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Structural basis for herbicidal inhibitor selectivity revealed by comparison of crystal structures of plant and mammalian 4-hydroxyphenylpyruvate dioxygenases.

Yang C, Pflugrath JW, Camper DL, Foster ML, Pernich DJ, Walsh TA
Biochemistry 43 10414-23 (2004)
Related entries: 1sqi, 1tfz, 1tg5

Cited: 44 times
EuropePMC logo PMID: 15301540

Abstract

A high degree of selectivity toward the target site of the pest organism is a desirable attribute for new safer agrochemicals. To assist in the design of novel herbicides, we determined the crystal structures of the herbicidal target enzyme 4-hydroxyphenylpyruvate dioxygenase (HPPD; EC 1.13.11.27) from the plant Arabidopsis thaliana with and without an herbicidal benzoylpyrazole inhibitor that potently inhibits both plant and mammalian HPPDs. We also determined the structure of a mammalian (rat) HPPD in complex with the same nonselective inhibitor. From a screening campaign of over 1000 HPPD inhibitors, six highly plant-selective inhibitors were found. One of these had remarkable (>1600-fold) selectivity toward the plant enzyme and was cocrystallized with Arabidopsis HPPD. Detailed comparisons of the plant and mammalian HPPD-ligand structures suggest a structural basis for the high degree of plant selectivity of certain HPPD inhibitors and point to design strategies to obtain potent and selective inhibitors of plant HPPD as agrochemical leads.

Reviews - 1sqd mentioned but not cited (1)

  1. Review on Structures of Pesticide Targets. Li X, Yang X, Zheng X, Bai M, Hu D. Int J Mol Sci 21 E7144 (2020)

Articles - 1sqd mentioned but not cited (6)

  1. 4-hydroxyphenylpyruvate dioxygenase catalysis: identification of catalytic residues and production of a hydroxylated intermediate shared with a structurally unrelated enzyme. Raspail C, Graindorge M, Moreau Y, Crouzy S, Lefèbvre B, Robin AY, Dumas R, Matringe M. J. Biol. Chem. 286 26061-26070 (2011)
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  3. Expression of Xhdsi-1VOC, a novel member of the vicinal oxygen chelate (VOC) metalloenzyme superfamily, is up-regulated in leaves and roots during desiccation in the resurrection plant Xerophyta humilis (Bak) Dur and Schinz. Mulako I, Farrant JM, Collett H, Illing N. J Exp Bot 59 3885-3901 (2008)
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  6. Crystal Structure of 4-Hydroxyphenylpyruvate Dioxygenase in Complex with Substrate Reveals a New Starting Point for Herbicide Discovery. Lin HY, Chen X, Chen JN, Wang DW, Wu FX, Lin SY, Zhan CG, Wu JW, Yang WC, Yang GF. Research (Wash D C) 2019 2602414 (2019)


Reviews citing this publication (8)

  1. Structural studies on 2-oxoglutarate oxygenases and related double-stranded beta-helix fold proteins. Clifton IJ, McDonough MA, Ehrismann D, Kershaw NJ, Granatino N, Schofield CJ. J. Inorg. Biochem. 100 644-669 (2006)
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  8. A review of the mode of toxicity and relevance to humans of the triketone herbicide 2-(4-methylsulfonyl-2-nitrobenzoyl)-1,3-cyclohexanedione. Lewis RW, Botham JW. Crit. Rev. Toxicol. 43 185-199 (2013)

Articles citing this publication (29)

