title: Mycobacterium tuberculosis Malate Synthase Structures with Fragments Reveal a Portal for Substrate/Product Exchange.
abstract: Fragment screening and high throughput screening are complementary approaches that combine with structural biology to explore the binding capabilities of an active site. We have used a fragment-based approach on malate synthase (GlcB) from Mycobacterium tuberculosis and discovered several novel binding chemotypes. In addition, the crystal structures of GlcB in complex with these fragments indicated conformational changes in the active site that represent the enzyme conformations during catalysis. Additional structures of the complex with malate and of the apo form of GlcB supported that hypothesis. Comparative analysis of GlcB structures in complex with 18 fragments allowed us to characterize the preferred chemotypes and their binding modes. The fragment structures showed a hydrogen bond to the backbone carbonyl of Met-631. We successfully incorporated an indole group from a fragment into an existing phenyl-diketo acid series. The resulting indole-containing inhibitor was 100-fold more potent than the parent phenyl-diketo acid with an IC50value of 20 nm.
authors.affiliation: From the Departments of Chemistry and.
authors.forename: Hsiao-Ling
authors.initials: HL
authors.lastname: Huang
authors.affiliation: Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77845.
authors.forename: Inna V
authors.initials: IV
authors.lastname: Krieger
authors.affiliation: Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77845.
authors.forename: Maloy K
authors.initials: MK
authors.lastname: Parai
authors.affiliation: Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77845.
authors.forename: Vijay B
authors.initials: VB
authors.lastname: Gawandi
authors.affiliation: From the Departments of Chemistry and sacchett@tamu.edu.|Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77845.
authors.forename: James C
authors.initials: JC
authors.lastname: Sacchettini
mesh_terms: D001665:Binding Sites; D002384:Catalysis; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D008292:Malate Synthase / Q000737:chemistry* / Q000378:metabolism*; D008293:Malates / Q000378:metabolism*; D008958:Models, Molecular; D009169:Mycobacterium tuberculosis / Q000201:enzymology*; D011487:Protein Conformation; D013379:Substrate Specificity
chemical_list: D008293:Malates; C030298:malic acid; D008292:Malate Synthase
keywords: crystal structure; drug design; enzyme inhibitor; enzyme mechanism; malate synthase; tuberculosis