Catalytic mechanisms for phosphotriesterases

Noncanonical Amino Acids: Bringing New-to-Nature Functionalities to Biocatalysis

Biocatalysis has become an important component of modern organic chemistry, presenting an efficient and environmentally friendly approach to synthetic transformations. Advances in molecular biology, computational modeling, and protein engineering have unlocked the full potential of enzymes in various industrial applications. However, the inherent limitations of the natural building blocks have sparked a revolutionary shift. In vivo genetic incorporation of noncanonical amino acids exceeds the conventional 20 amino acids, opening new avenues for innovation. This review provides a comprehensive overview of applications of noncanonical amino acids in biocatalysis. We aim to examine the field from multiple perspectives, ranging from their impact on enzymatic reactions to the creation of novel active sites, and subsequent catalysis of new-to-nature reactions. Finally, we discuss the challenges, limitations, and promising opportunities within this dynamic research domain.

Catalytic Redundancies and Conformational Plasticity Drives Selectivity and Promiscuity in Quorum Quenching Lactonases

Several enzymes from the metallo-β-lactamase-like family of lactonases (MLLs) degrade N-acyl L-homoserine lactones (AHLs). They play a role in a microbial communication system known as quorum sensing, which contributes to pathogenicity and biofilm formation. Designing quorum quenching (QQ) enzymes that can interfere with this communication allows them to be used in a range of industrial and biomedical applications. However, tailoring these enzymes for specific communication signals requires a thorough understanding of their mechanisms and the physicochemical properties that determine their substrate specificities. We present here a detailed biochemical, computational, and structural study of GcL, which is a highly proficient and thermostable MLL with broad substrate specificity. We show that GcL not only accepts a broad range of substrates but also hydrolyzes these substrates through at least two different mechanisms. Further, the preferred mechanism appears to depend on both the substrate structure and/or the nature of the residues lining the active site. We demonstrate that other lactonases, such as AiiA and AaL, show similar mechanistic promiscuity, suggesting that this is a shared feature among MLLs. Mechanistic promiscuity has been seen previously in the lactonase/paraoxonase PON1, as well as with protein tyrosine phosphatases that operate via a dual general acid mechanism. The apparent prevalence of this phenomenon is significant from both a biochemical and protein engineering perspective: in addition to optimizing for specific substrates, it may be possible to optimize for specific mechanisms, opening new doors not just for the design of novel quorum quenching enzymes but also of other mechanistically promiscuous enzymes.

Molecular Basis of the Substrate Specificity of Phosphotriesterase from Pseudomonas diminuta: A Combined QM/MM MD and Electron Density Study

The occurrence of organophosphorus compounds, pesticides, and flame-retardants in wastes is an emerging ecological problem. Bacterial phosphotriesterases are capable of hydrolyzing some of them. We utilize modern molecular modeling tools to study the hydrolysis mechanism of organophosphorus compounds with good and poor leaving groups by phosphotriesterase from Pseudomonas diminuta (Pd-PTE). We compute Gibbs energy profiles for enzymes with different cations in the active site: native Zn2+cations and Co2+cations, which increase the steady-state rate constant. Hydrolysis occurs in two elementary steps via an associative mechanism and formation of the pentacoordinated intermediate. The first step, a nucleophilic attack, occurs with a low energy barrier independently of the substrate. The second step has a low energy barrier and considerable stabilization of products for substrates with good leaving groups. For substrates with poor leaving groups, the reaction products are destabilized relative to the ES complex that suppresses the reaction. The reaction proceeds with low energy barriers for substrates with good leaving groups with both Zn2+and Co2+cations in the active site; thus, the product release is likely to be a limiting step. Electron density and geometry analysis of the QM/MM MD trajectories of the intermediate states with all considered compounds allow us to discriminate substrates by their ability to be hydrolyzed by the Pd-PTE. For hydrolyzable substrates, the cleaving bond between a phosphorus atom and a leaving group is elongated, and electron density depletion is observed on the Laplacian of electron density maps.

Improving stereoselectivity of phosphotriesterase (PTE) for kinetic resolution of chiral phosphates

Specific stereoisomer is paramount as it is vital for optimizing drug efficacy and safety. The quest for the isolation of desired stereoisomer of active pharmaceutical ingredients or key intermediates drives innovation in drug synthetic and biocatalytic methods. Chiral phosphoramidate is an important building block for the synthesis of antiviral drugs such as remdesivir and sofosbuvir. Given the clinical potency of the (Sp)-diastereomer of the drugs, an enzyme capable of completely hydrolyzing the (Rp)-diastereomer is needed to achieve the purified diastereomers via biocatalytic reaction. In this study, protein engineering of phosphotriesterase (PTE) was aimed to improve the specificity. Employing rational design and site-directed mutagenesis, we generated a small library comprising 24 variants for activity screening. Notably, W131M and I106A/W131M variants demonstrated successful preparation of pure (Sp)-diastereomer of remdesivir and sofosbuvir precursors within a remarkably short hydrolysis time (<20 min). Our work unveils a promising methodology for producing pure stereoisomeric compounds, utilizing novel biocatalysts to enable the chemoenzymatic synthesis of phosphoramidate nucleoside prodrugs.

Applications of Microbial Organophosphate-Degrading Enzymes to Detoxification of Organophosphorous Compounds for Medical Countermeasures against Poisoning and Environmental Remediation

Mining of organophosphorous (OPs)-degrading bacterial enzymes in collections of known bacterial strains and in natural biotopes are important research fields that lead to the isolation of novel OP-degrading enzymes. Then, implementation of strategies and methods of protein engineering and nanobiotechnology allow large-scale production of enzymes, displaying improved catalytic properties for medical uses and protection of the environment. For medical applications, the enzyme formulations must be stable in the bloodstream and upon storage and not susceptible to induce iatrogenic effects. This, in particular, includes the nanoencapsulation of bioscavengers of bacterial origin. In the application field of bioremediation, these enzymes play a crucial role in environmental cleanup by initiating the degradation of OPs, such as pesticides, in contaminated environments. In microbial cell configuration, these enzymes can break down chemical bonds of OPs and usually convert them into less toxic metabolites through a biotransformation process or contribute to their complete mineralization. In their purified state, they exhibit higher pollutant degradation efficiencies and the ability to operate under different environmental conditions. Thus, this review provides a clear overview of the current knowledge about applications of OP-reacting enzymes. It presents research works focusing on the use of these enzymes in various bioremediation strategies to mitigate environmental pollution and in medicine as alternative therapeutic means against OP poisoning.

