Evolutionary insights into the stereoselectivity of imine reductases based on ancestral sequence reconstruction

Engineering of ω-transaminase at binding pocket and access tunnel for preparation of (R)-1-phenoxypropan-2-amine

Transaminase-catalyzed amination of prochiral ketones is regarded as a promising route for optically active amines production. These chiral amines serve as key building blocks in the synthesis of agrochemicals and pharmaceuticals. However, the limited substrate scope and substrate/(co)product inhibition have significantly hindered the industrial-scale implementation of transaminase-catalyzed processes. Engineering of TAs at binding sites is an efficient strategy to expand the capacity of binding pocket, thereby improving the catalytic efficiency. Furthermore, modification of access tunnel is crucial for adjusting the transfer efficiency of ligand. In this endeavor, we engineered an ω-TA from Nocardioides sp. CER19(NsTA) at binding sites and access tunnel, and applied the mutants for enantioselective synthesis of (R)-1-phenoxypropan-2-amine. Mutation at residues H62 and Y122 increased catalytic activity of the TA towards 1-phenoxyacetone, the optimal mutants NsTAH62A and NsTAY122A with improved enzyme activity was obtained, which was 2.0 and 1.5-fold higher than that of the wild-type NsTA respectively. This allowed completely conversion of 5 mM 1-phenoxyacetone to (R)-1-phenoxypropan-2-amine at 4 h and > 99 % ee (in comparison to 66 % convesion with the wild-type NsTA). Molecular dynamic simulation suggested improved flexibility of NsTAH62A, which may result in eliminating of substrate inhibition. While mutant NsTAD7 (with deletion of 7 amino acids at N-terminal) exhibited about 1.6-fold increase of conversion. Tunnel analysis suggested that reshaping of the tunnel entrance may alter the shape and size of the tunnel, which might promote the release of the products. These results of our study lay the foundation for enantioselective synthesis of (R)-1-phenoxypropan-2-amine and provide a promising engineering strategy to enhance the activity of TAs and overcome substrate/(co)product inhibition of ω-TA towards bulky substrates.

Investigating the role of polar amino acids driven by evolution in the active site architecture of GH11 xylanase

Enzymes, as vital biomacromolecules, have developed significant plasticity, enabling adaptation to diverse environments and catalysis of numerous biochemical reactions. However, enzyme evolution is constrained by mutational limitations, as amino acid substitutions often impair structure or function, hampering optimization endeavors. To address this, we integrated structural bioinformatics with site-directed mutagenesis to investigate the evolutionary trends of four GH11 family xylanases (XynA, XynB, XynD, and XynE) from Aspergillus niger An76. Our analysis revealed that conserved residues in active sites are unevenly distributed, with highly conserved residues critical for catalysis and relatively conserved residues offering mutation potential. The mutation of Asp/Asn near catalytic residues at -1 subsite could not only alter the catalytic activity, but also shift the optimal pH by one unit. Additional mutants, including XynB-A143P, XynA-F142W, XynD-E20T, and XynD-E192Q, increased enzymatic activity by 17%, 46%, 82%, and 26%, respectively. More importantly, ancestral sequence reconstruction highlighted the importance of Arg at the -1 subsite of GH11 xylanases, and combinatorial mutation based on Y160R reinstated the pseudo-enzyme XynE's activity to 417.6 IU/mg. This study demonstrates the efficacy of evolutionary-informed mutagenesis for precise enzyme design, providing insights for optimizing GH11 family and other enzymes.

Imine Reductase-Catalyzed Remote Stereocontrol for Enantiodivergent Synthesis of Cyclohexylidene-Based Axially Chiral Amines

Cyclohexylidene-based amines exhibit unique axial chirality arising from the restricted double bond and have shown great potential in medicinal chemistry. However, their asymmetric synthesis remains challenging due to the long distance between the chirally relevant groups. Herein, we report a highly efficient and asymmetric synthesis of cyclohexylidene-based axially chiral amines from 4-substituted cyclohexanones and primary amines catalyzed by imine reductases (IREDs). Enantiodivergent IREDs were identified to provide convenient access to both enantiomers of chiral products with high yields and enantioselectivity (up to 99% yield, 99:1 or 1:99 enantiomeric ratio). A gram-scale synthesis of cyclohexylidene-based amines was also achieved. Moreover, protein X-ray crystallography and molecular modeling studies were conducted to provide structural insight into the remote stereocontrol of IREDs in generating cyclohexylidene-based axial chirality.

Phase-Separated Multienzyme Condensates for Efficient Synthesis of Imines from Carboxylic Acids with Enhanced Dual-Cofactor Recycling

Enzyme catalysis represents a promising approach for sustainable chemical synthesis, yet its industrial applications face limitations due to the inefficient regeneration and high cost of essential cofactors, such as adenosine-5'-triphosphate (ATP) and nicotinamide adenine dinucleotide phosphate (NADPH). While natural metabolic systems efficiently recycle cofactors through spatially organized enzymes, replicating this efficiency in vitro remains challenging. Here, we prepare a five-enzyme condensate system using liquid-liquid phase separation (LLPS) mediated by intrinsically disordered proteins (IDPs). By colocalizing a carboxylic acid reductase from Norcadia iowensis (NiCAR) with a reductive aminase from Aspergillus oryzae (AspRedAm) and three cofactor-regenerating enzymes, we generated a phase-separated catalytic condensate that enhanced ATP and NADPH recycling efficiency by 4.7-fold and 1.9-fold relative to free enzymes, respectively. Catalytic performance was correlated with the extent of phase separation, as confirmed by fluorescence microscopy, which revealed clear enrichment of ATP and NADPH within the condensates. This proximity effect enabled efficient cofactor turnover in the one-step reaction, achieving substrate conversion above 90% within 6 h and enhancing the space-time yield (STY) of the chiral imines 1.6-fold, with only one-fifth of the standard cofactor load. This approach creates a scalable and economic tool for performing multienzyme cascade reactions in vitro that are driven by the efficient recycling of multiple cofactors.