Pipecolic Acid Derivatives Research Articles

Molecular and Structural Basis for Cγ−C Bond Formation by PLP‐Dependent Enzyme Fub7

AbstractPyridoxal 5’‐phosphate (PLP)‐dependent enzymes that catalyze γ‐replacement reactions are prevalent, yet their utilization of carbon nucleophile substrates is rare. The recent discovery of two PLP‐dependent enzymes, CndF and Fub7, has unveiled unique C−C bond forming capabilities, enabling the biocatalytic synthesis of alkyl‐ substituted pipecolic acids from O‐acetyl‐L‐homoserine and β‐keto acid or aldehyde derived enolates. This breakthrough presents fresh avenues for the biosynthesis of pipecolic acid derivatives. However, the catalytic mechanisms of these enzymes remain elusive, and a dearth of structural information hampers their extensive application. Here, we have broadened the catalytic scope of Fub7 by employing ketone‐derived enolates as carbon nucleophiles, revealing Fub7’s capacity for substrate‐dependent regioselective α‐alkylation of unsymmetrical ketones. Through an integrated approach combining X‐ray crystallography, spectroscopy, mutagenesis, and computational docking studies, we offer a detailed mechanistic insight into Fub7 catalysis. Our findings elucidate the structural basis for its substrate specificity, stereoselectivity, and regioselectivity. Our work sets the stage ready for subsequent protein engineering effort aimed at expanding the synthetic utility of Fub7, potentially unlocking novel methods to access a broader array of noncanonical amino acids.

Diastereoselective synthesis of new zwitterionic bicyclic lactams, scaffolds for construction of 2-substituted-4-hydroxy piperidine and its pipecolic acid derivatives.

The synthesis of new chiral highly functionalized zwitterionic bicyclic lactams starting from acyclic β-enaminoesters derived from (R)-(−)-2-phenylglycinol is described. The key step involved an intramolecular non-classical Corey–Chaykovsky ring-closing reaction of the corresponding sulfonium salts derived from β-enaminoesters. This methodology permits the generation of two or three new stereogenic centers with high diastereoselectivity. The utility of these intermediates was demonstrated by the stereocontrolled total synthesis of cis-4-hydroxy-2-methyl piperidine and its corresponding pipecolic acid derivative.

A Stereoselective aza-Prins Reaction: Rapid Access to Enantiopure Piperidines and Pipecolic Acids

The aza-Prins reaction is a widely employed and highly efficient method for the preparation of saturated nitrogen-containing heterocycles. Its major drawback has always been a lack of diastereoselectivity and the formation of racemic products. Herein, we address these problems and report, for the first time, the synthesis of both diastereomerically and enantiopure multiply substituted piperidines via the aza-Prins reaction. This method is widely applicable for natural product synthesis and is exemplified here by the synthesis of enantiopure pipecolic acid derivatives.

An Aliphatic Bischler-Napieralski Reaction: Dihydropyridones by Cyclocarbonylation of 3-Allylimidazolidin-4-ones.

The N-chloroformylimidazolidinone derivative of enantiopure l-alanine was deprotonated to form an enolate and functionalized with a series of allylic halides. Treatment of the resulting carbamoyl chlorides with potassium iodide led to cyclization of the allylic substituent onto the carbonyl group in an intramolecular aliphatic Friedel-Crafts-type acylation that corresponds to an aliphatic Bischler-Napieralski reaction. The product 3,4-dihydropyridinones were amenable to further functionalization, and finally hydrolysis, to deliver a series of enantio-enriched pipecolic acid derivatives.

A Mild Synthesis of Bicyclic Alkoxyoxazolium Salts from Proline and Pipecolic Acid Derivatives.

A regio‐ and chemoselective preparation of bicyclic alkoxyoxazolium salts from amide derivatives of proline and pipecolic acid by electrophilic amide activation is reported. Mechanistic NMR experiments suggest an unusual role for the base and highlight the effect of substitution pattern of the substrates.

