The Interaction of Isopenicillin N Synthase with Homologated Substrate Analogues δ‐(L‐α‐Aminoadipoyl)‐L‐homocysteinyl‐D‐Xaa Characterised by Protein Crystallography

Isopenicillin N synthase (IPNS) converts the linear tripeptide δ‐(L ‐α‐aminoadipoyl)‐L ‐cysteinyl‐D ‐valine (ACV) into bicyclic isopenicillin N (IPN) in the central step in the biosynthesis of penicillin and cephalosporin antibiotics. Solution‐phase incubation experiments have shown that IPNS turns over analogues with a diverse range of side chains in the third (valinyl) position of the substrate, but copes less well with changes in the second (cysteinyl) residue. IPNS thus converts the homologated tripeptides δ‐(L ‐α‐aminoadipoyl)‐L ‐homocysteinyl‐D ‐valine (AhCV) and δ‐(L ‐α‐aminoadipoyl)‐L ‐homocysteinyl‐D ‐allylglycine (AhCaG) into monocyclic hydroxy‐lactam products; this suggests that the additional methylene unit in these substrates induces conformational changes that preclude second ring closure after initial lactam formation. To investigate this and solution‐phase results with other tripeptides δ‐(L ‐α‐aminoadipoyl)‐L ‐homocysteinyl‐D ‐Xaa, we have crystallised AhCV and δ‐(L ‐α‐aminoadipoyl)‐L ‐homocysteinyl‐D ‐S‐methylcysteine (AhCmC) with IPNS and solved crystal structures for the resulting complexes. The IPNS:Fe^II:AhCV complex shows diffuse electron density for several regions of the substrate, revealing considerable conformational freedom within the active site. The substrate is more clearly resolved in the IPNS:Fe^II:AhCmC complex, by virtue of thioether coordination to iron. AhCmC occupies two distinct conformations, both distorted relative to the natural substrate ACV, in order to accommodate the extra methylene group in the second residue. Attempts to turn these substrates over within crystalline IPNS using hyperbaric oxygenation give rise to product mixtures.     

The Role of a Nonribosomal Peptide Synthetase in l‐Lysine Lactamization During Capuramycin Biosynthesis

Capuramycins are one of several known classes of natural products that contain an l ‐Lys‐derived l ‐α‐amino‐?‐caprolactam (l ‐ACL) unit. The α‐amino group of l ‐ACL in a capuramycin is linked to an unsaturated hexuronic acid component through an amide bond that was previously shown to originate by an ATP‐independent enzymatic route. With the aid of a combined in vivo and in vitro approach, a predicted tridomain nonribosomal peptide synthetase CapU is functionally characterized here as the ATP‐dependent amide‐bond‐forming catalyst responsible for the biosynthesis of the remaining amide bond present in l ‐ACL. The results are consistent with the adenylation domain of CapU as the essential catalytic component for l ‐Lys activation and thioesterification of the adjacent thiolation domain. However, in contrast to expectations, lactamization does not require any additional domains or proteins and is likely a nonenzymatic event. The results set the stage for examining whether a similar NRPS‐mediated mechanism is employed in the biosynthesis of other l ‐ACL‐containing natural products and, just as intriguingly, how spontaneous lactamization is avoided in the numerous NRPS‐derived peptides that contain an unmodified l ‐Lys residue.     

Enzymatic preparation of L‐α‐glycerylphosphorylcholine in an aqueous medium

L ‐α‐Glycerylphosphorylcholine (L ‐α‐GPC) was successfully prepared from phosphatidylcholine (PC) of food‐grade soy lecithin powder using a novel enzymatic reaction in an aqueous medium. 94.5% yield of L ‐α‐GPC was obtained under the optimal conditions of 55°C, 6.67 mg/mL substrate, 2 mM CaCl₂, and 33.4 U/mL phospholipase A₁ (Lecitase Ultra). L ‐α‐GPC at 98% purity, 73.4% (wt%) recovery, and specific rotation ( ) of ?2.5° was achieved by silica gel column chromatography. Owing to its excellent catalytic efficiency, low cost, and ready availability, phospholipase A₁ (Lecitase Ultra) provides a very satisfactory option for converting PC to L ‐α‐GPC. Practical applications: L ‐α‐Glycerylphosphorylcholine (L ‐α‐GPC) has been studied recently for its potential use as a supplement that may support neurological functions, but it is only found in trace amounts in nature. The present results indicate that Lecitase Ultra can be used for producing L ‐α‐GPC from aqueous PC and suggest encouraging prospects for practical or industrial applications utilizing its notable catalytic performance, economy, and convenience.     

