Rational enzyme design for enabling biocatalytic Baldwin cyclization and asymmetric synthesis of chiral heterocycles

Engineering catalytically promiscuous enzymes to serve new functions

Catalytic promiscuity in enzymes refers to their ability to catalyze multiple chemically distinct reactions in addition to their native activity. The increasing discovery of additional enzymes exhibiting catalytic promiscuity has underscored the significance of this trait in nature. The catalytic promiscuity of enzymes offers new avenues for functional redesign. Through protein engineering, existing enzymes can be modified to expand their natural catalytic boundaries. Furthermore, de novo designed artificial enzymes can achieve novel enzymatic reactions, broadening the scope of enzyme-catalyzed applications. Given that catalytic promiscuity plays a fundamental role in enzyme evolution, comprehensive research on its origins and influencing factors is essential. In this review, we comprehensively examine the factors influencing catalytic promiscuity, including variations in substrate binding modes in pre-reaction states, the instability of key high-energy intermediates, and the roles of critical residues in catalytic mechanisms. Moreover, altering the enzyme's catalytic environment can also induce novel types of catalytic reactions, such as light-induced promiscuous reactions catalyzed by cofactor-dependent oxidoreductase enzymes. Additionally, we summarize the current protein engineering technologies and strategies aimed at enhancing the activity and stereoselectivity of target enzymes to meet industrial requirements.

Machine-Learning-Aided Engineering Hemoglobin as Carbene Transferase for Catalyzing Enantioselective Olefin Cyclopropanation

In this study, we developed a machine-learning-aided protein design strategy for engineering Vitreoscilla hemoglobin (VHb) as carbene transferase. A Natural Language Processing (NLP) model was used for the first time to construct an algorithm (EESP, enzyme enantioselectivity score predictor) and predict the enantioselectivity of VHb. We identified critical amino acid residue sites by molecular docking and established a simplified mutation library by site-saturated mutagenesis. Based on the simplified mutant library, the trianed EESP scored 160,000 virtual mutants, and 15 predicted high-score mutants were chosen for experimental validation. Among these mutants, VHb-WK (Y29W/P54K) demonstrated the highest diastereoselectivity and enantioselectivity of carbene transferase for the olefin cyclopropanation in aqueous conditions. Subsequently, molecular dynamics simulations were performed to explore the interaction between protein and substrates, finding that the high enantioselectivity of VHb-WK stems from the interactions of R47, Q53, and K84, which narrows the entrance of the enzyme's pocket, favoring the restriction of the formation of reaction intermediates. Integrating the NLP model and enzyme modification offers significant advantages by reducing economic costs and workloads associated with the protein engineering process.

Semi-rational design and modification of phosphoketolase to improve the yield of tyrosol in Saccharomyces cerevisiae

Tyrosol is an important component of pharmaceuticals, nutraceuticals, and cosmetics, and their biosynthetic pathways are currently a hot research topic. d-Erythrose 4-phosphate is a key precursor for the biosynthesis of tyrosol in Saccharomyces cerevisiae. Hence, the flux of d-Erythrose 4-phosphate determined the yield of tyrosol synthesis. In this study, we first obtained an S. cerevisiae strain S19 with a tyrosol yield of 247.66 mg/L by metabolic engineering strategy. To increase the production of d-Erythrose 4-phosphate, highly active phosphoketolase BA-C was obtained by bioinformatics combined with tyrosol yield assay. The key residue sites 183, 217, and 320 were obtained by molecular docking, kinetic simulation, and tyrosol yield verification. After mutation, the highly efficient phosphoketolase BA-CHis320Met was obtained, with a 37.32 % increase in enzyme activity. The tyrosol production of strain S26 with BA-CHis320Arg increased by 43.05 % than strain S25 with BA-C and increased by 151.19 % compared with the strain S19 without phosphoketolase in a 20 L fermenter. The mining and modification of phosphoketolase will provide strong support for the de novo synthesis of aromatic compounds.

Rational enzyme design by reducing the number of hotspots and library size

Biocatalysts that are eco-friendly, sustainable, and highly specific have great potential for applications in the production of fine chemicals, food, detergents, biofuels, pharmaceuticals, and more. However, due to factors such as low activity, narrow substrate scope, poor thermostability, or incorrect selectivity, most natural enzymes cannot be directly used for large-scale production of the desired products. To overcome these obstacles, protein engineering methods have been developed over decades and have become powerful and versatile tools for adapting enzymes with improved catalytic properties or new functions. The vastness of the protein sequence space makes screening a bottleneck in obtaining advantageous mutated enzymes in traditional directed evolution. In the realm of mathematics, there are two major constraints in the protein sequence space: (1) the number of residue substitutions (M); and (2) the number of codons encoding amino acids as building blocks (N). This feature review highlights protein engineering strategies to reduce screening efforts from two dimensions by reducing the numbers M and N, and also discusses representative seminal studies of rationally engineered natural enzymes to deliver new catalytic functions.

