| 1. |
- Benediktsdottir, Andrea, et al.
(författare)
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Design, synthesis, and in vitro biological evaluation of meta-sulfonamidobenzamide-based antibacterial LpxH inhibitors
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- New antibacterial compounds are urgently needed, especially for infections caused by the top-priority Gram-negative bacteria that are increasingly difficult to treat. Lipid A is a key component of the Gram-negative outer membrane and the LpxH enzyme plays an important role in its biosynthesis, making it an ideal antibacterial target. Inspired by previously reported ortho-N-methyl-sulfonamidobenzamide-based LpxH inhibitors, novel benzamide substitutions were explored in this work to assess their in vitro activity. Our findings reveal that maintaining wild-type antibacterial activity necessitates N-methyl removal when shifting the ortho-N-methyl-sulfonamide to the meta-position. This discovery led to the synthesis of meta-sulfonamidobenzamide analogs with potent antibacterial activity and enzyme inhibition. Moreover, we demonstrate that modifying the benzamide scaffold can alter hERG blocking. Furthermore, a LpxH-bound X-ray structure of the meta-sulfonamidobenzamide analog facilitated comparison with complexes with ortho-N-methyl-sulfonamidobenzamide analogs, and with the natural enzymatic reaction product lipid X, providing new insights into the enzyme-ligand interactions. Overall, our study has identified meta-sulfonamidobenzamide derivatives as promising LpxH-targeting hits with the potential for optimization in future antibacterial hit-to-lead programs.
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| 2. |
- Chofor, Rene, et al.
(författare)
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Synthesis and Bioactivity of beta-Substituted Fosmidomycin Analogues Targeting 1-Deoxy-D-xylulose-5-phosphate Reductoisomerase
- 2015
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Ingår i: Journal of Medicinal Chemistry. - : American Chemical Society (ACS). - 0022-2623 .- 1520-4804. ; 58:7, s. 2988-3001
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Tidskriftsartikel (refereegranskat)abstract
- Blocking the 2-C-methyl-d-erythrithol-4-phosphate (MEP) pathway for isoprenoid biosynthesis offers interesting prospects for inhibiting Plasmodium or Mycobacterium spp. growth. Fosmidomycin (1) and its homologue FR900098 (2) potently inhibit 1-deoxy-d-xylulose-5-phosphate reductoisomerase (Dxr), a key enzyme in this pathway. Here we introduced aryl or aralkyl substituents at the beta-position of the hydroxamate analogue of 2. While direct addition of a beta-aryl moiety resulted in poor inhibition, longer linkers between the carbon backbone and the phenyl ring were generally associated with better binding to the enzymes. X-ray structures of the parasite Dxr-inhibitor complexes show that the longer compounds generate a substantially different flap structure, in which a key tryptophan residue is displaced, and the aromatic group of the ligand lies between the tryptophan and the hydroxamates methyl group. Although the most promising new Dxr inhibitors lack activity against Escherichia coli and Mycobacterium smegmatis, they proved to be highly potent inhibitors of Plasmodium falciparum in vitro growth.
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| 3. |
- Dubey, Mukesh, et al.
(författare)
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The glyoxylate cycle is involved in pleotropic phenotypes, antagonism and induction of plant defence responses in the fungal biocontrol agent Trichoderma atroviride
- 2013
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845 .- 1096-0937. ; 58-59, s. 33-41
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Tidskriftsartikel (refereegranskat)abstract
- Isocitrate lyase (ICL), a signature enzyme of the glyoxylate cycle, is required for metabolism of non-fermentable carbon compounds like acetate or ethanol, and virulence in bacteria and fungi. In the present study, we investigate the role of the glyoxylate cycle in the fungal biocontrol agent Trichoderma atroviride by generating id deletion and complementation mutants. Phenotypic analyses of the deletion mutant Delta icl suggest that ICL is required for normal growth, conidial pigmentation and germination, and abiotic stress tolerance. The Delta icl strain display reduced antagonism towards Botrytis cinerea in plate confrontation assays. Secretion and sandwich assays further show that secreted factors are partly responsible for the reduced antagonism. Furthermore, in vitro root colonization assays shows that the Delta icl strain retains the ability to internally colonize Arabidopsis thaliana roots. However, the Delta icl strain has a reduced ability to induce systemic defence in A. thaliana leaves that results in reduced protection against B. cinerea. These data shows that ICL and the glyoxylate cycle are important for biocontrol traits in T. atroviride, including direct antagonism and induction of defence responses in plants.
