Trypsin-catalyzed direct asymmetric aldol reaction

Unnatural catalytic activity of trypsin from porcine pancreas for direct asymmetric aldol reaction was discovered. The reactions between aromatic aldehydes and various ketones gave products in moderate yields and enantioselectivities in the presence of a small amount of water. The influences of solvent, water content, temperature, mole ratio of substrates, and enzyme concentration were investigated. The mechanism of trypsin-catalyzed aldol reaction was discussed. This enzymatic promiscuity widens the application of trypsin to new chemical transformations.     

Synthesis of proline-derived dipeptides and their catalytic enantioselective direct aldol reactions: catalyst, solvent, additive and temperature effects

A series of dipeptides of l-proline-l-amino acid and l-proline-d-amino acid were synthesized to evaluate the catalytic effect for asymmetric direct aldol reactions. In the direct aldol reaction, a catalyst of l-proline-l-amino acid achieves better enantioselectivity than the corresponding l-proline-d-amino acid catalyst. Solubility of the dipeptide catalysts in the solvents is a key point for achieving a better yield of the direct aldol reaction, while hydrogen bonding of solvent does not play an important role in attaining better enantioselectivity and yield. Yield and enantioselectivity of the direct aldol reaction in water were improved by NMM and SDS additives, but the results that were done in plain DMSO were even better.     

Enzyme promiscuity: mechanism and applications

Introductory courses in biochemistry teach that enzymes are specific for their substrates and the reactions they catalyze. Enzymes diverging from this statement are sometimes called promiscuous. It has been suggested that relaxed substrate and reaction specificities can have an important role in enzyme evolution; however, enzyme promiscuity also has an applied aspect. Enzyme condition promiscuity has, for a long time, been used to run reactions under conditions of low water activity that favor ester synthesis instead of hydrolysis. Together with enzyme substrate promiscuity, it is exploited in numerous synthetic applications, from the laboratory to industrial scale. Furthermore, enzyme catalytic promiscuity, where enzymes catalyze accidental or induced new reactions, has begun to be recognized as a valuable research and synthesis tool. Exploiting enzyme catalytic promiscuity might lead to improvements in existing catalysts and provide novel synthesis pathways that are currently not available.     

Exploring the potential of some yeast strains in the stereoselective synthesis of aldol reaction products and its reduced 1,3-dialcohol derivatives

The behavior of two yeast strains has been studied under different conditions. Both microorganims catalyzed the aldol reaction between activated aldehydes and acetone when a large amount of the latter was present in the reaction medium producing, with moderate stereoselectivity, the aldol product with the R configuration. No reduction of any of the products present in the medium was detected. On the other hand, the carbonyl group of the racemic aldol was reduced to produce chiral 1,3-dialcohol derivatives when water was employed as the only solvent. In this case, the resolution of the racemic starting material was also possible with one of the biocatalysts, and the aldol was recovered with the S configuration. A complementary enantioselectivity was shown by both microorganisms in the generation of the new stereogenic center, which allowed access to 3 of the 4 possible diastereomeric diols with high enantiomerical purity.     

Synthesis of functional poly(phenyl isocyanide)s with macromolecular helicity memory and their use as asymmetric organocatalysts

To develop a novel polymer-based asymmetric organocatalyst, a series of helical poly(phenyl isocyanide)s with functional pendant groups were prepared by modifying the side groups of the optically active helical poly(4-carboxyphenyl isocyanide) with a macromolecular helicity memory. Helical polyisocyanides partially modified with achiral amines, such as piperazine, maintained their chiral memory and enantioselectively catalyzed a direct aldol reaction. Although the enantioselectivity was low, the original helical poly(4-carboxyphenyl isocyanide) showed no catalytic activity. These results indicated that the macromolecular helicity of the modified polyisocyanides together with bifunctional amino and carboxy acid pendant residues arranged in a helical array along the polymer backbones plays an important role in the enantioselectivity.     

