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Research Article

Composing Compound Libraries for Hit Discovery – Rationality-Driven Preselection or Random Choice by Structural Diversity?

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Pages 2057-2072 | Published online: 22 Dec 2014

References

  • Levy SB , MarshallB. Antibacterial resistance worldwide: causes, challanges and respones. Nat. Med.10 (12), S122–S129 (2004).
  • Kaitin KI , DimasiJA. Pharmaceutical innovation in the 21st century: new drug approvals in the first decade, 2000–2009.Clin. Pharmacol. Ther.89 (2), 183–188 (2011).
  • Talbot GH . What is in the pipeline for Gram-negative pathogens?Expert Rev. Anti Infect. Ther.6 (1), 39–49 (2008).
  • Livermore DM . Has the era of untreatable infections arrived?J. Antimicrob. Chemother.64 (4), 29–36 (2009).
  • Lambert PA . Mechanism of antibiotic resistance in Pseudomonas aeruginosa. J. R. Soc. Med.95, 22–26 (2002).
  • Nikaido H. Prevention of drug access to bacterial targets - permeability barriers and active efflux. Science. 264 (5157), 382–388 (1994).
  • Rivers EC , ManceraRL. New anti-tuberculosis drugs in clinical trials with novel mechanisms of action. Drug Discov. Today13 (23-24), 1090–1098 (2008).
  • Barrett CT , BarrettJF. Antibacterials: are the new entries enough to deal with the emerging resistance problems?Curr. Opin. Biotechnol.14 (6), 621–626 (2003).
  • Fischbach MA , WelshCT. Antibiotics for emerging pathogens. Science325 (5944), 1089–1093 (2009).
  • Gallant P , FinnJ, KeithD, WendlerP. The identification of quality antibacterial drug discovery targets: a case study with aminoacyl-tRNA synthetases. Expert Opin. Ther. Targets4 (1), 1–9 (2000).
  • Navratilova I , HopkinsAL. Fragment screening by surface plasmon resonance. ACS Med. Chem. Lett.1 (1), 44–48 (2010).
  • Wielens J , HeadeySJ, RhodesDIet al. Parallel screening of low molecular weight fragment libraries: do differences in methodology affect hit identification? J. Biomol. Screen. 18 (2), 147–159 (2013).
  • Siegal G , AbE, SchultzJ. Integration of fragment screening and library design. Drug Discov. Today12 (23–24), 1032–1039 (2007).
  • Mayr LM , BojanicD. Novel trends in high-throughput screening. Curr. Opin. Pharmacol.9 (5), 580–588 (2009).
  • Valler MJ , GreenD. Diversity screening versus focussed screening in drug discovery.Drug Discov. Today5 (7), 286–293 (2000).
  • Walters WP , StahlMT, MurckoMA. Virtual Screening - an overview.Drug Discov. Today3 (4), 160–178 (1998).
  • Marriott DP , DugallIG, MeghaniP, LiuYJ, FlowerDR. Lead generation using pharmacophore mapping and three-dimensional database searching: application to muscarin M(3) receptor antagonists. J. Med. Chem.42 (17), 3210–3216 (1999).
  • Boucher HW , TalbotGH, BradleyJSet al. Bad bugs, no drugs: no eskape! An update from infectious diseases society of America. Clin. Infect. Dis.48 (1), 1–12 (2009). 
  • Storz MP , MaurerCK, ZimmerCet al. Validation of PqsD as an anti-biofilm target in Pseudomonas aeruginosa by development of small-molecule inhibitors. JACS134 (39), 16143–16146 (2012).
  • Alhamadsheh MM , WatersNC, SachdevaS, LeeP, ReynoldsKA. Synthesis and biological evaluation of novel sulfonyl-naphtalene-1,4-diols as FabH inhibitors. Bioorg. Med. Chem. Lett.18 (24), 6402–6405 (2008).
  • Daines RA , PendrakI, ShamKet al. First x-ray cocrystal structure of a bacterial FabH condensing enzyme and a small molecule inhibitor achieved using rational design and homology modeling. J. Med. Chem. 46 (1), 5–8 (2003).
  • Al-Balas Q , AnthonyNG, Al-JaidiBet al. Identification of 2-aminothiazole-4-carboxylate derivates active against Mycobacterium tuberculosis H37Rv and the beta-keto-ACP synthase mtFabH. PloS ONE4 (5), e5617 (2009).
  • Senior SJ , IllarionovaPA, GurchaSSet al. Biphenyl-based analogues of thiolactomycin, active against Mycobacterium tuberculosis mtFabH fatty acid condensing enzyme. Bioorg. Med. Chem. Lett.13 (21), 3685–3688 (2003). 
  • Kim P , ZhangYM, ShenoyGet al. Structure-activity relationships at the 5-position of thiolactomycin: an intact (5R)-isoprene unit is required for activity against the condensing enzymes from Mycobacterium tuberculosis and Escherichia coli. J. Med. Chem.49 (1), 159–171 (2006). 
