1
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Oliw EH. Thirty years with three-dimensional structures of lipoxygenases. Arch Biochem Biophys 2024; 752:109874. [PMID: 38145834 DOI: 10.1016/j.abb.2023.109874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/17/2023] [Accepted: 12/17/2023] [Indexed: 12/27/2023]
Abstract
The X-ray crystal structures of soybean lipoxygenase (LOX) and rabbit 15-LOX were reported in the 1990s. Subsequent 3D structures demonstrated a conserved U-like shape of the substrate cavities as reviewed here. The 8-LOX:arachidonic acid (AA) complex showed AA bound to the substrate cavity carboxylate-out with C10 at 3.4 Å from the iron metal center. A recent cryo-electron microscopy (EM) analysis of the 12-LOX:AA complex illustrated AA in the same position as in the 8-LOX:AA complex. The 15- and 12-LOX complexes with isoenzyme-specific inhibitors/substrate mimics confirmed the U-fold. 5-LOX oxidizes AA to leukotriene A4, the first step in biosynthesis of mediators of asthma. The X-ray structure showed that the entrance to the substrate cavity was closed to AA by Phe and Tyr residues of a partly unfolded α2-helix. Recent X-ray analysis revealed that soaking with inhibitors shifted the short α2-helix to a long and continuous, which opened the substrate cavity. The α2-helix also adopted two conformations in 15-LOX. 12-LOX dimers consisted of one closed and one open subunit with an elongated α2-helix. 13C-ENDOR-MD computations of the 9-MnLOX:linoleate complex showed carboxylate-out position with C11 placed 3.4 ± 0.1 Å from the catalytic water. 3D structures have provided a solid ground for future research.
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Affiliation(s)
- Ernst H Oliw
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, SE 751 24, Uppsala, Sweden.
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2
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Lavrentaki V, Kousaxidis A, Theodosis-Nobelos P, Papagiouvannis G, Koutsopoulos K, Nicolaou I. Design, synthesis, and pharmacological evaluation of indazole carboxamides of N-substituted pyrrole derivatives as soybean lipoxygenase inhibitors. Mol Divers 2023:10.1007/s11030-023-10775-8. [PMID: 38145424 DOI: 10.1007/s11030-023-10775-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/17/2023] [Indexed: 12/26/2023]
Abstract
In this paper, we attempted to develop a novel class of compounds against lipoxygenase, a key enzyme in the biosynthesis of leukotrienes implicated in a series of inflammatory diseases. Given the absence of appropriate human 5-lipoxygenase crystallographic data, solved soybean lipoxygenase-1 and -3 structures were used as a template to generate an accurate pharmacophore model which was further used for virtual screening purposes. Eight compounds (1-8) have been derived from the in-house library consisting of N-substituted pyrroles conjugated with 5- or 6-indazole moieties through a carboxamide linker. This study led to the discovery of hit molecule 8 bearing a naphthyl group with the IC50 value of 22 μM according to soybean lipoxygenase in vitro assay. Isosteric replacement of naphthyl ring with quinoline moieties and reduction of carbonyl carboxamide group resulted in compounds 9-12 and 13, respectively. Compound 12 demonstrated the most promising enzyme inhibition. In addition, compounds 8 and 12 were found to reduce the carrageenan-induced paw edema in vivo by 52.6 and 49.8%, respectively. In view of the encouraging outcomes concerning their notable in vitro and in vivo anti-inflammatory activities, compounds 8 and 12 could be further optimized for the discovery of novel 5-lipoxygenase inhibitors in future. A structure-based 3D pharmacophore model was used in the virtual screening of in-house library to discover novel potential 5-lipoxygenase inhibitors.
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Affiliation(s)
- Vasiliki Lavrentaki
- Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Antonios Kousaxidis
- Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | | | - Georgios Papagiouvannis
- Department of Pharmacy, School of Health Sciences, Frederick University, 1036, Nicosia, Cyprus
| | | | - Ioannis Nicolaou
- Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.
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3
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Sharma A, Whittington C, Jabed M, Hill SG, Kostenko A, Yu T, Li P, Doan PE, Hoffman BM, Offenbacher AR. 13C Electron Nuclear Double Resonance Spectroscopy-Guided Molecular Dynamics Computations Reveal the Structure of the Enzyme-Substrate Complex of an Active, N-Linked Glycosylated Lipoxygenase. Biochemistry 2023; 62:1531-1543. [PMID: 37115010 PMCID: PMC10704959 DOI: 10.1021/acs.biochem.3c00119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Lipoxygenase (LOX) enzymes produce important cell-signaling mediators, yet attempts to capture and characterize LOX-substrate complexes by X-ray co-crystallography are commonly unsuccessful, requiring development of alternative structural methods. We previously reported the structure of the complex of soybean lipoxygenase, SLO, with substrate linoleic acid (LA), as visualized through the integration of 13C/1H electron nuclear double resonance (ENDOR) spectroscopy and molecular dynamics (MD) computations. However, this required substitution of the catalytic mononuclear, nonheme iron by the structurally faithful, yet inactive Mn2+ ion as a spin probe. Unlike canonical Fe-LOXs from plants and animals, LOXs from pathogenic fungi contain active mononuclear Mn2+ metallocenters. Here, we report the ground-state active-site structure of the native, fully glycosylated fungal LOX from rice blast pathogen Magnaporthe oryzae, MoLOX complexed with LA, as obtained through the 13C/1H ENDOR-guided MD approach. The catalytically important distance between the hydrogen donor, carbon-11 (C11), and the acceptor, Mn-bound oxygen, (donor-acceptor distance, DAD) for the MoLOX-LA complex derived in this fashion is 3.4 ± 0.1 Å. The difference of the MoLOX-LA DAD from that of the SLO-LA complex, 3.1 ± 0.1 Å, is functionally important, although is only 0.3 Å, despite the MoLOX complex having a Mn-C11 distance of 5.4 Å and a "carboxylate-out" substrate-binding orientation, whereas the SLO complex has a 4.9 Å Mn-C11 distance and a "carboxylate-in" substrate orientation. The results provide structural insights into reactivity differences across the LOX family, give a foundation for guiding development of MoLOX inhibitors, and highlight the robustness of the ENDOR-guided MD approach to describe LOX-substrate structures.