Synthesis of Amino Acid Conjugates and Further Derivatives of 3α‐Hydroxylup‐20(;29)ene‐23,28‐dioic acid

Triterpenes of betulinic acid type exhibit many interesting biological activities. Therefore a series of new 3α‐hydroxy‐lup‐20(29)‐ene‐23,28‐dioic acid derivatives 2a—22 with putative pharmacological activities were synthesized. As starting compounds 3α‐hydroxy‐lup‐20(29)‐ene‐23,28‐dioic acid ( 1a ), isolated from Schefflera octophylla, or its 3‐O‐acetyl derivative 1b were used. Mono‐ and diesters ( 2a—b from 1a , and 4d from 4c ) were prepared with CH₂N₂. Oxidation of the isopropenyl side chain with OsO₄ yielded the 20,29‐diols ( 4a—b from 1b , and 19 from 17 ), which were in the case of 4b further transformed to the 29‐norketones 8a/mdash;b . Oxidation of the isopropenyl side chain with m‐chloroperbenzoic acid afforded the 20,29‐epoxide 12 (from 1b ) and the 29‐aldehydes and a‐hydroxy aldehydes ( 13a—c from 2a, 14a—c from 2b , and 16a—c from 15a ). Ring A was modified by a tosylation—elimination sequence using p‐TsCl/NaOAc, which afforded diolefin 15a (from 2a ) with Δ^2,20(29) double bonds or 23‐nor‐Δ^3,20(29)diolefin 17 (from 1a ). Compounds 4b, 4c , and 8a were coupled with L ‐methionin, L ‐phenylalanin, L ‐alanin, L ‐serin, and L ‐glutaminic acid via amide bonds at positions 23 and 28 to afford the amino acid conjugates 5a—7b and 9a—11 .     

An Activator of an Adenylation Domain Revealed by Activity but Not Sequence Homology

Nonribosomal peptide synthetases (NRPSs), which are responsible for synthesizing many medicinally important natural products, frequently use adenylation domain activators (ADAs) to promote substrate loading. Although ADAs are usually MbtH‐like proteins (MLPs), a new type of ADA appears to promote an NRPS‐dependent incorporation of a dihydropyrrole unit into sibiromycin. The adenylation and thiolation didomain of the NRPS SibD catalyzes the adenylation of a limited number of amino acids including l ‐Tyr, the precursor in dihydropyrrole biosynthesis, as determined by a standard radioactivity exchange assay. LC‐MS/MS analysis confirmed loading of l ‐Tyr onto the thiolation domain. SibB, a small protein with no prior functional assignment or sequence homology to MLPs, was found to promote the exchange activity. MLPs from bacteria expressing homologous biosynthetic pathways were unable to replace this function of SibB. The discovery of this new type of ADA demonstrates the importance of searching beyond the conventional MLP standard for proteins affecting NRPS activity.     

Recombinant Δ4,5‐Steroid 5 β‐Reductases as Biocatalysts for the Reduction of Activated CC‐Double Bonds in Monocyclic and Acyclic Molecules

It was found that Δ^4,5‐steroid 5β‐reductases are capable of reducing also small molecules bearing an activated CC double bond such as monocyclic enones and acyclic enoate esters. As preferred Δ^4,5‐steroid 5β‐reductase (5β‐StR) for this purpose, 5β‐StR from Arabidopsis thaliana was used. In part, enzyme activities are even higher than that for progesterone. Successful preliminary biotransformations with enzymatic in situ cofactor recycling were also carried out. When using the prochiral compound isophorone as a substrate, a high enantioselective reaction course (>99% ee) was observed.     

