Dynamic Kinetic Resolution of Diarylmethanols with an Activated Lipoprotein Lipase

Mutexa: A Computational Ecosystem for Intelligent Protein Engineering

Protein engineering holds immense promise in shaping the future of biomedicine and biotechnology. This Review focuses on our ongoing development of Mutexa, a computational ecosystem designed to enable "intelligent protein engineering". In this vision, researchers will seamlessly acquire sequences of protein variants with desired functions as biocatalysts, therapeutic peptides, and diagnostic proteins through a finely-tuned computational machine, akin to Amazon Alexa's role as a versatile virtual assistant. The technical foundation of Mutexa has been established through the development of a database that combines and relates enzyme structures and their respective functions (e.g., IntEnzyDB), workflow software packages that enable high-throughput protein modeling (e.g., EnzyHTP and LassoHTP), and scoring functions that map the sequence-structure-function relationship of proteins (e.g., EnzyKR and DeepLasso). We will showcase the applications of these tools in benchmarking the convergence conditions of enzyme functional descriptors across mutants, investigating protein electrostatics and cavity distributions in SAM-dependent methyltransferases, and understanding the role of nonelectrostatic dynamic effects in enzyme catalysis. Finally, we will conclude by addressing the future steps and fundamental challenges in our endeavor to develop new Mutexa applications that assist the identification of beneficial mutants in protein engineering.

EnzyKR: a chirality-aware deep learning model for predicting the outcomes of the hydrolase-catalyzed kinetic resolution

Hydrolase-catalyzed kinetic resolution is a well-established biocatalytic process. However, the computational tools that predict favorable enzyme scaffolds for separating a racemic substrate mixture are underdeveloped. To address this challenge, we trained a deep learning framework, EnzyKR, to automate the selection of hydrolases for stereoselective biocatalysis. EnzyKR adopts a classifier-regressor architecture that first identifies the reactive binding conformer of a substrate-hydrolase complex, and then predicts its activation free energy. A structure-based encoding strategy was used to depict the chiral interactions between hydrolases and enantiomers. Different from existing models trained on protein sequences and substrate SMILES strings, EnzyKR was trained using 204 substrate-hydrolase complexes, which were constructed by docking. EnzyKR was tested using a held-out dataset of 20 complexes on the task of predicting activation free energy. EnzyKR achieved a Pearson correlation coefficient (R) of 0.72, a Spearman rank correlation coefficient (Spearman R) of 0.72, and a mean absolute error (MAE) of 1.54 kcal mol-1 in this task. Furthermore, EnzyKR was tested on the task of predicting enantiomeric excess ratios for 28 hydrolytic kinetic resolution reactions catalyzed by fluoroacetate dehalogenase RPA1163, halohydrin HheC, A. mediolanus epoxide hydrolase, and P. fluorescens esterase. The performance of EnzyKR was compared against that of a recently developed kinetic predictor, DLKcat. EnzyKR correctly predicts the favored enantiomer and outperforms DLKcat in 18 out of 28 reactions, occupying 64% of the test cases. These results demonstrate EnzyKR to be a new approach for prediction of enantiomeric outcomes in hydrolase-catalyzed kinetic resolution reactions.

Expanding the Synthetic Toolbox through Metal-Enzyme Cascade Reactions

The combination of metal-, photo-, enzyme-, and/or organocatalysis provides multiple synthetic solutions, especially when the creation of chiral centers is involved. Historically, enzymes and transition metal species have been exploited simultaneously through dynamic kinetic resolutions of racemates. However, more recently, linear cascades have appeared as elegant solutions for the preparation of valuable organic molecules combining multiple bioprocesses and metal-catalyzed transformations. Many advantages are derived from this symbiosis, although there are still bottlenecks to be addressed including the successful coexistence of both catalyst types, the need for compatible reaction media and mild conditions, or the minimization of cross-reactivities. Therefore, solutions are here also provided by means of catalyst coimmobilization, compartmentalization strategies, flow chemistry, etc. A comprehensive review is presented focusing on the period 2015 to early 2022, which has been divided into two main sections that comprise first the use of metals and enzymes as independent catalysts but working in an orchestral or sequential manner, and later their application as bionanohybrid materials through their coimmobilization in adequate supports. Each part has been classified into different subheadings, the first part based on the reaction catalyzed by the metal catalyst, while the development of nonasymmetric or stereoselective processes was considered for the bionanohybrid section.

Efficient synthesis of bepotastine and cloperastine intermediates using engineered alcohol dehydrogenase with a hydrophobic pocket

(S)-4-Chlorophenylpyridylmethanol and (R)-4-chlorobenzhydrol are key pharmaceutical intermediates for the synthesis of bepotastine and cloperastine, respectively. However, the biocatalytic approach to prepare these bulky diaryl ketones remains challenging because of the low activity of naturally occurring alcohol dehydrogenases (ADH). In the present study, ADH seq5, which has an adequate binding pocket volume and accepts bulky diaryl ketones, was further engineered with a binding pocket of increased hydrophobicity. Based on molecular simulation and binding free energy analyses, a small mutation library was constructed, and mutant seq5-D150I with a threefold increase in k_cat and a low K_m was obtained successfully. The comparison of kinetic parameters, binding free energy, docking conformation, and critical catalytic distances calculated by molecular dynamic simulations revealed the source of increased activity. To develop a practical approach with seq5-D150I, reaction conditions including pH, temperature, buffer, and metal ions were optimised and applied to synthesise (S)-4-chlorophenylpyridylmethanol and (R)-4-chlorobenzhydrol with high enantiomeric excess. The space-time yields for (S)-4-chlorophenylpyridylmethanol and (R)-4-chlorobenzhydrol increased dramatically to as high as 263.4 g∙L^-1 day^-1 and 150 g∙L^-1 day^-1, respectively, which, to our knowledge, is the highest reported yield to date. These results show that the biocatalytic approach with seq5-D150I may be practical for future industrial applications.Key points An alcohol dehydrogenase was engineered based on binding free energy analysis. The mutant seq5-D150I obtained a threefold increase in k_cat and a low K_m. Two important pharmaceutical intermediates were obtained with high space-time yield.

