140
Views
9
CrossRef citations to date
0
Altmetric
Research Articles

Novel and potent inhibitors for dihydropteroate synthase of Helicobacter pylori

, , & ORCID Icon
Pages 246-256 | Received 15 Sep 2019, Accepted 14 Feb 2020, Published online: 26 Feb 2020

References

  • Marshall BJ, Warren JR. Unidentified curved bacilli in the stomach of patients with gastritis and peptic ulceration. Lancet. 1984;8390:1311–1315.
  • Bravo D, Hoare A, Soto C, et al. Helicobacter pylori in human health and disease: mechanisms for local gastric and systemic effects. World J Gastroenterol. 2018;24:3071–3089.
  • Hu Y, Zhu Y, Lu NH. Novel and effective therapeutic regimens for Helicobacter pylori in an era of increasing antibiotic resistance. Front Cell Infect Microbiol. 2017;7:168.
  • Chiranjeevi P, Sandeep S, Pradeep N, et al. Inhibitor design for VacA toxin of Helicobacter pylori. J Proteomics Bioinform. 2016;9:220–225.
  • Pasala C, Chilamakuri CSR, Katari SK, et al. An in silico study: novel targets for potential drug and vaccine design against drug resistant H. pylori. Microb Pathog. 2018;122:156–161.
  • Bermingham A, Derrick JP. The folic acid biosynthesis pathway in bacteria: evaluation of potential for antibacterial drug discovery. Bioessays. 2002;24:637–648.
  • Griffin MJ, Brown GM. The biosynthesis of folic acid. III. Enzymatic formationof dihydrofolic acid from dihydropteroic acid and of tetrahydropteroylpolyglutamic acid compounds from tetrahydrofolic acid. J Biol Chem. 1964;239:310–316.
  • Bourne CR. Utility of the biosynthetic folate pathway for targets in antimicrobial discovery. Antibiotics. 2014;3:1–28.
  • Rossi M, Amaretti A, Raimondi S. Folate production by probiotic bacteria. Nutrients. 2011;3:118–134.
  • Matherly LH, Goldman DI. Membrane transport of folates. Vitam Horm. 2003;66:403–456.
  • Whetstine JR, Flatley RM, Matherly LH. The human reduced folate carrier gene is ubiquitously and differentially expressed in normal human tissues:identification of seven non-coding exons and characterization of a novel promoter. Biochem J. 2002;367:629–640.
  • Levin I, Giladi M, Altman-Price N, et al. An alternative pathway for reduced folate biosynthesis in bacteria and halophilic archaea. Mol Microbiol. 2004;54:1307–1318.
  • Roland S, Ferone R, Harvey RJ, et al. The characteristics and significance of sulfonamides as substrates for Escherichia coli dihydropteroate synthase. J Biol Chem. 1979;254:10337–10345.
  • Woods DD. The relation of p-aminobenzoic acid to the mechanism of the action of sulphanilamide. Br J Exp Pathol. 1940;21:74–90.
  • Chakraborty S, Gruber T, Barry CE, et al. Para-aminosalicylic acid acts as an alternative substrate of folate metabolism in Mycobacterium tuberculosis. Science. 2013;339:88–91.
  • Yun MK, Wu Y, Li Z, et al. Catalysis and sulfa drug resistance in dihydropteroate synthase. Science. 2012;335:1110–1114.
  • Then R, Angehrn P. Sulphonamide-induced ‘thymineless death’ in Escherichia coli. Microbiology. 1973;73:255–263.
  • Campbell ML, Marchaim D, Pogue JM, et al. Treatment of methicillin-resistant Staphylococcus aureus infections with a minimal inhibitory concentration of 2 μg/mL to vancomycin: old (trimethoprim/sulfamethoxazole) versus new (daptomycin or linezolid) agents. Ann Pharmacother. 2012;46:1587–1597.
  • Forgacs NL, Wengenack L, Hall SK, et al. Tuberculosis and trimethoprim-sulfamethoxazole. Antimicrob Agents Chemother. 2009;53:4789–4793.
  • Manyando C, Njunju EM, D’Alessandro U, et al. Safety and efficacy of co-trimoxazole for treatment and prevention of Plasmodium falciparum malaria: a systematic review. PLoS One. 2013;8:e56916.
  • Nzila A. Inhibitors of de novo folate enzymes in Plasmodium falciparum. Drug Discovery Today. 2006;11:939–944.
  • Walzer PD, Kim CK, Foy JM, et al. Inhibitors of folic acid synthesis in the treatment of experimental Pneumocystis carinii pneumonia. Antimicrob Agents Chemother. 1988;32:96–103.
  • Hampele IC, D’Arcy A, Dale GE, et al. Structure and function of the dihydropteroate synthase from Staphylococcus aureus. J Mol Biol. 1997;268:21–30.
  • Lawrence MC, Iliades P, Fernley RT, et al. The three-dimensional structure of the bifunctional 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase/dihydropteroate synthase of Saccharomyces cerevisiae. J Mol Biol. 2005;348:655–670.
  • Morgan RE, Batot GO, Dement JM, et al. Crystal structures of Burkholderia cenocepacia dihydropteroate synthase in the apo-form and complexed with the product 7,8-dihydropteroate. BMC Struct Biol. 2011;11:21.
  • Achari A, Somers DO, Champness JN, et al. Crystal structure of the anti-bacterial sulfonamide drug target dihydropteroate synthase. Nat Struct Mol Biol. 1997;4:490–497.
