Glycopeptide Antibiotics Impair Neutrophil Effector Functions.

INTRODUCTION: Neutrophilic granulocytes represent the first line of defense against microorganisms. Granulocytes phagocytose microorganisms and specifically synthesize oxygen radicals against them, which eventually kills the invaders. METHODS: Neutrophilic granulocytes were isolated from peripheral blood of healthy volunteer donors. Putative interference of new-generation antibiotics with neutrophil function was tested using a collection of granulocyte-stimulating agents and Amplex™ Red-based plate assay and flow cytometry-based respiratory burst assays. In addition, phagocytosis of E. coli, IL-8 production, bactericidal activity, and CD62L expression of granulocytes were evaluated. RESULTS: Of note, we found that the two glycopeptide antibiotics dalbavancin and teicoplanin inhibited ROS production upon granulocyte activation via different signaling pathways in a dose-dependent manner. Dalbavancin also blocked the PMA-induced shedding of CD62L. In contrast, the oxazolidinone antibiotics tedizolid and linezolid had no effect on neutrophil function, while the combination of ceftazidime/avibactam dose dependently inhibited the fMLP/Cytochalasin B-induced granulocyte burst in a dose-dependent manner. Additionally, we showed that dalbavancin and teicoplanin as well as sulfametrole/trimethoprim and ceftazidime/avibactam inhibited baseline and PMA-induced IL-8 production by neutrophilic granulocytes. Moreover, dalbavancin impaired the bactericidal activity of neutrophilic granulocytes. CONCLUSION: We here identified hitherto unknown inhibitory effects of several classes of antibiotics on the effector functions of neutrophilic granulocytes.

TIGAR Protects Cochlear Hair Cells against Teicoplanin-Induced Damage.

Teicoplanin is a glycopeptide antibiotic used to treat severe staphylococcal infections. It has been claimed that teicoplanin possesses ototoxic potential, although its toxic effects on cochlear hair cells (HCs) remain unknown. The TP53-induced glycolysis and apoptosis regulator (TIGAR) plays a crucial role in promoting cell survival. Prior research has demonstrated that TIGAR protects spiral ganglion neurons against cisplatin damage. However, the significance of TIGAR in damage to mammalian HCs has not yet been investigated. In this study, firstly, we discovered that teicoplanin caused dose-dependent cell death in vitro in both HEI-OC1 cells and cochlear HCs. Next, we discovered that HCs and HEI-OC1 cells treated with teicoplanin exhibited a dramatically decrease in TIGAR expression. To investigate the involvement of TIGAR in inner ear injury caused by teicoplanin, the expression of TIGAR was either upregulated via recombinant adenovirus or downregulated by shRNA in HEI-OC1 cells. Overexpression of TIGAR increased cell viability, decreased apoptosis, and decreased intracellular reactive oxygen species (ROS) level, whereas downregulation of TIGAR decreased cell viability, exacerbated apoptosis, and elevated ROS level following teicoplanin injury. Finally, antioxidant therapy with N-acetyl-L-cysteine decreased ROS level, prevented cell death, and restored p38/phosphorylation-p38 expression levels in HEI-OC1 cells injured by teicoplanin. This study demonstrates that TIGAR may be a promising novel target for the prevention of teicoplanin-induced ototoxicity.

Teicoplanin derivatives block spike protein mediated viral entry as pan-SARS-CoV-2 inhibitors.

The rapid emergence of highly transmissible SARS-CoV-2 variants poses serious threat to the efficacy of vaccines and neutralizing antibodies. Thus, there is an urgent need to develop new and effective inhibitors against SARS-CoV-2 and future outbreaks. Here, we have identified a series of glycopeptide antibiotics teicoplanin derivatives that bind to the SARS-CoV-2 spike (S) protein, interrupt its interaction with ACE2 receptor and selectively inhibit viral entry mediated by S protein. Computation modeling predicts that these compounds interact with the residues in the receptor binding domain. More importantly, these teicoplanin derivatives inhibit the entry of both pseudotyped SARS-CoV-2 Delta and Omicron variants. Our study demonstrates the feasibility of developing small molecule entry inhibitors by targeting the interaction of viral S protein and ACE2. Together, considering the proven safety and pharmacokinetics of teicoplanin as a glycopeptide antibiotic, the teicoplanin derivatives hold great promise of being repurposed as pan-SARS-CoV-2 inhibitors.

