One-Step Synthesis of 4-Octyl Itaconate through the Structure Control of Lipase

A general model for predicting enzyme functions based on enzymatic reactions

Accurate prediction of the enzyme comission (EC) numbers for chemical reactions is essential for the understanding and manipulation of enzyme functions, biocatalytic processes and biosynthetic planning. A number of machine leanring (ML)-based models have been developed to classify enzymatic reactions, showing great advantages over costly and long-winded experimental verifications. However, the prediction accuracy for most available models trained on the records of chemical reactions without specifying the enzymatic catalysts is rather limited. In this study, we introduced BEC-Pred, a BERT-based multiclassification model, for predicting EC numbers associated with reactions. Leveraging transfer learning, our approach achieves precise forecasting across a wide variety of Enzyme Commission (EC) numbers solely through analysis of the SMILES sequences of substrates and products. BEC-Pred model outperformed other sequence and graph-based ML methods, attaining a higher accuracy of 91.6%, surpassing them by 5.5%, and exhibiting superior F1 scores with improvements of 6.6% and 6.0%, respectively. The enhanced performance highlights the potential of BEC-Pred to serve as a reliable foundational tool to accelerate the cutting-edge research in synthetic biology and drug metabolism. Moreover, we discussed a few examples on how BEC-Pred could accurately predict the enzymatic classification for the Novozym 435-induced hydrolysis and lipase efficient catalytic synthesis. We anticipate that BEC-Pred will have a positive impact on the progression of enzymatic research.

4-octyl itaconate ameliorates alveolar macrophage pyroptosis against ARDS via rescuing mitochondrial dysfunction and suppressing the cGAS/STING pathway

Acute respiratory distress syndrome (ARDS) is a high-mortality pulmonary disorder characterized by an intense inflammatory response and a cytokine storm. As of yet, there is no proven effective therapy for ARDS. Itaconate, an immunomodulatory derivative accumulated during inflammatory macrophage activation, has attracted widespread attention for its potent anti-inflammatory and anti-oxidative properties. This study pointed to explore the protective impacts of 4-octyl itaconate (4-OI) on ARDS. The results showed that lung injury was attenuated markedly after 4-OI pre-treatment, as represented by decreased pulmonary edema, inflammatory cell infiltration, and production of inflammatory factors. LPS stimulation induced NLRP3-mediated pyroptosis in vitro and in vivo, as represented by the cleavage of gasdermin D (GSDMD), IL-18 and IL-1β release, and these changes could be prevented by 4-OI pretreatment. Mechanistically, 4-OI eliminated mitochondrial reactive oxygen species (mtROS) and mtDNA escaping to the cytosol through the opening mitochondrial permeability transition pore (mPTP) in alveolar macrophages (AMs) under oxidative stress. In addition, 4-OI pretreatment markedly downregulated cyclic GMP-AMP synthase (cGAS), stimulator of interferon genes (STING) expression, and interferon regulatory factor 3 (IRF3) phosphorylation in vitro and in vivo. Meanwhile, inhibition of STING/IRF3 pathway alleviated NLRP3-mediated pyroptosis induced by LPS in vitro. Taken together, this study indicated that 4-OI ameliorated ARDS by rescuing mitochondrial dysfunction and inhibiting NLRP3-mediated macrophage pyroptosis in a STING/IRF3-dependent manner, which further revealed the potential mechanism of itaconate in preventing inflammatory diseases.

Recent Advances on the Production of Itaconic Acid via the Fermentation and Metabolic Engineering

Itaconic acid (ITA) is one of the top 12 platform chemicals. The global ITA market is expanding due to the rising demand for bio-based unsaturated polyester resin and its non-toxic qualities. Although bioconversion using microbes is the main approach in the current industrial production of ITA, ecological production of bio-based ITA faces several issues due to: low production efficiency, the difficulty to employ inexpensive raw materials, and high manufacturing costs. As metabolic engineering advances, the engineering of microorganisms offers a novel strategy for the promotion of ITA bio-production. In this review, the most recent developments in the production of ITA through fermentation and metabolic engineering are compiled from a variety of perspectives, including the identification of the ITA synthesis pathway, the metabolic engineering of natural ITA producers, the design and construction of the ITA synthesis pathway in model chassis, and the creation, as well as application, of new metabolic engineering strategies in ITA production. The challenges encountered in the bio-production of ITA in microbial cell factories are discussed, and some suggestions for future study are also proposed, which it is hoped offers insightful views to promote the cost-efficient and sustainable industrial production of ITA.

