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

Potential Inhibitors of metalloproteinases (MMPs) and phospholipases from Nemopilema nomurai jellyfish peptides: An in-silico Pharmacokinetics and Molecular Docking Studies

Jellyfish stings, especially from Nemopilema nomurai, pose serious health risks due to its venom toxins like metalloproteinases (MMPs) and phospholipases A2 (PLAs A2). Thes toxin can induce severe reactions such as pain, tissue necrosis, inflammation, and in extreme cases, cardiac arrest. While the exact mechanisms of toxicity are not fully understood, MMPs and PLA2 enzymes are known to contribute significantly to tissue damage and inflammation. Thus, the inhibition of these toxins could reduce venom toxicity and provide new treatment options for jellyfish envenomation. This study utilized pharma informatic to evaluate Nemopilema nomurai jellyfish-derived peptides against Nemopilema nomurai venom toxins (metalloproteinase and phospholipase). After profiling absorption, distribution, metabolism, excretion, and toxicity (ADMET) parameters, two peptides, DN26779_N and DN26779_Q, were selected for docking analysis. DN26779_N exhibited higher binding energy to metalloproteinase (-13.3), and phospholipase (-12.6) than DN26779_Q. Molecular dynamics simulations confirmed the stability of these interactions, driven by hydrophobic affinity and hydrogen bonding. Overall, DN26779_N and DN26779_Q demonstrate significant potential as inhibitors of metalloproteinase, and phospholipase A2, presenting promising therapeutic avenues for treating and addressing jellyfish envenomation.

Inhibition of Glucosinolate Sulfatases to Combat Plutella xylostella: Development of Novel Phenylcarboxamide Derivatives for Plant-Integrated Pest Management

Glucosinolates in cruciferous plants are hydrolyzed by myrosinase to produce toxic isothiocyanates (ITCs). However, Plutella xylostella (P. xylostella), one of the top 10 global agricultural pests, utilizes glucosinolate sulfatases (GSSs) in its gut to convert glucosinolates into nontoxic desulfo-glucosinolates, thereby effectively avoiding the toxicity of ITCs. This study investigates the potential of inhibiting GSSs. Among 16 synthesized phenylcarboxamide derivatives, compound 1n exhibited strong inhibitory activity against GSS1 (59.72%) and GSS2 (88.47%), key enzymes involved in glucosinolate desulfation in P. xylostella, leading to toxic ITC accumulation and disrupted detoxification. This resulted in an approximately 30% reduction in larval weight, at a concentration of 100 mg/L, the mortality rate reached 96%. Importantly, in the absence of glucosinolates, these inhibitors showed no direct toxicity to the insect, indicating that their action relies on interaction with the plant's chemical defense system. These findings provide strong evidence supporting the development of GSSs inhibitions as more specific and selective insecticide, offering a promising alternative to conventional chemical pesticides.

Protonation State Insights into the Influence of Biocatalytic Function for Acetylcholinesterase Mediated by Neonicotinoids

The catalytic efficiency of acetylcholinesterase (AChE) is likely regulated by the protonation states and conformational adaptations of its catalytic residues. While neonicotinoid insecticides are recognized for impairing AChE function through neurotoxic mechanisms, the precise molecular mechanisms governing this inhibition remain poorly characterized. This investigation elucidates how structural variations among neonicotinoids modulate the protonation equilibria of Glu-202 and His-447 in AChE's catalytic triad. Comparative analysis reveals that nitro-substituted neonicotinoids (imidacloprid, clothianidin) induce more pronounced protonation state transitions compared to their cyano-containing counterparts (thiacloprid, acetamiprid). Specifically, the strong electron-withdrawing nitro groups facilitate the conversion of Glu-202 from the deprotonation (GLU) to protonation (GLH) state and His-447 from the δ- (HID) to ε-position protonation (HIE) state through enhanced electrostatic interactions. These electronic perturbations trigger structural reorganization within the active site, evidenced by nitro group-directed residue realignment and subsequent H-bond formation. Energy decomposition analysis identifies electrostatic contributions as the primary determinant of binding affinity differences, with nitro-neonicotinoids exhibiting stronger interactions than cyano-neonicotinoids. QM/MM metadynamics reveals that substantial protonation state alterations disrupt AChE's biocatalytic function, particularly its capacity for acetylcholine hydrolysis. Finally, SH-SY5Y-based cellular assays show that imidacloprid exhibits the strongest inhibitory effect on AChE intracellular activity, while thiacloprid and acetamiprid show weaker inhibitory effects, aligning with the computational predictions. This study provides insights into the protonation-state-induced biocatalytic function for acetylcholinesterase mediated by neonicotinoids, contributing to the assessment of exogenous ligand-induced potential ecological and human health risks.

