Stepwise Solid-Phase Synthesis of Polyamides as Linkers

Prion protein-Semisynthetic prion protein (PrP) variants with posttranslational modifications

Deciphering the pathophysiologic events in prion diseases is challenging, and the role of posttranslational modifications (PTMs) such as glypidation and glycosylation remains elusive due to the lack of homogeneous protein preparations. So far, experimental studies have been limited in directly analyzing the earliest events of the conformational change of cellular prion protein (PrP^C ) into scrapie prion protein (PrP^Sc ) that further propagates PrP^C misfolding and aggregation at the cellular membrane, the initial site of prion infection, and PrP misfolding, by a lack of suitably modified PrP variants. PTMs of PrP, especially attachment of the glycosylphosphatidylinositol (GPI) anchor, have been shown to be crucially involved in the PrP^Sc formation. To this end, semisynthesis offers a unique possibility to understand PrP behavior invitro and invivo as it provides access to defined site-selectively modified PrP variants. This approach relies on the production and chemoselective linkage of peptide segments, amenable to chemical modifications, with recombinantly produced protein segments. In this article, advances in understanding PrP conversion using semisynthesis as a tool to obtain homogeneous posttranslationally modified PrP will be discussed.

Primary Structure Control of Oligomers Based on Natural and Synthetic Building Blocks

Solid-phase synthesis was exploited for the preparation of oligomers constructed from natural and synthetic building blocks by combining the formation of amide bonds and copper-assisted alkyne-azide cycloaddition reactions extending the variety of oligomers with well-defined primary structures accessible through this technique and providing control over the spacing between amino acids.

Sequentially hetero-functional, topological polymers by step-growth thiol-yne approach

Sequence-controlled polymers (SCPs) such as DNA and proteins play an important role in biology. Many efforts have been devoted to synthesize SCPs in the past half a century. However, to our knowledge, the artificial sequences containing independently functional groups have never been reported. Here, we present a facile and scalable approach based on radical-initiated step-growth polymerization to synthesize sequence-controlled functional polymers (SCFPs) with various topologies, covering from linear to random and hyperbranched polymers. The functional groups, such as OH/NH2, OH/COOH, and NH2/N3, alternately arranged along the chain, which were further selectively functionalized to achieve DNA-mimic and hetero-multifunctional SCPs. This user-friendly strategy exhibits advantages of commercially available monomers, catalyst-free process, fast reaction, high yield and water solvent, opening a general approach to facile and scalable synthesis of SCFPs.

Bringing the science of proteins into the realm of organic chemistry: total chemical synthesis of SEP (synthetic erythropoiesis protein)

Erythropoietin, commonly known as EPO, is a glycoprotein hormone that stimulates the production of red blood cells. Recombinant EPO has been described as "arguably the most successful drug spawned by the revolution in recombinant DNA technology". Recently, the EPO glycoprotein molecule has re-emerged as a major target of synthetic organic chemistry. In this article I will give an account of an important body of earlier work on the chemical synthesis of a designed EPO analogue that had full biological activity and improved pharmacokinetic properties. The design and synthesis of this "synthetic erythropoiesis protein" was ahead of its time, but has gained new relevance in recent months. Here I will document the story of one of the major accomplishments of synthetic chemistry in a more complete way than is possible in the primary literature, and put the work in its contemporaneous context.

Facile and stabile linkages through tyrosine: bioconjugation strategies with the tyrosine-click reaction