Gastric proteases of the Greenland cod Gadus ogac. I. Isolation and kinetic properties

The zymogens of three gastric proteases of the Greenland cod (Gadus ogac) were isolated by exclusion chromatography and chromatofocusing. The cod zymogens were activated more rapidly at lower temperatures than porcine pepsinogen and, after activation, were further purified by exclusion chromatography. The cod proteases had more alkaline pH optima and were active over a wider range of pH than porcine pepsin. The specific activity of porcine pepsin on protein substrates was greater than that of the individual cod proteases. However, the cod proteases had cumulative activity on protein substrates that was greater than the sum of their individual activities. Cod protease 1 was active on pepsin-specific substrates, and cod proteases 2 and 3 were active as gastricsin-specific substrates. All three cod proteases had greater milk-clotting activity and hydrolysed hemoglobin to a greater extent than porcine pepsin. The Vmax and Km,app of the cod proteases were dependent upon the substrate, and Vmax/Km,app values of the cod proteases were generally lower than porcine pepsin. It is suggested that the cod proteases together exhibit broad substrate specificity and maintain activity over a wide range of conditions to enhance protein digestion in the cod stomach.     

Asymmetric organocatalysis with glycosyl-beta-amino acids: direct asymmetric aldol reaction of acetone with aldehydes

Direct asymmetric aldol reaction of acetone with aromatic aldehydes was achieved in good yields and high enantioselectivity using 5-amino-5-deoxy-beta-L-ido-(alpha-D-gluco)-heptofuranuronic acids as a new class of organocatalysts.     

Enantioselective Aldol Reaction Between Isatins and Cyclohexanone Catalyzed by Amino Acid Sulphonamides

Sulphonamides derived from primary α‐amino acid were successfully applied to catalyze the aldol reaction between isatin and cyclohexanone under neat conditions. More interestingly, molecular sieves, as privileged additives, were found to play a vital role in achieving high enantioselectivity. Consequently, high yields (up to 99%) along with good enantioselectivities (up to 92% ee) and diastereoselectivities (up to 95:5 dr) were obtained. In addition, this reaction was also conveniently scaled up, demonstrating the applicability of this protocol. Chirality 27:314‐319, 2015. © 2015 Wiley Periodicals, Inc.     

Was the serine protease cathepsin G discovered by S. G. Hedin in 1903 in bovine spleen?

In the beginning of the 20th century, enzymes with proteolytic activity were classified as peptidases, Erepsin, and proteases. Among these, pepsin, trypsin, and autolytic enzymes were of the protease class. Spleen-derived proteases were poorly characterized until Sven Gustaf Hedin performed several digestion experiments with bovine spleen. He incubated minced bovine spleen under acidic or neutral conditions and characterized two active proteases; the results were published in 1903. The first protease was named α-protease and was active under neutral conditions. The second was named β-protease and was active under acidic conditions. We replicated Hedin's experiments according to his methods and found, by using activity-based probes to visualize proteases, that the historical α-protease is the present-day serine protease cathepsin G (CatG), which is known to be important in several immune processes, including antigen processing, chemotaxis, and activation of surface receptors. The β-protease, however, comprised different proteases including CatX, B, S, and D. We suggest that Hedin described CatG activity in bovine spleen over 100 years ago.     