Stereodivergent Total Synthesis of Tacaman Alkaloids

This paper describes a concise, asymmetric and stereodivergent total synthesis of tacaman alkaloids. A key step in this synthesis is the biocatalytic Baeyer-Villiger oxidation of cyclohexanone, which was developed to produce seven-membered lactones and establish the required stereochemistry at the C14 position (92 % yield, 99 % ee, 500 mg scale). Cis- and trans-tetracyclic indoloquinolizidine scaffolds were rapidly synthesized through an acid-triggered, tunable acyl-Pictet-Spengler type cyclization cascade, serving as the pivotal reaction for building the alkaloid skeleton. Computational results revealed that hydrogen bonding was crucial in stabilizing intermediates and inducing different addition reactions during the acyl-Pictet-Spengler cyclization cascade. By strategically using these two reactions and the late-stage diversification of the functionalized indoloquinolizidine core, the asymmetric total syntheses of eight tacaman alkaloids were achieved. This study may potentially advance research related to the medicinal chemistry of tacaman alkaloids.

Stereoselective Synthesis of Oxetanes Catalyzed by an Engineered Halohydrin Dehalogenase

Although biocatalysis has garnered widespread attention in both industrial and academic realms, the enzymatic synthesis of chiral oxetanes remains an underdeveloped field. Halohydrin dehalogenases (HHDHs) are industrially relevant enzymes that have been engineered to accomplish the reversible transformation of epoxides. In this study, a biocatalytic platform was constructed for the stereoselective kinetic resolution of chiral oxetanes and formation of 1,3-disubstituted alcohols. HheC from Agrobacterium radiobacter AD1 was engineered to identify key variants capable of catalyzing the dehalogenation of γ-haloalcohols (via HheC M1-M3) and ring opening of oxetanes (via HheC M4-M5) to access both (R)- and (S)-configured products with high stereoselectivity and remarkable catalytic activity, yielding up to 49 % with enantioselectivities exceeding 99 % ee and E>200. The current strategy is broadly applicable as demonstrated by expansion of the substrate scope to include up to 18 examples for dehalogenation and 16 examples for ring opening. Additionally, the functionalized products are versatile building blocks for pharmaceutical applications. To shed light on the molecular recognition mechanisms for the relevant variants, molecular dynamic (MD) simulations were performed. The current strategy expands the scope of HHDH-catalyzed chiral oxetane ring construction, offering efficient access to both enantiomers of chiral oxetanes and 1,3-disubstituted alcohols.

Context-aware geometric deep learning for protein sequence design

Protein design and engineering are evolving at an unprecedented pace leveraging the advances in deep learning. Current models nonetheless cannot natively consider non-protein entities within the design process. Here, we introduce a deep learning approach based solely on a geometric transformer of atomic coordinates and element names that predicts protein sequences from backbone scaffolds aware of the restraints imposed by diverse molecular environments. To validate the method, we show that it can produce highly thermostable, catalytically active enzymes with high success rates. This concept is anticipated to improve the versatility of protein design pipelines for crafting desired functions.

A New Age of Biocatalysis Enabled by Generic Activation Modes

Biocatalysis is currently undergoing a profound transformation. The field moves from relying on nature's chemical logic to a discipline that exploits generic activation modes, allowing for novel biocatalytic reactions and, in many instances, entirely new chemistry. Generic activation modes enable a wide range of reaction types and played a pivotal role in advancing the fields of organo- and photocatalysis. This perspective aims to summarize the principal activation modes harnessed in enzymes to develop new biocatalysts. Although extensively researched in the past, the highlighted activation modes, when applied within enzyme active sites, facilitate chemical transformations that have largely eluded efficient and selective catalysis. This advance is attributed to multiple tunable interactions in the substrate binding pocket that precisely control competing reaction pathways and transition states. We will highlight cases of new synthetic methodologies achieved by engineered enzymes and will provide insights into potential future developments in this rapidly evolving field.

Maximizing Aqueous Drug Encapsulation: Small Nanoparticles Formation Enabled by Glycopolymers Combining Glucose and Tyrosine

Highly potent heterocyclic drugs are frequently poorly water soluble, leading to limited or abandoned further drug development. Nanoparticle technology offers a powerful delivery approach by enhancing the solubility and bioavailability of hydrophobic therapeutics. However, the common usage of organic solvents causes unwanted toxicity and process complexity, therefore limiting the scale-up of nanomedicine technology for clinical translation. Here, we show that an organic-solvent-free methodology for hydrophobic drug encapsulation can be obtained using polymers based on glucose and tyrosine. An aqueous solution based on a tyrosine-containing glycopolymer is able to dissolve solid dasatinib directly without adding an organic solvent, resulting in the formation of very small nanoparticles of around 10 nm loaded with up to 16 wt % of drug. This polymer is observed to function as both a drug solubilizer and a nanocarrier at the same time, offering a simple route for the delivery of insoluble drugs.

Deciphering the stereo-specific catalytic mechanisms of cis-epoxysuccinate hydrolases producing L(+)-tartaric acid

Microbial epoxide hydrolases, cis-epoxysuccinate hydrolases (CESHs), have been utilized for commercial production of enantiomerically pure L(+)- and D(-)-tartaric acids for decades. However, the stereo-catalytic mechanism of CESH producing L(+)-tartaric acid (CESH[L]) remains unclear. Herein, the crystal structures of two CESH[L]s in ligand-free, product-complexed, and catalytic intermediate forms were determined. These structures revealed the unique specific binding mode for the mirror-symmetric substrate, an active catalytic triad consisting of Asp-His-Glu, and an arginine providing a proton to the oxirane oxygen to facilitate the epoxide ring-opening reaction, which has been pursued for decades. These results provide the structural basis for the rational engineering of these industrial biocatalysts.