Gut microbial metalloproteins and its role in xenobiotics degradation and ROS scavenging

The gut microbial metalloenzymes play an important role in maintaining the balance between gut microbial ecosystem, human physiologically processes and immune system. The metals coordinated into active site contribute in various detoxification and defense strategies to avoid unfavourable environment and ensure bacterial survival in human gut. Metallo-β-lactamase is a potent degrader of antibiotics present in periplasmic space of both commensals and pathogenic bacteria. The resistance to anti-microbial agents developed in this enzyme is one of the global threats for human health. The organophosphorus eliminator, organophosphorus hydrolases have evolved over a course of time to hydrolyze toxic organophosphorus compounds and decrease its effect on human health. Further, the redox stress responders namely superoxide dismutase and catalase are key metalloenzymes in reducing both endogenous and exogenous oxidative stress. They hold a great importance for pathogens as they contribute in pathogenesis in human gut along with reduction of oxidative stress. The in-silico study on these enzymes reveals the importance of point mutation for the evolution of these enzymes in order to enhance their enzyme activity and stability. Various mutation studies were conducted to investigate the catalytic activity of these enzymes. By using the "directed evolution" method, the enzymes involved in detoxification and defense system can be engineered to produce new variants with enhance catalytic features, which may be used to predict the severity due to multi-drug resistance and degradation pattern of organophosphorus compounds in human gut.

Hydrolysis of Nerve Agent Simulants Accelerated by Stimuli-Responsive Dinuclear Catalysts

The ability to control the catalytic activity of enzymes in chemical transformations is essential for the design and development of artificial catalysts. Herein, we report the synthesis and characterization of functional ligands featuring two 1,4,7,10-tetraazacyclododecane units linked by an azobenzene group and their corresponding dinuclear Zn(II) complexes. We show that the configuration switching (E/Z) of the azobenzene spacer in the ligands and their dinuclear Zn(II) complexes is reversibly controlled by irradiation with UV and visible light. The Zn(II)-metal complexes are light-responsive catalysts for the hydrolytic cleavage of nerve agent simulants, i.e., p-nitrophenyl diphenyl phosphate and methyl paraoxon. The catalytic activity of the Z-isomers of the dinuclear Zn(II) complexes outperformed that of the E-counterparts. Moreover, combining the less active E-isomers with gold nanoparticles induced an enhancement in the hydrolysis rate of p-nitrophenyl diphenyl phosphate. Kinetic analysis has shown that the catalytic site appears to involve a single metal ion. We explain our results by considering the different desolvation effects occurring in the catalyst's configurations in the solution and the catalytic systems involving gold nanoparticles.

Catalytic Redundancies and Conformational Plasticity Drives Selectivity and Promiscuity in Quorum Quenching Lactonases

Several enzymes from the metallo-β-lactamase-like family of lactonases (MLLs) degrade N- acyl-L-homoserine lactones (AHLs). In doing so, they play a role in a microbial communication system, quorum sensing, which contributes to pathogenicity and biofilm formation. There is currently great interest in designing quorum quenching ( QQ ) enzymes that can interfere with this communication and be used in a range of industrial and biomedical applications. However, tailoring these enzymes for specific targets requires a thorough understanding of their mechanisms and the physicochemical properties that determine their substrate specificities. We present here a detailed biochemical, computational, and structural study of the MLL GcL, which is highly proficient, thermostable, and has broad substrate specificity. Strikingly, we show that GcL does not only accept a broad range of substrates but is also capable of utilizing different reaction mechanisms that are differentially used in function of the substrate structure or the remodeling of the active site via mutations. Comparison of GcL to other lactonases such as AiiA and AaL demonstrates similar mechanistic promiscuity, suggesting this is a shared feature across lactonases in this enzyme family. Mechanistic promiscuity has previously been observed in the lactonase/paraoxonase PON1, as well as with protein tyrosine phosphatases that operate via a dual general-acid mechanism. The apparent prevalence of this phenomenon is significant from both a biochemical and an engineering perspective: in addition to optimizing for specific substrates, it is possible to optimize for specific mechanisms, opening new doors not just for the design of novel quorum quenching enzymes, but also of other mechanistically promiscuous enzymes.

Fibrous Zr-MOF Nanozyme Aerogels with Macro-Nanoporous Structure for Enhanced Catalytic Hydrolysis of Organophosphate Toxins

Metal-organic frameworks (MOFs) with Lewis acid catalytic sites, such as zirconium-based MOFs (Zr-MOFs), comprise a growing class of phosphatase-like nanozymes that can degrade toxic organophosphate pesticides and nerve agents. Rationally engineering and shaping MOFs from as-synthesized powders into hierarchically porous monoliths is essential for their use in emerging applications, such as filters for air and water purification and personal protection gear. However, several challenges still limit the production of practical MOF composites, including the need for sophisticated reaction conditions, low MOF catalyst loadings in the resulting composites, and poor accessibility to MOF-based active sites. To overcome these limitations, a rapid synthesis method is developed to introduce Zr-MOF nanozyme coating into cellulose nanofibers, resulting in the formation of processable monolithic aerogel composites with high MOF loadings. These composites contain Zr-MOF nanozymes embedded in the structure, and hierarchical macro-micro porosity enables excellent accessibility to catalytic active sites. This multifaceted rational design strategy, including the selection of a MOF with many catalytic sites, fine-tuning the coating morphology, and the fabrication of a hierarchically structured monolithic aerogel, renders synergistic effects toward the efficient continuous hydrolytic detoxification of organophosphorus-based nerve agent simulants and pesticides from contaminated water.

Thermodynamic Insights into Phosphonate Binding in Metal-Azolate Frameworks

Organophosphorus chemicals, including chemical warfare agents (CWAs) and insecticides, are acutely toxic materials that warrant capture and degradation. Metal-organic frameworks (MOFs) have emerged as a class of tunable, porous, crystalline materials capable of hydrolytically cleaving, and thus detoxifying, several organophosphorus nerve agents and their simulants. One such MOF is M-MFU-4l (M = metal), a bioinspired azolate framework whose metal node is composed of a variety of divalent first-row transition metals. While Cu-MFU-4l and Zn-MFU-4l are shown to rapidly degrade CWA simulants, Ni-MFU-4l and Co-MFU-4l display drastically lower activities. The lack of reactivity was hypothesized to arise from the strong binding of the phosphate product to the node, which deactivates the catalyst by preventing turnover. No such study has provided detailed insight into this mechanism. Here, we leverage isothermal titration calorimetry (ITC) to monitor the binding of an organophosphorus compound with the M-MFU-4l series to construct a complete thermodynamic profile (Ka, ΔH, ΔS, ΔG) of this interaction. This study further establishes ITC as a viable technique to probe small differences in thermodynamics that result in stark differences in material properties, which may allow for better design of first-row transition metal MOF catalysts for organophosphorus hydrolysis.

