Synthesis, biological activity and molecular modelling studies of shikimic acid derivatives as inhibitors of the shikimate dehydrogenase enzyme of Escherichia coli

References

• Mir R, Jallu S, Singh TP. The shikimate pathway: review of amino acid sequence, function and three-dimensional structures of the enzymes. Crit Rev Microbiol 2015;41:172–89.
   PubMed Web of Science ®Google Scholar
• Maeda H, Dudareva N. The shikimate pathway and aromatic amino acid biosynthesis in plants. Annu Rev Plant Biol 2012;63:73–105.
   PubMed Web of Science ®Google Scholar
• Diaz Quiroz DC, Carmona SB, Bolivar F, Escalante A. Current perspectives on applications of shikimic and aminoshikimic acids in pharmaceutical chemistry. Res Rep Med Chem 2014;4:35–46.
   Google Scholar
• Martínez JA, Bolívar F, Escalante A. Shikimic acid production in Escherichia coli: from classical metabolic engineering strategies to omics applied to improve its production. Front Bioeng Biotechnol 2015;3:145.
   PubMed Web of Science ®Google Scholar
• Amer FA, El-behedy EM, Mohtady HA. New targets for antibacterial agents. Biotechnol Mol Biol Rev 2008;3:46–57.
   Google Scholar
• Gordon S, Simithy J, Goodwin D. Selective Mycobacterium tuberculosis shikimate kinase inhibitors as potential antibacterials. Perspect Medicin Chem 2015;7:9–20.
   PubMed Web of Science ®Google Scholar
• Gonzalez-Bello C. Inhibition of shikimate kinase and type II dehydroquinase for antibiotic discovery: structure-based design and simulation studies. Curr Top Med Chem 2016;16:960–77.
   PubMed Web of Science ®Google Scholar
• Derrer B, Macheroux P, Kappes B. The shikimate pathway in apicomplexan parasites: implications for drug development. Front Biosci 2013;18:944.
   Web of Science ®Google Scholar
• Roberts F, Roberts CW, Johnson JJ, et al. Evidence for the shikimate pathway in apicomplexan parasites. Nature 1998;393:801.
   PubMed Web of Science ®Google Scholar
• Steinrücken HC, Amrhein N. The herbicide glyphosate is a potent inhibitor of 5-enolpyruvyl-shikimic acid-3-phosphate synthase. Biochem Biophys Res Commun 1980;94:1207–12.
   PubMed Web of Science ®Google Scholar
• Bai SH, Ogbourne SM. Glyphosate: environmental contamination, toxicity and potential risks to human health via food contamination. Environ Sci Pollut Res Int 2016;23:18988–9001.
   PubMed Web of Science ®Google Scholar
• Peek J, Christendat D. The shikimate dehydrogenase family: functional diversity within a conserved structural and mechanistic framework. Arch Biochem Biophys 2015;566:85–99.
   PubMed Web of Science ®Google Scholar
• Balinsky D, Davies DD. Aromatic biosynthesis in higher plants. 2. Mode of attachment of shikimic acid and dehydroshikimic acid to dehydroshikimic reductase. Biochem J 1961;80:296–300.
   PubMed Web of Science ®Google Scholar
• Baillie AC, Corbett JR, Dowsett JR, McCloskey P. Inhibitors of shikimate dehydrogenase as potential herbicides. Pestic Sci 1972;3:113–20.
   Google Scholar
• Han C, Wang L, Yu K, et al. Biochemical characterization and inhibitor discovery of shikimate dehydrogenase from Helicobacter pylori. FEBS J 2006;273:4682–92.
   PubMed Web of Science ®Google Scholar
• Peek J, Shi T, Christendat D. Identification of novel polyphenolic inhibitors of shikimate dehydrogenase (AroE). J Biomol Screen 2014;19:1090–8.
   PubMedGoogle Scholar
• Avitia-Domínguez C, Sierra-Campos E, Salas-Pacheco J, et al. Inhibition and biochemical characterization of methicillin-resistant Staphylococcus aureus shikimate dehydrogenase: an in silico and kinetic study. Molecules 2014;19:4491–509.
   PubMed Web of Science ®Google Scholar
• Hsu K-C, Cheng W-C, Chen Y-F, et al. Pathway-based screening strategy for multitarget inhibitors of diverse proteins in metabolic pathways. PLoS Comput Biol 2013;9:e1003127.
   PubMed Web of Science ®Google Scholar
• Dell KA, Frost JW. Identification and removal of impediments to biocatalytic synthesis of aromatics from D-glucose: rate-limiting enzymes in the common pathway of aromatic amino acid biosynthesis. J Am Chem Soc 1993;115:11581–9.
