Probable novel MEP pathway inhibitor and its binding protein, IspG

Antibacterial and antibiofilm properties of two cyclic dipeptides produced by a new desert Streptomyces sp. HG-17 strain against multidrug-resistant pathogenic bacteria

INTRODUCTION

The emergence of multidrug-resistant bacteria and biofilms requires discovering new antimicrobial agents from unexplored environments.

OBJECTIVES

This study aims to isolate and characterize a new actinobacterial strain from the Hoggar Mountains in southern Algeria and evaluate its ability to produce bioactive molecules with potential antibacterial and antibiofilm activities.

METHODS

A novel halotolerant actinobacterial strain, designated HG-17, was isolated from the Hoggar Mountains, and identified based on phenotypic characterizations, 16S rDNA sequence analysis, and phylogenetic analysis. The antibacterial and antibiofilm activities of the strain were assessed, and the presence of biosynthetic genes (PKS-I and NRPS) was confirmed. Two active compounds, HG-7 and HG-9, were extracted butanol solvent, purified by HPLC, and their chemical structures were elucidated using ESI mass spectrometry and NMR spectroscopy.

RESULTS

The strain HG-17 was identified as Streptomyces purpureus NBRC with 98.8% similarity. It exhibited strong activity against multidrug-resistant and biofilm-forming bacteria. The two purified active compounds, HG-7 and HG-9, were identified as cyclo-(d-cis-hydroxyproline-l-phenylalanine) and cyclo-(l-prolone-l-tyrosine), respectively. The minimum inhibitory concentrations (MICs) of HG-7 and HG-9 ranged from 3 to 15 μg/mL, comparable to the MICs of tetracycline (8 to 15 μg/mL). Their minimum biofilm inhibitory concentration (MBIC 50%) showed good inhibition from 48.0 to 52.0% at concentrations of 1 to 7 μg/mL against the tested bacteria.

CONCLUSION

This is the first report of cyclo-(d-cis-hydroxyproline-l-phenylalanine) and cyclo-(l-prolone-l-tyrosine) antibiotics from S. purpureus and their anti-multi-drug-resistant and biofilm-forming bacteria. These results indicate that both antibiotics could be used as effective therapeutics to control infections associated with multidrug-resistant bacteria.

Antibacterial Activity of Allicin-Inspired Disulfide Derivatives against Xanthomonas axonopodis pv. citri

Xanthomonas axonopodis pv. citri (Xac) belongs to the Gram-negative species, causing citrus canker that seriously affects the fruit yield and quality of many rutaceae plants. Herein, we found that compound 2-(butyldisulfanyl) quinazolin-4(3H)-one exhibited remarkable anti-Xac activity in vitro with a half effective concentration (EC₅₀) of 2.6 μg/mL, while the positive controls thiodiazole-copper with 57 μg/mL and bismerthiazol with 68 μg/mL and this compound showed great anti-citrus canker activity in vivo. This active compound also was confirmed to reduce biofilm formation, increase the level of reactive oxygen species, damage the morphological structure of the bacteria, and cause bacterial death. Proteomics and RT-qPCR analysis results indicated that this compound down-regulated the expression of enzymes in the MEP (2-methyl-D-erythritol 4-phosphate) pathway and might achieve destructive ability of Xac. Overall, this study indicates that such derivatives could be a promising scaffold to develop novel bactericides to control citrus canker.

Synthesis and Antimicrobial Evaluation of γ-Borono Phosphonate Compounds in Escherichia coli and Mycobacterium smegmatis

Drug resistance in bacteria is a serious threat, and drugs with novel modes of action are constantly needed. Fosmidomycin is a naturally occurring antibiotic that inhibits the nonmevalonate pathway via inhibition of the enzyme 1-deoxylulose-5-phosphate reductoisomerase (DXR). This work is the first report in which a boronic acid is evaluated as an isostere of the retrohydroxamate moiety of fosmidomycin. We report the novel synthesis of a γ-borono phosphonate analog of fosmidomycin and its corresponding prodrugs. We evaluate the inhibition of DXR and the antimicrobial activity of γ-borono phosphonate compounds against Escherichia coli wild type, E. coli Δglycerol-3-phosphate transporter, and Mycobacterium smegmatis. Despite its structural similarities, the γ-borono phosphonate compound shows antimicrobial activity against E. coli with a mechanism of action that is different from fosmidomycin. This was proven with an underutilized method for studying in vitro inhibition of the MEP pathway in E. coli via isopentenyl pyrophosphate chemical rescue. These results indicate that these compounds may serve as a promising scaffold for developing a new class of antimicrobial agents.