Structural Basis for the Binding Mechanism of Human Serum Albumin Complexed with Cyclic Peptide Dalbavancin.

Cyclic peptides, with unique structural features, have emerged as new candidates for drug discovery; their association with human serum albumin (HSA; long blood half-life) is crucial to improve drug delivery and avoid renal clearance. Here, we present the crystal structure of HSA complexed with dalbavancin, a clinically used cyclic peptide. Small-angle X-ray scattering and isothermal titration calorimetry experiments showed that the HSA-dalbavancin complex exists in a monomeric state; dalbavancin is only bound to the subdomain IA of HSA in solution. Structural analysis and MD simulation revealed that the swing of Phe70 and movement of the helix near dalbavancin were necessary for binding. The flip of Leu251 promoted the formation of the binding pocket with an induced-fit mechanism; moreover, the movement of the loop region including Glu60 increased the number of noncovalent interactions with HSA. These findings may support the development of new cyclic peptides for clinical use, particularly the elucidation of their binding mechanism to HSA.

The reorganization of conformations, stability and aggregation of serum albumin isomers through the interaction of glycopeptide antibiotic teicoplanin: A thermodynamic and spectroscopy study.

The drugs-protein binding study is of growing importance for drug-repurposing against amyloidosis. In this work, we study the binding of teicoplanin (TPN), a glycopeptide antibiotic, with bovine serum albumin (BSA) in its neutral (N), physiological (P) and basic (B) forms, which exist at pH 6, pH 7.4 and pH 9, respectively. The binding and thermodynamic parameters of TPN binding were determined by isothermal titration calorimetry (ITC) and fluorescence quench titration methods. Two binding sites were observed for N and P forms, whereas B form showed only one binding site. ITC and molecular docking results indicated that TPN-BSA complex formation is stabilized by hydrogen bonds, salt bridges and hydrophobic interaction. The red-edge excitation shift (REES) study indicated an ordered compact and spatial arrangement of the TPN bound protein molecule. TPN was found to affect the secondary and tertiary structures of B form only. The TPN binding was observed to marginally stabilize BSA isomers. TPN was also found to inhibit BSA aggregation as monitored by Rayleigh light scattering and thioflavin T binding assay. The current in vitro study will open a new path to explore the possible use of TPN as potential drugs to treat amyloidosis.

A Two-Component regulatory system with opposite effects on glycopeptide antibiotic biosynthesis and resistance.

The glycopeptide A40926, produced by the actinomycete Nonomuraea gerenzanensis, is the precursor of dalbavancin, a second-generation glycopeptide antibiotic approved for clinical use in the USA and Europe in 2014 and 2015, respectively. The final product of the biosynthetic pathway is an O-acetylated form of A40926 (acA40926). Glycopeptide biosynthesis in N. gerenzanensis is dependent upon the dbv gene cluster that encodes, in addition to the two essential positive regulators Dbv3 and Dbv4, the putative members of a two-component signal transduction system, specifically the response regulator Dbv6 and the sensor kinase Dbv22. The aim of this work was to assign a role to these two genes. Our results demonstrate that deletion of dbv22 leads to an increased antibiotic production with a concomitant reduction in glycopeptide resistance. Deletion of dbv6 results in a similar phenotype, although the effects are not as strong as in the Δdbv22 mutant. Consistently, quantitative RT-PCR analysis showed that Dbv6 and Dbv22 negatively regulate the regulatory genes (dbv3 and dbv4), as well as some dbv biosynthetic genes (dbv23 and dbv24), whereas Dbv6 and Dbv22 positively regulate transcription of the single, cluster-associated resistance gene. Finally, we demonstrate that exogenously added acA40926 and its precursor A40926 can modulate transcription of dbv genes but with an opposite extent: A40926 strongly stimulates transcription of the Dbv6/Dbv22 target genes while acA40926 has a neutral or negative effect on transcription of those genes. We propose a model in which glycopeptide biosynthesis in N. gerenzanensis is modulated through a positive feedback by the biosynthetic precursor A40926 and a negative feedback by the final product acA40926. In addition to previously reported control systems, this sophisticated control loop might help the producing strain cope with the toxicity of its own product. This work, besides leading to improved glycopeptide producing strains, enlarges our knowledge on the regulation of glycopeptide biosynthesis in actinomycetes, setting N. gerenzanensis and its two-component system Dbv6-Dbv22 apart from other glycopeptide producers.