Engineering an alcohol dehydrogenase with enhanced activity and stereoselectivity toward diaryl ketones: reduction of steric hindrance and change of the stereocontrol element

Engineering an alcohol dehydrogenase with enhanced activity and stereoselectivity toward diaryl ketones: reduction of steric hindrance and change of the stereocontrol element.

Base-Free Dynamic Kinetic Resolution of Secondary Alcohols with a Ruthenium-Lipase Couple

We report the dynamic kinetic resolution (DKR) of various secondary alcohols by the combination of a ruthenium catalyst and an anionic surfactant-activated lipoprotein lipase. The DKR reactions performed under totally base-free conditions at room temperature provided the products of excellent enantiopurities (91-99% ee or greater) in high yields (92-99%). More importantly, the DKR of α-arylallyl alcohols was achieved for the first time with high yields (87-91%).

Enantioselective Extraction of Phenylalanine Enantiomers Using Environmentally Friendly Aqueous Two-Phase Systems

(1) Background: The environmentally friendly choline-amino acid ionic liquids (ChAAILs) and deep eutectic solvents (DESs) have been used as excellent alternatives to volatile organic compounds (VOCs) and ionic liquids (ILs) in recent years; (2) Methods: Thus, ChAAILs/salt and DESs/salt aqueous two-phase systems (ATPSs) were developed for the chiral extraction of phenylalanine enantiomers. The optimum ATPS of [Ch][L-Pro]/K3PO4 was chosen, and the influencing parameters were investigated, including ChAAILs concentration, salt concentration, chiral selector concentration, extraction temperature, phenylalanine concentration, and system pH; (3) Results: The phenylalanine enantiomers were mainly extracted into the top phase (ChAAIL-rich phase), meanwhile, the (S)-phenylalanine [(S)-Phe)] was preferentially recognized by the chiral selector in the top phase. The maximum separation factor (α) of 2.05 was obtained under the optimal conditions; and (4) Conclusions: This ATPS that was used for the chiral extraction of enantiomers is much more environmentally friendly, simple, and rapid, and has the potential to be used in the enantioselective extraction of other enantiomers.

Racemic and enantioselective metal-catalyzed synthesis of SF5-containing diarylmethanols

The racemic and enantioselective metal-catalyzed addition of arylboronic acids to 4- and 3-(pentafluorosulfur)benzaldehydes is reported. The racemic synthesis was accomplished using a Pd-based system and a wide range of arylboronic acids could be used, resulting in yields of 42 to 98% of the corresponding SF₅-containing diarylmethanols. A ruthenium-based system, along with (R,R)-Me-BIPAM as the chiral ligand, was investigated and optimized for the enantioselective version. In this case, while the chiral SF₅-containing diarylmethanols were generally obtained in good yields (up to 94%) and enantioselectivities (up to 98% ee), limitations were also observed. For instance, 4-(pentafluorosulfur)benzaldehyde generally provided slightly better yields than 3-(pentafluorosulfur)benzaldehyde. In addition, lower yields and enantioselectivities were observed when using either 4- and 3-substituted arylboronic acids bearing electron-withdrawing (e.g., CO₂Et, NO₂, CF₃) or 2-substituted arylboronic acids (regardless of the nature of the substituent). Overall, the SF₅-containing diarylmethanols described herein represent novel and potentially useful fluorinated building blocks for the synthesis of biologically active compounds.

Dynamic kinetic resolution of aromatic sec-alcohols by using a heterogeneous palladium racemization catalyst and lipase

A novel recyclable chemoenzymatic catalyst combination has been designed, which successfully converted sec-alcohols to chiral acetates under microwave irradiation.

Spatial effects of oxovanadium-immobilized mesoporous silica on racemization of alcohols and application in lipase-catalyzed dynamic kinetic resolution

The nano-scale pores of mesoporous silica and their polar environment accelerate the racemization to make the lipase/oxovanadium combo-catalysed DKR applicable to a wider range of alcohols.

Chemoenzymatic dynamic kinetic resolution: a powerful tool for the preparation of enantiomerically pure alcohols and amines

Chemoenzymatic dynamic kinetic resolution (DKR) constitutes a convenient and efficient method to access enantiomerically pure alcohol and amine derivatives. This Perspective highlights the work carried out within this field during the past two decades and pinpoints important avenues for future research. First, the Perspective will summarize the more developed area of alcohol DKR, by delineating the way from the earliest proof-of-concept protocols to the current state-of-the-art systems that allows for the highly efficient and selective preparation of a wide range of enantiomerically pure alcohol derivatives. Thereafter, the Perspective will focus on the more challenging DKR of amines, by presenting the currently available homogeneous and heterogeneous methods and their respective limitations. In these two parts, significant attention will be dedicated to the design of efficient racemization methods as an important means of developing milder DKR protocols. In the final part of the Perspective, a brief overview of the research that has been devoted toward improving enzymes as biocatalysts is presented.