Biodegradation of pesticide in agricultural soil employing entomopathogenic fungi: Current state of the art and future perspectives

Pesticides play a pivotal role in agriculture for the effective production of various crops. The indiscriminate use of pesticides results in the significant bioaccumulation of pesticide residues in vegetables. This situation is beyond the control of consumers and poses a serious health issue for human beings. Occupational exposure to pesticides may occur for farmers, agricultural workers, and industrial producers of pesticides. This occupational exposure primarily causes food and water contamination that gets into humans and environmental pollution. Depending on the toxicity of pesticides, the causes and effects differ in the environment and in human health. The number of criteria used and the method of implementation employed to assess the effect of pesticides on humans and the environment have been increasing, as they may provide characterization of pesticides that are already on the market as well as those that are on the way. The biological control of pests has been increasing nowadays to combat all these effects caused by synthetic pesticides. Myco-biocontrol has received great attention in research because it has no negative impact on humans, the environment, or non-target species. Entomopathogenic fungi are microbes that have the ability to kill insect pests. Fungi also make enzymes like the lytic enzymes, esterase, oxidoreductase, and cytochrome P450, which react with chemical residues in the field and break them down into nontoxic substances. In this review, the authors looked at how entomopathogenic fungi break down insecticides in the environment and how their enzymes break down insecticides on farms.

Unleashing potential of Pseudomonas aeruginosa RNC3 and Stenotrophomonas maltophilia RNC7 for chlorpyrifos biodegradation by genome analysis and kinetic studies

Chlorpyrifos (CP) is an extensively used organophosphate (OP) pesticide that inhibits the biogeochemical cycle with subsequent loss of soil fertility. In this view, indigenous soil bacteria with significant CP degradation capacity were identified as Pseudomonas aeruginosa RNC3 and Stenotrophomonas maltophilia RNC7 through 16 S rRNA. The optimum values of independent variables for CP degradation were found to be 30 ℃, pH 7, 100 mgL-1 of CP, and 1 OD600 cell culture. RNC3 and RNC7 showed 82.5 mgL-1 and 77.1 mgL-1 CP degradation within 5 days. A Michaelis-Menten kinetic model estimated the degradation rate (Vmax) and substrate binding affinity (Ks) for RNC3 were 1.23 mgL-1h-1 and 123 mgL-1 whereas for RNC7 as 1.19 mgL-1h -1 and 124.3 mgL-1, respectively. The major metabolites 3,5,6-trichloro-2-pyridinol (TCP) and 2-hydroxy pyridine were identified during CP degradation by RNC3 whereas, only TCP by RNC7 using GC-MS. Key enzymes encoded by opd and opch2 genes were annotated in the genomes of RNC3 and RNC7 along with the set of putative degradation genes (tcp, yieH, pho, prp). Protein-ligand docking between OPCH2 and CP found - 7.9 kcal mol -1 as a high binding affinity with the conserved catalytic triad (Ser155-Asp251-His281) in the active site. The study suggests that RNC3 can completely mineralize CP, whereas both strains have shown robust degradation ability of OP group of pesticides. The potential of rapid acclimatization to natural soil environment and non-virulent nature of the selected strains are beneficial for in situ application. Thus, selected indigenous strains can be applied for the bioremediation of OP-contaminated soil.

Warfare Nerve Agents and Paraoxonase-1 as a Potential Prophylactic Therapy against Intoxication

Nerve agents are a class of lethal neurotoxic chemicals used in chemical warfare. In this review, we have discussed a brief history of chemical warfare, followed by an exploration of the historical context surrounding nerve agents. The article explores the classification of these agents, their contemporary uses, their toxicity mechanisms, and the disadvantages of the current treatment options for nerve agent poisoning. It then discusses the possible application of enzymes as prophylactics against nerve agent poisoning, outlining the benefits and drawbacks of paraoxonase- 1. Finally, the current studies on paraoxonase-1 are reviewed, highlighting that several challenges need to be addressed in the use of paraoxonase-1 in the actual field and that its potential as a prophylactic antidote against nerve agent poisoning needs to be evaluated. The literature used in this manuscript was searched using various electronic databases, such as PubMed, Google Scholar, Web of Science, Elsevier, Springer, ACS, Google Patent, and books using the keywords chemical warfare agent, butyrylcholinesterase, enzyme, nerve agent, prophylactic, and paraoxonase-1, with the time scale for the analysis of articles between 1960 to 2023. The study has suggested that concerted efforts by researchers and agencies must be made to develop effective countermeasures against NA poisoning and that paraoxonase-1 has suitable properties for the development of efficient prophylaxis against NA poisoning.

Engineering Enzymes for Environmental Sustainability

The development and implementation of sustainable catalytic technologies is key to delivering our net-zero targets. Here we review how engineered enzymes, with a focus on those developed using directed evolution, can be deployed to improve the sustainability of numerous processes and help to conserve our environment. Efficient and robust biocatalysts have been engineered to capture carbon dioxide (CO2) and have been embedded into new efficient metabolic CO2 fixation pathways. Enzymes have been refined for bioremediation, enhancing their ability to degrade toxic and harmful pollutants. Biocatalytic recycling is gaining momentum, with engineered cutinases and PETases developed for the depolymerization of the abundant plastic, polyethylene terephthalate (PET). Finally, biocatalytic approaches for accessing petroleum-based feedstocks and chemicals are expanding, using optimized enzymes to convert plant biomass into biofuels or other high value products. Through these examples, we hope to illustrate how enzyme engineering and biocatalysis can contribute to the development of cleaner and more efficient chemical industry.

Engineering Enzymes for Environmental Sustainability

The development and implementation of sustainable catalytic technologies is key to delivering our net-zero targets. Here we review how engineered enzymes, with a focus on those developed using directed evolution, can be deployed to improve the sustainability of numerous processes and help to conserve our environment. Efficient and robust biocatalysts have been engineered to capture carbon dioxide (CO2 ) and have been embedded into new efficient metabolic CO2 fixation pathways. Enzymes have been refined for bioremediation, enhancing their ability to degrade toxic and harmful pollutants. Biocatalytic recycling is gaining momentum, with engineered cutinases and PETases developed for the depolymerization of the abundant plastic, polyethylene terephthalate (PET). Finally, biocatalytic approaches for accessing petroleum-based feedstocks and chemicals are expanding, using optimized enzymes to convert plant biomass into biofuels or other high value products. Through these examples, we hope to illustrate how enzyme engineering and biocatalysis can contribute to the development of cleaner and more efficient chemical industry.

The impact of molecular variants, crystallization conditions and the space group on ligand-protein complexes: a case study on bacterial phosphotriesterase

A bacterial phosphotriesterase was employed as an experimental paradigm to examine the effects of multiple factors, such as the molecular constructs, the ligands used during protein expression and purification, the crystallization conditions and the space group, on the visualization of molecular complexes of ligands with a target enzyme. In this case, the ligands used were organophosphates that are fragments of the nerve agents and insecticides on which the enzyme acts as a bioscavenger. 12 crystal structures of various phosphotriesterase constructs obtained by directed evolution were analyzed, with resolutions of up to 1.38 Å. Both apo forms and holo forms, complexed with the organophosphate ligands, were studied. Crystals obtained from three different crystallization conditions, crystallized in four space groups, with and without N-terminal tags, were utilized to investigate the impact of these factors on visualizing the organophosphate complexes of the enzyme. The study revealed that the tags used for protein expression can lodge in the active site and hinder ligand binding. Furthermore, the space group in which the protein crystallizes can significantly impact the visualization of bound ligands. It was also observed that the crystallization precipitants can compete with, and even preclude, ligand binding, leading to false positives or to the incorrect identification of lead drug candidates. One of the co-crystallization conditions enabled the definition of the spaces that accommodate the substituents attached to the P atom of several products of organophosphate substrates after detachment of the leaving group. The crystal structures of the complexes of phosphotriesterase with the organophosphate products reveal similar short interaction distances of the two partially charged O atoms of the P-O bonds with the exposed β-Zn2+ ion and the buried α-Zn2+ ion. This suggests that both Zn2+ ions have a role in stabilizing the transition state for substrate hydrolysis. Overall, this study provides valuable insights into the challenges and considerations involved in studying the crystal structures of ligand-protein complexes, highlighting the importance of careful experimental design and rigorous data analysis in ensuring the accuracy and reliability of the resulting phosphotriesterase-organophosphate structures.