Surface Design of Enantiomeric HPLC Separation on Vancomycin and Teicoplanin-Based Stationary Phases, a Tool for Chiral Recognition of Model ß-Blockers.

A quality-by-design approach was adopted for enantioseparation of atenolol on Vancomycin and Teicoplanin-based chiral stationary phases using reversed phase (RP) mode and polar ionic mode (PIM), respectively to account for major forces involved in enantiorecognition of ß-blockers on macrocyclics. A fractional factorial screening design for the two modes; followed by a central composite optimization design and regression analysis were able to point out critical factors and chromatographic responses and robust surface of the design. Within the studied range of flow the optimal was 0.3 mL/min for Chirobiotic T and 1 mL/min for Chirobiotic V. In PIM, a composition of 100% methanol was mandatory to compromise between best separation and least retention with equal amounts of the acid and base modifiers for enantiomers of atenolol, as model drug in addition to metoprolol and pindolol as structurally related compounds for possible extrapolation of results on members of the same class. However, in RP mode, only triethylamine acetate was needed as buffer for atenolol enantiomers. Chiral recognition of atenolol in both elution modes, further confirmed via extrapolation of the models on the two other ß-blockers showed that ionic interactions rather than any other forces governed chiral recognition on the two macrocyclic stationary phases in both modes.

Fluorescence assay to predict activity of the glycopeptide antibiotics.

Here, we describe a fluorescent assay developed to study competitive binding of the glycopeptide antibiotics to live bacteria cells. This assay demonstrated that the mechanism of action of the lipoglycopeptide antibiotics strongly depends on the hydrophobicity of the substitutes, with the best antibacterial activity of the glycopeptide antibiotics equally sharing properties of binding to D-Ala-D-Ala residues of the nascent peptidoglycan and to the membrane.

Specific chemiluminescent protocol for dual-site recognition of Streptococcus mutans utilizing strong affinity between teicoplanin and Gram-positive bacteria.

A novel dual-site recognition protocol was developed for chemiluminescent (CL) detection of Streptococcus mutans (S. mutans) based on a designed antibiotic-affinity strategy. Teicoplanin, a broad-spectrum antibiotic against Gram-positive bacteria, was adopted to functionalize magnetic particles and recognize S. mutans utilizing the strong affinity between this agent and D-Alanyl-D-Alanine peptide moieties in the bacterial cell wall. To achieve ideal specificity for S. mutans detection, rat immunoglobulin G2a (rat IgG2a) tagged with horseradish peroxidase (HRP) was used as the second recognition agent and signal tracer since Fab region of rat IgG2a could bind with streptococcal protein G highly expressed in the cell wall of S. mutans. Thus HRP-tagged sandwich complex of teicoplanin/S. mutans/rat IgG2a was formed on the magnetic particles, followed by a CL quantification of S. mutans based on a HRP-catalyzed luminol-H2O2-p-iodophenol CL reaction. This dual-site recognition protocol showed a linear range of 1.0 × 102-1.0 × 106 CFU mL-1 and a detection limit of 33 CFU mL-1 for S. mutans detection. The whole detection process could be completed within 70min. The recovery tests for food, environmental, pharmaceutical and biological samples showed acceptable recovery values between 83.0% and 110.0%, demonstrating its application potential for detection of bacteria in various sample matrixes.

Area under the curve predictions of dalbavancin, a new lipoglycopeptide agent, using the end of intravenous infusion concentration data point by regression analyses such as linear, log-linear and power models.