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| 4. |
- Hsiao, An-Shan, et al.
(författare)
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Arabidopsis cytosolic acyl-CoA-binding proteins ACBP4, ACBP5 and ACBP6 have overlapping but distinct roles in seed development
- 2014
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Ingår i: Bioscience Reports. - 0144-8463 .- 1573-4935. ; 34:6, s. 865-877
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Tidskriftsartikel (refereegranskat)abstract
- Eukaryotic cytosolic ACBPs (acyl-CoA-binding proteins) bind acyl-CoA esters and maintain a cytosolic acyl-CoA pool, but the thermodynamics of their protein-lipid interactions and physiological relevance in plants are not well understood. Arabidopsis has three cytosolic ACBPs which have been identified as AtACBP4, AtACBP5 and AtACBP6, and microarray data indicated that all of them are expressed in seeds; AtACBP4 is expressed in early embryogenesis, whereas AtACBP5 is expressed later. ITC (isothermal titration calorimetry) in combination with transgenic Arabidopsis lines were used to investigate the roles of these three ACBPs from Arabidopsis thaliana. The dissociation constants, stoichiometry and enthalpy change of AtACBP interactions with various acyl-CoA esters were determined using ITC. Strong binding of recombinant (r) AtACBP6 with long-chain acyl-CoA (C16-to C18-CoA) esters was observed with dissociation constants in the nanomolar range. However, the affinity of rAtACBP4 and rAtACBP5 to these acyl-CoA esters was much weaker (dissociation constants in the micromolar range), suggesting that they interact with acyl-CoA esters differently from rAtACBP6. When transgenic Arabidopsis expressing AtACBP6pro::GUS was generated, strong GUS (beta-glucuronidase) expression in cotyledonary-staged embryos and seedlings prompted us to measure the acyl-CoA contents of the acbp6 mutant. This mutant accumulated higher levels of C18:1-CoA and C18:1- and C18:2-CoAs in cotyledonary-staged embryos and seedlings, respectively, in comparison with the wild type. The acbp4acbp5acbp6 mutant showed the lightest seed weight and highest sensitivity to abscisic acid during germination, suggesting their physiological functions in seeds.
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| 5. |
- Jansson, Anna, 1979-, et al.
(författare)
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DXR Inhibition by Potent Mono- and Disubstituted Fosmidomycin Analogues
- 2013
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Ingår i: Journal of Medicinal Chemistry. - : American Chemical Society (ACS). - 0022-2623 .- 1520-4804. ; 56:15, s. 6190-6199
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Tidskriftsartikel (refereegranskat)abstract
- The antimalarial compound fosmidomycin targets DXR, the enzyme that catalyzes the first committed step in the MEP pathway producing the universally essential isoprenoid precursors, isopentenyl diphosphate and dimethylallyl diphosphate. The MEP pathway is used by a number of pathogens, including Mycobacterium tuberculosis and apicomplexan parasites, and differs from the classical mevalonate pathway that is essential in humans. Using a structure-based approach, we designed a number of analogues of fosmidomycin, including a series that are substituted in both the Cα and the hydroxamate positions. The latter proved to be a stable framework for the design of inhibitors that extend from the cramped substrate-binding site and can, for the first time, bridge the substrate and cofactor binding sites. A number of these compounds are more potent than fosmidomycin in terms of killing Plasmodium falciparum in an in vitro assay; the best has an IC50 of 40 nM.