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Affiliation(s)
- Ajay Sharma
- Department of Chemistry, Northwestern University, Evanston, IL 60208, United States
| | - Chris Whittington
- Department of Chemistry, East Carolina University, Greenville, NC 27858, United States
| | - Mohammed Jabed
- Department of Chemistry, University of North Dakota, Grand Forks, ND 58202, United States
| | - S. Gage Hill
- Department of Chemistry, East Carolina University, Greenville, NC 27858, United States
| | - Anastasiia Kostenko
- Department of Chemistry, East Carolina University, Greenville, NC 27858, United States
| | - Tao Yu
- Department of Chemistry, University of North Dakota, Grand Forks, ND 58202, United States
| | - Pengfei Li
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL 60660, United States
| | - Peter E. Doan
- Department of Chemistry, Northwestern University, Evanston, IL 60208, United States
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL 60208, United States
| | - Adam R. Offenbacher
- Department of Chemistry, East Carolina University, Greenville, NC 27858, United States
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4
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Engineering a lipoxygenase from cyclocybe aegerita towards long chain polyunsaturated fatty acids. AMB Express 2021; 11:37. [PMID: 33661405 PMCID: PMC7933318 DOI: 10.1186/s13568-021-01195-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/16/2021] [Indexed: 11/10/2022] Open
Abstract
The basidiomycetous lipoxygenase Lox1 from Cyclocybe aegerita catalyzes the oxygenation of polyunsaturated fatty acids (PUFAs) with a high preference towards the C18-PUFA linoleic acid (C18:2 (ω-6)). In contrast, longer PUFAs, generally not present in the fungal cell such as eicosatrienoic acid (C20:3(ω-3)) and docosatrienoic acid (C22:3 (ω-3)), are converted with drastically lower activities. With site-directed mutagenesis, we were able to create two variants with enhanced activities towards longer chain PUFAs. The W330L variant showed a ~ 20 % increased specific activity towards C20:3(ω-3), while a ~ 2.5-fold increased activity against C22:3 (ω-3) was accomplished by the V581 variant.
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5
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Figueiredo PR, Almeida BC, Dourado DFAR, Sousa AF, Silvestre AJD, Carvalho ATP. Enzymatic Synthesis of Poly(caprolactone): A QM/MM Study. ChemCatChem 2020. [DOI: 10.1002/cctc.202000780] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Pedro R. Figueiredo
- CNC – Center for Neuroscience and Cell Biology Institute for Interdisciplinary Research (IIIUC) University of Coimbra 3004-504 Coimbra Portugal
| | - Beatriz C. Almeida
- CNC – Center for Neuroscience and Cell Biology Institute for Interdisciplinary Research (IIIUC) University of Coimbra 3004-504 Coimbra Portugal
| | - Daniel F. A. R. Dourado
- Almac Sciences Department of Biocatalysis and Isotope Chemistry Almac House 20 Seagoe Industrial Estate Craigavon BT63 5QD Northern Ireland UK
| | | | | | - Alexandra T. P. Carvalho
- CNC – Center for Neuroscience and Cell Biology Institute for Interdisciplinary Research (IIIUC) University of Coimbra 3004-504 Coimbra Portugal
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6
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Hu S, Offenbacher AR, Lu ED, Klinman JP. Comparative kinetic isotope effects on first- and second-order rate constants of soybean lipoxygenase variants uncover a substrate-binding network. J Biol Chem 2019; 294:18069-18076. [PMID: 31624150 PMCID: PMC6885649 DOI: 10.1074/jbc.ra119.010826] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/14/2019] [Indexed: 01/08/2023] Open
Abstract
Lipoxygenases are widespread enzymes found in virtually all eukaryotes, including fungi, and, more recently, in prokaryotes. These enzymes act on long-chain polyunsaturated fatty acid substrates (C18 to C20), raising questions regarding how the substrate threads its way from solvent to the active site. Herein, we report a comparison of the temperature dependence of isotope effects on first- and second-order rate constants among single-site variants of the prototypic plant enzyme soybean lipoxygenase-1 substituted at amino acid residues inferred to impact substrate binding. We created 10 protein variants including four amino acid positions, Val-750, Ile-552, Ile-839, and Trp-500, located within a previously proposed substrate portal. The conversion of these bulky hydrophobic side chains to smaller side chains is concluded to increase the mobility of flanking helices, giving rise to increased off rates for substrate dissociation from the enzyme. In this manner, we identified a specific "binding network" that can regulate movement of the substrate from the solvent to the active site. Taken together with our previous findings on C-H and O2 activation of soybean lipoxygenase-1, these results support the emergence of multiple complementary networks within a single protein scaffold that modulate different steps along the enzymatic reaction coordinate.
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Affiliation(s)
- Shenshen Hu
- Department of Chemistry, University of California, Berkeley, California 94720; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720
| | - Adam R Offenbacher
- Department of Chemistry, University of California, Berkeley, California 94720; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720; Department of Chemistry, East Carolina University, Greenville, North Carolina 27858
| | - Edbert D Lu
- Department of Chemistry, University of California, Berkeley, California 94720; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720
| | - Judith P Klinman
- Department of Chemistry, University of California, Berkeley, California 94720; Department of Molecular and Cell Biology, University of California, Berkeley, California 94720; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720.
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7
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Hershelman D, Kahler KM, Price MJ, Lu I, Fu Y, Plumeri PA, Karaisz F, Bassett NF, Findeis PM, Clapp CH. Oxygenation reactions catalyzed by the F557V mutant of soybean lipoxygenase-1: Evidence for two orientations of substrate binding. Arch Biochem Biophys 2019; 674:108082. [PMID: 31473191 DOI: 10.1016/j.abb.2019.108082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/21/2019] [Accepted: 08/23/2019] [Indexed: 01/18/2023]
Abstract
Plant lipoxygenases oxygenate linoleic acid to produce 13(S)-hydroperoxy-9Z,11E-octadecadienoic acid (13(S)-HPOD) or 9-hydroperoxy-10E,12Z-octadecadienoic acid (9(S)-HPOD). The manner in which these enzymes bind substrates and the mechanisms by which they control regiospecificity are uncertain. Hornung et al. (Proc. Natl. Acad. Sci. USA96 (1999) 4192-4197) have identified an important residue, corresponding to phe-557 in soybean lipoxygenase-1 (SBLO-1). These authors proposed that large residues in this position favored binding of linoleate with the carboxylate group near the surface of the enzyme (tail-first binding), resulting in formation of 13(S)-HPOD. They also proposed that smaller residues in this position facilitate binding of linoleate in a head-first manner with its carboxylate group interacting with a conserved arginine residue (arg-707 in SBLO-1), which leads to 9(S)-HPOD. In the present work, we have tested these proposals on SBLO-1. The F557V mutant produced 33% 9-HPOD (S:R = 87:13) from linoleic acid at pH 7.5, compared with 8% for the wild-type enzyme and 12% with the F557V,R707L double mutant. Experiments with 11(S)-deuteriolinoleic acid indicated that the 9(S)-HPOD produced by the F557V mutant involves removal of hydrogen from the pro-R position on C-11 of linoleic acid, as expected if 9(S)-HPOD results from binding in an orientation that is inverted relative to that leading to 13(S)-HPOD. The product distributions obtained by oxygenation of 10Z,13Z-nonadecadienoic acid and arachidonic acid by the F557V mutant support the hypothesis that ω6 oxygenation results from tail-first binding and ω10 oxygenation from head-first binding. The results demonstrate that the regiospecificity of SBLO-1 can be altered by a mutation that facilitates an alternative mode of substrate binding and adds to the body of evidence that 13(S)-HPOD arises from tail-first binding.