A quantitative index of substrate promiscuity

Catalytic promiscuity is a widespread, but poorly understood, phenomenon among enzymes with particular relevance to the evolution of new functions, drug metabolism, and in vitro biocatalyst engineering. However, there is at present no way to quantitatively measure or compare this important parameter of enzyme function. Here we define a quantitative index of promiscuity (I) that can be calculated from the catalytic efficiencies of an enzyme toward a defined set of substrates. A weighted promiscuity index (J) that accounts for patterns of similarity and dissimilarity among the substrates in the set is also defined. Promiscuity indices were calculated for three different enzyme classes: eight serine and cysteine proteases, two glutathione S-transferase (GST) isoforms, and three cytochrome P450 (CYP) isoforms. The proteases ranged from completely specific (granzyme B, J = 0.00) to highly promiscuous (cruzain, J = 0.83). The four drug-metabolizing enzymes studied (GST A1-1 and the CYP isoforms) were highly promiscuous, with J values between 0.72 and 0.92; GST A4-4, involved in the clearance of lipid peroxidation products, is moderately promiscuous (J = 0.37). Promiscuity indices also allowed for studies of correlation between substrate promiscuity and an enzyme's activity toward its most-favored substrate, for each of the three enzyme classes.     

Discovery of new peptide-based catalysts for the direct asymmetric aldol reaction

A series of oligo-peptide based catalysts were prepared using Fmoc solid-phase peptide synthesis. It was found that peptides with N-terminal proline residues catalyzed an aldol reaction yielding enantiomeric enriched product. Peptide H-Pro-Glu-Leu-Phe-OH catalyzed the reaction with good activity and moderate enantioselectivity (66% ee). Furthermore, it was shown that an acidic side chain and/or C-termini are essential to catalysis.     

Improving enzyme properties: when are closer mutations better?

Study of mutations that improve enzyme properties reveals that in many, but not all, cases closer mutations are more effective than distant ones. For enantioselectivity, substrate selectivity and new catalytic activity (catalytic promiscuity) closer mutations improved enzymes more effectively than distant ones. However, both close and distant mutations can improve activity, thermal stability and also probably stability toward organic solvents. Typical random mutagenesis methods, such as error-prone PCR, create greater numbers of distant mutations than close mutations because enzymes contain more amino acids distant from the active site than close to the active site. This suggests that instead of mutating the entire enzyme, focusing mutations near the substrate-binding site might dramatically increase the success rate in many directed evolution experiments.     

Enzyme promiscuity – A light on the “darker” side of enzyme specificity

Abstract

Enzyme promiscuity can be defined as the capability of enzymes to catalyse side reaction in addition to its main reaction. The side reaction of an enzyme is termed as promiscuous or sometimes as the “darker” side of enzyme cross-reactivity/specificity. This unique property of enzyme allows organisms to adapt under varying environmental conditions. Promiscuous enzymes can modify their catalytic activities with altered substrates and can adjust their catalytic and kinetic mechanisms according to substrate properties. This group of enzymes evolved from ancestral proteins found in primitive organisms like archaea that survive under extreme environmental conditions. Such ancestral proteins possessed the potential to catalyse a wide range of reactions at low levels, hence create families or superfamilies of highly specialized enzymes. Further, some enzymes were identified which have non-catalytic functions in addition to their major catalytic activities. These enzymes are referred to as moonlighting enzymes. The study of these enzymes will provide important information regarding enzyme evolution and will help in optimizing protein engineering applications.     

Engineering enzyme access tunnels

Enzymes are efficient and specific catalysts for many essential reactions in biotechnological and pharmaceutical industries. Many times, the natural enzymes do not display the catalytic efficiency, stability or specificity required for these industrial processes. The current enzyme engineering methods offer solutions to this problem, but they mainly target the buried active site where the chemical reaction takes place. Despite being many times ignored, the tunnels and channels connecting the environment with the active site are equally important for the catalytic properties of enzymes. Changes in the enzymatic tunnels and channels affect enzyme activity, specificity, promiscuity, enantioselectivity and stability. This review provides an overview of the emerging field of enzyme access tunnel engineering with case studies describing design of all the aforementioned properties. The software tools for the analysis of geometry and function of the enzymatic tunnels and channels and for the rational design of tunnel modifications will also be discussed. The combination of new software tools and enzyme engineering strategies will provide enzymes with access tunnels and channels specifically tailored for individual industrial processes.     

