Identification of novel small molecule inhibitors of 4-diphosphocytidyl-2-C-methyl-d-erythritol (CDP-ME) kinase of Gram-negative bacteria

Abstract

The biosyntheses of isoprenoids is essential for the survival in all living organisms, and requires one of the two biochemical pathways: (a) Mevalonate (MVA) Pathway or (b) Methylerythritol Phosphate (MEP) Pathway. The latter pathway, which is used by all Gram-negative bacteria, some Gram-positive bacteria and a few apicomplexan protozoa, provides an attractive target for the development of new antimicrobials because of its absence in humans. In this report, we describe two different approaches that we used to identify novel small molecule inhibitors of Escherichia coli and Yersinia pestis 4-diphosphocytidyl-2-C-methyl D-erythritol (CDP-ME) kinases, key enzymes of the MEP pathway encoded by the E. coli ispE and Y. pestis ipk genes, respectively. In the first approach, we explored existing inhibitors of the GHMP kinases while in the second approach; we performed computational high-throughput screening of compound libraries by targeting the CDP-ME binding site of the two bacterial enzymes. From the first approach, we identified two compounds with 6-(benzylthio)-2-(2-hydroxyphenyl)-4-oxo-3,4-dihydro-2H-1,3-thiazine-5-carbonitrile and (Z)-3-methyl-4-((5-phenylfuran-2-yl)methylene)isoxazol-5(4H)-one scaffolds which inhibited Escherichia coli CDP-ME kinase in vitro. We then performed substructure search and docking experiments based on these two scaffolds and identified twenty three analogs for structure-activity relationship (SAR) studies. Three new compounds from the isoxazol-5(4H)-one series have shown inhibitory activities against E. coli and Y. pestis CDP-ME kinases with the IC50 values ranging from 7μM to 13μM. The second approach by computational high-throughput screening (HTS) of two million drug-like compounds yielded two compounds with benzenesulfonamide and acetamide moieties which, at a concentration of 20μM, inhibited 80% and 65%, respectively, of control CDP-ME kinase activity.

Epidemiology and Virulence of Klebsiella pneumoniae

“…For example, the use of probiotics to prevent E. coli UTIs has been investigated (146,147). In addition, small molecule inhibitors and competitors of essential bacterial metabolic processes are beginning to be evaluated as methods of therapy (148)(149)(150)(151)(152)(153)(154)(155). However, to date, no studies have been reported for the use of these molecules to prevent K. pneumoniae infections.…”

Innovative therapy for Classic Galactosemia — Tale of two HTS

“…A less selective GALK inhibitor may therefore cross-inhibit against CDP-ME kinase. In fact, close scrutiny of previous high-throughput screening for GALK inhibitors revealed that some of the GALK inhibitors could indeed inhibit CDP-ME kinase from E. coli (Tables 2) [121]. Therefore, the on-going development of GALK inhibitors provides new chemical templates for CDP-ME kinase inhibitors as novel antimicrobial agents.…”

Electrochemically Induced Facile and Efficient Multicomponent Approach to Medicinally Relevant 4‐[4‐oxo‐4H‐pyran‐2‐yl](aryl)‐methylisoxazol‐5(2H)‐one Scaffold

“…[11] Thus, isoxazol-5(4H)-one-containing compounds demonstrate inhibitory activities against Escherichia coli and Yersinia pestis CDP-ME kinases. [12] For benzylideneisoxazolones is known inhibition of fungal growth of Leptosphaeia nodorum and Blumeria graminis. [13] Isoxazol-5(4H)-one structures as well demonstrate antagonistic antiandrogen activity on human prostate tumor LNCaP cells.…”