A stereoselective fluorogenic assay for aldolases: Detection of an anti-selective aldolase catalytic antibody

Current state of and need for enzyme engineering of 2-deoxy-D-ribose 5-phosphate aldolases and its impact

Abstract

Deoxyribose-5-phosphate aldolases (DERAs, EC 4.1.2.4) are acetaldehyde-dependent, Class I aldolases catalyzing in nature a reversible aldol reaction between an acetaldehyde donor (C2 compound) and glyceraldehyde-3-phosphate acceptor (C3 compound, C3P) to generate deoxyribose-5-phosphate (C5 compound, DR5P). DERA enzymes have been found to accept also other types of aldehydes as their donor, and in particular as acceptor molecules. Consequently, DERA enzymes can be applied in C–C bond formation reactions to produce novel compounds, thus offering a versatile biocatalytic alternative for synthesis. DERA enzymes, found in all kingdoms of life, share a common TIM barrel fold despite the low overall sequence identity. The catalytic mechanism is well-studied and involves formation of a covalent enzyme-substrate intermediate. A number of protein engineering studies to optimize substrate specificity, enzyme efficiency, and stability of DERA aldolases have been published. These have employed various engineering strategies including structure-based design, directed evolution, and recently also machine learning–guided protein engineering. For application purposes, enzyme immobilization and usage of whole cell catalysis are preferred methods as they improve the overall performance of the biocatalytic processes, including often also the stability of the enzyme. Besides single-step enzymatic reactions, DERA aldolases have also been applied in multi-enzyme cascade reactions both in vitro and in vivo. The DERA-based applications range from synthesis of commodity chemicals and flavours to more complicated and high-value pharmaceutical compounds.

Key points

• DERA aldolases are versatile biocatalysts able to make new C–C bonds.

• Synthetic utility of DERAs has been improved by protein engineering approaches.

• Computational methods are expected to speed up the future DERA engineering efforts.

Graphical abstract

Colorimetric Carbonyl Sulfide (COS)/Hydrogen Sulfide (H2 S) Donation from γ-Ketothiocarbamate Donor Motifs

Hydrogen sulfide (H₂ S) is a biologically active molecule that exhibits protective effects in a variety of physiological and pathological processes. Although several H₂ S-related biological effects have been discovered by using H₂ S donors, knowing how much H₂ S has been released from donors under different conditions remains challenging. Now, a series of γ-ketothiocarbamate (γ-KetoTCM) compounds that provide the first examples of colorimetric H₂ S donors and enable direct quantification of H₂ S release, were reported. These compounds are activated through a pH-dependent deprotonation/β-elimination sequence to release carbonyl sulfide (COS), which is quickly converted into H₂ S by carbonic anhydrase. The p-nitroaniline released upon donor activation provides an optical readout that correlates directly to COS/H₂ S release, thus enabling colorimetric measurement of H₂ S donation.

Immobilization of 2-Deoxy-d-ribose-5-phosphate Aldolase in Polymeric Thin Films via the Langmuir-Schaefer Technique

A synthetic protocol for the fabrication of ultrathin polymeric films containing the enzyme 2-deoxy-d-ribose-5-phosphate aldolase from Escherichia coli (DERA_EC) is presented. Ultrathin enzymatically active films are useful for applications in which only small quantities of active material are needed and at the same time quick response and contact times without diffusion limitation are wanted. We show how DERA as an exemplary enzyme can be immobilized in a thin polymer layer at the air-water interface and transferred to a suitable support by the Langmuir-Schaefer technique under full conservation of enzymatic activity. The polymer in use is a poly(N-isopropylacrylamide-co-N-2-thiolactone acrylamide) (P(NIPAAm-co-TlaAm)) statistical copolymer in which the thiolactone units serve a multitude of purposes including hydrophobization of the polymer, covalent binding of the enzyme and the support and finally cross-linking of the polymer matrix. The application of this type of polymer keeps the whole approach simple as additional cocomponents such as cross-linkers are avoided.

