AI-driven de novo enzyme design: Strategies, applications, and future prospects

Enzymes are indispensable for biological processes and diverse applications across industries. While top-down modification strategies, such as directed evolution, have achieved remarkable success in optimizing existing enzymes, bottom-up de novo enzyme design has emerged as a transformative approach for engineering novel enzymes with customized catalytic functions, independent of natural templates. Recent advancements in artificial intelligence (AI) and computational power have significantly accelerated this field, enabling breakthroughs in enzyme engineering. These technologies facilitate the rapid generation of enzyme structures and amino acid sequences optimized for specific functions, thereby enhancing design efficiency. They also support functional validation and activity optimization, improving the catalytic performance, stability, and robustness of de novo designed enzymes. This review highlights recent advancements in AI-driven de novo enzyme design, discusses strategies for validation and optimization, and examines the challenges and future prospects of integrating these technologies into enzyme development.

Empowering Protein Engineering through Recombination of Beneficial Substitutions

Directed evolution stands as a seminal technology for generating novel protein functionalities, a cornerstone in biocatalysis, metabolic engineering, and synthetic biology. Today, with the development of various mutagenesis methods and advanced analytical machines, the challenge of diversity generation and high-throughput screening platforms is largely solved, and one of the remaining challenges is: how to empower the potential of single beneficial substitutions with recombination to achieve the epistatic effect. This review overviews experimental and computer-assisted recombination methods in protein engineering campaigns. In addition, integrated and machine learning-guided strategies were highlighted to discuss how these recombination approaches contribute to generating the screening library with better diversity, coverage, and size. A decision tree was finally summarized to guide the further selection of proper recombination strategies in practice, which was beneficial for accelerating protein engineering.

Sustainable isomaltulose production in Corynebacterium glutamicum by engineering the thermostability of sucrose isomerase coupled with one-step simplified cell immobilization

Sucrose isomerase (SI), catalyzing sucrose to isomaltulose, has been widely used in isomaltulose production, but its poor thermostability is still resisted in sustainable batches production. Here, protein engineering and one-step immobilized cell strategy were simultaneously coupled to maintain steady state for long-term operational stabilities. First, rational design of Pantoea dispersa SI (PdSI) for improving its thermostability by predicting and substituting the unstable amino acid residues was investigated using computational analysis. After screening mutagenesis library, two single mutants (PdSIV280L and PdSIS499F) displayed favorable characteristics on thermostability, and further study found that the double mutant PdSIV280L/S499F could stabilize PdSIWT better. Compared with PdSIWT, PdSIV280L/S499F displayed a 3.2°C-higher T m , and showed a ninefold prolonged half-life at 45°C. Subsequently, a one-step simplified immobilization method was developed for encapsulation of PdSIV280L/S499F in food-grade Corynebacterium glutamicum cells to further enhance the recyclability of isomaltulose production. Recombinant cells expressing combinatorial mutant (RCSI2) were successfully immobilized in 2.5% sodium alginate without prior permeabilization. The immobilized RCSI2 showed that the maximum yield of isomaltulose by batch conversion reached to 453.0 g/L isomaltulose with a productivity of 41.2 g/l/h from 500.0 g/L sucrose solution, and the conversion rate remained 83.2% after 26 repeated batches.

Towards a comprehensive understanding of malathion degradation: comparison of degradation reactions under alkaline and radical conditions

Malathion is a commercially available insecticide that functions by acting as an acetylcholinesterase inhibitor. Of significant concern, if left in the environment, some of the products observed from the degradation of malathion can function as more potent toxins than the parent compound. Accordingly, there are numerous studies revolving around possible degradation strategies to remove malathion from various environmental media. One of the possible approaches is the degradation of malathion by OH˙ radicals which could be produced from both artificial and biological means in the environment. While there is plenty of evidence that OH˙ does in fact degrade malathion, there is little understanding of the underlying mechanism by which OH˙ reacts with malathion. Moreover, it is not known how competitive the radical degradation pathway is with analogous alkaline degradation pathways. Even less is known about the reaction of additional OH˙ radicals with the degradation byproducts themselves. Herein, we demonstrate that OH˙ induced degradation pathways have variable competitiveness with OH^- driven degradation pathways and, in some cases, produce quite different reactivity.

