Assessing chemical hazard and unraveling binding affinity of priority pollutants to lignin modifying enzymes for environmental remediation

Laccase-based biocatalytic systems application in sustainable degradation of pharmaceutically active contaminants

The outflow of pharmaceutically active chemicals (PhACs) exerts a negative impact on biological systems even at extremely low concentrations. For instance, enormous threats to human and aquatic species have resulted from the widespread use of antibiotics in ecosystems, which stimulate the emergence and formation of antibiotic-resistant bacterial species and associated genes. Additionally, it is challenging to eliminate these PhACs by employing conventional physicochemical water treatment techniques. Enzymatic approaches, including laccase, have been identified as a promising alternative to eliminate a broad array of PhACs from water matrices. However, their application in environmental bioremediation is hindered by several factors, including the enzyme's stability and its location in the aqueous environment. Such obstacles may be surmounted by employing laccase immobilization, which enables enhanced stability (including inactivation caused by the substrate), and thus improved catalysis. This review emphasizes the potential hazards of PhACs to aquatic organisms within the detection concentration range of ngL-1 to µgL-1, as well as the deployment of laccase-based multifunctional biocatalytic systems for the environmentally friendly mitigation of anticancer drugs, analgesics/NSAIDs, antibiotics, antiepileptic agents, and beta blockers as micropollutants. This approach could reduce the underlying toxicological consequences. In addition, current developments, potential applications, and viewpoints have focused on computer-assisted investigations of laccase-PhACs binding at enzyme cavities and degradability prediction.

GRACE: Generative Redesign in Artificial Computational Enzymology

Designing de novo enzymes is complex and challenging, especially to maintain the activity. This research focused on motif design to identify the crucial domain in the enzyme and uncovered the protein structure by molecular docking. Therefore, we developed a Generative Redesign in Artificial Computational Enzymology (GRACE), which is an automated workflow for reformation and creation of the de novo enzymes for the first time. GRACE integrated RFdiffusion for structure generation, ProteinMPNN for sequence interpretation, CLEAN for enzyme classification, and followed by solubility analysis and molecular dynamic simulation. As a result, we selected two gene sequences associated with carbonic anhydrase from among 10,000 protein candidates. Experimental validation confirmed that these two novel enzymes, i.e., dCA12_2 and dCA23_1, exhibited favorable solubility, promising substrate-active site interactions, and achieved activity of 400 WAU/mL. This workflow has the potential to greatly streamline experimental efforts in enzyme engineering and unlock new avenues for rational protein design.

Time-dependent nonmonotonic concentration-response and synergism of alkyl glycosides with different alkyl side chain to Vibrio qinghaiensis sp. -Q67

Alkyl glycosides (AGs), commonly used nonionic surfactants, may have toxic effects on the environmental organisms. However, the complex concentration-response patterns of AGs with varying alkyl side chains and their mixtures have not been thoroughly studied. Therefore, the luminescence inhibition toxicities of six AGs with different alkyl side chains, namely, ethyl (AG02), butyl (AG04), hexyl (AG06), octyl (AG08), decyl (AG10), and dodecyl (AG12) glucosides, were determined in Vibrio qinghaiensis sp. -Q67 (Q67) at 0.25, 3, 6, 9, and 12 h. The six AGs exhibited time- and side-chain-dependent nonmonotonic concentration- responses toward Q67. AG02, with a short side chain, presented a concentration-response curve (CRC) with two peaks after 6 h and stimulated the luminescence of Q67 at both 6 and 9 h. AG04, AG06, and AG08 showed S-shaped CRCs at five exposure time points, and their toxicities increased with the side-chain length. AG10 and AG12, with long side chains, exhibited hormesis at 9 and 12 h. Molecular docking was performed to explore the mechanism governing the possible influence of AGs on the luminescence response. The effects of AGs on Q67 could be attributed to multiple luminescence-regulatory proteins, including LuxA, LuxC, LuxD, LuxG, LuxI, and LuxR. Notably, LuxR was identified as the primary binding protein among the six AGs. Given that they may co-exist, binary mixtures of AG10 and AG12 were designed to explore their concentration-response patterns and interactions. The results revealed that all AG10-AG12 binary mixture rays showed time-dependent hormesis on Q67, similar to that shown by their individual components. The interactions of these binary mixtures were mainly characterized by low-concentration additive action and high-concentration synergism at different times.

In Silico Insights into the Arsenic Binding Mechanism Deploying Application of Computational Biology-Based Toolsets

