107
Rienksma RA, Suarez-Diez M, Spina L, Schaap PJ, Martins dos Santos VAP (2014) Systemslevel modeling of mycobacterial metabolism for the identification of new (multi-)drug targets.
Semin Immunol 26(6):610–622. https://doi.org/10.1016/j.smim.2014.09.013
Rigottier-Gois L, Madec C, Navickas A, Matos RC, Akary-Lepage E, Mistou M-Y et al (2014) The
surface Rhamnopolysaccharide Epa of Enterococcus faecalis is a key determinant for intestinal
colonization. J Infect Dis 211:jiu402
Roca I, Akova M, Baquero F, Carlet J, Cavaleri M, Coenen S et al (2015) The global threat of antimicrobial resistance: science for intervention. New Microbes New Infections 6:22–29. https://
doi.org/10.1016/j.nmni.2015.02.007
Round JL, Mazmanian SK (2009) The gut microbiome shapes intestinal immune responses during
health and disease. Nat Rev Immunol 9(5):313–323. https://doi.org/10.1038/nri2515
Sanjuán R, Nebot MR, Chirico N, Mansky LM, Belshaw R (2010) Viral mutation rates. J Virol
84(19):9733–9748. https://doi.org/10.1128/JVI.00694-10
Santajit S, Indrawattana N (2016) Mechanisms of antimicrobial resistance in ESKAPE pathogens.
Biomed Res Int 2016:1–8. https://doi.org/10.1155/2016/2475067
Schilling CH, Palsson BO (2000) Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis. J Theor Biol 203(3):249–283. https://doi.
org/10.1006/jtbi.2000.1088
Secor WE, Bras JL, Clain Jr (2015) Mechanisms of resistance to antiparasitic agents. Manual of
clinical microbiology, 11th edn, pp 2550–2562. https://doi.org/10.1128/9781555817381.ch150
Semenyuta IV, Kobzar OL, Hodyna DM, Brovarets VS, Metelytsia LO (2019) In silico study of
4-phosphorylated derivatives of 1,3-oxazole as inhibitors of Candida albicans fructose- 1,6bisphosphate aldolase II. Heliyon 5(4):e01462. https://doi.org/10.1016/j.heliyon.2019.e01462
Singh V (2013) Antimicrobial resistance. Microbial pathogens and strategies for combating them.
Sci, Technol Educ 1:291–296
Singh NK, Selvam SM, Chakravarthy P (2006) T-iDT: tool for identification of drug target in bacteria and validation by Mycobacterium tuberculosis. Silico Biol 6(6):485–493
Skariyachan S, Manjunath M, Bachappanavar N (2019) Screening of potential lead molecules
against prioritised targets of multi-drug-resistant-Acinetobacter baumannii – insights from
molecular docking, molecular dynamic simulations and in vitro assays. J Biomol Struct Dyn
37(5):1146–1169. https://doi.org/10.1080/07391102.2018.1451387
Soares SC, Silva A, Trost E, Blom J, Ramos R, Carneiro A et al (2013) The pan-genome of the
animal pathogen Corynebacterium pseudotuberculosis reveals differences in genome plasticity between the Biovar ovis and equi strains. PLoS One 8(1):e53818. https://doi.org/10.1371/
journal.pone.0053818
Sosa EJ, Burguener G, Lanzarotti E, Defelipe L, Radusky L, Pardo AM et al (2018) Targetpathogen: a structural bioinformatic approach to prioritize drug targets in pathogens. Nucleic
Acids Res 46(D1):D413–D418. https://doi.org/10.1093/nar/gkx1015
Tanwar J, Das S, Fatima Z, Hameed S (2014) Multidrug resistance: an emerging crisis. Interdiscipl
Perspect Infect Dis 2014:1–7
Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL et al (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc Natl Acad Sci U S A 102(39):13950–13955. https://doi.org/10.1073/
pnas.0506758102
Tettelin H, Riley D, Cattuto C, Medini D (2008) Comparative genomics: the bacterial pan-genome.
Curr Opin Microbiol 11(5):472–477
Thiele I, Vo TD, Price ND, Palsson BO (2005) Expanded metabolic reconstruction of
Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants. J Bacteriol 187(16):5818–5830. https://doi.org/10.1128/
JB.187.16.5818-5830.2005
Ubeda C, Taur Y, Jenq RR, Equinda MJ, Son T, Samstein M et al (2010) Vancomycin-resistant
Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice
4 In Silico Approaches for Prioritizing Drug Targets in Pathogens
Rienksma RA, Suarez-Diez M, Spina L, Schaap PJ, Martins dos Santos VAP (2014) Systemslevel modeling of mycobacterial metabolism for the identification of new (multi-)drug targets.
