Biochemistry of Halogenated Carboxylic Acids

  • Kenneth L. Kirk
Part of the Biochemistry of the Elements book series (BOTE, volume 9A+B)


Mono-, di-, and tricarboxylic acids are key intermediates in several metabolic pathways. The ability of halogenated analogues of many of these acids to mimic their behavior, or to inhibit critical enzymes required for the processing of these acids, has made such analogues important research tools for the study of a broad spectrum of biological processes. For example, in the 1930s, extensive use of iodoacetic acid as an inhibitor was an important strategy in the elucidation of metabolic pathways. In another example having major impact on biochemistry, the studies on the mechanism of fluoroacetate toxicity carried out by Sir Rudolf Peters in the 1950s spurred intense interest in the development of fluorinated compounds as antimetabolites and mechanistic probes. Over the past few decades, an enormous number of halogenated carboxylic acids have been synthesized, and virtually every aspect of energy metabolism has been studied using such analogues. In this review, topics have been arranged progressively from simple to more complex carboxylic acids, with one exception. Because of the intimate biochemical and historical relationship between fluoroacetate and fluorocitrate, the biochemistry of these compounds will be considered together.


Pyruvate Kinase Pyruvate Dehydrogenase Malate Dehydrogenase Pyruvate Carboxylase Iodoacetic Acid 
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  1. Akhtar, M., Cohen, M. A., and Gani, D., 1986. Enzymic synthesis of 3-haloaspartic acids using ß-methylaspartase: Inhibition by 3-bromoaspartate, J. Chem. Soc., Chem. Commun. 1986: 1290–1291.CrossRefGoogle Scholar
  2. Birchmeier, W., and Christen, P., 1974. The reaction of cytoplasmic aspartate aminotransferase with bromopyruvate. Syncatalytic modification simulates affinity labeling, J. Biol. Chem. 249: 6311–6315.PubMedGoogle Scholar
  3. Bisswanger, H., 1981. Substrate specificity of the pyruvate dehydrogenase complex from Escherichia coli, J. Biol. Chem. 256: 815–822.PubMedGoogle Scholar
  4. Blumberg, K., and Stubbe, J., 1975. Chemical specificity of pyruvate kinase from yeast, Biochim. Biophys. Acta 384: 120–126.PubMedCrossRefGoogle Scholar
  5. Bosakowski, T., and Levin, A. A., 1986. Serum citrate as a peripheral indicator of fluoroacetate and fluorocitrate toxicity in rats and dogs, Toxicol. Appl. Pharmacol. 85: 428–436.PubMedCrossRefGoogle Scholar
  6. Bosakowski, T., and Levin, A. A., 1987. Comparative acute toxicity of chlorocitrate and fluorocitrate in dogs, Toxicol. Appl. Pharmacol. 89: 97–104.PubMedCrossRefGoogle Scholar
  7. Carrell, H. L., Glusker, J. P., Villafranca, J. J., Mildvan, A. S., Dummel, R. J., and Kun, E., 1970. Fluorocitrate inhibition of aconitase: Relative configuration of the inhibitory isomer by X-ray crystallography, Science 170: 1412–1414.PubMedCrossRefGoogle Scholar
  8. Conway, A., and Koshland, D. E., Jr., 1968. Negative cooperativity in enzyme action. The binding of diphosphopyridine nucleotide to glyceraldehyde 3-phosphate dehydrogenase, Biochemistry 7: 4011–4023.PubMedCrossRefGoogle Scholar
