Here we report a fully automated, flow-based approach to solid-phase polypeptide synthesis, with amide bond formation in 7 seconds and total synthesis times of 40 seconds per amino acid residue. Crude peptide purities and isolated yields were comparable to those for standard-batch solid-phase peptide synthesis. At full capacity, this approach can yield tens of thousands of individual 30-mer peptides per year.

Ribosomes can produce proteins in minutes and are largely constrained to proteinogenic amino acids. Here, we report highly efficient chemistry matched with an automated fast-flow instrument for the direct manufacturing of peptide chains up to 164 amino acids long over 327 consecutive reactions. The machine is rapid: Peptide chain elongation is complete in hours. We demonstrate the utility of this approach by the chemical synthesis of nine different protein chains that represent enzymes, structural units, and regulatory factors. After purification and folding, the synthetic materials display biophysical and enzymatic properties comparable to the biologically expressed proteins. High-fidelity automated flow chemistry is an alternative for producing single-domain proteins without the ribosome.

Conjugates between proteins and small molecules enable access to a vast chemical space that is not achievable with either type of molecule alone; however, the paucity of specific reactions capable of functionalizing proteins and natural products has presented a formidable challenge for preparing conjugates. Here we report a strategy for conjugating electron-rich (hetero)arenes to polypeptides and proteins. Our bioconjugation technique exploits the electrophilic reactivity of an oxidized selenocysteine residue in polypeptides and proteins, and the electron-rich character of certain small molecules to provide bioconjugates in excellent yields under mild conditions. This conjugation chemistry enabled the synthesis of peptide-vancomycin conjugates without prefunctionalization of vancomycin. These conjugates had enhanced in vitro potency for resistant Gram-positive and Gram-negative pathogens. Additionally, we showed that a 6 kDa affibody protein and a 150 kDa IgG antibody could be modified without diminishing bioactivity.

Pendant groups on polymers that have lower-critical solution temperature (LCST) properties experience a water-like environment below the LCST where the polymer is soluble but are less hydrated above the LCST when the polymer phase separates from solution. When these pendant groups are amphoteric groups like carboxylate salts or ammonium salts, the change in solvation that accompanies the polymer precipitation event significantly changes these groups' acidity or basicity. These changes in acidity or basicity can lead to carboxylate salts forming carboxylic acid groups by capturing protons from the bulk solvent or ammonium salts reverting to the neutral amine by release of protons to the bulk solvent, respectively. When polymers like poly(N-isopropylacrylamide) that contain a sufficient loading of such comonomers are dissolved in solutions whose pH is near the pK(a) of the pendant acid or basic group and undergo an LCST event, the LCST event can change the bulk solution pH. These changes are reversible. These effects were visually followed using common indicators with soluble polymers and or by monitoring solution pH as a function of temperature. LCST events triggered by the addition of a kosmotropic salt lead to similar reversible solution pH changes.

Chemical methods have enabled the total synthesis of protein molecules of ever-increasing size and complexity. However, methods to engineer synthetic proteins comprising noncanonical amino acids have not kept pace, even though this capability would be a distinct advantage of the total synthesis approach to protein science. In this work, we report a platform for protein engineering based on the screening of synthetic one-bead one-compound protein libraries. Screening throughput approaching that of cell surface display was achieved by a combination of magnetic bead enrichment, flow cytometry analysis of on-bead screens, and high-throughput MS/MS-based sequencing of identified active compounds. Direct screening of a synthetic protein library by these methods resulted in the de novo discovery of mirror-image miniprotein-based binders to a ∼150-kDa protein target, a task that would be difficult or impossible by other means.