1. Dalbavancin, a lipoglycopeptide, is approved for treating gram-positive bacterial infections. Area under plasma concentration versus time curve (AUCinf) of dalbavancin is a key parameter and AUCinf/MIC ratio is a critical pharmacodynamic marker. 2. Using end of intravenous infusion concentration (i.e. Cmax) Cmax versus AUCinf relationship for dalbavancin was established by regression analyses (i.e. linear, log-log, log-linear and power models) using 21 pairs of subject data. 3. The predictions of the AUCinf were performed using published Cmax data by application of regression equations. The quotient of observed/predicted values rendered fold difference. The mean absolute error (MAE)/root mean square error (RMSE) and correlation coefficient (r) were used in the assessment. 4. MAE and RMSE values for the various models were comparable. The Cmax versus AUCinf exhibited excellent correlation (r > 0.9488). The internal data evaluation showed narrow confinement (0.84-1.14-fold difference) with a RMSE < 10.3%. The external data evaluation showed that the models predicted AUCinf with a RMSE of 3.02-27.46% with fold difference largely contained within 0.64-1.48. 5. Regardless of the regression models, a single time point strategy of using Cmax (i.e. end of 30-min infusion) is amenable as a prospective tool for predicting AUCinf of dalbavancin in patients.

Effects of Teicoplanin on the PT-INR Controlled by Warfarin in Infection Patients.

Warfarin (WF) shows a number of interactions with other drugs, which alter its anticoagulant effects. The albumin binding interaction is one such pharmacokinetic mechanism of drug interaction with WF, which induces a rise in the free WF concentration and thus increases the risk of WF toxicity. Teicoplanin (TEIC) is an anti-methicillin-resistant Staphylococcus aureus drug, which also binds strongly to albumin in the plasma. Therefore, co-administration of TEIC may displace WF from the albumin binding site, and possibly result in a toxicity. The present study was performed to investigate the drug-drug interaction between WF and TEIC in comparison with controls treated with vancomycin (VCM), which has the same spectrum of activity as TEIC but a lower albumin binding ratio.The records of 49 patients treated with WF and TEIC or VCM at Fukuoka University Hospital between 2010 and 2015 were retrospectively reviewed. These 49 patients consisted of 18 treated with TEIC in combination with WF, while 31 received VCM in combination with WF. Prothrombin time-international normalized ratio (PT-INR) showed a significant increase of 80.9 (52.0-155.3) % after co-administration of TEIC with WF. In contrast, the rate of PT-INR elevation associated with VCM plus WF was 30.6 (4.5-44.1) %. These observations suggested that TEIC can cause a rise in free WF concentration by albumin binding interaction. Therefore, careful monitoring of PT-INR elevation is necessary in patients receiving WF plus TEIC.

Characterisation of the selective binding of antibiotics vancomycin and teicoplanin by the VanS receptor regulating type A vancomycin resistance in the enterococci.

A-type resistance towards "last-line" glycopeptide antibiotic vancomycin in the leading hospital acquired infectious agent, the enterococci, is the most common in the UK. Resistance is regulated by the VanRASA two-component system, comprising the histidine sensor kinase VanSA and the partner response regulator VanRA. The nature of the activating ligand for VanSA has not been identified, therefore this work sought to identify and characterise ligand(s) for VanSA. In vitro approaches were used to screen the structural and activity effects of a range of potential ligands with purified VanSA protein. Of the screened ligands (glycopeptide antibiotics vancomycin and teicoplanin, and peptidoglycan components N-acetylmuramic acid, D-Ala-D-Ala and Ala-D-y-Glu-Lys-D-Ala-D-Ala) only glycopeptide antibiotics vancomycin and teicoplanin were found to bind VanSA with different affinities (vancomycin 70µM; teicoplanin 30 and 170µM), and were proposed to bind via exposed aromatic residues tryptophan and tyrosine. Furthermore, binding of the antibiotics induced quicker, longer-lived phosphorylation states for VanSA, proposing them as activators of type A vancomycin resistance in the enterococci.

How To Make a Glycopeptide: A Synthetic Biology Approach To Expand Antibiotic Chemical Diversity.

Modification of natural product backbones is a proven strategy for the development of clinically useful antibiotics. Such modifications have traditionally been achieved through medicinal chemistry strategies or via in vitro enzymatic activities. In an orthogonal approach, engineering of biosynthetic pathways using synthetic biology techniques can generate chemical diversity. Here we report the use of a minimal teicoplanin class glycopeptide antibiotic (GPA) scaffold expressed in a production-optimized Streptomyces coelicolor strain to expand GPA chemical diversity. Thirteen scaffold-modifying enzymes from 7 GPA biosynthetic gene clusters in different combinations were introduced into S. coelicolor, enabling us to explore the criteria for in-cell GPA modification. These include identifying specific isozymes that tolerate the unnatural GPA scaffold and modifications that prevent or allow further elaboration by other enzymes. Overall, 15 molecules were detected, 9 of which have not been reported previously. Some of these compounds showed activity against GPA-resistant bacteria. This system allows us to observe the complex interplay between substrates and both non-native and native tailoring enzymes in a cell-based system and establishes rules for GPA synthetic biology and subsequent expansion of GPA chemical diversity.