  9. Comforth, J. W., Redmond, J. W., Eggerer, H., Buckel, W., and Gutschow, C., 1969. Asymmetric methyl groups, and the mechanism of malate synthase, Nature 221: 1212–1213.CrossRefGoogle Scholar
  10. Crabb, D. W., and Harris, R. A., 1979. Mechanism responsible for the hypoglycemic actions of dichloroacetate and 2-chloropropionate, Arch. Biochem. Biophys. 198: 145–152.PubMedCrossRefGoogle Scholar
  11. Crabb, D. W., Yount, E. A., and Harris, R. A., 1981. The metabolic effects of dichloroacetate, Metabolism 30: 1024–1039.PubMedCrossRefGoogle Scholar
  12. Crestfield, A. M., Moore, S., and Stein, W. H., 1963. The preparation and enzymatic hydrolysis of reduced and S-carboxymethylated proteins, J. Biol. Chem. 238: 622–627.PubMedGoogle Scholar
  13. Demaugre, F., Buc, H. A., Cepanec, C., Moncion, A., and Leroux, J.-P., 1983. Comparison of the effects of 2-chloropropionate and dichloroacetate on ketogenesis and lipogenesis in isolated rat hepatocytes, Biochem. Pharmacol. 32: 1881–1885.PubMedCrossRefGoogle Scholar
  14. Duffy, T. H., and Nowak, T., 1984. Stereoselectivity of interaction of phosphoenolpyruvate analogues with various phosphoenolpyruvate-utilizing enzymes, Biochemistry 23: 661–670.PubMedCrossRefGoogle Scholar
  15. Eanes, R. Z., Skilleter, D. N., and Kun, E., 1972. Inactivation of the tricarboxylate carrier of liver mitochondria by erythrofluorocitrate, Biochem. Biophys. Res. Commun. 46: 1618–1622.PubMedCrossRefGoogle Scholar
  16. Fanshier, D. W., Gottwald, L. K., and Kun, E., 1962. Enzymatic synthesis of monofluorocitrate from ß-fluoro-oxaloacetate, J. Biol. Chem. 237: 3588–3596.Google Scholar
  17. Filler, R., and Naqvi, S. M., 1982. Fluorine in biomedicinal chemistry. An overview of recent advances and selected topics, in Biomedicinal Aspects of Fluorine Chemistry ( R. Filler and Y. Kobayashi, eds.), Kodansha Ltd., Tokyo; Elsevier Biomedical Press, Amsterdam, pp. 1–32.Google Scholar
  18. Flournoy, D. S., and Frey, P. A., 1986. Pyruvate dehydrogenase and 3-fluoropyruvate: Chemical competence of 2-acetylthiamin pyrophosphate as an acetyl group donor to diyhydrolipoamide, Biochemistry 25: 6036–6043.PubMedCrossRefGoogle Scholar
  19. Fonda, M. L., 1976. Bromopyruvate inactivation of glutamate apodecarboxylase. Kinetics and specificity, J. Biol. Chem. 251: 229–235.PubMedGoogle Scholar
  20. Foxall, D. L., Brindle, K. M., Campbell, R. D., and Simpson, I. J., 1984. The inhibition of erythrocyte glyceraldehyde-3-phosphate dehydrogenase. In situ PMR studies, Biochim. Biophys. Acta. 804: 209–215.PubMedCrossRefGoogle Scholar
  21. Goldman, P., 1969. The carbon-fluorine bond in compounds of biological interest, Science 164: 1123–1133.PubMedCrossRefGoogle Scholar
  22. Goldstein, J. A., Cheung, Y.-F., Marietta, M. A., and Walsh, C., 1978. Fluorinated substrate analogues as stereochemical probes of enzymatic reaction mechanisms, Biochemistry 17: 5567–5575.PubMedCrossRefGoogle Scholar
  23. Han, A. C., Goodwin, G. W., Paxton, R., and Harris, R. A., 1987. Activation of branched-chain a-ketoacid dehydrogenase in isolated hepatocytes by branched-chain a-ketoacids, Arch. Biochem. Biophys. 258: 85–94.PubMedCrossRefGoogle Scholar
  24. Harris, J. I., and Perham, R N, 1968. Glyceraldehyde 3-phosphate dehydrogenase from pig muscle, Nature 219: 1025–1028.PubMedCrossRefGoogle Scholar