  • Nie Z. , PerrettaC, LuJet al. Structure-based design, synthesis, and study of potent inhibitors of beta-ketoacyl-acyl carrier protein synthase III as potential antimicrobial agents. J. Med. Chem.48 (5), 1596–1609 (2005).
  • Bera AK , AtanasovaV, RobinsonHet al. Structure of PqsD, a Pseudomonas quinolone signal biosynthetic enzyme, in complex with anthranilate. Biochem.48 (36), 8644–8655 (2009).
  • Weidel E , De JongJC, BrengelCet al. Structure optimization of 2-benzamidobenzoic acids as PqsD inhibitors for Pseudomonas aeruginosa infections and elucidation of binding mode by SPR, STD NMR, and molecular docking. J. Med. Chem.56 (15), 6146–6155 (2013).
  • Storz MP , BrengelC, WeidelEet al. Biochemical and biophysical analysis of a chiral PqsD inhibitor revealing tight-binding behavior and enantiomers with contrary thermodynamic signatures. ACS Chem. Biol.8 (12), 2794–2801 (2013).
  • Davies C , HeathRJ, WhiteSW, RockCO. The 1.8 angstrom crystal structure and active-site architecture of beta-ketoacyl-acyl carrier protein synthase III (FabH) from Escherichia coli. Structure8 (2), 185–195 (2000).
  • Pistorius D , UllrichA, LucasS, HartmannRW, KazmaierU, MüllerR Biosynthesis of 2-alkyl-4(1H)-quinolones in Pseudomonas aeruginosa: potential for therapeutic interference with pathogenicity. Chembiochem12 (6), 850–853 (2011).
  • Henn C , BoettcherS, SteinbachA, HartmannRW Catalytic enzyme activity on a biosensor chip: combination of surface plasmon resonance and mass spectrometry. Anal. Biochem428 (1), 28–30 (2012). 
  • Zhang JH , ChungTDY, OldenburgKR. A simple statistic parameter for use in evaluation and validation of high throughput screening assays. J. Biomol. Screen.4 (2), 67–73 (1999).
  • Jones G , WillettP, GlenRC, LeachAR, TaylorR. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol.267 (3), 727–748 (1997).
  • Verdonk ML , ColeJC, HartshornMJ, MurrayCW, TaylorRD. Improved protein-ligand docking using GOLD. Proteins52 (4), 609–623 (2003).
  • Molecular Operating Environment (MOE)2010.10. Chemical Computing Group, Quebec, Canada (2010).
  • Perspicace S , BannerD, BenzJ, MüllerF, SchlatterD, HuberW. Fragment-based screening using surface plasmon resonance technology. J. Biomol. Screen.14 (4), 337–349 (2009).
  • Giannetti AM , KochBD, BrownerMF. Surface plasmon resonance based assay for the detection and characterization of promiscuous inhibitors. J. Med. Chem.51 (3), 574–580 (2008).
  • Rees DC , CongreveM, MurrayCW, CarrR. Fragment-based lead discovery. Nat. Rev. Drug Discov.3 (8), 660–672 (2004). 
  • Yuan YQ , LeedsJA, MeredithTC. Pseudomonas aeruginosa directly shunts beta-oxidation degradation intermediates into de novo fatty acid biosynthesis. J. Bacteriol.194 (19), 5185–5196 (2012). 
  • Yuan YQ , SachdevaM, LeedsJA, MeredithTC. Fatty acid biosynthesis in Pseudomonas aeruginosa is initiated by the FabY class of beta-ketoacyl acyl carrier protein synthases. J. Bacteriol.194 (19), 5171–5184 (2012).
  • Shelat AA , GuyRK. Scaffold composition and biological relevance of screening libraries.. Nat. Chem. Biol.3 (8), 442–446 (2007).
  • Hann MM , LeachAR, HarperG. Molecular complexity and its impact on the probability of finding leads for drug discovery;. J. Chem. Inf. Comput. Sci.41 (3), 856–864 (2001).
  • Hopkins AL , GroomCR, AlexA. Ligand efficiency: a useful metric for lead selection. Drug Discov. Today9 (10), 430–431 (2004).
  • Howard S , BerdiniV, BoulstridgeJAet al. Fragment-based discovery of the pyrazol-4-yl-urea (AT9283), a multitargeted kinase inhibitor with potent aurora kinase activity. J. Med. Chem.52 (2), 379–388 (2009).
  • Villemagno B , FlipoM, BlondiauxNet al. Ligand efficiency driven design of new inhibitors of Mycobacterium tuberculosis transcriptional repressor EthR using fragment growing, merging and linking approaches. J. Med. Chem.57 (11), 4876–4888 (2014).
  • Johnson CN , BerdiniV, BekeLet al. Fragment-based discovery of type I inhibitors of maternal embryonic leucine zipper kinase. J. Med. Chem. Lett. (2014) ( Epub ahead of print).
  • Sahner JH , BrengelC, StorzMPet al. Combining in silico and biophysical methods for the development of Pseudomonas aeruginosa quorum sensing inhibitors: an alternative approach for structure-based drug design. J. Med. Chem.56 (21), 8656–8664 (2013).

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