Application of molecular docking for the degradation of organic pollutants in the environmental remediation: A review

Haloketones: A class of unregulated priority DBPs with high contribution to drinking water cytotoxicity

Although unregulated aliphatic disinfection byproducts (DBPs) had a much higher concentration and cytotoxicity than known aromatic DBPs, a recent study indicated that seven classes of regulated and unregulated priority DBPs (one and two-carbon-atom DBPs) just accounted for 16.2% of disinfected water cytotoxicity in the U.S., meaning some of the highly toxic aliphatic DBPs may be overlooked. Haloketones (HKs) are an essential class of priority DBPs with a 1-100 µg/L concentration in drinking water but lack cytotoxicity data. This study investigated the cytotoxicity of seven HKs using Chinese hamster ovary (CHO) cells. The order for cytotoxicity of HKs from most to least toxic was: 1,3-dichloroacetone (LC50: 1.0 ± 0.20 μM) ≈ 1,3-dibromoacetone (1.5 ± 0.19 μM) ≈ bromoacetone (1.9 ± 0.49 μM) > chloroacetone (4.3 ± 0.22 μM) > 1,1,3-trichloropropanone (6.6 ± 0.46 μM) > 1,1,1-trichloroacetone (222 ± 7.7 μM) > hexachloroacetone (3269 ± 344 μM). The cytotoxicity of HKs was higher than most regulated and priority aliphatic DBPs in mono-halogenated, di-halogenated, and tri-halogenated categories. A prediction model of HK cytotoxicity was developed based on the quantitative structure-activity relationship (QSAR), optimizing structures and computing descriptors with Gaussian 09 W. The average concentrations of HKs in representative drinking water samples from South Carolina (U.S.) and Suzhou (China) were 12.4 and 0.9 μg/L, respectively, accounting for 18.8% and 1.7% of their specific total DBPs measured (i.e. not TOX). For South Carolina drinking water, their contributions to total calculated additive cytotoxicity of aliphatic DBPs and overall drinking water cytotoxicity were 86.7% and 14.0%, respectively, demonstrating that HKs are an essential class of overlooked DBPs with a high contribution to drinking water cytotoxicity. Our study can help to explain the conflict that why regulated and priority DBPs (except HKs) just accounted for 16% of chlorinated drinking water cytotoxicity even enough they had much higher concentration and cytotoxicity than known aromatic DBPs.

Insights into the biodegradation of fipronil through soil microcosm-omics analyses of Pseudomonas sp. FIP_ A4

Fipronil, a phenylpyrazole insecticide, is used to kill insects resistant to conventional insecticides. Though its regular and widespread use has substantially reduced agricultural losses, it has also caused its accumulation in various environmental niches. The biodegradation is an effective natural process that helps in reducing the amount of residual insecticides. This study deals with an in-depth investigation of fipronil degradation kinetics and pathways in Pseudomonas sp. FIP_A4 using multi-omics approaches. Soil-microcosm results revealed ∼87% degradation within 40 days. The whole genome of strain FIP_A4 comprises 4.09 Mbp with 64.6% GC content. Cytochrome P450 monooxygenase and enoyl-CoA hydratase-related protein, having 30% identity with dehalogenase detected in the genome, can mediate the initial degradation process. Proteome analysis revealed differential enzyme expression of dioxygenases, decarboxylase, and hydratase responsible for subsequent degradation. Metabolome analysis displayed fipronil metabolites in the presence of the bacterium, supporting the proposed degradation pathway. Molecular docking and dynamic simulation of each identified enzyme in complex with the specific metabolite disclosed adequate binding and high stability in the enzyme-metabolite complex. This study provides in-depth insight into genes and their encoded enzymes involved in the fipronil degradation and formation of different metabolites during pollutant degradation. The outcome of this study can contribute immensely to developing efficient technologies for the bioremediation of fipronil-contaminated soils.

Disinfectant-induced ammonia oxidation disruption in microbial N-cycling process in aquatic ecosystem after the COVID-19 outbreak

Anthropogenic activities significantly impact the elemental cycles in aquatic ecosystems, with the N-cycling playing a critical role in potential nutrient turnover and substance cycling. We hypothesized that measures to prevent COVID-19 transmission profoundly altered the nitrogen cycle in riverine ecosystems. To investigate this, we re-analyzed metagenomic data and identified 60 N-cycling genes and 21 host metagenomes from four urban reaches (one upstream city, Wuhan, and two downstream cities) along the Yangtze River. Our analyses revealed a marked decrease in the abundance of bacterial ammonia monooxygenase genes, as well as in the host, ammonia-oxidizing autotrophic Nitrosomonas, followed by a substantial recovery post-pandemic. We posited that discharge of sodium hypochlorite (NaOCl) disinfectant may be a primary factor in the reduction of N-cycling process. To test this hypothesis, we exposed pure cultures of Nitrosomonas europaea to NaOCl to explore the microbial stress response. Results indicated that NaOCl exposure rapidly compromised the cell structure and inhibited ammonia oxidation of N. europaea, likely due to oxidative stress damage and reduced expression of nitrogen metabolism-related ammonia monooxygenase. Using the functional tagging technique, we determined that NaOCl directly destroyed the ammonia monooxygenase protein and DNA structure. This study highlights the negative impacts of chlorine disinfectants on the function of aquatic ecosystems and elucidates potential mechanisms of action.

Biodegradation of atrazine and nicosulfuron by Streptomyces nigra LM01: Performance, degradative pathway, and possible genes involved

Microbial herbicide degradation is an efficient bioremediation method. In this study, a strain of Streptomyces nigra, LM01, which efficiently degrades atrazine and nicosulfuron, was isolated from a corn field using a direct isolation method. The degradation effects of the identified strain on two herbicides were investigated and optimized using an artificial neural network. The maximum degradation rates of S. nigra LM01 were 58.09 % and 42.97 % for atrazine and nicosulfuron, respectively. The degradation rate of atrazine in the soil reached 67.94 % when the concentration was 108 CFU/g after 5 d and was less effective than that of nicosulfuron. Whole genome sequencing of strain LM01 helped elucidate the possible degradation pathways of atrazine and nicosulfuron. The protein sequences of strain LM01 were aligned with the sequences of the degraded proteins of the two herbicides by using the National Center for Biotechnology Information platform. The sequence (GE005358, GE001556, GE004212, GE005218, GE004846, GE002487) with the highest query cover was retained and docked with the small-molecule ligands of the herbicides. The results revealed a binding energy of - 6.23 kcal/mol between GE005358 and the atrazine ligand and - 6.66 kcal/mol between GE002487 and the nicosulfuron ligand.

Evaluation of surfactant-aided polycyclic aromatic hydrocarbon biodegradation by molecular docking and molecular dynamic simulation in the marine environment

Marine oil spills directly cause polycyclic aromatic hydrocarbons (PAHs) pollution and affect marine organisms due to their toxic property. Chemical and bio-based dispersants composed of surfactants and solvents are considered effective oil spill-treating agents. Dispersants enhance oil biodegradation in the marine environment by rapidly increasing their solubility in the water column. However, the effect of dispersants, especially surfactants, on PAHs degradation by enzymes produced by microorganisms has not been studied at the molecular level. The role of the cytochrome P450 (CYP) enzyme in converting contaminants into reactive metabolites during the biodegradation process has been evidenced, but the activity in the presence of surfactants is still ambiguous. Thus, this study focused on the evaluation of the impact of chemical and bio-surfactants (i.e., Tween 80 (TWE) and Surfactin (SUC)) on the biodegradation of naphthalene (NAP), chrysene (CHR), and pyrene (PYR), the representative components of PAHs, with CYP enzyme from microalgae Parachlorella kessleri using molecular docking and molecular dynamics (MD) simulation. The molecular docking analysis revealed that PAHs bound to residues at the CYP active site through hydrophobic interactions for biodegradation. The MD simulation showed that the surfactant addition changed the enzyme conformation in the CYP-PAH complexes to provide more interactions between the enzyme and PAHs. This led to an increase in the enzyme's capability to degrade PAHs. Binding free energy (ΔG‌‌Bind) calculations confirmed that surfactant treatment could enhance PAHs degradation by the enzyme. The SUC gave a better result on NAP and PYR biodegradation based on ΔG‌‌Bind, while TWE facilitated the biodegradation of CHR. The research outputs could greatly facilitate evaluating the behaviors of oil spill-treating agents and oil spill response operations in the marine environment.