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Affiliation(s)
| | - Kirsten M Kahler
- Department of Chemistry, Bucknell University, Lewisburg, PA, USA
| | - Morgan J Price
- Department of Chemistry, Bucknell University, Lewisburg, PA, USA
| | - Iris Lu
- Department of Chemistry, Bucknell University, Lewisburg, PA, USA
| | - Yuhan Fu
- Department of Chemistry, Bucknell University, Lewisburg, PA, USA
| | | | - Fred Karaisz
- Department of Chemistry, Bucknell University, Lewisburg, PA, USA
| | | | - Peter M Findeis
- Department of Chemistry, Bucknell University, Lewisburg, PA, USA
| | - Charles H Clapp
- Department of Chemistry, Bucknell University, Lewisburg, PA, USA.
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8
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Djian B, Hornung E, Ischebeck T, Feussner I. The green microalga Lobosphaera incisa harbours an arachidonate 15S-lipoxygenase. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21 Suppl 1:131-142. [PMID: 30277010 PMCID: PMC6587457 DOI: 10.1111/plb.12920] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 09/22/2018] [Indexed: 06/08/2023]
Abstract
The green microalga Lobosphaera incisa is an oleaginous eukaryotic alga that is rich in arachidonic acid (20:4). Being rich in this polyunsaturated fatty acid (PUFA), however, makes it sensitive to oxidation. In plants, lipoxygenases (LOXs) are the major enzymes that oxidise these molecules. Here, we describe, to our best knowledge, the first characterisation of a cDNA encoding a LOX (LiLOX) from a green alga. To obtain first insights into its function, we expressed it in E. coli, purified the recombinant enzyme and analysed its enzyme activity. The protein sequence suggests that LiLOX and plastidic LOXs from bryophytes and flowering plants may share a common ancestor. The fact that LiLOX oxidises all PUFAs tested with a consistent oxidation on the carbon n-6, suggests that PUFAs enter the substrate channel through their methyl group first (tail first). Additionally, LiLOX form the fatty acid hydroperoxide in strict S configuration. LiLOX may represent a good model to study plastid LOX, because it is stable after heterologous expression in E. coli and highly active in vitro. Moreover, as the first characterised LOX from green microalgae, it opens the possibility to study endogenous LOX pathways in these organisms.
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Affiliation(s)
- B. Djian
- Department of Plant BiochemistryUniversity of GoettingenAlbrecht‐von‐Haller‐Institute for Plant SciencesGoettingenGermany
| | - E. Hornung
- Department of Plant BiochemistryUniversity of GoettingenAlbrecht‐von‐Haller‐Institute for Plant SciencesGoettingenGermany
| | - T. Ischebeck
- Department of Plant BiochemistryUniversity of GoettingenAlbrecht‐von‐Haller‐Institute for Plant SciencesGoettingenGermany
- Goettingen Metabolomics and Lipidomics LaboratoryUniversity of GoettingenGoettingen Center for Molecular Biosciences (GZMB)GoettingenGermany
| | - I. Feussner
- Department of Plant BiochemistryUniversity of GoettingenAlbrecht‐von‐Haller‐Institute for Plant SciencesGoettingenGermany
- Goettingen Metabolomics and Lipidomics LaboratoryUniversity of GoettingenGoettingen Center for Molecular Biosciences (GZMB)GoettingenGermany
- Department of Plant BiochemistryUniversity of GoettingenGoettingen Center for Molecular Biosciences (GZMB)GoettingenGermany
- Department of Plant BiochemistryUniversity of GoettingenInternational Center for Advanced Studies of Energy Conversion (ICASEC)GoettingenGermany
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9
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Horitani M, Offenbacher AR, Carr CAM, Yu T, Hoeke V, Cutsail GE, Hammes-Schiffer S, Klinman JP, Hoffman BM. 13C ENDOR Spectroscopy of Lipoxygenase-Substrate Complexes Reveals the Structural Basis for C-H Activation by Tunneling. J Am Chem Soc 2017; 139:1984-1997. [PMID: 28121140 PMCID: PMC5322796 DOI: 10.1021/jacs.6b11856] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Indexed: 12/20/2022]
Abstract
In enzymatic C-H activation by hydrogen tunneling, reduced barrier width is important for efficient hydrogen wave function overlap during catalysis. For native enzymes displaying nonadiabatic tunneling, the dominant reactive hydrogen donor-acceptor distance (DAD) is typically ca. 2.7 Å, considerably shorter than normal van der Waals distances. Without a ground state substrate-bound structure for the prototypical nonadiabatic tunneling system, soybean lipoxygenase (SLO), it has remained unclear whether the requisite close tunneling distance occurs through an unusual ground state active site arrangement or by thermally sampling conformational substates. Herein, we introduce Mn2+ as a spin-probe surrogate for the SLO Fe ion; X-ray diffraction shows Mn-SLO is structurally faithful to the native enzyme. 13C ENDOR then reveals the locations of 13C10 and reactive 13C11 of linoleic acid relative to the metal; 1H ENDOR and molecular dynamics simulations of the fully solvated SLO model using ENDOR-derived restraints give additional metrical information. The resulting three-dimensional representation of the SLO active site ground state contains a reactive (a) conformer with hydrogen DAD of ∼3.1 Å, approximately van der Waals contact, plus an inactive (b) conformer with even longer DAD, establishing that stochastic conformational sampling is required to achieve reactive tunneling geometries. Tunneling-impaired SLO variants show increased DADs and variations in substrate positioning and rigidity, confirming previous kinetic and theoretical predictions of such behavior. Overall, this investigation highlights the (i) predictive power of nonadiabatic quantum treatments of proton-coupled electron transfer in SLO and (ii) sensitivity of ENDOR probes to test, detect, and corroborate kinetically predicted trends in active site reactivity and to reveal unexpected features of active site architecture.
