Improved microalgae carbon fixation and microplastic sedimentation in the lake through in silico method

The impact of microplastics in lake water environments on microalgae carbon fixation and microplastic sedimentation has attracted global attention. The molecular dynamic simulation method was used to design microplastic additive proportioning schemes for improving microalgae carbon fixation and microplastic sedimentation. Results showed that the harm of microplastics can be effectively alleviated by adjusting the proportioning scheme of plastic additives. Besides, the decabromodiphenyl oxide (DBDPO) was identified as the main additive that affect the microalgae carbon fixation and microplastic sedimentation. Thus, a molecular modification based on CiteSpace visual analysis was firstly used and 12 DBDPO derivatives were designed. After the screening, DBDPO-2 and DBDPO-5 became the environmentally friendly DBDPO alternatives, with the highest microalgae carbon fixation and microplastic sedimentation ability enhancement of over 25 %. Compared to DBDPO, DBDPO derivatives were found easier to stimulate the adsorption and binding ability of surrounding hotspot amino acids to CO2 and ribulose-5-phosphate, increasing the solvent-accessible surface area of microplastics, thus improving the microalgae carbon fixation and microplastic sedimentation ability. This study provides theoretical support for simultaneously promoting the microalgae carbon fixation and microplastic sedimentation in the lake water environment and provides scientific basis for the protection and sustainable development of lake water ecosystem.

Construction of An Oral Bioavailability Prediction Model Based on Machine Learning for Evaluating Molecular Modifications

OBJECTIVE

This study aims to explore the impact of ADME on the Oral Bioavailability (OB) of drugs and to construct a machine learning model for OB prediction. The model is then applied to predict the OB of modified berberine and atenolol molecules to obtain structures with higher OB.

METHODS

Initially, a drug OB database was established, and corresponding ADME characteristics were obtained. The relationship between ADME and OB was analyzed using machine learning, with Morgan fingerprints serving as molecular descriptors. Compounds from the database were input into Random Forest, XGBoost, CatBoost, and LightGBM machine learning models to train the OB 7prediction model and evaluate its performance. Subsequently, berberine and atenolol were modified using Chemdraw software with ten different substituents for mono-substitution, and chlorine atoms for a full range of double substitutions. The modified molecular structures were converted into the same format as the training set for OB prediction. The predicted OB values of the modified structures of berberine and atenolol were compared.

RESULTS

An OB database of 386 drugs was obtained. It was found that smaller molecular weight and a higher number of rotatable bonds (ten or less) could potentially lead to higher OB. The four machine learning models were evaluated using MSE, R2 score, MAE, and MFE as metrics, with Random Forest performing the best. The models' predictions for the test set were particularly accurate when OB ranged from 30% to 90%. After mono-substitution and double substitution of berberine and atenolol, the OB of both drugs was significantly improved.

CONCLUSIONS

This study found that some ADME properties of molecules do not have an absolute impact on OB. The database played a decisive role in the process of the machine learning OB prediction model, and the performance of the model was evaluated based on predictions within a range of strong generalization ability. In most cases, mono-substitution and double substitution were beneficial for enhancing the OB of berberine and atenolol. In summary, this study successfully constructed a machine learning regression prediction model that can accurately predict drug OB, which can guide drug design to achieve higher OB to some extent.

Research and application progress of microbial β-mannanases: a mini-review

Mannan is a predominant constituent of cork hemicellulose and is widely distributed in various plant tissues. β-Mannanase is the principal mannan-degrading enzyme, which breaks down the β-1,4-linked mannosidic bonds in mannans in an endo-acting manner. Microorganisms are a valuable source of β-mannanase, which exhibits catalytic activity in a wide range of pH and temperature, making it highly versatile and applicable in pharmaceuticals, feed, paper pulping, biorefinery, and other industries. Here, the origin, classification, enzymatic properties, molecular modification, immobilization, and practical applications of microbial β-mannanases are reviewed, the future research directions for microbial β-mannanases are also outlined.

Recent advances of silk fibroin materials: From molecular modification and matrix enhancement to possible encapsulation-related functional food applications

Silk fibroin materials are emergingly explored for food applications due to their inherent properties including safe oral consumption, biocompatibility, gelatinization, antioxidant performance, and mechanical properties. However, silk fibroin possesses drawbacks like brittleness owing to its inherent specific composition and structure, which limit their applications in this field. This review discusses current progress about molecular modification methods on silk fibroin such as extraction, blending, self-assembly, enzymatic catalysis, etc., to address these limitations and improve their physical/chemical properties. It also summarizes matrix enhancement strategies including freeze drying, spray drying, electrospinning/electrospraying, microfluidic spinning/wheel spinning, desolvation and supercritical fluid, to generate nano-, submicron-, micron-, or bulk-scale materials. It finally highlights the food applications of silk fibroin materials, including nutraceutical improvement, emulsions, enzyme immobilization and 3D/4D printing. This review also provides insights on potential opportunities (like safe modification, toxicity risk evaluation, and digestion conditions) and possibilities (like digital additive manufacturing) in functional food industry.

MgO-modified biochar by modifying hydroxyl and amino groups for selective phosphate removal: Insight into phosphate selectivity adsorption mechanism through experimental and theoretical

Metal oxides-modified biochars have been widely studied as promising adsorbents for removing phosphate from wastewater discharge. Yet, the low adsorption selectivity towards phosphate severely limits its potential in practical applications. In this study, MgO-modified biochar modified by hydroxyl and amino groups (OH/NH2@MBC) is developed for selective phosphorus recovery from wastewater. As major results, the OH/NH2@MBC exhibits favorable phosphate adsorption performance is superior to that of MBC resin in the presence of co-existing anions (NO3-, Cl-, HCO3- and SO42-) and natural organic matter (humic acid) even actual wastewater, suggesting its superior selectivity towards phosphate. The OH/NH2@MBC shows an excellent phosphate adsorption capacity (43.27 mg/g) and desorption ratio (82.34 %) after five cycles under the condition of anion coexistence (100 mg/L). The experimental and DFT theoretical study reveals that attaching hydroxyl and amino groups onto the MBC surface, which facilitates to inhibiting the side effects of anions (NO3-, Cl-, HCO3-, and SO42-) through Lewis acid-base sites, hydrogen bonds, and metal affinity, and preferentially select adsorption P, contributing greatly to improve phosphate adsorption selectivity. Importantly, the presence of amino and hydroxyl groups can reduce the Fermi level of OH/NH2@MgO(220) and OH/NH2@MgO(200) and improve the adsorption selection for HPO42-. This study provides an effective strategy for enhancing the adsorption selectivity of metal oxides-modified biochars towards phosphate through modifying functional groups.