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| 6. |
- Lu, Lu, 1984-, et al.
(författare)
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MEPicides : α,β-Unsaturated Fosmidomycin N-acyl Analogsas inhibitors that selectively target DXR from Plasmodium falciparum, the deadliest causative parasite of human Malaria
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Fosmidomycin and FR-9000098 have been confirmed to show parasiticidal activity against Plasmodium falciparum, targeting DXR involved in the MEP pathway. We designed a construct of PfDXR that has successfully been overexpressed in E. coli BL21(DE3) C43, and purified by IMAC and SEC, with the final yield of 1.2 mg/ 8 L culture. PfDXR was concentrated to 20 mg/ml, and co-crystallized with previously tested inhibitors in the FR-9000098 scaffold in the presence of Mn2+. Three FR-9000098 analogues with double-bonded Ca-Cband/or a phenyl ring with various lengths to N1, showed inhibitory activities with IC50s roughly 50 nM. Three crystals were in triclinic P1space group, with similar dimensions in the unit cell (51Å, 56Å, 86Å, 103°, 103°, 101°). All four complex structures have been crystallographically determined at resolutions in the range 1.86 Å, 2.45 Å, 2.13Å, 2.05 Å. Given the high similarity in structures, the initial phases were determined by rigid body refinement with search model PfDXR-FN3 complex, followed by restrained refinement in refmac5. Subsequently, the ligands and surrounding amino acid residues were manually rebuilt with theqdstools in O. the Ca-Cbbonds of the three ligands were altered from a single to double bond based on the structure of FR9000098. In addition, two ligands were extended at the Cdwith a phenyl group, and with the benzyl group connected by two carbons. N-terminal NADPH binding domains from four complexes undergo minor rigid body movement, and more details of conformational changes in the flap region are discussed.
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| 7. |
- Sooriyaarachchi, Sanjeewani, et al.
(författare)
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A new class of Scots pine antimicrobial proteins, which act by binding beta-glucan
- 2011
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Konferensbidrag (refereegranskat)abstract
- Scots pine (Pinus sylvestris) produces several small, highly homologous, disulfide-rich proteins (Sp-AMPs) in response to fungal pathogenic attacks. We report here the expression, structure and function of these proteins. One of the Sp-AMPs was cloned into and over-expressed in Pichia pastoris. The purified protein shows antifungal activity against Heterobasidion annosum, causing morphological changes in spores and hyphae. Binding studies revealed that it binds to soluble and insoluble beta-(1,3)-glucans, major components of the fungal cell wall, with high affinity. Homology modeling studies suggest a Greek-key-beta-barrel fold having a conserved patch on the surface that can accommodate at least 4 sugar units. We conclude that these proteins represent a new class of antimicrobial proteins that can be classified as pathogenesis related (PR) protein family 18.
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| 8. |
- Sooriyaarachchi, Sanjeewani, et al.
(författare)
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Conformational Changes and Ligand Recognition of Escherichia coli d-Xylose Binding Protein Revealed
- 2010
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Ingår i: Journal of Molecular Biology. - : Elsevier BV. - 0022-2836 .- 1089-8638. ; 402:4, s. 657-668
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Tidskriftsartikel (refereegranskat)abstract
- ABC transport systems account for most import of necessary nutrients in bacteria. The periplasmic binding component (or an equivalent membrane-anchored protein) is critical to recognizing the cognate ligand and directing it to the appropriate membrane permease. Here we report X-ray structures of D-xylose-binding protein from Escherichia coli in ligand-free open, ligand-bound open and ligand-bound closed forms, at 2.15, 2.2, and 2.2-Å resolution, respectively. The ligand-bound open form is the first such structure to be reported at high resolution; the combination of the three different forms from the same protein furthermore gives unprecedented detail concerning the conformational changes involved in binding protein function. As is typical for the structural family, the protein has two similar globular domains, which are connected by a three-stranded hinge region. The open liganded structure shows that xylose binds first to the C-terminal domain, with only very small conformational changes resulting. After a 34° closing motion, additional interactions are formed with the N-terminal domain; changes in this domain are larger, and serve to make the structure more ordered near the ligand. An analysis of the interactions suggests why xylose is the preferred ligand. Further, a comparison with the most closely related proteins in the structural family shows that the conformational changes are distinct in each type of binding protein, which may have implications for how the individual proteins act in concert with their respective membrane permeases.
