Development of a Coupled VanA/VanX Assay: Screening for Inhibitors of Glycopeptide Resistance

Resistance in Enterococcus faecium to the glycopeptide antibiotics vancomycin and teicoplanin is encoded by five genes: vanR, vanS, vanH, vanA, and vanX.1 The mechanism of resistance involves replacement of the dipeptide D-Ala-D-Ala, destined for the peptidoglycan layer with the depsipeptide D-Ala-D-lactate. This alteration lowers the binding affinity of vancomycin for the bacterial cell wall by a factor of 1000. The functions of VanA and VanX are the ligation of D-Ala and D-lactate, and the hydrolysis of D-Ala-D-Ala, respectively. We report here the overexpression of both genes as well as the D-Ala-D-Ala ligase (Ddl) from Enterococcus faecium, development of a coupled assay and several inhibitors obtained by high-throughput screening (HTS). All genes were expressed in E. coli by translational coupling to kdsB, the CMP-KDO synthetase gene, under control of a modified lac promoter. The coupled VanA/VanX assay employs colorimetric detection of inorganic phosphate (Pi) released in the VanA ligation reaction, with the VanX dipeptidase activity providing the D-Ala substrate for VanA. A secondary VanX assay uses cadmium-ninhydrin calorimetric detection of free amino acid released by the dipeptidase activity of the enzyme on D-Ala-D-Ala. We have also developed an assay using Ddl ligase. Over 250,000 compounds have been screened to date using the coupled assay.

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Novel Mechanism of Resistance to Glycopeptide Antibiotics in Enterococcus faecium

Journal of Biological Chemistry ◽

10.1074/jbc.m606920200 ◽

2006 ◽

Vol 281 (43) ◽

pp. 32254-32262 ◽

Cited By ~ 27

Author(s):

Julie Cremniter ◽

Jean-Luc Mainardi ◽

Nathalie Josseaume ◽

Jean-Charles Quincampoix ◽

Lionel Dubost ◽

...

Keyword(s):

Enterococcus Faecium ◽

Peptide Bond ◽

Cross Resistance ◽

Glycopeptide Antibiotics ◽

Penicillin Binding Proteins ◽

Gram Positive Bacteria ◽

High Level ◽

Hydrolysis Of ◽

Link Formation ◽

Level Resistance

Glycopeptides and β-lactams are the major antibiotics available for the treatment of infections due to Gram-positive bacteria. Emergence of cross-resistance to these drugs by a single mechanism has been considered as unlikely because they inhibit peptidoglycan polymerization by different mechanisms. The glycopeptides bind to the peptidyl-d-Ala4-d-Ala5 extremity of peptidoglycan precursors and block by steric hindrance the essential glycosyltransferase and d,d-transpeptidase activities of the penicillin-binding proteins (PBPs). The β-lactams are structural analogues of d-Ala4-d-Ala5 and act as suicide substrates of the d,d-transpeptidase module of the PBPs. Here we have shown that bypass of the PBPs by the recently described β-lactam-insensitive l,d-transpeptidase from Enterococcus faecium (Ldtfm) can lead to high level resistance to glycopeptides and β-lactams. Cross-resistance was selected by glycopeptides alone or serially by β-lactams and glycopeptides. In the corresponding mutants, UDP-MurNAc-pentapeptide was extensively converted to UDP-MurNAc-tetrapeptide following hydrolysis of d-Ala5, thereby providing the substrate of Ldtfm. Complete elimination of d-Ala5, a residue essential for glycopeptide binding, was possible because Ldtfm uses the energy of the l-Lys3-d-Ala4 peptide bond for cross-link formation in contrast to PBPs, which use the energy of the d-Ala4-d-Ala5 bond. This novel mechanism of glycopeptide resistance was unrelated to the previously identified replacement of d-Ala5 by d-Ser or d-lactate.

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Directed Evolution of P450 Fatty Acid Decarboxylases via High-Throughput Screening Towards Improved Catalytic Activity

10.26434/chemrxiv.9791162 ◽

2019 ◽

Author(s):

Huifang Xu ◽

Weinan Liang ◽

Linlin Ning ◽

Yuanyuan Jiang ◽

Wenxia Yang ◽

...