Facile Synthetic Access to Glycopeptide Antibiotic Precursor Peptides for the Investigation of Cytochrome P450 Action in Glycopeptide Antibiotic Biosynthesis.

The glycopeptide antibiotics are an important class of complex, medically relevant peptide natural products. Given that the production of such compounds all stems from in vivo biosynthesis, understanding the mechanisms of the natural assembly system--consisting of a nonribosomal-peptide synthetase machinery (NRPS) and further modifying enzymes--is vital. In order to address the later steps of peptide biosynthesis, which are catalyzed by Cytochrome P450s that interact with the peptide-producing nonribosomal peptide synthetase, peptide substrates are required: these peptides must also be in a form that can be conjugated to carrier protein domains of the nonribosomal peptide synthetase machinery. Here, we describe a practical and effective route for the solid phase synthesis of glycopeptide antibiotic precursor peptides as their Coenzyme A (CoA) conjugates to allow enzymatic conjugation to carrier protein domains. This route utilizes Fmoc-chemistry suppressing epimerization of racemization-prone aryl glycine derivatives and affords high yields and excellent purities, requiring only a single step of simple solid phase extraction for chromatographic purification. With this, comprehensive investigations of interactions between various NRPS-bound substrates and Cytochrome P450s are enabled.

Advancing cell wall inhibitors towards clinical applications.

Natural products represent a major source of approved drugs and still play an important role in supplying chemical diversity. Consistently, 2014 has seen new, natural product-derived antibiotics approved for human use by the US Food and Drug Administration. One of the recently approved second-generation glycopeptides is dalbavancin, a semi-synthetic derivative of the natural product A40,926. This compound inhibits bacterial growth by binding to lipid intermediate II (Lipid II), a key intermediate in peptidoglycan biosynthesis. Like other recently approved antibiotics, dalbavancin has a complex history of preclinical and clinical development, with several companies contributing to different steps in different years. While our work on dalbavancin development stopped at the previous company, intriguingly our current pipeline includes two more Lipid II-binding natural products or derivatives thereof. In particular, we will focus on the properties of NAI-107 and related lantibiotics, which originated from recent screening and characterization efforts.

High-yield production of lipoglycopeptide antibiotic A40926 using a mutant strain Nonomuraea sp. DP-13 in optimized medium.

The lipoglycopeptide antibiotic A40926 produced by Nonomuraea sp. is a complex of structurally related components differing in the fatty acid moiety. Besides showing an intrinsic antibacterial activity, A40926 is the precursor of the semisynthetic antibiotic Dalvance. In this work, A40926 production by a mutant strain Nonomuraea sp. DP-13 was investigated. It was found that A40926 production was markedly promoted by using poorly assimilated carbon source maltodextrin and nitrogen source soybean meal. Addition of Cu(2+) resulted in a stimulation of A40926 production, but Co(2+) had an inhibitory effect. L-Leucine addition greatly improved total A40926 production and modified the complex composition toward factor B0. An optimized production medium IM-3 was developed and a maximum A40926 production of 1096 mg/L was obtained in the 10-L fermenter. This was the highest A40926 productivity so far reported.

X-domain of peptide synthetases recruits oxygenases crucial for glycopeptide biosynthesis.