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Affiliation(s)
- Masaki Horitani
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Adam R. Offenbacher
- Department of Chemistry and California Institute for Quantitative
Biosciences (QB3), Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
| | - Cody A. Marcus Carr
- Department of Chemistry and California Institute for Quantitative
Biosciences (QB3), Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
| | - Tao Yu
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Veronika Hoeke
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - George E. Cutsail
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Sharon Hammes-Schiffer
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Judith P. Klinman
- Department of Chemistry and California Institute for Quantitative
Biosciences (QB3), Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
| | - Brian M. Hoffman
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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10
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Bian J, Jin M, Yue M, Wang M, Zhang H, Gui C. Tryptophan Residue Located at the Middle of Putative Transmembrane Domain 11 Is Critical for the Function of Organic Anion Transporting Polypeptide 2B1. Mol Pharm 2016; 13:3553-3563. [DOI: 10.1021/acs.molpharmaceut.6b00648] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jialin Bian
- Department of Pharmaceutical Analysis, College of Pharmaceutical
Sciences, Soochow University, Suzhou 215123, China
| | - Meng Jin
- Department of Pharmaceutical Analysis, College of Pharmaceutical
Sciences, Soochow University, Suzhou 215123, China
| | - Mei Yue
- Department of Pharmaceutical Analysis, College of Pharmaceutical
Sciences, Soochow University, Suzhou 215123, China
| | - Meiyu Wang
- Department of Pharmaceutical Analysis, College of Pharmaceutical
Sciences, Soochow University, Suzhou 215123, China
| | - Hongjian Zhang
- Department of Pharmaceutical Analysis, College of Pharmaceutical
Sciences, Soochow University, Suzhou 215123, China
| | - Chunshan Gui
- Department of Pharmaceutical Analysis, College of Pharmaceutical
Sciences, Soochow University, Suzhou 215123, China
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11
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Deschamps JD, Ogunsola AF, Jameson JB, Yasgar A, Flitter BA, Freedman CJ, Melvin JA, Nguyen JVMH, Maloney DJ, Jadhav A, Simeonov A, Bomberger JM, Holman TR. Biochemical and Cellular Characterization and Inhibitor Discovery of Pseudomonas aeruginosa 15-Lipoxygenase. Biochemistry 2016; 55:3329-40. [PMID: 27226387 DOI: 10.1021/acs.biochem.6b00338] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that can cause nosocomial and chronic infections in immunocompromised patients. P. aeruginosa secretes a lipoxygenase, LoxA, but the biological role of this enzyme is currently unknown. LoxA is poorly similar in sequence to both soybean LOX-1 (s15-LOX-1) and human 15-LOX-1 (37 and 39%, respectively) yet has kinetics comparably fast versus those of s15-LOX-1 (at pH 6.5, Kcat = 181 ± 6 s(-1) and Kcat/KM = 16 ± 2 μM(-1) s(-1)). LoxA is capable of efficiently catalyzing the peroxidation of a broad range of free fatty acid (FA) substrates (e.g., AA and LA) with high positional specificity, indicating a 15-LOX. Its mechanism includes hydrogen atom abstraction [a kinetic isotope effect (KIE) of >30], yet LoxA is a poor catalyst against phosphoester FAs, suggesting that LoxA is not involved in membrane decomposition. LoxA also does not react with 5- or 15-HETEs, indicating poor involvement in lipoxin production. A LOX high-throughput screen of the LOPAC library yielded a variety of low-micromolar inhibitors; however, none selectively targeted LoxA over the human LOX isozymes. With respect to cellular activity, the level of LoxA expression is increased when P. aeruginosa undergoes the transition to a biofilm mode of growth, but LoxA is not required for biofilm growth on abiotic surfaces. However, LoxA does appear to be required for biofilm growth in association with the host airway epithelium, suggesting a role for LoxA in mediating bacterium-host interactions during colonization.
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Affiliation(s)
- Joshua D Deschamps
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - Abiola F Ogunsola
- Department of Microbiology and Molecular Genetics, University of Pittsburgh , Pittsburgh, Pennsylvania 15219, United States
| | - J Brian Jameson
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - Adam Yasgar
- National Center for Advancing Translational Sciences, National Institutes of Health , 9800 Medical Center Drive, MSC 3370, Bethesda, Maryland 20892, United States
| | - Becca A Flitter
- Department of Microbiology and Molecular Genetics, University of Pittsburgh , Pittsburgh, Pennsylvania 15219, United States
| | - Cody J Freedman
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - Jeffrey A Melvin
- Department of Microbiology and Molecular Genetics, University of Pittsburgh , Pittsburgh, Pennsylvania 15219, United States
| | - Jason V M H Nguyen
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - David J Maloney
- National Center for Advancing Translational Sciences, National Institutes of Health , 9800 Medical Center Drive, MSC 3370, Bethesda, Maryland 20892, United States
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institutes of Health , 9800 Medical Center Drive, MSC 3370, Bethesda, Maryland 20892, United States
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health , 9800 Medical Center Drive, MSC 3370, Bethesda, Maryland 20892, United States
| | - Jennifer M Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh , Pittsburgh, Pennsylvania 15219, United States
| | - Theodore R Holman
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
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12
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Huang J, Li N, Hong W, Zhan K, Yu X, Huang H, Hong M. Conserved tryptophan residues within putative transmembrane domain 6 affect transport function of organic anion transporting polypeptide 1B1. Mol Pharmacol 2013; 84:521-7. [PMID: 23858103 DOI: 10.1124/mol.113.085977] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The organic anion-transporting polypeptides (OATPs, gene symbol SLCO) are a family of transporters that play important roles in the absorption, distribution, metabolism, and excretion of various drugs. Although substrate specificity of transporter proteins is under extensive study, the underlying mechanisms for substrate binding and/or recognition remain largely unknown. Transmembrane domain 6 (TM6) is a relatively conserved region within OATP family members, and several amino acid residues on its extracellular half are part of the OATP family signature sequence D-X-RW-(I,V)-GAWWX-G-(F,L)-L. In the present study, two adjacent tryptophan residues (Trp258 and Trp259) within TM6 were identified as critical amino acids for the transport function of OATP1B1. Kinetic studies showed that substitution of Trp258 with alanine resulted in monophasic kinetics for estrone-3-sulfate uptake, with a significantly higher Km value (Km = 12.0 ± 2.8 μM) than the high-affinity component of wild-type OATP1B1 (Km = 0.38 ± 0.06 μM). On the other hand, W259A retained the biphasic characteristic of the transporter. Km values of the high- and low-affinity components for estrone-3-sulfate of W259A are 1.93 ± 0.76 μM and 30.8 ± 4.4 μM, respectively. Further studies revealed that W258A retained transport function of another prototypic substrate, taurocholate, while W259A displayed a dramatically reduced uptake of the substrate and exhibited an 8-fold increase in the Km value compared with that of the wild-type and W258A. Our results suggest that Trp258 and Trp259 may play different roles in the uptake of different substrates by OATP1B1.
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Affiliation(s)
- Jiujiu Huang
- College of Life Science, South China Agricultural University, Guangzhou, China (J.H., N.L., W.H., K.Z., X.Y., M.H.); and School of Information, University of South Florida, Tampa, Florida (H.H.)