Keyword(s):

Catalytic Activity ◽

Fatty Acid ◽

Directed Evolution ◽

High Throughput ◽

High Throughput Screening ◽

Colorimetric Detection ◽

Screening Method ◽

Random Mutagenesis ◽

Direct Production ◽

Consumption Activity

P450 fatty acid decarboxylases (FADCs) have recently been attracting considerable attention owing to their one-step direct production of industrially important 1-alkenes from biologically abundant feedstock free fatty acids under mild conditions. However, attempts to improve the catalytic activity of FADCs have met with little success. Protein engineering has been limited to selected residues and small mutant libraries due to lack of an effective high-throughput screening (HTS) method. Here, we devise a catalase-deficient Escherichia coli host strain and report an HTS approach based on colorimetric detection of H2O2-consumption activity of FADCs. Directed evolution enabled by this method has led to effective identification for the first time of improved FADC variants for medium-chain 1-alkene production from both DNA shuffling and random mutagenesis libraries. Advantageously, this screening method can be extended to other enzymes that stoichiometrically utilize H2O2 as co-substrate.

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Large-scale High-throughput Screening Revealed 5'-(carbonylamino)-2,3'- bithiophene-4'-carboxylate as Novel Template for Antibacterial Agents

Current Drug Discovery Technologies ◽

10.2174/1570163816666190603095521 ◽

2020 ◽

Vol 17 (5) ◽

pp. 716-724

Author(s):

Yan A. Ivanenkov ◽

Renat S. Yamidanov ◽

Ilya A. Osterman ◽

Petr V. Sergiev ◽

Vladimir A. Aladinskiy ◽

...

Keyword(s):

Antibacterial Activity ◽

High Throughput ◽

High Throughput Screening ◽

Large Scale ◽

Antibacterial Agents ◽

Sos Response ◽

Luciferase Assay ◽

Translational Machinery ◽

E Coli ◽

New Class

Background: The key issue in the development of novel antimicrobials is a rapid expansion of new bacterial strains resistant to current antibiotics. Indeed, World Health Organization has reported that bacteria commonly causing infections in hospitals and in the community, e.g. E. Coli, K. pneumoniae and S. aureus, have high resistance vs the last generations of cephalosporins, carbapenems and fluoroquinolones. During the past decades, only few successful efforts to develop and launch new antibacterial medications have been performed. This study aims to identify new class of antibacterial agents using novel high-throughput screening technique. Methods: We have designed library containing 125K compounds not similar in structure (Tanimoto coeff.< 0.7) to that published previously as antibiotics. The HTS platform based on double reporter system pDualrep2 was used to distinguish between molecules able to block translational machinery or induce SOS-response in a model E. coli system. MICs for most active chemicals in LB and M9 medium were determined using broth microdilution assay. Results: In an attempt to discover novel classes of antibacterials, we performed HTS of a large-scale small molecule library using our unique screening platform. This approach permitted us to quickly and robustly evaluate a lot of compounds as well as to determine the mechanism of action in the case of compounds being either translational machinery inhibitors or DNA-damaging agents/replication blockers. HTS has resulted in several new structural classes of molecules exhibiting an attractive antibacterial activity. Herein, we report as promising antibacterials. Two most active compounds from this series showed MIC value of 1.2 (5) and 1.8 μg/mL (6) and good selectivity index. Compound 6 caused RFP induction and low SOS response. In vitro luciferase assay has revealed that it is able to slightly inhibit protein biosynthesis. Compound 5 was tested on several archival strains and exhibited slight activity against gram-negative bacteria and outstanding activity against S. aureus. The key structural requirements for antibacterial potency were also explored. We found, that the unsubstituted carboxylic group is crucial for antibacterial activity as well as the presence of bulky hydrophobic substituents at phenyl fragment. Conclusion: The obtained results provide a solid background for further characterization of the 5'- (carbonylamino)-2,3'-bithiophene-4'-carboxylate derivatives discussed herein as new class of antibacterials and their optimization campaign.

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Hydrolysis of the brain dipeptide N-acetyl-L-aspartyl-L-glutamate. Identification and characterization of a novel N-acetylated alpha-linked acidic dipeptidase activity from rat brain.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)47823-4 ◽

1987 ◽

Vol 262 (30) ◽

pp. 14498-14506

Author(s):

M B Robinson ◽

R D Blakely ◽

R Couto ◽

J T Coyle

Keyword(s):

Rat Brain ◽

Hydrolysis Of ◽

The Brain ◽

Identification And Characterization ◽

Dipeptidase Activity

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A High-Throughput Approach To Identify Compounds That Impair Envelope Integrity in Escherichia coli

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00537-16 ◽

2016 ◽

Vol 60 (10) ◽

pp. 5995-6002 ◽

Cited By ~ 7

Author(s):

Kristin R. Baker ◽

Bimal Jana ◽

Henrik Franzyk ◽

Luca Guardabassi

Keyword(s):