Designed Metal-Containing Peptoid Membranes as Enzyme Mimetics for Catalytic Organophosphate Degradation

The detoxification of lethal organophosphate (OP) residues in the environment is crucial to prevent human exposure and protect modern society. Despite serving as excellent catalysts for OP degradation, natural enzymes require costly preparation and readily deactivate upon exposure to environmental conditions. Herein, we designed and prepared a series of phosphotriesterase mimics based on stable, self-assembled peptoid membranes to overcome these limitations of the enzymes and effectively catalyze the hydrolysis of dimethyl p-nitrophenyl phosphate (DMNP)─a nerve agent simulant. By covalently attaching metal-binding ligands to peptoid N-termini, we attained enzyme mimetics in the form of surface-functionalized crystalline nanomembranes. These nanomembranes display a precisely controlled arrangement of coordinated metal ions, which resemble the active sites found in phosphotriesterases to promote DMNP hydrolysis. Moreover, using these highly programmable peptoid nanomembranes allows for tuning the local chemical environment of the coordinated metal ion to achieve enhanced hydrolysis activity. Among the crystalline membranes that are active for DMNP degradation, those assembled from peptoids containing bis-quinoline ligands with an adjacent phenyl side chain showed the highest hydrolytic activity with a 219-fold rate acceleration over the background, demonstrating the important role of the hydrophobic environment in proximity to the active sites. Furthermore, these membranes exhibited remarkable stability and were able to retain their catalytic activity after heating to 60 °C and after multiple uses. This work provides insights into the principal features to construct a new class of biomimetic materials with high catalytic efficiency, cost-effectiveness, and reusability applied in nerve agent detoxification.

Distinct chemical factors in hydrolytic reactions catalyzed by metalloenzymes and metal complexes

The selective hydrolysis of the extremely stable phosphoester, peptide and ester bonds of molecules by bio-inspired metal-based catalysts (metallohydrolases) is required in a wide range of biological, biotechnological and industrial applications. Despite the impressive advances made in the field, the ultimate goal of designing efficient enzyme mimics for these reactions is still elusive. Its realization will require a deeper understanding of the diverse chemical factors that influence the activities of both natural and synthetic catalysts. They include catalyst-substrate complexation, non-covalent interactions and the electronic nature of the metal ion, ligand environment and nucleophile. Based on our computational studies, their roles are discussed for several mono- and binuclear metallohydrolases and their synthetic analogues. Hydrolysis by natural metallohydrolases is found to be promoted by a ligand environment with low basicity, a metal bound water and a heterobinuclear metal center (in binuclear enzymes). Additionally, peptide and phosphoester hydrolysis is dominated by two competing effects, i.e. nucleophilicity and Lewis acid activation, respectively. In synthetic analogues, hydrolysis is facilitated by the inclusion of a second metal center, hydrophobic effects, a biological metal (Zn, Cu and Co) and a terminal hydroxyl nucleophile. Due to the absence of the protein environment, hydrolysis by these small molecules is exclusively influenced by nucleophile activation. The results gleaned from these studies will enhance the understanding of fundamental principles of multiple hydrolytic reactions. They will also advance the development of computational methods as a predictive tool to design more efficient catalysts for hydrolysis, Diels-Alder reaction, Michael addition, epoxide opening and aldol condensation.

Unusual Relationship between Iron Deprivation and Organophosphate Hydrolase Expression

Organophosphate hydrolases (OPH), hitherto known to hydrolyze the third ester bond of organophosphate (OP) insecticides and nerve agents, have recently been shown to interact with outer membrane transport components, namely, TonB and ExbB/ExbD. In an OPH negative background, Sphingopyxis wildii cells failed to transport ferric enterobactin and showed retarded growth under iron-limiting conditions. We now show the OPH-encoding organophosphate degradation (opd) gene from Sphingobium fuliginis ATCC 27551 to be part of the iron regulon. A fur-box motif found to be overlapping with the transcription start site (TSS) of the opd gene coordinates with an iron responsive element (IRE) RNA motif identified in the 5' coding region of the opd mRNA to tightly regulate opd gene expression. The fur-box motif serves as a target for the Fur repressor in the presence of iron. A decrease in iron concentration leads to the derepression of opd. IRE RNA inhibits the translation of opd mRNA and serves as a target for apo-aconitase (IRP). The IRP recruited by the IRE RNA abrogates IRE-mediated translational inhibition. Our findings establish a novel, multilayered, iron-responsive regulation that is crucial for OPH function in the transport of siderophore-mediated iron uptake. IMPORTANCE Sphingobium fuliginis, a soil-dwelling microbe isolated from agricultural soils, was shown to degrade a variety of insecticides and pesticides. These synthetic chemicals function as potent neurotoxins, and they belong to a class of chemicals termed organophosphates. S. fuliginis codes for OPH, an enzyme that has been shown to be involved in the metabolism of several organophosphates and their derivatives. Interestingly, OPH has also been shown to facilitate siderophore-mediated iron uptake in S. fuliginis and in another Sphingomonad, namely, Sphingopyxis wildii, implying that this organophosphate-metabolizing protein has a role in iron homeostasis, as well. Our research dissects the underlying molecular mechanisms linking iron to the expression of OPH, prompting a reconsideration of the role of OPH in Sphingomonads and a reevaluation of the evolutionary origins of the OPH proteins from soil bacteria.

Different Strategies Affect Enzyme Packaging into Bacterial Outer Membrane Vesicles

All Gram-negative bacteria are believed to produce outer membrane vesicles (OMVs), proteoliposomes shed from the outermost membrane. We previously separately engineered E. coli to produce and package two organophosphate (OP) hydrolyzing enzymes, phosphotriesterase (PTE) and diisopropylfluorophosphatase (DFPase), into secreted OMVs. From this work, we realized a need to thoroughly compare multiple packaging strategies to elicit design rules for this process, focused on (1) membrane anchors or periplasm-directing proteins (herein "anchors/directors") and (2) the linkers connecting these to the cargo enzyme; both may affect enzyme cargo activity. Herein, we assessed six anchors/directors to load PTE and DFPase into OMVs: four membrane anchors, namely, lipopeptide Lpp', SlyB, SLP, and OmpA, and two periplasm-directing proteins, namely, maltose-binding protein (MBP) and BtuF. To test the effect of linker length and rigidity, four different linkers were compared using the anchor Lpp'. Our results showed that PTE and DFPase were packaged with most anchors/directors to different degrees. For the Lpp' anchor, increased packaging and activity corresponded to increased linker length. Our findings demonstrate that the selection of anchors/directors and linkers can greatly influence the packaging and bioactivity of enzymes loaded into OMVs, and these findings have the potential to be utilized for packaging other enzymes into OMVs.