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| 9. |
- Sooriyaarachchi, Sanjeewani, et al.
(författare)
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Expression and beta-glucan binding properties of Scots pine (Pinus sylvestris L.) antimicrobial protein (Sp-AMP)
- 2011
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Ingår i: Plant Molecular Biology. - : Springer Science and Business Media LLC. - 0167-4412 .- 1573-5028. ; 77:1-2, s. 33-45
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Tidskriftsartikel (refereegranskat)abstract
- Scots pine (Pinus sylvestris) secretes a number of small, highly-related, disulfide-rich proteins (Sp-AMPs) in response to challenges with fungal pathogens such as Heterobasidion annosum, although their biological role has been unknown. Here, we examined the expression patterns of these genes, as well as the structure and function of the encoded proteins. Northern blots and quantitative real time PCR showed increased levels of expression that are sustained during the interactions of host trees with pathogens, but not non-pathogens, consistent with a function in conifer tree defenses. Furthermore, the genes were up-regulated after treatment with salicylic acid and an ethylene precursor, 1-aminocyclopropane-1-carboxylic-acid, but neither methyl jasmonate nor H(2)O(2) induced expression, indicating that Sp-AMP gene expression is independent of the jasmonic acid signaling pathways. The cDNA encoding one of the proteins was cloned and expressed in Pichia pastoris. The purified protein had antifungal activity against H. annosum, and caused morphological changes in its hyphae and spores. It was directly shown to bind soluble and insoluble beta-(1,3)-glucans, specifically and with high affinity. Furthermore, addition of exogenous glucan is linked to higher levels of Sp-AMP expression in the conifer. Homology modeling and sequence comparisons suggest that a conserved patch on the surface of the globular Sp-AMP is a carbohydrate-binding site that can accommodate approximately four sugar units. We conclude that these proteins belong to a new family of antimicrobial proteins (PR-19) that are likely to act by binding the glucans that are a major component of fungal cell walls.
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| 10. |
- Sooriyaarachchi, Sanjeewani
(författare)
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Structural studies of sugar binding proteins
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Binding proteins, which are themselves non-enzymatic, play an important role in enzymatic reactions as well as non-enzymatic processes by providing a binding platform for the specific recognition of particular molecules. For example, periplasmic binding proteins play a vital role in nutrient uptake in Gram-negative bacteria. In the present study, three sugar binding proteins, including two periplasmic binding proteins and a β-glucan binding protein, are described. The glucose/galactose binding protein in complex with (2R)-glyceryl-β-D-galactopyranoside, another physiologically relevant ligand for the protein, was revealed. The structure was solved using the molecular replacement method and refined to 1.87 Å with R and R free values 17% and 22%. The structure displays the closest form among the available glucose/galactose binding protein structures with three additional binding residues, which are conserved among the group. We also present three different conformations of E. coli xylose binding protein structures, open ligand free, open liganded and closed liganded. This is the first structure of the open liganded form in the pentose/hexose sugar-binding cluster. The structures were solved using molecular replacement method and refined to 2.15 Å, 2.1 Å and to 2.2 Å respectively. The new family of antimicrobial protein, secreted upon fungal attacks from Pinus sylvestris was present here with the binding and activity assays. The inhibition of vegetative growth and the spore germination of the causative agent of the disease, root and butt rot was proved with low concentrations of the peptide. The assays determined its ability to bind with β-(1,3)-D-glucans. The homology model was made using the PDB structure 1C01, the antimicrobial protein from Macadamia integrifolia, which has 64% sequence identity.
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