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13
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Chohany LE, Bishop KA, Camic H, Sup SJ, Findeis PM, Clapp CH. Cationic substrates of soybean lipoxygenase-1. Bioorg Chem 2011; 39:94-100. [PMID: 21257189 DOI: 10.1016/j.bioorg.2010.12.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Revised: 12/20/2010] [Accepted: 12/21/2010] [Indexed: 11/18/2022]
Abstract
Soybean lipoxygenase-1 (SBLO-1) catalyzes the oxygenation of 1,4-dienes to produce conjugated diene hydroperoxides. The best substrates are anions of fatty acids; for example, linoleate is converted to 13(S)-hydroperoxy-9(Z),11(E)-octadecadienoate. The manner in which SBLO-1 binds substrates is uncertain. In the present work, it was found that SBLO-1 will oxygenate linoleyltrimethylammonium ion (LTMA) to give primarily13(S)-hydroperoxy-9(Z),11(E)-octadecadienyltrimethylammonium ion. The rate of this process is about the same at pH 7 and pH 9 and is about 30% of the rate observed with linoleate at pH 9. At pH 7, SBLO-1 oxygenates linoleyldimethylamine (LDMA) to give primarily 13(S)-hydroperoxy-9(Z),11(E)-octadecadienyldimethylamine. The oxygenation of LDMA occurs at about the same rate as LTMA at pH 7, but more slowly at pH 9. The results demonstrate that SBLO-1 will readily oxygenate substrates in which the carboxylate of linoleate is replaced with a cationic group, and the products of these reactions have the same stereo- and regiochemistry as the products obtained from fatty acid substrates.
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Affiliation(s)
- Lucas E Chohany
- Department of Chemistry, Bucknell University, Lewisburg, PA 17837, United States
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14
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Osipova EV, Chechetkin IR, Gogolev YV, Tarasova NB. Recombinant maize 9-lipoxygenase: expression, purification, and properties. BIOCHEMISTRY. BIOKHIMIIA 2010; 75:861-5. [PMID: 20673209 DOI: 10.1134/s0006297910070072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Expression of maize 9-lipoxygenase was performed and optimized in Escherichia coli Rosetta(DE3)pLysS. The purity of recombinant protein obtained during Q-Sepharose and Octyl-Sepharose chromatographies in an LP system at 4 degrees C was >95%. Maximum activity of the lipoxygenase reaction was observed at pH 7.5. Enzyme stability was studied at pH 4.5 to 9.5 and in the presence of different compounds: phenylmethanesulfonyl fluoride, beta-mercaptoethanol, ammonium sulfate, and glycerol. HPLC and GC-MS analysis showed that enzyme produced 99% 9S-hydroperoxide from linoleic acid. 13-Hydroperoxide (less than 1%) consisted of S- and R-enantiomers in ratio 2 : 3.
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Affiliation(s)
- E V Osipova
- Kazan Institute of Biochemistry and Biophysics, Kazan Research Center, Russian Academy of Sciences, Russia
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15
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Wecksler AT, Garcia NK, Holman TR. Substrate specificity effects of lipoxygenase products and inhibitors on soybean lipoxygenase-1. Bioorg Med Chem 2009; 17:6534-9. [PMID: 19716306 PMCID: PMC2737062 DOI: 10.1016/j.bmc.2009.08.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Revised: 07/29/2009] [Accepted: 08/04/2009] [Indexed: 11/30/2022]
Abstract
Recently, it has been shown that lipoxygenase (LO) products affect the substrate specificity of human 15-LO. In the current paper, we demonstrate that soybean LO-1 (sLO-1) is not affected by its own products, however, inhibitors which bind the allosteric site, oleyl sulfate (OS) and palmitoleyl sulfate (PS), not only lower catalytic activity, but also change the substrate specificity, by increasing the arachidonic acid (AA)/linoleic acid (LA) ratio to 4.8 and 4.0, respectively. The fact that LO inhibitors can lower activity and also change the LO product ratio is a new concept in lipoxygenase inhibition, where the goal is to not only reduce the catalytic activity but also alter substrate selectivity towards a physiologically beneficial product.
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Affiliation(s)
- Aaron T. Wecksler
- Chemistry and Biochemistry Department, University of California, Santa Cruz, CA 95064 Phone 831-459-5884, FAX 831-459-2935
| | - Natalie K. Garcia
- Chemistry and Biochemistry Department, University of California, Santa Cruz, CA 95064 Phone 831-459-5884, FAX 831-459-2935
| | - Theodore R. Holman
- Chemistry and Biochemistry Department, University of California, Santa Cruz, CA 95064 Phone 831-459-5884, FAX 831-459-2935
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16
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Andreou A, Feussner I. Lipoxygenases - Structure and reaction mechanism. PHYTOCHEMISTRY 2009; 70:1504-10. [PMID: 19767040 DOI: 10.1016/j.phytochem.2009.05.008] [Citation(s) in RCA: 240] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Revised: 05/13/2009] [Accepted: 05/14/2009] [Indexed: 05/20/2023]
Abstract
Lipid oxidation is a common metabolic reaction in all biological systems, appearing in developmentally regulated processes and as response to abiotic and biotic stresses. Products derived from lipid oxidation processes are collectively named oxylipins. Initial lipid oxidation may either occur by chemical reactions or is derived from the action of enzymes. In plants this reaction is mainly catalyzed by lipoxygenase (LOXs) enzymes and during recent years analysis of different plant LOXs revealed insights into their enzyme mechanism. This review aims at giving an overview of concepts explaining the catalytic mechanism of LOXs as well as the different regio- and stereo-specificities of these enzymes.
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Affiliation(s)
- Alexandra Andreou
- Georg-August-University, Albrecht-von-Haller-Institute for Plant Science, Department of Plant Biochemistry, D-37077 Göttingen, Germany
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17
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Wecksler AT, Jacquot C, van der Donk WA, Holman TR. Mechanistic investigations of human reticulocyte 15- and platelet 12-lipoxygenases with arachidonic acid. Biochemistry 2009; 48:6259-67. [PMID: 19469483 DOI: 10.1021/bi802332j] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human reticulocyte 15-lipoxygenase-1 (15-hLO-1) and human platelet 12-lipoxygenase (12-hLO) have been implicated in a number of diseases, with differences in their relative activity potentially playing a central role. In this work, we characterize the catalytic mechanism of these two enzymes with arachidonic acid (AA) as the substrate. Using variable-temperature kinetic isotope effects (KIE) and solvent isotope effects (SIE), we demonstrate that both k(cat)/K(M) and k(cat) for 15-hLO-1 and 12-hLO involve multiple rate-limiting steps that include a solvent-dependent step and hydrogen atom abstraction. A relatively low k(cat)/K(M) KIE of 8 was determined for 15-hLO-1, which increases to 18 upon the addition of the allosteric effector molecule, 12-hydroxyeicosatetraenoic acid (12-HETE), indicating a tunneling mechanism. Furthermore, the addition of 12-HETE lowers the observed k(cat)/K(M) SIE from 2.2 to 1.4, indicating that the rate-limiting contribution from a solvent sensitive step in the reaction mechanism of 15-hLO-1 has decreased, with a concomitant increase in the C-H bond abstraction contribution. Finally, the allosteric binding of 12-HETE to 15-hLO-1 decreases the K(M)[O(2)] for AA to 15 microM but increases the K(M)[O(2)] for linoleic acid (LA) to 22 microM, such that the k(cat)/K(M)[O(2)] values become similar for both substrates (approximately 0.3 s(-1) microM(-1)). Considering that the oxygen concentration in cancerous tissue can be less than 5 microM, this result may have cellular implications with respect to the substrate specificity of 15-hLO-1.