  25. Harris, R. A., Paxton, R., and DePaoli-Roach, A. A., 1982. Inhibition of branched chain a-ketoacid dehydrogenase kinase activity by a-chloroisocaproate, J. Biol. Chem. 257: 13915–13918.PubMedGoogle Scholar
  26. Harris, R. A., Paxton, R., Powell, S. M., Goodwin, G. W., Kuntz, M. J., and Han, A. C., 1986. Regulation of branched-chain a-ketoacid dehydrogenase complex by covalent modification, Adv. Enzyme Regul. 25: 219–237.PubMedCrossRefGoogle Scholar
  27. Hartman, F. C., 1977. Haloketones as affinity labeling reagents, Methods Enzymol. 46: 130–153.PubMedCrossRefGoogle Scholar
  28. Heinrikson, R. I., Stein, W. H., Crestfield, A. M., and Moore, S., 1965. The reactivities of the histidine residues at the active site of ribonuclease toward halo acids of different structures, J. Biol. Chem. 240: 2921–2934.PubMedGoogle Scholar
  29. Hoving, H., Nowak, T., and Robillard, G. T., 1983. Escherichia coli phosphoenolpyruvatedependent phospho-transcarboxylase system: Stereospecificity of proton transfer in the phosphorylation of enzyme I from (Z)-phosphoenolbutyrate, Biochemistry 22: 2832–2838.Google Scholar
  30. Hoving, H., Crysell, B., and Leadlay, P. F., 1985. Fluorine NMR studies on stereochemical aspects of reactions catalyzed by transcarboxylase, pyruvate kinase, and enzyme I, Biochemistry 24: 6163–6169.PubMedCrossRefGoogle Scholar
  31. Hudson, P. J., Keech, D. B., and Wallace, J. C., 1975. Pyruvate carboxylase: Affinity labelling of the pyruvate binding site, Biochem. Biophys. Res. Commun. 65: 213–219.PubMedCrossRefGoogle Scholar
  32. Hwang, S. H., and Nowak, T., 1986. Stereochemistry of phosphoenolpyruvate carboxylation catalyzed by phosphoenolpyruvate carboxykinase, Biochemistry 25: 5590–5595.PubMedCrossRefGoogle Scholar
  33. Keck, R., Haas, H., and Retey, J., 1980. Synthesis of stereospecifically deuterated fluoroacetic acid and its behavior in enzymic aldol-type condensations, FEBS Lett. 114: 287–290.PubMedCrossRefGoogle Scholar
  34. Kennedy, M. C., Spoto, G., Emptage, M. H., and Beinert, H., 1988. The active site sulfhydryl of aconitase is not required for catalytic activity, J. Biol. Chem. 263: 8190–8193.PubMedGoogle Scholar
  35. Kirsten, E., Sharma, M. L., and Kun, E., 1978. Molecular toxicology of erythro fluorocitrate: Selective inhibition of citrate transport in mitochondria and the binding of fluorocitrate to mitochondrial proteins, Mol. Pharmacol. 14: 172–184.PubMedGoogle Scholar
  36. Kun, E., 1976. Fluorocarboxylic acids as enzymatic and metabolic probes, in Biochemistry Involving Carbon-Fluorine Bonds (R. Filler, ed.), ACS Symposium Series, No. 28, American Chemical Society, Washington, D.C., pp. 1–22.Google Scholar
  37. Kun, E., Kirsten, E., and Sharma, M. L., 1977. Enzymatic formation of glutathione-citryl thioester by a mitochondrial system and its inhibition by (-)-erythro-fluorocitrate, Proc. Natl. Acad. Sci. USA 74: 4942–4946.PubMedCrossRefGoogle Scholar
  38. Kuo, D. J., and Rose, I. A., 1982. Utilization of enolpyruvate by the carboxybiotin form of transcarboxylase: Evidence for a nonconcerted mechanism, J. Am. Chem. Soc. 104: 3235–3236.CrossRefGoogle Scholar