Effective remediation and decontamination of organophosphorus compounds using enzymes: From rational design to potential applications

Organophosphorus compounds (OPs) have been widely used in agriculture for decades because of their high insecticidal efficiency, which maintains and increases crop yields worldwide. More importantly, OPs, as typical chemical warfare agents, are a serious concern and significant danger for military and civilian personnel. The widespread use of OPs, superfluous and unreasonable use, has caused great harm to the environment and food chain. Developing efficient and environmentally friendly solutions for the decontamination of OPs is a long-term challenge. Microbial enzymes show potential application as natural and green biocatalysts. Thus, utilizing OP-degrading enzymes for environmental decontamination presents significant advantages, as these enzymes can rapidly hydrolyze OPs; are environmentally friendly, nonflammable, and noncorrosive; and can be discarded safely and easily. Here, the properties, structure and catalytic mechanism of various typical OP-degrading enzymes are reviewed. The methods and effects utilized to improve the expression level, catalytic performance and stability of OP-degrading enzymes were systematically summarized. In addition, the immobilization of OP-degrading enzymes was explicated emphatically, and the latest progress of cascade reactions based on immobilized enzymes was discussed. Finally, the latest applications of OP-degrading enzymes were summarized, including biosensors, nanozyme mimics and medical detoxification. This review provides guidance for the future development of OP-degrading enzymes and promotes their application in the field of environmental bioremediation and medicine.

Structure-Activity Relationship Insights for Organophosphonate Hydrolysis at Ti(IV) Active Sites in Metal-Organic Frameworks

Organophosphorus nerve agents are among the most toxic chemicals known and remain threats to humans due to their continued use despite international bans. Metal-organic frameworks (MOFs) have emerged as a class of heterogeneous catalysts with tunable structures that are capable of rapidly detoxifying these chemicals via hydrolysis at Lewis acidic active sites on the metal nodes. To date, the majority of studies in this field have focused on zirconium-based MOFs (Zr-MOFs) that contain hexanuclear Zr(IV) clusters, despite the large toolbox of Lewis acidic transition metal ions that are available to construct MOFs with similar catalytic properties. In particular, very few reports have disclosed the use of a Ti-based MOF (Ti-MOF) as a catalyst for this transformation even though Ti(IV) is a stronger Lewis acid than Zr(IV). In this work, we explored five Ti-MOFs (Ti-MFU-4l, NU-1012-NDC, MIL-125, Ti-MIL-101, MIL-177(LT), and MIL-177(HT)) that each contains Ti(IV) ions in unique coordination environments, including monometallic, bimetallic, octanuclear, triangular clusters, and extended chains, as catalysts to explore how both different node structures and different linkers (e.g., azolate and carboxylate) influence the binding and subsequent hydrolysis of an organophosphorus nerve agent simulant at Ti(IV)-based active sites in basic aqueous solutions. Experimental and theoretical studies confirm that Ti-MFU-4l, which contains monometallic Ti(IV)-OH species, exhibits the best catalytic performance among this series with a half-life of roughly 2 min. This places Ti-MFU-4l as one of the best nerve agent hydrolysis catalysts of any MOF reported to date.

Ultrahigh-Throughput Directed Evolution of a Metal-Free α/β-Hydrolase with a Cys-His-Asp Triad into an Efficient Phosphotriesterase

Finding new mechanistic solutions for biocatalytic challenges is key in the evolutionary adaptation of enzymes, as well as in devising new catalysts. The recent release of man-made substances into the environment provides a dynamic testing ground for observing biocatalytic innovation at play. Phosphate triesters, used as pesticides, have only recently been introduced into the environment, where they have no natural counterpart. Enzymes have rapidly evolved to hydrolyze phosphate triesters in response to this challenge, converging onto the same mechanistic solution, which requires bivalent cations as a cofactor for catalysis. In contrast, the previously identified metagenomic promiscuous hydrolase P91, a homologue of acetylcholinesterase, achieves slow phosphotriester hydrolysis mediated by a metal-independent Cys-His-Asp triad. Here, we probe the evolvability of this new catalytic motif by subjecting P91 to directed evolution. By combining a focused library approach with the ultrahigh throughput of droplet microfluidics, we increase P91's activity by a factor of ≈360 (to a k_cat/K_M of ≈7 × 10⁵ M^-1 s^-1) in only two rounds of evolution, rivaling the catalytic efficiencies of naturally evolved, metal-dependent phosphotriesterases. Unlike its homologue acetylcholinesterase, P91 does not suffer suicide inhibition; instead, fast dephosphorylation rates make the formation of the covalent adduct rather than its hydrolysis rate-limiting. This step is improved by directed evolution, with intermediate formation accelerated by 2 orders of magnitude. Combining focused, combinatorial libraries with the ultrahigh throughput of droplet microfluidics can be leveraged to identify and enhance mechanistic strategies that have not reached high efficiency in nature, resulting in alternative reagents with novel catalytic machineries.

Promiscuous Catalytic Activity of a Binuclear Metallohydrolase: Peptide and Phosphoester Hydrolyses

In this study, chemical promiscuity of a binuclear metallohydrolase Streptomyces griseus aminopeptidase (SgAP) has been investigated using DFT calculations. SgAP catalyzes two diverse reactions, peptide and phosphoester hydrolyses, using its binuclear (Zn-Zn) core. On the basis of the experimental information, mechanisms of these reactions have been investigated utilizing leucine p-nitro aniline (Leu-pNA) and bis(4-nitrophenyl) phosphate (BNPP) as the substrates. The computed barriers of 16.5 and 16.8 kcal/mol for the most plausible mechanisms proposed by the DFT calculations are in good agreement with the measured values of 13.9 and 18.3 kcal/mol for the Leu-pNA and BNPP hydrolyses, respectively. The former was found to occur through the transfer of two protons, while the latter with only one proton transfer. They are in line with the experimental observations. The cleavage of the peptide bond was the rate-determining process for the Leu-pNA hydrolysis. However, the creation of the nucleophile and its attack on the electrophile phosphorus atom was the rate-determining step for the BNPP hydrolysis. These calculations showed that the chemical nature of the substrate and its binding mode influence the nucleophilicity of the metal bound hydroxyl nucleophile. Additionally, the nucleophilicity was found to be critical for the Leu-pNA hydrolysis, whereas double Lewis acid activation was needed for the BNPP hydrolysis. That could be one of the reasons why peptide hydrolysis can be catalyzed by both mononuclear and binuclear metal cofactors containing hydrolases, while phosphoester hydrolysis is almost exclusively by binuclear metallohydrolases. These results will be helpful in the development of versatile catalysts for chemically distinct hydrolytic reactions.