Loop‐Grafted Old Yellow Enzymes in the Bienzymatic Cascade Reduction of Allylic Alcohols

The enzymatic reduction of C=C bonds in allylic alcohols with Old Yellow Enzymes represents a challenging task, due to insufficient activation through the hydroxy group. In our work, we coupled an alcohol dehydrogenase with three wild‐type ene reductases—namely nicotinamide‐dependent cyclohex‐2‐en‐1‐one reductase (NCR) from Zymomonas mobilis, OYE1 from Saccharomyces pastorianus and morphinone reductase (MR) from Pseudomonas putida M10—and four rationally designed β/α loop variants of NCR in the bienzymatic cascade hydrogenation of allylic alcohols. Remarkably, the wild type of NCR was not able to catalyse the cascade reaction whereas MR and OYE1 demonstrated high to excellent activities. Through the rational loop grafting of two intrinsic β/α surface loop regions near the entrance of the active site of NCR with the corresponding loops from OYE1 or MR we successfully transferred the cascade reduction activity from one family member to another. Further we observed that loop grafting revealed certain influences on the interaction with the nicotinamide cofactor.     

Structure,Activity and Stereoselectivity of NADPH‐Dependent Oxidoreductases Catalysing the S‐Selective Reduction of the Imine Substrate 2‐Methylpyrroline

Oxidoreductases from Streptomyces sp. GF3546 [3546‐IRED], Bacillus cereus BAG3X2 (BcIRED) and Nocardiopsis halophila (NhIRED) each reduce prochiral 2‐methylpyrroline (2MPN) to (S)‐2‐methylpyrrolidine with >95 % ee and also a number of other imine substrates with good selectivity. Structures of BcIRED and NhIRED have helped to identify conserved active site residues within this subgroup of imine reductases that have S selectivity towards 2MPN, including a tyrosine residue that has a possible role in catalysis and superimposes with an aspartate in related enzymes that display R selectivity towards the same substrate. Mutation of this tyrosine residue—Tyr169—in 3546‐IRED to Phe resulted in a mutant of negligible activity. The data together provide structural evidence for the location and significance of the Tyr residue in this group of imine reductases, and permit a comparison of the active sites of enzymes that reduce 2MPN with either R or S selectivity.     

Helix‐Grafted Pleckstrin Homology Domains Suppress HIV‐1 Infection of CD4‐Positive Cells

The size, functional group diversity and three‐dimensional structure of proteins often allow these biomolecules to bind disease‐relevant structures that challenge or evade small‐molecule discovery. Additionally, folded proteins are often much more stable in biologically relevant environments compared to their peptide counterparts. We recently showed that helix‐grafted display—extensive resurfacing and elongation of an existing solvent‐exposed helix in a pleckstrin homology (PH) domain—led to a new protein that binds a surrogate of HIV‐1 gp41, a validated target for inhibition of HIV‐1 entry. Expanding on this work, we prepared a number of human‐derived helix‐grafted‐display PH domains of varied helix length and measured properties relevant to therapeutic and basic research applications. In particular, we showed that some of these new reagents expressed well as recombinant proteins in Escherichia coli, were relatively stable in human serum, bound a mimic of pre‐fusogenic HIV‐1 gp41 in vitro and in complex biological environments, and significantly lowered the incidence of HIV‐1 infection of CD4‐positive cells.     

Functional Characterization of PyrG,an Unusual Nonribosomal Peptide Synthetase Module from the Pyridomycin Biosynthetic Pathway

Pyridomycin is an antimycobacterial cyclodepsipeptide assembled by a nonribosomal peptide synthetase/polyketide synthase hybrid system. Analysis of its cluster revealed a nonribosomal peptide synthetase (NRPS) module, PyrG, that contains two tandem adenylation domains and a PKS‐type ketoreductase domain. In this study, we biochemically validated that the second A domain recognizes and activates α‐keto‐β‐methylvaleric acid (2‐KVC) as the native substrate; the first A domain was not functional but might play a structural role. The KR domain catalyzed the reduction of the 2‐KVC tethered to the peptidyl carrier protein of PyrG in the presence of the MbtH family protein, PyrH. PyrG was demonstrated to recognize many amino acids. This substrate promiscuity provides the potential to generate pyridomycin analogues with various enolic acids moiety; this is important for binding InhA, a critical enzyme for cell‐wall biosynthesis in Mycobacterium tuberculosis.     

