14 research outputs found
Interfering with DNA Decondensation as a Strategy Against Mycobacteria
Tuberculosis is once again a major global threat, leading to more than 1 million deaths each year. Treatment options for tuberculosis patients are limited, expensive and characterized by severe side effects, especially in the case of multidrug-resistant forms. Uncovering novel vulnerabilities of the pathogen is crucial to generate new therapeutic strategies. Using high resolution microscopy techniques, we discovered one such vulnerability of Mycobacterium tuberculosis. We demonstrate that the DNA of M. tuberculosis can condense under stressful conditions such as starvation and antibiotic treatment. The DNA condensation is reversible and specific for viable bacteria. Based on these observations, we hypothesized that blocking the recovery from the condensed state could weaken the bacteria. We showed that after inducing DNA condensation, and subsequent blocking of acetylation of DNA binding proteins, the DNA localization in the bacteria is altered. Importantly under these conditions, Mycobacterium smegmatis did not replicate and its survival was significantly reduced. Our work demonstrates that agents that block recovery from the condensed state of the nucleoid can be exploited as antibiotic. The combination of fusidic acid and inhibition of acetylation of DNA binding proteins, via the Eis enzyme, potentiate the efficacy of fusidic acid by 10 and the Eis inhibitor to 1,000-fold. Hence, we propose that successive treatment with antibiotics and drugs interfering with recovery from DNA condensation constitutes a novel approach for treatment of tuberculosis and related bacterial infections
Deciphering Natureās Intricate Way of <i>N</i>,<i>S</i>-Dimethylating lāCysteine: Sequential Action of Two Bifunctional Adenylation Domains
Dimethylation
of amino acids consists of an interesting and puzzling
series of events that could be achieved, during nonribosomal peptide
biosynthesis, either by a single adenylation (A) domain interrupted
by a methyltransferase (M) domain or by the sequential action of two
of such independent enzymes. Herein, to establish the method by which
Nature <i>N</i>,<i>S</i>-dimethylates l-Cys, we studied its formation during thiochondrilline A biosynthesis
by evaluating TioSĀ(A<sub>3a</sub>M<sub>3S</sub>A<sub>3b</sub>T<sub>3</sub>) and TioNĀ(A<sub>a</sub>M<sub>N</sub>A<sub>b</sub>). This
study not only led to identification of the exact pathway followed
in Nature by these two enzymes for <i>N</i>,<i>S</i>-dimethylation of l-Cys, but also revealed that a single
interrupted A domain can <i>N</i>,<i>N</i>-dimethylate
amino acids, a novel phenomenon in the nonribosomal peptide field.
These findings offer important and useful insights for the development
and engineering of novel interrupted A domain enzymes to serve, in
the future, as tools for combinatorial biosynthesis
CCDC 890236: Experimental Crystal Structure Determination
Related Article: Atefeh Garzan, Arvind Jaganathan, Nastaran SalehiāMarzijarani, Roozbeh Yousefi, Daniel C. Whitehead, James E. Jackson, Babak Borhan|2013|Chem.-Eur.J.|19|9015|doi:10.1002/chem.201300189,An entry from the Cambridge Structural Database, the worldās repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures
Sulfonamide-Based Inhibitors of Aminoglycoside Acetyltransferase Eis Abolish Resistance to Kanamycin in Mycobacterium tuberculosis
Discovery and Optimization of Two Eis Inhibitor Families as Kanamycin Adjuvants against Drug-Resistant <i>M. tuberculosis</i>
Drug-resistant
tuberculosis (TB) is a global threat and innovative
approaches such as using adjuvants of anti-TB therapeutics are required
to combat it. High-throughput screening yielded two lead scaffolds
of inhibitors of <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>) acetyltransferase Eis, whose upregulation causes resistance
to the anti-TB drug kanamycin (KAN). Chemical optimization on these
scaffolds resulted in potent Eis inhibitors. One compound restored
the activity of KAN in a KAN-resistant <i>Mtb</i> strain.
Model structures of Eis-inhibitor complexes explain the structureāactivity
relationship
Discovery of Allosteric and Selective Inhibitors of Inorganic Pyrophosphatase from <i>Mycobacterium tuberculosis</i>
Inorganic
pyrophosphatase (PPiase) is an essential enzyme that
hydrolyzes inorganic pyrophosphate (PP<sub>i</sub>), driving numerous
metabolic processes. We report a discovery of an allosteric inhibitor
(2,4-bisĀ(aziridin-1-yl)-6-(1-phenylpyrrol-2-yl)-<i>s</i>-triazine) of bacterial PPiases. Analogues of this lead compound
were synthesized to target specifically <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>) PPiase (<i>Mt</i>PPiase). The best
analogue (compound <b>16</b>) with a <i>K</i><sub>i</sub> of 11 Ī¼M for <i>Mt</i>PPiase is a species-specific
inhibitor. Crystal structures of <i>Mt</i>PPiase in complex
with the lead compound and one of its analogues (compound <b>6</b>) demonstrate that the inhibitors bind in a nonconserved interface
between monomers of the hexameric <i>Mt</i>PPiase in a yet
unprecedented pairwise manner, while the remote conserved active site
of the enzyme is occupied by a bound PP<sub>i</sub> substrate. Consistent
with the structural studies, the kinetic analysis of the most potent
inhibitor has indicated that it functions uncompetitively, by binding
to the enzymeāsubstrate complex. The inhibitors appear to allosterically
lock the active site in a closed state causing its dysfunctionalization
and blocking the hydrolysis. These inhibitors are the first examples
of allosteric, species-selective inhibitors of PPiases, serving as
a proof-of-principle that PPiases can be selectively targeted
Pyrimidone inhibitors targeting Chikungunya Virus nsP3 macrodomain by fragment-based drug design.
