His6 tag-assisted chemical protein synthesis

Total Chemical Synthesis of the SARS-CoV-2 Spike Receptor-Binding Domain

SARS-CoV-2 and its global spread have created an unprecedented public health crisis. The spike protein of SARS-CoV-2 has gained significant attention due to its crucial role in viral entry into host cells and its potential as both a prophylactic and a target for therapeutic interventions. Herein, we report the first successful total synthesis of the SARS-CoV-2 spike protein receptor binding domain (RBD), highlighting the key challenges and the strategies employed to overcome them. Appropriate utilization of advanced solid phase peptide synthesis and cutting-edge native chemical ligation methods have facilitated the synthesis of this moderately large protein molecule. We discuss the problems encountered during the chemical synthesis and approaches taken to optimize the yield and the purity of the synthetic protein molecule. Furthermore, we demonstrate that the chemically synthesized homogeneous spike RBD efficiently binds to the known mini-protein binder LCB1. The successful chemical synthesis of the spike RBD presented here can be utilized to gain valuable insights into SARS-CoV-2 spike RBD biology, advancing our understanding and aiding the development of intervention strategies to combat future coronavirus outbreaks. The modular synthetic approach described in this study can be effectively implemented in the synthesis of other mutated variants or enantiomer of the spike RBD for mirror-image drug discovery.

Revealing the extracellular function of HMGB1 N-terminal region acetylation assisted by a protein semi-synthesis approach

HMGB1 (high-mobility group box 1) is a non-histone chromatin-associated protein that has been widely reported as a representative damage-associated molecular pattern (DAMP) and to play a pivotal role in the proinflammatory process once it is in an extracellular location. Accumulating evidence has shown that HMGB1 undergoes extensive post-translational modifications (PTMs) that actively regulate its conformation, localization, and intermolecular interactions. However, fully characterizing the functional implications of these PTMs has been challenging due to the difficulty in accessing homogeneous HMGB1 with site-specific PTMs of interest. In this study, we developed a streamlined protein semi-synthesis strategy via salicylaldehyde ester-mediated chemical ligations (Ser/Thr ligation and Cys/Pen ligation, STL/CPL). This methodology enabled us to generate a series of N-terminal region acetylated HMGB1 proteins. Further studies revealed that acetylation regulates HMGB1-heparin interaction and modulates HMGB1's stability against thrombin, representing a regulatory switch to control HMGB1's extracellular activity.

Traceless parallel peptide purification by a first-in-class reductively cleavable linker system featuring a safety-release

Hundreds of peptides can be synthesized by automated parallel synthesizers in a single run. In contrast, the most widely used peptide purification method - high-pressure liquid chromatography (HPLC) - only allows one-by-one processing of each sample. The chromatographic purification of many peptides, therefore, remains a time-consuming and costly effort. Catch-and-release methods can be processed in parallel and potentially provide a remedy. However, no such system has yet provided a true alternative to HPLC. Herein we present the development of a side-reaction free, reductively cleavable linker. The linker is added to the target peptide as the last building block during peptide synthesis. After acidic cleavage from synthetic resin, the linker-tagged full-length peptide is caught onto an aldehyde-modified solid support by rapid oxime ligation, allowing removal of all impurities lacking the linker by washing. Reducing the aryl azide to an aniline sensitizes the linker for cleavage. However, scission does not occur at non-acidic pH enabling wash out of reducing agent. Final acidic treatment safely liberates the peptide by an acid-catalysed 1,6-elimination. We showcase this first-in-class reductively cleavable linker system in the parallel purification of a personalized neoantigen cocktail, containing 20 peptides for cancer immunotherapy within six hours.

Photo-cleavable purification/protection handle assisted synthesis of giant modified proteins with tandem repeats

Proteins with tandem repeats have essential physical or biological roles in cells and have been widely investigated as biomaterials or vaccines. Chemically derived proteins with tandem repeats would be beneficial for research, owing to their accurate structures, possibly with precise modifications, produced by chemical synthesis. Traditional protein synthesis often leads to severe handling loss due to multiple ligations and HPLC purifications. To improve the protein synthesis efficiency, we developed a purification/protection handle consisting of a His6 tag and a photo-labile linker. This handle has great potential to facilitate purification with immobilized metal affinity chromatography techniques and also provides orthogonal protection for N-terminal Cys. The synthesis of the model proteins Muc1 and antifreeze glycoprotein mimics shows that the handle decreases the requirement for HPLC and enables both convergent and sequential assembly of peptide segments.

A clickable glutamine (CliQ) derivative for the traceless reversible modification of peptides and proteins

The Cu(i)-mediated click reaction of proteins with affinity tags enables their selective isolation from complex mixtures.