Metabolic pathway promiscuity in the archaeon Sulfolobus solfataricus revealed by studies on glucose dehydrogenase and 2-keto-3-deoxygluconate aldolase

The hyperthermophilic Archaeon Sulfolobus solfataricus metabolizes glucose by a non-phosphorylative variant of the Entner-Doudoroff pathway. In this pathway glucose dehydrogenase and gluconate dehydratase catalyze the oxidation of glucose to gluconate and the subsequent dehydration of gluconate to 2-keto-3-deoxygluconate. 2-Keto-3-deoxygluconate (KDG) aldolase then catalyzes the cleavage of 2-keto-3-deoxygluconate to glyceraldehyde and pyruvate. The gene encoding glucose dehydrogenase has been cloned and expressed in Escherichia coli to give a fully active enzyme, with properties indistinguishable from the enzyme purified from S. solfataricus cells. Kinetic analysis revealed the enzyme to have a high catalytic efficiency for both glucose and galactose. KDG aldolase from S. solfataricus has previously been cloned and expressed in E. coli. In the current work its stereoselectivity was investigated by aldol condensation reactions between D-glyceraldehyde and pyruvate; this revealed the enzyme to have an unexpected lack of facial selectivity, yielding approximately equal quantities of 2-keto-3-deoxygluconate and 2-keto-3-deoxygalactonate. The KDG aldolase-catalyzed cleavage reaction was also investigated, and a comparable catalytic efficiency was observed with both compounds. Our evidence suggests that the same enzymes are responsible for the catabolism of both glucose and galactose in this Archaeon. The physiological and evolutionary implications of this observation are discussed in terms of catalytic and metabolic promiscuity.     

Preparation of Immobilized L‐Prolinamide Via Enzymatic Polymerization of Phenolic L‐Prolinamide and Evaluation of Its Catalytic Performance for Direct Asymmetric Aldol Reaction

Phenolic L‐prolinamide was allowed to participate in enzymatic polymerization with horseradish peroxidase as the catalyst, generating immobilized L‐prolinamide. The catalytic performance of the resultant polymer‐supported L‐prolinamide for direct asymmetric aldol reaction between aromatic aldehyde and cyclohexanone was studied. The results show that as prepared L‐prolinamide can catalyze the aldol reaction at room temperature in the presence of H₂O. Relevant aldol addition products are obtained with good yields (up to 91%), high diastereoselectivities (up to 6:94 dr), and medium enantioselectivities (up to 87% ee). Moreover, the title polymer‐supported catalyst can be recovered and reused for at least five cycles while the activity remains almost unchanged. Chirality 26:209–213, 2014. © 2014 Wiley Periodicals, Inc.     

Accessing the reproducibility and specificity of pepsin and other aspartic proteases

The aspartic protease pepsin is less specific than other endoproteinases. Because aspartic proteases like pepsin are active at low pH, they are utilized in hydrogen deuterium exchange mass spectrometry (HDX MS) experiments for digestion under hydrogen exchange quench conditions. We investigated the reproducibility, both qualitatively and quantitatively, of online and offline pepsin digestion to understand the compliment of reproducible pepsin fragments that can be expected during a typical pepsin digestion. The collection of reproducible peptides was identified from > 30 replicate digestions of the same protein and it was found that the number of reproducible peptides produced during pepsin digestion becomes constant above 5–6 replicate digestions. We also investigated a new aspartic protease from the stomach of the rice field eel (Monopterus albus Zuiew) and compared digestion efficiency and specificity to porcine pepsin and aspergillopepsin. Unique cleavage specificity was found for rice field eel pepsin at arginine, asparagine, and glycine. Different peptides produced by the various proteases can enhance protein sequence coverage and improve the spatial resolution of HDX MS data. This article is part of a Special Issue entitled: Mass spectrometry in structural biology.     