Improving Catalytic Activity and Thermal Stability of Methyl-Parathion Hydrolase for Degrading the Pesticide of Methyl-Parathion

Pesticides are indispensable in today’s agriculture. Methyl-parathion hydrolase (MPH, E.C.3.1.8.1) could hydrolyze organophosphorus pesticides, including methyl-parathion. MPH could rehabilitate soil and water resources contaminated by organophosphorus pesticides. However, natural MPHs generally exhibited a low tolerance to high temperatures and low catalytic efficiency. In this study, we improved the catalytic efficiency toward methyl-parathion and the thermal stability of the MPH from Pseudomonas sp. WBC-3 through saturation mutagenesis and fusion with self-assembling amphipathic peptides (SAP). The experimental characterization showed that compared to the wild-type enzyme, the kcat/Km of the mutant T271S yielded by saturation mutagenesis was increased by 224.3% compared to the wild-type MPH. T50 and Tm of SAP3-MPH with an SAP fused at the N-terminus were increased by 6.2°C and 6.0°C, respectively. Compared to the wild-type enzyme, T271S fused with SAP3 at the N-terminus (SAP3-T271S) exhibited a 2.1-fold increase in kcat/Km without significantly affecting the thermal stability. The simultaneous improvement of the catalytic efficiency and thermal stability of MPH would be beneficial for its application in the degradation and detection of organophosphorus pesticides. Furthermore, our study provides a potential combination strategy for the design of the other enzyme preparations of pollutant degradation.

A novel organophosphate hydrolase from Arthrobacter sp. HM01: Characterization and applications

Bioremediation systems coupled to efficient microbial enzymes have emerged as an attractive approach for the in-situ removal of hazardous organophosphates (OPs) pesticides from the polluted environment. However, the role of engineered enzymes in OPs-degradation is rarely studied. In this study, the potential OPs-hydrolase (opdH) gene (Arthrobacter sp. HM01) was isolated, cloned, expressed, and purified. The recombinant organophosphate hydrolase (ropdH) was ∼29 kDa; which catalyzed a broad-range of OPs-pesticides in organic-solvent (∼99 % in 30 min), and was found to increase the catalytic efficiency by 10-folds over the native enzyme (k_cat/K_m: 10⁷ M^-1s^-1). The degraded metabolites were analyzed using HPLC/GCMS. Through site-directed mutagenesis, it was confirmed that, conserved metal-bridged residue (Lys-127), plays a crucial role in OPs-degradation, which shows ∼18-folds decline in OPs-degradation. Furthermore, the catalytic activity and its stability has been enhanced by >2.0-fold through biochemical optimization. Thus, the study suggests that ropdH has all the required properties for OPs bioremediation.

Degradation insight of organophosphate pesticide chlorpyrifos through novel intermediate 2,6-dihydroxypyridine by Arthrobacter sp. HM01

Organophosphates (OPs) are hazardous pesticides, but an indispensable part of modern agriculture; collaterally contaminating agricultural soil and surrounding water. They have raised serious food safety and environmental toxicity that adversely affect the terrestrial and aquatic ecosystems and therefore, it become essential to develop a rapid bioremediation technique for restoring the pristine environment. A newly OPs degrading Arthrobacter sp. HM01 was isolated from pesticide-contaminated soil and identified by a ribotyping (16S rRNA) method. Genus Arthrobacter has not been previously reported in chlorpyrifos (CP) degradation, which shows 99% CP (100 mg L-1) degradation within 10 h in mMSM medium and also shows tolerance to a high concentration (1000 mg L-1) of CP. HM01 utilized a broad range of OPs pesticides and other aromatic pollutants including intermediates of CP degradation as sole carbon sources. The maximum CP degradation was obtained at pH 7 and 32 °C. During the degradation, a newly identified intermediate 2,6-dihydroxypyridine was detected through TLC/HPLC/LCMS analysis and a putative pathway was proposed for its degradation. The study also revealed that the organophosphate hydrolase (opdH) gene was responsible for CP degradation, and the opdH-enzyme was located intracellularly. The opdH enzyme was characterized from cell free extract for its optimum pH and temperature requirement, which was 7.0 and 50 °C, respectively. Thus, the results revealed the true potential of HM01 for OPs-bioremediation. Moreover, the strain HM01 showed the fastest rate of CP degradation, among the reported Arthrobacter sp.

Structure and chemistry of enzymatic active sites that play a role in the switch and conformation mechanism

Enzymes, which are biological molecules, are constructed from polypeptide chains, and these molecules are activated through reaction mechanisms. It is the role of enzymes to speed up chemical reactions that are used to build or break down cell structures. Activation energy is reduced by the enzymes' selective binding of substrates in a protected environment. In enzyme tertiary structures, the active sites are commonly situated in a "cleft," which necessitates the diffusion of substrates and products. The amino acid residues of the active site may be far apart in the primary structure owing to the folding required for tertiary structure. Due to their critical role in substrate binding and attraction, changes in amino acid structure at or near the enzyme's active site usually alter enzyme activity. At the enzyme's active site, or where the chemical reactions occur, the substrate is bound. Enzyme substrates are the primary targets of the enzyme's active site, which is designed to assist in the chemical reaction. This chapter elucidates the summary of structure and chemistry of enzymes, their active site features, charges and role of water in the structures to clarify the biochemistry of the enzymes in the depth of atomic features.

Green MIP-202(Zr) Catalyst: Degradation and Thermally Robust Biomimetic Sensing of Nerve Agents

Rapid and robust sensing of nerve agent (NA) threats is necessary for real-time field detection to facilitate timely countermeasures. Unlike conventional phosphotriesterases employed for biocatalytic NA detection, this work describes the use of a new, green, thermally stable, and biocompatible zirconium metal-organic framework (Zr-MOF) catalyst, MIP-202(Zr). The biomimetic Zr-MOF-based catalytic NA recognition layer was coupled with a solid-contact fluoride ion-selective electrode (F-ISE) transducer, for potentiometric detection of diisopropylfluorophosphate (DFP), a F-containing G-type NA simulant. Catalytic DFP degradation by MIP-202(Zr) was evaluated and compared to the established UiO-66-NH₂ catalyst. The efficient catalytic DFP degradation with MIP-202(Zr) at near-neutral pH was validated by ³¹P NMR and FT-IR spectroscopy and potentiometric F-ISE and pH-ISE measurements. Activation of MIP-202(Zr) using Soxhlet extraction improved the DFP conversion rate and afforded a 2.64-fold improvement in total percent conversion over UiO-66-NH₂. The exceptional thermal and storage stability of the MIP-202/F-ISE sensor paves the way toward remote/wearable field detection of G-type NAs in real-world environments. Overall, the green, sustainable, highly scalable, and biocompatible nature of MIP-202(Zr) suggests the unexploited scope of such MOF catalysts for on-body sensing applications toward rapid on-site detection and detoxification of NA threats.