Thermophilic β-mannanases from bacteria: production, resources, structural features and bioengineering strategies

β-mannanases are pivotal enzymes that cleave the mannan backbone to release short chain mannooligosaccharides, which have tremendous biotechnological applications including food/feed, prebiotics and biofuel production. Due to the high temperature conditions in many industrial applications, thermophilic mannanases seem to have great potential to overcome the thermal impediments. Thus, structural analysis of thermostable β-mannanases is extremely important, as it could open up new avenues for genetic engineering, and protein engineering of these enzymes with enhanced properties and catalytic efficiencies. Under this scope, the present review provides a state-of-the-art discussion on the thermophilic β-mannanases from bacterial origin, their production, engineering and structural characterization. It covers broad insights into various molecular biology techniques such as gene mutagenesis, heterologous gene expression, and protein engineering, that are employed to improve the catalytic efficiency and thermostability of bacterial mannanases for potential industrial applications. Further, the bottlenecks associated with mannanase production and process optimization are also discussed. Finally, future research related to bioengineering of mannanases with novel protein expression systems for commercial applications are also elaborated.

Tire additives: Evaluation of joint toxicity, design of new derivatives and mechanism analysis of free radical oxidation

N-(1,3-Dimethylbutyl)-N'-phenyl-p-phenylenediamine (6PPD) is one of the most widely used antioxidant agents in tire additives. Its ozonation by-product 6PPD-quinone has recently been recognized as inducing acute mortality in aquatic organisms such as coho salmon. In this study, we aimed to develop an in-silico method to design environmentally friendly 6PPD derivatives and evaluate the joint toxicity of 6PPD with other commonly used tire additives on coho salmon through full factorial design-molecular docking and molecular dynamic simulation. The toxicity mentioned in this study is represented by the binding energy of chemical(s) binding to the coho salmon growth hormone. The recommended formula for tire additives with relatively low toxicity was then proposed. To further reduce the toxicity of 6PPD, 129 6PPD derivatives were designed based on the N-H bond dissociation reaction, and three of these derivatives showed improved antioxidant activity and 6PPD-106 was finally screened as the optimum alternative with lower toxicity to coho salmon. Besides, the mechanism of free radical oxidation (i.e., antioxidation and ozonation metabolic pathway) for 6PPD-106 was also analyzed and found that after ozonation, the toxicity of 6PPD-106's by-products is much lower than that of 6PPD's by-products. This study provided a molecular modelling-based examination of 6PPD, which comprehensively advanced the understanding of 6PPD's environmental behaviors and provided more environmentally friendly 6PPD alternatives with desired functional property and lower ecological risks.

Advances in alginate lyases and the potential application of enzymatic prepared alginate oligosaccharides: A mini review

Alginate is mainly a linear polysaccharide composed of randomly arranged β-D-mannuronic acid and α-L-guluronic acid linked by α, β-(1,4)-glycosidic bonds. Alginate lyases degrade alginate mainly adopting a β-elimination mechanism, breaking the glycosidic bonds between the monomers and forming a double bond between the C4 and C5 sugar rings to produce alginate oligosaccharides consisting of 2-25 monomers, which have various physiological functions. Thus, it can be used for the continuous industrial production of alginate oligosaccharides with a specific degree of polymerization, in accordance with the requirements of green exploitation of marine resources. With the development of structural analysis, the quantity of characterized alginate lyase structures is progressively growing, leading to a concomitant improvement in understanding the catalytic mechanism. Additionally, the use of molecular modification methods including rational design, truncated expression of non-catalytic domains, and recombination of conserved domains can improve the catalytic properties of the original enzyme, enabling researchers to screen out the enzyme with the expected excellent performance with high success rate and less workload. This review presents the latest findings on the catalytic mechanism of alginate lyases and outlines the methods for molecular modifications. Moreover, it explores the connection between the degree of polymerization and the physiological functions of alginate oligosaccharides, providing a reference for enzymatic preparation development and utilization.

Modification of the Loop Region Near the Substrate Tunnel to Alter the Hydrolytic Process of Dextranase

Dextranases are hydrolases that exclusively catalyze the disruption of α-1,6 glycosidic bonds. A series of variant enzymes were obtained by comparing the sequences of dextranases from different sources and introducing sequence substitutions. A correlation was found between the number of amino acids in the 397-401 region and the hydrolytic process. When there were no more than 5 amino acids in the 397-401 region, the enzyme first hydrolyzed the dextran T70 to a low molecular weight dextran with a molecular weight of about 5000, then IMOs1 appeared in the system if the degradation continued, showing a clear sequential relationship. And when there are more than 5 amino acids in the 397-401 region, IMOs were produced at the beginning of hydrolysis and continue to increase throughout the hydrolytic process. At the same time, we investigated the enzymatic properties of the variants and found that the hydrolytic rate of A-Ca was 11 times higher than that of the original enzyme. The proportion of IMOs produced by A-Ca was 80.68%, which was nearly10% higher than the original enzyme, providing a new enzyme for the industrial preparation of IMOs.