Computational identification of aspartic protease inhibitors for antimalarial drug development against Plasmodium Vivax

Malaria is a parasitic disease that has caused suffering to humans since ancient times and remains a major public health concern in tropical and subtropical regions.The development of novel antimalarials therefore becomes of utmost importance by targeting aspartic protease. The computational study utilized a molecular docking approach to identify hit compounds. In this stuyda molecular docking approach was employed to identify potential hit compounds. The molecular docking analysis yielded three hit compounds CMNPD229, ZINC000000018635, and ZINC000005425464 along with the reference drug chloroquine, with binding energy scores of -8.1 kcal/mol, -8.0 kcal/mol, -7.8 kcal/mol, and - 6.8 kcal/mol, respectively. These compounds were further to assess their potential as optimal drug candidates. Subsequently density function theory (DFT) was performed. Afterward, the protein-ligand (PL) complexes were subjected to molecular dynamic simulation (MDS) to identify the stability and rigidity of the complexes in a fleeting and dynamic setting. The complex CMNPD229 exhibited good stability followed by ZINC000000018635, ZINC000005425464, and the Control. The compounds showed good MM-PBSA/GBSA, WaterSwap, and entropy energy values. The calculated MM-PBSA/GBSA binding free energy scores were - 120.78 kcal/mol, -107.16 kcal/mol, -91.00 kcal/mol, and - 97.49 kcal/mol for CMNPD229, ZINC000000018635, ZINC000005425464, and the reference drug, respectively.Additionally, salt bridge analysis and secondary structure evaluation revealed that CMNPD229 formed the highest number of interactions (Glu290-Arg23 and Glu305-Lys306), indicating its stability as a potential drug candidate. This study suggests that CMNPD229 holds promise as a potent antimalarial drug by effectively inhibiting Plasmodium falciparum and Plasmodium vivax aspartic proteases.

Borylated 5-Membered Ring Iminosugars: Detailed Nuclear Magnetic Resonance Spectroscopic Characterisation, and Method for Analysis of Anomeric and Boron Equilibria

This paper describes the first detailed NMR analysis of the borylated intermediates and target compounds for a small library of pyrrolidine iminosugars of l-gulose absolute stereochemical configuration. The iminosugars were functionalised via N-alkylation to bear a boronate ester or boronic acid groups. The addition of the organic boron pharmacophore allows to further explore the chemical space around and in the active sites, where the boron atom has the capability to make reversible covalent bonds with enzyme nucleophiles and other nucleophiles. We discuss the concurrent complex equilibrium processes of mutarotation and borarotation as studied by NMR.

Computer-assisted enzyme cocktails enhance fermentation by overcoming toxic inhibitors from pretreatment processes

Lignocellulosic biomass is the most abundant form of biomass available for fuel production, serving as the fourth leading energy source globally. However, inhibitors generated during pretreatment processes often hinder fermentation performance and conversion efficiency. In this study, we developed an enhanced computer-assisted enzyme cocktail strategy (ComEC 2.0) to mitigate the inhibitory effects. Through experimental studies and molecular dynamics simulations, eight optimization strategies were developed for enzyme cocktail formulation (comprising CBHI, EG, BG, XYN, LPMO). Notably, Strategy 4b, which accounts for both overall hydration and the synergistic effects between LPMO and CBHI/EG/BG/XYN, increased glucose and xylose yields by 20.7 % and 21 %, respectively, using corn stover, reducing Process Mass Intensity (PMI) by 70.78 % and water use by 80 % during ethanol fermentation. Applying Strategy 4b to industrial corn cob increased glucose and xylose yields by 22.1 % and 21.6 %, surpassing the commercial Ctec3 blend. This scalable approach significantly enhances biomass conversion and resource efficiency, offering broad industrial potential.