Design, synthesis of benzimidazole tethered 3,4-dihydro-2H-benzo[e] [1, 3] oxazines as anticancer agents

A series of novel 3-(1H-benzo[d]imidazol-2-yl)-3,4-dihydro-2H-benzo[e][1,3] oxazine analogues synthesized through a two-step synthetic protocol. The structure of the compounds were established by interpretation 1H NMR, 13C NMR and Mass spectral data recorded after purification. All the title compounds 4a-k were screened for their in vitro anti-cancer activity against two breast cancer cell lines MCF 7 and MDA-MB-231 by using Doxorubicin as standard reference. Compound 4e displayed superior activity against both the cell lines MCF-7 and MDA-MB-231 with IC50 values of 8.60 ± 0.75 and 6.30 ± 0.54 µM respectively, compared to the Doxorubicin IC50 value of 9.11 ± 0.54 and 8.47 ± 0.47 µM. Compound 4i also indicated good activity with IC50 value of 9.85 ± 0.69 μM on par with Doxorubicin against MCF-7 cells. Compound 4g demonstrated best activity on par with standard reference to IC50 value of 8.52 ± 0.62 μM against MDA-MB-231 cell line. And all other compounds demonstrated good to moderate activity compared to Doxorubicin. Docking studies against EGFR showed that all the compounds have very good binding affinities towards the target. The predicted drug-likeness properties of all compounds enable them to be used as therapeutic agents.

Emerging technologies for the removal of pesticides from contaminated soils and their reuse in agriculture

Pesticides are becoming more prevalent in agriculture to protect crops and increase crop yields. However, nearly all pesticides used for this purpose reach non-target crops and remain as residues for extended periods. Contamination of soil by widespread pesticide use, as well as its toxicity to humans and other living organisms, is a global concern. This has prompted us to find solutions and develop alternative remediation technologies for sustainable management. This article reviews recent technological developments for remediating pesticides from contaminated soil, focusing on the following major points: (1) The application of various pesticide types and their properties, the sources of pesticides related to soil pollution, their transport and distribution, their fate, the impact on soil and human health, and the extrinsic and intrinsic factors that affect the remediation process are the main points of focus. (2) Sustainable pesticide degradation mechanisms and various emerging nano- and bioelectrochemical soil remediation technologies. (3) The feasible and long-term sustainable research and development approaches that are required for on-site pesticide removal from soils, as well as prospects for applying them directly in agricultural fields. In this critical analysis, we found that bioremediation technology has the potential for up to 90% pesticide removal from the soil. The complete removal of pesticides through a single biological treatment approach is still a challenging task; however, the combination of electrochemical oxidation and bioelectrochemical system approaches can achieve the complete removal of pesticides from soil. Further research is required to remove pesticides directly from soils in agricultural fields on a large-scale.

Enhanced Drug Carriage Efficiency of Curcumin-Loaded PLGA Nanoparticles in Combating Diabetic Nephropathy via Mitigation of Renal Apoptosis

Objectives

The Curcuma-derived diferuloylmethane compound CUR, loaded on Poly (lactide-co-glycolic) acid (PLGA) nanoparticles was utilized to combat DN-induced renal apoptosis by selectively targeting and modulating Bcl2.

Methods

Upon in silico molecular docking and screening study CUR was selected as the core phytocompound for nanoparticle formulation. PLGA-nano-encapsulated-curcumin (NCUR) were synthesized following standard solvent displacement method. The NCUR were characterized for shape, size and other physico-chemical properties by Atomic Force Microscopy (AFM), Dynamic Light Scattering (DLS) and Fourier-Transform Infrared (FTIR) Spectroscopy studies. For in vivo validation of nephro-protective effects, Mus musculus were pre-treated with CUR at a dose of 50 mg/kg b.w. and NCUR at a dose of 25 mg/kg b.w. (dose 1), 12.5 mg/kg b.w (dose 2) followed by alloxan administration (100 mg/kg b.w) and serum glucose levels, histopathology and immunofluorescence study were conducted.

Results

The in silico study revealed a strong affinity of CUR towards Bcl2 (dock score -10.94 Kcal/mol). The synthesized NCUR were of even shape, devoid of cracks and holes with mean size of ~80 nm having -7.53 mV zeta potential. Dose 1 efficiently improved serum glucose levels, tissue-specific expression of Bcl2 and reduced glomerular space and glomerular sclerosis in comparison to hyperglycaemic group.

Conclusion

This study essentially validates the potential of NCUR to inhibit DN by reducing blood glucose level and mitigating glomerular apoptosis by selectively promoting Bcl2 protein expression in kidney tissue.

Natural autophagy activators: A promising strategy for combating photoaging

BACKGROUND

Photodamage to the skin stands out as one of the most widespread epidermal challenges globally. Prolonged exposure to sunlight containing ultraviolet radiation (UVR) instigates stress, thereby compromising the skin's functionality and culminating in photoaging. Recent investigations have shed light on the importance of autophagy in shielding the skin from photodamage. Despite the acknowledgment of numerous phytochemicals possessing photoprotective attributes, their potential to induce autophagy remains relatively unexplored.

PURPOSE

Diminished autophagy activity in photoaged skin underscores the potential benefits of restoring autophagy through natural compounds to enhance photoprotection. Consequently, this study aims to highlight the role of natural compounds in safeguarding against photodamage and to assess their potential to induce autophagy via an in-silico approach.

METHODS

A thorough search of the literature was done using several databases, including PUBMED, Science Direct, and Google Scholar, to gather relevant studies. Several keywords such as Phytochemical, Photoprotection, mTOR, Ultraviolet Radiation, Reactive oxygen species, Photoaging, and Autophagy were utilized to ensure thorough exploration. To assess the autophagy potential of phytochemicals through virtual screening, computational methodologies such as molecular docking were employed, utilizing tools like AutoDock Vina. Receptor preparation for docking was facilitated using MGLTools.

RESULTS

The initiation of structural and functional deterioration in the skin due to ultraviolet radiation (UVR) or sunlight-induced reactive oxygen species/reactive nitrogen species (ROS/RNS) involves the modulation of various pathways. Natural compounds like phenolics, flavonoids, flavones, and anthocyanins, among others, possess chromophores capable of absorbing light, thereby offering photoprotection by modulating these pathways. In our molecular docking study, these phytochemicals have shown binding affinity with mTOR, a negative regulator of autophagy, indicating their potential as autophagy modulators.

CONCLUSION

This integrated review underscores the photoprotective characteristics of natural compounds, while the in-silico analysis reveals their potential to modulate autophagy, which could significantly contribute to their anti-photoaging properties. The findings of this study hold promise for the advancement of cosmeceuticals and therapeutics containing natural compounds aimed at addressing photoaging and various skin-related diseases. By leveraging their dual benefits of photoprotection and autophagy modulation, these natural compounds offer a multifaceted approach to combatting skin aging and related conditions.

Molecular docking and metagenomics assisted mitigation of microplastic pollution

Microplastics, tiny, flimsy, and direct progenitors of principal and subsidiary plastics, cause environmental degradation in aquatic and terrestrial entities. Contamination concerns include irrevocable impacts, potential cytotoxicity, and negative health effects on mortals. The detection, recovery, and degradation strategies of these pollutants in various biota and ecosystems, as well as their impact on plants, animals, and humans, have been a topic of significant interest. But the natural environment is infested with several types of plastics, all having different chemical makeup, structure, shape, and origin. Plastic trash acts as a substrate for microbial growth, creating biofilms on the plastisphere surface. This colonizing microbial diversity can be glimpsed with meta-genomics, a culture-independent approach. Owing to its comprehensive description of microbial communities, genealogical evidence on unconventional biocatalysts or enzymes, genomic correlations, evolutionary profile, and function, it is being touted as one of the promising tools in identifying novel enzymes for the degradation of polymers. Additionally, computational tools such as molecular docking can predict the binding of these novel enzymes to the polymer substrate, which can be validated through in vitro conditions for its environmentally feasible applications. This review mainly deals with the exploration of metagenomics along with computational tools to provide a clearer perspective into the microbial potential in the biodegradation of microplastics. The computational tools due to their polymathic nature will be quintessential in identifying the enzyme structure, binding affinities of the prospective enzymes to the substrates, and foretelling of degradation pathways involved which can be quite instrumental in the furtherance of the plastic degradation studies.

Remediation of multifarious metal ions and molecular docking assessment for pathogenic microbe disinfection in aqueous solution by waste-derived Ca-MOF

The present study demonstrates an eco-friendly and cost-effective synthesis of calcium terephthalate metal-organic frameworks (Ca-MOF). The Ca-MOF were composed of metal ions (Ca2+) and organic ligands (terephthalic acid; TPA); the former was obtained from egg shells, and the latter was obtained from processing waste plastic bottles. Detailed characterization using standard techniques confirmed the synthesis of Ca-MOF with an average particle size of 461.9 ± 15 nm. The synthesized Ca-MOF was screened for its ability to remove multiple metal ions from an aqueous solution. Based on the maximum sorption capacity, Pb2+, Cd2+, and Cu2+ ions were selected for individual parametric batch studies. The obtained results were interpreted using standard isotherms and kinetic models. The maximum sorption capacity (qm) obtained from the Langmuir model was found to be 644.07 ± 47, 391.4 ± 26, and 260.5 ± 14 mg g-1 for Pb2+, Cd2+, and Cu2+, respectively. Moreover, Ca-MOF also showed an excellent ability to remove all three metal ions simultaneously from a mixed solution. The metal nodes and bonded TPA from Ca-MOF were dissociated by the acid dissolution method, which protonated and isolated TPA for reuse. Further, the crystal structure of Ca-MOF was prepared and docked with protein targets of selected pathogenic water-borne microbes, which showed its disinfection potential. Overall, multiple metal sorption capability, regeneration studies, and broad-spectrum antimicrobial activity confirmed the versatility of synthesized Ca-MOF for industrial wastewater treatment.