The scope, chemoselectivity, and utility of the click-like tyrosine labeling reaction with 4-phenyl-3H-1,2,4-triazoline-3,5(4H)-diones (PTADs) is reported. To study the utility and chemoselectivity of PTAD derivatives in peptide and protein chemistry, we synthesized PTAD derivatives possessing azide, alkyne, and ketone groups and studied their reactions with amino acid derivatives and peptides of increasing complexity. With proteins we studied the compatibility of the tyrosine click reaction with cysteine and lysine-targeted labeling approaches and demonstrate that chemoselective trifunctionalization of proteins is readily achieved. In particular cases, we noted that PTAD decomposition resulted in formation of a putative isocyanate byproduct that was promiscuous in labeling. This side reaction product, however, was readily scavenged by the addition of a small amount of 2-amino-2-hydroxymethyl-propane-1,3-diol (Tris) to the reaction medium. To study the potential of the tyrosine click reaction to introduce poly(ethylene glycol) chains onto proteins (PEGylation), we demonstrate that this novel reagent provides for the selective PEGylation of chymotrypsinogen, whereas traditional succinimide-based PEGylation targeting lysine residues provided a more diverse range of PEGylated products. Finally, we applied the tyrosine click reaction to create a novel antibody-drug conjugate. For this purpose, we synthesized a PTAD derivative linked to the HIV entry inhibitor aplaviroc. Labeling of the antibody trastuzumab with this reagent provided a labeled antibody conjugate that demonstrated potent HIV-1 neutralization activity demonstrating the potential of this reaction in creating protein conjugates with small molecules. The tyrosine click linkage demonstrated stability to extremes of pH, temperature, and exposure to human blood plasma indicating that this linkage is significantly more robust than maleimide-type linkages that are commonly employed in bioconjugations. These studies support the broad utility of this reaction in the chemoselective modification of small molecules, peptides, and proteins under mild aqueous conditions over a broad pH range using a wide variety of biologically acceptable buffers such as phosphate buffered saline (PBS) and 2-amino-2-hydroxymethyl-propane-1,3-diol (Tris) buffers as well as others and mixed buffered compositions.

Sequence control in polymer synthesis

The control over comonomer sequences is barely studied in macromolecular science nowadays. This is an astonishing situation, taking into account that sequence-defined polymers such as nucleic acids and proteins are key components of the living world. In fact, fascinating biological machines such as enzymes, transport proteins, cytochromes or sensory receptors would certainly not exist if evolution had not favored chemical pathways for controlling chirality and sequences. Thus, it seems obvious that synthetic polymers with controlled monomer sequences have an enormous role to play in the materials science of the next centuries. The goal of this tutorial review is to shed light on this highly important but embryonic field of research. Both biological and synthetic mechanisms for controlling sequences in polymerization processes are critically discussed herein. This state-of-the-art overview may serve as a source of inspiration for the development of new generations of synthetic macromolecules.

Bioorthogonal chemistry: fishing for selectivity in a sea of functionality

The study of biomolecules in their native environments is a challenging task because of the vast complexity of cellular systems. Technologies developed in the last few years for the selective modification of biological species in living systems have yielded new insights into cellular processes. Key to these new techniques are bioorthogonal chemical reactions, whose components must react rapidly and selectively with each other under physiological conditions in the presence of the plethora of functionality necessary to sustain life. Herein we describe the bioorthogonal chemical reactions developed to date and how they can be used to study biomolecules.

Semisynthetic Murine Prion Protein Equipped with a GPI Anchor Mimic Incorporates into Cellular Membranes

Conversion of cellular prion protein (PrP(C)) into the pathological conformer (PrP(Sc)) has been studied extensively by using recombinantly expressed PrP (rPrP). However, due to inherent difficulties of expressing and purifying posttranslationally modified rPrP variants, only a limited amount of data is available for membrane-associated PrP and its behavior in vitro and in vivo. Here, we present an alternative route to access lipidated mouse rPrP (rPrP(Palm)) via two semisynthetic strategies. These rPrP variants studied by a variety of in vitro methods exhibited a high affinity for liposomes and a lower tendency for aggregation than rPrP. In vivo studies demonstrated that double-lipidated rPrP is efficiently taken up into the membranes of mouse neuronal and human epithelial kidney cells. These latter results enable experiments on the cellular level to elucidate the mechanism and site of PrP-PrP(Sc) conversion.

Multivalency—a way to enhance binding avidities and bioactivity—preliminary applications to EPO

Multivalency has advantages over monovalency for binding interactions and even for activity. In particular, avidity is higher since the off-rate of a multivalent species is much slower than that of a monomer. This is particularly profitable for ligand-binding receptors that require dimerization for activity, such as the receptor of erythropoietin (EPOR). Peptides that mimic the action of erythropoietin (EPO) have been described with no sequence similarity with the human hormone: erythropoietin mimetic peptide (EMP) and EPO receptor peptide (ERP). These two peptides have similar activity but interact through different sites on the EPOR. Here, we describe the construction of several new synthetic homo- and hetero-dimers based on EMP-ERP sequences. To link the monomeric molecules together, several monodisperse polyamide linkers of different lengths were synthesized with dialdehyde functionalities. Chemoselective oxime chemistry was used to obtain homogeneous constructs. Certain chemical incompatibilities were dealt with via a protection approach. The oximes are stable under normal conditions and so lend themselves to biological testing.