Impact of ultrasonic pretreatment on pumpkin seed protein: Effect on protease activities, protein structure, hydrolysis kinetics and functional properties

Adding value to food by-products, such as pumpkin seeds, is an important strategy for the complete utilization of plant foods and advancing sustainability goals. This study aimed to maximize the production of bioactive peptides from pumpkin seed protein (PSP) by combining ultrasonic (US) pretreatment (40 kHz, 23.8 W/L) with enzymatic hydrolysis. The PSP's structure after sonication and its effects on the commercial proteases (Brauzyn®, Flavourzyme®, Neutrase®) activity and degree of hydrolysis were studied. The hydrolysis consequences regarding solubility and antioxidant activity of the resulting peptides were also evaluated. Sonication of PSP increased enzymatic activity by up to 21.3 % for Brauzyn®, 24.8 % for Flavourzyme® and 19.2 % for Neutrase®. Consequently, there was an increase in the degree of hydrolysis (up to 89 %) using sonicated PSP, particularly at 60 min/40 °C. These effects can be attributed to ultrasound-induced protein conformation changes, including increased intrinsic fluorescence intensity (<22 %), shifts in UV spectra, and alterations in FTIR amide bands, especially a decrease in β-sheet content (<7.14 %). Additionally, ultrasonic pretreatment reduced particle size (<43.9 %) and polydispersity index (<58 %), enhancing enzyme accessibility by fragmenting protein aggregates, as observed via scanning electron microscopy. As a result, the peptides obtained from the hydrolysis of sonicated PSP exhibited higher protein solubility (12 % to 49 % at pH 6.0) and improved antioxidant activity (5.6 % to 77 %). Overall, sonication of PSP for 60 min at 40 °C followed by hydrolysis with Neutrase® proved to be the most effective strategy for producing highly soluble peptides with enhanced antioxidant properties, highlighting the potential of ultrasound as a valuable tool for optimizing bioactive peptide production. Based on these results, the developed process is ready for scale-up by the food industry, aiming to obtain protein hydrolysates with improved functional and/or nutritional properties from a low-cost raw material. In parallel, further researches can focus on the potential application of these hydrolysates as ingredients in bakery, meet or dairy products.

Cellulase from Halomonas elongata for biofuel application: enzymatic characterization and inhibition tolerance investigation

Halophilic bacteria are promising candidates for biofuel production because of their efficient cellulose degradation. Their cellulases exhibit high activity, even in the presence of inhibitors and under extreme conditions, making them ideal for biorefinery applications. In this study, we isolated a strain of Halomonas elongata (Kadal6) from decomposed cotton cloth on a Rameshwaram seashore. Morphological, biochemical, and 16S rRNA analyses revealed that Kadal6 was 99.93% similar to the cellulase-producing strain, H. elongata MH25661. The tolerance of the cellulase to inhibitors was assessed through molecular docking with a cellulase model of MH25661 generated by I-TASSER and experimentally using response surface methodology (RSM) with Kadal6. A molecular docking study indicated a high inhibition constant for ethanol, hydroxymethylfurfural (HMF), and furfural. Cellulase from H. elongata Kadal6 (CellHe) showed a maximum inhibition rate of 44.27% at 55 °C, 15% ethanol, and 6.5 g/L furfural and HMF. The enzyme retained 50% of its activity in the presence of these inhibitors, and remained unaffected at 1 g/L furfural and HMF, although inhibition occurred at 3 g/L. H. elongata cellulase demonstrated significant tolerance to inhibition both in vitro (RSM) and in silico, indicating its potential for biorefinery applications in harsh environments.

