Researchers Discover a Potent Anti-Pneumococcal Agent

Pneumonia kills over 2 million children each year worldwide and is considered the leading killer of children. The emergency of multidrug-resistant bacteria threatens the treatment of the disease. It is urgent to develop new anti-pneumococcal agents with no cross-resistance to current drugs. Recently, researchers from Shanghai Institute of Biochemistry and Cell Biology (SIBCB), Chinese Academy of Sciences discover a potent benzoxaborole-based anti-pneumococcal agent targeting leucyl-tRNA synthetase.

Leucyl-tRNA synthetase (LeuRS) plays an essential role in cellular translation and is an attractive drug target for antimicrobial development. The known structures discovered several differences in the editing domain CP1 among eukaryal and bacterial LeuRSs, which could serve as valuable targets for the development of novel selective antibacterial agents against LeuRS. PhD student HU Qing-Hua and Dr. LIU Ru-Juan and their colleagues, led by Prof. WANG Enduo from SIBCB, in collaboration with Prof. ZHOU Hu-Chen from Shanghai Jiao Tong University, reported a compound ZCL039，6-(1-phenyl-1-hydroxylmethyl)]-1,3- dihydro-1-hydroxy-2,1-benzoxaborole, as a potent anti-pneumococcal agent, elucidated the inhibitory mechanism and indicated the potential of benzoxaboroles in the development of antimicrobials.

A variety of AN2690 (5-fluoro-1,3-dihydro-1-hydroxy-2,1- benzoxaborole) derivatives were designed and synthesized based on the homologous structure of bacterial LeuRS. Their activities against S. pneumoniae LeuRS (SpLeuRS) aminoacylation were examined, and a strong inhibitor was identified as ZCL039. Activity examination against LeuRSs from E. coli, human cytoplasm and mitochondrion suggested that ZCL039 was a selective inhibitor to bacterial LeuRS. ZCL039 could suppress the growth of S. pneumoniae with a MIC value of 1/80-fold of ampicillin.

Through the kinetic and biochemical analyses combined with the crystal structure of ZCL039-AMP in complex with the separated SpLeuRS editing domain, the uncompetitive inhibition mechanism of ZCL039 was revealed. ZCL039 formed a stable covalent adduct with the 3’ end of tRNA in the CP1 domain of LeuRS, which blocked tRNA charging and further the protein synthesis. To study the selectivity of ZCL039, docking models were made to establish that ZCL039 clashes with the eukaryal/archaeal specific insertion I4ae helix within the CP1 domains. These findings demonstrated the potential of benzoxaboroles as the effective LeuRS inhibitors for pneumococcus infection therapy, and provided a structure background for further drug design and optimization.

This study entitled “Discovery of a potent benzoxaborole-based anti-pneumococcal agent targeting leucyl-tRNA synthetase” was published online in Scientific Reports on Aug 20^th, 2013. This work was supported by the National Natural Science Foundation of China, the National Key Basic Research Foundation of China and the Chinese Academy of Sciences.

Insight into the structure of ZCL039 bound with SpLeuRS-CP1 and the selectivity of ZCL039 (Image by Prof. WANG Enduo’s group)