Inhibition of algal blooms by residual antibiotics in aquatic environments: Design, screening, and validation of antibiotic alternatives

Water blooms frequently appear in the aquatic environment with global warming. However, traditional methods for treating water bloom usually require the addition of algaecides, which may lead to secondary environmental pollution problems in the water environment. To solve this problem, researchers have initiated efforts to harness pre-existing chemical substances within aquatic environments to regulate algal blooms, thereby pioneering novel avenues for water body management. Therefore, an integrated approach involving molecular docking, molecular dynamics simulations, three-dimensional quantitative structure-activity relationship (3D-QSAR), and toxicokinetics methods were utilized for the molecular modification of fluoroquinolone antibiotics, to design and screen fluoroquinolone substitutes with improved toxicity of cyanobacteria and green algae, functionality, and environmental friendliness. A total of 143 fluoroquinolone alternatives were designed in this study, and lomefloxacin-6 (LOM6) was found as the optimum alternative to lomefloxacin (LOM), with increased toxicity to cyanobacteria and green algae by 31 % and 72 %. Molecular docking of LOM before and after modification with seven other cyanobacterial and green algal photosynthetic proteins revealed that LOM6 exhibited varying degrees of increased toxicity towards 6 of these photosynthetic proteins, of which 2J96 protein increased the most (136.25 %). It shows that the residual LOM6 in the water environment has a certain inhibitory effect on the algae bloom. In addition, results showed that LOM6 had synergistic toxic effects on cyanobacteria and green algae with other pollutants residual in the aqueous environment, such as trichloroethyl phosphate, triethyl phosphate, perfluorononanoic acid, perfluorooctanoic acid. This indicates that LOM6 has better algal removal effectiveness in aqueous environments where organophosphate flame retardants and perfluorinated compounds exist together. In this paper, a novel method was developed to remove cyanobacteria and green algae in water environment and reduce the secondary pollution through theoretical simulation, which provides theoretical support for the control of water blooms.

strain K30 in Escherichia coli through fermentation condition optimization and molecular modification

Latex clearing protein from Streptomyces sp. strain K30 (LcpK30) is a natural oxidoreductase that can catalyse the cleavage of rubber through dioxygenation. It has significant potential applications in polymer degradation. However, its limited expression in engineered strains restricts its utility. This study aimed to enhance the soluble expression and enzyme activity of LcpK30 in E. coli BL21 (DE3) by optimizing fermentation conditions and making molecular modifications. The enzyme activity reached 5.05 U·mL-1 by optimizing the induction conditions, adding cofactors, and using chemical chaperones, which was 237.1 % of the initial case. Further enhancements in soluble expression were achieved through site mutations guided by the PROSS server, resulting in 8 out of 13 mutants with increased protein expression, a high positive mutation rate of 61.5 %. Subsequently, combined mutants were created by merging single mutants with enhanced protein expression and enzyme activity. The top three double mutants, G91D/S149A, G91D/A210H, and G91D/H296P, displayed expression levels at 173.3 %, 173.3 %, and 153.3 % of the wild-type LcpK30, respectively. These mutants also exhibited enhanced fermentation enzyme activity, reaching 149.5 %, 250.0 %, and 420.2 % compared to the wild-type, along with improved specific activities. This study provides insights for the efficient production of LcpK30 and a practical foundation for its application.

Maltogenic amylase: Its structure, molecular modification, and effects on starch and starch-based products

Maltogenic amylase (MAA) (EC3.2.1.133), a member of the glycoside hydrolase family 13 that mainly produces α-maltose, is widely used to extend the shelf life of bread as it softens bread, improves its elasticity, and preserves its flavor without affecting dough processing. Moreover, MAA is used as an improver in flour products. Despite its antiaging properties, the hydrolytic capacity and thermal stability of MAA can't meet the requirements of industrial application. However, genetic engineering techniques used for the molecular modification of MAA can alter its functional properties to meet application-specific requirements. This review briefly introduces the structure and functions of MAA, its application in starch modification, its effects on starch-based products, and its molecular modification to provide better insights for the application of genetically modified MAA in starch modification.

Engineering the thermostability of d-lyxose isomerase from Caldanaerobius polysaccharolyticus via multiple computer-aided rational design for efficient synthesis of d-mannose

d-Mannose is an attractive functional sugar that exhibits many physiological benefits on human health. The demand for low-calorie sugars and sweeteners in foods are increasingly available on the market. Some sugar isomerases, such as d-lyxose isomerase (d-LIase), can achieve an isomerization reaction between d-mannose and d-fructose. However, the weak thermostability of d-LIase limits its efficient conversion from d-fructose to d-mannose. Nonetheless, few studies are available that have investigated the molecular modification of d-LIase to improve its thermal stability. In this study, computer-aided tools including FireProt, PROSS, and Consensus Finder were employed to jointly design d-LIase mutants with improved thermostability for the first time. Finally, the obtained five-point mutant M5 (N21G/E78P/V58Y/C119Y/K170P) showed high thermal stability and catalytic activity. The half-life of M5 at 65 °C was 10.22 fold, and the catalytic efficiency towards 600 g/L of d-fructose was 2.6 times to that of the wild type enzyme, respectively. Molecular dynamics simulation and intramolecular forces analysis revealed a thermostability mechanism of highly rigidity conformation, newly formed hydrogen bonds and π-cation interaction between and within protein domains, and redistributed surface electrostatic charges for the mutant M5. This research provided a promising d-LIase mutant for the industrial production of d-mannose from d-fructose.

Recent advances in polygalacturonase: Industrial applications and challenges

This review focuses on the applications of polygalacturonase (PG), one of the most commercially produced enzymes on the biocatalyst market, in the food, beverage, feed, textile, and paper industries. Most PGs are acidic mesophilic enzymes, as shown by a summary of their biochemical properties. However, the acidic PGs discovered to date are insufficiently effective for industrial applications. The sequence and structural characteristics of thermophilic PGs are analyzed based on the results of extensive discussions regarding the catalytic mechanism and structural characteristics of PGs with shared right-handed parallel β-helical structures. In addition, the molecular modification methods for obtaining thermostable PGs are systematically presented. Notably, the demand for alkaline heat-resistant PGs has increased significantly concurrent with the biomanufacturing industry development. Therefore, this review also provides a theoretical guideline for mining heat-resistant PG gene resources and modifying PG thermostability.