Exploiting enzyme evolution for computational protein design

Recent years have seen an explosion of interest in understanding the physicochemical parameters that shape enzyme evolution, as well as substantial advances in computational enzyme design. This review discusses three areas where evolutionary information can be used as part of the design process: (i) using ancestral sequence reconstruction (ASR) to generate new starting points for enzyme design efforts; (ii) learning from how nature uses conformational dynamics in enzyme evolution to mimic this process in silico; and (iii) modular design of enzymes from smaller fragments, again mimicking the process by which nature appears to create new protein folds. Using showcase examples, we highlight the importance of incorporating evolutionary information to continue to push forward the boundaries of enzyme design studies.

Disposable Paper-Based Biosensors for the Point-of-Care Detection of Hazardous Contaminations-A Review

The fast detection of trace amounts of hazardous contaminations can prevent serious damage to the environment. Paper-based sensors offer a new perspective on the world of analytical methods, overcoming previous limitations by fabricating a simple device with valuable benefits such as flexibility, biocompatibility, disposability, biodegradability, easy operation, large surface-to-volume ratio, and cost-effectiveness. Depending on the performance type, the device can be used to analyze the analyte in the liquid or vapor phase. For liquid samples, various structures (including a dipstick, as well as microfluidic and lateral flow) have been constructed. Paper-based 3D sensors are prepared by gluing and folding different layers of a piece of paper, being more user-friendly, due to the combination of several preparation methods, the integration of different sensor elements, and the connection between two methods of detection in a small set. Paper sensors can be used in chromatographic, electrochemical, and colorimetric processes, depending on the type of transducer. Additionally, in recent years, the applicability of these sensors has been investigated in various applications, such as food and water quality, environmental monitoring, disease diagnosis, and medical sciences. Here, we review the development (from 2010 to 2021) of paper methods in the field of the detection and determination of toxic substances.

Hydrolytic cleavage of nerve agent simulants by gold nanozymes

Although banned by the Chemical Weapons Convention, organophosphorus nerve agents are still available and have been used in regional wars, terroristic attacks or for other crtaiminal purposes. Their degradation is of primary importance for the severe toxicity of these compounds. Here we report that gold nanoparticles passivated with thiolated molecules bearing 1,3,7-triazacyclononane and 1,3,7,10-tetraazacyclododecane ligands efficiently hydrolyze nerve agents simulants p-nitrophenyl diphenyl phosphate and methylparaoxon as transition metal complexes at 25 °C and pH 8 with half-lives of the order of a few minutes. Mechanistically, these catalysts show an enzyme-like behavior, hence they constitute an example of nanozymes. The catalytic site appears to involve a single metal ion and its recognition of the substrates is driven mostly by hydrophobic interactions. The ease of preparation and the mild conditions at which they operate, make these nanozymes appealing catalysts for the detoxification after contamination with organophosphorus nerve agents, particularly those poorly soluble in water.

Product Inhibition and the Catalytic Destruction of a Nerve Agent Simulant by Zirconium-Based Metal-Organic Frameworks

Rapid degradation/destruction of chemical warfare agents, especially ones containing a phosphorous-fluorine bond, is of notable interest due to their extreme toxicity and typically rapid rate of human incapacitation. Recent studies of the hydrolytic destruction of a key nerve agent simulant, dimethyl 4-nitrophenylphosphate (DMNP), catalyzed by Zr₆-based metal-organic frameworks (MOFs), have suggested deactivation of the active sites due to inhibition by the products as the reaction progresses. In this study, the interactions of two MOFs, NU-1000 and MOF-808, and two hydrolysis products, dimethyl phosphate (DMP) and ethyl methyl phosphonate (EMP), from the hydrolysis of the simulant (DMNP) and nerve agent ethyl methylphosphonofluoridate (EMPF), resembling the hydrolysis degradation product of the G-series nerve agent, Sarin (GB), have been investigated to deconvolute the effect of product inhibition from other effects on catalytic activity. Kinetic studies via in situ nuclear magnetic resonance spectroscopy indicated substantial product inhibition upon catalyst activity after several tens to several thousand turnovers, depending on specific conditions. Apparent product binding constants were obtained by fitting initial reaction rates at pH 7.0 and pH 10.5 to a Langmuir-Freundlich binding/adsorption model. For the fits, varying amounts/concentrations of candidate inhibitors were introduced before the start of catalytic hydrolysis. The derived binding constants proved suitable for quantitatively describing product inhibition effects upon reaction rates over the extended time course of simulant hydrolysis by aqua-ligand-bearing hexa-zirconium(IV) nodes.

Insights into Catalytic Hydrolysis of Organophosphonates at M-OH Sites of Azolate-Based Metal Organic Frameworks

Organophosphorus nerve agents, a class of extremely toxic chemical warfare agents (CWAs), have remained a threat to humanity because of their continued use against civilian populations. To date, Zr(IV)-based metal organic framework (MOFs) are the most prevalent nerve agent hydrolysis catalysts, and relatively few reports disclose MOFs containing nodes with other Lewis acidic transition metals. In this work, we leveraged this synthetic tunability to explore how the identity of the transition metal node in the M-MFU-4l series of MOFs (M = Zn, Cu, Ni, Co) influences the catalytic performance toward the hydrolysis of the nerve agent simulant dimethyl (4-nitrophenyl)phosphate (DMNP). Experimental studies reveal that Cu-MFU-4l exhibits the best performance in this series with a half-life for hydrolysis of ∼2 min under these conditions. In contrast, both Ni- and Co-MFU-4l demonstrate significantly slower reactivity toward DMNP, as they both fail to surpass 30% conversion of DMNP after 1 h under analogous conditions. Further modification of the active site within Cu-MFU-4l is possible, and we found that although the identity of the anion coordinated to the Cu(II)-X (X = Cl^-, HCOO^-, ClO₄^-, NO₃^-) active site has little influence on the catalytic performance, reduction of the Cu(II) sites yields nodes that contain Cu(I) ions in a trigonal geometry with open metal sites, leading to remarkable catalytic activity with a half-life for hydrolysis less than 2 min. Computational studies indicate the Cu(I) sites exhibit stronger binding affinities than Cu(II) to both water and DMNP, which corroborates the experimental results.