An assortment of environmental matrices includes arsenic (As) in its different oxidation states, which is often linked to concerns that pose a threat to public health worldwide. The current difficulty lies in addressing toxicological concerns and achieving sustained detoxification of As. Multiple conventional degradation methods are accessible; however, they are indeed labor-intensive, expensive, and reliant on prolonged laboratory evaluations. Molecular interaction and atomic level degradation mechanisms for enzyme-As exploration are, however, underexplored in those approaches. A feasible approach in this case for tackling this accompanying concern of As might be to cope with undertaking multivalent computational methodologies and tools. This work aimed to provide molecular-level insight into the enzyme-aided As degradation mechanism. AutoDock Vina, CABS-flex 2.0, and Desmond high-performance molecular dynamics simulation (MDS) were utilized in the current investigation to simulate multivalent molecular processes on two protein sets: arsenate reductase (ArsC) and laccase (LAC) corresponding arsenate (ART) and arsenite (AST), which served as model ligands to comprehend binding, conformational, and energy attributes. The structural configurations of both proteins exhibited variability in flexibility and structure framework within the range of 3.5-4.5 Å. The LAC-ART complex exhibited the lowest calculated binding affinity, measuring -5.82 ± 0.01 kcal/mol. Meanwhile, active site residues ILE-200 and HIS-206 were demonstrated to engage in H-bonding with the ART ligand. In contrast to ArsC, the ligand binding affinity of this bound complex was considerably greater. Additional validation of docked complexes was carried out by deploying Desmond MDS of 100 ns to capture protein and ligand conformation behavior. The system achieved stability during the 100 ns simulation run, as confirmed by the average P-L RMSD, which was ∼1 Å. As a preliminary test of the enzyme's ability to catalyze As species, corresponding computational insights might be advantageous for bridging gaps and regulatory consideration.

Enzyme-linked carbon nanotubes as biocatalytic tools to degrade and mitigate environmental pollutants

A wide array of organic compounds have been recognized as pollutants of high concern due to their controlled or uncontrolled presence in environmental matrices. The persistent prevalence of diverse organic pollutants, including pharmaceutical compounds, phenolic compounds, synthetic dyes, and other hazardous substances, necessitates robust measures for their practical and sustainable removal from water bodies. Several bioremediation and biodegradation methods have been invented and deployed, with a wide range of materials well-suited for diverse environments. Enzyme-linked carbon-based materials have been considered efficient biocatalytic platforms for the remediation of complex organic pollutants, mostly showing over 80% removal efficiency of micropollutants. The advantages of enzyme-linked carbon nanotubes (CNTs) in enzyme immobilization and improved catalytic potential may thus be advantageous for environmental research considering the current need for pollutant removal. This review outlines the perspective of current remediation approaches and highlights the advantageous features of enzyme-linked CNTs in the removal of pollutants, emphasizing their reusability and stability aspects. Furthermore, different applications of enzyme-linked CNTs in environmental research with concluding remarks and future outlooks have been highlighted. Enzyme-linked CNTs serve as a robust biocatalytic platform for the sustainability agenda with the aim of keeping the environment clean and safe from a variety of organic pollutants.

Predictionof Environmental FateandToxicityofInsecticidesUsing Multi-Target QSAR Approach

Ecotoxicological risk assessments form the foundation of regulatory decisions for industrial chemicals used in various sectors. In this study, a multi-target-QSAR model established by a backpropagation neural network trained with the Levenberg-Marquardt (LM) algorithm was used to construct a statistically robust and easily interpretable Mt-QSAR model with high external predictability for the simultaneous prediction of the environmental fate in form of octanol-water partition coefficient (LogP), (BCF) and acute oral toxicity in mammals and birds (LD50rat ) and (LD50bird ) for a wide range of chemical structural classes of insecticides. Principal component analysis was performed on descriptors selected by the SW-MLR method, and the selected PCs were used for constructing the SW-MLR-PCA-ANN model. The developed well-trained model (RMSE=0.83, MPE=0.004, CCC=0.82, IIC=0.78, R2 =0.69) was statistically robust as indicated by the external validation parameters (RMSE=0.93, MPE=0.008, CCC=0.77, IIC=0.68, R2 =0.61). The AD of the developed Mt-QSAR model was also defined to identify the most reliable predictions. Finally, the missing values in the dataset for the aforementioned targets were predicted using the constructed Mt-QSAR model. The proposed approach can be used for simultaneous prediction of the environmental fate of new insecticides, especially ones that haven't been tested yet.

Structural insights, biocatalytic characteristics, and application prospects of lignin-modifying enzymes for sustainable biotechnology

Lignin modifying enzymes (LMEs) have gained widespread recognition in depolymerization of lignin polymers by oxidative cleavage. LMEs are a robust class of biocatalysts that include lignin peroxidase (LiP), manganese peroxidase (MnP), versatile peroxidase (VP), laccase (LAC), and dye-decolorizing peroxidase (DyP). Members of the LMEs family act on phenolic, non-phenolic substrates and have been widely researched for valorization of lignin, oxidative cleavage of xenobiotics and phenolics. LMEs implementation in the biotechnological and industrial sectors has sparked significant attention, although its potential future applications remain underexploited. To understand the mechanism of LMEs in sustainable pollution mitigation, several studies have been undertaken to assess the feasibility of LMEs in correlating to diverse pollutants for binding and intermolecular interactions at the molecular level. However, further investigation is required to fully comprehend the underlying mechanism. In this review we presented the key structural and functional features of LMEs, including the computational aspects, as well as the advanced applications in biotechnology and industrial research. Furthermore, concluding remarks and a look ahead, the use of LMEs coupled with computational framework, built upon artificial intelligence (AI) and machine learning (ML), has been emphasized as a recent milestone in environmental research.