Lactulose production from lactose isomerization by chemo-catalysts and enzymes: Current status and future perspectives

Lactulose, a semisynthetic nondigestive disaccharide with versatile applications in the food and pharmaceutical industries, has received increasing interest due to its significant health-promoting effects. Currently, industrial lactulose production is exclusively carried out by chemical isomerization of lactose via the Lobry de Bruyn-Alberda van Ekenstein (LA) rearrangement, and much work has been directed toward improving the conversion efficiency in terms of lactulose yield and purity by using new chemo-catalysts and integrated catalytic-purification systems. Lactulose can also be produced by an enzymatic route offering a potentially greener alternative to chemo-catalysis with fewer side products. Compared to the controlled trans-galactosylation by β-galactosidase, directed isomerization of lactose with high isomerization efficiency catalyzed by the most efficient lactulose-producing enzyme, cellobiose 2-epimerase (CE), has gained much attention in recent decades. To further facilitate the industrial translation of CE-based lactulose biotransformation, numerous studies have been reported on improving biocatalytic performance through enzyme mediated molecular modification. This review summarizes recent developments in the chemical and enzymatic production of lactulose. Related catalytic mechanisms are also highlighted and described in detail. Emerging techniques that aimed at advancing lactulose production, such as the boronate affinity-based technique and molecular biological techniques, are reviewed. Finally, perspectives on challenges and opportunities in lactulose production and purification are also discussed.

Research progress of anthocyanin prebiotic activity: A review

BACKGROUND

Anthocyanins are a kind of flavonoids and natural water-soluble pigments, which endow fruits, vegetables, and plants with multiple colors. They are important source of new products with prebiotic activity. However, there is no systematic review documenting prebiotic activity of anthocyanins and their structural analogues. This study aims to fill this gap in literature.

PURPOSE

The objective of this review is to summarize and evaluate the prebiotic activity of anthocyanin's, and discuss the physical and molecular modification methods to improve their biological activities.

STUDY DESIGN AND METHODS

In this review, the databases (PubMed, Google Scholar, Web of Science, Researchgate and Elsevier) were searched profoundly with keywords (anthocyanin's, prebiotics, probiotics, physical embedding and molecular modification).

RESULTS

A total of 34 articles were considered for reviewing. These studies approved that anthocyanins play an important role in promoting the proliferation of probiotics, inhibiting the growth of harmful bacteria and improving the intestinal environment. In addition, physical embedding and molecular modification have also been proved to be effective methods to improve the prebiotic activity of anthocyanins. Anthocyanins could promote the production of short chain fatty acids, accelerate self degradation and improve microbial related enzyme activities to promote the proliferation of probiotics. They inhibited the growth of harmful bacteria by inhibiting the expression of harmful bacteria genes, interfering with the role of metabolism related enzymes and affecting respiratory metabolism. They promoted the formation of a complete intestinal barrier and regulated the intestinal environment to keep the body healthy. Physical embedding, including microencapsulation and colloidal embedding, greatly improved the stability of anthocyanins. On the other hand, molecular modification, especially enzymatic modification, significantly improved the biological activities (antioxidant, prebiotic activity and so on) of anthocyanins.

CONCLUSION

All these research results displayed by this review indicate that anthocyanins are a useful tool for developing prebiotic products. The better activities of the new anthocyanins formed by embedding and modification may make them become more effective raw materials. Our review provides a scientific basis for the future research and application of anthocyanins.

Effect of carbon numbers and structures of monosaccharides on the glycosylation and emulsion stabilization ability of gelatin

Herein, the effect of saccharide glycosylation by nine monosaccharides on bovine bone gelatin for the stabilization of fish oil-loaded emulsions was explored. The gelatin modification was analyzed and then the emulsifying properties of monosaccharide-modified gelatins were analyzed at pH 9.0 and 3.0. The results demonstrated that glycosylated gelatin structure, droplet stability, creaming stability, and liquid-gel transition time were dependent on monosaccharide carbon numbers, monosaccharide structures, and solution pH. Glycosylation modification of gelatins did not obviously change the emulsion droplet stability at pH 9.0, whereas it increased the emulsion droplet stability at pH 3.0. Glycosylation modification of gelatins did not obviously change the emulsion creaming index values (5.1%-8.4% at pH 9.0 and 25.8%-33.1% at pH 3.0). Three-carbon and four-carbon monosaccharides glycosylation significantly increased emulsion liquid-gel transition times. This work provided useful information to understand the effects of carbon numbers and structures of monosaccharides on the protein modification.

Evolving strategies for marine enzyme engineering: recent advances on the molecular modification of alginate lyase

Alginate, an acidic polysaccharide, is formed by β-d-mannuronate (M) and α-l-guluronate (G). As a type of polysaccharide lyase, alginate lyase can efficiently degrade alginate into alginate oligosaccharides, having potential applications in the food, medicine, and agriculture fields. However, the application of alginate lyase has been limited due to its low catalytic efficiency and poor temperature stability. In recent years, various structural features of alginate lyase have been determined, resulting in modification strategies that can increase the applicability of alginate lyase, making it important to summarize and discuss the current evidence. In this review, we summarized the structural features and catalytic mechanisms of alginate lyase. Molecular modification strategies, such as rational design, directed evolution, conserved domain recombination, and non-catalytic domain truncation, are also described in detail. Lastly, the application of alginate lyase is discussed. This comprehensive summary can inform future applications of alginate lyases.