Recent Advances in the Enzymatic Synthesis of Polyester

Polyester is a kind of polymer composed of ester bond-linked polybasic acids and polyol. This type of polymer has a wide range of applications in various industries, such as automotive, furniture, coatings, packaging, and biomedical. The traditional process of synthesizing polyester mainly uses metal catalyst polymerization under high-temperature. This condition may have problems with metal residue and undesired side reactions. As an alternative, enzyme-catalyzed polymerization is evolving rapidly due to the metal-free residue, satisfactory biocompatibility, and mild reaction conditions. This article presented the reaction modes of enzyme-catalyzed ring-opening polymerization and enzyme-catalyzed polycondensation and their combinations, respectively. In addition, the article also summarized how lipase-catalyzed the polymerization of polyester, which includes (i) the distinctive features of lipase, (ii) the lipase-catalyzed polymerization and its mechanism, and (iii) the lipase stability under organic solvent and high-temperature conditions. In addition, this article also focused on the advantages and disadvantages of enzyme-catalyzed polyester synthesis under different solvent systems, including organic solvent systems, solvent-free systems, and green solvent systems. The challenges of enzyme optimization and process equipment innovation for further industrialization of enzyme-catalyzed polyester synthesis were also discussed in this article.

Access to valuable building blocks by the regio- and enantioselective ring opening of itaconic anhydride by lipase catalysis

Herein, we report for the first time the highly regio- and enantioselective ring opening of a biobased itaconic anhydride catalyzed by the Pseudomonas cepacia lipase (PCL) in tert-butyl methyl ether (TBME) at room temperature. This method is easy, efficient and eco-friendly and can be performed in one step with a series of highly valuable monoester itaconates (achiral or enantioenriched) using various alcohols as nucleophiles with 100% atom economy. In all cases, the β-monoester isomer was the predominant product of the reaction. Using achiral primary alcohols as substrates, a variety of novel itaconates were obtained in moderate to excellent yields (50-90%). For select examples, product characterization was carried out using X-ray diffraction, in addition to the standard techniques. The application of this approach was performed for the preparation of enantioenriched 4-monoester itaconates via enzymatic kinetic resolution.

Immune-responsive gene 1 protects against liver injury caused by concanavalin A via the activation Nrf2/HO-1 pathway and inhibition of ROS activation pathways

Itaconate is produced by an enzyme encoded by the immune-responsive gene 1 (IRG1) and exerts antibacterial, anti-inflammatory, and antioxidant effects via multiple mechanisms. However, the role of IRG1/itaconate in liver injury caused by Concanavalin A (Con A) is not fully understood. In this study, we explored the therapeutic effect of IRG1/four-octyl itaconate (4-OI), a derivative of itaconate, on liver injury caused by Con A and its possible underlying mechanisms. In vivo experiments, we found that Con A promoted IRG1 expression in the liver tissue. Deletion of IRG1 in mice aggravated Con A-induced liver injury. Compared to wild-type (WT) mice, the inflammatory response, hepatocyte apoptosis, and serum cytokine levels were significantly increased, while the antioxidant capacity was significantly attenuated in IRG1^-/- mice. In addition, we found that Con A promoted the nucleotide-binding oligomerization domain-like receptor family pyrin domain-containing 3 inflammasome, caspase-1, and gasdermin D activation, and pyroptosis was more obvious in IRG1^-/- mice, while 4-OI inhibited pyroptosis. In vivo experiments showed that Con A promoted hepatocyte apoptosis by promoting reactive oxygen species (ROS) expression, and 4-OI reduced ROS-mediate apoptosis in NCTC 1469 cells. In RAW264.7 cells, we demonstrated that 4-OI inhibited the inflammatory response by promoting the nuclear factor erythroid 2 [NF-E2]-related factor 2 (Nrf2)/heme oxygenase-1 (HO-1) pathway and inhibiting the nuclear factor-kappa B (NF-κB)/mitogen-activated protein kinases signaling pathway. To further confirm that Nrf2 is the target of itaconate, we pretreated WT mice with ML385, an Nrf2 inhibitor, and found that ML385 could weaken the protection of 4-OI in Con A-induced liver injury mouse model. Furthermore, when we knocked down the Nrf2 gene in NCTC 1469 and RAW264.7 cells, the effect of 4-OI in inhibiting inflammation and apoptosis also decreased. In conclusion, our study shows the importance of IRG1 in inflammation and oxidative stress, and suggests that it plays a vital protective role in Con A-induced liver injury. These findings indicate IRG1/itaconate is a potential therapeutic strategy for immune liver injury, which requires further clinical exploration.