Towards a comprehensive understanding of malathion degradation: theoretical investigation of degradation pathways and related kinetics under alkaline conditions

Malathion is a commercially available insecticide that functions by acting as an acetylcholinesterase inhibitor. Of more significant concern, if left in the environment, some of the products observed from the degradation of malathion can function as more potent toxins than the parent compound. These compounds may threaten human life if they are present in high quantities during operation in contaminated or industrial areas. Several experimental studies have been performed to elucidate the possible degradation products of malathion under various conditions to probe both the application of potential remediation methods and the environmental fate of the degradation products. However, only limited computational studies have been reported to delineate the mechanism by which malathion degrades under environmental conditions and how these degradation mechanisms are intertwined with one another. Herein, M06-2X DFT computations were employed to develop comprehensive degradation pathways from the parent malathion compound to a multitude of experimentally observed degradation products. These data corroborate experimental observations that multiple degradation pathways (ester hydrolysis and elimination) are in competition with each other, and the end-products can therefore be influenced by environmental factors such as temperature. Furthermore, the products resulting from any of the initial degradation pathways (ester hydrolysis, elimination, or P-S hydrolysis) can continue to degrade under the same conditions into compounds that are also reported to be toxic.

Mechanisms of deleterious effects of some pesticide exposure on pigs

The increase in the size of the global population increases the food and energy demand, making the use of pesticides in agricultural and livestock industries unavoidable. Exposure to pesticides can be toxic to the non-target species, such as humans, wildlife, and livestock, in addition to the target organisms. Various chemicals are used in the livestock industry to control harmful organisms, such as insects, weeds, and parasites. Pigs are one of the most important food sources for humans. In addition, pigs can be used as promising models for assessing the risk of absorption of environmental pollutants through the skin and oral exposure since they are physiologically similar to humans. Exposure to numerous environmental pollutants, such as mycotoxins, persistent organic pollutants, and heavy metals, has been reported to adversely affect growth, fertility, and endocrine homeostasis in pigs. Various pesticides have been observed in porcine tissues, blood, urine, and processed foods; however, there is a lack of comprehensive understanding of their effects on porcine health. This review provides a comprehensive description of the characteristics of pesticides that pigs can be exposed to and how their exposure affects porcine reproductive function, intestinal health, and endocrine homeostasis in vivo and in vitro.

Organophosphorus poisoning in animals and enzymatic antidotes

Organophosphorus compounds (OPs) are neurotoxic molecules developed as pesticides and chemical warfare nerve agents (CWNAs). Most of them are covalent inhibitors of acetylcholinesterase (AChE), a key enzyme in nervous systems, and are therefore responsible for numerous poisonings around the world. Many animal models have been studied over the years in order to decipher the toxicity of OPs and to provide insights for therapeutic and decontamination purposes. Environmental impact on wild animal species has been analyzed to understand the consequences of OP uses in agriculture. In complement, various laboratory models, from invertebrates to aquatic organisms, rodents and primates, have been chosen to study chronic and acute toxicity as well as neurobehavioral impact, immune response, developmental disruption, and other pathological signs. Several decontamination approaches were developed to counteract the poisoning effects of OPs. Among these, enzyme-based strategies are particularly attractive as they allow efficient external decontamination without toxicity or environmental impact and may be of interest for treatment. Approaches using bioscavengers for prophylaxis, treatment, and external decontamination are emphasized and their potential is discussed in the light of toxicological observations from various animal models. The relevance of animal models, regarding their cholinergic system and the abundance of naturally protecting enzymes, is also discussed for better extrapolation of results to human.

Recent advances and future prospective of organophosphorus-degrading enzymes: identification, modification, and application

The organophosphorus-based OPs) nerve agents and pesticides have been applied in the agriculture industry for a long time. However, they were found to have a persistent effect on the environment and threaten human health. Traditional methods, including incineration and landfilling, could not thoroughly remove these organophosphorus compounds (OPs). Meanwhile, chemical hydrolysis for decontamination was also inhibited due to the presence of corrosive materials and high costs. Biological remediation for OPs employing microorganisms and organophosphorus-degrading enzymes is promising due to a mild and controllable procedure, environmental-friendly reactions, and high efficacy. A wide variety of enzymes have shown latent ability in degrading OPs hazards like organophosphorus hydrolase (OPH), organophosphorus acid anhydrolase (OPAA), the diisopropylfluorophosphatase (DFPase), and mammalian paraoxonase 1 (PON 1). To this end, increasing efforts have been made on these intriguing enzymes to increase their expression level, enhance the catalytic activity, modify the optimal substrate, and expand the practical application. In this review, the enzyme resource, crystal structure, molecular modification, and industry application were compared and discussed in detail. Moreover, the proposed ideas and positive results could be useful for the other relevant OPs-degrading enzymes.

