scholarly journals A unique peptide deformylase platform to rationally design and challenge novel active compounds

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Sonia Fieulaine ◽  
Rodolphe Alves de Sousa ◽  
Laure Maigre ◽  
Karim Hamiche ◽  
Mickael Alimi ◽  
...  
Keyword(s):  
Multidrug Resistant ◽  
Peptide Deformylase ◽  
Binding Modes ◽  
Proof Of Concept ◽  
Compound Structure ◽  
3 Dimensional ◽  
Design And Synthesis ◽  
Relationship Analysis

Abstract Peptide deformylase (PDF) is considered an excellent target to develop antibiotics. We have performed an extensive characterization of a new PDF from the pathogen Streptococcus agalactiae, showing properties similar to other known PDFs. S. agalactiae PDF could be used as PDF prototype as it allowed to get complete sets of 3-dimensional, biophysical and kinetic data with virtually any inhibitor compound. Structure-activity relationship analysis with this single reference system allowed us to reveal distinct binding modes for different PDF inhibitors and the key role of a hydrogen bond in potentiating the interaction between ligand and target. We propose this protein as an irreplaceable tool, allowing easy and relevant fine comparisons between series, to design, challenge and validate novel series of inhibitors. As proof-of-concept, we report here the design and synthesis of effective specific bacterial PDF inhibitors of an oxadiazole series with potent antimicrobial activity against a multidrug resistant clinical isolate.

scholarly journals Characterization of RelA in Acinetobacter baumannii

2020 ◽  
Vol 202 (12) ◽  
Author(s):  
María Pérez-Varela ◽  
Aimee R. P. Tierney ◽  
Ju-Sim Kim ◽  
Andrés Vázquez-Torres ◽  
Philip Rather
Keyword(s):  
Acinetobacter Baumannii ◽  
Galleria Mellonella ◽  
Multidrug Resistant ◽  
Cell Physiology ◽  
Content Type ◽  
Content Model ◽  
Transposon Insertion ◽  
Downstream Effectors

ABSTRACT In response to nutrient depletion, the RelA and SpoT proteins generate the signaling molecule (p)ppGpp, which then controls a number of downstream effectors to modulate cell physiology. In Acinetobacter baumannii strain AB5075, a relA ortholog (ABUW_3302) was identified by a transposon insertion that conferred an unusual colony phenotype. An in-frame deletion in relA (ΔrelA) failed to produce detectable levels of ppGpp when amino acid starvation was induced with serine hydroxamate. The ΔrelA mutant was blocked from switching from the virulent opaque colony variant (VIR-O) to the avirulent translucent colony variant (AV-T), but the rate of AV-T to VIR-O switching was unchanged. In addition, the ΔrelA mutation resulted in a pronounced hypermotile phenotype on 0.35% agar plates. This hypermotility was dependent on the activation of a LysR regulator ABUW_1132, which was required for expression of AbaR, a LuxR family quorum-sensing regulator. In the ΔrelA mutant, ABUW_1132 was also required for the increased expression of an operon composed of the ABUW_3766-ABUW_3773 genes required for production of the surfactant-like lipopeptide acinetin 505. Additional phenotypes identified in the ΔrelA mutant included (i) cell elongation at high density, (ii) reduced formation of persister cells tolerant to colistin and rifampin, and (iii) decreased virulence in a Galleria mellonella model. IMPORTANCE Acinetobacter baumannii is a pathogen of worldwide importance. Due to the increasing prevalence of antibiotic resistance, these infections are becoming increasingly difficult to treat. New therapies are required to combat multidrug-resistant isolates. The role of RelA in A. baumannii is largely unknown. This study demonstrates that like in other bacteria, RelA controls a variety of functions, including virulence. Strategies to inhibit the activity of RelA and the resulting production of ppGpp could inhibit virulence and may represent a new therapeutic approach.

scholarly journals The lone S41 family C-terminal processing protease in Staphylococcus aureus is localized to the cell wall and contributes to virulence

Microbiology ◽  
2014 ◽  
Vol 160 (8) ◽  
pp. 1737-1748 ◽  
Author(s):  
Ronan K. Carroll ◽  
Frances E. Rivera ◽  
Courtney K. Cavaco ◽  
Grant M. Johnson ◽  
David Martin ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Cell Wall ◽  
Critical Role ◽  
Multidrug Resistant ◽  
Health Concern ◽  
Host Immune System ◽  
Increased Sensitivity ◽  
Processing Protease

