Computer-assisted design of pro-drugs for antimalarial atovaquone

Chemical Biology and Drug Design

Volumn 76, Issue 4, 2010, Pages 350-360

  Karaman, Rafik ^a   Hallak, Hussein ^a  

^a AL QUDS UNIVERSITY   (Palestine)

Author keywords

ab initio calculations; antimalarial pro drugs; atovaquone pro drugs; DFT calculations; Kirby's enzyme models; proton transfer reaction

Indexed keywords

ATOVAQUONE; PRODRUG;

AB INITIO CALCULATION; ARTICLE; COMPUTER AIDED DESIGN; DENSITY FUNCTIONAL THEORY; DRUG CONFORMATION; DRUG DESIGN; GEOMETRY; HYDROGEN BOND; PRIORITY JOURNAL; PROTON TRANSPORT;

ANTIMALARIALS; ATOVAQUONE; COMPUTER SIMULATION; DRUG DESIGN; HYDROGEN BONDING; KINETICS; MOLECULAR CONFORMATION; PRODRUGS; PROTONS; THERMODYNAMICS;

EID: 77956414921     PISSN: 17470277     EISSN: 17470285     Source Type: Journal    
DOI: 10.1111/j.1747-0285.2010.01018.x     Document Type: Article

References (52)

1. Reinaldo T. (2003) Antimalarial drug discovery: old and new approaches. J Exp Biol 206 : 3735 3744.
2. Comley J., Yeates C., Frend T. (1995) Antipneumocystis activity of 17C91, a prodrug of atovaquone. Antimicrob Agents Chemother 39 : 2217 2219.
3. Testa B., Mayer J. (2003) Hydrolysis in Drug and Prodrug Metabolism-Chemistry, Biochemistry and Enzymology. Zurich : Wiley-VHCA.
4. Testa B., Mayer J.M. (2001) Concepts in prodrug design to overcome pharmacokinetic problems. In : Testa B., van de Waterbeemd H., Folkers G., Guy R., editors. Pharmacokinetic Optimization in Drug Research: Biological, Physiochemical and Computational Strategies. Zurich : Wiley-VHCA pp. 85 95.
5. Wang W., Jiang J., Ballard C.E., Wang B. (1999) Prodrug approaches in the improved delivery of peptide drugs. Curr Pharm Design 5 : 265 287.
6. Karaman R. (2008) Analysis of Menger's 'spatiotemporal hypothesis. Tet Lett 49 : 5998 6002.
7. Karaman R. (2009) Reevaluation of Bruice's proximity orientation. Tet Lett 50 : 452 456.
8. Karaman R. (2009) A new mathematical equation relating activation energy to bond angle and distance: a key for understanding the role of acceleration in the lactonization of the trimethyl lock system. Bioorg Chem 37 : 11 25.
9. Karaman R. (2009) Accelerations in the lactonization of trimethyl lock systems are due to proximity orientation and not to strain effects. Res Lett Org Chem doi: /240253.
10. Karaman R. (2009) The Effective Molarity (EM) Puzzle in Proton Transfer Reactions. Bioorg Chem 37 : 106 110.
11. Karaman R. (2009) Cleavage of Menger's Aliphatic Amide: a model for peptidase enzyme solely explained by proximity orientation in intramolecular proton transfer. J Mol Struct (Theochem) 910 : 27 33.
12. Karaman R. (2009) The gem-Disubstituent Effect-Computational Study that Exposes the Relevance of Existing Theoretical Models. Tet Lett 50 : 6083 6087.
13. Karaman R. (2010) Effects of substitution on the Effective Molarity (EM) for five membered ring-closure reactions-a computational approach. J Mol Struct (Theochem) 939 : 69.
14. Karaman R. (2009) Analyzing Kirby's amine olefin - a model for amino-acid ammonia lyases. Tet Lett 50 : 7304 7309.
15. Karaman R. (2010) The Effective Molarity (EM) Puzzle in Intramolecular Ring-Closing Reactions. J Mol Struct (Theochem) 940 : 70 75.
16. Milstien S., Cohen L.A. (1970) Concurrent general-acid and general-base catalysis of esterification. J Am Chem Soc 92 : 4377 4382.
17. Milstien S., Cohen L.A. (1970) Rate acceleration by stereopopulation control: models for enzyme action. Proc Natl Acad Sci U S A 67 : 1143 1147.
18. Milstien S., Cohen L.A. (1972) Stereopopulation control. I. Rate enhancement in the lactonizations of o-hydroxyhydrocinnamic acids. J Am Chem Soc 94 : 9158 9165.
19. Winans R.E., Wilcox C.F. Jr. (1976) Comparison of stereopopulation control with conventional steric effects in lactonization of hydrocoumarinic acids. J Am Chem Soc 98 : 4281 4285.
20. Dorigo A.E., Houk K.N. (1987) The origin of proximity effects on reactivity: a modified MM2 model for the rates of acid-catalyzed lactonizations of hydroxy acids. J Am Chem Soc 109 : 3698 3708.
21. Houk K.N., Tucker J.A., Dorigo A.E. (1990) Quantitative modeling of proximity effects on organic reactivity. Acc Chem Res 23 : 107 113.
22. Menger F.M. (1985) On the source of intramolecular and enzymatic reactivity. Acc Chem Res 18 : 128 134.
23. Menger F.M., Chow J.F., Kaiserman H., Vasquez P.C. (1983) Directionality of proton transfer in solution. Three systems of known angularity. J Am Chem Soc 105 : 4996 5002.
24. Menger F.M. (1983) Directionality of organic reactions in solution. Tetrahedron 39 : 1013 1040.
25. Menger F.M., Grossman J., Liotta D.C. (1983) Transition-state pliability in nitrogen-to-nitrogen proton transfer. J Org Chem 48 : 905 907.