The macrodomain of nsP3 (nsP3MD) is highly conserved among the alphaviruses and ADP-ribosylhydrolase activity of Chikungunya Virus (CHIKV) nsP3MD is critical for CHIKV viral replication and virulence. No small molecule drugs targeting CHIKV nsP3 have been identified to date. Here we report small fragments that bind to nsP3MD which were discovered by virtually screening a fragment library and X-ray crystallography. These identified fragments share a similar scaffold, 2-pyrimidone-4-carboxylic acid, and are specifically bound to the ADP-ribose binding site of nsP3MD. Among the fragments, 2-oxo-5,6-benzopyrimidine-4-carboxylic acid showed anti-CHIKV activity with an IC50 of 23 Ī¼M. Our fragment-based drug discovery approach provides valuable information to further develop a specific and potent nsP3 inhibitor of CHIKV viral replication based on the 2-pyrimidone-4-carboxylic acid scaffold. In silico studies suggest this pyrimidone scaffold could also bind to the macrodomains of other alphaviruses and coronaviruses and thus, have potential pan-antiviral activity
Activation and Loading of the Starter Unit during Thiocoraline Biosynthesis
The
initiation of the nonribosomal peptide synthetase (NRPS) assembly
of the bisintercalator natural product thiocoraline involves key enzymatic
steps for AMP activation and carrier protein loading of the starter
unit 3-hydroxyquinaldic acid (3HQA). Gene cluster data combined with
protein sequence homology analysis originally led us to propose that
TioJ could be responsible for the AMP activation step, whereas TioO
could act as the thiolation (T) domain, facilitating the transfer
of 3HQA to the next NRPS module, TioR. Herein, we confirmed the involvement
of TioJ in thiocoraline biosynthesis by <i>tioJ</i> knockout
and <i>in vitro</i> activation of 3HQA studies. However,
we demonstrated that TioJ-activated 3HQA is not loaded onto the T
domain TioO, as originally believed, but instead onto a fatty acid
synthase (FAS) acyl carrier protein (ACP) domain FabC, which is located
outside of the thiocoraline gene cluster. We showed a strong interaction
between TioJ and FabC. By generating TioJ point mutants mimicking
the active site of highly homologous enzymes activating different
molecules, we showed that the identity of the substrate activated
by adenylation domains such as TioJ is not determined by only the
active site residues that directly interact with the substrate. The
insights gained from these enzymatic transformations are valuable
in the efforts toward deciphering the complete biosynthetic pathway
of thiocoraline and bisintercalators in general
Sulfonamide-Based Inhibitors of Aminoglycoside Acetyltransferase Eis Abolish Resistance to Kanamycin in Mycobacterium tuberculosis
A two-drug combination
therapy where one drug targets an offending
cell and the other targets a resistance mechanism to the first drug
is a time-tested, yet underexploited approach to combat or prevent
drug resistance. By high-throughput screening, we identified a sulfonamide
scaffold that served as a pharmacophore to generate inhibitors of Mycobacterium tuberculosis acetyltransferase Eis,
whose upregulation causes resistance to the aminoglycoside (AG) antibiotic
kanamycin A (KAN) in Mycobacterium tuberculosis. Rational systematic derivatization of this scaffold to maximize
Eis inhibition and abolish the Eis-mediated KAN resistance of M. tuberculosis yielded several highly potent agents.
A crystal structure of Eis in complex with one of the most potent
inhibitors revealed that the inhibitor bound Eis in the AG-binding
pocket held by a conformationally malleable region of Eis (residues
28ā37) bearing key hydrophobic residues. These Eis inhibitors
are promising leads for preclinical development of innovative AG combination
therapies against resistant TB
Optimization of pyrazole-containing 1,2,4-triazolo-[3,4-b]thiadiazines, a new class of STAT3 pathway inhibitors
Structure-activity relationship studies of a 1,2,4-triazolo-[3,4-b]thiadiazine scaffold, identified in an HTS campaign for selective STAT3 pathway inhibitors, determined that a pyrazole group and specific aryl substitution on the thiadiazine were necessary for activity. Improvements in potency and metabolic stability were accomplished by the introduction of an Ī±-methyl group on the thiadiazine. Optimized compounds exhibited anti-proliferative activity, reduction of phosphorylated STAT3 levels and effects on STAT3 target genes. These compounds represent a starting point for further drug discovery efforts targeting the STAT3 pathway