Catalytic Characteristics of New Antibacterials Based on Hexahistidine-Containing Organophosphorus Hydrolase

A new understanding on the prerequisite of antibiotic biodegradation in wastewater treatment: Adhesive behavior between antibiotic-degrading bacteria and ciprofloxacin

The extensive exploration of antibiotic biodegradation by antibiotic-degrading bacteria in biological wastewater treatment processes has left a notable gap in understanding the behavior of these bacteria when exposed to antibiotics and the initiation of biodegradation processes. This study, therefore, delves into the adhesive behavior of Paraclostridium bifermentans, isolated from a bioreactor treating ciprofloxacin-laden wastewater, towards ciprofloxacin molecules. For the first time, this behavior is observed and characterized through quartz crystal microbalance with dissipation (QCM-D) and atomic force microscopy. The investigation further extends to identify key regulatory factors and mechanisms governing this adhesive behavior through a comparative proteomics analysis. The results reveal the dominance of extracellular proteins, particularly those involved in nucleotide binding, hydrolase, and transferase, in the adhesion process. These proteins play pivotal roles through direct chemical binding and the regulation of signaling molecule. Furthermore, QCM-D measurements provide evidence that transferase-related signaling molecules, especially tyrosine, augment the binding between ciprofloxacin and transferases, resulting in enhance ciprofloxacin removal by P. bifermentans (increased by ∼1.2-fold). This suggests a role for transferase-related signaling molecules in manipulating the adhesive behavior of P. bifermentans towards ciprofloxacin. These findings contribute to a new understanding of the prerequisites for antibiotic biodegradation and offer potential strategies for improving the application of antibiotic-degrading bacteria in the treatment of antibiotics-laden wastewater.

Combination of Enzymes with Materials to Give Them Antimicrobial Features: Modern Trends and Perspectives

Multidrug-resistant bacteria form serious problems in many areas, including medicine and the food industry. At the same time, great interest is shown in the transfer or enhancement of antimicrobial properties to various materials by modifying them with enzymes. The use of enzymes in biomaterials with antimicrobial properties is important because enzymes can be used as the main active components providing antimicrobial properties of functionalized composite biomaterials, or can serve as enhancers of the antimicrobial action of certain substances (antibiotics, antimicrobial peptides, metal nanoparticles, etc.) against cells of various microorganisms. Enzymes can simultaneously widen the spectrum of antimicrobial activity of biomaterials. This review presents the most promising enzymes recently used for the production of antibacterial materials, namely hydrolases and oxidoreductases. Computer modeling plays an important role in finding the most effective combinations between enzymes and antimicrobial compounds, revealing their possible interactions. The range of materials that can be functionalized using enzymes looks diverse. The physicochemical characteristics and functionalization methods of the materials have a significant impact on the activity of enzymes. In this context, fibrous materials are of particular interest. The purpose of this review is to analyze the current state of the art in this area.

Carrier Variety Used in Immobilization of His6-OPH Extends Its Application Areas

Organophosphorus hydrolase, containing a genetically introduced hexahistidine sequence (His6-OPH), attracts the attention of researchers by its promiscuous activity in hydrolytic reactions with various substrates, such as organophosphorus pesticides and chemical warfare agents, mycotoxins, and N-acyl homoserine lactones. The application of various carrier materials (metal-organic frameworks, polypeptides, bacterial cellulose, polyhydroxybutyrate, succinylated gelatin, etc.) for the immobilization and stabilization of His6-OPH by various methods, enables creation of biocatalysts with various properties and potential uses, in particular, as antidotes, recognition elements of biosensors, in fibers with chemical and biological protection, dressings with antimicrobial properties, highly porous sorbents for the degradation of toxicants, including in flow systems, etc. The use of computer modeling methods in the development of immobilized His6-OPH samples provides in silico prediction of emerging interactions between the enzyme and immobilizing polymer, which may have negative effects on the catalytic properties of the enzyme, and selection of the best options for experiments in vitro and in vivo. This review is aimed at analysis of known developments with immobilized His6-OPH, which allows to recognize existing recent trends in this field of research, as well as to identify the reasons limiting the use of a number of polymer molecules for the immobilization of this enzyme.

Not a Mistake but a Feature: Promiscuous Activity of Enzymes Meeting Mycotoxins

Mycotoxins are dangerous compounds and find multiple routes to enter living bodies of humans and animals. To solve the issue and degrade the toxicants, (bio)catalytic processes look very promising. Hexahistidine-tagged organophosphorus hydrolase (His6-OPH) is a well-studied catalyst for degradation of organophosphorus neurotoxins and lactone-containing quorum-sensing signal molecules. Moreover, the catalytic characteristics in hydrolysis of several mycotoxins (patulin, deoxynivalenol, zearalenone, and sterigmatocystin) were studied in this investigation. The best Michaelis constant and catalytic constant were estimated in the case of sterigmatocystin and patulin, respectively. A possible combination of His6-OPH with inorganic sorbents treated by low-temperature plasma was investigated. Further, enzyme–polyelectrolyte complexes of poly(glutamic acid) with His6-OPH and another enzymatic mycotoxin degrader (thermolysin) were successfully used to modify fiber materials. These catalytically active prototypes of protective materials appear to be useful for preventing surface contact and exposure to mycotoxins and other chemicals that are substrates for the enzymes used.