Paper-Based Enzymatic Colorimetric Assay for Rapid Malathion Detection

Due to their unique properties, paper-based biosensors have attracted attention as inexpensive devices for on-site analysis. To achieve fast and sensitive detection of analytes, immobilization of enzymes with high apparent activities on paper is highly desirable; however, this is challenging. Herein, we report an improved approach to attach a malathion degrading enzyme, PoOPH_M9, on paper via an interlocking network of Pluronic F127 (PF127)-poly(acrylic acid)-enzyme conjugates. The addition of PF127 improved retention of enzymatic activity as the apparent kinetic constant V_max of the immobilized enzyme increased two-fold compared with the paper prepared without PF127. The PF127-poly(acrylic acid)-PoOPH_M9 papers provided rapid colorimetric detection of malathion at 0.1-50 mM. The detection was completed within 5 min using a smartphone and image analysis software. As a proof-of-concept, malathion-contaminated water, plant, and apple samples were analyzed with the papers successfully. This material is promising for on-site rapid analysis of malathion-contaminated samples.

Statistical noise from recombinant plasmids can be abated via complementation of a ribosomal protein gene deletion

The phenotypes conferred by recombinant plasmids upon host cells often exhibit variability between replicate populations. This statistical noise is mostly a consequence of adaptive evolution in response to fitness burdens imposed by the plasmids themselves. We developed a novel strategy, 'ribosome pegging', to exclude common unwanted mutations that benefit host cells at the expense of heterologous gene expression. Plasmids that constitutively co-expressed the fluorescent reporter tagRFP and ribosomal protein L23 (rplW) were used to transform Escherichia coli cells that lacked the essential chromosomal rplW gene. Cells within the population that expressed too little L23, or too much, were evidently inviable. Ribosome pegging obviates the need for antibiotics, thus facilitating the deployment of recombinant bacteria in uncontrolled environments. We show that ribosome-pegged E. coli carrying a plasmid that constitutively expresses L23 and an artificially evolved enzyme protects fruit flies from otherwise toxic doses of the insecticide malathion.

Simple Purification and Immobilization of His-Tagged Organophosphohydrolase from Cell Culture Supernatant by Metal Organic Frameworks for Degradation of Organophosphorus Pesticides

Coordinating unsaturated metal sites (CUS) on the surface of metal-organic frameworks (MOFs) could be used to adsorb His-tagged proteins. The specific adsorption between CUS and His-tagged proteins could reduce preparation steps, shorten preparation time, and could also avoid the binding between the metal ion of metalloenzyme active center and the chelating agent to ensure the enzyme activity. In this study, MIL-88A was synthesized by hydrothermal method and used to purify and immobilize His-tagged organophosphohydrolase (OpdA) in one step for organophosphate bioremediation. Under optimized conditions, OpdA@MIL-88A had a maximal activity of 1554 U/g_protein, which was nearly 5 times higher than free OpdA. Compared with free OpdA, OpdA@MIL-88A exhibited improved organic solvent tolerance, SDS tolerance, thermal stability, and storage stability. OpdA@MIL-88A was used to degrade organophosphorus pesticides on grapes and cucumbers. After reuse 6 times, OpdA@MIL-88A retained more than 66% and 61% of the initial activity, respectively. Therefore, this proposed strategy provided a facile and effective method for degradation of organophosphorus pesticides.

A comprehensive review on enzymatic degradation of the organophosphate pesticide malathion in the environment

A comprehensive review of available bioremediation technologies for the pesticide malathion is presented. This review article describes the usage and consequences of malathion in the environment, along with a critical discussion on modes of metabolism of malathion as a sole source of carbon, phosphorus, and sulfur for bacteria, and fungi along with the biochemical and molecular aspects involved in its biodegradation. Additionally, the recent approaches of genetic engineering are discussed for the manipulation of important enzymes and microorganisms for enhanced malathion degradation along with the challenges that lie ahead.

