QSAR study on the antimalarial activity of Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) inhibitors

References

• WHO, World malarial report, World Health Organization, Geneva, Switzerland, 2014.
   Google Scholar
• V.K. Vyas, H. Parikh, and M. Ghate, 3D QSAR studies on 5-(2-methylbenzimidazol-1-yl)-N-alkylthiophene-2-carboxamide derivatives as P. falciparum dihydroorotate dehydrogenase (PfDHODH) inhibitors, Med. Chem. Res. 22 (2013), pp. 2235–2243.
   Web of Science ®Google Scholar
• D.F. Caroline, Pyrimidine synthesis in Neurospora crassa: Gene-enzyme relationships, J. Bacteriol. 100 (1969), pp. 1371–1377.
   PubMed Web of Science ®Google Scholar
• M.L. Taylor, W.H. Taylor, and D.F. Eames, Biosynthetic dihydroorotate dehydrogenase from Lactobacillus bulgaricus, J. Bacteriol. 105 (1971), pp. 1015–1027.
   PubMed Web of Science ®Google Scholar
• J.C. Williams and G.A. O'Donovan, Repression of enzyme synthesis of the pyrimidine pathway in Salmonella typhimurium, J. Bacteriol. 115 (1973), pp. 1071–1076.
   PubMed Web of Science ®Google Scholar
• M.E. Jones, Pyrimidine nucleotide biosynthesis in animals: Genes, enzymes, and regulation of UMP biosynthesis, Annu. Rev. Biochem. 49 (1980), pp. 253–279.
   PubMed Web of Science ®Google Scholar
• R.T. Eakin and H.K. Mitchell, A mitochondrial dihydroorotate oxidase system in Neurospora crassa, Arch. Biochem. Biophys. 134 (1969), pp. 160–171.
   PubMed Web of Science ®Google Scholar
• M. Fry and J.E. Beesley, Mitochondria of mammalian Plasmodium spp, Parasitology 102 (1991), pp. 17–26.
   PubMed Web of Science ®Google Scholar
• N.J. White, Drug resistance in malaria, Br. Med. Bull. 54 (1998), pp. 703–715.
   PubMed Web of Science ®Google Scholar
• I.N. Subbayya, S.S. Ray, and P. Balaram, Metabolic enzymes as potential drug targets in Plasmodium falciparum, Indian J. Med. Res. 106 (1997), pp. 79–94.
   PubMed Web of Science ®Google Scholar
• V. Patel, M. Booker, and M. Kramer, Identification and characterization of small molecule inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase, J. Biol. Chem. 283 (2008), pp. 35078–35085.
   PubMed Web of Science ®Google Scholar
• S. Liu, E.A. Neidhardt, and T.H. Grossman, Structures of human dihydroorotate dehydrogenase in complex with antiproliferative agents, Structure. 8 (2000), pp. 25–33.
   PubMed Web of Science ®Google Scholar
• J. Baldwin, C.H. Michnoff, and N.A. Malmquist, High-throughput screening for potent and selective inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase, J. Bio. Chem. 280 (2005), pp. 21847–21853.
   PubMed Web of Science ®Google Scholar
• M.A. Phillips, R. Gujjar, and N.A. Malmquist, Triazolopyrimidine-based dihydroorotate dehydrogenase inhibitors with potent and selective activity against the malaria parasite Plasmodium falciparum, J. Med. Chem. 51 (2008), pp. 3649–3653.
   PubMed Web of Science ®Google Scholar
• R. Gujjar, F. El Mazouni, and K.L. White, Lead optimization of aryl and aralkyl amine-based triazolopyrimidine inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase with antimalarial activity in mice, J. Med. Chem. 54 (2011), pp. 3935–3949.
   PubMed Web of Science ®Google Scholar
• R.T. Skerlj, C.M. Bastos, and M.L. Booker, Optimization of potent inhibitors of P. falciparum dihydroorotate dehydrogenase for the treatment of malaria, ACS Med. Chem. Lett. 2 (2011), pp. 708–713.
   PubMed Web of Science ®Google Scholar
• P.T. Bedingfield, D. Cowen, and P. Acklam, Factors influencing the specificity of inhibitor binding to the human and malaria parasite dihydroorotate dehydrogenases, J. Med. Chem. 55 (2012), pp. 5841–5850.
