We here report four biocatalytic approaches for the synthesis of the protected amino acid building block α-benzyl L-glutamate. Screenings of these routes to identify active and selective enzymes were conducted, and major hits were confirmed in retest reactions. In the first approach, N-Boc L-glutamic acid is mono-benzylesterified by the protease Alcalase with 81% yield; and in the other three approaches, a biocatalytic γ-selective hydrolysis of α,γ-dibenzyl L-glutamate, a selective amide hydrolysis of α-benzyl L-glutamine, and a selective lactam hydrolysis of alpha-benzyl L-pyroglutamate is performed with up to 71% yield.

The hydrogenative conversions of the biobased platform molecules 4-hydroxycyclopent-2-enone and cyclopentane-1,3-dione to their corresponding 1,3-diols are established using a pre-activated Knölker-type iron catalyst. The catalyst exhibits a high selectivity for ketone reduction, and does not induce dehydration. Moreover, by using different substituents of the ligand, the cis-trans ratio of the products can be affected substantially. A decent compatibility of this catalytic system with various structurally related substrates is demonstrated.

Cyclopentane-1,3-diol (4b) has gained renewed attention as a potential building block for polymers and fuels because its synthesis from hemicellulose-derived 4-hydroxycyclopent-2-enone (3) was recently disclosed. However, cyclopentane-1,3-dione (4), which is a constitutional isomer of 3, possesses a higher chemical stability and can therefore afford higher carbon mass balances and higher yields of 4b in the hydrogenation reaction under more concentrated conditions. In this work, the hydrogenation of 4 into 4b over a commercial Ru/C catalyst was systematically investigated on a bench scale through kinetic studies and variation of reaction conditions. Herein, the temperature, H2-pressure, and the solvent choice were found to have significant effects on the reaction rate and suppression of undesired dehydration of 4. The cis-trans ratio of 4b is naturally generated as 7:3 in these reactions. However, at elevated reaction temperatures, 4b epimerizes, yielding more trans products. This effect was also studied and rationalized from a thermodynamic perspective using DFT. The combined optimized reaction conditions provided 78% yield for 4b, and successful applications to 8-fold scaled up reactions (40 g) and a substrate scope of several 1,3-diones demonstrate the general applicability of this catalytic approach.

Synthesis of cyclopentane-1,3-diamine from hemi-cellulosic origin is established for the first time, with useful chemical insights and potential applications demonstrated.

The synthesis of thymosin-α1, an acetylated 28 amino acid long therapeutic peptide, via conventional chemical methods is exceptionally challenging. The enzymatic coupling of unprotected peptide segments in water offers great potential for a more efficient synthesis of peptides that are difficult to synthesize. Based on the design of a highly engineered peptide ligase, we developed a fully convergent chemo-enzymatic peptide synthesis (CEPS) process for the production of thymosin-α1via a 14-mer + 14-mer segment condensation strategy. Using structure-inspired enzyme engineering, the thiol-subtilisin variant peptiligase was tailored to recognize the respective 14-mer thymosin-α1 segments in order to create a clearly improved biocatalyst, termed thymoligase. Thymoligase catalyzes peptide bond formation between both segments with a very high efficiency (>94% yield) and is expected to be well applicable to many other ligations in which residues with similar characteristics (e.g. Arg and Glu) are present in the respective positions P1 and P1'. The crystal structure of thymoligase was determined and shown to be in good agreement with the model used for the engineering studies. The combination of the solid phase peptide synthesis (SPPS) of the 14-mer segments and their thymoligase-catalyzed ligation on a gram scale resulted in a significantly increased, two-fold higher overall yield (55%) of thymosin-α1 compared to those typical of existing industrial processes.

Strategies for the efficient synthesis of peptide macrocycles have been a long-standing goal. In this paper, we demonstrate the use of the peptide ligase termed omniligase-1 as a versatile and broadly applicable enzymatic tool for peptide cyclization. Several head-to-tail (multi) cyclic peptides have been synthesized, including the cyclotide MCoTI-II. Cyclization and oxidative folding of the cyclotide MCoTI-II were efficiently performed in a one-pot reaction on a 1-gram scale. The native cyclotide was isolated and the correct disulfide bonding pattern was confirmed by NMR structure determination. Furthermore, compatibility of chemo-enzymatic peptide synthesis (CEPS) using omniligase-1 with methods such as chemical ligation of peptides onto scaffolds (CLIPS) was successfully demonstrated by synthesizing a kinase-inhibitor derived tricyclic peptide. Our studies indicate that the minimal ring size for omniligase-1 mediated cyclization is 11 amino acids, whereas the cyclization of peptides longer than 12 amino acids proceeds with remarkable efficiency. In addition, several macrocycles containing non-peptidicbackbones (e.g., polyethylene glycol), isopeptide bonds (amino acid sidechain attachment) as well as d-amino acids could be efficiently cyclized.