  39. Leung, S. L., and Frey, P. A., 1978. Fluoropyruvate: An unusual substrate for Escherichia coli pyruvate dehydrogenase, Biochem. Biophys. Res. Commun. 81: 274–279.PubMedCrossRefGoogle Scholar
  40. Lew, V. L., and Ferreira, H. G., 1978. Calcium transport and the properties of a calcium-activated potassium channel in the red cell membrane, Curr. Top. Membr. Transport 10: 217–277.CrossRefGoogle Scholar
  41. Lowe, P. N., and Perham, R. N., 1984. Bromopyruvate as an active-site-directed inhibitor of the pyruvate dehydrogenase multienzyme complex from Escherichia coli, Biochemistry 23: 91–97.PubMedCrossRefGoogle Scholar
  42. Luthy, J., Retey, J., and Arigoni, D., 1969. Preparation and detection of chiral methyl groups, Nature 221: 1213–1215.PubMedCrossRefGoogle Scholar
  43. MacQuarrie, R. A., and Bernhard, S. A., 1971. Mechanism of alkylation of rabbit muscle glyceraldehyde 3-phosphate dehydrogenase, Biochemistry 10: 2456–2466.PubMedCrossRefGoogle Scholar
  44. Maldonado, M. E., Oh, K.-J., and Frey, P. A., 1972. Studies on Escherichia coli pyruvate dehydrogenase complex. I. Effect of bromopyruvate on the catalytic activities of the complex, J. Biol. Chem. 247: 2711–2716.PubMedGoogle Scholar
  45. Mariash, C. N., and Schwartz, H. L., 1986. Effect of dichloroacetate on rat hepatic messenger RNA activity profiles, Metabolism 35: 452–456.PubMedCrossRefGoogle Scholar
  46. Marietta, M. A., Srere, P. A., and Walsh, C., 1981. Stereochemical outcome of processing of fluorinated substances by ATP citrate lyase and malate synthase, Biochemistry 20: 3719–3723.CrossRefGoogle Scholar
  47. Marietta, M. A., Cheung, Y.-F., and Walsh, C., 1982. Stereochemical studies on the hydration of monofluorofumarate and 2,3-difluorofumarate by fumarase, Biochemistry 21: 2637–2644.CrossRefGoogle Scholar
  48. Meloche, H. P., 1967. Bromopyruvate inactivation of 2-keto-3-deoxy-6-phosphogluconic aldolase. I. Kinetic evidence for active site specificity, Biochemistry 6: 2273–2280.PubMedCrossRefGoogle Scholar
  49. Meloche, H. P., 1970. Reaction of the substrate analog bromopyruvate with two active-site conformers of 2-keto-3-deoxy-6 phosphogluconic aldolase, Biochemistry 9: 5050–5055.PubMedCrossRefGoogle Scholar
  50. Meloche, H. P., and Glusker, J. P., 1973. Aldolase catalysis: Single base-mediated proton activation, Science 181: 350–352.PubMedCrossRefGoogle Scholar
  51. Monti, C. T., Waterbor, J. W., and Meloche, H. P., 1979. Interaction of the chiral pyruvate analog, 2-keto-3-bromobutyrate with pyruvate lyases. 2-Keto-3-deoxygluconate-6phosphate aldolase of Pseudomonas putida, J. Biol. Chem. 254: 5862–5865.PubMedGoogle Scholar
  52. Murray-Rust, P., Stallings, W. C., Monti, C. T., Preston, R. K., and Glusker, J. P., 1983. Intermolecular interactions of the C–F bond: The crystallographic environment of fluorinated carboxylic acids and related structures, J. Am. Chem. Soc. 105: 3206–3214.CrossRefGoogle Scholar
  53. Nitta, N., Kuga, O., Yui, S., Tsugawa, A., Negishi, K., and Hayatsu, H., 1984. A new reaction useful for chemical cross-linking between nucleic acids and proteins, FEBS Lett. 166: 194–198.PubMedCrossRefGoogle Scholar
  54. Okamoto, M., and Morino, Y., 1973. Affinity labeling of aspartate aminotransferase isozymes by bromopyruvate, J. Biol. Chem. 248: 82–90.PubMedGoogle Scholar