   PubMed Web of Science ®Google Scholar
• M. Davies, T. Heikkila, and G.A. McConkey, Structure-based design, synthesis, and characterization of inhibitors of human and Plasmodium falciparum dihydroorotate dehydrogenases, J. Med. Chem. 52 (2009), pp. 2683–2693.
   PubMed Web of Science ®Google Scholar
• P.K. Ojha and K. Roy, Chemometric modeling, docking and in silico design of triazolopyrimidine-based dihydroorotate dehydrogenase inhibitors as antimalarials, Eur J Med Chem 45 (2010), pp. 4645–4656.
   PubMed Web of Science ®Google Scholar
• P. Shah, S. Kumar, and S. Tiwari, 3D-QSAR studies of triazolopyrimidine derivatives of Plasmodium falciparum dihydroorotate dehydrogenase inhibitors using a combination of molecular dynamics, docking, and genetic algorithm-based methods, J. Chem. Biol. 5 (2012), pp. 91–103.
   PubMedGoogle Scholar
• A. Wadood and Z.U. Ulhaq, In silico identification of novel inhibitors against Plasmodium falciparum dihydroorate dehydrogenase, J. Mol. Graph. Model. 40 (2013), pp. 40–47.
   PubMed Web of Science ®Google Scholar
• R.B. Aher and K. Roy, Understanding the structural requirements in diverse scaffolds for the inhibition of P. falciparum dihydroorotate dehydrogenase (PfDHODH) using 2D-QSAR, 3D-pharmacophore and structure-based energy- optimized pharmacophore models, Comb. Chem. High. Throughput, Screen. 18 (2015), pp. 217–226.
   Web of Science ®Google Scholar
• ChEMBL Web Services; available at: https://www.ebi.ac.uk/chembl/ws (accessed July 2015).
   Google Scholar
• J.M. Coteron, M. Marco, and J. Esquivias, Structure-guided lead optimization of triazolopyrimidine-ring substituents identifies potent Plasmodium falciparum dihydroorotate dehydrogenase inhibitors with clinical candidate potential, J. Med. Chem. 54 (2011), pp. 5540–5561.
   PubMed Web of Science ®Google Scholar
• X. Deng, R. Gujjar, and F. El Mazouni, Structural plasticity of malaria dihydroorotate dehydrogenase allows selective binding of diverse chemical scaffolds, J. Biol. Chem. 284 (2009), pp. 26999–27009.
   PubMed Web of Science ®Google Scholar
• R. Sharma and S. Patil, Three dimensional quantitative structure analysis substituted 1,3-diaryl propenone derivatives as antimalarial activity Der, Pharma. Chemica. 5 (2013), pp. 80–86.
   Google Scholar
• M.L. Booker, C.M. Bastos, and M.L. Kramer, Novel inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase with anti-malarial activity in the mouse model, J. Biol. Chem. 285 (2010), pp. 33054–33064.
   PubMed Web of Science ®Google Scholar
• A.N. Boa, S.P. Canavan, and P.R. Hirst, Synthesis of brequinar analogue inhibitors of malaria parasite dihydroorotate dehydrogenase, Bioorg. Med. Chem. 13 (2005), pp. 1945–1967.
   PubMed Web of Science ®Google Scholar
• T. Heikkila, C. Ramsey, and M. Davies, Design and synthesis of potent inhibitors of the malaria parasite dihydroorotate dehydrogenase, J. Med. Chem. 50 (2007), pp. 186–191.
   PubMed Web of Science ®Google Scholar
• R. Gujjar, A. Marwaha, and F. El Mazouni, Identification of a metabolically stable triazolopyrimidine-based dihydroorotate dehydrogenase inhibitor with antimalarial activity in mice, J. Med. Chem. 52 (2009), pp. 1864–1872.
   PubMed Web of Science ®Google Scholar
• A. Yan, H. Liang, and Y. Chong, In-silico prediction of blood-brain barrier permeability, SAR QSAR Environ. Res. 24 (2013), pp. 61–74.
   PubMed Web of Science ®Google Scholar
• J. Sadowski and J. Gasteiger, From atoms and bonds to three-dimensional atomic coordinates: Automatic model builders, Chem. Rev. 93 (1993), pp. 2567–2581.