The inside cover picture, provided by Nuijens and co-workers, illustrates the power and versatility of the peptide ligase omniligase-1. This ligase provides a promising green and clean alternative to chemical approaches used for peptide cyclization, peptide fragment condensation and protein labelling. The ligations are traceless, proceed with very high catalytic efficiency and result in high product yields. Details on omniligase-mediated peptide cyclization can be found in the communication on pages 2050–2055 (M. Schmidt, A. Toplak, P. J. L. M. Quaedflieg, H. Ippel, G. J. J. Richelle, T. M. Hackeng, J. H. van Maarseveen, T. Nuijens, Adv. Synth. Catal. 2017, 359, 2050–2055; DOI: 10.1002/adsc.201700314).

With the steadily increasing complexity and quantity requirements for peptides in industry and academia, the efficient and site-selective ligation of peptides and proteins represents a highly desirable goal. Within this context, enzyme-mediated ligation technologies for peptides and proteins have attracted great interest in recent years as they represent an extremely powerful extension to the scope of chemical methodologies (e.g. native chemical ligation) in basic and applied research. Compared to chemical ligation methods, enzymatic strategies using ligases such as sortase, butelase, peptiligase or omniligase generally feature excellent chemoselectivity, therefore making them valuable tools for protein and peptide chemists.

The recent advancement of peptide macrocycles as promising therapeutics creates a need for novel methodologies for their efficient synthesis and (large scale) production. Within this context, due to the favorable properties of biocatalysts, enzyme-mediated methodologies have gained great interest. Enzymes such as sortase A, butelase 1, peptiligase and omniligase-1 represent extremely powerful and valuable enzymatic tools for peptide ligation, since they can be applied to generate complex cyclic peptides with exquisite biological activity. Therefore, the use of enzymatic strategies will effectively supplement the scope of existing chemical methodologies and will accelerate the development of future cyclic peptide therapeutics. The advantages and disadvantages of the different enzymatic methodologies will be discussed in this review.

The substrate profile of peptiligase, a stable enzyme designed for peptide ligation in aqueous environments, was mapped using six different peptide libraries. The most discriminating substrate binding pocket proved to be the first nucleophile binding subsite (S1′), which is crucial for the peptide ligation yield. Two important amino acids shaping the S1′ pocket are M213 and L208. A site-saturation library of the M213 position yielded two variants with a significantly broadened substrate profile, i.e., M213G and M213P. Next, examination of two libraries with M213G+L208X and M213P+L208X (with X being any proteinogenic amino acid) resulted in a toolbox of enzymes which can accommodate any proteinogenic amino acid in the S1′ pocket, except proline. The applicability of a particular enzyme variant in chemoenzymatic peptide synthesis was demonstrated by coupling at the gram scale of two peptide segments to yield exenatide, a 39-mer therapeutic peptide used in the treatment of diabetes type II. The overall yield of 43% is at least 2-fold higher than yields reported for conventional syntheses of exenatide by full solid-phase peptide synthesis; large-scale production costs are expected to be significantly reduced if the enzymatic coupling process is employed to manufacture this peptide.

We describe a novel, organic cosolvent-stable and cation-independent engineered enzyme for peptide coupling reactions. The enzyme is a variant of a stable calcium-independent mutant of subtilisin BPN, with the catalytic Ser212 mutated to Cys and Pro216 converted to Ala. The enzyme, called peptiligase, catalyzes exceptionally efficient peptide coupling in water with a surprisingly high synthesis over hydrolysis (S/H) ratio. The S/H ratio of the peptide ligation reaction is correlated to the length of the peptide substrate and proved to be >100 for the synthesis of a 13-mer peptide, which corresponds to >99% conversion to the ligated peptide product and <1% hydrolytic side-reaction. Furthermore, peptiligase does not require a particular recognition motif resulting in a broadly applicable and traceless peptide ligation technology. Peptiligase is very robust, easy to produce in Bacillus subtilis, and its purification is straightforward. It shows good activity and stability in the presence of organic cosolvents and chelating or denaturing agents, enabling the ligation of poorly soluble (hydrophobic) or folded peptides. This enzyme could be useful for the (industrial) synthesis of diverse (pharmaceutical) peptides. In addition, peptiligase is able to efficiently catalyze head-to-tail peptide cyclization reactions.