Escherichia Coli ◽

High Throughput ◽

High Throughput Screening ◽

Gram Negative Bacteria ◽

Chromogenic Substrate ◽

Intrinsic Resistance ◽

Gram Negative ◽

Content Type ◽

E Coli ◽

Screening Platform

ABSTRACTThe envelope of Gram-negative bacteria constitutes an impenetrable barrier to numerous classes of antimicrobials. This intrinsic resistance, coupled with acquired multidrug resistance, has drastically limited the treatment options against Gram-negative pathogens. The aim of the present study was to develop and validate an assay for identifying compounds that increase envelope permeability, thereby conferring antimicrobial susceptibility by weakening of the cell envelope barrier in Gram-negative bacteria. A high-throughput whole-cell screening platform was developed to measureEscherichia colienvelope permeability to a β-galactosidase chromogenic substrate. The signal produced by cytoplasmic β-galactosidase-dependent cleavage of the chromogenic substrate was used to determine the degree of envelope permeabilization. The assay was optimized by using known envelope-permeabilizing compounds andE. coligene deletion mutants with impaired envelope integrity. As a proof of concept, a compound library comprising 36 peptides and 45 peptidomimetics was screened, leading to identification of two peptides that substantially increased envelope permeability. Compound 79 reduced significantly (from 8- to 125-fold) the MICs of erythromycin, fusidic acid, novobiocin and rifampin and displayed synergy (fractional inhibitory concentration index, <0.2) with these antibiotics by checkerboard assays in two genetically distinctE. colistrains, including the high-risk multidrug-resistant, CTX-M-15-producing sequence type 131 clone. Notably, in the presence of 0.25 μM of this peptide, both strains were susceptible to rifampin according to the resistance breakpoints (R> 0.5 μg/ml) for Gram-positive bacterial pathogens. The high-throughput screening platform developed in this study can be applied to accelerate the discovery of antimicrobial helper drug candidates and targets that enhance the delivery of existing antibiotics by impairing envelope integrity in Gram-negative bacteria.

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Caracterización de microorganismos con potencial probiótico aislados de estiércol de terneros Brahman en Sucre, Colombia

Revista de Investigaciones Veterinarias del Perú ◽

10.15381/rivep.v29i2.14482 ◽

2018 ◽

Vol 29 (2) ◽

pp. 438

Author(s):

Pedro Luis Castillo Arroyo ◽

César Augusto Betancur Hurtado ◽

Enrique Pardo Pérez

Keyword(s):

Escherichia Coli ◽

Enterococcus Faecium ◽

Candida Krusei ◽

E Coli

El objetivo del estudio fue caracterizar microorganismos con potencial probiótico de estiércol de terneros lactantes Brahman en Sucre (Colombia). Se aislaron bacterias y levaduras de las muestras de estiércol y se determinó la capacidad probiótica de estas cepas mediante pruebas de resistencia a sales biliares (0.05, 0.1, 0.15 y 0.3%), resistencia a pH ácido (pH 3, 4, 5.6, 7), tolerancia a NaCl (2, 4, 6, 8, 10%) y actividad antagónica (Salmonella sp y Escherichia coli). Nueve microorganismos fueron identificados y tres pasaron las pruebas de tolerancia. Se determinó la capacidad antagónica frente a bacterias patógenas (Salmonella sp y E. coli), evidenciada por halos (mm) de las tres cepas seleccionadas. La identificación de las cepas se realizó por los métodos bioquímicos API 50 CHL V5.1 para Lactobacillus y API 20 AUX para levaduras. El análisis molecular de dos cepas (M13a y 103M2) identificó la cepa M13a como Enterococcus faecium y la cepa 103M2 como Candida krusei. En conclusión, Enterococcus faecium se convierte en una alternativa viable para la formulación de un biopreparado para mejorar los parámetros productivos y disminuir los trastornos gastrointestinales en los terneros lactantes.

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Enterohemorrhagic Escherichia coli Colony Check Assay for the Identification of Serogroups O26, O45, O103, O111, O121, O145, and O157 Colonies Isolated on Plating Media

Journal of Food Protection ◽

10.4315/0362-028x.jfp-13-555 ◽

2014 ◽

Vol 77 (7) ◽

pp. 1212-1218 ◽

Cited By ~ 1

Author(s):

BURTON BLAIS ◽

MYLÈNE DESCHÊNES ◽

GEORGE HUSZCZYNSKI ◽

MARTINE GAUTHIER

Keyword(s):