A Protocol for the Design of Protein and Peptide Nanostructure Self-Assemblies Exploiting Synthetic Amino Acids

In recent years there has been increasing interest in nanostructure design based on the self-assembly properties of proteins and polymers. Nanodesign requires the ability to predictably manipulate the properties of the self-assembly of autonomous building blocks, which can fold or aggregate into preferred conformational states. The design includes functional synthetic materials and biological macromolecules. Autonomous biological building blocks with available 3D structures provide an extremely rich and useful resource. Structural databases contain large libraries of protein molecules and their building blocks with a range of sizes, shapes, surfaces, and chemical properties. The introduction of engineered synthetic residues or short peptides into these building blocks can greatly expand the available chemical space and enhance the desired properties. Herein, we summarize a protocol for designing nanostructures consisting of self-assembling building blocks, based on our recent works. We focus on the principles of nanostructure design with naturally occurring proteins and synthetic amino acids, as well as hybrid materials made of amyloids and synthetic polymers.

Total chemical synthesis of proteins without HPLC purification

This work presents the first method for the rapid chemical total on-resin synthesis of proteins that proceeds without a single HPLC-purification step.

The total chemical synthesis of proteins is a tedious and time-consuming endeavour. The typical steps involve solid phase synthesis of peptide thioesters and cysteinyl peptides, native chemical ligation (NCL) in solution, desulfurization or removal of ligation auxiliaries in the case of extended NCL as well as many intermediary and final HPLC purification steps. With an aim to facilitate and improve the throughput of protein synthesis we developed the first method for the rapid chemical total on-resin synthesis of proteins that proceeds without a single HPLC-purification step. The method relies on the combination of three orthogonal protein tags that allow sequential immobilization (via the N-terminal and C-terminal ends), extended native chemical ligation and release reactions. The peptide fragments to be ligated are prepared by conventional solid phase synthesis and used as crude materials in the subsequent steps. An N-terminal His₆ unit permits selective immobilization of the full length peptide thioester onto Ni-NTA agarose beads. The C-terminal peptide fragment carries a C-terminal peptide hydrazide and an N-terminal 2-mercapto-2-phenyl-ethyl ligation auxiliary, which serves as a reactivity tag for the full length peptide. As a result, only full length peptides, not truncation products, react in the subsequent on-bead extended NCL. After auxiliary removal the ligation product is liberated into solution upon treatment with mild acid, and is concomitantly captured by an aldehyde-modified resin. This step allows the removal of the most frequently observed by-product in NCL chemistry, i.e. the hydrolysed peptide thioester (which does not contain a C-terminal peptide hydrazide). Finally, the target protein is released with diluted hydrazine or acid. We applied the method in the synthesis of 46 to 126 amino acid long MUC1 proteins comprising 2–6 copies of a 20mer tandem repeat sequence. Only three days were required for the parallel synthesis of 9 MUC1 proteins which were obtained in 8–33% overall yield with 90–98% purity despite the omission of HPLC purification.

The road to the synthesis of "difficult peptides"

The last decade has witnessed a renaissance of peptides as drugs. This progress, together with advances in the structural behavior of peptides, has attracted the interest of the pharmaceutical industry in these molecules as potential APIs. In the past, major peptide-based drugs were inspired by sequences extracted from natural structures of low molecular weight. In contrast, nowadays, the peptides being studied by academic and industrial groups comprise more sophisticated sequences. For instance, they consist of long amino acid chains and show a high tendency to form aggregates. Some researchers have claimed that preparing medium-sized proteins is now feasible with chemical ligation techniques, in contrast to medium-sized peptide syntheses. The complexity associated with the synthesis of certain peptides is exemplified by the so-called "difficult peptides", a concept introduced in the 80's. This refers to sequences that show inter- or intra-molecular β-sheet interactions significant enough to form aggregates during peptide synthesis. These structural associations are stabilized and mediated by non-covalent hydrogen bonds that arise on the backbone of the peptide and-depending on the sequence-are favored. The tendency of peptide chains to aggregate is translated into a list of common behavioral features attributed to "difficult peptides" which hinder their synthesis. In this regard, this manuscript summarizes the strategies used to overcome the inherent difficulties associated with the synthesis of known "difficult peptides". Here we evaluate several external factors, as well as methods to incorporate chemical modifications into sequences, in order to describe the strategies that are effective for the synthesis of "difficult peptides". These approaches have been classified and ordered to provide an extensive guide for achieving the synthesis of peptides with the aforementioned features.