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.

Fungal enzyme degradation of lignin-PLA composites: Insights from experiments and molecular docking simulations

Fungal enzymes are effective in degrading various polymeric materials. In this study, we assessed the initial degradation of composites consisting of lignin-poly(lactic acid) (PLA) with both unmodified lignin (LIG) and oxypropylated lignin (oLIG) incorporated at 10 % and 40 % weight within the PLA matrix in a fungal environment. Trametes versicolor fungi were used, and the samples were treated only for eight weeks. Although there was no significant difference in weight loss, the degradation process impacted the chemical and thermal properties of the composites, as shown by Fourier transform infrared spectroscopy (FTIR) and Differential scanning calorimetry (DSC) analyses. After the degradation process, the carbonyl index values decreased for all composites and the hydroxyl index values increased for LIG/PLA and a reverse trend was observed for oLIG/PLA composites. The first heating scan from DSC results showed that the melting peak and the cold crystallization peak disappeared after the degradation process. Microscopic analysis revealed that LIG/PLA exhibited higher roughness than oLIG/PLA. Molecular docking simulations were carried out using guaiacylglycerol-β-guaiacyl ether (GGE) and lactic acid (LA) as model compounds for lignin and PLA, respectively, with laccase (Lac) enzyme for Trametes versicolor. The docking results showed that GGE had the strongest binding interaction and affinity with Lac than lactic acid and oxypropylated GGE. The oxypropylated GGE formed a shorter hydrogen bonding with the Lac enzyme than GGE and LA. The trend associated with the degradation of composites from experimental and molecular docking findings was consistent. This combined approach provided insights into the degradation process using fungi and had the potential to be applied to different polymeric composites.

Molecular Mechanism and Structure-activity Relationship of the Inhibition Effect between Monoamine Oxidase and Selegiline Analogues

INTRODUCTION

To investigate the inhibition properties and structure-activity relationship between monoamine oxidase (MAO) and selected monoamine oxidase inhibitors (MAOIs, including selegiline, rasagiline and clorgiline).

METHODS

The inhibition effect and molecular mechanism between MAO and MAOIs were identified via the half maximal inhibitory concentration (IC50) and molecular docking technology.

RESULTS

It was indicated that selegiline and rasagiline were MAO B inhibitors, but clorgiline was MAO-A inhibitor based on the selectivity index (SI) of MAOIs (0.000264, 0.0197 and 14607.143 for selegiline, rasagiline and clorgiline, respectively). The high-frequency amino acid residues of the MAOIs and MAO were Ser24, Arg51, Tyr69 and Tyr407 for MAO-A and Arg42 and Tyr435 for MAO B. The MAOIs and MAO A/B pharmacophores included the aromatic core, hydrogen bond acceptor, hydrogen bond donor-acceptor and hydrophobic core.

CONCLUSION

This study shows the inhibition effect and molecular mechanism between MAO and MAOIs and provides valuable findings on the design and treatment of Alzheimer's and Parkinson's diseases.

Exploring the role of microbial proteins in controlling environmental pollutants based on molecular simulation

Molecular simulation has been widely used to study microbial proteins' structural composition and dynamic properties, such as volatility, flexibility, and stability at the microscopic scale. Herein, this review describes the key elements of molecular docking and molecular dynamics (MD) simulations in molecular simulation; reviews the techniques combined with molecular simulation, such as crystallography, spectroscopy, molecular biology, and machine learning, to validate simulation results and bridge information gaps in the structure, microenvironmental changes, expression mechanisms, and intensity quantification; illustrates the application of molecular simulation, in characterizing the molecular mechanisms of interaction of microbial proteins with four different types of contaminants, namely heavy metals (HMs), pesticides, dyes and emerging contaminants (ECs). Finally, the review outlines the important role of molecular simulations in the study of microbial proteins for controlling environmental contamination and provides ideas for the application of molecular simulation in screening microbial proteins and incorporating targeted mutagenesis to obtain more effective contaminant control proteins.

Exploring the potential of Halalkalibacterium halodurans laccase for endosulfan and chlorophacinone degradation: insights from molecular docking and molecular dynamics simulations

Pesticides are widely used in agriculture but at the same time, a majority of them are known to cause serious harm to health and the environment. In the recent past, laccases have been reported as key enzymes having the ability to degrade pollutants by converting them into less toxic forms. In this investigation, laccase from polyextremophilic bacterium Halalkalibacterium halodurans C-125 was analyzed for its structural, physicochemical, and functional characterization using in silico approaches. The 3D model of the said enzyme is unknown; therefore, the model was generated by template-independent modeling using ROBETTA, I-TASSER, and Alphafold server. The best-generated model from Alphafold with a confidence of 0.95 was validated from ERRAT and Verify 3D scores of 89.95 and 91.80%, respectively. The Ramachandran plot generated using the PROCHECK server further predicted the accuracy of the model with 93.7% and 5.9% of residues present in most favored and additional allowed regions of the plot respectively. The active sites, ion binding sites, and subcellular localization of laccase were also predicted. The generated model was docked with 121 pollutants (pesticides, insecticides, herbicides, fungicides, and rodenticides) for its degradation potential towards these pollutants. Two ligands chlorophacinone (based on the highest binding energy) and endosulfan (based on agricultural uses) were selected for molecular dynamic simulation studies. Endosulfan as a pesticide is banned but in some countries governments allow its use for special purposes which need serious consideration on developing bioremediation approaches for endosulfan degradation. MD simulation studies revealed that both chlorophacinone and endosulfan form hydrogen bonds and hydrophobic bonds with the active site of laccase and chlorophacinone-laccase complex were more stable in comparison to endosulfan. The present investigation provides insight into the structural features of laccase and its potential for the degradation of pesticides which can be further validated by experimental data.Communicated by Ramaswamy H. Sarma.

Biodegradation mechanisms of polycyclic aromatic hydrocarbons: Combination of instrumental analysis and theoretical calculation

Polycyclic aromatic hydrocarbons (PAHs) are a common class of petroleum hydrocarbons, widely encountered in both environment and industrial pollution sources. Owing to their toxicity, environmental persistence, and potential bioaccumulation properties, a mounting interest has been kindled in addressing the remediation of PAHs. Biodegradation is widely employed for the removal and remediation of PAHs due to its low cost, lack of second-contamination and ease of operation. This paper reviews the degradation efficiency of degradation and the underlying mechanisms exhibited by algae, bacteria, and fungi in remediation. Additionally, it delved into the application of modern instrumental analysis techniques and theoretical investigations in the realm of PAH degradation. Advanced instrumental analysis methods such as mass spectrometry provide a powerful tool for identifying intermediates and metabolites throughout the degradation process. Meanwhile, theoretical calculations could guide the optimization of degradation processes by revealing the reaction mechanisms and energy changes in PAH degradation. The combined use of instrumental analysis and theoretical calculations allows for a comprehensive understanding of the degradation mechanisms of PAHs and provides new insights and approaches for the development of environmental remediation technologies.

Investigation on toxicity mechanism of halogenated aromatic disinfection by-products to zebrafish based on molecular docking and QSAR model

Halogenated aromatic disinfection by-products (DBPs) are a new type of DBPs that have been detected in various water bodies. Previous studies have shown that most of them can induce in vivo toxicity in aquatic organisms. In this study, in order to further investigate the toxic effects and mechanisms of aromatic DBPs, the toxicity and ecological risks of 10 halogenated aromatic DBPs were assessed using the model organism zebrafish. It was found that the toxicity of DBPs was related to the number, type, and position of halogen and the type of substituent, and the 24 h-toxicity value of DBPs in this experiment could replace their 96 h-toxicity value to reduce the test time and save the test cost. Halogenated phenol and halogenated nitrophenol were more toxic, but the current ecological risks of DBPs were relatively low. In addition, the toxicity mechanism of DBPs was analyzed based on molecular docking and quantitative structure-activity relationship (QSAR) models. The molecular docking results showed that all 10 DBPs could bind to zebrafish's catalase (CAT), cytochrome P450 (CYP450), p53, and acetylcholinesterase (AChE), thereby affecting their normal life activities. QSAR models indicated that the toxicity of halogenated aromatic DBPs to zebrafish mainly depended on their hydrophobicity (log D), the interaction with CAT (ECAT), and hydrogen bonding acidity (A).