Development of self-immolative dendrimers for drug delivery and sensing

Traditional dendrimers possess unique cascade-branched structural properties that allow for multivalent modifications with drug cargos, targeting/delivery agents and imaging tools. In addition to multivalency, the dendrimer's macromolecular size also brings about the enhanced permeability and retention (EPR) effect, which makes it an attracting agent for drug delivery and biosensing. Similar to other macromolecules, therapeutic application of dendrimers in the human body faces practical challenges such as target specificity and toxicity. The latter represents a substantial issue due to the dendrimer's unnatural chemical structure and relatively large size, which prohibit its in vivo degradation and excretion from the body. To date, a class of self-immolative dendrimers has been developed to overcome these obstacles, which takes advantage of its unique structural backbone to allow for cascade decompositions upon a simple triggering event. The specific drug release can be achieved through a careful design of the trigger, and as a result of the fragmentation, the generated small molecules are either biodegradable or easily excreted from the body. Though still at a preliminary stage, the development of this novel approach represents an important direction in nanoparticle-mediated drug delivery and sensor design, thereby opening up an insightful frontier of dendrimer based applications.

Enzyme assays

Enzyme assays are analytical tools to visualize enzyme activities. In recent years a large variety of enzyme assays have been developed to assist the discovery and optimization of industrial enzymes, in particular for "white biotechnology" where selective enzymes are used with great success for economically viable, mild and environmentally benign production processes. The present article highlights the aspects of fluorogenic and chromogenic substrates, sensors, and enzyme fingerprinting, which are our particular areas of interest.

Molecular probe for enzymatic activity with dual output

A novel molecular probe for enzymatic activity with a dual output detection-mode has been developed. The probe effectively detected the presence of the bacterial protease penicillin-G-amidase; a single cleavage by the enzyme initiated the fragmentation of a self immolative dendritic platform to release two reporter units. The signals of the free reporters were detected by two different spectroscopic techniques, fluorescence and UV-vis. This is the first reported molecular probe with two different chromogenic reporter units activated by a specific stimulus.

Screening systems

Enzyme screening technology has undergone massive developments in recent years, particularly in the area of high-throughput screening and microarray methods. Screening consists of testing each sample of a sample library individually for the targeted reaction. This requires enzyme assays that accurately test relevant parameters of the reaction, such as catalytic turnover with a given substrate and selectivity parameters such as enantio- and regioselectivity. Enzyme assays also play an important role outside of enzyme screening, in particular for drug screening, medical diagnostics, and in the area of cellular and tissue imaging. In the 1990s, methods for high-throughput screening of enzyme activities were perceived as a critical bottleneck. As illustrated partly in this chapter, a large repertoire of efficient screening strategies are available today that allow testing of almost any reaction with high-throughput.

Amperometric assay for aldolase activity: antibody-catalyzed ferrocenylamine formation

Screening of new catalysts for aldolase activity is a major task in bioorganic chemistry. For this purpose, fast and convenient methods are required for the detection of the catalysts. We have developed the first amperometric assay for aldol or retro-aldol catalytic activity. A new ferrocene-aldol derivative was synthesized with redox activity significantly different from that of ferrocenylamine. It was shown that the reaction between aldolase antibody 38C2 and a ferrocene-aldol substrate generated free ferrocenylamine, which could be detected and quantified by simple electrochemical measurement. The amperometric assay was applied to perform a Michaelis-Menten analysis of catalytic antibody 38C2 in order to determine the enzymatic kinetic parameters.

A new visual screening assay for catalytic antibodies with retro-aldol retro-Michael activity

Fast and convenient methods are required for the detection of novel catalysts. We have developed a new assay to allow direct visualization of retro-aldol retro-Michael catalytic activity and have demonstrated it with catalytic antibody 38C2. The assay is based on a catalytic cleavage of a physiologically stable substrate to release 3,4-cyclohexeneoesculetin. The latter then reacts with iron(III) to generate a non-soluble complex that precipitates in the form of a black dye. This assay may be used for screening new catalysts for retro-aldol retro-Michael activity with improved efficiency for specific prodrug activation.

Artificial aldolases from peptide dendrimer combinatorial libraries

Peptide dendrimers were investigated as synthetic models for aldolase enzymes. Combinatorial libraries were prepared with aldolase active residues such as lysine and proline placed at the dendrimer core or near the surface. On-bead selection for aldolase activity was carried out using the dye-labelled 1,3-diketone 1a, suitable for covalent trapping of enamine-reactive side-chains, and the fluorogenic enolization probe 6. Aldolase dendrimers catalyzed the aldol reaction of acetone, dihydroxyacetone and cyclohexanone with nitrobenzaldehyde. Much like enzymes, the dendrimers exhibited strong aldolase activity in aqueous medium, but were also active in organic solvent. Dendrimer-catalyzed aldol reactions reached complete conversion in 3 h at 25 degrees C with 1 mol% catalyst and gave aldol products with up to 65% ee. A positive dendritic effect in catalysis was observed with both lysine and proline based aldolase dendrimer catalysts.