[Organophosphorus poisoning: Towards enzymatic treatments]

Organophosphorus compounds (OP) are toxic molecules developed as insecticides and chemical warfare nerve agents (CWNAs). Most OP are neurotoxic and act as nervous system disruptors by blocking cholinergic transmission. They are therefore responsible for many poisonings worldwide. OP toxicity may result either from acute or chronic exposure, and their poisoning effect were evaluated using several animal models. These latter were also used for evaluating the efficacy of antidotes. Strategies based on enzymes that can trap (stoichiometric bioscavengers) or degrade (catalytic bioscavengers) OP, were particularly studied since they allow effective decontamination, without toxicity or environmental impact. This review summarizes the results obtained in vivo with enzymes through three levels: prophylaxis, treatment and external decontamination. The efficiency of enzymatic treatments in different animal models is presented and the relevance of these models is also discussed for a better extrapolation to humans.

Toxic effects and possible mechanisms following malathion exposure in porcine granulosa cells

Malathion is a wide spectrum organophosphorothionate insecticide that is frequently found in drinking water, food and foodstuffs. Ovarian granulosa cells modulate oogenesis by providing metabolic nutrients to oocytes. They can decide the fate of folliculogenesis and oocyte maturation by supplying regulatory cues that help in reproduction. However, little is known about the underlying mechanisms of malathion as a reproductive toxicant in porcine granulosa cells. In the present study, we found that malathion has obvious toxic effects on cultured porcine granulosa cells in a dose-dependent manner. Malathion exposure resulted in significantly increased oxidative stress levels and DNA damage response, which was measured by the mRNA expression levels of homologous recombination (HR) pathway and non-homologous end-joining (NHEJ) pathway-related genes. Subsequently, it was found that malathion exposure could induce apoptosis and autophagy by qRT-PCR and fluorescence intensity analysis. In conclusion, malathion is a reproductive toxicant by inhibiting granulosa cell proliferation by multiple pathways connected to oxidative stress, DNA damage, apoptosis and autophagy.

Identifying and engineering a critical amino acid residue to enhance the catalytic efficiency of Pseudomonas sp. methyl parathion hydrolase

Methyl parathion hydrolase (MPH) that hydrolyzes a wide range of organophosphorus pesticides can be used to remediate land polluted by the pesticides. Here, the catalytic efficiency of methyl parathion hydrolase from Pseudomonas sp. (WBC-3) was enhanced by searching and engineering a critical site far away from the binding pocket. In the first round, a four-site mutant with a modest increased catalytic efficiency (3.2-fold k_cat/K_m value of the wild type) was obtained with random mutagenesis. By splitting and re-combining the four substitutions in the mutant, the critical site S277, was identified to show the most significant effects of improving binding affinity and catalytic efficiency. With further site-saturation mutagenesis focused on the residue S277, another two substitutions were discovered to have even more significant decrease in K_m (40.2 and 47.6 μM) and increased in k_cat/K_m values (9.5- and 10.3-fold of the wild type) compared to the original four-site mutant (3.0- and 3.2-fold). In the three-dimensional structure, residue S277 is located at a hinge region of a loop, which could act as a "lid" at the substrate entering to the binding pocket. This suggests that substitutions of residue S277 could affect substrate binding via conformational change in substrate entrance region. This work provides a valuable protocol combining random mutagenesis, site-saturation mutagenesis, structural and bioinformatics analyses to obtain mutants with high catalytic efficiency from a screening library of a modest size (3200 strains).

Enhancing fructosylated chondroitin production in Escherichia coli K4 by balancing the UDP-precursors

Microbial production of chondroitin and chondroitin-like polysaccharides from renewable feedstock is a promising and sustainable alternative to extraction from animal tissues. In this study, we attempted to improve production of fructosylated chondroitin in Escherichia coli K4 by balancing intracellular levels of the precursors UDP-GalNAc and UDP-GlcA. To this end, we deleted pfkA to favor the production of Fru-6-P. Then, we identified rate-limiting enzymes in the synthesis of UDP-precursors. Third, UDP-GalNAc synthesis, UDP-GlcA synthesis, and chondroitin polymerization were combinatorially optimized by altering the expression of relevant enzymes. The ratio of intracellular UDP-GalNAc to UDP-GlcA increased from 0.17 in the wild-type strain to 1.05 in a 30-L fed-batch culture of the engineered strain. Titer and productivity of fructosylated chondroitin also increased to 8.43 g/L and 227.84 mg/L/h; the latter represented the highest productivity level achieved to date.