Anti-cervical cancer mechanism of bioactive compounds from Alangium platanifolium based on the 'compound-target-disease' network

In this study, we analyzed the chemical compositions of Alangium platanifolium (Sieb. et Zucc.) Harms (AP) using ultraperformance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) non-targeted plant metabolomics integration MolNetEnhancer strategy. A total of 75 compounds, including flavonoids, alkaloids, terpenes, C21 steroids, among others, were identified by comparing accurate mass-to-charge ratios, MS2 cleavage fragments, retention times, and MolNetenhancer-integrated analytical data, and the cleavage rules of the characteristic compounds were analyzed. A total of 125 potential cervical cancer (CC) therapeutic targets were obtained through Gene Expression Omnibus (GEO) data mining, differential analysis, and database screening. Hub targets were obtained by constructing protein-protein interaction (PPI) networks and CytoNCA topology analysis, including SRC, STAT3, TP53, PIK3R1, MAPK3, and PIK3CA. According to Gene ontology (GO) analysis, AP was primarily against CC by influencing gland development, oxidative stress processes, serine/threonine kinase, and tyrosine kinase activity. Enrichment analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated that the PI3K/AKT and MAPK signaling pathways play a crucial role in AP treatment for CC. The compound-target-pathway (C-T-P) network revealed that quercetin, methylprednisolone, and caudatin may play key roles in the treatment of CC. The results of molecular docking revealed that the core compound could bind significantly to the core target. In this study, the compounds in AP were systematically analyzed qualitatively, and the core components, core targets, and mechanisms of action of AP in the treatment of CC were screened through a combination of network pharmacology tools. Providing a scientific reference for the therapeutic material basis and quality control of AP.

Biodegradation of polyurethanes by Serratia liquefaciens L135 and its polyurethanase: In silico and in vitro analyses

Polyurethanes (PUs) are found in many everyday products and their disposal leads to environmental accumulation. Therefore, there is an urgent need to develop ecologically sustainable techniques to biodegrade and recycle this recalcitrant polymer and replace traditional methods that form harmful by-products. Serratia liquefaciens L135 secretes a polyurethanase with lipase activity, and this study explores the biodegradation of PUs by this bacterium and its enzyme through in silico and in vitro analyses. PUs monomers and tetramers were constructed in silico and tested with modeled and validated structure of the polyurethanase from S. liquefaciens. The molecular docking showed that all PUs monomers presented favorable interactions with polyurethanase (values of binding energy between -84.75 and -121.71 kcal mol-1), including PU poly[4,4'-methylenebis (phenyl isocyanate)-alt-1,4-butanediol/di (propylene glycol)/polycaprolactone] (PCLMDI). Due to repulsive steric interactions, tetramers showed less favorable interactions (values between 24.26 and -45.50 kcal mol-1). In vitro analyses evaluated the biodegradation of PUs: Impranil® and PCLMDI; this latter showed high binding energy with this polyurethanase in silico. The biodegradation of Impranil® by S. liquefaciens and its partially purified polyurethanase was confirmed in agar by forming a transparent halo. Impranil® disks inoculated with S. liquefaciens and incubated at 30 °C for six days showed rupture of the PU structure, possibly due to the formation of cracks visualized by scanning electron microscopy (SEM). PCLMDI films were also biodegraded by S. liquefaciens after 60 days of incubation, with the formation of pores and cracks visualized by SEM. The biodegradation may have occurred due to the action of polyurethanase produced by this bacterium. This work provides essential information on the potential of S. liquefaciens to biodegrade PUs through in silico analyses combined with in vitro analyses.

Computational design of a multi-epitope vaccine candidate against Langya henipavirus using surface proteins

In July 2022, Langya henipavirus (LayV) was identified in febrile patients in China. There is currently no approved vaccine against this virus. Therefore, this research aimed to design a multi-epitope vaccine against LayV using reverse vaccinology. The best epitopes were selected from LayV's fusion protein (F) and glycoprotein (G), and a multi-epitope vaccine was designed using these epitopes, adjuvant, and appropriate linkers. The physicochemical properties, antigenicity, allergenicity, toxicity, and solubility of the vaccine were evaluated. The vaccine's secondary and 3D structures were predicted, and molecular docking and molecular dynamics (MD) simulations were used to assess the vaccine's interaction and stability with toll-like receptor 4 (TLR4). Immune simulation, codon optimization, and in silico cloning of the vaccine were also performed. The vaccine candidate showed good physicochemical properties, as well as being antigenic, non-allergenic, and non-toxic, with acceptable solubility. Molecular docking and MD simulation revealed that the vaccine and TLR4 have stable interactions. Furthermore, immunological simulation of the vaccine indicated its ability to elicit immune responses against LayV. The vaccine's increased expression was also ensured using codon optimization. This study's findings were encouraging, but in vitro and in vivo tests are needed to confirm the vaccine's protective effect.Communicated by Ramaswamy H. Sarma.

Network pharmacology based anti-diabetic attributes of bioactive compounds from Ocimum gratissimum L. through computational approach

The present research was framed to determine the key compounds present in the plant Ocimum gratissimum L. targeting protein molecules of Diabetes Mellitus (DM) by employing In-silico approaches. Phytochemicals previously reported to be present in this herb were collated through literature survey and public phytochemical databases, and their probable targets were anticipated using BindingDB (p ≥ 0.7). STRING and KEGG pathway databases were employed for pathway enrichment analysis. Homology modelling was executed to elucidate the structures of therapeutic targets. Further, Phytocompounds from O. gratissimum were subjected for docking with four therapeutic targets of DM by using AutoDock vina through POAP pipeline implementation. 30 compounds were predicted to target 136 protein molecules including aldose reductase, DPP4, alpha-amylase, and alpha-glucosidase. Neuroactive ligand-receptor interaction, MAPK, PI3K-Akt, starch and insulin resistance were predicted to have potentially modulation by phytocompounds. Based on the phytocompound's binding score with the four targets of DM, Rutin scored the lowest binding energy (-11 kcal/mol) with Aldose reductase by forming 17 intermolecular interactions. In conclusion, based on the network and binding score, phytocompounds from O. gratissimum have a synergistic and considerable effect in the management of DM via multi-compound, multi-target, and multi-pathway mechanisms.

Affinity maturation of antibody fragments: A review encompassing the development from random approaches to computational rational optimization

Routinely screened antibody fragments usually require further in vitro maturation to achieve the desired biophysical properties. Blind in vitro strategies can produce improved ligands by introducing random mutations into the original sequences and selecting the resulting clones under more and more stringent conditions. Rational approaches exploit an alternative perspective that aims first at identifying the specific residues potentially involved in the control of biophysical mechanisms, such as affinity or stability, and then to evaluate what mutations could improve those characteristics. The understanding of the antigen-antibody interactions is instrumental to develop this process the reliability of which, consequently, strongly depends on the quality and completeness of the structural information. Recently, methods based on deep learning approaches critically improved the speed and accuracy of model building and are promising tools for accelerating the docking step. Here, we review the features of the available bioinformatic instruments and analyze the reports illustrating the result obtained with their application to optimize antibody fragments, and nanobodies in particular. Finally, the emerging trends and open questions are summarized.

Reaction mechanism and detecting properties of a novel molecularly imprinted electrochemical sensor for microcystin based on three-dimensional AuNPs@MWCNTs/GQDs

Microcystins with leucine arginine (MC-LR) is a virulent hepatotoxin, which is commonly present in polluted water with its demethylated derivatives [Dha7] MC-LR. This study reported a low-cost molecularly imprinted polymer network-based electrochemical sensor for detecting MC-LR. The sensor was based on a three-dimensional conductive network composed of multi-walled carbon nanotubes (MWCNTs), graphene quantum dots (GQDs), and gold nanoparticles (AuNPs). The molecularly imprinted polymer was engineered by quantum chemical computation utilizing p-aminothiophenol (p-ATP) and methacrylic acid (MAA) as dual functional monomers and L-arginine as a segment template. The electrochemical reaction mechanism of MC-LR on the sensor was studied for the first time, which is an irreversible electrochemical oxidation reaction involving an electron and two protons, and is controlled by a mixed adsorption-diffusion mechanism. The sensor exhibited a great detection response to MC-LR in the linear range of 0.08-2 μg/L, and the limit of detection (LOD) is 0.0027 μg/L (S/N = 3). In addition, the recoveries of the total amount of MC-LR and [Dha7] MC-LR in the actual sample by the obtained sensor were in the range from 91.4 to 116.7%, which indicated its great potential for environmental detection.