  55. O’Leary, M. H., and Diaz, E., 1982. Phosphoenol-3-bromopyruvate. A mechanism-based inhibitor of phosphoenolpyruvate carboxylase from maize, J. Biol. Chem. 257: 14603–14605.PubMedGoogle Scholar
  56. Patel, S. S., and Walt, D. R., 1987. Substrate specificity of acetyl coenzyme A synthase, J. Biol. Chem. 262: 7132–7134.PubMedGoogle Scholar
  57. Paulsen, R. E., Contestabile, A., Villani, L., and Fonnum, F., 1987. An in vivo model for studying function of brain tissue temporarily devoid of glial cell metabolism: The use of fluorocitrate, J. Neurochem. 48: 1377–1385.PubMedCrossRefGoogle Scholar
  58. Paxton, R., and Harris, R. A., 1984. Clofibric acid, phenylpyruvate, and dichloroacetate inhibition of branched-chain a-ketoacid dehydrogenase in vitro and in perfused rat heart, Arch. Biochem. Biophys. 231: 58–66.PubMedCrossRefGoogle Scholar
  59. Paxton, R., Harris, R. A., Sener, A., and Malaisse, W. J., 1988. Branched chain a-ketoacid dehydrogenase and pyruvate dehydrogenase activity in isolated rat pancreatic islets, Horm. Metabol. Res. 20: 317–322.CrossRefGoogle Scholar
  60. Peters, R., 1972. Some metabolic aspects of fluoroacetate especially related to fluorocitrate, in Ciba Foundation Symposium: Carbon-Fluorine Compounds: Chemistry, Biochemistry, and Biological Activities, Elsevier, Amsterdam, 1972, pp. 55–76.Google Scholar
  61. Plishker, G. A., 1985. Iodoacetic acid inhibition of calcium-dependent potassium efflux in red blood cells, Am. J. Physiol. 248: C419 - C424.PubMedGoogle Scholar
  62. Polgar, L., 1975. Ion-pair formation as a source of enhanced reactivity of the essential thiol group of D-glyceraldehyde-3-phosphate dehydrogenase, Eur. J. Biochem. 51: 63–71.PubMedCrossRefGoogle Scholar
  63. Prestwich, G. D., Yamaoka, R., Phirwa, S., and DePalma, A., 1984. Isolation of 2-fluorocitrate produced by in vivo dealkylation of 20-fluorostigmasterol in an insect, J. Biol. Chem. 259: 11022–11026.PubMedGoogle Scholar
  64. Rokita, S. E., Srere, P. A., and Walsh, C. T., 1982. 3-Fluoro-3-deoxycitrate: A probe for mechanistic study of citrate-utilizing enzymes, Biochemistry 21: 3765–3774.Google Scholar
  65. Shapiro, R., Strydom, D. J., Weremowicz, S., and Vallee, B. L., 1988. Sites of modification of human angiogenin by bromoacetate at pH 5.5, Biochem. Biophys. Res. Commun. 156: 530–536.PubMedCrossRefGoogle Scholar
  66. Skilleter, D. N., Dummel, R. J., and Kun, E., 1972. Specific enzyme inhibitors. XIV. Effects of enzymically synthesized erythro-fluoromalic acid on malate dehydrogenase and on anion carriers of liver mitochondria, Mol. Pharmacol. 8: 139–148.PubMedGoogle Scholar
  67. Stacpoole, P. W., Lorenz, A. C., Thomas, R. G., and Harman, E. M., 1988. Dichloroacetate in the treatment of lactic acidosis, Ann. Internal Med. 108: 58–63.CrossRefGoogle Scholar
  68. Stryer, L., 1988. Biochemistry, 3rd ed., W. H. Freeman and Company, New York, pp. 379–382.Google Scholar
  69. Stubbe, J., and Abeles, R. H., 1977. Biotin carboxylations-concerted or nonconcerted? That is the question, J. Biol. Chem. 252: 8338–8340.PubMedGoogle Scholar