Semin Immunol 26(6):610–622. https://doi.org/10.1016/j.smim.2014.09.013
Rigottier-Gois L, Madec C, Navickas A, Matos RC, Akary-Lepage E, Mistou M-Y et al (2014) The
surface Rhamnopolysaccharide Epa of Enterococcus faecalis is a key determinant for intestinal
colonization. J Infect Dis 211:jiu402
Roca I, Akova M, Baquero F, Carlet J, Cavaleri M, Coenen S et al (2015) The global threat of antimicrobial resistance: science for intervention. New Microbes New Infections 6:22–29. https://
doi.org/10.1016/j.nmni.2015.02.007
Round JL, Mazmanian SK (2009) The gut microbiome shapes intestinal immune responses during
health and disease. Nat Rev Immunol 9(5):313–323. https://doi.org/10.1038/nri2515
Sanjuán R, Nebot MR, Chirico N, Mansky LM, Belshaw R (2010) Viral mutation rates. J Virol
84(19):9733–9748. https://doi.org/10.1128/JVI.00694-10
Santajit S, Indrawattana N (2016) Mechanisms of antimicrobial resistance in ESKAPE pathogens.
Biomed Res Int 2016:1–8. https://doi.org/10.1155/2016/2475067
Schilling CH, Palsson BO (2000) Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis. J Theor Biol 203(3):249–283. https://doi.
org/10.1006/jtbi.2000.1088
Secor WE, Bras JL, Clain Jr (2015) Mechanisms of resistance to antiparasitic agents. Manual of
clinical microbiology, 11th edn, pp 2550–2562. https://doi.org/10.1128/9781555817381.ch150
Semenyuta IV, Kobzar OL, Hodyna DM, Brovarets VS, Metelytsia LO (2019) In silico study of
4-phosphorylated derivatives of 1,3-oxazole as inhibitors of Candida albicans fructose- 1,6bisphosphate aldolase II. Heliyon 5(4):e01462. https://doi.org/10.1016/j.heliyon.2019.e01462
Singh V (2013) Antimicrobial resistance. Microbial pathogens and strategies for combating them.
Sci, Technol Educ 1:291–296
Singh NK, Selvam SM, Chakravarthy P (2006) T-iDT: tool for identification of drug target in bacteria and validation by Mycobacterium tuberculosis. Silico Biol 6(6):485–493
Skariyachan S, Manjunath M, Bachappanavar N (2019) Screening of potential lead molecules
against prioritised targets of multi-drug-resistant-Acinetobacter baumannii – insights from
molecular docking, molecular dynamic simulations and in vitro assays. J Biomol Struct Dyn
37(5):1146–1169. https://doi.org/10.1080/07391102.2018.1451387
Soares SC, Silva A, Trost E, Blom J, Ramos R, Carneiro A et al (2013) The pan-genome of the
animal pathogen Corynebacterium pseudotuberculosis reveals differences in genome plasticity between the Biovar ovis and equi strains. PLoS One 8(1):e53818. https://doi.org/10.1371/
journal.pone.0053818
Sosa EJ, Burguener G, Lanzarotti E, Defelipe L, Radusky L, Pardo AM et al (2018) Targetpathogen: a structural bioinformatic approach to prioritize drug targets in pathogens. Nucleic
Acids Res 46(D1):D413–D418. https://doi.org/10.1093/nar/gkx1015
Tanwar J, Das S, Fatima Z, Hameed S (2014) Multidrug resistance: an emerging crisis. Interdiscipl
Perspect Infect Dis 2014:1–7
Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL et al (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc Natl Acad Sci U S A 102(39):13950–13955. https://doi.org/10.1073/
pnas.0506758102
Tettelin H, Riley D, Cattuto C, Medini D (2008) Comparative genomics: the bacterial pan-genome.
Curr Opin Microbiol 11(5):472–477
Thiele I, Vo TD, Price ND, Palsson BO (2005) Expanded metabolic reconstruction of
Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants. J Bacteriol 187(16):5818–5830. https://doi.org/10.1128/
JB.187.16.5818-5830.2005
Ubeda C, Taur Y, Jenq RR, Equinda MJ, Son T, Samstein M et al (2010) Vancomycin-resistant
Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice
4 In Silico Approaches for Prioritizing Drug Targets in Pathogens