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Affiliation(s)
- Aaron T Wecksler
- Chemistry and Biochemistry Department, University of California, Santa Cruz, California 95064, USA
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18
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Chechetkin IR, Osipova EV, Tarasova NB, Mukhitova FK, Hamberg M, Gogolev YV, Grechkin AN. Specificity of oxidation of linoleic acid homologs by plant lipoxygenases. BIOCHEMISTRY. BIOKHIMIIA 2009; 74:855-61. [PMID: 19817685 DOI: 10.1134/s0006297909080069] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The lipoxygenase-catalyzed oxidation of linoleic acid homologs was studied. While the linoleic acid oxidation by maize 9-lipoxygenase (9-LO) specifically produced (9S)-hydroperoxide, the dioxygenation of (11Z,14Z)-eicosadienoic (20:2) and (13Z,16Z)-docosadienoic (22:2) acids by the same enzyme lacked regio- and stereospecificity. The oxidation of 20:2 and 22:2 by 9-LO afforded low yields of racemic 11-, 12-, 14-, and 15-hydroperoxides or 13- and 17-hydroperoxides, respectively. Soybean 13-lipoxygenase-1 (13-LO) specifically oxidized 20:2, 22:2, and linoleate into (omega6S)-hydroperoxides. Dioxygenation of (9Z,12Z)-hexadecadienoic acid (16:2) by both 9-LO and 13-LO occurred specifically, affording (9S)- and (13S)-hydroperoxides, respectively. The data are consistent with the "pocket theory of lipoxygenase catalysis" (i.e. with the penetration of a substrate into the active center with the methyl end first). Our findings also demonstrate that the distance between carboxyl group and double bonds substantially determines the positioning of substrates within the active site.
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Affiliation(s)
- I R Chechetkin
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Center, Russian Academy of Sciences, Kazan, 420111, Russia.
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19
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Jacquot C, Peng S, van der Donk WA. Kinetic isotope effects in the oxidation of arachidonic acid by soybean lipoxygenase-1. Bioorg Med Chem Lett 2008; 18:5959-62. [PMID: 18793849 PMCID: PMC2652760 DOI: 10.1016/j.bmcl.2008.08.108] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Revised: 08/23/2008] [Accepted: 08/26/2008] [Indexed: 11/22/2022]
Abstract
The reaction of soybean lipoxygenase-1 with linoleic acid has been extensively studied and displays very large kinetic isotope effects. In this work, substrate and solvent kinetic isotope effects as well as the viscosity dependence of the oxidation of arachidonic acid were investigated. The hydrogen atom abstraction step was rate-determining at all temperatures, but was partially masked by a viscosity-dependent step at ambient temperatures. The observed KIEs on k(cat) were large ( approximately 100 at 25 degrees C).
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Affiliation(s)
- Cyril Jacquot
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, 600 S. Mathews Avenue, Urbana, IL 61801, USA
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20
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Somvanshi RK, Singh AK, Saxena M, Mishra B, Dey S. Development of novel peptide inhibitor of Lipoxygenase based on biochemical and BIAcore evidences. BIOCHIMICA ET BIOPHYSICA ACTA 2008; 1784:1812-7. [PMID: 18691678 DOI: 10.1016/j.bbapap.2008.07.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2008] [Revised: 06/19/2008] [Accepted: 07/07/2008] [Indexed: 10/21/2022]
Abstract
Lipoxygenase (LOX) are enzymes implicated in a broad range of inflammatory diseases, cancer, asthma and atherosclerosis. These diverse biological properties lead to the interesting target for the inhibition of this metabolic pathway of LOX. The drugs available in the market against LOX reported to have various side effects. To develop potent and selective therapeutic agents against LOX, it is essential to have the knowledge of its active site. Due to the lack of structural data of human LOX, researchers are using soybean LOX (sLOX) because of their availability and similarities in the active site structure. Based on the crystal structure of sLOX-3 and its complex with known inhibitors, we have designed a tripeptide, FWY which strongly inhibits sLOX-3 activity. The inhibition by peptide has been tested with purified sLOX-3 and with LOX present in blood serum of breast cancer patients in the presence of substrate linoleic acid and arachidonic acid respectively. The dissociation constant (K(D)) of the peptide with sLOX-3 as determined by Surface Plasmon Resonance (SPR) was 3.59x10(-9) M. The kinetic constant (K(i)) and IC(50), as determined biochemical methods were 7.41x10(-8) M and 0.15x10(-6) M respectively.
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Affiliation(s)
- Rishi Kumar Somvanshi
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110 029, India
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21
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Wecksler AT, Kenyon V, Deschamps JD, Holman TR. Substrate specificity changes for human reticulocyte and epithelial 15-lipoxygenases reveal allosteric product regulation. Biochemistry 2008; 47:7364-75. [PMID: 18570379 DOI: 10.1021/bi800550n] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Human reticulocyte 15-lipoxygenase (15-hLO-1) and epithelial 15-lipoxygenase (15-hLO-2) have been implicated in a number of human diseases, with differences in their substrate specificity potentially playing a central role. In this paper, we present a novel method for accurately measuring the substrate specificity of the two 15-hLO isozymes and demonstrate that both cholate and specific LO products affect substrate specificity. The linoleic acid (LA) product, 13-hydroperoxyoctadienoic acid (13-HPODE), changes the ( k cat/ K m) (AA)/( k cat/ K m) (LA) ratio more than 5-fold for 15-hLO-1 and 3-fold for 15-hLO-2, while the arachidonic acid (AA) product, 12-( S)-hydroperoxyeicosatetraenoic acid (12-HPETE), affects only the ratio of 15-hLO-1 (more than 5-fold). In addition, the reduced products, 13-( S)-hydroxyoctadecadienoic acid (13-HODE) and 12-( S)-hydroxyeicosatetraenoic acid (12-HETE), also affect substrate specificity, indicating that iron oxidation is not responsible for the change in the ( k cat/ K m) (AA)/( k cat/ K m) (LA) ratio. These results, coupled with the dependence of the 15-hLO-1 k cat/ K m kinetic isotope effect ( (D) k cat/ K m) on the presence of 12-HPETE and 12-HETE, indicate that the allosteric site, previously identified in 15-hLO-1 [Mogul, R., Johansen, E., and Holman, T. R. (1999) Biochemistry 39, 4801-4807], is responsible for the change in substrate specificity. The ability of LO products to regulate substrate specificity may be relevant with respect to cancer progression and warrants further investigation into the role of this product-feedback loop in the cell.
