Biochemical characterization and molecular docking analysis of novel esterases from Sphingobium chungbukense DJ77

Enhancing catalytic efficiency of two microbial uricases making by directed evolution

Uricase is a key enzyme in purine metabolism that catalyzes the oxidation of uric acid to allantoin, widely used in the treatment of hyperuricemia and gout. In this study, error-prone PCR and one high-throughput screening method were employed to generate uricase mutants with enhanced enzymatic activity from Aspergillus flavus and Candida utilis. After several rounds of mutation and selection, an A. flavus uricase mutant, af-UAM, with activity of 46.21 U/mg, and a C. utilis uricase mutant, cu-UAM, with activity of 31.43 U/mg, were obtained-representing the highest uricase activities reported up to date. Site-directed mutagenesis revealed that the Thr231Ala substitution in A. flavus uricase and the Val234Met substitution in C. utilis uricase were key factors driving their enhanced activities. Furthermore, in vivo experiments demonstrated significant clinical potential of these mutants. These findings offer new insights into the structure-function relationship of uricase and present promising candidates for therapeutic applications in hyperuricemia treatment.

Structural Insights into Cold-Active Lipase from Glaciozyma antarctica PI12: Alphafold2 Prediction and Molecular Dynamics Simulation

Cold-active enzymes have recently gained popularity because of their high activity at lower temperatures than their mesophilic and thermophilic counterparts, enabling them to withstand harsh reaction conditions and enhance industrial processes. Cold-active lipases are enzymes produced by psychrophiles that live and thrive in extremely cold conditions. Cold-active lipase applications are now growing in the detergency, synthesis of fine chemicals, food processing, bioremediation, and pharmaceutical industries. The cold adaptation mechanisms exhibited by these enzymes are yet to be fully understood. Using phylogenetic analysis, and advanced deep learning-based protein structure prediction tool Alphafold2, we identified an evolutionary processes in which a conserved cold-active-like motif is presence in a distinct subclade of the tree and further predicted and simulated the three-dimensional structure of a putative cold-active lipase with the cold active motif, Glalip03, from Glaciozyma antarctica PI12. Molecular dynamics at low temperatures have revealed global stability over a wide range of temperatures, flexibility, and the ability to cope with changes in water and solvent entropy. Therefore, the knowledge we uncover here will be crucial for future research into how these low-temperature-adapted enzymes maintain their overall flexibility and function at lower temperatures.

Paeoniflorin-mediated downregulation of VEGFA: unveiling the therapeutic mechanism of buyang huanwu decoction in diabetic retinopathy

Diabetic retinopathy (DR) is a leading cause of blindness globally. Buyang Huanwu decoction (BHD) is a traditional Chinese medicine for treating DR, but its therapeutic mechanisms are not fully understood. This study aimed to elucidate and validate the underlying mechanisms of BHD in DR treatment through network pharmacology and in vitro experiments. We identified active compounds in BHD and their associated targets using the TCMSP and SwissTargetPrediction. DR-related targets were sourced from GeneCards, NCBI, and OMIM databases. The protein-protein interaction (PPI) network and enrichment analyses were employed to predict common targets and pathways. Subsequent molecular docking and in vitro experiments, including cell viability assays, RT-qPCR, flow cytometry, and Western blot, were conducted to validate the anti-DR mechanism of BHD. Network pharmacology identified paeoniflorin as a key active compound in BHD for treating DR, with VEGFA emerging as a central target. Molecular docking suggested a strong binding affinity between paeoniflorin and VEGFA. In vitro experiments confirmed that paeoniflorin attenuated high glucose-induced increases in cell viability, migration, apoptosis, and inflammatory cytokine expression in retinal pigment epithelial cells. The therapeutic effect of paeoniflorin was primarily mediated through the downregulation of VEGFA expression. Our study demonstrates that paeoniflorin, a key active compound in BHD, effectively mitigates DR by downregulating VEGFA expression and reducing high glucose-induced cellular alterations, thereby highlighting its potential as a therapeutic agent for DR.

Targeted blocking of EGFR and GLUT1 by compound H reveals a new strategy for treatment of triple-negative breast cancer and nasopharyngeal carcinoma

BACKGROUND

Cytoplasmic epidermal growth factor receptor (EGFR) is overexpressed in both nasopharyngeal carcinoma (NPC) and triple-negative breast cancer (TNBC), while clinical outcome and prognosis vary greatly among patients treated with gefitinib, and all patients eventually develop resistance to this agent. Therefore, we propose a new concept for synthesizing multitarget compounds and reveal new therapeutic strategies for NPC and TNBC expressing EGFR.