Salivary cysteine levels as a potential biochemical indicator of oral cancer risk in tobacco consumers

Aim: Oral cancer is the leading cause of mortality, with a survival rate of less than 5 years, and is predominantly influenced by tobacco mutagens. Invasive diagnostic methods hinder early detection of oral cancer biomarkers. The present study performed salivary biochemical analysis for early oral cancer screening in tobacco consumers.Materials & methods: Three study groups included healthy controls (n = 25), tobacco users (n = 25) and oral cancer patients (n = 25). Salivary total protein, amylase, TNF-α and amino acid levels were evaluated using enzymatic tests, Enzyme linked Immunosorbent Assay (ELISA) and High-Performance Liquid Chromatography (HPLC).Results: Compared with healthy controls, salivary total protein and TNF-α levels were significantly (p = 0.04) higher in oral cancer patients. Salivary amylase levels were significantly lower in tobacco smokers (p = 0.02) and higher in oral cancer patients (p = 0.01). Interestingly, the amino acid cysteine concentration was significantly higher (p = 0.02) in tobacco consumers (62.5 ± 10) than in healthy controls (116.1 ± 28).Conclusion: In high-risk populations, such as tobacco users, salivary biochemical analysis can serve as a promising noninvasive diagnostic method for early oral cancer screening. As a salivary biomarker, the amino acid cysteine exhibits potential as a means of detecting the progression of oral cancer in individuals who consume tobacco.

Use of ultrasound to improve the activity of cyclodextrin glycosyltransferase in the producing of β-cyclodextrins: Impact on enzyme activity, stability and insights into changes on enzyme macrostructure

This work explored the impact of ultrasound (US) on the activity, stability, and macrostructural conformation of cyclodextrin glycosyltransferase (CGTase) and how these changes could maximize the production of β-cyclodextrins (β-CDs). The results showed that ultrasonic pretreatment (20 kHz and 38 W/L) at pH 6.0 promoted increased enzymatic activity. Specifically, after sonication at 25 °C/30 min, there was a maximum activity increase of 93 % and 68 % when biocatalysis was carried out at 25 and 55 °C, respectively. For activity measured at 80 °C, maximum increase (31 %) was observed after sonication at 25 °C/60 min. Comparatively, US pretreatment at low pH (pH = 4.0) resulted in a lower activity increase (max. 28 %). These activation levels were maintained after 24 h of storage at 8 °C, suggesting that changes on CGTase after ultrasonic pretreatment were not transitory. These pretreatments altered the conformational structure of CGTase, revealed by an up to 11 % increase in intrinsic fluorescence intensity, and resulted in macrostructural modifications, such as a decrease in particle size and polydispersion index (up to 85 % and 45.8 %, respectively). Therefore, the sonication of CGTase under specific conditions of pH, time, and temperature (especially at pH 6.0/ 30 min/ 25 °C) promotes macrostructural changes in CGTase that induce enzyme activation and, consequently, higher production of β-CDs.

Assessment of polyphenols in purple and red rice bran: Phenolic profiles, antioxidant activities, and mechanism of inhibition against amylolytic enzymes

Pigmented Thai rice varieties, including purple (Riceberry) and red (Hommali), are gaining popularity due to their health benefits as a source of polyphenols that may exert a hypoglycemic effect through specific inhibition of amylolytic enzymes. This study determined the free phenolic extract from purple rice bran (PFE) to exhibit notably greater content of phytochemical compounds than did phenolic extracts from red rice bran, whether free (RFE) or bound fractions. This phytochemical content correlated with increased antioxidant activity and strong inhibition capacity against amylolytic enzymes, suppressing the conversion of carbohydrates into glucose. Several polyphenol compounds were identified in pigmented rice bran extracts, including benzoic acid, chlorogenic acid, ferulic acid, apigenin, and rutin; among these, flavonoids exhibited greater effect on inhibition capacity. Mechanistically, PFE was found to act as a competitive and uncompetitive inhibitor of α-amylase and α-glucosidase respectively, while RFE showed respective uncompetitive and competitive inhibitory modes.

Cellular and Biophysical Applications of Genetic Code Expansion

Despite their diverse functions, proteins are inherently constructed from a limited set of building blocks. These compositional constraints pose significant challenges to protein research and its practical applications. Strategically manipulating the cellular protein synthesis system to incorporate novel building blocks has emerged as a critical approach for overcoming these constraints in protein research and application. In the past two decades, the field of genetic code expansion (GCE) has achieved significant advancements, enabling the integration of numerous novel functionalities into proteins across a variety of organisms. This technological evolution has paved the way for the extensive application of genetic code expansion across multiple domains, including protein imaging, the introduction of probes for protein research, analysis of protein-protein interactions, spatiotemporal control of protein function, exploration of proteome changes induced by external stimuli, and the synthesis of proteins endowed with novel functions. In this comprehensive Review, we aim to provide an overview of cellular and biophysical applications that have employed GCE technology over the past two decades.