Staphylococcus aureus is a versatile pathogen of humans and a continued public health concern due to the rise and spread of multidrug-resistant strains. As part of an ongoing investigation into the pathogenic mechanisms of this organism we previously demonstrated that an intracellular N-terminal processing protease is required for S. aureus virulence. Following on from this, here we examine the role of CtpA, the lone C-terminal processing protease of S. aureus. CtpA, a member of the S41 family, is a serine protease whose homologues in Gram-negative bacteria have been implicated in a range of biological functions, including pathogenesis. We demonstrate that S. aureus CtpA is localized to the bacterial cell wall and expression of the ctpA gene is maximal upon exposure to conditions encountered during infection. Disruption of the ctpA gene leads to decreased heat tolerance and increased sensitivity when exposed to components of the host immune system. Finally we demonstrate that the ctpA − mutant strain is attenuated for virulence in a murine model of infection. Our results represent the first characterization of a C-terminal processing protease in a pathogenic Gram-positive bacterium and show that it plays a critical role during infection.

Structural Design and Synthesis of H3O+-β”/βAl2O3 and NH4-β”/β-Al2O3 Polycrystals

1988 ◽  
Vol 135 ◽  
Author(s):  
Patrick S. Nicholson
Keyword(s):  
Ion Exchange ◽  
Structural Design ◽  
Synthesis And Characterization ◽  
Total Weight Loss ◽  
Chemical Formula ◽  
Two Phase ◽  
Design And Synthesis ◽  
And Control

AbstractThe synthesis and characterization of H3Oβ”/β-Al2O3 and NH4 + -H3O+β”/β-Al2O3 poly-crystals is described. The role of stress development and control in the intermediate stages of ion-exchange of the NaK-β”/βA12O3 ceramics is analysed and identifies the β-Al2O3 phase as acting as inert reinforcement for the two-phase composite. The Rb + ion-exchange of the intermediate K + β”/β-Al2O3 requisite for NH4+/H3O + ion-exchange to NH4-H3O+β”/βAl2O3 is described as also is the NH4NO3 exchange to the final ceramic. The total weight loss on heating NH4-H3O+β”/βAl2O3 polycrystals to 810°C is 7.4% which agrees with the value expected from the chemical formula. The 25°C conductivity of the grains of NH4 +-H3O + β”/βAl2O3 was 1.7 × 10−4 (ω-cm)−1 and the bulk conductivity was 3 × 10−5(ω-cm)−1.

scholarly journals Atomic-scale characterization of mature HIV-1 capsid stabilization by inositol hexakisphosphate (IP6)

2020 ◽  
Vol 6 (38) ◽  
pp. eabc6465 ◽  
Author(s):  
Alvin Yu ◽  
Elizabeth M. Y. Lee ◽  
Jaehyeok Jin ◽  
Gregory A. Voth
Keyword(s):  
Kinetic Studies ◽  
Binding Pocket ◽  
Free Energy Calculations ◽  
Atomic Scale ◽  
Binding Modes ◽  
Ligand Density ◽  
Scale Characterization ◽  
Dynamics Simulations

Inositol hexakisphosphates (IP6) are cellular cofactors that promote the assembly of mature capsids of HIV. These negatively charged molecules coordinate an electropositive ring of arginines at the center of pores distributed throughout the capsid surface. Kinetic studies indicate that the binding of IP6 increases the stable lifetimes of the capsid by several orders of magnitude from minutes to hours. Using all-atom molecular dynamics simulations, we uncover the mechanisms that underlie the unusually high stability of mature capsids in complex with IP6. We find that capsid hexamers and pentamers have differential binding modes for IP6. Ligand density calculations show three sites of interaction with IP6 including at a known capsid inhibitor binding pocket. Free energy calculations demonstrate that IP6 preferentially stabilizes pentamers over hexamers to enhance fullerene modes of assembly. These results elucidate the molecular role of IP6 in stabilizing and assembling the retroviral capsid.

scholarly journals Direct Glutaminyl-tRNA Biosynthesis and Indirect Asparaginyl-tRNA Biosynthesis in Pseudomonas aeruginosa PAO1

2004 ◽  
Vol 186 (3) ◽  
pp. 767-776 ◽  
Author(s):  
Pierre-Marie Akochy ◽  
Dominic Bernard ◽  
Paul H. Roy ◽  
Jacques Lapointe
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Genomic Sequence ◽  
Multidrug Resistant ◽  
Open Reading Frames ◽  
Indirect Pathway ◽  
Biochemical Tests ◽  
Trna Synthetases ◽  
Gram Positive Bacteria