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Affiliation(s)
- Aaron T Wecksler
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
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22
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Pudney CR, Hay S, Pang J, Costello C, Leys D, Sutcliffe MJ, Scrutton NS. Mutagenesis of morphinone reductase induces multiple reactive configurations and identifies potential ambiguity in kinetic analysis of enzyme tunneling mechanisms. J Am Chem Soc 2007; 129:13949-56. [PMID: 17939663 DOI: 10.1021/ja074463h] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have identified multiple reactive configurations (MRCs) of an enzyme-coenzyme complex that have measurably different kinetic properties. In the complex formed between morphinone reductase (MR) and the NADH analogue 1,4,5,6-tetrahydro-NADH (NADH4) the nicotinamide moiety is restrained close to the FMN isoalloxazine ring by hydrogen bonds from Asn-189 and His-186 as determined from the X-ray crystal structure. Molecular dynamic simulations indicate that removal of one of these hydrogen bonds in the N189A MR mutant allows the nicotinamide moiety to occupy a region of configurational space not accessible in wild-type enzyme. Using stopped-flow spectroscopy, we show that reduction of the FMN cofactor by NADH in N189A MR is multiphasic, identifying at least four different reactive configurations of the MR-NADH complex. This contrasts with wild-type MR in which hydride transfer occurs by environmentally coupled tunneling in a single kinetic phase [Pudney et al. J. Am. Chem. Soc. 2006, 128, 14053-14058]. Values for primary and alpha-secondary kinetic isotope effects, and their temperature dependence, for three of the kinetic phases in the N189A MR are consistent with hydride transfer by tunneling. Our analysis enables derivation of mechanistic information concerning different reactive configurations of the same enzyme-coenzyme complex using ensemble stopped-flow methods. Implications for the interpretation from kinetic data of tunneling mechanisms in enzymes are discussed.
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Affiliation(s)
- Christopher R Pudney
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester, M1 7DN, U.K
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23
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Camargo AB, Marchevsky E, Luco JM. QSAR study for the soybean 15-lipoxygenase inhibitory activity of organosulfur compounds derived from the essential oil of garlic. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2007; 55:3096-103. [PMID: 17367159 DOI: 10.1021/jf063020e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
In this study, multiple linear regression (MLR) and partial least-squares (PLS) techniques were used for modeling the soybean 15-lipoxygenase inhibitory activity of a varied group of mono-, di-, and trisulfides derived from the essential oil of garlic. The structures of the compounds under study were characterized by means of calculated physicochemical parameters and several nonempirical descriptors, such as topological, geometrical, and quantum chemical indices. The results obtained indicate that the inhibitory activity is strongly dependent on the ability of the compounds to participate in dispersive interactions with the enzyme, as expressed by the solvent-accessible surface area (SASA) and the average distance/distance degree descriptor (ADDD) index. On the other hand, the high contribution of the lowest unoccupied molecular orbit term (LUMO) in the PLS models derived for the di- and trisulfides suggests that the solute's electron-acceptor capacity plays a fundamental role in the inhibitory activity exhibited for these compounds. Finally, the geometric features as expressed by the shape parameters included in the models indicate a low but not negligible positive contribution of molecular linearity in the enzyme-inhibitor binding. In summary, the developed quantitative structure-activity relationship approach successfully accounts for the potencies of organosulfur compounds acting on soybean 15-lipoxygenase and thereby offers both a guide for the synthesis of new compounds and a hypothesis for the molecular basis of their activity.
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Affiliation(s)
- Alejandra B Camargo
- Laboratorio de AnAlisis de Residuos Tóxicos, Facultad de Ciencia Agrarias, Universidad Nacional de Cuyo, Alte. Brown 500, Chacras de Coria 5505 Mendoza, Argentina
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24
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Tejero I, Garcia-Viloca M, Gonzalez-Lafont A, Lluch JM, York DM. Enzyme dynamics and tunneling enhanced by compression in the hydrogen abstraction catalyzed by soybean lipoxygenase-1. J Phys Chem B 2006; 110:24708-19. [PMID: 17134234 DOI: 10.1021/jp066263i] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A fully microscopical simulation of the rate-limiting hydrogen abstraction catalyzed by soybean lipoxygenase-1 (SLO-1) has been carried out. This enzyme exhibits the largest, and weakly temperature dependent, experimental H/D kinetic isotope effect (KIE) reported for a biological system. The theoretical model used here includes the complete enzyme with a solvation shell of water molecules, the Fe(III)-OH- cofactor, and the linoleic acid substrate. We have used a hybrid QM(PM3/d-SRP)/MM method to describe the potential energy surface of the whole system, and the ensemble-averaged variational transition-state theory with multidimensional tunneling (EA-VTST/MT) to calculate the rate constant and the primary KIE. The computational results show that the compression of the wild-type active site enzyme results in the huge contribution of tunneling (99%) to the rate of the hydrogen abstraction. Importantly, the active site becomes more flexible in the Ile553Ala mutant reactant complex simulation (for which a markedly temperature dependent KIE has been experimentally determined), thus justifying the proposed key role of the gating promoting mode in the reaction catalyzed by SLO-1. Finally, the results indicate that the calculated KIE for the wild-type enzyme has an important dependence on the barrier width.
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Affiliation(s)
- Ismael Tejero
- Departament de Química and Institut de Biotecnologia i de Biomedicina, Universitat Autonoma de Barcelona, 08193, Bellaterra (Barcelona), Spain
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25
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Wu F, Gaffney BJ. Dynamic behavior of fatty acid spin labels within a binding site of soybean lipoxygenase-1. Biochemistry 2006; 45:12510-8. [PMID: 17029406 PMCID: PMC2515559 DOI: 10.1021/bi061415l] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The putative substrate-binding site in lipoxygenases is long and internal. There is little direct evidence about how the unsaturated fatty acid substrates enter and move within the cavity to position themselves correctly for electron transfer reactions with the catalytic non-heme iron. An EPR spectroscopy approach, with spin-labeled fatty acids, is taken here to investigate dynamic behavior of fatty acids bound to soybean lipoxygenase-1. The probes are labeled on C5, C8, C10, C12, and C16 of stearic acid. The EPR-determined affinity for the enzyme increases as the length of the alkyl end of the probe increases, with a DeltaDeltaG of -190 cal/methylene. The probes in the series exhibit similar enhanced paramagnetic relaxation by the iron center. These results indicate that the members of the series have a common binding site. All of the bound probes undergo considerable local mobility. The stearate spin-labeled at C5 has the highest affinity for the lipoxygenase, and it is a competitive inhibitor, with a K(i) of 9 muM. Surprisingly, this stearate labeled near the carboxyl end undergoes more local motion than those labeled in the middle of the chain, when it is bound. This shows that the carboxyl end of the fatty-acid spin label is not rigidly docked on the protein. During catalysis, repositioning of the substrate carboxyl on the protein surface may be coupled to motion of portions of the chain undergoing reaction.
