Mycobacterium tuberculosis Malate Synthase Structures with Fragments Reveal a Portal for Substrate/Product Exchange

Hsiao-Ling Huang; Inna V. Krieger; Maloy K. Parai; Vijay B. Gawandi; James C. Sacchettini

doi:10.1074/jbc.M116.750877

Mycobacterium tuberculosis Malate Synthase Structures with Fragments Reveal a Portal for Substrate/Product Exchange*

From the Departments of ^‡Chemistry and
^§Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77845

↵2 To whom correspondence should be addressed: Texas A&M University, 3474 TAMU College Station, TX 77843-3474. Tel.: 979-862-7637; Fax: 979-862-7638; E-mail: sacchett{at}tamu.edu.

↵1 Both authors contributed equally to this work.
Edited by Ruma Banerjee

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 IC₅₀ value of 20 nm.

Footnotes

↵* This work was supported by Welch Foundation Grant A-0015 and National Institutes of Health Grant P01 AI095208 (to J. C. S.). The authors declare that they have no conflicts of interest with the contents of this article. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
↵ This article contains supplemental Tables S1–S3; Scheme S1, and Figs. S1–S5.
The atomic coordinates and structure factors (codes 5C9R, 5T8G, 5C9U, 5C9W, 5C9X, 5CAH, 5E9X, 5C7V, 5CAK, 5CJN, 5CC3, 5CBB, 5CJM, 5CBI, 5CBJ, 5CCZ, 5DX7, 5CEW, 5DRC, 5DRI, 5ECV, 5H8P, 5H8U, and 5H8M) have been deposited in the Protein Data Bank (http://wwpdb.org/).