26 research outputs found
Phosphonate as a Stable Zinc-Binding Group for "Pathoblocker" Inhibitors of Clostridial Collagenase H (ColH)
Microbial infections are a significant threat to public health, and resistance is on the rise, so new antibiotics with novel modes of action are urgently needed. The extracellular zinc metalloprotease collagenase H (ColH) from Clostridium histolyticum is a virulence factor that catalyses tissue damage, leading to improved host invasion and colonisation. Besides the major role of ColH in pathogenicity, its extracellular localisation makes it a highly attractive target for the development of new antivirulence agents. Previously, we had found that a highly selective and potent thiol prodrug (with a hydrolytically cleavable thiocarbamate unit) provided efficient ColH inhibition. We now report the synthesis and biological evaluation of a range of zinc‐binding group (ZBG) variants of this thiol‐derived inhibitor, with the mercapto unit being replaced by other zinc ligands. Among these, an analogue with a phosphonate motif as ZBG showed promising activity against ColH, an improved selectivity profile, and significantly higher stability than the thiol reference compound, thus making it an attractive candidate for future drug development
Identification of a 1-deoxy-D-xylulose-5-phosphate synthase (DXS) mutant with improved crystallographic properties
In this report, we describe a truncated Deinococcus radiodurans 1-deoxy-D-xylulose-5-phosphate synthase (DXS) protein that retains enzymatic activity, while slowing protein degradation and showing
improved crystallization properties. With modern drug-design approaches relying heavily on the
elucidation of atomic interactions of potential new drugs with their targets, the need for co-crystal
structures with the compounds of interest is high. DXS itself is a promising drug target, as it catalyzes
the first reaction in the 2-C-methyl-D-erythritol 4-phosphate (MEP)-pathway for the biosynthesis of the
universal precursors of terpenes, which are essential secondary metabolites. In contrast to many bacteria
and pathogens, which employ the MEP pathway, mammals use the distinct mevalonate-pathway for the
biosynthesis of these precursors, which makes all enzymes of the MEP-pathway potential new targets for
the development of anti-infectives. However, crystallization of DXS has proven to be challenging: while
the first X-ray structures from Escherichia coli and D. radiodurans were solved in 2004, since then only
two additions have been made in 2019 that were obtained under anoxic conditions. The presented site of
truncation can potentially also be transferred to other homologues, opening up the possibility for the
determination of crystal structures from pathogenic species, which until now could not be crystallized.
This manuscript also provides a further example that truncation of a variable region of a protein can lead
to improved structural data
Substrate-Inspired Fragment Merging and Growing Affords Efficacious LasB Inhibitors
Extracellular virulence factors have emerged as
attractive targets in the current antimicrobial resistance crisis.
The Gram-negative pathogen Pseudomonas aeruginosa secretes the virulence factor elastase B (LasB), which plays an
important role in the infection process. Here, we report a submicromolar, non-peptidic, fragment-like inhibitor of LasB
discovered by careful visual inspection of structural data.
Inspired by the natural LasB substrate, the original fragment
was successfully merged and grown. The optimized inhibitor
is accessible via simple chemistry and retained selectivity with
a substantial improvement in activity, which can be rationalized by the crystal structure of LasB in complex with the
inhibitor. We also demonstrate an improved in vivo efficacy
of the optimized hit in Galleria mellonella larvae, highlighting the significance of this class of compounds as
promising drug candidates
First crystal structures of 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Mycobacterium tuberculosis indicate a distinct mechanism of intermediate stabilization
The development of drug resistance by Mycobacterium tuberculosis and other pathogenic bacteria
emphasizes the need for new antibiotics. Unlike animals, most bacteria synthesize isoprenoid
precursors through the MEP pathway. 1-Deoxy-d-xylulose 5-phosphate synthase (DXPS) catalyzes the
frst reaction of the MEP pathway and is an attractive target for the development of new antibiotics.