Semirational Protein Engineering of CYP153AM.aq.‐CPRBM3 for Efficient Terminal Hydroxylation of Short‐ to Long‐Chain Fatty Acids

The regioselective terminal hydroxylation of alkanes and fatty acids is of great interest in a variety of industrial applications, such as in cosmetics, in fine chemicals, and in the fragrance industry. The chemically challenging activation and oxidation of non‐activated C?H bonds can be achieved with cytochrome P450 enzymes. CYP153A_M.aq.‐CPR_BM3 is an artificial fusion construct consisting of the heme domain from Marinobacter aquaeolei and the reductase domain of CYP102A1 from Bacillus megaterium. It has the ability to hydroxylate medium‐ and long‐chain fatty acids selectively at their terminal positions. However, the activity of this interesting P450 construct needs to be improved for applications in industrial processes. For this purpose, the design of mutant libraries including two consecutive steps of mutagenesis is demonstrated. Targeted positions and residues chosen for substitution were based on semi‐rational protein design after creation of a homology model of the heme domain of CYP153A_M.aq., sequence alignments, and docking studies. Site‐directed mutagenesis was the preferred method employed to address positions within the binding pocket, whereas diversity was created with the aid of a degenerate codon for amino acids located at the substrate entrance channel. Combining the successful variants led to the identification of a double variant—G307A/S233G—that showed alterations of one position within the binding pocket and one position located in the substrate access channel. This double variant showed twofold increased activity relative to the wild type for the terminal hydroxylation of medium‐chain‐length fatty acids. This variant furthermore showed improved activity towards short‐ and long‐chain fatty acids and enhanced stability in the presence of higher concentrations of fatty acids.     

New Insights into Additive Structure Effect on Crystal Agglomeration of L‐Valine

Specific small amounts of amino acids caused agglomeration of L‐valine (L‐Val) crystals during evaporative crystallization from aqueous solutions. The agglomeration of L‐Val occurred only under acidic condition when guest amino acids satisfied several conditions. Only L‐form amino acids that have carboxylic acid groups and sufficiently long alkyl chain in the side‐chains could induce agglomeration of L‐Val. The length of alkyl chain in the side‐chains controls the degree of agglomeration. Data indicated only 0.5 wt % of L‐2‐aminoadipic acid, which has a similar chemical structure to L‐glutamic acid (L‐Glu), produced the large agglomerates > 1000 μm. The particle size was ～ 500 μm when using the same amount of L‐Glu. Based on the results from previous tests and this paper, the whole mechanism for the L‐Val agglomeration in the presence of specific guest amino acids has been revealed.     

Stereo‐Controlled Asymmetric Bioreduction of α,β‐Dehydroamino Acid Derivatives

α,β‐Dehydroamino acid derivatives proved to be a novel substrate class for ene‐reductases from the ‘old yellow enzyme’ (OYE) family. Whereas N‐acylamino substituents were tolerated in the α‐position, β‐analogues were generally unreactive. For aspartic acid derivatives, the stereochemical outcome of the bioreduction using OYE3 could be controlled by variation of the N‐acyl protective group to furnish the corresponding (S)‐ or (R)‐amino acid derivatives. This switch of stereopreference was explained by a change in the substrate binding, by exchange of the activating ester group, which was proven by ²H‐labelling experiments.     

Exploiting the Catalytic Diversity of Short‐Chain Dehydrogenases/Reductases: Versatile Enzymes from Plants with Extended Imine Substrate Scope

Numerous short‐chain dehydrogenases/reductases (SDRs) have found biocatalytic applications in C=O and C=C (enone) reduction. For NADPH‐dependent C=N reduction, imine reductases (IREDs) have primarily been investigated for extension of the substrate range. Here, we show that SDRs are also suitable for a broad range of imine reductions. The SDR noroxomaritidine reductase (NR) is involved in Amaryllidaceae alkaloid biosynthesis, serving as an enone reductase. We have characterized NR by using a set of typical imine substrates and established that the enzyme is active with all four tested imine compounds (up to 99 % conversion, up to 92 % ee). Remarkably, NR reduced two keto compounds as well, thus highlighting this enzyme family's versatility. Using NR as a template, we have identified an as yet unexplored SDR from the Amaryllidacea Zephyranthes treatiae with imine‐reducing activity (≤95 % ee). Our results encourage the future characterization of SDR family members as a means of discovering new imine‐reducing enzymes.     