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Affiliation(s)
- Fayi Wu
- Department of Biological Sciences, BIO Unit I, Florida State University, Tallahassee, FL 32306-4370.
| | - Betty J. Gaffney
- Department of Biological Sciences, BIO Unit I, Florida State University, Tallahassee, FL 32306-4370.
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26
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Terp N, Göbel C, Brandt A, Feussner I. Lipoxygenases during Brassica napus seed germination. PHYTOCHEMISTRY 2006; 67:2030-40. [PMID: 16884747 DOI: 10.1016/j.phytochem.2006.06.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2006] [Revised: 06/18/2006] [Accepted: 06/19/2006] [Indexed: 05/11/2023]
Abstract
The peroxidation of polyunsaturated fatty acids is mostly catalyzed by members of the lipoxygenase enzyme family. Lipoxygenase products can be metabolized further in the oxylipin pathway and are known as signalling substances that play a role in plant development as well as in plant responses to wounding and pathogen attack. Apart from accumulating data in model plants like Arabidopsis, information on the relevance of lipid peroxide metabolism in the crop plant oilseed rape is scarce. Thus we aimed to analyze lipoxygenases and oxylipin patterns in seedlings of oilseed rape. RNA isolated from 3 day etiolated seedlings contains mRNAs for at least two different lipoxygenases. These have been cloned as cDNAs and named Bn-Lox-1fl and Bn-Lox-2fl. The protein encoded by Bn-Lox-2fl was identified as a 13-lipoxygenase by expression in Escherichia coli. The Bn-Lox-1fl yielded an inactive protein when expressed in E. coli. Based on Bn-Lox-1fl active site determinants and on sequence homology the Bn-Lox-1fl is most likely a 9-lipoxygenase. Both genes are expressed in light-grown and etiolated cotyledons as well as in leaves. Bn-Lox-2fl protein is more abundant in cotyledons of etiolated seedlings than in cotyledons of green seedlings. Both 13- and 9-lipoxygenase-derived hydroperoxides can be detected during germination. Etiolated seedlings contain more lipoxygenase-derived hydroperoxides in non esterified fatty acids than green seedlings. The 13-lipoxygenase derivatives are 6-8-fold more abundant than the 9-derivatives. Lipoxygenase-derived hydroperoxides in esterified lipids are almost not present during germination. These results suggest that 13-lipoxygenases acting on free fatty acids dominate during B. napus seed germination.
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Affiliation(s)
- Nina Terp
- Carlsberg Laboratory, Department of Physiology, Gamle Carlsberg Vej 10, DK-2500 Copenhagen, Denmark
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27
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Pu J, Gao J, Truhlar DG. Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions. Chem Rev 2006; 106:3140-69. [PMID: 16895322 PMCID: PMC4478620 DOI: 10.1021/cr050308e] [Citation(s) in RCA: 288] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jingzhi Pu
- Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Jiali Gao
- Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
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Kenyon V, Chorny I, Carvajal WJ, Holman TR, Jacobson MP. Novel human lipoxygenase inhibitors discovered using virtual screening with homology models. J Med Chem 2006; 49:1356-63. [PMID: 16480270 DOI: 10.1021/jm050639j] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the discovery of new, low micromolar, small molecule inhibitors of human platelet-type 12- and reticulocyte 15-lipoxygenase-1 (12-hLO and 15-hLO) using structure-based methods. Specifically, we created homology models of 12-hLO and 15-hLO, based on the structure of rabbit 15-lipoxygenase, for in silico screening of a large compound library followed by in vitro screening of 20 top scoring molecules. Eight of these compounds inhibited either 12- or 15-human lipoxygenase with lower than 100 microM affinity. Of these, we obtained IC50 values for the three best inhibitors, all of which displayed low micromolar inhibition. One compound showed specificity for 15-hLO versus 12-hLO; however, a selective inhibitor for 12-hLO was not identified. As a control we screened 20 randomly selected compounds, of which none showed low micromolar inhibition. The new low-micromolar inhibitors appear to be suitable as leads for further inhibitor development efforts against 12-hLO and 15-hLO, based on the fact their size and chemical properties are appropriate to classify them as drug-like compounds. The models of these protein-inhibitor complexes suggest strategies for future development of selective lipoxygenase inhibitors.
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Affiliation(s)
- Victor Kenyon
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143-2240, USA
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Coffa G, Imber AN, Maguire BC, Laxmikanthan G, Schneider C, Gaffney BJ, Brash AR. On the relationships of substrate orientation, hydrogen abstraction, and product stereochemistry in single and double dioxygenations by soybean lipoxygenase-1 and its Ala542Gly mutant. J Biol Chem 2005; 280:38756-66. [PMID: 16157595 PMCID: PMC1351262 DOI: 10.1074/jbc.m504870200] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recent findings associate the control of stereochemistry in lipoxygenase (LOX) catalysis with a conserved active site alanine for S configuration hydroperoxide products, or a corresponding glycine for R stereoconfiguration. To further elucidate the mechanistic basis for this stereocontrol we compared the stereoselectivity of the initiating hydrogen abstraction in soybean LOX-1 and an Ala542Gly mutant that converts linoleic acid to both 13S and 9R configuration hydroperoxide products. Using 11R-(3)H- and 11S-(3)H-labeled linoleic acid substrates to examine the initial hydrogen abstraction, we found that all the primary hydroperoxide products were formed with an identical and highly stereoselective pro-S hydrogen abstraction from C-11 of the substrate (97-99% pro-S-selective). This strongly suggests that 9R and 13S oxygenations occur with the same binding orientation of substrate in the active site, and as the equivalent 9R and 13S products were formed from a bulky ester derivative (1-palmitoyl-2-linoleoylphosphatidylcholine), one can infer that the orientation is tail-first. Both the EPR spectrum and the reaction kinetics were altered by the R product-inducing Ala-Gly mutation, indicating a substantial influence of this Ala-Gly substitution extending to the environment of the active site iron. To examine also the reversed orientation of substrate binding, we studied oxygenation of the 15S-hydroperoxide of arachidonic acid by the Ala542Gly mutant soybean LOX-1. In addition to the usual 5S, 15S- and 8S, 15S-dihydroperoxides, a new product was formed and identified by high-performance liquid chromatography, UV, gas chromatography-mass spectrometry, and NMR as 9R, 15S-dihydroperoxyeicosa-5Z,7E,11Z,13E-tetraenoic acid, the R configuration "partner" of the normal 5S,15S product. This provides evidence that both tail-first and carboxylate end-first binding of substrate can be associated with S or R partnerships in product formation in the same active site.
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Affiliation(s)
- Gianguido Coffa
- From the Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, U.S.A., and
| | | | | | - Gurunathan Laxmikanthan
- Chemistry & Biochemistry (Institute of Molecular Biophysics), Florida State University, Tallahassee, FL, 32306, U.S.A
| | - Claus Schneider
- From the Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, U.S.A., and
| | | | - Alan R. Brash
- From the Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, U.S.A., and
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