Probing antibacterial drugs for Fusobacterium nucleatum subsp. nucleatum ATCC 25586 targeting UDP-N-acetylglucosamine 1-carboxyltransferase

Fusobacterium nucleatum is a Gram-negative anaerobic bacteria that is commonly found in oral cavities and is associated with connective tissue destruction in periodontitis. UDP-N-acetylglucosamine 1-carboxyltransferase with enzyme commission number 2.5.1.7 is a transferases enzyme that plays a role in bacterial pathogenesis. Inhibiting binding sites of UDP-N-acetylglucosamine 1-carboxyltransferase is needed to find potential antibiotic candidates for periodontitis treatment. Hence, the research aimed to present potential UDP-N-acetylglucosamine 1-carboxyltransferase inhibiting compounds through molecular docking simulation by in silico analysis. DrugBank database was used to obtain the antibacterial candidates, which were further screened computationally using the AutoDock Vina program on Google Colab Pro. The top nine compounds yielded binding affinity ranging from -12.1 to -12.8 kcal/mol, with conivaptan as one of the three compounds having the highest binding affinity. Molecular dynamic study revealed that the ligand-protein complex for conivaptan had root-mean-square deviation values of 0.05-1.1 nm, indicating likeliness for stable interaction. Our findings suggest that conivaptan is the potent UDP-N-acetylglucosamine 1-carboxyltransferase inhibitor, hence its efficacy against periodontitis-causing bacteria.

Characterization of 17β-estradiol-degrading enzyme from Microbacterium sp. MZT7 and its function on E2 biodegradation in wastewater

BACKGROUND

17β-estradiol (E2) residues exhibit harmful effects both for human and animals and have got global attention of the scientific community. Microbial enzymes are considered as one of the effective strategies having great potential for removal E2 residues from the environment. However, limited literature is available on the removal of E2 from wastewater using short-chain dehydrogenase.

RESULTS

In this study, 17β-estradiol degrading enzyme (17β-HSD-0095) was expressed and purified from Microbacterium sp. MZT7. The optimal pH and temperature for reaction was 7 and 40 °C, respectively. Molecular docking studies have shown that the ARG215 residue form a hydrogen bond with oxygen atom of the substrate E2. Likewise, the point mutation results have revealed that the ARG215 residue play an important role in the E2 degradation by 17β-HSD-0095. In addition, 17β-HSD-0095 could remediate E2 contamination in synthetic livestock wastewater.

CONCLUSIONS

These findings offer some fresh perspectives on the molecular process of E2 degradation and the creation of enzyme preparations that can degrade E2.

Effect of co-pigments on anthocyanins of Rhododendron arboreum and insights into interaction mechanism

The impact of intermolecular copigmentation between five phenolic acids, two flavonoid and three amino acids with R. arboreum anthocyanins (ANS) and its isolated cyanidin-3-O-monoglycosides were investigated through experimental and theoretical approach. On addition of different copigments, phenolic acid induced strong hyperchromic (0.26-0.55 nm) and bathochromic shift (6.6-14.2 nm). The color intensity and stability of ANS with, storage at 4 °C & 25 °C, sunlight, oxidation and heat were evaluated by chromaticity, anthocyanin content, kinetic and structural simulation analysis. The strongest copigmentation reaction was observed with narningin (NA) and also showed high thermostability and highest half-life i.e. 3.39 h-1.24 h at 90-160 °C. The cyanidin-3-O-monoglycosides were analysed for their copigmentation effect and observations revealed that NA displayed best copigmentation effect to cyanidin-3-O-arabinoside (B) followed by cyanidin-3-O-galactoside (A), and cyanidin-3-O-rhamnoside (C). Additionally, structural simulation and steered molecular dynamics insights NA is the most favourable co-pigment involving π-π stacking and H-bonding.

Catalytic resilience of multicomponent aromatic ring-hydroxylating dioxygenases in Pseudomonas for degradation of polycyclic aromatic hydrocarbons

Hydrophobic organic compounds, either natural or introduced through anthropogenic activities, pose a serious threat to all spheres of life, including humankind. These hydrophobic compounds are recalcitrant and difficult to degrade by the microbial system; however, microbes have also evolved their metabolic and degradative potential. Pseudomonas species have been reported to have a multipotential role in the biodegradation of aromatic hydrocarbons through aromatic ring-hydroxylating dioxygenases (ARHDs). The structural complexity of different hydrophobic substrates and their chemically inert nature demands the explicit role of evolutionary conserved multicomponent enzyme ARHDs. These enzymes catalyze ring activation and subsequent oxidation by adding two molecular oxygen atoms onto the vicinal carbon of the aromatic nucleus. This critical metabolic step in the aerobic mode of degradation of polycyclic aromatic hydrocarbons (PAHs) catalyzed by ARHDs can also be explored through protein molecular docking studies. Protein data analysis enables an understanding of molecular processes and monitoring complex biodegradation reactions. This review summarizes the molecular characterization of five ARHDs from Pseudomonas species already reported for PAH degradation. Homology modeling for the amino acid sequences encoding the catalytic α-subunit of ARHDs and their docking analyses with PAHs suggested that the enzyme active sites show flexibility around the catalytic pocket for binding of low molecular weight (LMW) and high molecular weight (HMW) PAH substrates (naphthalene, phenanthrene, pyrene, benzo[α]pyrene). The alpha subunit harbours variable catalytic pockets and broader channels, allowing relaxed enzyme specificity toward PAHs. ARHD's ability to accommodate different LMW and HMW PAHs demonstrates its 'plasticity', meeting the catabolic demand of the PAH degraders.

Deciphering the recent trends in pesticide bioremediation using genome editing and multi-omics approaches: a review

Pesticide pollution in recent times has emerged as a grave environmental problem contaminating both aquatic and terrestrial ecosystems owing to their widespread use. Bioremediation using gene editing and system biology could be developed as an eco-friendly and proficient tool to remediate pesticide-contaminated sites due to its advantages and greater public acceptance over the physical and chemical methods. However, it is indispensable to understand the different aspects associated with microbial metabolism and their physiology for efficient pesticide remediation. Therefore, this review paper analyses the different gene editing tools and multi-omics methods in microbes to produce relevant evidence regarding genes, proteins and metabolites associated with pesticide remediation and the approaches to contend against pesticide-induced stress. We systematically discussed and analyzed the recent reports (2015-2022) on multi-omics methods for pesticide degradation to elucidate the mechanisms and the recent advances associated with the behaviour of microbes under diverse environmental conditions. This study envisages that CRISPR-Cas, ZFN and TALEN as gene editing tools utilizing Pseudomonas, Escherichia coli and Achromobacter sp. can be employed for remediation of chlorpyrifos, parathion-methyl, carbaryl, triphenyltin and triazophos by creating gRNA for expressing specific genes for the bioremediation. Similarly, systems biology accompanying multi-omics tactics revealed that microbial strains from Paenibacillus, Pseudomonas putida, Burkholderia cenocepacia, Rhodococcus sp. and Pencillium oxalicum are capable of degrading deltamethrin, p-nitrophenol, chlorimuron-ethyl and nicosulfuron. This review lends notable insights into the research gaps and provides potential solutions for pesticide remediation by using different microbe-assisted technologies. The inferences drawn from the current study will help researchers, ecologists, and decision-makers gain comprehensive knowledge of value and application of systems biology and gene editing in bioremediation assessments.

Exploration of binding mechanism of apigenin to pepsin: Spectroscopic analysis, molecular docking, enzyme activity and antioxidant assays

Pepsin plays an important role in nutrient metabolism. Apigenin (AP) is a beneficial polyphenol to human health. To enhance the bioavailability of AP and elucidate the inhibitory effect of AP on pepsin, the interaction mechanism of AP with pepsin was investigated using spectroscopic analysis and molecular docking, and the activity of pepsin and antioxidant activity of AP was also evaluated. Specifically, AP performed static quenching of pepsin and had only one binding site on pepsin. More interestingly, the interaction between AP and pepsin was spontaneous, while hydrogen bonds and van der Waals forces were the main binding forces. Generally, synchronous and three-dimensional fluorescence confirmed that AP induced the conformational changes of pepsin, and molecular docking proved the above results and illustrated the specific binding patterns. Specifically, AP inhibited the activity of pepsin, while pepsin decreased the antioxidant activity of AP. These results provided useful information for elucidating the interactions between AP and pepsin.

Understanding the biodegradation pathways of azo dyes by immobilized white-rot fungus, Trametes hirsuta D7, using UPLC-PDA-FTICR MS supported by in silico simulations and toxicity assessment

No biodegradation methods are absolute in the treatment of all textile dyes, which leads to structure-dependent degradation. In this study, biodegradation of three azo dyes, reactive black 5 (RB5), acid blue 113 (AB113), and acid orange 7 (AO7), was investigated using an immobilized fungus, Trametes hirsuta D7. The degraded metabolites were identified using UPLC-PDA-FTICR MS and the biodegradation pathway followed was proposed. RB5 (92%) and AB113 (97%) were effectively degraded, whereas only 30% of AO7 was degraded. Molecular docking simulations were performed to determine the reason behind the poor degradation of AO7. Weak binding affinity, deficiency in H-bonding interactions, and the absence of interactions between the azo (-NN-) group and active residues of the model laccase enzyme were responsible for the low degradation efficiency of AO7. Furthermore, cytotoxicity and genotoxicity assays confirmed that the fungus-treated dye produced non-toxic metabolites. The observations of this study will be useful for understanding and further improving enzymatic dye biodegradation.