PGK1 : An Essential Player in Modulating Tumor Metabolism

Phosphoglycerate kinase 1 (PGK1) is the first enzyme in glycolysis to generate a molecule of ATP in the conversion of 1,3-bisphosphoglycerate (1,3-BPG) to 3-phosphoglycerate (3-PG). In addition to the role of glycolysis, PGK-1 acts as a polymerase alpha cofactor protein, with effects on the tricarboxylic acid cycle, DNA replication and repair. Posttranslational modifications such as methylation, phosphorylation, and acetylation have been seen to activate PGK1 in cancer. High levels of intracellular PGK1 are associated with tumorigenesis and progression, and chemoradiotherapy resistance. However, high levels of extracellular PGK1 suppress angiogenesis and subsequently counteract cancer malignancy. Here we have summarized the current knowledge on the mechanisms and effects of PGK1 in various tumor types and evaluated its potential prognostic and therapeutic value in cancer. The data summarized here aims at providing molecular information and new ideas of employing natural products to combat cancer associated with PGK1.

Advances in research on calf rennet substitutes and their effects on cheese quality

Milk coagulation is an important step in cheese production, and milk-clotting enzymes (MCEs) play a major role in this process. Calf rennet is the most widely used MCE in the cheese industry. The use of calf rennet substitutes is becoming necessary due to the limited availability of calf rennet and the increase in cheese consumption. The objective of this review is to summarize the latest findings on calf rennet substitutes (animal MCEs, plant-derived MCEs, recombinant MCEs and microbial MCEs) and their application in cheese production. Special emphasis has been placed on aspects of the effects of these substitutes on hydrolysis, functional peptides, cheese variety and cheese yield. The advantages and disadvantages of different calf rennet substitutes are discussed, in which microbial MCEs have the advantages of less expensive production, greater biochemical diversity, easier genetic modification, etc. In particular, some of these MCEs have suitable characteristics for cheese production and are considered to be the most potential calf rennet substitutes. Moreover, challenges and future perspectives are presented to provide inspiration for the development of excellent calf rennet substitutes.

Research status of Bacillus phytase

Phytic acid is abundant in seeds, roots and stems of plants, it acts as an anti-nutrient in food and feed industry, since it affects the absorption of nutrients by humans and monogastric animals. Furthermore, phosphorus produced through its decomposition by microorganisms can cause environmental pollution. Phytase degrades phytic acid generating precursors of inositol that can be used in clinical practice; in addition, phytase treatment can minimize the anti-nutritional effect of phytic acid. The use of phytase synthesized from Bacillus is more advantageous due to its high activity. Additionally, its good heat resistance under neutral conditions greatly fills the gap of commercial utilization of acid phytase. In this review, we summarize the latest research results on Bacillus phytase, including its physiological and biochemical characteristics, molecular structure information, calcium effects on its catalytic activity and stability, its catalytic mechanism and molecular modification.

Emerging technologies for genetic modification of solventogenic clostridia: From tool to strategy development

Solventogenic clostridia has been considered as one of the most potential microbial cell factories for biofuel production in the biorefinery industry. However, the inherent shortcomings of clostridia strains such as low productivity, by-products formation and toxic tolerance still strongly restrict the large-scale application. Therefore, concerns regarding the genetic modification of solventogenic clostridia have spurred interests into the development of modern gene-editing tools. In this review, we summarize the latest advances of genetic tools involved in modifying solventogenic clostridia. Following a systematic comparison on their respective characteristics, we then review the corresponding strategies for overcoming the obstacles to the enhanced production. Discussing the progress of other microbial cell factories for solventogenesis, we finally describe the key challenges and trends with valuable recommendations for future large-scale biosolvent industrial application.

Molecular modification, structural characterization, and biological activity of xylans

The differences in the source and structure of xylans make them have various biological activities. However, due to their inherent structural limitations, the various biological activities of xylans are far lower than those of commercial drugs. Currently, several types of molecular modification methods have been developed to address these limitations, and many derivatives with specific biological activity have been obtained. Further research on structural characteristics, structure-activity relationship and mechanism of action is of great significance for the development of xylan derivatives. Therefore, the major molecular modification methods of xylans are introduced in this paper, and the primary structure and conformation characteristics of xylans and their derivatives are summarized. In addition, the biological activity and structure-activity relationship of the modified xylans are also discussed.

An adjusted 3D-QSAR model for the combined activity of fluoroquinolones photodegradation and microbial degradation assisted by dynamic simulation and its application in molecular modification

This study developed a comprehensive characterization method for the combined degradation effect of modified fluoroquinolones (FQs) photodegradation and microbial degradation. A combination of revised 3D-QSAR model, molecular docking, path simulation inference, pharmacokinetics, molecular dynamics (MD) simulation and toxicokinetics simulation was used to construct a systematic environment-friendly drug screening system. Five derivatives were screened with significantly improved combined degradation effect (over 20%) and functional characteristics and human health parameters through combined model verification, functional and human health risk assessment. The simulation path of photo- and microbial-degradation of gatifloxacin and new gatifloxacin molecules was derived, and the reaction energy barrier was also calculated. The ratio of the total rate-determining steps change rate of the decreased energy barrier (14.10%:26.30%) was consistent with the ratio of the increased degradation performance predicted by the model (22.87%:19.77%), demonstrating the reliability of revised 3D-QSAR model and it could be applied in molecular modification. MD and toxicokinetics simulation were used to predict the binding energy and aquatic toxicity between photo- and microbial-degradation products and the degradation enzymes, which further to screen the degradation pathways with low potential environmental risks. The findings will be helpful to screen environment-friendly drug and develop appropriate strategies for its risk management.