Asymmetric Cα‐Alkylation of Pipecolic Acid via Curtin‐Hammett Controlled Diastereoselective N‐Alkylation

AbstractAn efficient asymmetric synthetic approach for the synthesis of Cα‐substituted pipecolic acid has been investigated through utilizing an N‐fused bicyclic system. Despite the fluxionality of the pipecolic imidazolidinone, N‐alkylation proceeded in high yield with excellent selectivity. The subsequent [2,3]‐Stevens rearrangement afforded Cα‐substituted pipecolic acid derivatives successfully. The computational study revealed that the diastereoselectivity during N‐alkylation is governed by Curtin‐Hammett kinetics.

The Asymmetric Aza-silyl-Prins Reaction: Synthesis of Enantiopure Piperidines.

The design and development of the first asymmetric aza-silyl-Prins reaction is reported, giving rise to valuable and diverse piperidines and pipecolic acid derivatives in both high yields and as single enantiomers. The creation of a novel chiral auxiliary-homoallylic amine for the aza-silyl-Prins reaction is essential to its success.

Biochemical and genetic characterization of fungal proline hydroxylase in echinocandin biosynthesis.

An intriguing structural feature of echinocandins is the incorporation of hydroxylated amino acids. Elucidation of the machinery and the mechanism responsible for this modification is critical to generate new echinocandin derivatives with enhanced antifungal activity. In our present study, we biochemically characterized the α-ketoglutarate/Fe2+-dependent proline hydroxylase (HtyE) from two Aspergillus species, Aspergillus pachycristatus and Aspergillus aculeatus, in the respective echinocandin B and aculeacin A biosynthetic gene clusters. Our results showed that both Ap- and Aa-HtyE converted L-proline to trans-4- and trans-3-hydroxyproline, but at different ratios. Both enzymes also effectively hydroxylated C-3 of 4R-methyl-proline, L-pipecolic acid, and D-proline. Our homology modeling and site-directed mutagenesis studies identified Leu182 of Ap-HtyE as a key residue in determining the regioselectivity of Ap-HtyE. Notably, we found that the efficiency in C-3 hydroxylation of 4R-methyl-proline has no direct correlation with the ratio of trans-4-hydroxylproline to trans-3-hydroxylproline catalyzed by HtyE. Deletion of Ap-htyE abolished A. pachycristatus anti-Candida activity and the production of echinocandin B, demonstrating that HtyE is the enzyme responsible for the hydroxylation of L-proline and 4R-methyl-proline in vivo and is essential for the anti-Candida activity of echinocandin B. Our present study thus sheds light on the biochemical basis for the selective hydroxylation of L-proline and 4R-methyl-proline and reveals a new type of biocatalyst with potential for the custom production of hydroxylated proline and pipecolic acid derivatives.

Pipped at the Post: Pipecolic Acid Derivative Identified as SAR Regulator

The non-protein amino acid pipecolic acid (Pip) is a lysine catabolite involved in plant systemic acquired resistance (SAR). In this issue of Cell, Hartmann etal. (2018) demonstrate that a flavin-dependent monooxygenase converts Pip to N-hydroxypipecolic acid (NHP), which functions as a critical metabolic regulator of SAR in Arabidopsis.

Synthesis of cis- and trans-(±)-3-mercaptoproline and pipecolic acid derivatives via thio-Michael addition

The reactivity of 2,3-dehydroproline and 2,3-dehydropipecolic acid methyl ester derivatives with S-nucleophiles in the thio-Michael addition reaction has been explored. The addition of triphenylmethanethiol and subsequent trityl cleavage led to the corresponding cis- and trans-(±)-3-mercaptoproline and pipecolic acid derivatives in good yields.