Solid phase chemical ligation employing a rink amide linker for the synthesis of histone H2B protein

Presented here is a solid phase chemical ligation strategy employing native chemical ligation and the commercially available Rink-amide linker as a key element in our approach. The method was applied for the synthesis of histone H2B, which sets the ground for the rapid preparation of posttranslationally modified analogues of this protein.

Native chemical ligation: a boon to peptide chemistry

The use of chemical ligation within the realm of peptide chemistry has opened various opportunities to expand the applications of peptides/proteins in biological sciences. Expansion and refinement of ligation chemistry has made it possible for the entry of peptides into the world of viable oral therapeutic drugs through peptide backbone cyclization. This progression has been a journey of chemical exploration and transition, leading to the dominance of native chemical ligation in the present advances of peptide/protein applications. Here we illustrate and explore the historical and current nature of peptide ligation, providing a clear indication to the possibilities and use of these novel methods to take peptides outside their typically defined boundaries.

Repeat protein engineering: creating functional nanostructures/biomaterials from modular building blocks

There is enormous interest in molecular self-assembly and the development of biological systems to form smart nanostructures for biotechnology (so-called 'bottom-up fabrications'). Repeat proteins are ideal choices for development of such systems as they: (i) possess a relatively simple relationship between sequence, structure and function; (ii) are modular and non-globular in structure; (iii) act as diverse scaffolds for the mediation of a diverse range of protein-protein interactions; and (iv) have been extensively studied and successfully engineered and designed. In the present review, we summarize recent advances in the use of engineered repeat proteins in the self-assembly of novel materials, nanostructures and biosensors. In particular, we show that repeat proteins are excellent monomeric programmable building blocks that can be triggered to associate into a range of morphologies and can readily be engineered as stimuli-responsive biofunctional materials.

Solid phase protein chemical synthesis

The chemical synthesis of peptides or small proteins is often an important step in many research projects and has stimulated the development of numerous chemical methodologies. The aim of this review is to give a substantial overview of the solid phase methods developed for the production or purification of polypeptides. The solid phase peptide synthesis (SPPS) technique has facilitated considerably the access to short peptides (<50 amino acids). However, its limitations for producing large homogeneous peptides have stimulated the development of solid phase covalent or non-covalent capture purification methods. The power of the native chemical ligation (NCL) reaction for protein synthesis in aqueous solution has also been adapted to the solid phase by the combination of novel linker technologies, cysteine protection strategies and thioester or N,S-acyl shift thioester surrogate chemistries. This review details pioneering studies and the most recent publications related to the solid phase chemical synthesis of large peptides and proteins.

Challenges in the chemical synthesis of average sized proteins: sequential vs. convergent ligation of multiple peptide fragments

This review examines the challenges in the chemical synthesis of average sized proteins. Recent progress on sequential and convergent ligation methods, two approaches to the synthesis of proteins, is outlined. An examination of these challenges could aid in the process of finding new methodologies for the efficient chemical synthesis of average sized protein molecules.

Protein engineering of redox-active enzymes

Redox-active enzymes perform many key biological reactions. The electron transfer process is complex, not only because of its versatility, but also because of the intricate and delicate modulation exerted by the protein scaffold on the redox properties of the catalytic sites. Nowadays, there is a wealth of information available about the catalytic mechanisms of redox-active enzymes and the time is propitious for the development of projects based on the protein engineering of redox-active enzymes. In this review, we aim to provide an updated account of the available methods used for protein engineering, including both genetic and chemical tools, which are usually reviewed separately. Specific applications to redox-active enzymes are mentioned within each technology, with emphasis on those cases where the generation of novel functionality was pursued. Finally, we focus on two emerging fields in the protein engineering of redox-active enzymes: the construction of novel nucleic acid-based catalysts and the remodeling of intra-molecular electron transfer networks. We consider that the future development of these areas will represent fine examples of the concurrence of chemical and genetic tools.

De Novo Tubular Nanostructure Design Based on Self-Assembly of β-Helical Protein Motifs

We present an approach for designing self-assembled nanostructures from naturally occurring building block segments obtained from native protein structures. We focus on structural motifs from left-handed beta-helical proteins. We selected 17 motifs. Copies of each of the motifs are stacked one atop the other. The obtained structures were simulated for long periods by using Molecular Dynamics to test their ability to retain their organization over time. We observed that a structural model based on the self-assembly of a motif from E. coli galactoside acetyltransferase produced a very stable tube. We studied the interactions that help maintain the conformational stability of the systems, focusing on the role of specific amino acids at specific positions. Analysis of these systems and a mutational study of selected candidates revealed that the presence of proline and glycine residues in the loops of beta-helical structures greatly enhances the structural stability of the systems.