The large-scale chemical manufacture of peptides with a length exceeding ca. 30 amino acids is still a huge challenge. Using chemical approaches such as solid phase peptide synthesis (SPPS) synthetic yields decrease significantly with increasing peptide chain length. The crude purity and overall yield can be dramatically improved using a fragment condensation strategy. Unfortunately, chemical fragment condensation leads to epimerization (except of Gly and Pro residues) and native chemical ligation is often not feasible (no Cys present) and difficult to scale-up due to the thioester instability. Alternatively, enzymes can be used for peptide fragment condensation without any epimerization. To minimize the intrinsic hydrolytic activity of enzymes, peptide coupling enzymes can be improved by protein engineering. Recently, we described the discovery of peptiligase, an efficient biocatalyst for assembling linear and cyclic peptides. Herein, we describe the further engineering of peptiligase to improve the enzyme's synthetic efficiency, substrate scope and activity. Several peptiligase variants with a unique substrate specificity were found. By combining multiple positive mutations, a variant called omniligase was obtained that can couple virtually any peptide sequence. The application of specific peptiligases and omniligase for the synthesis of linear and cyclic peptides, and peptide-to-protein conjugates is discussed.

Peptide C-terminal carboxyamidomethyl (Cam-)esters are pivotal building blocks for enzymatic segment condensation and their yield and purity are crucial for the overall efficiency of this strategy. Although a few methods for their preparation have been disclosed, the solid phase synthesis of peptide C-terminal Cam-esters is not straightforward. Herein, we describe two novel method types for their synthesis in high yield and good purity. The first type is based on the coupling of hydroxyl protected glycolic acid to a solid support, followed by ester synthesis using an N-protected amino acid and dicyclohexyl carbodiimide with catalytic 4-dimethylaminopyridine. The second type is based on the synthesis of amino acid carboxymethyl ester building blocks, which are coupled to the solid support using standard coupling reagents and procedures. The latter procedure is easily implemented in peptide synthesizer protocols and applicable to all standard Fmoc-protected amino acid building blocks. (C) 2016 Elsevier Ltd. All rights reserved.

The properties of synthetic peptides, including potency, stability, and bioavailability, are strongly influenced by modification of the peptide chain termini. Unfortunately, generally applicable methods for selective and mild C-terminal peptide functionalization are lacking. In this work, we explored the peptide amidase from Stenotrophomonas maltophilia as a versatile catalyst for diverse carboxy-terminal peptide modification reactions. Because the scope of application of the enzyme is hampered by its mediocre stability, we used computational protein engineering supported by energy calculations and molecular dynamics simulations to discover a number of stabilizing mutations. Twelve mutations were combined to yield a highly thermostable (ΔTm = 23 °C) and solvent-compatible enzyme. Protein crystallography and molecular dynamics simulations revealed the biophysical effects of mutations contributing to the enhanced robustness. The resulting enzyme catalyzed the selective C-terminal modification of synthetic peptides with small nucleophiles such as ammonia, methylamine, and hydroxylamine in various organic (co)solvents. The use of a nonaqueous environment allowed modification of peptide free acids with >85% product yield under thermodynamic control. On the basis of the crystal structure, further mutagenesis gave a biocatalyst that favors introduction of larger functional groups. Thus, the use of computational and rational protein design provided a tool for diverse enzymatic peptide modification.

Biocatalytic peptide synthesis will benefit from enzymes that are active at low water levels in organic solvent compositions that allow good substrate and product solubility. To explore the use of proteases from thermophiles for peptide synthesis under such conditions, putative protease genes of the subtilase class were cloned from Thermus aquaticus and Deinococcus geothermalis and expressed in Escherichia coli. The purified enzymes were highly thermostable and catalyzed efficient peptide bond synthesis at 80°C and 60°C in neat acetonitrile with excellent conversion (>90%). The enzymes tolerated high levels of N,N-dimethylformamide (DMF) as a cosolvent (40-50% v/v), which improved substrate solubility and gave good conversion in 5+3 peptide condensation reactions. The results suggest that proteases from thermophiles can be used for peptide synthesis under harsh reaction conditions.

The γ-amino alcohol structural motif is often encountered in drugs and natural products. We developed two complementary catalytic diastereoselective methods for the synthesis of N-PMP-protected γ-amino alcohols from the corresponding ketones. The anti-products were obtained through Ir-catalyzed asymmetric transfer hydrogenation, the syn-products via Rh-catalyzed asymmetric hydrogenation.