  70. Stubbe, J., Fish, S., and Abeles, R. H., 1980. Are carboxylations involving biotin concerted or nonconcerted? J. Biol. Chem. 255: 236–242.PubMedGoogle Scholar
  71. Sullivan, A. C., Dairman, W., and Triscari, J., 1981. Threo-Chlorocitric acid: A novel anorectic agent, Pharmacol. Biochem. Behay. 15: 303–310.CrossRefGoogle Scholar
  72. Szerb, J. C., and Issekutz, B., 1987. Increase in the stimulation-induced overflow of glutamate by fluoroacetate, a selective inhibitor of the glial tricarboxylic acid cycle, Brain Res. 410: 116–120.PubMedCrossRefGoogle Scholar
  73. Teipel, J. W., Hass, G. M., and Hill, R. L., 1968. The substrate specificity of fumarase, J. Biol. Chem. 243: 5684–5694.PubMedGoogle Scholar
  74. Toshima, K., Kuroda, Y., Yokota, I., Naito, E., Ito, M., Watanabe, T., Takeda, E., and Miyao, M., 1985. Activation of branched-chain x-ketoacid dehydrogenase by a-chloroisocaproate in normal and enzyme deficient fibroblast, Clin. Chim. Acta 147: 103–108.PubMedCrossRefGoogle Scholar
  75. Triscari, J., and Sullivan, A. C., 1981. Studies on the mechanism of a novel anorectic agent, threo-chlorocitric acid, Pharmacol. Biochem. Behay. 15: 311–318.CrossRefGoogle Scholar
  76. Urban, P., Alliel, P. M., and Lederer, F., 1983. On the transhydrogenase activity of baker’s yeast flavocytochrome b 2, Eur. J. Biochem. 134: 275–281.PubMedCrossRefGoogle Scholar
  77. Vary, T. C., Siegel, J. H., Tall, B. D., and Morris, J. G., 1988. Metabolic effects of partial reversal of pyruvate dehydrogenase activity by dichloroacetate in sepsis, Circ. Shock 24: 3–18.PubMedGoogle Scholar
  78. Walsh, C., 1983. Fluorinated substrate analogues: Routes of metabolism and selective toxicity, Adv. Enzymol. 55: 197–289.PubMedGoogle Scholar
  79. Wang, Z.-X., Preiss, B., and Tsou, C.-L., 1988. Kinetics of inactivation of creatine kinase during modification of its thiol groups, Biochemistry 27: 5095–5100.PubMedCrossRefGoogle Scholar
  80. Webb, J. L., 1966. Enzyme and Metabolic Inhibitors, Vol. III, Academic Press, New York, pp. 1–283.Google Scholar
  81. Welch, J. T., 1987. Advances in the preparation of biologically active organofluorine compounds, Tetrahedron 43: 3123–3197.CrossRefGoogle Scholar
  82. Whitehouse, S., Cooper, R. H., and Randle, P. J., 1974. Mechanism of activation of pyruvate dehydrogenase by dichloroacetate and other halogenated carboxylic acids, Biochem. J. 141: 761–774.PubMedGoogle Scholar
  83. Wilchek, M., and Givol, D., 1977. Haloacetyl derivatives, Methods Enzymol. 46: 153–157.PubMedCrossRefGoogle Scholar
  84. Wold, F., 1977. Affinity labeling—an overview, Methods Enzymol. 46: 3–14.PubMedCrossRefGoogle Scholar
  85. Yoshida, H., and Wood, H. G., 1978. Crystalline pyruvate, phosphate dikinase from Bacteroides symbiosus. Modification of essential histidyl residues by bromopyruvate inactivation, J. Biol. Chem. 253: 7650–7655.PubMedGoogle Scholar
  86. Zimmerle, C. T., Tung, P. P., and Alter, G. M., 1987. Ligand-induced symmetry between active sites of cytoplasmic malate dehydrogenase: A chemical modification study, Biochemistry 26: 8535–8541.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 1991

Authors and Affiliations

  • Kenneth L. Kirk
    • 1
  1. 1.National Institutes of HealthBethesdaUSA

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