A stepwise docking and molecular dynamics approach for enzymatic biolubricant production using Lipase Eversa® Transform as a biocatalyst

Cavalcante, Francisco Sales Ávila; Fonseca, Aluísio Marques da; Alexandre, Jeferson Yves Nunes Holanda; Santos, José Cleiton Sousa dos

doi:10.1016/j.indcrop.2022.115450

Cited by 35 publications

(20 citation statements)

References 78 publications

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“…rcsb.org/) while being able to handle the complexity and diversity of structured data. 44 When applying AI technology to enzyme engineering, an understanding of additional fields is also needed, e.g., molecular simulation, 56 synthetic biology, 133 residue interaction networks, 134 dynamics, 135,136 and other knowledge that needs to be involved. In molecular simulation, quantum mechanics/molecular mechanics (QM/MM) is considered to be an excellent method for simulating the mechanism of enzyme-catalyzed reactions.…”

Section: Lipase Modification and Predictionmentioning

confidence: 99%

Artificial Intelligence Aided Lipase Production and Engineering for Enzymatic Performance Improvement

Ge,

Chen,

Qian

et al. 2023

J. Agric. Food Chem.

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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.

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Section: Lipase Modification and Predictionmentioning

confidence: 99%

Artificial Intelligence Aided Lipase Production and Engineering for Enzymatic Performance Improvement

Ge,

Chen,

Qian

et al. 2023

J. Agric. Food Chem.

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“…This technology has greatly promoted the development of the pharmaceutical industry. Lipases can catalyze a series of reactions, including esterification, transesterification, ester polymerization, and amide synthesis, under mild reaction conditions without the need for harsh reaction conditions. − In drug synthesis, lipase catalysis relies on its high selectivity, including chiral, positional, and functional group specificity, which is also superior to that of traditional chemical catalysts. During the catalytic reaction, it can reduce the production of byproducts or even have no byproducts, especially in the process of catalyzing esterification, where the byproduct is only water, which not only avoids waste production but also facilitates the separation of the target product, thereby reducing environmental problems .…”

Section: Introductionmentioning

confidence: 99%

Application of Lipase B from Candida antarctica in the Pharmaceutical Industry

Wang,

Zhang,

et al. 2023

Ind. Eng. Chem. Res.

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The use of biocatalysts in pharmaceutical production is an important approach for the pharmaceutical industry to achieve green manufacturing. Compared to other lipases, Candida antarctica lipase B (CALB) possesses numerous excellent characteristics due to its unique structure. It exhibits relatively strong catalytic activity toward both water-insoluble and water-soluble substances. It shows high selectivity in hydrolysis and organic synthesis reactions. These properties are crucial for drug synthesis. However, current research shows that the use of CALB as a catalyst still faces challenges such as high cost, poor stability, and difficulty in large-scale production. Therefore, this paper mainly explores the advantages of CALB in the pharmaceutical industry and the challenges that still need to be overcome. It introduces the application progress of CALB in the pharmaceutical industry and finally provides a prospect for future research directions, hoping to provide appropriate references for related research.

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“…Application-driven enzyme engineering has shown great potential for industrial-scale implementation of challenging chemical reactions. Recent examples include applications of engineered lipases toward biofuel production − and enantiopure synthesis of important drug precursor molecules . Immobilization has been shown to further enhance the versatility of enzymes in industrial contexts. ,− Discovery and engineering of plastic degrading enzymes have shown that biodegradation of microplastics in the wastewater treatment system is a strategy with high potential for success .…”

Section: Introductionmentioning

confidence: 99%

Directed Immobilization of PETase on Mesoporous Silica Enables Sustained Depolymerase Activity in Synthetic Wastewater Conditions

Zurier

Goddard

2022

ACS Appl. Bio Mater.

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Microplastic accumulation in terrestrial and aquatic environments is a growing environmental challenge. Biodegradation has shown promise as an intervention strategy for reducing the spread of microplastics. The wastewater treatment system is a key intervention point in microplastic biodegradation due to its pivotal role in the water cycle at the interface between human activity and the environmental. However, the best characterized microplastic degradation enzyme, PETase, lacks the stability to perform at scale in wastewater treatment. In this work, we show that genetic fusion of PETase to a silica binding peptide enables directed immobilization of the enzyme onto silica nanoparticles. PETase activity in simulated wastewater conditions is quantified by linear regression from time zero to the time of maximum fluorescence of a fluorescent oxidized product of PETase degradation of PET microfibers. Mesoporous silica is shown to be a superior support material to nonporous silica. The resulting biocatalytic nanomaterial has up to 2.5-fold enhanced stability and 6.2-fold increased activity compared to free enzyme in unbuffered, 40 °C simulated influent (ionic strength ∼15 mM). In unbuffered, 40 °C simulated effluent (ionic strength ∼700 μM), reaction velocity and overall catalytic activity were increased by the biocatalytic material 2.1-fold relative to free PETase. All reactions were performed in 0.2 mL volumes, and enzyme concentrations were normalized across both free and immobilized samples to 9 μg/mL. Site-directed mutagenesis is shown to be a complementary technique to directed immobilization, which may aid in optimization of the biomaterial for wastewater applications. PETase stabilization in application-relevant environments as shown here enables progress toward application of PETase for microplastic biodegradation in wastewater treatment.

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A stepwise docking and molecular dynamics approach for enzymatic biolubricant production using Lipase Eversa® Transform as a biocatalyst

Cited by 35 publications

References 78 publications

Artificial Intelligence Aided Lipase Production and Engineering for Enzymatic Performance Improvement

Artificial Intelligence Aided Lipase Production and Engineering for Enzymatic Performance Improvement

Application of Lipase B from Candida antarctica in the Pharmaceutical Industry

Directed Immobilization of PETase on Mesoporous Silica Enables Sustained Depolymerase Activity in Synthetic Wastewater Conditions

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