Cell-penetrating proline-rich peptidomimetics

Cell-penetrating peptides (CPPs) offer potential as delivery agents for the cellular administration of drugs. However, the pharmacological utility of CPPs that are derived from natural amino acids is limited by their rapid metabolic degradation, low membrane permeability, and toxicity. Various peptidomimetics able to overcome these problems have been described, including peptides formed by D-amino acids and beta-peptides. This chapter summarizes the synthesis of gamma-proline-derived peptides and polyproline dendrimers for drug delivery applications, and includes descriptions of several modifications in the gamma-peptides (mimicking the side chains of the alpha-amino acids) or modulating the dendrimer surface. 5(6)-Carboxyfluorescein labeling of the aforementioned peptidomimetics for use in cell translocation studies is also described. Furthermore, different protocols for the study of the drug delivery capabilities of these compounds are reviewed, including enzymatic stability studies, cellular uptake measurements by plate fluorimetry and flow cytometry, confocal laser scanning microscopy, and cytotoxicity assays.

Solid Phase Synthesis of Dual Labeled Peptides: Development of Cell Permeable Calpain Specific Substrates

A step-by-step evaluation of dual-labeled FRET substrates for the protease calpain is reported. The study led to cell permeable selections, with optimized specificity and effectiveness for the target enzyme, and improved stability to non-specific degrading enzymes.

Synthesis and screening of a small library of proline-based biodendrimers for use as delivery agents

A small library of defined peptide dendrimers based on polyproline sequences was designed to demonstrate the feasibility of generating a new type of polymeric agent for therapeutic use. Structural modifications to dendrimer surfaces further enriched the diversity of the library. Data show that the prolinerich dendrimers can be internalized in human epithelial (HeLa) cells, demonstrating the importance of the dendrimeric motif. The promising results described herein suggest that controlled modification of the dendrimer surface should eventually yield proline dendrimers with therapeutic potential.

Chemical and biological properties of polymer-modified proteins

Modification with polymers such as polyethylene glycol (PEG) can increase circulating lifetime, reduce immunogenicity and simplify the handling of pharmaceutical proteins. These benefits are currently exploited in six marketed polymer-modified protein therapeutics and about a dozen product candidates in clinical trials. However, traditional protein modification techniques are restricted by the limited control over polymer structure and the location and number of polymer attachment sites. New technology, in the form of chemical protein synthesis and the generation of precision polymers, has been applied to generate synthetic erythropoiesis protein (SEP). This promising treatment for anaemia has been synthesised with precision polymer modification methodology to improve the target protein pharmaceutical. The chemical and biological properties of proteins prepared by both traditional and novel approaches are contrasted in this discussion of chemical protein synthesis and polymer modification in protein drug discovery.

Synthetic Erythropoietic Proteins: Tuning Biological Performance by Site-Specific Polymer Attachment

Chemical synthesis in combination with precision polymer modification allows the systematic exploration of the effect of protein properties, such as charge and hydrodynamic radius, on potency using defined, homogeneous conjugates. A series of polymer-modified synthetic erythropoiesis proteins were constructed that had a polypeptide chain similar to the amino acid sequence of human erythropoietin but differed significantly in the number and type of attached polymers. The analogs differed in charge from +5 to -26 at neutral pH and varied in molecular weight from 30 to 54 kDa. All were active in an in vitro cell proliferation assay. However, in vivo potency was found to be strongly dependent on overall charge and size. The trends observed in this study may serve as starting points for the construction of more potent synthetic EPO analogs in the future.

Conversion of a mechanosensitive channel protein from a membrane-embedded to a water-soluble form by covalent modification with amphiphiles

Covalent modification of integral membrane proteins with amphiphiles may provide a general approach to the conversion of membrane proteins into water-soluble forms for biophysical and high-resolution structural studies. To test this approach, we mutated four surface residues of the pentameric Mycobacterium tuberculosis mechanosensitive channel of large conductance (MscL) to cysteine residues as anchors for amphiphile attachment. A series of modified ion channels with four amphiphile groups attached per channel subunit was prepared. One construct showed the highest water solubility to a concentration of up to 4mg/ml in the absence of detergent. This analog also formed native-like, alpha-helical homo-pentamers in the absence of detergent as judged by circular dichroism spectroscopy, size-exclusion chromatography and various light-scattering techniques. Proteins with longer, or shorter polymers attached, or proteins modified exclusively with polar cysteine-reactive small molecules, exhibited reduced to no solubility and higher-order aggregation. Electron microscopy revealed a homogeneous population of particles consistent with a pentameric channel. Solubilization of membrane proteins by covalent attachment of amphiphiles results in homogeneous particles that may prove useful for crystallization, solution NMR spectroscopy, and electron microscopy.