METHODS

Compound H was synthesized in our previous study. Molecular docking, and cell thermal shift assays (CETSAs) and drug affinity responsive target stability(DARTS) were used to confirm the binding of compound H to EGFR and GLUT1. Methylthiazolyldiphenyl-tetrazolium bromide(MTT), annexin V-PE assays, mitochondrial membrane potential (MMP) assays, and animal models were used to evaluate the inhibitory effect of compound H on TNBC cell lines. Energy metabolism tests, Western blotting, and immunofluorescence staining were performed to evaluate the synergistic effects on EGFR- and glucose transporter type 1(GLUT1)-mediated energy metabolism.

RESULTS

Compound H can simultaneously act on the EGFR tyrosine kinase ATP-binding site and inhibit GLUT1-mediated energy metabolism, resulting in reductions in ATP, MMP, intra-cellular lactic acid, and EGFR nuclear transfer. The anti-tumor activity of compound H is significantly superior to the combination of GLUT1 inhibitor BAY876 and EGFR inhibitor gefitinib. Compound H has remarkable anti-proliferative effects on TNBC MDA-MB231 cells, and importantly, no obvious toxicity effects of compound H were found in vivo.

CONCLUSIONS

Synergistic effects of inhibition of EGFR- and GLUT1-mediated energy metabolism by compound H may present a new strategy for the treatment of TNBC and NPC.

Engineered Geobacillus lipolytic enzymes - Attractive polyesterases that degrade polycaprolactones and simultaneously produce esters

Plastic pollution is one of the biggest environmental problems plaguing the modern world. Polyester-based plastics contribute significantly to this ecological safety concern. In this study, lipolytic biocatalysts GD-95RM and GDEst-lip developed based on lipase/esterase produced by Geobacillus sp. 95 strain were applied for the degradation of polycaprolactone films (Mn 45.000 (PCL45000) and Mn 80.000 (PCL80000)). The degradation efficiency was significantly enhanced by the addition of short chain alcohols. Lipase GD-95RM (1 mg) can depolymerize 264.0 mg and 280.7 mg of PCL45000 and PCL80000, films respectively, in a 24 h period at 30 °C, while the fused enzyme GDEst-lip (1 mg) is capable of degrading 145.5 mg PCL45000 and 134.0 mg of PCL80000 films in 24 h. The addition of ethanol (25 %) improves the degradation efficiency ~2.5 fold in the case of GD-95RM. In the case of GDEst-lip, 50 % methanol was found to be the optimal alcohol solution and the degradation efficiency was increased by ~3.25 times. The addition of alcohols not only increased degradation speeds but also allowed for simultaneous synthesis of industrially valuable 6-hydroxyhexonic acid esters. The suggested system is an attractive approach for removing of plastic waste and supports the principles of bioeconomics.

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.

Fabrication, Characterization, and Emulsifying Properties of Complex Based on Pea Protein Isolate / Pectin for the Encapsulation of Pterostilbene

In this study, pectin (PEC) and pea protein isolate(PPI) was successfully used to create complexes as a novel delivery system for pterostilbene (PT). When the mass ratio of PEC to PPI was 0.5, the particle size and ζ-potential of PPI-PEC-PT were 119.41 ± 5.68 nm and -23.26 ± 0.61 mV, respectively, and the encapsulation efficiency (EE) of PT was 90.92 ± 2.08%. The photochemical stability of PT was enhanced after encapsulation. The results of the molecular docking and multispectral analysis demonstrated that the PPI and PT binding was spontaneous and mostly fueled by hydrophobic interactions. The hydrophobicity of PPI was significantly decreased and the emulsification activity and emulsion stability were significantly improved after production with PEC and PT. The best emulsification impact was demonstrated by the PPI-PEC-PT complex. PPI-PEC is an effective PT delivery material, and the PPI-PEC-PT complex is a new functional emulsification material with significant potential in liquid and semi-liquid food and health products.

Cold-Active Lipases and Esterases: A Review on Recombinant Overexpression and Other Essential Issues

Cold environments characterised by diverse temperatures close to or below the water freezing point dominate about 80% of the Earth's biosphere. One of the survival strategies adopted by microorganisms living in cold environments is their expression of cold-active enzymes that enable them to perform an efficient metabolic flux at low temperatures necessary to thrive and reproduce under those constraints. Cold-active enzymes are ideal biocatalysts that can reduce the need for heating procedures and improve industrial processes' quality, sustainability, and cost-effectiveness. Despite their wide applications, their industrial usage is still limited, and the major contributing factor is the lack of complete understanding of their structure and cold adaptation mechanisms. The current review looked at the recombinant overexpression, purification, and recent mechanism of cold adaptation, various approaches for purification, and three-dimensional (3D) crystal structure elucidation of cold-active lipases and esterase.

Combining in silico and in vitro approaches to identify endogenous hypoglycemic peptides from human milk

Potential endogenous hypoglycemic peptides derived from breast milk were screened by in silico approaches against intestinal glucose absorption- and metabolism-related membrane proteins (i.e., SGLT1, ATPase, and GPR40), and their inhibitory...