Publications
(selected publications)
Korzekwa KR, Jones JP, and Gillette JR. (1990) Theoretical studies on cytochrome P-450 mediated hydroxylation: A predictive model for hydrogen atom abstractions. J. Amer. Chem. Soc. 112: 7042-7046.
Jones JP, and Urbauer JL. (1991) Theoretical kinetic isotope effects for hydride transfer from formate to carbon dioxide: A comparison of theory with experiment. J. Comp. Chem. 12: 1134-1141.
Jones JP, Trager WF, and Carlson TJ. (1993) The binding and regioselectivity of reaction of (R) and (S)-nicotine with cytochrome P-450cam: Parallel experimental and theoretical studies. J. Amer. Chem. Soc. 115: 381-387.
Korzekwa KR, Jones JP. (1993) Predicting the cytochrome P450 mediated metabolism of xenobiotics. Pharmacogenetics 3: 1-18.
Dinnocenzo JP, Karki SB, and Jones JP (1993) Isotope effects for the cytochrome P-450 oxidation of substituted N,N-dimethyl anilines. J. Amer. Chem. Soc. 115: 7111-7116.
Yin H, Bennett G, and Jones JP. (1994) Mechanistic studies of UDP-glucuronosyltransferase. Chemico-Biol. Interact. 90: 47-58.
Jones JP, Shou M, and Korzekwa KR (1995). Stereospecific activation of the procarcinogen benzo[a]pyrene to probe the active site of the cytochrome P450 superfamily. Biochemistry, 34: 6956-6961.
Dinnocenzo JP, Karki SB, Jones JP, and Korzekwa KR. (1995) The mechanism of oxidative amine dealkylation by cytochrome P450: Application of isotope effect profiles. J. Am. Chem. Soc., 117: 3657-3664.
Yin H, Anders MW, and Jones JP. (1996) Metabolism of 1,2-dichloro-1-fluoroethane and 1-fluoro-1,2,2-trichloroethane: Electronic factors govern the regioselectivity of cytochrome P450-dependent oxidation. Chem. Res. Toxicol. 9: 50-57.
Jones JP, He M, Trager WF, and Rettie AW (1996) 3D-QSAR for inhibitors of cytochrome P450 2C9. Drug Metabolism and Disposition24: 1-6.
Jones JP, and Korzekwa KR. (1997) Predicting binding affinities and rates of reaction for the P450 superfamily. In: “Methods in Enzymology.” Ed. E. F. Johnson, and M. R. Waterman. Invited Chapter, Vol. 272b, pp. 326-335.
Manchester JI, Dinnocenzo JP, Higgins L and Jones JP. (1997) A new mechanistic probe for cytochrome P450. J. Am. Chem. Soc. 119: 5069-5070.
Iyer KR, Jones JP, Darbyshire JF, and Trager WF. (1997) Intramolecular isotope effects of benzylic hydroxylation of isomeric xylenes and 4,4’-dimethylbiphenyl by cytochrome P450: Relationship between distance of methyl groups and masking of the intrinsic isotope effect. Biochemistry 36: 7136-7143.
Higgins, L, Bennett, G. A., Shimoji, M. & Jones, J.P (1998) Evaluation of Cytochrome P450 Mechanism and Kinetics Using Kinetic Deuterium Isotope Effects. Biochemistry 37: 7036-7046.
Shimoji, M., Yin, H., Higgins, L. Jones, J.P. (1998) Design of a Novel P450: A Functional Bacterial/Human Cytochrome P450 Chimera. Biochemistry, 37: 8848-8852.
Goto, Y., Watanabe, Y., Fukuzumi, S., Jones, J. P. Dinnocenzo, J. P. (1998) Mechanisms of N-Demethylations Catalyzed by High-Valent Species of Heme Enzymes: Novel Use of Isotope Effects and Direct Observation of Intermediates. J. Amer. Chem. Soc. 120: 10762-10763.
Audergon, C., Iyer, K.R., Jones, J.P., Darbyshire, J.F, Trager, W.F. (1999) Experimental and theoretical approaches to study the active site topography of CYP101 (P450cam). J. Amer, Chem. Soc. 121, 41-47.
Haining, R.L., Jones, J.P., Henne, K., Fisher, M.B., Trager, W.F., Rettie, A.E. (1999) Phenylalanine 114 is a Critical, Substrate-Dependent Determinant of Specificity in Human Cytochrome P450 2C9. Biochemistry, 38: 3285-3292.
Koenigs, L.L., Jones, J.P., Friedberg, T., Pritchard, M. P., Shou, M., Rushmore, T.H., Trager, W. F. (2000) Mechanism-Based Inactivation of Cytochrome P450 3A4 by L-754,394. Biochemistry; 39:4276-87.
Rao S, Aoyama R, Schrag M, Trager WF, Rettie A, Jones JP. (2000) A refined 3-dimensional QSAR of cytochrome P450 2C9: computational predictions of drug interactions.J Med Chem; 43:2789-96.
Higgins, L., Korzekwa, K.R., Shou, M., Jones, J.P. (2001) A Method for the Assessment of Reaction Energetics for Cytochrome P450 Mediated Reactions. Archives of Biochemistry and Biophysics, 385, 220-230.
Ekins, S., de Groot, M.J., Jones, J.P. (2001) Pharmacophores and three Dimensional Quantitative Structure Activity Relationship Methods for Modeling Cytochrome P450 Active Sites. Drug Metabolism and Disposition, 29: 936-944.