Dual mechanism of zinc-proline catalyzed aldol reactions in water

The aldol reaction of acetone with aldehydes in aqueous medium under catalysis by zinc-proline (Zn(L-Pro)2) and secondary amines such as proline, (2S,4R)-4-hydroxyproline (Hyp) and (S)-(+)-1-(2-pyrrolidinomethyl)pyrrolidine (PMP) is shown to proceed by an enamine mechanism, as evidenced by reductive trapping of the iminium intermediate, while the aldol reaction of dihydroxyacetone (DHA) under catalysis by zinc-proline and by general bases such as N-methylmorpholine (NMM) is shown to occur under rate-limiting deprotonation of the alpha-carbon and formation of an enolate intermediate.

Catalytic antibodies: hapten design strategies and screening methods

Catalytic antibodies have emerged as powerful tools for the efficient and specific catalysis of a wide range of chemical transformations. Generating antibody catalysts that achieve enzymatic efficiency remains a challenging task, which has long been the source of great interest both in the design of more effective haptens for immunization and in the development of more direct and efficient screening methods for the selection of antibodies with desired catalytic capacities. In this review, we describe the development of different hapten design strategies, including a transition state analog (TSA) approach, 'bait-and-switch' catalysis, and reactive immunization. We also comment on recent developments in the screening process that allow for a more efficient identification of antibody catalysts.

Recent advances in enzyme assays

Enzyme assays for high-throughput screening and enzyme engineering, which are often based on derivatives of coumarin, nitrophenol, fluorescein, nitrobenzofurazane or rhodamine dyes, can be divided into two categories: those that depend on labelled substrates, and those that depend on sensing the reactions of unmodified substrates. Labelled substrates include, for example, fluorogenic and chromogenic substrates that generate a reporter molecule by beta-elimination, fluorescence resonance energy transfer (FRET) substrates and isotopic labels for enantioselectivity screening. By contrast, endpoint sensing can be done using amine reagents, fluorescent affinity labels for phosphorylated proteins, or synthetic multifunctional pores. Sensing assays can also be done in real time by using, for example, aldehyde trapping to follow vinyl ester acylation in organic solvent or calcein-copper fluorescence for sensing amino acids. The current trend is to assemble many such assays in parallel for enzyme profiling and enzyme fingerprinting.

Fluorescent detection of carbon-carbon bond formation

We have developed a new spectroscopic system for detecting carbon-carbon bond formation by fluorescence to enhance high-throughput catalyst screening and rapid characterization of catalysts on a small scale. Fluorogenic substrates composed of a fluorophore possessing an amino group are readily prepared as amides of alpha,beta-unsaturated carbonyl compounds and generally exhibit low fluorescence, while Michael or Diels-Alder reactions of these fluorogenic substrates provide products of significantly increased fluorescence. The product's fluorescence is approximately 20- to 100-fold higher than that of the substrate. The assay system was validated by screening potential catalysts of the Michael reaction and in solvent optimization experiments. The covalent combination of fluorophores possessing an amino group with alpha,beta-unsaturated carbonyl compounds should provide a diverse range of fluorogenic substrates that may be used to rapidly screen catalysts and to optimize reaction conditions.

Visualizing antibody-catalyzed retro-aldol-retro-Michael reactions

We developed a visible detection system for antibody-catalyzed retro-aldol-retro-Michael reactions. Aldolase antibody 38C2 catalyzed the reaction of substrate 1 to provide 6-bromo-2-napthol that forms a visible colored azo dye with diazonium salts. This system has potential for the screening of novel catalysts.

Fluorogenic polypropionate fragments for detecting stereoselective aldolases

A series of fluorogenic polypropionate fragments has been prepared. These undergo retroaldolization to an intermediate aldehyde that liberates the fluorescent product umbelliferone by a secondary beta-elimination reaction. leading to a >20-fold increase in fluorescence (lambda(em) = 460 +/- 20 nm, lambdaex = 360 +/- 20 nm). By applying the principle of microscopic reversibility to the reversible aldol reaction, we can use these substrates to detect stereoselective aldolases. Test substrates are available to probe the classical cases of syn- and anti-selective aldolization (11a-d), Cram/ anti-Cram-selective aldolization (10a-d), and double stereoselective aldolization (3a-h). The selectivity of aldolase antibody 38C2 for these substrates is demonstrated as an example. The assay is suitable for high-throughput screening for catalysis in microtiter plates, and therefore provides a convenient tool for the isolation of new stereoselective aldolases from catalyst libraries.