  1. Herbicide-binding sites revealed in the structure of plant acetohydroxyacid synthase. McCourt JA, Pang SS, King-Scott J, Guddat LW, Duggleby RG. Proc. Natl. Acad. Sci. U.S.A. 103 569-573 (2006)
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  3. Broad 4-hydroxyphenylpyruvate dioxygenase inhibitor herbicide tolerance in soybean with an optimized enzyme and expression cassette. Siehl DL, Tao Y, Albert H, Dong Y, Heckert M, Madrigal A, Lincoln-Cabatu B, Lu J, Fenwick T, Bermudez E, Sandoval M, Horn C, Green JM, Hale T, Pagano P, Clark J, Udranszky IA, Rizzo N, Bourett T, Howard RJ, Johnson DH, Vogt M, Akinsola G, Castle LA. Plant Physiol. 166 1162-1176 (2014)
  4. Conversion of hydroxyphenylpyruvate dioxygenases into hydroxymandelate synthases by directed evolution. O'Hare HM, Huang F, Holding A, Choroba OW, Spencer JB. FEBS Lett. 580 3445-3450 (2006)
  5. Adaptation of phenylalanine and tyrosine catabolic pathway to hibernation in bats. Pan YH, Zhang Y, Cui J, Liu Y, McAllan BM, Liao CC, Zhang S. PLoS ONE 8 e62039 (2013)
  6. A discoidin domain receptor 1 knock-out mouse as a novel model for osteoarthritis of the temporomandibular joint. Schminke B, Muhammad H, Bode C, Sadowski B, Gerter R, Gersdorff N, Bürgers R, Monsonego-Ornan E, Rosen V, Miosge N. Cell. Mol. Life Sci. 71 1081-1096 (2014)
  7. Proteomic analysis of hepatic tissue in adult female zebrafish (Danio rerio) exposed to atrazine. Jin Y, Zhang X, Lu D, Fu Z. Arch. Environ. Contam. Toxicol. 62 127-134 (2012)
  8. Mechanism of resistance to mesotrione in an Amaranthus tuberculatus population from Nebraska, USA. Kaundun SS, Hutchings SJ, Dale RP, Howell A, Morris JA, Kramer VC, Shivrain VK, Mcindoe E. PLoS ONE 12 e0180095 (2017)
  9. A computational tool to optimize ligand selectivity between two similar biomacromolecular targets. Chen DL, Kellogg GE. J. Comput. Aided Mol. Des. 19 69-82 (2005)
  10. Pyrazolone-quinazolone hybrids: a novel class of human 4-hydroxyphenylpyruvate dioxygenase inhibitors. Xu YL, Lin HY, Cao RJ, Ming ZZ, Yang WC, Yang GF. Bioorg. Med. Chem. 22 5194-5211 (2014)
  11. Novel bacterial bioassay for a high-throughput screening of 4-hydroxyphenylpyruvate dioxygenase inhibitors. Rocaboy-Faquet E, Noguer T, Romdhane S, Bertrand C, Dayan FE, Barthelmebs L. Appl. Microbiol. Biotechnol. 98 7243-7252 (2014)
  12. Chiral hydroxylation at the mononuclear nonheme Fe(II) center of 4-(S) hydroxymandelate synthase--a structure-activity relationship analysis. Di Giuro CM, Konstantinovics C, Rinner U, Nowikow C, Leitner E, Straganz GD. PLoS ONE 8 e68932 (2013)
  13. Molecular insights into the mechanism of 4-hydroxyphenylpyruvate dioxygenase inhibition: enzyme kinetics, X-ray crystallography and computational simulations. Lin HY, Yang JF, Wang DW, Hao GF, Dong JQ, Wang YX, Yang WC, Wu JW, Zhan CG, Yang GF. FEBS J 286 975-990 (2019)
  14. 3D Pharmacophore-Based Virtual Screening and Docking Approaches toward the Discovery of Novel HPPD Inhibitors. Fu Y, Sun YN, Yi KH, Li MQ, Cao HF, Li JZ, Ye F. Molecules 22 (2017)
  15. Combination of Virtual Screening Protocol by in Silico toward the Discovery of Novel 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors. Fu Y, Sun YN, Yi KH, Li MQ, Cao HF, Li JZ, Ye F. Front Chem 6 14 (2018)