Synthesis and performance characterization of an efficient coal dust suppressant for synergistic combustion with coal dust

Coal dust diffusion during coal transportation and storage causes serious environmental pollution. The existing dust suppressant in previous studies was unable to achieve the expected effects owing to severe wind damage and rain erosion. Therefore, the current study synthesized and prepared an efficient and applicable dust suppressant for coal transportation and storage. Infrared spectroscopy and scanning electron microscope experiments were conducted during the synthesis to analyze the microstructure changes in the synthetic products. Moreover, viscosity was used as the evaluation index in the single-factor experiments to obtain the optimal synthesis conditions. Performance measurement results showed that the prepared dust suppressant had a strong protective effect on coal powder and could effectively resist the impact of wind damage and rain erosion. Compared with other dust suppressants, the proposed dust suppressant prepared showed more evident positive effects and longer lasting action time in the quantitative test. Moreover, the dried product could synergistically combust with coal powder, thereby possibly mitigating the tedious post-treatment process and increasing the utilization rate of resources.

Efficacy coefficient method assisted quadruple-activities 3D-QSAR pharmacophore model for application in environmentally friendly PAE molecular modification

Phthalate acid esters (PAEs) are among the most widely used plasticizers in plastic products. They are easily diffused from plastic during use and seriously affect the environment and human health. Therefore, designing environmentally friendly PAE derivatives has important practical applications. In this paper, the environmentally friendly molecular modification of PAEs was carried out according to a comprehensive structural evaluation based on a three-dimensional quantitative structure-activity relationship (3D-QSAR) pharmacophore model of four activity modes. First, the efficacy coefficient method was used to process the mobility, toxicity, degradation and bioconcentration data of the PAEs to calculate comprehensive evaluation values. The PAE 3D-QSAR pharmacophore complex model was constructed based on the PAE four-activity comprehensive evaluation value (a comprehensive value representing the mobility, toxicity, degradation and bioconcentration of the PAEs), and a total of 4 PAE derivatives with reduced comprehensive evaluation values were obtained. Functional evaluation of the derivatives showed that the five PAEs with lower comprehensive evaluation values were stable in the environment, while the insulating properties of the derivative molecules were less affected. Following the four-activity pharmacophore model (Hypo 1) of the target molecules, dimethyl phthalate (DMP) and di-n-octyl phthalate (DNOP), comprehensive evaluation models and their mobility, toxicity, degradation and bioconcentration single-activity models, the substitution sites selected by the comprehensive evaluation model were demonstrated to be highly representative. By constructing a two-dimensional quantitative structure-activity relationship (2D-QSAR) model of the comprehensive evaluation values of the PAEs and the four single-effect 2D-QSAR models of their derivatives, the different effects of the five key parameters on the comprehensive evaluation values, toxicity, degradation, mobility and bioconcentration of molecules were analysed.

Exploring how structural changes to new Licarin A derivatives effects their bioactive properties against rapid growing mycobacteria and biofilm formation

Several species of rapidly growing mycobacteria (RGM) have been associated with biofilms in areas such as biomedical devices, water distribution systems, cosmetic surgery, and catheter-related blood infections. Biofilms which exhibit antimicrobial resistance such as those formed by the genus Mycobacterium pose a significant risk to health and are of particular interest to researchers. Licarin A (a neolignan found in numerous plant species e.g. nutmeg) has been reported to show a wide range of biological actions including anti-inflammatory, antioxidant, and antibacterial properties. The aim of this study was to prepare a set of Licarin A derivatives and investigate the impact of specific structural changes on its antimycobacterial ability, and its effect on the biofilm formation of RGM species. Initially, the phenolic sub-unit and alkenyl side chain of Licarin A were modified to create derivatives with a higher partition coefficient; as the activity of a compound against mycobacteria seems to be strongly influenced by its hydrophobicity. Further, polar groups were inserted into the side chain to change the hydrophilic-lipophilic profile of the molecules. Results showed variability in the susceptibility profile of mycobacteria against the Licarin A derivatives under analysis. A number of the derivatives showed significant inhibitory activity of planktonic growth of the three strains of mycobacteria used, with even lower MIC values than those observed with reference drugs and Licarin A itself. Cytotoxicity assays showed they also have low toxicity, confirming that structural modifications to the Licarin A have made improvements to its antimycobacterial properties.

Highly biodegradable fluoroquinolone derivatives designed using the 3D-QSAR model and biodegradation pathways analysis

A three-dimensional quantitative structure-activity relationship (3D-QSAR) model was established based on molecular structures and docking scores (representing the biodegradability); the scores were obtained for 23 fluoroquinolones (FQs) and the oxidoreductase (PDB ID: 1YZP) of Phanerochaete chrysosporium in the aerobic process of municipal wastewater treatment plants. In the Comparative Molecular Field Analysis (CoMFA) model, q² was 0.516 and r²_pred was 0.727, which showed that the model was reliable and robust. The modification information obtained by the contour maps showed that introducing electronegative, bulky or electropositive groups at different active sites could increase the biodegradability of fluoroquinolone derivatives. Using levofloxacin (LEV) as a modified molecule, 35 fluoroquinolone derivatives with higher biodegradability than LEV were designed. After the evaluation of genotoxicity, bioconcentration and photodegradation, Derivative-15, with higher biodegradability (increased by 27.85%), higher genotoxicity, higher photodegradation and lower bioconcentration, was identified as the most environmentally friendly fluoroquinolone derivative. The 2D-QSAR model of FQ biodegradability was established through the quantization parameters, and q⁺ was identified as the main parameter affecting the biodegradability of FQs through sensitivity analysis. In addition, the docking results of LEV and Derivative-15 with the oxidoreductase in P. chrysosporium showed that the electrostatic field force between Derivative-15 and the amino acid residues promoted the binding of the donor to the receptor protein, thereby increasing the biodegradability of Derivative-15. Additionally, molecular dynamics simulations revealed that the enhancement of the electrostatic field force with Derivative-15 could promote the binding of the ligand to the receptor, which was basically consistent with the conclusion of molecular docking. Finally, the three microbial degradation pathways of LEV and Derivative-15 were also proposed. The total energy barrier value of the pathway with the lowest total energy barrier of biodegradation was reduced by 32.07%, which was basically consistent with the enhancement of biodegradability of Derivative-15.