Bacterial Cellulose Containing Combinations of Antimicrobial Peptides with Various QQ Enzymes as a Prototype of an "Enhanced Antibacterial" Dressing: In Silico and In Vitro Data

To improve the action of already in use antibiotics or new antimicrobial agents against different bacteria, the development of effective combinations of antimicrobial peptides (AMPs) with enzymes that can quench the quorum (QQ) sensing of bacterial cells was undertaken. Enzymes hydrolyzing N-acyl homoserine lactones (AHLs) and peptides that are signal molecules of Gram-negative and Gram-positive bacterial cells, respectively, were estimated as "partners" for antibiotics and antimicrobial peptides in newly designed antimicrobial-enzymatic combinations. The molecular docking of six antimicrobial agents to the surface of 10 different QQ enzyme molecules was simulated in silico. This made it possible to choose the best variants among the target combinations. Further, bacterial cellulose (BC) was applied as a carrier for uploading such combinations to generally compose prototypes of effective dressing materials with morphology, providing good absorbance. The in vitro analysis of antibacterial activity of prepared BC samples confirmed the significantly enhanced efficiency of the action of AMPs (including polymyxin B and colistin, which are antibiotics of last resort) in combination with AHL-hydrolyzing enzymes (penicillin acylase and His₆-tagged organophosphorus hydrolase) against both Gram-negative and Gram-positive cells.

Simultaneous molecular docking of different ligands to His6-tagged organophosphorus hydrolase as an effective tool for assessing their effect on the enzyme

Background

Enzymatic hydrolysis of N-acyl homoserine lactones (AHLs), which are signaling molecules responsible for the development of antibiotic resistance in gram-negative bacteria, is a potential solution to overcoming antibiotic resistance problem. It has been established that hexahistidine-tagged organophosphorus hydrolase (His₆-OPH) exhibits lactonase activity against a number of AHLs and that the combined application of His₆-OPH with β-lactam antibiotics leads to an increase in the efficiency of the action of both the enzyme and antibiotics. The use of computational methods can be an effective way to search for and select from the known antibiotics to find the most rational "partners" for combining with this enzyme and creating effective antibacterial agents with a dual (lactonase and antibacterial) functional activity.

Methods

In this study, by using AutoDock Vina and Gromacs softwares the molecular docking and the molecular dynamics methods were adopted to simulate models of puromycin, ceftiofur, and/or AHLs docked to the surface of a dimer molecule of His₆-OPH and to study their binding properties. GABEDIT and GAMESS-US packages were used to generate and simulate electron densities of docked AHLs.

Results

Interactions of N-butyryl-DL-homoserine lactone (C4-HSL), N-(3-oxooctanoyl)-L-homoserine lactone (C8-HSL) and N-(3-oxododecanoyl)-L-homoserine lactone (C12-HSL) with His₆-OPH dimer active sites in the presence of puromycin and ceftiofur were simulated and studied. The possible intersection of long-chain AHLs with antibiotic molecules in the active sites of the enzyme was revealed. The binding energies of antibiotics and AHLs with the His₆-OPH surface were estimated. Statistically significant differences (p = 0.003) were observed between the values calculated for both C4-HSL and C12-HSL, whereas there were no statistically significant differences between the values of the other groups (p ≥ 0.100). The binding energies of AHLs with His₆-OPH were slightly higher as compared with the binding energies of antibiotics with the enzyme. The dynamics of the most probable models obtained from docking were investigated. RMSD and RMSF analysis of His₆-OPH-AHL complexes in the absence and presence of antibiotics were performed. The interaction energy values of antibiotics and AHLs with the His₆-OPH were assessed. Significant increase of the AHLs steadiness in enzyme-substrate complexes in the presence of antibiotics was revealed. The interaction between His₆-OPH and C12-HSL was established as thermodynamically more favored.

Conclusions

It has been established that the studied antibiotics puromycin and ceftiofur steady the enzyme-substrate complexes, but at the same time lead to a decrease in the long-chain AHL-hydrolytic activity of His₆-OPH in such a combination as compared to a native enzyme, and, therefore, it should be taken into account when creating a therapeutic composition based on combining antibiotics with His₆-OPH.

Charges' interaction in polyelectrolyte (nano)complexing of His6-OPH with peptides: Unpredictable results due to imperfect or useless concept?