Hibiscus sabdariffa L. polyphenolic-rich extract promotes muscle glucose uptake and inhibits intestinal glucose absorption with concomitant amelioration of Fe2+ -induced hepatic oxidative injury

In this current study, the antidiabetic effectiveness of Hibiscus sabdariffa and its protective function against Fe²⁺ -induced oxidative hepatic injury were elucidated using in vitro, in silico, and ex vivo studies. The oxidative damage was induced in hepatic tissue by incubation with 0.1 mMolar ferrous sulfate (FeSO4) and then treated with different concentrations of crude extracts (ethyl acetate, ethanol, and aqueous) of H. sabdariffa flowers for 30 min at 37°C. When compared to ethyl acetate and aqueous extracts, the ethanolic extract displayed the most potent scavenging activity in ferric-reducing antioxidant power (FRAP), 1,1-diphenyl-2-picrylhydrazyl (DPPH), and nitric oxide (NO) assays, with IC₅₀ values of 2.8 μl/ml, 3.3 μl/ml, and 9.2 μl/ml, respectively. The extracts significantly suppressed α-glucosidase and α-amylase activities (p < .05), with the ethanolic extract demonstrating the highest activity. H. sabdariffa significantly (p < .05) raised reduced glutathione (GSH) levels while simultaneously decreasing malondihaldehyde (MDA) and NO levels and increasing superoxide dismutase (SOD) and catalase activity in Fe²⁺ induced oxidative hepatic injury. The extract of the plant inhibited intestinal glucose absorption and increased muscular glucose uptake. The extract revealed the presence of several phenolic compounds when submitted to gas chromatography-mass Spectroscopy (GC-MS) screening, which was docked with α-glucosidase and α- amylase. The molecular docking displayed the compound 4-(3,5-Di-tert-butyl-4-hydroxyphenyl)butyl acrylate strongly interacted with α-glucosidase and α-amylase and had the lowest free binding energy compared to other compounds and acarbose. These results suggest that H. sabdariffa has promising antioxidant and antidiabetic activity. PRACTICAL APPLICATIONS: In recent years, there has been increased concern about the side effects of synthetic anti-diabetic drugs, as well as their expensive cost, especially in impoverished nations. This has instigated a radical shift towards the use of traditional plants, which are rich in phytochemicals many years ago. Among these plants, H. sabdariffa has been used to treat diabetes in traditional medicine. In this present study, H. sabdariffa extracts demonstrated the ability to inhibit carbohydrate digesting enzymes, facilitate muscle glucose uptake and attenuate oxidative stress in oxidative hepatic injury. Hence, demonstrating H. sabdariffa's potential to protect against oxidative damage and the complications associated with diabetes. Consumption of Hibiscus tea or juice may be a potential source for developing an anti-diabetic drug.

Molecular dynamics simulation study of covalently bound hybrid coagulants (CBHyC): Molecular structure and coagulation mechanisms

Covalently-bound organic silicate-aluminum hybrid coagulants (CBHyC) have been shown to efficiently remove low molecular weight organic contaminants from wastewater. However, the interaction dynamics and motivations during the coagulation of contaminant molecules by CBHyC are limited. In this study, a molecular dynamics (MD) simulation showed that CBHyC forms core-shell structure with the aliphatic carbon chains gather inside as a core and the hydrophilic quaternary ammonium-Si-Al complexes disperse outside as a shell. This wrapped structure allowed the coagulant to diffuse into solutions easily and capture target contaminants. The adsorption of anionic organic contaminants (e.g., diclofenac) onto the CBHyC aggregates was driven equally by van der Waals forces and electrostatic interactions. Cationic organic contaminants (e.g., tetracycline) were seldom bound to CBHyC because of substantial repulsive forces between cationic molecules and CBHyC. Neutrally-charged organic molecules were generally bound through hydrophobic interactions. For adenine and thymine deoxynucleotide, representatives of antibiotic resistance genes, van der Waals forces and electrostatic interaction became the dominant driving force with further movement for adenine and thymine, respectively. Driving forces between target contaminant and coagulant directly affect the size and stability of formed aggregate, following the coagulation efficiency of wastewater treatment. The findings of this study enrich the database of aggregation behavior between low molecular weight contaminants and CBHyC and contribute to further and efficient application of CBHyC in wastewater treatment.

A Theoretical and Experimental Study for Enzymatic Biodiesel Production from Babassu Oil (Orbignya sp.) Using Eversa Lipase

A theoretical and experimental study was carried out on the biocatalytic production of babassu biodiesel through enzymatic hydroesterification. The complete hydrolysis of babassu oil was carried out using a 1:1 mass solution at 40 °C for 4 h using 0.4% of lipase from Thermomyces lanuginosus (TLL). Then, with the use of Eversa® Transform 2.0 lipase in the esterification step, a statistical design was used, varying the temperature (25–55 °C), the molar ratio between free fatty acids (FFAs) and methanol (1:1 to 1:9), the percentage of biocatalyst (0.1% to 0.9%), and the reaction time (1–5 h) using the Taguchi method. The ideal reaction levels obtained after the statistical treatment were 5 h of reaction at 40 °C at a molar ratio of 1:5 (FFAs/methanol) using 0.9% of the biocatalyst. These optimal conditions were validated by chromatographic analysis; following the EN 14103 standard, the sample showed an ester concentration of 95.76%. A theoretical study was carried out to evaluate the stability of Eversa with FFAs. It was observed in the molecular docking results that the ligands interacted directly with the catalytic site. Through molecular dynamics studies, it was verified that there were no significant conformational changes in the studied complexes. Theoretical and experimental results show the feasibility of this process.

Identification of antiviral peptide inhibitors for receptor binding domain of SARS-CoV-2 omicron and its sub-variants: an in-silico approach

Omicron, a variant of concern (VOC) of SARS-CoV-2, emerged in South Africa in November 2021. Omicron has been continuously acquiring a series of new mutations, especially in the spike (S) protein that led to high infectivity and transmissibility. Peptides targeting the receptor-binding domain (RBD) of the spike protein by which omicron and its variants attach to the host receptor, angiotensin-converting enzyme (ACE2) can block the viral infection at the first step. This study aims to identify antiviral peptides from the Antiviral peptide database (AVPdb) and HIV-inhibitory peptide database (HIPdb) against the RBD of omicron by using a molecular docking approach. The lead RBD binder peptides obtained through molecular docking were screened for allergenicity and physicochemical criteria (isoelectric point (pI) and net charge) required for peptide-based drugs. The binding affinity of the best five peptide inhibitors with the RBD of omicron was validated further by molecular dynamics (MD) simulation. Our result introduces five antiviral peptides, including AVP1056, AVP1059, AVP1225, AVP1801, and HIP755, that may effectively hinder omicron-host interactions. It is worth mentioning that all the three major sub-variants of omicron, BA.1 (B.1.1.529.1), BA.2 (B.1.1.529.2), and BA.3 (B.1.1.529.3), exhibits conserved ACE-2 interacting residues. Hence, the screened antiviral peptides with similar affinity can also interrupt the RBD-mediated invasion of different major sub-variants of omicron. Altogether, these peptides can be considered in the peptide-based therapeutics development for omicron treatment after further experimentation.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03258-4.

Dibutyl phthalate-induced oxidative stress and apoptosis in swine testis cells and therapy of naringenin via PTEN/PI3K/AKT signaling pathway

Dibutyl phthalate (DBP) is a phthalic acid ester (PAE) that has posed a health hazard to the organisms. Naringenin (NRG) is a flavanone compound that has shown protection against several environmental chemicals through suppression of oxidative stress and activation of phosphatidylinositol 3-kinase/threonine kinase (PI3K/AKT) signaling pathway. Herein, swine testis (ST) cells were treated with 1.8 μM of DBP or/and 25.39 nM of NRG for 24 h, we described the discovery path of NRG inhibition on apoptosis in DBP-exposed ST cells through targeting phosphatase and tensin homologue deleted on chromosome 10 (PTEN). We first found that the anti-apoptosis effect of NRG is dependent on mitochondrial pathway through flow cytometry and related gene/protein expression, and then we detected PI3K/AKT pathway-related gene/protein expression, and established a computational docking assay between NRG and PTEN. We found that NRG specifically binds to three basic residues (His93, Lys125, Lys128) of P loop in PTEN, as well as phosphatase domains (Asp92, His93, Cys124, Lys125, Ala126, Lys128, and Arg130) in active dephosphorylation pockets, thereby reducing PTEN level and activating PI3K/AKT signaling pathway, and further inhibiting oxidative stress and mitochondrial pathway apoptosis. Taken together, our results push forward that NRG deserves further attention as a potential antagonistic therapy against DBP through targeting PTEN to inhibit oxidative stress and activate PI3K/AKT signaling pathway.