ABSTRACT The genomic sequence of Pseudomonas aeruginosa PAO1 was searched for the presence of open reading frames (ORFs) encoding enzymes potentially involved in the formation of Gln-tRNA and of Asn-tRNA. We found ORFs similar to known glutamyl-tRNA synthetases (GluRS), glutaminyl-tRNA synthetases (GlnRS), aspartyl-tRNA synthetases (AspRS), and trimeric tRNA-dependent amidotransferases (AdT) but none similar to known asparaginyl-tRNA synthetases (AsnRS). The absence of AsnRS was confirmed by biochemical tests with crude and fractionated extracts of P. aeruginosa PAO1, with the homologous tRNA as the substrate. The characterization of GluRS, AspRS, and AdT overproduced from their cloned genes in P. aeruginosa and purified to homogeneity revealed that GluRS is discriminating in the sense that it does not glutamylate tRNAGln, that AspRS is nondiscriminating, and that its Asp-tRNAAsn product is transamidated by AdT. On the other hand, tRNAGln is directly glutaminylated by GlnRS. These results show that P. aeruginosa PAO1 is the first organism known to synthesize Asn-tRNA via the indirect pathway and to synthesize Gln-tRNA via the direct pathway. The essential role of AdT in the formation of Asn-tRNA in P. aeruginosa and the absence of a similar activity in the cytoplasm of eukaryotic cells identifies AdT as a potential target for antibiotics to be designed against this human pathogen. Such novel antibiotics could be active against other multidrug-resistant gram-negative pathogens such as Burkholderia and Neisseria as well as all pathogenic gram-positive bacteria.

Emerging role of carbonic anhydrase inhibitors

2021 ◽  
Vol 135 (10) ◽  
pp. 1233-1249
Author(s):  
Claudiu T. Supuran
Keyword(s):  
Carbonic Anhydrase ◽  
Pathogenic Bacteria ◽  
Acute Mountain Sickness ◽  
Proof Of Concept ◽  
Mountain Sickness ◽  
Antiobesity Agents ◽  
New Applications ◽  
Human Isoforms

Abstract Inhibition of carbonic anhydrase (CA, EC 4.2.1.1) was clinically exploited for decades, as most modern diuretics were obtained considering as lead molecule acetazolamide, the prototypical CA inhibitor (CAI). The discovery and characterization of multiple human CA (hCA) isoforms, 15 of which being known today, led to new applications of their inhibitors. They include widely clinically used antiglaucoma, antiepileptic and antiobesity agents, antitumor drugs in clinical development, as well as drugs for the management of acute mountain sickness and idiopathic intracranial hypertension (IIH). Emerging roles of several CA isoforms in areas not generally connected to these enzymes were recently documented, such as in neuropathic pain, cerebral ischemia, rheumatoid arthritis, oxidative stress and Alzheimer’s disease. Proof-of-concept studies thus emerged by using isoform-selective inhibitors, which may lead to new clinical applications in such areas. Relevant preclinical models are available for these pathologies due to the availability of isoform-selective CAIs for all human isoforms, belonging to novel classes of compounds, such as coumarins, sulfocoumarins, dithiocarbamates, benzoxaboroles, apart the classical sulfonamide inhibitors. The inhibition of CAs from pathogenic bacteria, fungi, protozoans or nematodes started recently to be considered for obtaining anti-infectives with a new mechanism of action.

Digital x-ray mapping of nanometer-size supported bimetallic catalysts

1988 ◽  
Vol 46 ◽  
pp. 530-531
Author(s):  
L. T. Germinario
Keyword(s):  
Background Radiation ◽  
Metal Cluster ◽  
Single Element ◽  
Beam Diameter ◽  
X Rays ◽  
X Ray ◽  
Major Interest ◽  
Induced Changes

Understanding the role of metal cluster composition in determining catalytic selectivity and activity is of major interest in heterogeneous catalysis. The electron microscope is well established as a powerful tool for ultrastructural and compositional characterization of support and catalyst. Because the spatial resolution of x-ray microanalysis is defined by the smallest beam diameter into which the required number of electrons can be focused, the dedicated STEM with FEG is the instrument of choice. The main sources of errors in energy dispersive x-ray analysis (EDS) are: (1) beam-induced changes in specimen composition, (2) specimen drift, (3) instrumental factors which produce background radiation, and (4) basic statistical limitations which result in the detection of a finite number of x-ray photons. Digital beam techniques have been described for supported single-element metal clusters with spatial resolutions of about 10 nm. However, the detection of spurious characteristic x-rays away from catalyst particles produced images requiring several image processing steps.

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