Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei.

Abstract

As part of the Seattle Structural Genomics Center for Infectious Disease, we seek to enhance structural genomics with ligand-bound structure data which can serve as a blueprint for structure-based drug design. We have adapted fragment-based screening methods to our structural genomics pipeline to generate multiple ligand-bound structures of high priority drug targets from pathogenic organisms. In this study, we report fragment screening methods and structure determination results for 2C-methyl-D-erythritol-2,4-cyclo-diphosphate (MECP) synthase from Burkholderia pseudomallei, the gram-negative bacterium which causes melioidosis. Screening by nuclear magnetic resonance spectroscopy as well as crystal soaking followed by X-ray diffraction led to the identification of several small molecules which bind this enzyme in a critical metabolic pathway. A series of complex structures obtained with screening hits reveal distinct binding pockets and a range of small molecules which form complexes with the target. Additional soaks with these compounds further demonstrate a subset of fragments to only bind the protein when present in specific combinations. This ensemble of fragment-bound complexes illuminates several characteristics of MECP synthase, including a previously unknown binding surface external to the catalytic active site. These ligand-bound structures now serve to guide medicinal chemists and structural biologists in rational design of novel inhibitors for this enzyme.

• Authors: Darren W Begley, Robert C Hartley, Douglas R Davies, Thomas E Edwards, Jess T Leonard, Jan Abendroth, Courtney A Burris, Janhavi Bhandari, Peter J Myler, Bart L Staker, Lance J Stewart
• Journal: Journal of structural and functional genomics (J Struct Funct Genomics) Vol. 12 Issue 2 Pg. 63-76 (Jul 2011) ISSN: 1570-0267 [Electronic] Netherlands
• PMID: 21359640 (Publication Type: Journal Article, Research Support, N.I.H., Extramural)

Chemical References

• Bacterial Proteins
• Ligands
• Phosphorus-Oxygen Lyases

Topics

• Bacterial Proteins (chemistry)
• Binding Sites
• Burkholderia pseudomallei (enzymology)
• Catalytic Domain
• Crystallography, X-Ray
• Drug Design
• Ligands
• Magnetic Resonance Spectroscopy
• Phosphorus-Oxygen Lyases (chemistry)