Non-ribosomal peptide synthetase (NRPS) mega-enzyme complexes are modular assembly lines that are involved in the biosynthesis of numerous peptide metabolites independently of the ribosome. The multiple interactions between catalytic domains within the NRPS machinery are further complemented by additional interactions with external enzymes, particularly focused on the final peptide maturation process. An important class of NRPS metabolites that require extensive external modification of the NRPS-bound peptide are the glycopeptide antibiotics (GPAs), which include vancomycin and teicoplanin. These clinically relevant peptide antibiotics undergo cytochrome P450-catalysed oxidative crosslinking of aromatic side chains to achieve their final, active conformation. However, the mechanism underlying the recruitment of the cytochrome P450 oxygenases to the NRPS-bound peptide was previously unknown. Here we show, through in vitro studies, that the X-domain, a conserved domain of unknown function present in the final module of all GPA NRPS machineries, is responsible for the recruitment of oxygenases to the NRPS-bound peptide to perform the essential side-chain crosslinking. X-ray crystallography shows that the X-domain is structurally related to condensation domains, but that its amino acid substitutions render it catalytically inactive. We found that the X-domain recruits cytochrome P450 oxygenases to the NRPS and determined the interface by solving the structure of a P450-X-domain complex. Additionally, we demonstrated that the modification of peptide precursors by oxygenases in vitro--in particular the installation of the second crosslink in GPA biosynthesis--occurs only in the presence of the X-domain. Our results indicate that the presentation of peptidyl carrier protein (PCP)-bound substrates for oxidation in GPA biosynthesis requires the presence of the NRPS X-domain to ensure conversion of the precursor peptide into a mature aglycone, and that the carrier protein domain alone is not always sufficient to generate a competent substrate for external cytochrome P450 oxygenases.

Structure of the terminal PCP domain of the non-ribosomal peptide synthetase in teicoplanin biosynthesis.

The biosynthesis of the glycopeptide antibiotics, of which teicoplanin and vancomycin are representative members, relies on the combination of non-ribosomal peptide synthesis and modification of the peptide by cytochrome P450 (Oxy) enzymes while the peptide remains bound to the peptide synthesis machinery. We have structurally characterized the final peptidyl carrier protein domain of the teicoplanin non-ribosomal peptide synthetase machinery: this domain is believed to mediate the interactions with tailoring Oxy enzymes in addition to its function as a shuttle for intermediates between multiple non-ribosomal peptide synthetase domains. Using solution state NMR, we have determined structures of this PCP domain in two states, the apo and the post-translationally modified holo state, both of which conform to a four-helix bundle assembly. The structures exhibit the same general fold as the majority of known carrier protein structures, in spite of the complex biosynthetic role that PCP domains from the final non-ribosomal peptide synthetase module must play in glycopeptide antibiotic biosynthesis. These structures thus support the hypothesis that it is subtle rearrangements, rather than dramatic conformational changes, which govern carrier protein interactions and selectivity during non-ribosomal peptide synthesis.

Application of a computational neural network to optimize the fluorescence signal from a receptor-ligand interaction on a microfluidic chip.

We describe the use of a computational neural network platform to optimize the fluorescence upon binding 5-carboxyfluorescein-d-Ala-d-Ala-d-Ala (5-FAM(DA)3 ) (1) to the antibiotic teicoplanin covalently attached to a glass slide. A three-level response surface experimental design was used as the first stage of investigation. Subsequently, three defined experimental parameters were examined by the neural network approach: (i) the concentration of teicoplanin used to derivatize a glass platform on the microfluidic device, (ii) the time required for the immobilization of teicoplanin on the platform, and (iii) the length of time 1 is allowed to equilibrate with teicoplanin in the microfluidic channel. Optimal neural structure provided a best fit model, both for the training set (r(2) = 0.961) and test set (r(2) = 0.934) data. Model simulated results were experimentally validated with excellent agreement (% difference) between experimental and predicted fluorescence shown, thus demonstrating efficiency of the neural network approach.

Cytochrome P450 OxyBtei catalyzes the first phenolic coupling step in teicoplanin biosynthesis.

Bacterial cytochrome P450s form a remarkable clade of the P450 superfamily of oxidative hemoproteins, and are often involved in the biosynthesis of complex natural products. Those in a subgroup known as "Oxy enzymes" play a crucial role in the biosynthesis of glycopeptide antibiotics, including vancomycin and teicoplanin. The Oxy enzymes catalyze crosslinking of aromatic residues in the non-ribosomal antibiotic precursor peptide while it remains bound to the non-ribosomal peptide synthetase (NRPS); this crosslinking secures the three-dimensional structure of the glycopeptide, crucial for antibiotic activity. We have characterized OxyBtei , the first of the Oxy enzymes in teicoplanin biosynthesis. Our results reveal that OxyBtei possesses a structure similar to those of other Oxy proteins and is active in crosslinking NRPS-bound peptide substrates. However, OxyBtei displays a significantly altered activity spectrum against peptide substrates compared to its well-studied vancomycin homologue.