  • Qi J, Virga KG, Das S, et al. Synthesis of bi-substrate state mimics of dihydropteroate synthase as potential inhibitors and molecular probes. Bioorg Med Chem. 2011;19:1298–1305.
  • Zhao Y, Shadrick WR, Wallace MJ, et al. Pterin-sulfa conjugates as dihydropteroate synthase inhibitors and antibacterial agents. Bioorg Med Chem Lett. 2016;26:3950–3954.
  • Pradhan D, Priyadarshini V, Munikumar M, et al. Para-(benzoyl)-phenylalanine as a potential inhibitor against LpxC of Leptospira spp.: homology modeling, docking, and molecular dynamics study. J Biomol Struct Dyn. 2014;32:171–185.
  • Webb B, Sali A. Comparative protein structure modeling using MODELLER. Curr Protoc Bioinformatics. 2016;54:5.6.1–5.6.37.
  • Altschul SF, Madden TL, Schäffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–3402.
  • Thompson JD, Gibson TJ, Plewniak F, et al. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997;24:4876–4882.
  • Amineni U, Pradhan D, Marisetty H. In silico identification of common putative drug targets in Leptospira interrogans. J Chem Biol. 2010;3:165–173.
  • Laskowski RA, MacArthur MW, Moss DS, et al. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr. 1993;26:283–291.
  • Wiederstein M, Sippl MJ. ProSA-web: interactive web service for the recognition of errors in threedimensional structures of proteins. Nucleic Acids Res. 2007;35:W407–W410.
  • Wallner B, Elofsson A. Can correct protein models be identified? Protein Sci. 2003;12:1073–1086.
  • Delano WL. 2002. PYMOL. San Carlos, CA: DeLano Scientific LLC.
  • Pasala C, Katari SK, Nalamolu RM, et al. Hierarchical-clustering, scaffold-mining exercises and dynamics simulations for effectual inhibitors against lipid-A biosynthesis of Helicobacter pylori. Cel Mol Bioeng. 2019;12:255–274.
  • Friesner RA, Banks JL, Murphy RB, et al. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem. 2004;47:1739–1749.
  • Shelley JC, Cholleti A, Frye LL, et al. Epik: a software program for pKa prediction and protonation state generation for drug-like molecules. J Comput Aided Mol Des. 2007;21:681–691.
  • Sudheer Kumar K, Chiranjeevi P, Ravina Madhulitha N, et al. Potent MMP-14 antagonist design through screening, docking and dynamics studies. J Biomol Struct Dyn. 2019;37:40–42.
  • Toledo Warshaviak D, Golan G, Borrelli KW, et al. Structure-based virtual screening approach for discovery of covalently bound ligands. J Chem Inf Model. 2014;54:1941–1950.
  • Madhulitha NR, Pradeep N, Sandeep S, et al. E-Pharmacophore model assisted discovery of novel antagonists of nNOS. Biochem Anal Biochem. 2017;6:1–9.
  • Mobley DL, Dill KA. Binding of small-molecule ligands to proteins: “what you see” is not always “what you get”. Structure. 2009;17:489–498.
  • Lyne PD, Lamb ML, Saeh JC. Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring. J Med Chem. 2006;49:4805–4808.
  • Fornabaio M, Spyrakis F, Mozzarelli A, et al. Simple, intuitive calculations of free energy of binding for protein-ligand complexes. 3. The free energy contribution of structural water molecules in HIV-1 protease complexes. J Med Chem. 2004;47:4507–4516.
  • Martyna GJ, Tobias DJ, Klein ML. Constant pressure molecular dynamics algorithms. J Chem Phys. 1994;101:4177–4189.
  • Pasala C, Chilamakuri CSR, Katari SK, et al. Epitope-driven common subunit vaccine design against H. pylori strains. J Biomol Struct Dyn. 2019;37:3740–3750.
  • Sudheer Kumar K, Pradeep N, Sandeep S, et al. Inhibitor design against JNK1 through e-pharmacophore modeling docking and molecular dynamics simulations. J Recept Signal Transduction. 2016;36:558–571.
  • Pasala C, Katari SK, Nalamolu RM, et al. In silico probing exercises, bioactive-conformational and dynamic simulations strategies for designing and promoting selective therapeutics against Helicobacter pylori strains. J Mol Graph Model. 2019;92:167–179.
  • Pasala C, Katari SK, Nalamolu RM, et al. Integration of core hopping, quantum-mechanics, molecular mechanics coupled binding-energy estimations and dynamic simulations for fragment-based novel therapeutic scaffolds against Helicobacter pylori strains. Comput Biol Chem. 2019;83:107126.
  • Ghosh S, Nie A, An J, et al. Structure-based virtual screening of chemical libraries for drug discovery. Curr Opin Chem Biol. 2006;10:194–202.
  • Sudheer Kumar K, Chiranjeevi P, Ravina Madhulitha N, et al. Design and validation of novel antagonists of stromelysin-1 (MMP-3) through core hopping, ROC metrics and molecular dynamics simulations. J Proteins Proteomics. 2017;8:22–23.
  • Umamaheswari A, Pradhan D, Hemanthkumar M. Identification of potential Leptospira phosphoheptose isomerase inhibitors through virtual high-throughput screening. Genomics Proteomics Bioinformatics. 2010;8:246–255.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.