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Original Article

A common feature-based 3D-pharmacophore model generation and virtual screening: identification of potential PfDHFR inhibitors

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Pages 635-645 | Received 26 Jul 2009, Accepted 07 Oct 2009, Published online: 08 Dec 2009

References

  • Kompis IM, Islam K, Then RL. DNA and RNA synthesis: antifolates. Chem Rev 2005;105:593–620.
  • Da Cuhan EF, Ramlho TC, Maia ER, de Alenncastro RB. The search for new DHFR inhibitors: a review of patents, January 2001–February 2005. Expert Opin Ther Patents 2005;15:1–20.
  • Nzila A. Inhibitors of de novo folate enzymes in P. falciparum. Drug Discov Today 2006;11:939–44.
  • Anderson AC, Wright DL. Targeting DHFR in parasitic protozoa. Drug Discov Today 2005;10:121–8.
  • Schenell JR, Dyson HJ, Wright PE. Structure, dynamics, and catalytic function of dihydrofolate reductase. Annu Rev Biophys Biomol Struct 2004;33:119–40.
  • Lemeke T, Christensen IT, Jorgensen FS. Towards understanding of drug resistance in malaria: three-dimensional structure of P. falciparum DHFR by homology building. Bioorg Med Chem 1999;7:1003–11.
  • Rastelli G, Sirawaraporn W, Sompornpisut P, Vilaivan T, Kamchonwongpaisan S, Quarrell R, et al. Interaction of pyrimethamine, cycloguanil, WR99210 and their analogues with P. falciparum dihydrofolate reductase: structural basis of antifolate. Bioorg Med Chem 2000;8:1117–28.
  • Delfino RT, Santos-Filho OA, Figueroa-Villar JD. Molecular modeling of wild-type and antifolate resistant mutant P. falciparum DHFR. Biophys Chem 2002;98:287–300.
  • Santos-Filho OA, de Alencastrob RD, Figueroa-Villar JD. Homology modeling of wild-type and pyrimethamine/cycloguanil-cross-resistant mutant type P. falciparum DHFR: a model for antimalarial chemotherapy resistance. Biophys Chem 2001;91:305–17.
  • Sirawaraporn W, Sathitkul T, Sirawaraporn R, Yuthavong Y, Santi DV. Antifolate-resistant mutants of P. falciparum dihydrofolate reductase. Proc Natl Acad Sci USA 1997;94:1124–9.
  • Yuvaniyama J, Chitnumsub P, Kamchonwongpaisan S, Vanichatanankul J, Sirawaraporn W, Taylor P, et al. Insights into antifolate resistance from malarial DHFR-TS structures. Nat Struct Biol 2003;10:357–65.
  • Warhurst DV. Antimalarial drug discovery: development of inhibitors of dihydrofolate reductase active in drug resistance. Drug Discov Today 1998;3:538–46.
  • Warhurst DV. Resistance to antifolate in P. falciparum DHFR, the causative agent of tropical malaria. Sci Prog 2002;85:89–111.
  • McKie JH, Douglas KT, Chan C, Roser SA, Yates R, Read M, et al. Rational drug design approach for overcoming drug resistance: application to pyrimethamine resistance in malaria. J Med Chem 1998;41:1367–70.
  • Sardarian A, Douglas KT, Read M, Sims PFG., Hyde JE, Chitnumsub P, et al. Pyrimethamine analogs as strong inhibitors of double and quadruple mutants of dihydrofolate reductase in human malaria. J Biol Chem 2003;1:960–4.
  • Kamchonwongpaisan S, Quarrell R, Charoensetakul N, Ponsinet R, Vilaivan T, Vanichtanankul J, et al. Inhibitors of multiple mutants of P. falciparum dihydrofolate reductase and their antimalarial activities. J Med Chem 2004;47:673–80.
  • Yuthavong Y, Vilainvan T, Chareonsethakul N, Kamchonwongpaisan S, Sirawaraporn W, Quarrell R, et al. Development of a lead inhibitor for the A16V+S108T mutant of dihydrofolate reductase from the cycloguanil-resistant strain (T9/94) of P. falciparum. J Med Chem 2000;43:2738–44.
  • Sichaiwat C, Intaraudom C, Kamchonwongpaisan S, Vanichtanankul J, Thebtaranonth Y, Yuthavong Y. Target guided synthesis of 5-benzyl-2,4-diamonopyrimidines: their antimalarial activities and binding affinities to wild type and mutant dihydrofolate reductases from P. falciparum. J Med Chem 2004;47:345–54.
  • Hunt SY, Detering C, Varani G, Jacobus DP, Schiehser GA, Shieh HM, et al. Identification of the optimal third generation antifolate against P. falciparum and P. vivax. Mol Biochem Parasitol 2005;144:198–205.