Liquid chromatographic resolution of proline and pipecolic acid derivatives on chiral stationary phases based on (+)‐(18‐crown‐6)‐2,3,11,12‐tetracarboxylic acid

Two liquid chromatographic chiral stationary phases based on (+)-(18-crown-6)-2,3,11,12-tetracarboxylic acid were applied to the resolution of the amide derivatives of cyclic α-amino acids including proline and pipecolic acid. Among the five amide derivatives of proline, aniline amide was resolved best on the first chiral stationary phase, which contains two N-H tethering amide groups, with the separation factor of 1.31 and the resolution of 2.60, and on the second chiral stationary phase, which contains two N-CH3 tethering amide groups, with the separation factor of 1.57 and the resolution of 5.50. Among the five amide derivatives of pipecolic acid, 2-naphthyl amide was resolved best on the first chiral stationary phase with the separation factor of 1.30 and the resolution of 1.75, but 1-naphthylmethyl amide was resolved best on the second chiral stationary phase with the separation factor of 1.30 and the resolution of 2.26. In general, the second chiral stationary phase was found to be better than the first chiral stationary phase in the resolution of the amide derivatives of cyclic α-amino acids. In this study, the second chiral stationary phase was first demonstrated to be useful for the resolution of secondary amino compounds.

Exploring the Chemistry of Bicyclic Isoxazolidines for the Multicomponent Synthesis of Glycomimetic Building Blocks.

Starting from a chiral furanone, the nitrone-olefin [3 + 2] cycloaddition can be used to obtain bicyclic isoxazolidines for which we report a set of reactions to selectively modify each functional position. These synthetically versatile bicyclic isoxazolidines allowed us to obtain complex glycomimetic building blocks, like iminosugars, via multicomponent chemistry. For example, a library of 20 pipecolic acid derivatives, a recurring motif in various prescription drugs, could be obtained via a one-pot Staudinger/aza-Wittig/Ugi three-component reaction of a bicyclic isoxazolidine-derived azido-hemiacetal. Notably, specific pipecolic acids in this library were obtained via hydrolysis of an unique tricyclic imidate side product of the Ugi reaction. The azido-hemiacetal was also converted into an aza-C-glycoside iminosugar via an unprecendented one-pot Staudinger/aza-Wittig/Mannich reaction.

Development, synthesis and structure–activity-relationships of inhibitors of the macrophage infectivity potentiator (Mip) proteins of Legionella pneumophila and Burkholderia pseudomallei

The bacteria Burkholderia pseudomallei and Legionella pneumophila cause severe diseases like melioidosis and Legionnaire’s disease with high mortality rates despite antibiotic treatment. Due to increasing antibiotic resistances against these and other Gram-negative bacteria, alternative therapeutical strategies are in urgent demand. As a virulence factor, the macrophage infectivity potentiator (Mip) protein constitutes an attractive target. The Mip proteins of B. pseudomallei and L. pneumophila exhibit peptidyl-prolyl cis/trans isomerase (PPIase) activity and belong to the PPIase superfamily. In previous studies, the pipecolic acid moiety proved to be a valuable scaffold for inhibiting this PPIase activity. Thus, a library of pipecolic acid derivatives was established guided by structural information and computational analyses of the binding site and possible binding modes. Stability and toxicity considerations were taken into account in iterative extensions of the library. Synthesis and evaluation of the compounds in PPIase assays resulted in highly active inhibitors. The activities can be interpreted in terms of a common binding mode obtained by docking calculations.

One‐Step Ruthenium‐Catalysed Transformation of 1,7‐Enynes into Strained Bicyclic Amino Esters

The reaction of 1,7‐enynes, synthesised from α‐amino acids, carried out with diazo compounds in the presence of the Cp*RuCl(cod) catalyst allowed the one‐step preparation of various strained bicyclic pipecolic acid derivatives in good yields under mild conditions. The stereoselectivity of the created double bond depends on the nature of the diazoalkane, and the diastereoselectivity arises essentially from steric factors.

