Ribosomal Incorporation of Aromatic Oligoamides as Peptide Sidechain Appendages

Abstract

Derivatives of 4‐aminomethyl‐l‐phenylalanine with aromatic oligoamide foldamers as sidechain appendages were successfully charged on tRNA by means of flexizymes. Their subsequent incorporation both at the C‐terminus of, and within, peptide sequences by the ribosome, was demonstrated. These results expand the registry of chemical structures tolerated by the ribosome to sidechains significantly larger and more structurally defined than previously demonstrated.

Conformational interplay in hybrid peptide–helical aromatic foldamer macrocycles

“…3 Recently, it was shown that ribosomal translation tolerates peptide appendages consisting of aromatic amide foldamer sequences of quinoline-based monomer Q Xxx and pyridinebased monomer P (Figure 1a). [4][5][6] These appendages are far larger and more remote from peptides than what had been previously envisaged. They can be placed either at the Nterminus, i.e.…”

“…on the peptide chain initiator, 4,5 or within the sequence on an -amino acid side chain. 6 They can also be included within thioether peptide macrocycles such as 3 (Figure 1b). Interest for such peptide modifications stems from the high propensity of Q Xxx /P sequences to adopt stable helically folded conformations, particularly in water.…”

Engineering molecular translation systems

“…In one recent study, four chemically diverse non-canonical scaffolds (phenylalanine, benzoic acid, heteroaromatic, and aliphatic acid analogs) were investigated for the compatibility of their substrates with the three flexizymes (Lee et al, 2019). Based on the molecular characteristics and yields in Fx-catalyzed reaction in several studies (Lee et al, 2021(Lee et al, , 2020b(Lee et al, , 2019(Lee et al, , 2020cPassioura and Suga, 2014;Rogers et al, 2018;Tsiamantas et al, 2020), several general substrate design rules were identified for efficient tRNA charging (Figure 4E). First, substrates with a similar molecular structure to…”

“…Taken together, numerous non-canonical substrates have now been acylated to tRNA by Fx and subsequently incorporated site-specifically into a peptide in a reconstituted PURE system. The substrates include a- (Obexer et al, 2017), b-(Fujino et al, 2016, g- (Ohshiro et al, 2011), D-amino acids (Katoh et al, 2017) Review (Lee et al, 2021), non-amino (aromatic, aliphatic) acids (Lee et al, 2019), foldamers Rogers et al, 2018), oligomeric peptides (Tsiamantas et al, 2020), malonyl (polyketide-like) acids (Ad et al, 2019), hydroxyacids (Ohta et al, 2007(Ohta et al, , 2008, and thioacids (Takatsuji et al, 2019).…”

“…For decades, the ribosome has been exploited to site-specifically incorporate >200 non-canonical amino acids (ncAAs) into proteins. These ncAAs include non-canonical a-amino acids (e.g., p-azidophenylalanine), as well as cyclic Lee et al, 2020c), backbone-extended (e.g., b-, g-, d-) (Fujino et al, 2016;Lee et al, 2020b;Takatsuji et al, 2019), N-alkylated (Iwane et al, 2016;Kawakami et al, 2013), and oligomeric analogs (Tsiamantas et al, 2020), among others. Site-specific incorporation of such diverse chemical entities into peptides and proteins has yielded new biopolymer structures and functions (e.g., antibodydrug conjugates and macrocyclic foldamer-peptide drugs).…”