  • Japrung D, Leartsakulpanich U, Chusacultanachai S, Yuthavong Y. Conflicting requirements of P. falciparum dihydrofolate reductase mutations conferring resistance to pyrimethamine-WR99210 combination. Antimicrob Agents Chemother 2007;51:4356–60.
  • Klebe G. Foundation review: virtual ligand screening: strategies, perspectives and limitations. Drug Discov Today 2006;11:580–94.
  • Muegge I, Oloff S. Advances in virtual screening. Drug Discov Today Tech 2006;3:405–11.
  • Alvarez J, Shoichet B. Virtual Screening in Drug Design. Boca Raton, FL: Taylor & Francis, 2005.
  • Toyoda T, Brobey RK, Sano G, Horii T, Tomioka N, Itai A. Lead discovery of inhibitors of the dihydrofolate reductase domain of P. falciparum dihydrofolate reductase-thymidylate synthase. Biochem Biophys Res Commun 1997;235:515–19.
  • Rastelli G, Pacchioni S, Sirawaraporn W, Sirawaraporn R, Parenti MD, Ferrari AM. Docking and database screening reveal new classes of P. falciparum dihydrofolate reductase inhibitors. J Med Chem 2003;46:2834–45.
  • Dasgupta T, Chitnumsub P, Kamchonwongpaisan S, Maneeruttanarungroj C, Nichols SE, Lyons TM, et al. Exploiting structural analysis, in silico screening, and serendipity to identify novel inhibitors of drug-resistant Falciparum malaria. ACS Chem Biol 2009;4:29–40.
  • Ommeh S, Nduati E, Mberu E, Kokwaro G, Marsh K, Rosowsky A, et al. In vitro activities of 2,4-diaminoquinazoline and 2,4-diaminopteridine derivatives against P. falciparum. Antimicrob Agents Chemother 2004;48:3711–14.
  • Guner OF. Pharmacophore: Perception, Development and Use in Drug Design. La Jolla, CA: International University Line, 2000.
  • Kurogi Y, Guner OF. Pharmacophore modeling and three-dimensional database searching for drug design using catalyst. Curr Med Chem 2001; 8:1035–55.
  • Rarey M, Kramer B, Lengauer T. Multiple automatic base selection: protein-ligand docking based on incremental construction without manual intervention. J Comput Aided Mol Des 1997;11:369–84.
  • Rarey M, Kramer B, Lengauer T, Klebe G. A fast flexible docking method using an incremental construction algorithm. J Mol Biol 1996;261:470–89.
  • Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, et al. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 2004;47:1739–49.
  • Halgren TA, Murphy RB, Friesner RA, Beard HS, Frye LL, Pollard WT, et al. Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem 2004;47:1750–9.
  • Catalyst, Version 4.10. San Diego, CA: Accelrys Inc., 2005.
  • Smellie A, Teig SL, Towbin P. Polling: promoting conformational variation. J Comput Chem 1995;16:171–87.
  • Smellie A, Kahn SD, Teig SL. An analysis of conformational coverage 2. Applications of conformational models. J Chem Inf Comput Sci 1995;35:295–304.
  • Catalyst manual, available at http://www.accelrys.com.
  • Lipinski CA, Lombardo F, Dominy BW, Feeney PJ. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 1997;23:3–25.
  • Muegge I. Selection criteria for drug-like compounds. Med Res Rev 2003;23:302–21.
  • Oprea TI. Property distribution of drug-related chemical databases. J Comput Aided Mol Des 2000;14:251–64.
  • SYBYL 7.1. St. Louis, MO: Tripose Inc., 2005.
  • Jones G, Willett P, Glen RC, Leach AR, Taylor R. Development and validation of a genetic algorithm for flexible docking. J Mol Biol 1997;267:727–48.
  • Muegge I., Martin YC. A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J Med Chem 1999;42:791–804.
  • Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE. A geometric approach to macromolecule-ligand interactions. J Mol Biol 1982;161:269–88.
  • Eldridge MD, Murray CW, Auton TR, Paolini GV, Mee RP. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J Comput Aided Mol Des 1997;11:425–45.
  • Schrödinger Suite 2007. New York: Schrödinger, LLC, 2007.
  • Proudfoot JR. Drugs, leads, and drug-likeness: an analysis of some recently launched drugs. Bioorg Med Chem Lett 2002;12:1647–50.
  • Oprea TI, Allu TK, Fara DC, Rad RF, Ostopovici L, Bologa CG. Lead-like, drug-like or “pub-like”: how different are they? J Comput Aided Mol Des 2007;21:113–19.

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