A novel suicide plasmid for efficient gene mutation in Listeria monocytogenes

Although several plasmids have been used in Listeria monocytogenes for generating mutants by allelic exchange, construction of L. monocytogenes mutants has been inefficient due to lack of effective selection markers for first and second recombination events. To address this problem, we have developed a new suicide plasmid, pHoss1, by using the pMAD plasmid backbone and anhydrotetracycline selection marker (secY antisense RNA) driven by an inducible Pxyl/tetO promoter. Expression of the secY antisense RNA eliminates merodiploids and selects for the loss of plasmid via a second allelic exchange, which enriches the number of mutants with deleted genes. To assess the effectiveness of pHoss1 for the generation of stable in-frame deletion mutations, we deleted the ispG and ispH genes of L. monocytogenes serotype 4b strain F2365. Results showed that identification of the second allelic exchange mutants was very efficient with 80-100% of the colonies yielding desired deletion mutants. L. monocytogenes' intestinal cell attachment was not altered when ispG and ispH genes were deleted. We expect that this new plasmid will be very useful for construction of marker-free deletion mutants in L. monocytogenes and in other Gram-positive bacteria, including Staphylococcus aureus and Bacillus cereus.

Atomic-Resolution Structures of Discrete Stages on the Reaction Coordinate of the [Fe4S4] Enzyme IspG (GcpE)

IspG is the penultimate enzyme in non-mevalonate biosynthesis of the universal terpene building blocks isopentenyl diphosphate and dimethylallyl diphosphate. Its mechanism of action has been the subject of numerous studies but remained unresolved due to difficulties in identifying distinct reaction intermediates. Using a moderate reducing agent and an epoxide substrate analogue, we were now able to trap and crystallographically characterize various stages in the IspG-catalyzed conversion of 2-C-methyl-D-erythritol-2,4-cyclo-diphosphate into (E)-1-hydroxy-2-methylbut-2-enyl-4-diphosphate. In addition, the enzyme's structure was determined in complex with several inhibitors. These results, combined with recent electron paramagnetic resonance data, allowed us to deduce a detailed and complete IspG catalytic mechanism, which describes all stages from initial ring opening to formation of (E)-1-hydroxy-2-methylbut-2-enyl-4-diphosphate via discrete radical and carbanion intermediates. The data presented in this article provide a guide for the design of selective drugs against many prokaryotic and eukaryotic pathogens to which the non-mevalonate pathway is essential for survival and virulence.

Kinetic characterization and allosteric inhibition of the Yersinia pestis 1-deoxy-D-xylulose 5-phosphate reductoisomerase (MEP synthase)

The methylerythritol phosphate (MEP) pathway found in many bacteria governs the synthesis of isoprenoids, which are crucial lipid precursors for vital cell components such as ubiquinone. Because mammals synthesize isoprenoids via an alternate pathway, the bacterial MEP pathway is an attractive target for novel antibiotic development, necessitated by emerging antibiotic resistance as well as biodefense concerns. The first committed step in the MEP pathway is the reduction and isomerization of 1-deoxy-D-xylulose-5-phosphate (DXP) to methylerythritol phosphate (MEP), catalyzed by MEP synthase. To facilitate drug development, we cloned, expressed, purified, and characterized MEP synthase from Yersinia pestis. Enzyme assays indicate apparent kinetic constants of KMDXP = 252 µM and KMNADPH = 13 µM, IC50 values for fosmidomycin and FR900098 of 710 nM and 231 nM respectively, and Ki values for fosmidomycin and FR900098 of 251 nM and 101 nM respectively. To ascertain if the Y. pestis MEP synthase was amenable to a high-throughput screening campaign, the Z-factor was determined (0.9) then the purified enzyme was screened against a pilot scale library containing rationally designed fosmidomycin analogs and natural product extracts. Several hit molecules were obtained, most notably a natural product allosteric affector of MEP synthase and a rationally designed bisubstrate derivative of FR900098 (able to associate with both the NADPH and DXP binding sites in MEP synthase). It is particularly noteworthy that allosteric regulation of MEP synthase has not been described previously. Thus, our discovery implicates an alternative site (and new chemical space) for rational drug development.