Potential molecular mechanism of reuterin on the inhibition of Aspergillus flavus conidial germination: An in silico study

Reuterin is a natural antifungal agent derived from certain strains of Limosilactobacillus reuteri. Our previous study revealed that 6 mM reuterin inhibited completely the conidial germination of aflatoxigenic Aspergillus flavus. This study investigated the potential molecular mechanism of reuterin in inhibiting A. flavus conidial germination, which was pre-assumed that it correlated to the inhibition of some essential enzyme activity involved in conidial germination, specifically 1,3-β-glucan synthase, chitin synthase, and catalases (catalase, bifunctional catalase-peroxidase, and spore-specific catalase). The complex of 1,3-β-glucan synthase and chitin synthase with reuterin had a lower binding affinity than that with the substrate. Conversely, the complex of catalases with reuterin had a higher binding affinity than that with the substrate. It was suggested that 1,3-β-glucan synthase and chitin synthase tended to bind the substrate rather than bind reuterin. In contrast, catalases tended to bind reuterin rather than bind the substrate. Therefore, reuterin could be a potential inhibitor of catalases but may not be an inhibitor of 1,3-β-glucan synthase and chitin synthase. In this in silico study, we predicted that the potential molecular mechanism of reuterin in inhibiting A. flavus conidial germination was due to the inhibition of catalases activities by competitively binding to the enzymes active sites, thus resulting in the accumulation of reactive oxygen species in cells, leading to cells damage. PRACTICAL APPLICATION: This in silico study revealed that reuterin is a potential inhibitor of catalases in A. flavus, thereby interfering with the antioxidant system during conidial germination. This finding shows that reuterin can be used as an antifungal agent in food or agricultural products, inhibiting conidial germination completely.

Exploration of the structural mechanism of hydrogen (H2)-promoted horseradish peroxidase (HRP) activity via multiple spectroscopic and molecular dynamics simulation techniques

Horseradish peroxidase (HRP) is an enzyme that is widely used in various fields. In this study, the effects of molecular hydrogen (H2) on the activity and structural characteristics of HRP were investigated by employing multiple spectroscopic techniques, atomic force microscopy (AFM) and molecular dynamics (MD) simulations. The results demonstrated that H2 could enhance HRP activity, especially in 1.5 mg/L hydrogen-rich water (HRW). The structural analysis results showed that H2 might alter HRP activity by affecting the active sites, secondary structure, hydrogen bonding network, CS groups, and morphological characteristics. The MD results also confirmed that H2 could increase the FeN bond distance in the active site, affect the secondary structure, and increase the number of hydrogen bonds. The MD results further suggested that H2 could increase the number of salt bridges, and lengthen the SS bonds in HRP. This study primarily revealed the mechanism by which H2 enhances the HRP activity, providing insight into the interactions between gas and macromolecular proteins. However, some of the results obtained via MD simulations still need to be verified experimentally. In addition, our study also provided a new convenient strategy to enhance enzyme activity.

Artificial Intelligence Aided Lipase Production and Engineering for Enzymatic Performance Improvement

With the development of artificial intelligence (AI), tailoring methods for enzyme engineering have been widely expanded. Additional protocols based on optimized network models have been used to predict and optimize lipase production as well as properties, namely, catalytic activity, stability, and substrate specificity. Here, different network models and algorithms for the prediction and reforming of lipase, focusing on its modification methods and cases based on AI, are reviewed in terms of both their advantages and disadvantages. Different neural networks coupled with various algorithms are usually applied to predict the maximum yield of lipase by optimizing the external cultivations for lipase production, while one part is used to predict the molecule variations affecting the properties of lipase. However, few studies have directly utilized AI to engineer lipase by affecting the structure of the enzyme, and a set of research gaps needs to be explored. Additionally, future perspectives of AI application in enzymes, including lipase engineering, are deduced to help the redesign of enzymes and the reform of new functional biocatalysts. This review provides a new horizon for developing effective and innovative AI tools for lipase production and engineering and facilitating lipase applications in the food industry and biomass conversion.