Quorum Quenching (QQ) enzymes can be used to prevent bacterial antibiotic resistance by degradation of Quorum Sensing (QS) signaling molecules, for example N-acyl homoserine lactones (AHLs). This paper is aimed at the in silico investigation of the possible combinations of hexahistidine-tagged organophosphorus hydrolase (His₆-OPH) with antimicrobial peptides (AMPs) to improve the enzyme activity and, promisingly, stability. This shall help creating a nanosized QQ preparation capable to hydrolyze different AHLs and possessing an antimicrobial activity. To achieve this, binding of AMPs and His₆-OPH was simulated by molecular docking, and various interaction parameters (affinity, charge, contact area, etc.) of the generated models were studied. Both anionic and cationic polypeptides were shown to bind to His₆-OPH with negligible effect of their charge, that significantly deviates from the charge-to-charge interaction concept. The (nano)complexes of His₆-OPH with Indolicidin and Temporin A appear to have the most balanced characteristics which were issued experimentally also.

Enzymes for Detoxification of Various Mycotoxins: Origins and Mechanisms of Catalytic Action

Mycotoxins are highly dangerous natural compounds produced by various fungi. Enzymatic transformation seems to be the most promising method for detoxification of mycotoxins. This review summarizes current information on enzymes of different classes to convert various mycotoxins. An in-depth analysis of 11 key enzyme mechanisms towards dozens of major mycotoxins was realized. Additionally, molecular docking of mycotoxins to enzymes' active centers was carried out to clarify some of these catalytic mechanisms. Analyzing protein homologues from various organisms (plants, animals, fungi, and bacteria), the prevalence and availability of natural sources of active biocatalysts with a high practical potential is discussed. The importance of multifunctional enzyme combinations for detoxification of mycotoxins is posed.

Novel approach to quorum quenching: rational design of antibacterials in combination with hexahistidine-tagged organophosphorus hydrolase

N-acyl homoserine lactones (AHLs) are quorum sensing (QS) signal molecules used by most Gram-negative pathogenic bacteria. In this article the lactonase activity of the preparations based on hexahistidine-tagged organophosphorus hydrolase (His6-OPH) towards AHLs was studied. Initially, three of the most interesting β-lactam antibiotics were selected from seven that were trialed during molecular docking to His6-OPH. Combinations of antibiotics (meropenem, imipenem, ceftriaxone) and His6-OPH taken in the native form or in the form of non-covalent enzyme-polyelectrolyte complexes (EPCs) with poly(glutamic acid) or poly(aspartic acid) were obtained and investigated. The lactonase activity of the preparations was investigated under different physical-chemical conditions in the hydrolysis of AHLs [N-butyryl-D,L-homoserine lactone, N-(3-oxooctanoyl)-D,L-homoserine lactone, N-(3-oxododecanoyl)-L-homoserine lactone]. An increased efficiency of catalytic action and stability of the lactonase activity of His6-OPH was shown for its complexes with antibiotics and was confirmed in trials with bacterial strains. The broadening of the catalytic action of the enzyme against AHLs was revealed in the presence of the meropenem. Results of molecular docking of AHLs to the surface of the His6-OPH dimer in the presence of antibiotics allowed proposing the mechanism of such interference based on a steric repulsion of the carbon chain of hydrolyzed AHLs by the antibiotics bounded to the enzyme surface.

[The influence of enzymatic removal of chlorpyrifos from feed grain-mixture on the biochemical parameters of rat blood]

Organophosphorus pesticides (OP) are used to protect crops from pests. Treatment of plants and animals with pesticides can be done during their growth or creation of conditions necessary for the long-shelf life of the agricultural products. Currently, there are many remedies for prevention and removal of intoxication consequences developed under the action of OP in living organisms. The development of biologics for the degradation of OP and biotechnologies for their application in agriculture is relevant. New biologics based on the stabilized forms of such enzyme as hexahistidine-tagged organophosphorus hydrolase (His6-OPH) in the form of nano-sized particles were tried for OP detoxification. These biologics (enzyme-polyelectrolyte complexes, EPC) were obtained in accordance to previously developed procedure by mixing solutions of His6-OPH and polyanion under certain conditions. The main purpose of this work was to evaluate the usage efficiency of EPC based on His6-OPH and polyglutamic acid for OP detoxification by analyzing biochemical blood parameters of rats consumed the grain-mixture containing chlorpyrifos. The experiment was conducted using female Sprague Dawley albino rats. Treatment of feeding grain-mixture initially containing chlopyrifos (48 mg/kg of the mixture) with EPC based on His6-OPH (1000 U/kg of the mixture) for 24 h was the most effective. The results showed that rats from the group consuming food after enzymatic removal of chlorpyrifos, had comparable acetyl cholinesterase activity in blood of rats consuming pure food (without any OP intoxication).