No abstract

Strategies for the efficients ynthesis of peptide macrocyclesh ave been al ong-standing goal. In this paper, we demonstrate the use of the peptide ligase termedo mniligase-1 as av ersatile and broadly applicable enzymatic toolf or peptide cyclization. Severalh ead-to-tail (multi)cyclic peptides have been synthesized, including the cyclotide MCoTI-II. Cyclization ando xidative foldingo ft he cyclotide MCoTI-II were efficiently performed in ao ne-pot reactiono na1 -gram scale.T he native cyclotide was isolated andt he correct disulfide bonding pattern was confirmed by NMRs tructure determination. Furthermore,c ompatibility of chemo-enzymatic peptide synthesis( CEPS) using omniligase1w ith methods such as chemical ligation of peptides onto scaffolds( CLIPS)w as successfully demonstrated by synthesizing ak inase-inhibitor derived tricyclic peptide.O ur studies indicate that the minimal ring size for omniligase-1 mediated cyclization is 11 amino acids,w hereas the cyclization of peptides longer than 12 amino acids proceeds with remarkablee fficiency.I na ddition,s everal macrocycles containing non-peptidic backbones( e.g.,p olyethylene glycol), isopeptide bonds (aminoa cid sidechain attachment) as well as d-amino acids couldbe efficiently cyclized.Keywords: chemo-enzymatic peptide synthesis (CEPS);c yclic peptides; cyclization;c yclotide synthesis;c yclotides;e nzyme catalysis;h ead-to-tail cyclization; ligases;m acrocycles;o mniligase-1;p eptides Peptide macrocyclesr epresent an extremely diverse class of molecules that attracti ncreased attentiona s drug leads and prospective pharmaceuticals,w ith currently over 30 cyclic peptides registered or in clinical trials.[1-3] Togetherw ith linearp eptides, they fill the gap between small-molecule drugs (less than 500 Da) and biologics (over 5000 Da) andh avet he potential to address previously "undruggable" targets. Many cyclicp eptides are characterized by their unique structural and enhancedb iopharmaceutical properties,s uch as an improved metabolic stability due to ar educed sensitivity to proteolytic cleavage.T he increasing number of cyclic peptidesu sed as therapeutics is accompanied by the need for efficient andc osteffectiver outes that enable their synthesis on al arge scale.M oreover, efficients ynthesiso fl arge libraries of cyclic peptides (e.g.,f or screeningp urposes) or of cyclicp eptides containing non-canonical amino acids (e.g., d-o ru nnatural amino acids to increase stability and diversity) is of importance.H owever, efficient cyclization of peptidesu sing traditional synthetic methodsi ss till ac hallenge.[4] Classical coupling reagents are often used to cyclize side-chain protected peptides in anhydrous organic solvents.H owever, heavy dilution to prevent polymerization,r isk of epimerization and ap oors olubility of side-chain protected peptideslimitthis approach, especially for peptides longer than 20 amino acids.[5] Native chemical ligation (NCL) [6] is often used to cyclize unprotected peptides in aqueous solution. However, not all pep...

We describe a novel, organic cosolventstable 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 headto-tail peptide cyclization reactions.

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 (Δ T m = 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.

Thes ubstrate profile of peptiligase, as table enzyme designed for peptide ligation in aqueous environments,w as mapped using six different peptide libraries.T he most discriminatings ubstrate binding pocket provedt ob et he first nucleophile binding subsite (S1'), which is crucial for the peptide ligation yield. Tw oi mportant amino acids shaping the S1' pocket are M213 and L208. As itesaturation library of the M213 position yielded two variants with as ignificantly broadened substrate profile,i .e., M213G and M213P.N ext, examination of two libraries with M213G + + L208X and M213P + + L208X (with Xb eing any proteinogenic amino acid) resulted in at oolbox of enzymes which can accommodate any proteinogenic amino acid in the S1' pocket, exceptp roline.T he applicability of ap articu-lar enzyme variant in chemoenzymatic peptide synthesis was demonstrated by coupling at the gram scale of two peptide segments to yield exenatide, a3 9-mert herapeutic peptide usedi nt he treatment of diabetes type II. Theo verally ield of 43% is at least 2-fold higher than yieldsr eported for conventional syntheses of exenatide by full solid-phase peptide synthesis;l arge-scale production costs are expectedt ob es ignificantly reduced if the enzymatic coupling process is employed to manufacture this peptide.