Identification of Effective and Nonpromiscuous Antidiabetic Drug Molecules from Penicillium Species

Diabetes mellitus (DM) is a very common metabolic disorder/disease. The deterioration of β-cells by autoimmune system is the hallmark of this disease. Thioredoxin-Interacting Protein (TXNIP) is responsible for β-cells degradation by T-cells in the pancreas. This protein had been declared a good drug target for controlling DM. Lots of side effects have been reported as a result of long-time consumption of conventional antidiabetic drugs. The development of new and effective drugs with the minimal side effects needs time. TXNIP was selected as a target for Computer-Aided Drug Design. The antidiabetic fungal metabolite compounds were selected from the literature. The compounds were screened for their drug-likeness properties by DruLiTo and DataWarior tools. Twenty-two drug-like fungal compounds were subjected to Quantitative Structure-Activity Relationship (QSAR) analysis by using CheS-Mapper 2.0. The lowest (0.01) activity cliff was found for three compounds: Pinazaphilone A, Pinazaphilone B, and Chermesinone A. The highest value for apol (81.76) was shown by Asperphenamate, while Albonoursin and Sterenin L showed highest score (40.66) for bpol. The lowest value (0.46) for fractional molecular frame (FMF) was calculated for Pinazaphilone A and Pinazaphilone B. TPSA for Pinazaphilone A and Pinazaphilone B was 130.51 Å2. $\log P<5$ was observed for all the twenty-two compounds. Molecular docking of fungal compounds with TXNIP was done by AutoDock Vina. The binding energy for complexes ranged between −9.2 and −4.6 kcal/mol. Four complexes, TXNIP-Pinazaphilone A, TXNIP-Pinazaphilone B, TXNIP-Asperphenamate, and TXNIP-Sterenin L, were selected for MD simulation to find out the best lead molecule. Only one complex, TXNIP-Pinazaphilone B, showed a stable conformation throughout the 80 ns run of MD simulation. Pinazaphilone B derived from the Penicillium species fungi was selected as the lead molecule for development of antidiabetic drug having the least side effects.

Bioinformatics analysis of amino acid decarboxylases related to four major biogenic amines in pickles

Microbial amino acid decarboxylases (AADs) produce biogenic amines (BAs) in fermented food. However, a systematic comparison of the AADs' properties from different microorganisms in pickle fermentation remains unexplored. Here, we bioinformatically analyzed the amino acid sequences of AADs corresponding to four major BAs for common microorganisms in pickle fermentation. We showed that their sequences, besides tyrosine decarboxylase, differed among microorganisms. Overall, the AAD sequences varied lesser among bacterial species than between bacteria and fungi, with those in Lactobacillus sharing occasionally high similarity with other bacteria. Most AADs were predicted as stable cytosolic endoenzymes. Molecular docking showed that most commonly used spice components in pickle production, especially pepper, chili, and ginger, strongly bind to the AAD active sites, thus may inhibit the enzymes and reduce the BA accumulation. This study provides insights for deeply understanding the different microbial AAD properties in pickle fermentation and reducing BAs by appropriately using spices.

Tyrosinase-functionalized polyhydroxyalkanoate bio-beads as a novel biocatalyst for degradation of bisphenol analogues

Bisphenol compounds are emerging contaminants of high concerns with known endocrine-disrupting effects. Biocatalysis provides a green chemistry alternative for advanced treatment in water reclamation. This study createda novel biocatalyst through genetically immobilizing the Bacillus megaterium tyrosinase enzyme (BmTyr) on the surface ofself-assembled polyhydroxyalkanoate (PHA) biopolymer beads (termed PHA-BmTyr) by using synthetic biology techniques and demonstrated one-pot in vivo production of the biocatalyst for effective degradation and detoxification of various bisphenol analogues for the first time. The degradation pathway of bisphenols was determined to be mediated by the monophenolase and diphenolase activity of BmTyr. Notably, biocatalytic bisphenol degradation by PHA-BmTyr could substantially reduce or eliminate estrogenic activity of the contaminants, and the degradation products had remarkably lower acute and chronic toxicity than their parent compounds. Furthermore, the PHA-BmTyr biocatalyst had high reusability for multiple bisphenol degradation reaction cycles and showed excellent stability that retained 100% and 86.6% of the initial activity when stored at 4 °C and room temperature, respectively for 30 days. Also, the PHA-BmTyr biocatalyst could efficiently degrade bisphenol analogues in real wastewater effluent matrix. This study provides a promising approach to develop innovative biocatalysis technologies for sustainable water reclamation.

Chemoprotection mediated by açaí berry (Euterpe oleracea) in white shrimp Litopenaeus vannamei exposed to the cyanotoxin saxitoxin analyzed by in vivo assays and docking modeling

Saxitoxin (STX) is a neurotoxic cyanotoxin that also generate reactive oxygen species, leading to a situation of oxidative stress and altered metabolism. The Amazonian fruit açaí Euterpe oleracea possesses a high concentration of antioxidant molecules, a fact that prompted us to evaluate its chemoprotection activity against STX toxicity (obtained from samples of Trichodesmium sp. collected in the environment) in the shrimp Litopenaeus vannamei. For 30 days, shrimps were maintained in 16 aquaria containing 10 shrimps (15% salinity, pH 8.0, 24 °C, 12C/12D photoperiod) and fed twice daily with a diet supplemented with lyophilized açaí pulp (10%), in addition to the control diet. After, shrimps (7.21 ± 0.04 g) were exposed to the toxin added to the feed for 96 h. Four treatments were defined: CTR (control diet), T (lyophilized powder of Trichodesmium sp. 0.8 μg/g), A (10% of açaí) and the combination T + A. HPLC analysis showed predominance of gonyautoxin-1 concentrations (GTX-1) and gonyautoxin-4 concentrations (GTX-4). The results of molecular docking simulations indicated that all variants of STX, including GTX-1, can be a substrate of isoform mu of the glutathione-S-transferase (GST) enzyme since these molecules obtained similar values of estimated Free Energy of Binding (FEB), as well as similar final positions on the binding site. GSH levels were reduced in muscle tissues of shrimp in the T, A, and T + A treatments. Increased GST activity was observed in shrimp hepatopancreas of the T treatment and the gills of the A and T + A treatments. A decrease of protein sulfhydryl groups (P-SH) was observed in gills of shrimps from T + A treatment. A reduction in malondialdehyde (MDA) levels was registered in the hepatopancreas of the T + A treatment in respect to the Control, T, and A treatments. The use of açaí supplements in L. vannamei feed was able to partially mitigate the toxic effects caused by Trichodesmium sp. extracts, and points to mu GST isoform as a key enzyme for saxitoxin detoxification in L. vannamei, an issue that deserves further investigation.

Synthesis, molecular docking and extensive structure activity relationship of substituted DHP derivatives: a new class of herbicides

In the present study, twenty-two derivatives of dihydropyridine (DHP) have been synthesized using the Boric acid catalyst in solventless conditions. The synthesis was confirmed by FTIR analysis, 1HNMR, and 13CNMR analysis. The quantitative structure-activity relationship for all the synthesized derivatives was performed using an artificial neural network with correlation coefficient (R²) 0.8611, mean standard error 0.19, and Comparative molecular field analysis (CoMFA) with correlation coefficient (R²) 0.713, mean standard error 0.27. The molecular docking activity of synthesized compounds was tested using "AUTODOCK VINA" against "Acetohydroxyacid synthase protein receptors (PDB code 1YHZ)" acquired from the "RCSB Protein Data Bank". Docking experiments demonstrated favorable interaction among synthesized DHP derivatives and protein receptors with significant binding energy values. These synthesized derivatives have been screened for their pre-emergence herbicidal bioassay against weed species Echinochola crus galli, and the IC50 value were calculated and activity was compared with Butachlor, significant activity was exhibited by all the derivatives. All the synthesized compounds were also screened for their post emergence herbicidal activity against Echinochola crus galli, and the activity of DHPs were compared with penoxulum. All the synthesized compounds show good to moderate activity. Thus, it is concluded that substituted DHP derivatives may be developed as potential herbicides.

In silico analytical toolset for predictive degradation and toxicity of hazardous pollutants in water sources

Different phenolic compounds, including multimeric lignin derivatives in the β-O-4 form, are among the most prevalent compounds in wastewater, often generated from paper industries. Relatively small concentrations of lignin are hazardous to aquatic organisms and can trigger severe environmental hazards. Herein, we present a predictive toolset to insight the induced toxic hazards prediction, and their Lignin peroxidase (LiP)-assisted degradation mechanism of selected multimeric lignin model compounds. T.E.ST and Toxtree toolset were deployed for toxic hazards estimation in different endpoints. To minimize the concerning hazards, we screened multimeric compounds for binding affinity with LiP. The binding affinity was found to be significantly lower than the reference compound. An Extra precision (XP) Glide score of -6.796 kcal/mol was found for dimer (guaiacyl 4-O-5 guaiacyl) complex as lowest compared to reference compound (-4.007 kcal/mol). The active site residues ASP-153, HIP-226, VAL-227, ARG-244, GLU-215, 239, PHE-261 were identified as site-specific key binding AA residues actively involved with corresponding ligands, forming Hydrophobic, H-Bond, π-Stacking, π-π type interactions. The DESMOND-assisted molecular dynamics simulation's (MDS) trajectories of protein-ligand revealed the considerable binding behavior and attained stability and system equilibrium state. Such theoretical and predictive conclusions indicted the feasibility of LiP assisted sustainable mitigation of lignin-based compounds, and such could be used to protect the environment from the potential hazards posed by recognized similar pollutants.