Rock D, Rock D, Jones JP. (2001) Inexpensive purification of P450 reductase and other proteins using 2 ',5 '-adenosine diphosphate agarose affinity columns. Prot. Express. Pur. , 22: 82-83
French, K. J., Strickler, M. D., Rock, D. A., Rock, D. A., Bennett, G. A., Wahlstrom, J. L. Goldstein, B. M., Jones, J. P. (2001) Benign Synthesis of 2-ethylhexanoic acid by Cytochrome P450cam: Enzymatic, Crystallographic, and Theoretical Studies. Biochemistry, 40: 9532-9538.
Kevin J. French, Dan A. Rock, Denise A. Rock, John I. Manchester, Barry M. Goldstein, and Jeffrey P. Jones* (2002) “Rational Design of Cytochrome P450cam: Understanding the structural basis for the oxidase shunt and improving the benign synthesis of 2-Ethylhexanoic Acid” Arch. Biochem. Biophysics, 398, 188-97.
Jeffrey P. Jones*, Michael Mysinger, Kenneth Ray Korzekwa (2002) “Computational Models for Cytochrome P450: Predictive Electronic Model for Aromatic Oxidation and Hydrogen Atom abstraction” Drug Metabolism and Disposition, 1, 7-12.
Dan A. Rock, Anthony E. Boitano, Jan L. Wahlstrom, Denise A. Rock, and Jeffrey P. Jones* (2002) “The Use of Kinetic Isotope Effects to Delineate the Role of Phenylalanine 87 in P450BM-3 “ Bioorganic Chemistry, 30, 107-118.
Volz, T., Rock, D.A., Jones, J.P. (2002) “Direct Evidence for Two Different Active Oxygen Species in Cytochrome P450BM3 Mediated Sulfoxidation and N-Dealkylkation Reactions.” Journal of the American Chemical Society, 124(33); 9724-9725.
Strickler M, Goldstein BM, Maxfield K, Shireman L, Kim G, Matteson DS, Jones JP.(2003) “ Crystallographic studies on the complex behavior of nicotine binding to P450cam (CYP101).” Biochemistry. Oct 21;42(41):11943-50
Rock DA, Perkins BNS, Wahlstrom J, Jones JP.(2003) “A method for determining two substrates binding in the same active site of cytochrome P450(BM3): an explanation of high energy omega product formation.” Arch. Biochem. Biophysics. 416 (1): 9-16 AUG 1 2003.
Tornero-Velez R, Ross MK, Granville C, Laskey J, Jones JP, DeMarini DM,Evans MV “Metabolism and mutagenicity of source water contaminants 1,3-dichloropropane and 2,2-dichloropropane”Drug Metabolism and Disposition, 32 (1): 123-131 JAN 1 2004.
Dowers TS, Rock DA, Rock DA, Perkins BNS, Jones JP (2004) “An analysis of the regioselectivity of aromatic hydroxylation and N-oxygenation by cytochrome P450 enzymes.”Drug Metabolism and Disposition, 32 (3): 328-332.
Dickmann, L. J., Locuson, C. W., Jones, J. P. and Rettie. A.E. (2004) “Differential Roles of Arg97, Asp293, and Arg108 in Enzyme Stability and Substrate Specificity of CYP2C9.” Mol Pharmacol 65: 842-850.
Locuson,C.W. II, Rock, D.A., and Jones, J.P. (2004), “Quantitative Binding Models for CYP2C9 Based on Benzbromarone Analogues." Biochemistry, Web Release Date: 13-May-2004.
Dowers, T. S., D. A. Rock, D. A. Rock and J. P. Jones (2004). "Kinetic isotope effects implicate the iron-oxene as the sole oxidant in P450-catalyzed N-dealkylation." Journal of the American Chemical Society 126(29): 8868-8869.
Rettie, A., Jones, J.P. (2005) “Clinical and toxicological relevance of CYP2C9: Drug- drug interactions and pharmacogenetics” Annual Review of Pharmacology and Toxicology 45 477-494.
Locuson, C.W., Wienkers, L.C., Jones, J.P., Tracy, T.(2007) "CYP2C9 Protein Interactions with Cytochrome b5: Effects on the Coupling of Catalysis"Drug Metabolism and Disposition, 35(7): 1174-81
Cho, K. B.;Moreau, Y.;Kumar, D.;Rock, D. A.;Jones, J. P.;Shaik, S.
(2007). "Formation of the Active Species of Cytochrome P450 by Using Iodosylbenzene: A Case for Spin-Selective Reactivity." Chemistry: A European Journal 13: 4103-4115.
Torres, R. A.; Korzekwa, K. R.; McMasters, D. R.; Fandozzi, C. M.; Jones, J. P. (2007) "Use of Density Functional Calculations To Predict the Regioselectivity of Drugs and Molecules Metabolized by Aldehyde Oxidase" . J. Med. Chem.; (Article); ASAP Article; DOI: 10.1021/jm0703690
Hudelson, M. G.; Ketkar, N. S.; Holder, L. B.; Carlson, T. J.; Peng, C.; Waldher, B. J.; Jones, J. P. (2008). High Confidence Predictions of Drug−Drug Interactions: Predicting Affinities for Cytochrome P450 2C9 with Multiple Computational Methods, J. Med. Chem.; 2008 Feb 14;51(3):648-54. Epub 2008 Jan 19 DOI: 10.1021/jm701130z
Chi-Chi Peng, Tom Rushmore, Gregory J. Crouch, and Jeffrey P. Jones ” Modeling and Synthesis of Novel Tight-Binding Inhibitors of Cytochrome P450 2C9". Bioorganic and Medicinal Chemistry, 2008 Aor 1; 16(7): 4064-74 Epub 2008 Jan 18. PMID: 18255300
.