Improving the catalytic performance of Proteinase K from Parengyodontium album for use in feather degradation

Proteinase K (PROK) from Parengyodontium album hydrolyzes keratin, a major protein component of poultry feathers, which are an inexpensive and renewable protein resource. Based on structural studies for analysis of amino acid flexibility near the catalytic center, identification of highly conserved residues, and experimental screening, we obtained a mutant R218S with residual activity 1.6-fold higher than that of PROK after incubation at 60 °C for 1 h. Molecular dynamics simulation indicated that substitution of Arg218 with Ser leads to three hydrogen bonds being introduced into the structure, stabilizing the β-sheet in which Ser218 is located, and thus improvement of thermostability. Additionally, the mutant R218S had a 15% increase in specific activity compared to PROK and improvement in the rate and thoroughness of feather degradation compared with PROK. We confirmed the positive effects of enhancing catalytic center rigidity on enzyme thermostability, a finding which may have broad applications.

Designing modified polybrominated diphenyl ether BDE-47, BDE-99, BDE-100, BDE-183, and BDE-209 molecules with decreased estrogenic activities using 3D-QSAR, pharmacophore models coupled with resolution V of the 210-3 fractional factorial design and molecular docking

A 3D-QSAR model was constructed to predict polybrominated diphenyl ether (PBDE) estrogenic activities expressed as median effective concentrations (pEC₅₀), and resolution V of the 2^10-3 fractional factorial design and a pharmacophore model were used to modify the target PBDE molecules BDE-47, BDE-99, BDE-100, BDE-183, and BDE-209 to decrease the estrogenic activities. The persistent-organic-pollutant-related and flame-retardant properties of the modified molecules were evaluated. The mechanisms involved in decreasing PBDE estrogenic activities were explored through molecular docking. The 3D-QSAR model gave a cross-validated correlation coefficient (q²) of 0.682 (i.e., >0.5) and a non-cross-validated correlation coefficient (r²) of 0.980 (i.e., >0.9). Mono- and di-substitutions and hydrophobic substituent groups gave 40 modified molecules with decreased estrogenic activities, including modified BDE-47 and BDE-99 with pEC₅₀ decreased by >10% and modified BDE-100, BDE-183, and BDE-209 with pEC₅₀ decreased by >20%. The modified molecules had similar flame-retardancy to the unmodified molecules, and lower biotoxicities (by a maximum of 17.27%), persistences (by a maximum of 55.68%), bioconcentration (by 4.28%-23.91%), and long-range transport potentials (by 0.72%-18.47%). Docking indicated that hydrophobic interactions were the main factors affecting PBDE estrogenic activities. The results provide a theoretical basis for designing less estrogenic flame retardants than are currently available.

Evolutionary analysis and structural characterization of Aquilaria sinensis sesquiterpene synthase in agarwood formation: A computational study

Agarwood originating from Aquilaria sinensis contains sesquiterpenoids that have tremendous commercial value in the pharmaceutical and fragrance industries. Aquilaria sinensis sesquiterpene synthase (AsSTS) is the key enzyme in the agarwood biosynthesis pathway, and its activity directly affects the chemical composition of agarwood; however, its role in species evolution remains unclear. In this study, we performed an evolutionary analysis based on 68 plant sesquiterpene synthase (STS) genes and further structural characterization of the gene encoding AsSTS to explore its molecular evolution. The phylogenetic tree indicated that these STS genes included three subfamilies. Additionally, 23 positively selected sites were detected, and no influence of recombination was found. Furthermore, the protein structure of AsSTS was characterized using primary sequence and structural analyses as having a functional active site lid domain, a substrate binding site, two post-translational modification sites and four conserved motifs. Finally, most virtual mutations of positively selected sites could be stabilized against thermal denaturation by a decrease in free energy, and three virtual mutations (D403R, G470Q and S538K) were shown to play important roles in the function and stability of AsSTS. The molecular evolutionary analysis of plant STSs provides essential clues for further experimental site-directed mutagenesis and molecular modification of AsSTS.

Site-directed mutation of β-galactosidase from Aspergillus candidus to reduce galactose inhibition in lactose hydrolysis

β-Galactosidase is widely used for hydrolysis of whey lactose. However, galactose inhibition has acted as a major constraint on the catalytic process. Thus, it is sensible to improve upon this defect in β-galactosidase through protein modification. To reduce the galactose inhibition of Aspergillus candidus β-galactosidase (LACB), four amino acid positions were selected for mutation based on their molecular bindings with galactose. Four mutant libraries (Tyr96, Asn140, Glu142, and Tyr364) of the LACB were constructed using site-directed mutagenesis. Among all of the mutants, Y364F was superior to the wild-type enzyme. The Y364F mutant has a galactose inhibition constant (K_i) of 282 mM, 15.7-fold greater than that of the wild-type enzyme (K_i = 18 mM). When 18 mg/ml galactose was added, the activity of the wild-type enzyme fell to 57% of its initial activity, whereas Y364F activity was maintained at over 90% of its initial activity. The wild-type enzyme hydrolyzed 78% of the initial lactose (240 mg/ml) after 48 h, while the Y364F mutant had a hydrolysis rate greater than 90%. The β-galactosidase Y364F mutant with reduced galactose inhibition may have greater potential applications in whey treatment compared to wild-type LACB.