Inhibitors of macrophage infectivity potentiator-like PPIases affect neisserial and chlamydial pathogenicity

The pathogenic bacteria Chlamydia trachomatis, Neisseria gonorrhoeae and Neisseria meningitidis express the surface-exposed macrophage infectivity potentiator (MIP)-like protein, which plays a role in their pathogenicity. MIP exhibits a peptidyl-prolyl isomerase (PPIase) activity that is inhibited by rapamycin and FK506. In this study, pipecolic acid derivatives were tested for their activity against the chlamydial and neisserial MIP. Two MIP inhibitors were identified, PipN3 and PipN4, that affected the developmental cycle of C. trachomatis in HeLa cells. Furthermore, we could show that deletion of neisserial MIP or addition of the two MIP inhibitors affected the survival of N. gonorrhoeae in the presence of neutrophils. Furthermore, both compounds inhibited the adherence, invasion and/or survival of N. meningitidis in epithelial cells. These results confirm the importance of MIP-like proteins in infection and indicate the relevance of pipecolic acid derivatives as antimicrobials against C. trachomatis, N. gonorrhoeae and N. meningitidis.

Betaines and related ammonium compounds in chestnut (Castanea sativa Mill.)

Chestnut fruits, being poor of simple sugars and consisting mainly of fibers and starch, are among the constituents of Mediterranean diet. While numerous studies report on content of proteins and amino acids in chestnut, no one has appeared so far on betaines, an important class of nitrogen compounds ubiquitous in plants for their protective action in response to abiotic stress. In this study, we analyzed by HPLC–ESI-tandem mass spectrometry, in fruits and flours of varieties of chestnut cultivated in Italy, the composition of betaines and ammonium compounds intermediates of their biosynthesis. Besides the parent amino acids, the compounds quantified were choline, glycerophosphocholine, phosphocholine, glycine betaine, N-methylproline, proline betaine (stachydrine), β-alanine betaine, 4-guanidinobutyric acid, trigonelline, N,N,N-trimethyllysine. Interestingly, some uncommon derivatives of pipecolic acid, such as N-methylpipecolic acid, 4-hydroxypipecolic acid and 4-hydroxy-N-methylpipecolic acid were identified for the first time in chestnut samples and characterized by MSn tandem mass spectrometry.

Improved Synthesis of the Unnatural Amino Acids AHMOD and AMD, Components of the Anticancer Peptaibol Culicinin D.

An improved second-generation synthesis of the unnatural amino acid components of the anticancer peptaibol culicinin D has been developed. With a protected glutamic acid derivate as the starting material, the process readily delivered the Fmoc-protected free acid derivatives of AHMOD ((2S)-amino-(6R)-hydroxy-(4S)-methyl-8-oxodecanoic acid) and AMD ((2S)-amino-(4S)-methyldecanoic acid) required to support solid phase peptide synthesis (SPPS) for structure-activity studies of the natural product. The same approach also provides improved access to pipecolic acid derivatives. A novel Wittig reagent for one-carbon homologation of aldehydes, developed during this work, is also reported.

Asymmetric Synthesis of Tetrahydropyridines via a Brønsted Acid Catalyzed Aza-Diels–Alder Reaction

The asymmetric synthesis of tetrahydropyridines employing a normal electron-demanding aza-Diels–Alder reaction has been developed. The [4+2] cycloaddition of ethyl glyoxylate imine with aryl-substituted 2-silyloxy-1,3-butadienes is catalyzed by 5 mol% of a BINOL-derived phosphoric acid and in general leads to good yields and ee values with good to excellent diastereoselectivities. The cycloadducts can be further converted into the corresponding piperidinones, which are important pipecolic acid derivatives.

ChemInform Abstract: Nucleophilic Addition Reaction to the Iminium Salts Generated from Pipecolic Acid Derivatives and Application to the Synthesis of Bicyclic Compounds.

AbstractNucleophilic addition of Grignard reagents to the iminium salts generated by the oxidation of cyclic amino ketene silyl acetals derived from pipecolic acid give α‐quaternary amino ester derivatives.

ChemInform Abstract: Sequential Biocatalytic Aldol Reactions in Multistep Asymmetric Synthesis: Pipecolic Acid, Piperidine and Pyrrolidine (Homo)Iminocyclitol Derivatives from Achiral Building Blocks.

AbstractTwo consecutive enzymatic and asymmetric aldol reactions allow the synthesis of stereodefined pipecolic acid (I), piperidine, and pyrrolidine (homo)iminocyclitol [(II) and (III)] derivatives from dimethoxy acetaldehyde and glycine.