Molecular basis for the inhibition of β-hydroxyacyl-ACP dehydratase HadAB complex from Mycobacterium tuberculosis by flavonoid inhibitors.

Yu Dong,Xiaodi Qiu,Yueyang Xu,Neil Shaw,Yuna Sun,Zihe Rao,Jun Li,Xuemei Li

doi:10.1007/s13238-015-0181-1

Abstract

Dehydration is one of the key steps in the biosynthesis of mycolic acids and is vital to the growth of Mycobacterium tuberculosis (Mtb). Consequently, stalling dehydration cures tuberculosis (TB). Clinically used anti-TB drugs like thiacetazone (TAC) and isoxyl (ISO) as well as flavonoids inhibit the enzyme activity of the β-hydroxyacyl-ACP dehydratase HadAB complex. How this inhibition is exerted, has remained an enigma for years. Here, we describe the first crystal structures of the MtbHadAB complex bound with flavonoid inhibitor butein, 2’,4,4’-trihydroxychalcone or fisetin. Despite sharing no sequence identity from Blast, HadA and HadB adopt a very similar hotdog fold. HadA forms a tight dimer with HadB in which the proteins are sitting side-by-side, but are oriented anti-parallel. While HadB contributes the catalytically critical His-Asp dyad, HadA binds the fatty acid substrate in a long channel. The atypical double hotdog fold with a single active site formed by MtbHadAB gives rise to a long, narrow cavity that vertically traverses the fatty acid binding channel. At the base of this cavity lies Cys61, which upon mutation to Ser confers drug-resistance in TB patients. We show that inhibitors bind in this cavity and protrude into the substrate binding channel. Thus, inhibitors of MtbHadAB exert their effect by occluding substrate from the active site. The unveiling of this mechanism of inhibition paves the way for accelerating development of next generation of anti-TB drugs.Electronic supplementary materialThe online version of this article (doi:10.1007/s13238-015-0181-1) contains supplementary material, which is available to authorized users.

Highlights

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is the second most common cause of death due to a single infectious pathogen with an enormous global medical burden
The crystal structure of MtbHadAB complex was solved by single wavelength anomalous dispersion (SAD) method using X-ray diffraction data collected from crystals of selenomethionine labeled protein
The overall structure of the MtbHadAB complex reveals that both proteins adopt a similar hotdog fold (Fig. 3B)

Summary

Introduction

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is the second most common cause of death due to a single infectious pathogen with an enormous global medical burden. In the year of 2013, approximately 30% of the world’s population were latently infected with Mtb, and there were nearly 9 million new TB cases and 1.5 million TB deaths (WHO 2014; Jiang et al, 2014; Zumla et al, 2013). The cell wall of mycobacteria is unique primarily because of its lipid content (Goldberg et al, 2012). 2-alkyl, 3-hydroxy long-chain fatty acids known as mycolic acids (MAs) and their derivates form a dense outer sheath for shielding the inner cytoskeleton of the cell wall (Carel et al, 2014). One approach to Crystal structure of Mtb HadAB-inhibitor complex overpower mycobacteria is to scuttle the biosynthesis of mycolic acids (Jackson et al, 2013)

Methods

Results

Conclusion