• 1
    Hansch C. (1969) A quantitative approach to biochemical structure-activity relationships. Acc Chem Res;2:232239.
  • 2
    Hansch C., Fujita T. (1964) Rho-Sigma-Pi analysis. Method for correlation of biological activity + chemical structure. J Am Chem Soc;86:16161626.
  • 3
    Cramer R.D., Patterson D.E., Bunce J.D. (1988) Comparative molecular-field analysis (CoMFA) .1. Effect of shape on binding of steroids to carrier proteins. J Am Chem Soc;110:59595967.
  • 4
    Hopfinger A.J., Wang S., Tokarski J.S., Jin B.Q., Albuquerque M., Madhav P.J., Duraiswami C. (1997) Construction of 3D-QSAR models using the 4D-QSAR analysis formalism. J Am Chem Soc;119:1050910524.
  • 5
    Pan D., Tseng Y., Hopfinger A.J. (2003) Quantitative structure-based design: formalism and application of receptor-dependent RD-4D-QSAR analysis to a set of glucose analogue inhibitors of glycogen phosphorylase. J Chem Inf Comput Sci;43:15911607.
  • 6
    Pan D., Liu J., Senese C., Hopfinger A.J., Tseng Y. (2004) Characterization of a ligand-receptor binding event using receptor-dependent four-dimensional quantitative structure-activity relationship analysis. J Med Chem;47:30753088.
  • 7
    Santos O.A., Hopfinger A.J. (2006) Structure-based QSAR analysis of a set of 4-hydroxy-5,6-dihydropyrones as inhibitors of HIV-1 protease: an application of the receptor-dependent (RD) 4D-QSAR formalism. J Chem Inf Model;46:345354.
  • 8
    Hong X., Hopfinger A.J. (2003) 3D-pharmacophores of flavonoid binding at the benzodiazepine GABA(A) receptor site using 4D-QSAR analysis. J Chem Inf Comput Sci;43:324336.
  • 9
    Pasqualoto K.F., Ferreira E.I., Santos-Filho O.A., Hopfinger A.J. (2004) Rational design of new antituberculosis agents: receptor-independent four-dimensional quantitative structure-activity relationship analysis of a set of isoniazid derivatives. J Med Chem;47:37553764.
  • 10
    Urbina J.A., Docampo R. (2003) Specific chemotherapy of Chagas disease: controversies and advances. Trends Parasitol;19:495501.
  • 11
    Bond C.S., Zhang Y., Berriman M., Cunningham M.L., Fairlamb A.H., Hunter W.N. (1999) Crystal structure of Trypanosoma cruzi trypanothione reductase in complex with trypanothione, and the structure-based discovery of new natural product inhibitors. Structure;7:8189.
  • 12
    McKie J.H., Garforth J., Jaouhari R., Chan C., Yin H., Besheya T., Fairlamb A.H., Douglas K.T. (2001) Specific peptide inhibitors of trypanothione reductase with backbone structures unrelated to that of substrate: potential rational drug design lead frameworks. Amino Acids;20:145153.
  • 13
    Schirmer R.H., Müller J.G., Krauth-Siegel R.L. (1995) Disulfide-reductase inhibitors as chemotherapeutic agents: the design of drugs for trypanosomiasis and malaria. Angew Chem Int Ed Engl;34:141154.
  • 14
    Schmidt A., Krauth-Siegel R.L. (2002) Enzymes of the trypanothione metabolism as targets for antitrypanosomal drug development. Curr Top Med Chem;2:12391259.
  • 15
    Benson T.J., McKie J.H., Garforth J., Borges A., Fairlamb A.H., Douglas K.T. (1992) Rationally designed selective inhibitors of trypanothione reductase. Phenothiazines and related tricyclics as lead structures. Biochem J;286(Pt 1):911.
  • 16
    Chan C., Yin H., Garforth J., McKie J.H., Jaouhari R., Speers P., Douglas K.T., Rock P.J., Yardley V., Croft S.L., Fairlamb A.H. (1998) Phenothiazine inhibitors of trypanothione reductase as potential antitrypanosomal and antileishmanial drugs. J Med Chem;41:148156.
  • 17
    Chan C., Yin H., McKie J.H., Fairlamb A.H., Douglas K.T. (2002) Peptoid inhibition of trypanothione reductase as a potential antitrypanosomal and antileishmanial drug lead. Amino Acids;22:297308.
  • 18
    Faerman C.H., Savvides S.N., Strickland C., Breidenbach M.A., Ponasik J.A., Ganem B., Ripoll D., Krauth-Siegel R.L., Karplus P.A. (1996) Charge is the major discriminating factor for glutathione reductase versus trypanothione reductase inhibitors. Bioorg Med Chem;4:12471253.
  • 19
    Garforth J., Mckie J.H., Jaouhari R., Benson T.J., Fairlamb A.H., Douglas K.T. (1994) Rational design of peptide-based inhibitors of trypanothione reductase as potential antitrypanosomal drugs. Amino Acids;6:295299.
  • 20
    Garforth J., Yin H., McKie J.H., Douglas K.T., Fairlamb A.H. (1997) Rational design of selective ligands for trypanothione reductase from Trypanosoma cruzi. Structural effects on the inhibition by dibenzazepines based on imipramine. J Enzyme Inhib;12:161173.
