PMID: 24234753
  • Horecker, B.L., Melloni, E., Pontremoli, S., Fructose 1,6-bisphosphatase: Properties of the neutral enzyme and its modification by proteolytic enzymes (1975) Adv Enzymol Relat Areas Mol Biol, 42, pp. 193-226. , PMID: 236638
  • Wright, S.W., Carlo, A.A., Carty, M.D., Danley, D.E., Hageman, D.L., Karam, G.A., Anilinoquinazoline inhibitors of fructose 1,6-bisphosphatase bind at a novel allosteric site: Synthesis, in vitro characterization, and X-ray crystallography (2002) J Med Chem, 45 (18), pp. 3865-3877. , PMID: 12190310
  • Sassetti, C.M., Rubin, E.J., Genetic requirements for mycobacterial survival during infection (2003) Proc Natl Acad Sci U S A, 100 (22), pp. 12989-12994. , https://doi.org/10.1073/pnas.2134250100, PMID: 14569030; PubMed Central PMCID: PMCPMC240732
  • Gopal, B., Haire, L.F., Cox, R.A., Jo Colston, M., Major, S., Brannigan, J.A., The crystal structure of NusB from Mycobacterium tuberculosis (2000) Nat Struct Biol, 7 (6), pp. 475-478. , https://doi.org/10.1038/75876, PMID: 10881194
  • Brogan, A.P., Verghese, J., Widger, W.R., Kohn, H., Bismuth-dithiol inhibition of the Escherichia coli rho transcription termination factor (2005) J Inorg Biochem, 99 (3), pp. 841-851. , https://doi.org/10.1016/j.jinorgbio.2004.12.019, PMID: 15708806
  • Yates, J.L., Arfsten, A.E., Nomura, M., In vitro expression of Escherichia coli ribosomal protein genes: Autog-enous inhibition of translation (1980) Proc Natl Acad Sci U S A, 77 (4), pp. 1837-1841. , PMID: 6445562; PubMed Central PMCID: PMCPMC348603
  • Davies, C., Ramakrishnan, V., White, S.W., Structural evidence for specific S8-RNA and S8-protein interactions within the 30S ribosomal subunit: Ribosomal protein S8 from Bacillus stearothermophilus at 1.9 A resolution (1996) Structure, 4 (9), pp. 1093-1104. , PMID: 8805594
  • Berkovitch, F., Nicolet, Y., Wan, J.T., Jarrett, J.T., Drennan, C.L., Crystal structure of biotin synthase, an S-ade-nosylmethionine-dependent radical enzyme (2004) Science, 303 (5654), pp. 76-79. , https://doi.org/10.1126/science.1088493, PMID: 14704425; PubMed Central PMCID: PMCPMC1456065
  • Javid-Majd, F., Yang, D., Ioerger, T.R., Sacchettini, J.C., The 1.25 A resolution structure of phosphoribosyl-ATP pyrophosphohydrolase from Mycobacterium tuberculosis (2008) Acta Crystallogr D Biol Crystallogr, 64, pp. 627-635. , https://doi.org/10.1107/S0907444908007105, PMID: 18560150; PubMed Central PMCID: PMCPMC2631106
  • Gutmann, S., Haebel, P.W., Metzinger, L., Sutter, M., Felden, B., Ban, N., Crystal structure of the transfer-RNA domain of transfer-messenger RNA in complex with SmpB (2003) Nature, 424 (6949), pp. 699-703. , https://doi.org/10.1038/nature01831, PMID: 12904796
  • Finn, R.D., Bateman, A., Clements, J., Coggill, P., Eberhardt, R.Y., Eddy, S.R., Pfam: The protein families database (2014) Nucleic Acids Res, 42, pp. D222-D230. , https://doi.org/10.1093/nar/gkt1223, (Database issue): PMID: 24288371; PubMed Central PMCID: PMCPMC3965110
  • Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, S.R., The Pfam protein families database (2002) Nucleic Acids Res, 30 (1), pp. 276-280. , PMID: 11752314; PubMed Central PMCID: PMCPMC99071
  • Dzurova, L., Forneris, F., Savino, S., Galuszka, P., Vrabka, J., Frebort, I., The three-dimensional structure of "Lonely Guy" from Claviceps purpurea provides insights into the phosphoribohydrolase function of Rossmann fold-containing lysine decarboxylase-like proteins (2015) Proteins, 83 (8), pp. 1539-1546. , https://doi.org/10.1002/prot.24835, PMID: 26010010
  • Lohinai, Z., Keremi, B., Szoko, E., Tabi, T., Szabo, C., Tulassay, Z., Biofilm lysine Decarboxylase, a New Therapeutic Target for Periodontal Inflammation (2015) J Periodontol, pp. 1-15. , https://doi.org/10.1902/jop.2015.140490, PMID: 26110450
  • Veeresham, C., Natural products derived from plants as a source of drugs (2012) J Adv Pharm Technol Res, 3 (4), pp. 200-201. , https://doi.org/10.4103/2231-4040.104709, PMID: 23378939; PubMed Central PMCID: PMCPMC3560124

Citas:

---------- APA ----------
Jamal, S.B., Hassan, S.S., Tiwari, S., Viana, M.V., De Jesus Benevides, L., Ullah, A., Turjanski, A.G.,..., Azevedo, V.A.C. (2017) . An integrative in-silico approach for therapeutic target identification in the human pathogen Corynebacterium diphtheriae. PLoS ONE, 12(10).
http://dx.doi.org/10.1371/journal.pone.0186401
---------- CHICAGO ----------
Jamal, S.B., Hassan, S.S., Tiwari, S., Viana, M.V., De Jesus Benevides, L., Ullah, A., et al. "An integrative in-silico approach for therapeutic target identification in the human pathogen Corynebacterium diphtheriae" . PLoS ONE 12, no. 10 (2017).
http://dx.doi.org/10.1371/journal.pone.0186401
---------- MLA ----------
Jamal, S.B., Hassan, S.S., Tiwari, S., Viana, M.V., De Jesus Benevides, L., Ullah, A., et al. "An integrative in-silico approach for therapeutic target identification in the human pathogen Corynebacterium diphtheriae" . PLoS ONE, vol. 12, no. 10, 2017.
http://dx.doi.org/10.1371/journal.pone.0186401
---------- VANCOUVER ----------
Jamal, S.B., Hassan, S.S., Tiwari, S., Viana, M.V., De Jesus Benevides, L., Ullah, A., et al. An integrative in-silico approach for therapeutic target identification in the human pathogen Corynebacterium diphtheriae. PLoS ONE. 2017;12(10).
http://dx.doi.org/10.1371/journal.pone.0186401