Carbon Nanomaterials (CNMs) and Enzymes: From Nanozymes to CNM-Enzyme Conjugates and Biodegradation

Carbon nanomaterials (CNMs) and enzymes differ significantly in terms of their physico-chemical properties—their handling and characterization require very different specialized skills. Therefore, their combination is not trivial. Numerous studies exist at the interface between these two components—especially in the area of sensing—but also involving biofuel cells, biocatalysis, and even biomedical applications including innovative therapeutic approaches and theranostics. Finally, enzymes that are capable of biodegrading CNMs have been identified, and they may play an important role in controlling the environmental fate of these structures after their use. CNMs’ widespread use has created more and more opportunities for their entry into the environment, and thus it becomes increasingly important to understand how to biodegrade them. In this concise review, we will cover the progress made in the last five years on this exciting topic, focusing on the applications, and concluding with future perspectives on research combining carbon nanomaterials and enzymes.

Molecular Docking and Dynamics Studies to Explore Effective Inhibitory Peptides Against the Spike Receptor Binding Domain of SARS-CoV-2

The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a pandemic due to the high transmission and mortality rate of this virus. The world health and economic sectors have been severely affected by this deadly virus, exacerbated by the lack of sufficient efficient vaccines. The design of effective drug candidates and their rapid development is necessary to combat this virus. In this study, we selected 23 antimicrobial peptides from the literature and predicted their structure using PEP-FOLD 3.5. In addition, we docked them to the SARS-CoV-2 spike protein receptor-binding domain (RBD) to study their capability to inhibit the RBD, which plays a significant role in virus binding, fusion and entry into the host cell. We used several docking programs including HDOCK, HPEPDOCK, ClusPro, and HawkDock to calculate the binding energy of the protein-peptide complexes. We identified four peptides with high binding free energy and docking scores. The docking results were further verified by molecular dynamics (MD) simulations to characterize the protein-peptide complexes in terms of their root-mean-square fluctuation (RMSF), root-mean-square deviation (RMSD), radius of gyration (Rg), solvent-accessible surface area (SASA), and hydrogen bond formation. Allergenicity and toxicity predictions suggested that the peptides we identified were non-allergenic and non-toxic. This study suggests that these four antimicrobial peptides could inhibit the RBD of SARS-CoV-2. Future in vitro and in vivo studies are necessary to confirm this.

Naringenin protects swine testis cells from bisphenol A-induced apoptosis via Keap1/Nrf2 signaling pathway

Bisphenol A (BPA) has caused serious pathologies in varying organs of humans and animals, especially reproductive organs. Naringenin (NRG) is a flavanone compound that has shown protective effects against several environmental chemicals through suppression of oxidative stress and activation of nuclear factor erythroid 2-related factor 2 (Nrf2) pathway. Herein, we described the discovery path of NRG inhibition on apoptosis in BPA exposed swine testis (ST) cells through targeting Kelch-like ech-associated protein (Keap1). We found that NRG could specifically bound to the active residues of DGR domain in Keap1, thereby activating Nrf2 signaling pathway, and then increasing the levels of SOD, GPx and CAT, and finally inhibiting oxidative stress and mitochondrial apoptosis induced by BPA in ST cells. Altogether, our results showed that NRG inhibits oxidative stress and mitochondrial apoptosis induced by BPA in ST cells by targeting Keap1/Nrf2 signaling pathway, indicating that NRG could serve as an antagonistic therapy against BPA.

Binding interaction of a ring-hydroxylating dioxygenase with fluoranthene in Pseudomonas aeruginosa DN1

Pseudomonas aeruginosa DN1 can efficiently utilize fluoranthene as its sole carbon source, and the initial reaction in the biodegradation process is catalyzed by a ring-hydroxylating dioxygenase (RHD). To clarify the binding interaction of RHD with fluoranthene in the strain DN1, the genes encoding alpha subunit (RS30940) and beta subunit (RS05115) of RHD were functionally characterized through multi-technique combination such as gene knockout and homology modeling as well as molecular docking analysis. The results showed that the mutants lacking the characteristic alpha subunit and/or beta subunit failed to degrade fluoranthene effectively. Based on the translated protein sequence and Ramachandran plot, 96.5% of the primary amino-acid sequences of the alpha subunit in the modeled structure of the RHD were in the permitted region, 2.3% in the allowed region, but 1.2% in the disallowed area. The catalytic mechanism mediated by key residues was proposed by the simulations of molecular docking, wherein the active site of alpha subunit constituted a triangle structure of the mononuclear iron atom and the two oxygen atoms coupled with the predicted catalytic ternary of His₂₁₇-His₂₂₂-Asp₃₇₂ for the dihydroxylation reaction with fluoranthene. Those amino acid residues adjacent to fluoranthene were nonpolar groups, and the C₇-C₈ positions on the fluoranthene ring were estimated to be the best oxidation sites. The distance of C₇-O and C₈-O was 3.77 Å and 3.04 Å respectively, and both of them were parallel. The results of synchronous fluorescence and site-directed mutagenesis confirmed the roles of the predicted residues during catalysis. This binding interaction could enhance our understanding of the catalytic mechanism of RHDs and provide a solid foundation for further enzymatic modification.

Antiviral peptides against the main protease of SARS-CoV-2: A molecular docking and dynamics study

The recent coronavirus outbreak has changed the world's economy and health sectors due to the high mortality and transmission rates. Because the development of new effective vaccines or treatments against the virus can take time, an urgent need exists for the rapid development and design of new drug candidates to combat this pathogen. Here, we obtained antiviral peptides obtained from the data repository of antimicrobial peptides (DRAMP) and screened their predicted tertiary structures for the ability to inhibit the main protease of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using multiple combinatorial docking programs, including PatchDock, FireDock, and ClusPro. The four best peptides, DRAMP00877, DRAMP02333, DRAMP02669, and DRAMP03804, had binding energies of -1125.3, -1084.5, -1005.2, and -924.2 Kcal/mol, respectively, as determined using ClusPro, and binding energies of -55.37, -50.96, -49.25, -54.81 Kcal/mol, respectively, as determined using FireDock, which were better binding energy values than observed for other peptide molecules. These peptides were found to bind with the active cavity of the SARS-CoV-2 main protease; at Glu166, Cys145, Asn142, Phe140, and Met165, in addition to the substrate-binding sites, Domain 2 and Domain 3, whereas fewer interactions were observed with Domain 1. The docking studies were further confirmed by a molecular dynamics simulation study, in which several descriptors, including the root-mean-square difference (RMSD), root-mean-square fluctuation (RMSF), solvent-accessible surface area (SASA), radius of gyration (Rg), and hydrogen bond formation, confirmed the stable nature of the peptide-main protease complexes. Toxicity and allergenicity studies confirmed the non-allergenic nature of the peptides. This present study suggests that these identified antiviral peptide molecules might inhibit the main protease of SARS-CoV-2, although further wet-lab experiments remain necessary to verify these findings.

Bioremediation of lignin derivatives and phenolics in wastewater with lignin modifying enzymes: Status, opportunities and challenges

Lignin modifying enzymes from fungi and bacteria are potential biocatalysts for sustainable mitigation of different potentially toxic pollutants in wastewater. Notably, the paper and pulp industry generates enormous amounts of wastewater containing high amounts of complex lignin-derived chlorinated phenolics and sulfonated pollutants. The presence of these compounds in wastewater is a critical issue from environmental and toxicological perspectives. Some chloro-phenols are harmful to the environment and human health, as they exert carcinogenic, mutagenic, cytotoxic, and endocrine-disrupting effects. In order to address these most urgent concerns, the use of oxidative lignin modifying enzymes for bioremediation has come into focus. These enzymes catalyze modification of phenolic and non-phenolic lignin-derived substances, and include laccase and a range of peroxidases, specifically lignin peroxidase (LiP), manganese peroxidase (MnP), versatile peroxidase (VP), and dye-decolorizing peroxidase (DyP). In this review, we explore the key pollutant-generating steps in paper and pulp processing, summarize the most recently reported toxicological effects of industrial lignin-derived phenolic compounds, especially chlorinated phenolic pollutants, and outline bioremediation approaches for pollutant mitigation in wastewater from this industry, emphasizing the oxidative catalytic potential of oxidative lignin modifying enzymes in this regard. We highlight other emerging biotechnical approaches, including phytobioremediation, bioaugmentation, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based technology, protein engineering, and degradation pathways prediction, that are currently gathering momentum for the mitigation of wastewater pollutants. Finally, we address current research needs and options for maximizing sustainable biobased and biocatalytic degradation of toxic industrial wastewater pollutants.