NUIJENS TIMO*¹, TOPLAK ANA¹, VAN DE MEULENREEK MATHIJS B. A. C.¹, SCHMIDT M.¹, GOLDBACH MICHEL¹, JANSSEN DICK B.², QUAEDFLIEG PETER J. L. M.¹
*Corresponding author
1. Enzypep, Urmonderbaan 22, 6167 RD, Geleen, Netherlands
2. University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands

Abstract

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.

INTRODUCTION

By 2020 an estimated 50% of the 50 top-selling drugs world-wide will be biologics, most of which will be polypeptides (proteins, peptides and their conjugates) (1).

With the exception of natural products and their semi-synthetic modified derivatives, polypeptides are typically manufactured by recombinant procedures (i.e., fermentation), by synthetic chemistry, or by a combination of these technologies. Despite their versatility and applicability, both recombinant and chemical approaches have intrinsic limitations. Whereas recombinant procedures have no relevant upper chain length limits, their large-scale application is typically restricted to polypeptide sequences that are composed exclusively of naturally occurring amino acids. Chemical approaches can incorporate unnatural moieties, but the synthetic yields decrease significantly with increasing peptide chain length. While it may be possible to assemble amino acid chains of over 100 amino acids by sequential coupling, the low yields exclude the development of commercial manufacturing processes. Currently, single sequences of approximately 50 amino acids represent the upper ...