Role of chemistry versus substrate binding in recruiting promiscuous enzyme functions

Two different scenarios for the recruitment of evolutionary starting points and their subsequent divergence to give new enzymes have been described. The coincidental, promiscuous starting activity may regard the same reaction chemistry on a new substrate (substrate ambiguity). Alternatively, substrate binding guides the recruitment of an enzyme whose reaction chemistry differs from that of the newly evolving one (catalytic promiscuity). While substrate ambiguity seems to underlie the divergence of most enzyme families, the relative levels of occurrence of these scenarios remain unknown. Screening the Escherichia coli proteome with a comparative series of xenobiotic substrates, we found that substrate ambiguity was, as anticipated, more frequent than reaction promiscuity. However, for at least one unnatural reaction (phosphonoesterase), a promiscuous enzyme was identified only when the substrate was decorated with the naturally abundant phosphate group. These findings support the prevailing hypothesis of chemistry-driven divergence but also suggest that recognition of familiar substrate motifs plays a role. In the absence of enzymes catalyzing the same chemistry, having a familiar, naturally occurring substrate motif (chemophore) such as phosphate may increase the likelihood of catalytic promiscuity. Chemophore anchoring may also find practical applications in identifying catalysts for unnatural reactions.     

Catalytic versus inhibitory promiscuity in cytochrome P450s: implications for evolution of new function

Catalytically promiscuous enzymes are intermediates in the evolution of new function from an existing pool of protein scaffolds. However, promiscuity will only confer an evolutionary advantage if other useful properties are not compromised or if there is no "negative trade-off" induced by the mutations that yield promiscuity. Therefore, identification and characterization of negative trade-offs incurred during the emergence of promiscuity are required to further develop the evolutionary models and to optimize in vitro evolution. One potential negative trade-off of catalytic promiscuity is increased susceptibility to inhibition, or inhibitory promiscuity. Here we exploit cytochrome P450s (CYPs) as a model protein scaffold that spans a vast range of catalytic promiscuity and apply a quantitative index to determine the relationship between promiscuity of catalysis and promiscuity of inhibition for a series of homologues. The aim of these studies is to begin to identify properties that, in general, correlate with catalytic promiscuity, hypothetically such as inhibitory promiscuity. Interestingly, the data indicate that the potential negative trade-off of inhibitory promiscuity is nearly insignificant because even highly substrate specific CYPs have high inhibitory promiscuity, with little incremental increase in susceptibility to inhibitory interactions as the substrate promiscuity increases across the series of enzymes. In the context of evolution, inhibitory promiscuity is not an obligate negative trade-off for catalytic promiscuity.     

Gastric proteases of the Greenland cod Gadus ogac. II. Structural properties

Three gastric proteases were isolated from the stomach mucosa of the Greenland cod (Gadus ogac). The cod proteases were all less stable to heating and protease 1 retained less activity at 5 degrees C when the pH was greater than 5 in comparison with porcine pepsin. The activities of cod proteases 1 and 2, with hemoglobin as the substrate, were doubled in the presence of 25 mM NaCl, while cod protease 3 and porcine pepsin were not stimulated by the salt. The cod proteases did not cross-react with antibodies raised against porcine pepsin. However, some cross-reactivity was noted with antibodies raised against proteases from psychotrophic pseudomonads. The molecular weights of all the cod proteases were in the range of 36,000-38,000. The amino acid compositions of the cod proteases as compared by the Metzger difference index differed from the mammalian gastric proteases by about the same extent that pepsin, gastricsin, and chymosin differ from each other. Of the cod enzymes, protease 1 differed from mammalian gastric proteases, while cod proteases 3 was more like chymosin with respect to amino acid composition. Cod protease 1 had the lowest hydrophobicity index and chymosin had the highest. The hydrophobicity indices of cod proteases 2 and 3 were intermediate between that of porcine pepsin and bovine chymosin. It is suggested that the Greenland cod proteases represent less differentiated forms of gastric proteases than the mammalian pepsins, gastricsins, and chymosins.