  16. Manifestation of hawkinsinuria in a patient compound heterozygous for hawkinsinuria and tyrosinemia III. Item CB, Mihalek I, Lichtarge O, Jalan A, Vodopiutz J, Muhl A, Bodamer OA. Mol. Genet. Metab. 91 379-383 (2007)
  17. Molecular dynamics simulations and free energy calculations on the enzyme 4-hydroxyphenylpyruvate dioxygenase. De Beer SB, Glättli A, Hutzler J, Vermeulen NP, Oostenbrink C. J Comput Chem 32 2160-2169 (2011)
  18. The interactions in the carboxyl terminus of human 4-hydroxyphenylpyruvate dioxygenase are critical to mediate the conformation of the final helix and the tail to shield the active site for catalysis. Lin JF, Sheih YL, Chang TC, Chang NY, Chang CW, Shen CP, Lee HJ. PLoS ONE 8 e69733 (2013)
  19. Synthesis and bioevaluation of pyrazole-benzimidazolone hybrids as novel human 4-Hydroxyphenylpyruvate dioxygenase inhibitors. Xu YL, Lin HY, Ruan X, Yang SG, Hao GF, Yang WC, Yang GF. Eur J Med Chem 92 427-438 (2015)
  20. Novel HPPD inhibitors: triketone 2H-benzo[b][1,4]oxazin-3(4H)-one analogs. Li HB, Li L, Li JX, Han TF, He JL, Zhu YQ. Pest Manag. Sci. 74 579-589 (2018)
  21. Structural and functional characterization of 4-hydroxyphenylpyruvate dioxygenase from the thermoacidophilic archaeon Picrophilus torridus. Frick E, Spatzal T, Gerhardt S, Krämer A, Einsle O, Hüttel W. Extremophiles 18 641-651 (2014)
  22. Case Reports Case Report: Two Families With HPDL Related Neurodegeneration. Micule I, Lace B, Wright NT, Chrestian N, Strautmanis J, Diriks M, Stavusis J, Kidere D, Kleina E, Zdanovica A, Laflamme N, Rioux N, Setty ST, Pajusalu S, Droit A, Lek M, Rivest S, Inashkina I. Front Genet 13 780764 (2022)
  23. Efficient synthesis of fused bicyclic ethers and their application in herbicide chemistry. Schaetzer J, Edmunds AJF, Gaus K, Rendine S, De Mesmaeker A, Rueegg W. Bioorg. Med. Chem. Lett. 24 4643-4649 (2014)
  24. Electronic structure and molecular properties of nitisinone and mesotrione in water. Imrich R, Štofko J, Boča R, Rajnák C. J Mol Model 29 370 (2023)
  25. Free energy calculations elucidate substrate binding, gating mechanism, and tolerance-promoting mutations in herbicide target 4-hydroxyphenylpyruvate dioxygenase. Schindler CEM, Hollenbach E, Mietzner T, Schleifer KJ, Zacharias M. Protein Sci 28 1048-1058 (2019)
  26. Mechanism of action and selectivity of a novel herbicide, fenquinotrione. Yamamoto S, Tanetani Y, Uchiyama C, Nagamatsu A, Kobayashi M, Ikeda M, Kawai K. J Pestic Sci 46 249-257 (2021)
  27. Profiles of phenolics and their synthetic pathways in Asparagus officinalis L. Li Y, Brown SE, Li Y, Cheng Q, Wu H, Wei S, Li X, Lin C, Liu Z, Mao Z. Food Chem (Oxf) 8 100187 (2024)
  28. Quantitative Structure Activity Relationship Studies and Molecular Dynamics Simulations of 2-(Aryloxyacetyl)cyclohexane-1,3-Diones Derivatives as 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors. Fu Y, Liu YX, Yi KH, Li MQ, Li JZ, Ye F. Front Chem 7 556 (2019)
  29. Synthesis and herbicidal activities of aryloxyacetic acid derivatives as HPPD inhibitors. Wang MM, Huang H, Shu L, Liu JM, Zhang JQ, Yan YL, Zhang DY. Beilstein J Org Chem 16 233-247 (2020)


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