Escherichia Coli ◽

Shiga Toxin ◽

High Throughput Screening ◽

Enterohemorrhagic Escherichia Coli ◽

Test Results ◽

Bacterial Strains ◽

Enrichment Broth ◽

Substrate Solution ◽

E Coli ◽

Assay Performance

A simple immunoenzymatic enterohemorrhagic Escherichia coli (EHEC) colony check (ECC) assay was developed for the presumptive identification of priority EHEC colonies isolated on plating media from enrichment broth cultures of foods. With this approach, lipopolysaccharide extracted from a colony is spotted on the grid of a polymyxin-coated polyester cloth strip, and bound E. coli serogroup O26, O45, O103, O111, O121, O145, and O157 antigens are subsequently detected by sequential reactions with a pool of commercially available peroxidase-conjugated goat antibodies and tetramethylbenzidine substrate solution. Each strip can accommodate up to 15 colonies, and test results are available within 30 min. Assay performance was verified using colonies from a total of 73 target EHEC isolates covering the range of designated priority serogroups (all of which were reactive), 41 nontarget E. coli isolates including several nontarget Shiga toxin–producing E. coli serogroups (all unreactive), and 33 non–E. coli strains (all unreactive except two bacterial strains possessing O-antigenic structures in common with those of the priority EHEC). The ECC assay was reactive with target colonies grown on several types of selective and nonselective plating media designed for their cultivation. These results support the use of the ECC assay for high-throughput screening of colonies isolated on plating media for detecting priority EHEC strains in foods.

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Effects of the Movement of Insertion Sequences on the Structure of VanA Glycopeptide Resistance Elements in Enterococcus faecium

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.44.5.1362-1364.2000 ◽

2000 ◽

Vol 44 (5) ◽

pp. 1362-1364 ◽

Cited By ~ 25

Author(s):

Ana L. C. Darini ◽

Marie-France I. Palepou ◽

Neil Woodford

Keyword(s):

Structural Change ◽

Inverted Repeat ◽

Enterococcus Faecium ◽

Insertion Sequence ◽

Host Strain ◽

Insertion Sequences ◽

Glycopeptide Resistance ◽

Related Element

ABSTRACT A Tn1546-related element with IS1216V at position 8839 underwent a structural change after storage of the host strain of Enterococcus faecium at 4°C. The element acquired IS1542 at position 3932, nucleotides 8732 to 8831 were deleted, and the first 3417 nucleotides were lost and replaced by an inverted copy of the IS1216V–vanY–vanZ-inverted-repeat block from the 3′ end. Insertion sequence movement is likely to play a key role in the evolution of VanA resistance elements.

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Potential Probiotic Enterococcus faecium OV3-6 and Its Bioactive Peptide as Alternative Bio-Preservation

Foods ◽

10.3390/foods10102264 ◽

2021 ◽

Vol 10 (10) ◽

pp. 2264

Author(s):

Thiwanya Choeisoongnern ◽

Sasithorn Sirilun ◽

Rungaroon Waditee-Sirisattha ◽

Komsak Pintha ◽

Sartjin Peerajan ◽

...

Keyword(s):

Enterococcus Faecium ◽

Ribosomal Proteins ◽

Starter Culture ◽

Heat Stability ◽

Fermented Food ◽

E Coli ◽

Active Peptide ◽

Wide Ph Range ◽

Small Intestinal ◽

Ph Range

Probiotic Enterococcus faecium OV3-6 and its secreted active peptide were characterized and investigated. The strain survived in simulated gastric and small intestinal conditions at 88.16% and 94.33%, respectively. The safety assessment revealed that the strain was shown α-hemolysis and susceptible to most clinically relevant antibiotics, but intermediate sensitivity to erythromycin and kanamycin was found. It does not harbor any virulence genes except for the efaAfm gene. Both of its living cells and the cell-free supernatants (CFS) of the strain significantly reduced the adhesion of E. coli and S. Typhi on Caco-2 cells. The strain can regulate the secretion of pro and inflammatory cytokines, IL-6 and IL-12 and induce the secretion of anti-inflammatory IL-10 of the Caco-2 cell. The strain can prevent the growth of Gram-positive strains belonging to the genera Bacillus, Carnobacterium, Listeria, and Staphylococcus. It also presented the entP gene that involves the production of bacteriocin named enterocin P. The antimicrobial peptide was matched 40% with 50S ribosomal proteins L29 (7.325 kDa), as revealed by LC-MS/MS. This active peptide exhibits heat stability, is stable over a wide pH range of 2−10, and maintains its activity at −20 and 4 °C for 12 weeks of storage. Altogether, E. faecium OV3-6 thus has potential for consideration as a probiotic and bio-preservative for applied use as a fermented food starter culture and in functional food or feed industries.

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