A Multiple‐Labeling Strategy for Nonribosomal Peptide Synthetases Using Active‐Site‐Directed Proteomic Probes for Adenylation Domains

Genetic approaches have greatly contributed to our understanding of nonribosomal peptide biosynthetic machinery; however, proteomic investigations are limited. Here, we developed a highly sensitive detection strategy for multidomain nonribosomal peptide synthetases (NRPSs) by using a multiple‐labeling technique with active‐site‐directed probes for adenylation domains. When applied to gramicidin S‐producing and ‐nonproducing strains of Aneurinibacillus migulanus (DSM 5759 and DSM 2895, respectively), the multiple technique sensitively detected an active multidomain NRPS (GrsB) in lysates obtained from the organisms. This functional proteomics method revealed an unknown inactive precursor (or other inactive form) of GrsB in the nonproducing strain. This method provides a new option for the direct detection, functional analysis, and high‐resolution identification of low‐abundance active NRPS enzymes in native proteomic environments.     

Multi‐Enzymatic Synthesis of Optically Pure β‐Hydroxy α‐Amino Acids

A novel enzymatic production system of optically pure β‐hydroxy α‐amino acids was developed. Two enzymes were used for the system: an N‐succinyl L ‐amino acid β‐hydroxylase (SadA) belonging to the iron(II)/α‐ketoglutarate‐dependent dioxygenase superfamily and an N‐succinyl L ‐amino acid desuccinylase (LasA). The genes encoding the two enzymes are part of a gene set responsible for the biosynthesis of peptidyl compounds found in the Burkholderia ambifaria AMMD genome. SadA stereoselectively hydroxylated several N‐succinyl aliphatic L ‐amino acids and produced N‐succinyl β‐hydroxy L ‐amino acids, such as N‐succinyl‐L ‐β‐hydroxyvaline, N‐succinyl‐L ‐threonine, (2S,3R)‐N‐succinyl‐L ‐β‐hydroxyisoleucine, and N‐succinyl‐L ‐threo‐β‐hydroxyleucine. LasA catalyzed the desuccinylation of various N‐succinyl‐L ‐amino acids. Surprisingly, LasA is the first amide bond‐forming enzyme belonging to the amidohydrolase superfamily, and has succinylation activity towards the amino group of L ‐leucine. By combining SadA and LasA in a preparative scale production using N‐succinyl‐L ‐leucine as substrate, 2.3 mmol of L ‐threo‐β‐hydroxyleucine were successfully produced with 93% conversion and over 99% of diastereomeric excess. Consequently, the new production system described in this study has advantages in optical purity and reaction efficiency for application in the mass production of several β‐hydroxy α‐amino acids.

     

β‐Aminopeptidase‐Catalyzed Biotransformations of β2‐Dipeptides: Kinetic Resolution and Enzymatic Coupling

We have previously shown that the β‐aminopeptidases BapA from Sphingosinicella xenopeptidilytica and DmpA from Ochrobactrum anthropi can catalyze reactions with non‐natural β³‐peptides and β³‐amino acid amides. Here we report that these exceptional enzymes are also able to utilize synthetic dipeptides with N‐terminal β²‐amino acid residues as substrates under aqueous conditions. The suitability of a β²‐peptide as a substrate for BapA or DmpA was strongly dependent on the size of the C_α substituent of the N‐terminal β²‐amino acid. BapA was shown to convert a diastereomeric mixture of the β²‐peptide H‐β²hPhe‐β²hAla‐OH, but did not act on diastereomerically pure β²,β³‐dipeptides containing an N‐terminal β²‐homoalanine. In contrast, DmpA was only active with the latter dipeptides as substrates. BapA‐catalyzed transformation of the diastereomeric mixture of H‐β²hPhe‐β²hAla‐OH proceeded along two highly S‐enantioselective reaction routes, one leading to substrate hydrolysis and the other to the synthesis of coupling products. The synthetic route predominated even at neutral pH. A rise in pH of three log units shifted the synthesis‐to‐hydrolysis ratio (v_S/v_H) further towards peptide formation. Because the equilibrium of the reaction lies on the side of hydrolysis, prolonged incubation resulted in the cleavage of all peptides that carried an N‐terminal β‐amino acid of S configuration. After completion of the enzymatic reaction, only the S enantiomer of β²‐homophenylalanine was detected (ee>99 % for H‐(S)‐β²‐hPhe‐OH, E>500); this confirmed the high enantioselectivity of the reaction. Our findings suggest interesting new applications of the enzymes BapA and DmpA for the production of enantiopure β²‐amino acids and the enantioselective coupling of N‐terminal β²‐amino acids to peptides.     