We report here the successful use of a loop truncation to crystallize and solve the frst DXPS structures
of a pathogen, namely M. tuberculosis (MtDXPS). The main diference found to other DXPS structures
is in the active site where a highly coordinated water was found, showing a new mechanism for
the enamine-intermediate stabilization. Unlike other DXPS structures, a “fork-like” motif could be
identifed in the enamine structure, using a diferent residue for the interaction with the cofactor,
potentially leading to a decrease in the stability of the intermediate. In addition, electron density
suggesting a phosphate group could be found close to the active site, provides new evidence for
the D-GAP binding site. These results provide the opportunity to improve or develop new inhibitors
specifc for MtDXPS through structure-based drug design
First crystal structures of 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Mycobacterium tuberculosis indicate a distinct mechanism of intermediate stabilization
The development of drug resistance by Mycobacterium tuberculosis and other pathogenic bacteria emphasizes the need for new antibiotics. Unlike animals, most bacteria synthesize isoprenoid precursors through the MEP pathway. 1-Deoxy-D-xylulose 5-phosphate synthase (DXPS) catalyzes the first reaction of the MEP pathway and is an attractive target for the development of new antibiotics. We report here the successful use of a loop truncation to crystallize and solve the first DXPS structures of a pathogen, namely M. tuberculosis (MtDXPS). The main difference found to other DXPS structures is in the active site where a highly coordinated water was found, showing a new mechanism for the enamine-intermediate stabilization. Unlike other DXPS structures, a "fork-like" motif could be identified in the enamine structure, using a different residue for the interaction with the cofactor, potentially leading to a decrease in the stability of the intermediate. In addition, electron density suggesting a phosphate group could be found close to the active site, provides new evidence for the D-GAP binding site. These results provide the opportunity to improve or develop new inhibitors specific for MtDXPS through structure-based drug design
Identification of Inhibitors of the Anti-Infective Target DXS Using Dynamic Combinatorial Chemistry
Antibiotic resistance is one of the biggest threats to humankind [1,2]. [...
Successful pregnancy under fibrinogen substitution in a woman with congenital afibrinogenaemia complicated by a postpartum venous thrombosis
Phosphonate as Stable Zinc-binding Group for Inhibitors of Clostridial Collagenase H (ColH) as Pathoblocker Agents.
Microbial infections are a significant threat to public health and resistances are on the rise, so new antibiotics with novel modes of action are urgently needed. The extracellular zinc metalloprotease collagenase H (ColH) from Clostridium histolyticum is a virulence factor that catalyzes tissue damage, leading to improved host invasion and colonisation. Besides the major role of ColH in pathogenicity, its extracellular localisation makes it a highly attractive target for the development of new antivirulence agents. Previously, we had found that a highly selective and potent thiol prodrug (with a hydrolytically cleavable thiocarbamate unit) provided efficient ColH inhibition. We now report the synthesis and biological evaluation of a range of zinc-binding group (ZBG) variants of this thiol-derived inhibitor, with the mercapto unit being replaced by other zinc ligands. Among these, an analogue with a phosphonate motif as ZBG showed promising activity against ColH, an improved selectivity profile, and significantly higher stability than the thiol reference compound, thus making it an attractive candidate for future drug development
Identification of a 1-deoxy-D-xylulose-5-phosphate synthase (DXS) mutant with improved crystallographic properties
In this report, we describe a truncated Deinococcus radiodurans 1-deoxy-D-xylulose-5-phosphate synthase (DXS) protein that retains enzymatic activity, while slowing protein degradation and showing improved crystallization properties. With modern drug-design approaches relying heavily on the elucidation of atomic interactions of potential new drugs with their targets, the need for co-crystal structures with the compounds of interest is high. DXS itself is a promising drug target, as it catalyzes the first reaction in the 2-C-methyl-D-erythritol 4-phosphate (MEP)-pathway for the biosynthesis of the universal precursors of terpenes, which are essential secondary metabolites. In contrast to many bacteria and pathogens, which employ the MEP pathway, mammals use the distinct mevalonate-pathway for the biosynthesis of these precursors, which makes all enzymes of the MEP-pathway potential new targets for the development of anti-infectives. However, crystallization of DXS has proven to be challenging: while the first X-ray structures from Escherichia coli and D. radiodurans were solved in 2004, since then only two additions have been made in 2019 that were obtained under anoxic conditions. The presented site of truncation can potentially also be transferred to other homologues, opening up the possibility for the determination of crystal structures from pathogenic species, which until now could not be crystallized. This manuscript also provides a further example that truncation of a variable region of a protein can lead to improved structural data