FoldX as Protein Engineering Tool: Better Than Random Based Approaches?

Improving protein stability is an important goal for basic research as well as for clinical and industrial applications but no commonly accepted and widely used strategy for efficient engineering is known. Beside random approaches like error prone PCR or physical techniques to stabilize proteins, e.g. by immobilization, in silico approaches are gaining more attention to apply target-oriented mutagenesis. In this review different algorithms for the prediction of beneficial mutation sites to enhance protein stability are summarized and the advantages and disadvantages of FoldX are highlighted. The question whether the prediction of mutation sites by the algorithm FoldX is more accurate than random based approaches is addressed.

Efficient Degradation of Malathion in the Presence of Detergents Using an Engineered Organophosphorus Hydrolase Highly Expressed by Pichia pastoris without Methanol Induction

The biodegradation of pesticides by organophosphorus hydrolases (OPHs) requires an efficient enzyme production technology in industry. Herein, a Pichia pastoris strain was constructed for the extracellular expression of PoOPH_M9, an engineered malathion-degrading enzyme. After optimization, the maximum titer and yield of fermentation reached 50.8 kU/L and 4.1 g_protein/L after 3 days, with the highest space-time yield (STY) reported so far, 640 U L^-1 h^-1. PoOPH_M9 displayed its high activity and stability in the presence of 0.1% (w/w) plant-derived detergent. Only 0.04 mg/mL enzyme could completely remove 0.15 mM malathion in aqueous solution within 20 min. Furthermore, 12 μmol malathion on apples and cucumbers surfaces was completely removed by 0.05 mg/mL PoOPH_M9 in tap water after 35 min washing. The efficient production of the highly active PoOPH_M9 has cleared a major barrier to biodegradation of pesticide residues in food industry.

Biocatalysts for the pharmaceutical industry created by structure-guided directed evolution of stereoselective enzymes

Enzymes have been used for a long time as catalysts in the asymmetric synthesis of chiral intermediates needed in the production of therapeutic drugs. However, this alternative to man-made catalysts has suffered traditionally from distinct limitations, namely the often observed wrong or insufficient enantio- and/or regioselectivity, low activity, narrow substrate range, and insufficient thermostability. With the advent of directed evolution, these problems can be generally solved. The challenge is to develop and apply the most efficient mutagenesis methods which lead to highest-quality mutant libraries requiring minimal screening. Structure-guided saturation mutagenesis and its iterative form have emerged as the method of choice for evolving stereo- and regioselective mutant enzymes needed in the asymmetric synthesis of chiral intermediates. The number of (industrial) applications in the preparation of chiral pharmaceuticals is rapidly increasing. This review features and analyzes typical case studies.

Engineering 7β-Hydroxysteroid Dehydrogenase for Enhanced Ursodeoxycholic Acid Production by Multiobjective Directed Evolution

Ursodeoxycholic acid (UDCA) is the main active ingredient of natural bear bile powder with multiple pharmacological functions. 7β-Hydroxysteroid dehydrogenase (HSDH) is a key biocatalyst for the synthesis of UDCA. However, all the 7β-HSDHs reported commonly suffer from poor activity and thermostability, resulting in limited productivity of UDCA. In this study, a multiobjective directed evolution (MODE) strategy was proposed and applied to improve the activity, thermostability, and pH optimum of a 7β-HSDH. The best variant (V_3-1) showed a specific activity 5.5-fold higher than and a half-life 3-fold longer than those of the wild type. In addition, the pH optimum of the variant was shifted to a weakly alkaline value. In the cascade reaction, the productivity of UDCA with V_3-1 increased to 942 g L^-1 day^-1, in contrast to 141 g L^-1 day^-1 with the wild type. Therefore, this study provides a useful strategy for improving the catalytic efficiency of a key enzyme that significantly facilitated the bioproduction of UDCA.