   Web of Science ®Google Scholar
• Flores N, Flores S, Escalante A, et al. Adaptation for fast growth on glucose by differential expression of central carbon metabolism and gal regulon genes in an Escherichia coli strain lacking the phosphoenolpyruvate: carbohydrate phosphotransferase system. Metab Eng 2005;7:70–87.
   PubMed Web of Science ®Google Scholar
• Baba T, Ara T, Hasegawa M, et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2006;2:2006.0008.
   PubMed Web of Science ®Google Scholar
• Bradford MM. A rapid and sensitive method for the quantitation microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 1976;72:248–54.
   PubMed Web of Science ®Google Scholar
• Alimoradi N, Ashrafi-kooshk MR, Shahlaei M, et al. Diethylalkylsulfonamido (4- methoxyphenyl)methyl) phosphonate/phosphonic acid derivatives act as acid phosphatase inhibitors: synthesis accompanied by experimental and molecular modeling assessments. J Enzyme Inhib Med Chem 2017;32:20–8.
   PubMed Web of Science ®Google Scholar
• Cheng Y-C, Prusoff WH. Relationship between the inhibition constant (K1) and the concentration of inhibitor which causes 50 per cent inhibition (I50) of an enzymatic reaction. Biochem Pharmacol 1973;22:3099–108.
   PubMed Web of Science ®Google Scholar
• Andrews JM. Determination of minimum inhibitory concentrations. J Antimicrob Chemother 2001;48(suppl 1):5.
   PubMed Web of Science ®Google Scholar
• Sastry GM, Adzhigirey M, Sherman W. Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. J Comput Aided Mol Des 2013;27:221–34.
   PubMed Web of Science ®Google Scholar
• Schrödinger. Maestro. LLC, New York, NY; 2014.
   Google Scholar
• Krieger E, Koraimann G, Vriend G. Increasing the precision of comparative models with YASARA NOVA – a self-parameterizing force field. Proteins 2002;47:393–402.
   PubMed Web of Science ®Google Scholar
• Bikadi Z, Hazai E. Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock. J Cheminform 2009;1:1–16.
   PubMed Web of Science ®Google Scholar
• Michel G, Roszak AW, Sauvé V, et al. Structures of shikimate dehydrogenase AroE and its paralog YdiB: a common structural framework for different activities. J Biol Chem 2003;278:19463–72.
   PubMed Web of Science ®Google Scholar
• Schrödinger L. The PyMOL Molecular Graphics System, Version 1.8. 2015.
   Google Scholar
• Sánchez-Abella L, Fernández S, Verstuyf A, et al. Synthesis, conformational analysis, and biological evaluation of 19- nor -vitamin D3 analogues with A-ring modifications. J Med Chem 2009;52:6158–62.
   PubMed Web of Science ®Google Scholar
• Ramkumar N, Raghavendra MS, Nagarajan R. Friedel–Crafts cyclodehydration approach toward the synthesis of ellipticine and 9-methoxyellipticine. SYNLETT 2014;25:2791–3.
   Web of Science ®Google Scholar
• Sánchez-Abella L, Fernández S, Verstuyf A, et al. Synthesis and biological evaluation of new 6-s-cis locked 1,2,25-trihydroxyprevitamin D3 analogues. Bioorg Med Chem 2007;15:4193–202.
   PubMed Web of Science ®Google Scholar
• Sumiyoshi T, Nishimura K, Nakano M, et al. Molecular assembly of C2-symmetric r, ω -alkylidenediamines into coiled coil and twisted ribbon aggregates. JACS 2003;125:12137–42.
   PubMed Web of Science ®Google Scholar
• Segel IH. Enzyme kinetics: behaviour and analysis of rapid equilibria and steady-state equilibria. New York: John Wiley and Sons; 1993.
   Google Scholar
• Whipp MJ, Camakaris H, Pittard AJ. Cloning and analysis of the shiA gene, which encodes the shikimate transport system of Escherichia coli K-12. Gene 1998;209:185–92.
   PubMed Web of Science ®Google Scholar
• Prabhala BK, Aduri NG, Jensen JM, et al. New insights into the substrate specificities of proton-coupled oligopeptide transporters from E. coli by a pH sensitive assay. FEBS Lett 2014;588:560–5.
   PubMed Web of Science ®Google Scholar
• Harder D, Stolz J, Casagrande F, et al. DtpB (YhiP) and DtpA (TppB, YdgR) are prototypical proton-dependent peptide transporters of Escherichia coli. FEBS J 2008;275:3290–8.
   PubMed Web of Science ®Google Scholar
• Payne JW. Peptide transport in Escherichia coli: permease specificity towards terminal amino group substituents. J Gen Microbiol 1974;80:269–76.
   PubMedGoogle Scholar