Molecular modification, expression and purification of new subtype antioxidant peptide from Pinctada fucata by recombinant Escherichia coli to improve antioxidant-activity

The aim of this study was to establish a system for the efficient expression and purification of new subtype of antioxidant peptide from Pinctada fucata meat (NPFMAP), which is designed by molecular modification technology based on the sequence of purified and identified antioxidant peptide from Pinctada fucata meat (PFMAP, Gly-Ala-Gly-Leu-Pro-Gly-Lys-Arg-Glu-Arg), and to better understand the relationship between structure and antioxidant activity. Meanwhile, gene codon usage was optimized and the glutathione S-transferase (GST) tag of pGEX-6P-1 was added to facilitate expression and purification NPFMAP in Escherichia coli. The results of antioxidant activity assay in vitro showed a higher antioxidant activity in NPFMAP than that in enzymatic hydrolysis digested or chemically synthesized PFMAP. In particular, the DPPH scavenging radical activity increased by about 4.7 times after molecular modification. Structural bioanalysis indicated that new subtype antioxidant peptide had spatial conformation and good hydrophilic after modification, which was confirmed by antioxidant activity assays. Thus, the proposed method could be used to obtain NPFMAP with high antioxidant activity.

Synthesis, antiplatelet and antithrombotic activities of resveratrol derivatives with NO-donor properties

Resveratrol (RVT) is a stilbene with a protective effect on the cardiovascular system; however, drawbacks including low bioavailability and fast metabolism limit its efficacy. In this work we described new resveratrol derivatives with nitric oxide (NO) release properties, ability to inhibit platelet aggregation and in vivo antithrombotic effect. Compounds (4a-f) were able to release NO in vitro, at levels ranging from 24.1% to 27.4%. All compounds (2a-f and 4a-f) have exhibited platelet aggregation inhibition using as agonists ADP, collagen and arachidonic acid. The most active compound (4f) showed reduced bleeding time compared to acetylsalicylic acid (ASA) and protected up to 80% against in vivo thromboembolic events. These findings suggest that hybrid resveratrol-furoxan (4f) is a novel lead compound able to prevent platelet aggregation and thromboembolic events.

Novel capsaicin analogues as potential anticancer agents: synthesis, biological evaluation, and in silico approach

A novel class of benzo[d][1,3]dioxol-5-ylmethyl alkyl/aryl amide and ester analogues of capsaicin were designed, synthesized, and evaluated for their cytotoxic activity against human and murine cancer cell lines (B16F10, SK-MEL-28, NCI-H1299, NCI-H460, SK-BR-3, and MDA-MB-231) and human lung fibroblasts (MRC-5). Three compounds (5f, 6c, and 6e) selectively inhibited the growth of aggressive cancer cells in the micromolar (µM) range. Furthermore, an exploratory data analysis pointed at the topological and electronic molecular properties as responsible for the discrimination process regarding the set of investigated compounds. The findings suggest that the applied designing strategy, besides providing more potent analogues, indicates the aryl amides and esters as well as the alkyl esters as interesting scaffolds to design and develop novel anticancer agents.

Biological properties of adrenomedullin conjugated with polyethylene glycol

Adrenomedullin (AM) is a vasodilator peptide with pleiotropic effects, including cardiovascular protection and anti-inflammation. Because of these beneficial effects, AM appears to be a promising therapeutic tool for human diseases, while intravenous injection of AM stimulates sympathetic nerve activity due to short-acting potent vasodilation, resulting in increased heart rate and renin secretion. To lessen these acute reactions, we conjugated the N-terminal of human AM peptide with polyethylene glycol (PEG), and examined the biological properties of PEGylated AM in the present study. PEGylated AM stimulated cAMP production, an intracellular second messenger of AM, in cultured human embryonic kidney cells expressing a specific AM receptor in a dose-dependent manner, as did native human AM. The pEC50 value of PEGylated AM was lower than human AM, but no difference was noted in maximum response (Emax) between the PEGylated and native peptides. Intravenous bolus injection of 10nmol/kg PEGylated AM lowered blood pressure in anesthetized rats, but the acute reduction became significantly smaller by PEGylation as compared with native AM. Plasma half-life of PEGylated AM was significantly longer than native AM both in the first and second phases in rats. In summary, N-terminal PEGylated AM stimulated cAMP production in vitro, showing lessened acute hypotensive action and a prolonged plasma half-life in comparison with native AM peptide in vivo.

Recent advances in discovery, heterologous expression, and molecular engineering of cyclodextrin glycosyltransferase for versatile applications

Cyclodextrin glycosyltransferase (CGTase) is an important enzyme with multiple functions, in particular the production of cyclodextrins. It is also widely applied in baking and carbohydrate glycosylation because it participates in various types of catalytic reactions. New applications are being found with novel CGTases being isolated from various organisms. Heterologous expression is performed for the overproduction of CGTases to meet the requirements of these applications. In addition, various directed evolution techniques have been applied to modify the molecular structure of CGTase for improved performance in industrial applications. In recent years, substantial progress has been made in the heterologous expression and molecular engineering of CGTases. In this review, we systematically summarize the heterologous expression strategies used for enhancing the production of CGTases. We also outline and discuss the molecular engineering approaches used to improve the production, secretion, and properties (e.g., product and substrate specificity, catalytic efficiency, and thermal stability) of CGTase.

Molecular docking studies of quercetin and its analogues against human inducible nitric oxide synthase

Nitric oxide synthases (NOS) catalyze to produce nitric oxide (NO) from L-arginine. The isoform of NOS i.e. inducible nitric oxide synthases (iNOS) expression is observed in various human malignant tumors such as breast, lung, prostate and bladder, colorectal cancer, and malignant melanoma. Also an increased level of iNOS expression and activity has been found in the tumor cells of gynecological malignancies, stroma of breast cancer and tumor cells of head and neck cancer. Because of its importance in causing tumors and cancer, iNOS enzyme has become a new target in finding novel inhibitors as anti cancer agents. The present work focuses on the molecular docking analysis of quercetin and its analogues against iNOS enzyme. Earlier there are reports of quercetin inhibiting iNOS enzyme in certain experiments as anti cancer agent. But the clinical use of quercetin is limited by its low oral bioavailability and therefore needed its molecular modification to improve its pharmacological properties. In the present study ten analogues of quercetin were found to be docked at the active site cavity with favorable ligand-protein molecular interaction and interestingly from the ADME-Toxicity analysis these analogues have enhanced pharmacological properties than quercetin.