Engineered Artificial Carboligases Facilitate Regioselective Preparation of Enantioenriched Aldol Adducts

Ancestral terpene cyclases: From fundamental science to applications in biosynthesis

Terpenes constitute one of the largest family of natural products with potent applications as renewable platform chemicals and medicines. The low activity, selectivity and stability displayed by terpene biosynthetic machineries can constitute an obstacle towards achieving expedient biosynthesis of terpenoids in processes that adhere to the 12 principles of green chemistry. Accordingly, engineering of terpene synthase enzymes is a prerequisite for industrial biotechnology applications, but obstructed by their complex catalysis that depend on reactive carbocationic intermediates that are prone to undergo bifurcation mechanisms. Rational redesign of terpene synthases can be tedious and requires high-resolution structural information, which is not always available. Furthermore, it has proven difficult to link sequence space of terpene synthase enzymes to specific product profiles. Herein, the author shows how ancestral sequence reconstruction (ASR) can favorably be used as a protein engineering tool in the redesign of terpene synthases without the need of a structure, and without excessive screening. A detailed workflow of ASR is presented along with associated limitations, with a focus on applying this methodology on terpene synthases. From selected examples of both class I and II enzymes, the author advocates that ancestral terpene cyclases constitute valuable assets to shed light on terpene-synthase catalysis and in enabling accelerated biosynthesis.

Ultrahigh-Throughput Screening of an Artificial Metalloenzyme using Double Emulsions

The potential for ultrahigh-throughput compartmentalization renders droplet microfluidics an attractive tool for the directed evolution of enzymes. Importantly, it ensures maintenance of the phenotype-genotype linkage, enabling reliable identification of improved mutants. Herein, we report an approach for ultrahigh-throughput screening of an artificial metalloenzyme in double emulsion droplets (DEs) using commercially available fluorescence-activated cell sorters (FACS). This protocol was validated by screening a 400 double-mutant streptavidin library for ruthenium-catalyzed deallylation of an alloc-protected aminocoumarin. The most active variants, identified by next-generation sequencing, were in good agreement with hits obtained using a 96-well plate procedure. These findings pave the way for the systematic implementation of FACS for the directed evolution of (artificial) enzymes and will significantly expand the accessibility of ultrahigh-throughput DE screening protocols.

Leveraging Regio- and Stereoselective C(sp3)-H Functionalization of Silyl Ethers to Train a Logistic Regression Classification Model for Predicting Site-Selectivity Bias

The C-H functionalization of silyl ethers via carbene-induced C-H insertion represents an efficient synthetic disconnection strategy. In this work, site- and stereoselective C(sp³)-H functionalization at α, γ, δ, and even more distal positions to the siloxy group has been achieved using donor/acceptor carbene intermediates. By exploiting the predilections of Rh₂(R-TCPTAD)₄ and Rh₂(S-2-Cl-5-BrTPCP)₄ catalysts to target either more electronically activated or more spatially accessible C-H sites, respectively, divergent desired products can be formed with good diastereocontrol and enantiocontrol. Notably, the reaction can also be extended to enable desymmetrization of meso silyl ethers. Leveraging the broad substrate scope examined in this study, we have trained a machine learning classification model using logistic regression to predict the major C-H functionalization site based on intrinsic substrate reactivity and catalyst propensity for overriding it. This model enables prediction of the major product when applying these C-H functionalization methods to a new substrate of interest. Applying this model broadly, we have demonstrated its utility for guiding late-stage functionalization in complex settings and developed an intuitive visualization tool to assist synthetic chemists in such endeavors.

Redesigning Enzymes for Biocatalysis: Exploiting Structural Understanding for Improved Selectivity

The discovery of new enzymes, alongside the push to make chemical processes more sustainable, has resulted in increased industrial interest in the use of biocatalytic processes to produce high-value and chiral precursor chemicals. Huge strides in protein engineering methodology and in silico tools have facilitated significant progress in the discovery and production of enzymes for biocatalytic processes. However, there are significant gaps in our knowledge of the relationship between enzyme structure and function. This has demonstrated the need for improved computational methods to model mechanisms and understand structure dynamics. Here, we explore efforts to rationally modify enzymes toward changing aspects of their catalyzed chemistry. We highlight examples of enzymes where links between enzyme function and structure have been made, thus enabling rational changes to the enzyme structure to give predictable chemical outcomes. We look at future directions the field could take and the technologies that will enable it.

