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The AEROPATH project targeting Pseudomonas aeruginosa: crystallographic studies for assessment of potential targets in early-stage drug discovery.

Moynie L, Schnell R, McMahon SA, Sandalova T, Boulkerou WA, Schmidberger JW, Alphey M, Cukier C, Duthie F, Kopec J, Liu H, Jacewicz A, Hunter WN, Naismith JH, Schneider G - Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. (2012)

Bottom Line: A major concern is Gram-negative bacteria, for which the discovery of new antimicrobial drugs has been particularly scarce.The crystal structures of eight of these targets, ranging from hypothetical unknown proteins to metabolic enzymes from different functional classes (PA1645, PA1648, PA2169, PA3770, PA4098, PA4485, PA4992 and PA5259), are reported here.The structural information is expected to provide a firm basis for the improvement of hit compounds identified from fragment-based and high-throughput screening campaigns.

View Article: PubMed Central - HTML - PubMed

Affiliation: Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, Scotland.

ABSTRACT
Bacterial infections are increasingly difficult to treat owing to the spread of antibiotic resistance. A major concern is Gram-negative bacteria, for which the discovery of new antimicrobial drugs has been particularly scarce. In an effort to accelerate early steps in drug discovery, the EU-funded AEROPATH project aims to identify novel targets in the opportunistic pathogen Pseudomonas aeruginosa by applying a multidisciplinary approach encompassing target validation, structural characterization, assay development and hit identification from small-molecule libraries. Here, the strategies used for target selection are described and progress in protein production and structure analysis is reported. Of the 102 selected targets, 84 could be produced in soluble form and the de novo structures of 39 proteins have been determined. The crystal structures of eight of these targets, ranging from hypothetical unknown proteins to metabolic enzymes from different functional classes (PA1645, PA1648, PA2169, PA3770, PA4098, PA4485, PA4992 and PA5259), are reported here. The structural information is expected to provide a firm basis for the improvement of hit compounds identified from fragment-based and high-throughput screening campaigns.

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Schematic view of the structure of the subunit (a) and tetramer (b) of the putative inosine-5′-monophosphate dehydrogenase PA3770. The location of the missing subdomain and active-site flap are highlighted in the structure of the subunit.
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fig6: Schematic view of the structure of the subunit (a) and tetramer (b) of the putative inosine-5′-monophosphate dehydrogenase PA3770. The location of the missing subdomain and active-site flap are highlighted in the structure of the subunit.

Mentions: The three-dimensional structure of IMPDH has been well characterized and has recently been reviewed (Hedstrom, 2009 ▶). The catalytic domain folds into an eight-stranded β/α-barrel (Fig. 6 ▶ and Supplementary Fig. S1f). The closest structural homologue to PA3770 is IMPDH from the Gram-negative bacterium Borrelia burgdorferi (PDB entry 1eep; McMillan et al., 2000 ▶). The two proteins align over 313 residues with an r.m.s.d. of 0.8 Å. Like many of the IMPDH structures deposited in the PDB, no electron density is visible in our structure for the subdomain residues 91–204. In addition, electron density for residues 385–420 corresponding to the so-called ‘active-site flap’ is also missing. Nevertheless, the overall architecture of the proposed active site in PA3770 is the same as that found in the B. burgdorferi enzyme.


The AEROPATH project targeting Pseudomonas aeruginosa: crystallographic studies for assessment of potential targets in early-stage drug discovery.

Moynie L, Schnell R, McMahon SA, Sandalova T, Boulkerou WA, Schmidberger JW, Alphey M, Cukier C, Duthie F, Kopec J, Liu H, Jacewicz A, Hunter WN, Naismith JH, Schneider G - Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. (2012)

Schematic view of the structure of the subunit (a) and tetramer (b) of the putative inosine-5′-monophosphate dehydrogenase PA3770. The location of the missing subdomain and active-site flap are highlighted in the structure of the subunit.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3539698&req=5

fig6: Schematic view of the structure of the subunit (a) and tetramer (b) of the putative inosine-5′-monophosphate dehydrogenase PA3770. The location of the missing subdomain and active-site flap are highlighted in the structure of the subunit.
Mentions: The three-dimensional structure of IMPDH has been well characterized and has recently been reviewed (Hedstrom, 2009 ▶). The catalytic domain folds into an eight-stranded β/α-barrel (Fig. 6 ▶ and Supplementary Fig. S1f). The closest structural homologue to PA3770 is IMPDH from the Gram-negative bacterium Borrelia burgdorferi (PDB entry 1eep; McMillan et al., 2000 ▶). The two proteins align over 313 residues with an r.m.s.d. of 0.8 Å. Like many of the IMPDH structures deposited in the PDB, no electron density is visible in our structure for the subdomain residues 91–204. In addition, electron density for residues 385–420 corresponding to the so-called ‘active-site flap’ is also missing. Nevertheless, the overall architecture of the proposed active site in PA3770 is the same as that found in the B. burgdorferi enzyme.

Bottom Line: A major concern is Gram-negative bacteria, for which the discovery of new antimicrobial drugs has been particularly scarce.The crystal structures of eight of these targets, ranging from hypothetical unknown proteins to metabolic enzymes from different functional classes (PA1645, PA1648, PA2169, PA3770, PA4098, PA4485, PA4992 and PA5259), are reported here.The structural information is expected to provide a firm basis for the improvement of hit compounds identified from fragment-based and high-throughput screening campaigns.

View Article: PubMed Central - HTML - PubMed

Affiliation: Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, Scotland.

ABSTRACT
Bacterial infections are increasingly difficult to treat owing to the spread of antibiotic resistance. A major concern is Gram-negative bacteria, for which the discovery of new antimicrobial drugs has been particularly scarce. In an effort to accelerate early steps in drug discovery, the EU-funded AEROPATH project aims to identify novel targets in the opportunistic pathogen Pseudomonas aeruginosa by applying a multidisciplinary approach encompassing target validation, structural characterization, assay development and hit identification from small-molecule libraries. Here, the strategies used for target selection are described and progress in protein production and structure analysis is reported. Of the 102 selected targets, 84 could be produced in soluble form and the de novo structures of 39 proteins have been determined. The crystal structures of eight of these targets, ranging from hypothetical unknown proteins to metabolic enzymes from different functional classes (PA1645, PA1648, PA2169, PA3770, PA4098, PA4485, PA4992 and PA5259), are reported here. The structural information is expected to provide a firm basis for the improvement of hit compounds identified from fragment-based and high-throughput screening campaigns.

Show MeSH
Related in: MedlinePlus