Cycloaddition Reactions of 1,3‐Diaza‐2‐azoniaallene Salts and Glycals

The 1,3‐diaza‐2‐azoniaallene salt 3a reacts stereoselectively with glycals ( 5a—e ) to afford pyrano[2,3‐d]‐1,2,3‐ triazolium salts 6a—e . In contrast to other 1,3‐dipolar cycloadditions of glycals reported so far, the stereoselectivity of compounds 6 is not determined by the substituent on C‐3 of the glycal. Both cis ( 6a,b ) and trans ( 6d,e ) substitutions on C‐7 and C‐7a were found for bicyclic compounds 6 (crystal structure of 6a ). Under the influence of acid 6e opens the pyran ring to give the triazolium salt 9 . Addition of antimony pentachloride to a solution of the glycal 5e and the chlorotriazene 2a results in the formation of the pyranotriazene 12 containing two triazene units. In the presence of acid the pyranotriazene 6c reacts with alcohols to afford 2‐hydrazino glycosides 13a,b, 15 , which with zinc dust in acetic acid are reduced to 2‐amino glycosides 14a,b .     

Synthesis of 2H‐Thiopyrans by Rhodium(II) Acetate‐Catalyzed Reaction of 4‐Amino‐2,5‐dihydro‐3‐thiophenecarbonitriles with α‐Diazocarbonyl Compounds. Part 1

4‐Amino‐2,5‐dihydro‐3‐thiophenecarbonitriles 1 reacted with dimethyl diazomalonate in the presence of rhodium(II) acetate to give regioselectively 4‐cyano‐2H‐thio‐pyrans 2 (C ₂— S insertion), and 5‐cyano‐2H‐thiopyrans (C ₅— S insertion) were not isolated. Similar insertion was also observed in the reaction of 1 with methyl diazoacetoacetate and ethyl diazobenzoylacetate. The starting compounds 1 were synthesized by the reaction of tetrahydro‐4‐oxo‐3‐thiophene‐carbonitrile with morpholine, piperidine, and pyrrolidine in the presence of formic acid in ethanol.     

Phenolic antioxidants – radical‐scavenging and chain‐breaking activity: A comparative study

Fifty phenolic antioxidants (AH) (42 individual compounds and 8 binary mixtures of two antioxidants) were chosen for a comparative analysis of their radical‐scavenging (H‐donating) and chain‐breaking (antioxidant) activity. Correlations between experimental (antiradical and antioxidant) and predictable (theoretical) activities of 15 flavonoids, 15 hydroxy cinnamic acid derivatives, 5 hydroxy chalcones, 4 dihydroxy coumarins and 3 standard antioxidants (butylated hydroxytoluene, hydroquinone, DL ‐α‐tocopherol) were summarized and discussed. The following models were applied to explain the structure‐activity relationships of phenolic antioxidants of natural origin: (a) model 1, a DPPH assay used for the determination of the radical‐scavenging capacity (AH + DPPH? → A? + DPPH‐H); (b) model 2, chemiluminescence of a model substrate RH (cumene or diphenylmethane) used for the determination of the rate constant of a reaction with model peroxyl radicals (AH + RO₂? → ROOH + A?); (c) model 3, lipid autoxidation used for the determination of the chain‐breaking antioxidant efficiency and reactivity (AH + LO₂? → LOOH + A?; A? + LH (+O₂) → AH + LO₂?); and (d) model 4, theoretical methods used for predicting the activity (predictable activity). The highest lipid oxidation stability was found for antioxidants with a catecholic structure and for their binary mixtures with DL ‐α‐tocopherol, as a result of synergism between them.