Selective Synthesis of Lysine Peptides and the Prebiotically Plausible Synthesis of Catalytically Active Diaminopropionic Acid Peptide Nitriles in Water

Abstract

Why life encodes specific proteinogenic amino acids remains an unsolved problem, but a non-enzymatic synthesis that recapitulates biology’s universal strategy of stepwise N-to-C terminal peptide growth may hold the key to this selection. Lysine is an important proteinogenic amino acid that, despite its essential structural, catalytic, and functional roles in biochemistry, has widely been assumed to be a late addition to the genetic code. Here, we demonstrate that lysine thioacids undergo coupling with aminonitriles in neutral water to afford peptides in near-quantitative yield, whereas non-proteinogenic lysine homologues, ornithine, and diaminobutyric acid cannot form peptides due to rapid and quantitative cyclization that irreversibly blocks peptide synthesis. We demonstrate for the first time that ornithine lactamization provides an absolute differentiation of lysine and ornithine during (non-enzymatic) N-to-C-terminal peptide ligation. We additionally demonstrate that the shortest lysine homologue, diaminopropionic acid, undergoes effective peptide ligation. This prompted us to discover a high-yielding prebiotically plausible synthesis of the diaminopropionic acid residue, by peptide nitrile modification, through the addition of ammonia to a dehydroalanine nitrile. With this synthesis in hand, we then discovered that the low basicity of diaminopropionyl residues promotes effective, biomimetic, imine catalysis in neutral water. Our results suggest diaminopropionic acid, synthesized by peptide nitrile modification, can replace or augment lysine residues during early evolution but that lysine’s electronically isolated sidechain amine likely provides an evolutionary advantage for coupling and coding as a preformed monomer in monomer-by-monomer peptide translation.

A model for N-to-C direction in prebiotic peptide synthesis

“…4 However, the spontaneous occurrence of dehydrated condensation reactions in aqueous solution poses significant challenges due to formidable barriers associated with peptide formation from abiotic polycondensation of prebiotic amino acids, including high activation energy, 5 unfavorable thermodynamics, and side reactions. Various approaches have been applied into the condensation of amino acids in an aqueous solution, including mineral surface catalysis, [6][7][8][9] a-Aminonitrile polymerization in neutral aqueous solution, [10][11][12] ester-amide exchange between a-amino acids and a-hydroxyl acids, 13,14 formation of amyloid aggregates is induced by volcanic gas carbonyl sulfide (COS), 15 and drying reactions of mercaptoacids and amino acids. 16 Additionally, various prebiotic activators such as DAP (diaminophosphate), 17 trimetaphosphate, 14 methylisonitrile, 18 and boric acid 19 have been employed in the process of peptide polymerization.…”

“…10,28 Building on this, Powner utilized acetylated cysteine nitrile (Ac-Cys-CN) and acetylated lysine nitrile (Ac-Lys-CN) to successfully achieve N -C peptide synthesis. 11,12 The bionic Ac-AA-NH 2 , derived from the above biopeptide synthesis with a modification of the first amino acid at the N-terminal of the peptide, may serves as the initial amino acid for prebiotic peptide synthesis. Meanwhile, AA-NH 2 also used as the raw material for peptide extension.…”

“…10,28 Building on this, Powner utilized acetylated cysteine nitrile (Ac-Cys-CN) and acetylated lysine nitrile (Ac-Lys-CN) to successfully achieve N → C peptide synthesis. 11,12…”

Spontaneous Peptide Ligation Mediated by Cysteamine

“…We reasoned that if 5 (or it is oxidized disulfide, cystamine 6 ) were to participate in Strecker synthesis, with hydrogen cyanide (HCN) and an aldehyde 7 , the reaction would afford β-mercaptoethyl-aminonitrile 8 (Figure ), where a thiol catalyst, a nucleophilic amine, and an electrophilic nitrile are built into one molecule. We anticipated that tethering a thiol-catalyst, required for catalytic peptide ligation (CPL; Figure B), , to the amine coupling partner ( 9 ) would greatly enhance the rate of peptide ligation and importantly would lead to spontaneous peptide ligation in near-neutral water (Figure D). − We also recognize that the thiol-tethered ligation products would be β-mercaptoethyl-peptoids 10 , which undergo reductive fragmentation to yield proteinogenic peptides 11 (Figure D). − …”

“…Seeking to explore the advantages of the biomimetic strategy, we have previously recognized that aminonitriles 1 and peptide nitriles 2 are thermodynamically activated but kinetically stable substrates for prebiotic peptide synthesis (Figure ). − Coupling these nitriles, through transformation into thioacids 3 or thioimidates 4 (Figure B), allows efficient protecting-group-free peptide synthesis in water. However, despite these advances, the spontaneous synthesis of peptides remains an elusive goal with direct ligation of α-aminonitriles yielding amino-imidazoles that block peptide synthesis (Figure A) …”