Droplet Microfluidics and Directed Evolution of Enzymes: An Intertwined Journey

Evolution is essential to the generation of complexity and ultimately life. It relies on the propagation of the properties, traits, and characteristics that allow an organism to survive in a challenging environment. It is evolution that shaped our world over about four billion years by slow and iterative adaptation. While natural evolution based on selection is slow and gradual, directed evolution allows the fast and streamlined optimization of a phenotype under selective conditions. The potential of directed evolution for the discovery and optimization of enzymes is mostly limited by the throughput of the tools and methods available for screening. Over the past twenty years, versatile tools based on droplet microfluidics have been developed to address the need for higher throughput. In this Review, we provide a chronological overview of the intertwined development of microfluidics droplet-based compartmentalization methods and in vivo directed evolution of enzymes.

Varying the Directionality of Protein Catalysts for Aldol and Retro-Aldol Reactions

Natural aldolase enzymes and created retro-aldolase protein catalysts often catalyze both aldol and retro-aldol reactions depending on the concentrations of the reactants and the products. Here, we report that the directionality of protein catalysts can be altered by replacing one amino acid. The protein catalyst derived from a scaffold of a previously reported retro-aldolase catalyst, catalyzed aldol reactions more efficiently than the previously reported retro-aldolase catalyst. The retro-aldolase catalyst efficiently catalyzed the retro-aldol reaction but was less efficient in catalyzing the aldol reaction. The results indicate that protein catalysts with varying levels of directionality in usually reversibly catalyzed aldol and retro-aldol reactions can be generated from the same protein scaffold.

The Unexplored Importance of Fleeting Chiral Intermediates in Enzyme-Catalyzed Reactions

Decades of extensive research efforts by biochemists, organic chemists, and protein engineers have led to an understanding of the basic mechanisms of essentially all known types of enzymes, but in a formidable number of cases an essential aspect has been overlooked. The occurrence of short-lived chiral intermediates formed by symmetry-breaking of prochiral precursors in enzyme catalyzed reactions has been systematically neglected. We designate these elusive species as fleeting chiral intermediates and analyze such crucial questions as "Do such intermediates occur in homochiral form?" If so, what is the absolute configuration, and why did Nature choose that particular stereoisomeric form, even when the isolable final product may be achiral? Does the absolute configuration of a chiral product depend in any way on the absolute configuration of the fleeting chiral precursor? How does this affect the catalytic proficiency of the enzyme? If these issues continue to be unexplored, then an understanding of the mechanisms of many enzyme types remains incomplete. We have systematized the occurrence of these chiral intermediates according to their structures and enzyme types. This is followed by critical analyses of selected case studies and by final conclusions and perspectives. We hope that the fascinating concept of fleeting chiral intermediates will attract the attention of scientists, thereby opening an exciting new research field.

Directed Evolution: Methodologies and Applications

Directed evolution aims to expedite the natural evolution process of biological molecules and systems in a test tube through iterative rounds of gene diversifications and library screening/selection. It has become one of the most powerful and widespread tools for engineering improved or novel functions in proteins, metabolic pathways, and even whole genomes. This review describes the commonly used gene diversification strategies, screening/selection methods, and recently developed continuous evolution strategies for directed evolution. Moreover, we highlight some representative applications of directed evolution in engineering nucleic acids, proteins, pathways, genetic circuits, viruses, and whole cells. Finally, we discuss the challenges and future perspectives in directed evolution.

Looking Back: A Short History of the Discovery of Enzymes and How They Became Powerful Chemical Tools

Enzymatic approaches to challenges in chemical synthesis are increasingly popular and very attractive to industry given their green nature and high efficiency compared to traditional methods. In this historical review we highlight the developments across several fields that were necessary to create the modern field of biocatalysis, with enzyme engineering and directed evolution at its core. We exemplify the modular, incremental, and highly unpredictable nature of scientific discovery, driven by curiosity, and showcase the resulting examples of cutting-edge enzymatic applications in industry.

Enhancing promiscuous chemistries of a Schiff-base forming enzyme by divergent evolution

Directed evolution has emerged as a powerful technique for the rapid tailoring of enzymes toward particular synthetic demands, spawning a number of enzymes capable of complex chemical transformations. During random mutagenesis of a protein, changes in fitness must be assayed in order to quantify and understand the relative effect a given mutation has, and the assay employed must be carefully chosen to report directly on the transformation of interest. Here, we describe a series of medium-throughput screening techniques that have been utilized for the evolution and engineering of an artificial carboligase, RA95.5-8, resulting in improvement of catalytic efficiency of a number of promiscuous chemistries. The methods make use of common analytical chemistry equipment and low-cost materials, and may help inspire development of novel screening workflows for related transformations.