   Web of Science ®Google Scholar
• J. Sadowski and J. Gasteiger, Comparison of automatic three-dimensional model builders using 639 X-ray structures, J. Chem. Inf. Comput. Sci. 34 (1994), pp. 1000–1008.
   Google Scholar
• ADRIANA.Code, Molecular Networks GmbH, Erlangen, Germany; available at: http://www.molecular-networks.com (accessed July 2014).
   Google Scholar
• K.J. Miller, Additivity methods in molecular polarizability, J. Am. Chem. Soc. 112 (1990), pp. 8533–8542.
   Web of Science ®Google Scholar
• P. Ertl, B. Rohde, and P. Selzer, Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties, J. Med. Chem. 43 (2000), pp. 3714–3717.
   PubMed Web of Science ®Google Scholar
• C.A. Lipinski, F. Lombardo, and B.W. Dominy, Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings, Adv. Drug. Deliv. Rev. 46 (2001), pp. 3–26.
   PubMed Web of Science ®Google Scholar
• J. Gasteiger, An algorithm for the perception of synthetically important rings, J. Chem. Inf. Comput. Sci. 19 (1979), pp. 43–48.
   Google Scholar
• H. Bauknecht, A. Zell, and H. Bayer, Locating biologically active compounds in medium-sized heterogeneous datasets by topological autocorrelation vectors: Dopamine and benzodiazepine agonists, J. Chem. Inf. Comput. Sci. 36 (1996), pp. 1205–1213.
   PubMedGoogle Scholar
• A. Yan and J. Gasteiger, Prediction of aqueous solubility of organic compounds based on a 3D structure representation, J. Chem. Inf. Comput. Sci. 43 (2003), pp. 429–434.
   PubMedGoogle Scholar
• M.C. Hemmer, V. Steinhauer, and J. Gasteiger, Deriving the 3D structure of organic molecules from their infrared spectra, Vib. Spectrosc. 19 (1999), pp. 151–164.
   Web of Science ®Google Scholar
• C.-C. Chang and C.-J. Lin, LIBSVM: A library for support vector machines, ACM TIST. 2 (2011), pp. 1–39.
   Google Scholar
• MOE, Chemical Computing Group, Montreal, Canada; available at: http://www.chemcomp.com (accessed July 2015).
   Google Scholar
• C. Rucker, G. Rucker, and M. Meringer, y-Randomization and its variants in QSPR/QSAR, J. Chem. Inf. Model. 47 (2007), pp. 2345–2357.
   PubMed Web of Science ®Google Scholar
• RCSB Protein Data Bank, 4CQ8, Plasmodium falciparum dihydroorotate dehydrogenase (DHODH) in complex with Genz-669178; available at: http://www.rcsb.org/pdb/explore/explore.do?structureId=4CQ8 (accessed July. 2015).
   Google Scholar
• L.S. Ross, F.J. Gamo, and M.J. Lafuente-Monasterio, In vitro resistance selections for Plasmodium falciparum dihydroorotate dehydrogenase inhibitors give mutants with multiple point mutations in the drug-binding site and altered growth, J. Biol. Chem. 289 (2014), pp. 17980–17995.
   PubMed Web of Science ®Google Scholar
• K.R. Desai, M.S. Shaikh, and E.C. Coutinho, Robinson, Molecular modeling studies, synthesis and biological evaluation of derivatives of N-phenylbenzamide as Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) inhibitors, Med. Chem. Res. 20 (2011), pp. 321–332.
   Web of Science ®Google Scholar
• J.L. Atwood, F. Hamada, and K.D. Robinson, X-ray diffraction evidence for aromatic π-hydrogen bonding to water, Nature. 349 (1991), pp. 683–684.
   Web of Science ®Google Scholar
• SciFinder; available at: https://scifinder.cas.org/scifinder/view/scifinder/scifinderExplore.jsf (accessed December 2015).
   Google Scholar
• PubChem Compound Database; available at: http://www.ncbi.nlm.nih.gov/pccompound (accessed December 2015).
   Google Scholar
• ZINC Database; available at: http://zinc.docking.org/ (accessed December 2015).
   Google Scholar