  • 21
    Khan M.O., Austin S.E., Chan C., Yin H., Marks D., Vaghjiani S.N., Kendrick H., Yardley V., Croft S.L., Douglas K.T. (2000) Use of an additional hydrophobic binding site, the Z site, in the rational drug design of a new class of stronger trypanothione reductase inhibitor, quaternary alkylammonium phenothiazines. J Med Chem;43:31483156.
  • 22
    Linares G.E., Ravaschino E.L., Rodriguez J.B. (2006) Progresses in the field of drug design to combat tropical protozoan parasitic diseases. Curr Med Chem;13:335360.
  • 23
    Marsh I.R., Bradley M. (1997) Substrate specificity of trypanothione reductase. Eur J Biochem;243:690694.
  • 24
    Moutiez M., Aumercier M., Parmentier B., Tartar A., Sergheraert C. (1995) Compared recognition of di- and trisulfide substrates by glutathione and trypanothione reductases. Biochim Biophys Acta;1245:161166.
  • 25
    Bailey S., Smith K., Fairlamb A.H., Hunter W.N. (1993) Substrate interactions between trypanothione reductase and N1-glutathionylspermidine disulphide at 0.28-nm resolution. Eur J Biochem;213:6775.
  • 26
    Hopfinger A.J. (2001) 4D-QSAR Package User’s Manual, v.3.0. The Chem21 Group Inc, Lake Forest, IL, USA.
  • 27
    Hypercube (2001) HyperChem Professional v.7.0. Hypercube, Inc, 1115 NW, 4th street, Gainesville, FL, USA.
  • 28
    Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz K.M., Ferguson D.M., Spellmeyer D.C., Fox T., Caldwell J.W., Kollman P.A. (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc;117:51795197.
  • 29
    Dewar M.J.S., Zoebisch E.G., Healy E.F., Stewart J.J.P. (1985) The development and use of quantum-mechanical molecular-models .76. AM1 – a new general-purpose quantum-mechanical molecular-model. J Am Chem Soc;107:39023909.
  • 30
    Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. (2000) The protein data bank. Nucleic Acids Res;28:235242.
  • 31
    Molecular Simulation (2000) WebLab ViewerLite. v.4.0: Molecular Simulation, Inc., San Diego, California, USA.
  • 32
    Hunter W.N., Bailey S., Habash J., Harrop S.J., Helliwell J.R., Aboagye-Kwarteng T. et al. (1992) Active site of trypanothione reductase. A target for rational drug design. J Mol Biol;227:322333.
  • 33
    da Rocha Pita S.S., Cirino J.J., de Alencastro R.B., Castro H.C., Rodrigues C.R., Albuquerque M.G. (2009) Molecular docking of a series of peptidomimetics in the trypanothione binding site of T. cruzi trypanothione reductase. J Mol Graph Model;28:330335.
  • 34
    Doherty D.C. (1994) Molsim User’s Guide. Molsim v.3.0. The Chem21 Group, Inc,, 1780 Wilson Drive, Lake Forest, IL 60045, USA.
  • 35
    Ooms F. (2000) Molecular modeling and computer aided drug design. Examples of their applications in medicinal chemistry. Curr Med Chem;7:141158.
  • 36
    Liu J., Pan D., Tseng Y., Hopfinger A.J. (2003) 4D-QSAR analysis of a series of antifungal p450 inhibitors and 3D-pharmacophore comparisons as a function of alignment. J Chem Inf Comput Sci;43:21702179.
  • 37
    Dunn W.J. III, Scott D.R., Glen W.G. (1989) Principal components analysis and partial least squares regression. Tetrahedron Comput Methodol;2:349376.
  • 38
    Rogers D., Hopfinger A.J. (1994) Application of genetic function approximation to quantitative structure-activity-relationships and quantitative structure-property relationships. J Chem Inf Comput Sci;34:854866.
  • 39
    Friedman J. (1991) Multivariate Adaptive Regression Splines. Ann Statist;19:167.
  • 40
    Rogers D. (1991) G/SPLINES: a hybrid of Friedman’s multivariate adaptive regression splines (MARS) algorithm with Holland’s genetic algorithm. Eds. Belew R.K., Booker L.B., Proceedings of the Fourth International Conference on Genetic Algorithms. San Francisco: Morgan Kaufman Publishers; 91.10:384391.
  • 41
    Golbraikh A., Tropsha A. (2002) Beware of q2! J Mol Graph Model;20:269276.
  • 42
    Romeiro N.C., Albuquerque M.G., Alencastro R.B., Ravi M., Hopfinger A.J. (2005) Construction of 4D-QSAR models for use in the design of novel p38-MAPK inhibitors. J Comput Aided Mol Des;19:385400.
  • 43
    Bailey S., Fairlamb A.H., Hunter W.N. (1994) Structure of trypanothione reductase from Crithidia fasciculata at 2.6 A resolution; enzyme-NADP interactions at 2.8 A resolution. Acta Crystallogr D Biol Crystallogr;50:139154.
  • 44
    Leichus B.N., Bradley M., Nadeau K., Walsh C.T., Blanchard J.S. (1992) Kinetic isotope effect analysis of the reaction catalyzed by Trypanosoma congolense trypanothione reductase. Biochemistry;31:64146420.