26. Menger F.M., Galloway A.L., Musaev D.G. (2003) Relationship between rate and distance. Chem Comm 9 : 2370 2371.
27. Menger F.M. (2005) An alternative view of enzyme catalysis. Pure Appl Chem 77 : 1873 1886.
28. Brown R.F., Van Gulick N.M. (1956) The geminal alkyl effect on the rates of ring closure of bromobutylamines. J Org Chem 21 : 1046 1049.
29. Galli C., Mandolini L. (2000) The role of ring strain on the ease of ring closure of bifunctional chain molecules. Eur J Org Chem : 3117 3125. and references therein.
30. Bruice T.C., Pandit U.K. (1960) The effect of geminal substitution ring size and rotamer distribution on the intramolecular nucleophilic catalysis of the hydrolysis of monophenyl esters of dibasic acids and the solvolysis of the intermediate anhydrides. J Am Chem Soc 82 : 5858 5865.
31. Bruice T.C., Pandit U.K. (1960) Intramolecular models depicting the kinetic importance of "Fit" in enzymatic catalysis. Proc Natl Acad Sci U S A 46 : 402 404.
32. Kirby A.J. (1997) Efficiency of proton transfer catalysis in models and enzymes. Acc Chem Res 30 : 290 296.
33. Brown C.J., Kirby A.J. (1997) Efficiency of proton transfer catalysis. Intramolecular general acid catalysis of the hydrolysis of dialkyl acetals of benzaldehyde. J Chem Soc Perkin Trans 2 : 1081 1093.
34. Craze G.-A., Kirby A.J. (1974) The role of carboxy-group in intramolecular catalysis of acetal hydrolysis. The hydrolysis of substituted 2-methoxymethoxybenzoic acids. J Chem Soc Perkin Trans 2 : 61 66.
35. Barber S.E., Dean K.E.S., Kirby A. (1999) A mechanism for efficient proton-transfer catalysis. Intramolecular general acid catalysis of the hydrolysis of 1-arylethyl ethers of salicylic acid. Can J Chem 77 : 792 801.
36. Asaad N., Davies J.E., Hodgson D.R.W., Kirby A.J. (2005) The search for efficient intramolecular proton transfer from carbon: the kinetically silent intramolecular general base-catalyzed elimination reaction of o-phenyl 8-dimethylamino-1-naphthaldoximes. J. Phys. Org. Chem. 18 : 101 109.
37. Kirby A.J., Parkinson A. (1994) Most efficient intramolecular general acid catalysis of acetal hydrolysis by the carboxy group. J Chem Soc Chem Commun : 707 708.
38. Kirby A.J., Lima M.F., de Silva D., Roussev C.D., Nome F. (2006) Efficient intramolecular general acid catalysis of nucleophilic attack on a phosphodiester. J Am Chem Soc 128 : 16944 16952.
39. Hartwell E., Hodgson D.R.W., Kirby A.J. (2000) Exploring the limits of efficiency of proton-transfer catalysis in models and enzymes. J Am Chem Soc 122 : 9326 9327.
40. Kirby A.J., Williams N.H. (1994) Efficient intramolecular general acid catalysis of enol ether hydrolysis. Hydrogen-bonding stabilization of the transition state for proton transfer to carbon. J Chem Soc, Perkin Trans 2 : 643 648.
41. Kirby A.J., Williams N.H. (1991) Efficient intramolecular general acid catalysis of vinyl ether hydrolysis by the neighboring carboxylic acid group. J Chem Soc Chem Commun : 1643 1644.
42. Casewit C.J., Colwell K.S., Rappé A.K. (1992) Application of a universal force field to main group compounds. J Am Chem Soc 114 : 10046 10053.
43. Dewar M.J.S., Zoebisch E.G., Healy E.F., Stewart J.J.P. (1985) AM1: a new general purpose quantum mechanical molecular model. J Am Chem Soc 107 : 3902 3909.
44. Murrell J.N., Laidler K.J. (1968) Symmetries of activated complexes. Trans Faraday Soc 64 : 371 377.
45. Muller K. (1980) Reaction paths on multidimensional energy hypersurfaces. Angew Chem Int Ed Engl 19 : 1 13.
46. Cancès E., Mennucci B., Tomasi J. (1997) A new integral equation formalism for the polarizable continuum model: Theoretical background and applications to isotropic and anisotropic dielectrics. J Chem Phys 107 : 3032 3041.
47. Mennucci B., Tomasi J. (1997) Continuum solvation models: A new approach to the problem of solute's charge distribution and cavity boundaries. J Chem Phys 106 : 5151.
48. Mennucci B., Cancès E., Tomasi J. (1997) Evaluation of solvent effects in isotropic and anisotropic dielectrics and in ionic solutions with a unified integral equation method: Theoretical bases, computational implementation, and numerical applications. Journal of Physical Chemistry B 101 : 10506 10517.
49. Tomasi J., Mennucci B., Cancès E. (1999) The IEF version of the PCM solvation method: an overview of a new method addressed to study molecular solutes at the QM ab initio level. Journal of Molecular Structure-Theochem 464 : 211 226.
50. Enthalpic energy of 5 kcal/mol was needed to rotate the carboxyl group such that the attack angle increases from 48° to 88°.
51. Fife T.H., Przystas T.J. (1979) Intramolecular general acid catalysis in the hydrolysis of acetals with aliphatic alcohol leaving groups. J Am Chem Soc 101 : 1202 1210.
52. Kirby A.J. (1980) Effective molarities for intramolecular reactions. Adv Phys Org Chem 17 : 183 278.