Catalytic Performance of a Recombinant Organophosphate-Hydrolyzing Phosphotriesterase from Brevundimonas diminuta in the Presence of Surfactants

Phosphotriestease (PTE), also known as parathion hydrolase, has the ability to hydrolyze the triester linkage of organophosphate (OP) pesticides and chemical warfare nerve agents, making it highly suitable for environment remediation. Here, we studied the effects of various surfactants and commercial detergents on the esterase activity of a recombinant PTE (His6-tagged BdPTE) from Brevundimonas diminuta. Enzymatic assays indicated that His6-tagged BdPTE was severely inactivated by SDS even at lower concentrations and, conversely, the other three surfactants (Triton X-100, Tween 20, and Tween 80) had a stimulatory effect on the activity, especially at a pre-incubating temperature of 40 °C. The enzyme exhibited a good compatibility with several commercial detergents, such as Dr. Formula® and Sugar Bubble®. The evolution results of pyrene fluorescence spectroscopy showed that the enzyme molecules participated in the formation of SDS micelles but did not alter the property of SDS micelles above the critical micelle concentration (CMC). Structural analyses revealed a significant change in the enzyme’s secondary structure in the presence of SDS. Through the use of the intentionally fenthion-contaminated Chinese cabbage leaves as the model experiment, enzyme–Joy® washer solution could remove the pesticide from the contaminated sample more efficiently than detergent alone. Overall, our data promote a better understanding of the links between the esterase activity of His6-tagged BdPTE and surfactants, and they offer valuable information about its potential applications in liquid detergent formulations.

Pollen-inspired enzymatic microparticles to reduce organophosphate toxicity in managed pollinators

Pollinators support the production of the leading food crops worldwide. Organophosphates are a heavily used group of insecticides that pollinators can be exposed to, especially during crop pollination. Exposure to lethal or sublethal doses can impair fitness of wild and managed bees, risking pollination quality and food security. Here we report a low-cost, scalable in vivo detoxification strategy for organophosphate insecticides involving encapsulation of phosphotriesterase (OPT) in pollen-inspired microparticles (PIMs). We developed uniform and consumable PIMs capable of loading OPT at 90% efficiency and protecting OPT from degradation in the pH of a bee gut. Microcolonies of Bombus impatiens fed malathion-contaminated pollen patties demonstrated 100% survival when fed OPT-PIMs but 0% survival with OPT alone, or with plain sucrose within five and four days, respectively. Thus, the detrimental effects of malathion were eliminated when bees consumed OPT-PIMs. This design presents a versatile treatment that can be integrated into supplemental feeds such as pollen patties or dietary syrup for managed pollinators to reduce risk of organophosphate insecticides.

Enzymes, Reacting with Organophosphorus Compounds as Detoxifiers: Diversity and Functions

Organophosphorus compounds (OPCs) are able to interact with various biological targets in living organisms, including enzymes. The binding of OPCs to enzymes does not always lead to negative consequences for the body itself, since there are a lot of natural biocatalysts that can catalyze the chemical transformations of the OPCs via hydrolysis or oxidation/reduction and thereby provide their detoxification. Some of these enzymes, their structural differences and identity, mechanisms, and specificity of catalytic action are discussed in this work, including results of computational modeling. Phylogenetic analysis of these diverse enzymes was specially realized for this review to emphasize a great area for future development(s) and applications.

Structure-based redesign of the bacterial prolidase active-site pocket for efficient enhancement of methyl-parathion hydrolysis

Mutagenesis at four residues surrounding the active-site pocket of an old bacterial prolidase scaffold led to a 10 000-fold increase in methyl-parathion hydrolysis and broadening substrate specificity against organophosphorus compounds.

Enzymatic Degradation of Organophosphorus Pesticides and Nerve Agents by EC: 3.1.8.2

The organophosphorus substances, including pesticides and nerve agents (NAs), represent highly toxic compounds. Standard decontamination procedures place a heavy burden on the environment. Given their continued utilization or existence, considerable efforts are being made to develop environmentally friendly methods of decontamination and medical countermeasures against their intoxication. Enzymes can offer both environmental and medical applications. One of the most promising enzymes cleaving organophosphorus compounds is the enzyme with enzyme commission number (EC): 3.1.8.2, called diisopropyl fluorophosphatase (DFPase) or organophosphorus acid anhydrolase from Loligo Vulgaris or Alteromonas sp. JD6.5, respectively. Structure, mechanisms of action and substrate profiles are described for both enzymes. Wild-type (WT) enzymes have a catalytic activity against organophosphorus compounds, including G-type nerve agents. Their stereochemical preference aims their activity towards less toxic enantiomers of the chiral phosphorus center found in most chemical warfare agents. Site-direct mutagenesis has systematically improved the active site of the enzyme. These efforts have resulted in the improvement of catalytic activity and have led to the identification of variants that are more effective at detoxifying both G-type and V-type nerve agents. Some of these variants have become part of commercially available decontamination mixtures.

Organophosphorus Nerve Agents: Types, Toxicity, and Treatments

Organophosphorus compounds are extensively used worldwide as pesticides which cause great hazards to human health. Nerve agents, a subcategory of the organophosphorus compounds, have been produced and used during wars, and they have also been used in terrorist activities. These compounds possess physiological threats by interacting and inhibiting acetylcholinesterase enzyme which leads to the cholinergic crisis. After a general introduction, this review elucidates the mechanisms underlying cholinergic and noncholinergic effects of organophosphorus compounds. The conceivable treatment strategies for organophosphate poisoning are different types of bioscavengers which include stoichiometric, catalytic, and pseudocatalytic. The current research on the promising treatments specifically the catalytic bioscavengers including several wild-type organophosphate hydrolases such as paraoxonase and phosphotriesterase, phosphotriesterase-like lactonase, methyl parathion hydrolase, organophosphate acid anhydrolase, diisopropyl fluorophosphatase, human triphosphate nucleotidohydrolase, and senescence marker protein has been widely discussed. Organophosphorus compounds are reported to be the nonphysiological substrate for many mammalian organophosphate hydrolysing enzymes; therefore, the efficiency of these enzymes toward these compounds is inadequate. Hence, studies have been conducted to create mutants with an enhanced rate of hydrolysis and high specificity. Several mutants have been created by applying directed molecular evolution and/or targeted mutagenesis, and catalytic efficiency has been characterized. Generally, organophosphorus compounds are chiral in nature. The development of mutant enzymes for providing superior stereoselective degradation of toxic organophosphorus compounds has also been widely accounted for in this review. Existing enzymes have shown limited efficiency; hence, more effective treatment strategies have also been critically analyzed.

Enhancing organophosphate hydrolase efficacy via protein engineering and immobilization strategies

Organophosphorus compounds (OPs), developed as pesticides and chemical warfare agents, are extremely toxic chemicals that pose a public health risk. Of the different detoxification strategies, organophosphate-hydrolyzing enzymes have attracted much attention, providing a potential route for detoxifying those exposed to OPs. Phosphotriesterase (PTE), also known as organophosphate hydrolase (OPH), is one such enzyme that has been extensively studied as a catalytic bioscavenger. In this review, we will discuss the protein engineering of PTE aimed toward improving the activity and stability of the enzyme. In order to make enzyme utilization in OP detoxification more favorable, enzyme immobilization provides an effective means to increase enzyme activity and stability. Here, we present several such strategies that enhance the storage and operational stability of PTE/OPH.