Chemical synthesis and single channel properties of tetrameric and pentameric TASPs (template-assembled synthetic proteins) derived from the transmembrane domain of HIV virus protein u (Vpu)

Vpu, an 81-residue membrane protein encoded by the genome of HIV-1, is involved in CD4 degradation and facilitates virion budding from infected cells. The latter activity requires an intact transmembrane (TM) domain; however, the mechanism remains unclear. Vpu forms ion channels, an activity linked to the TM domain and envisioned to arise by oligomerization. The precise number of Vpu monomers that structure the channel is not yet known. To address this issue, we have synthesized tetrameric and pentameric proteins consisting of a carrier template to which four or five peptides corresponding to the TM domain of Vpu are attached. Ketoxime-forming chemoselective ligation efficiently ligated four and five copies, respectively, of the linear transmembrane peptide that was solubilized by the addition of a cleavable polyethylene glycol-polyamide auxiliary to a template. Purified tetrameric and pentameric proteins, denoted as T(4)Vpu and T(5)Vpu, exhibit the predicted mass as determined by MS analysis and fold with a high helical content as evidenced by CD. Both T(4)Vpu and T(5)Vpu, after reconstitution in lipid bilayers, form discrete ion channels of distinct conductance and high propensity to be open. The most frequent openings have a single channel conductance of 42 +/- 5 pS for T(4)Vpu and 76 +/- 5 pS for T(5)Vpu in 0.5m KCl. These findings validate the notion that the channels formed by Vpu result from the self-assembly of monomers. We conclude that a five-helix bundle of the TM of Vpu may approximate the structural motif underlying the oligomeric state of the conductive channel.

Synthesis of a functionalized high affinity mannose receptor ligand and its application in the construction of peptide-, polyamide- and PNA-conjugates

The synthesis of a high affinity mannose receptor ligand, appropriately functionalized for chemoselective ligation with an antigen or DNA-binding moieties is described. By a combination of solid- and solution-phase chemistry a versatile synthesis of the target structure was accomplished. Examples of subsequent ligation reactions are described.

Design and chemical synthesis of a homogeneous polymer-modified erythropoiesis protein

We report the design and total chemical synthesis of "synthetic erythropoiesis protein" (SEP), a 51-kilodalton protein-polymer construct consisting of a 166-amino-acid polypeptide chain and two covalently attached, branched, and monodisperse polymer moieties that are negatively charged. The ability to control the chemistry allowed us to synthesize a macromolecule of precisely defined covalent structure. SEP was homogeneous as shown by high-resolution analytical techniques, with a mass of 50,825 +/-10 daltons by electrospray mass spectrometry, and with a pI of 5.0. In cell and animal assays for erythropoiesis, SEP displayed potent biological activity and had significantly prolonged duration of action in vivo. These chemical methods are a powerful tool in the rational design of protein constructs with potential therapeutic applications.

A practical approach to the synthesis of hairpin polyamide-peptide conjugates through the use of a safety-catch linker

Hairpin polyamides are high-affinity, sequence selective DNA binders. The use of a safety-catch linker for the solid phase synthesis of hairpin polyamides allows for easy preparation of derivatives ready for chemoselective ligation with unprotected peptides. Examples of ligations reported include thioether bond formation and thioester-mediated amide bond formation ('Native Chemical Ligation').

Solution- and Solid-Phase Synthesis of Components for Tethered Bilayer Membranes

The synthesis of the novel compound PhCH(2)SS(C(24)H(44)N(4)O(10))(C(20)H(41)) (5) for the preparation of tethered bilayer membranes is described. The compound is the all-amide analogue of the previously reported ester-containing membrane-forming material PhCH(2)SS(C(24)H(40)O(14))(C(20)H(41)) (1). The advanced intermediate (C(20)H(41)) C(16)H(28)N(3)O(8) (17) was prepared from the same starting materials using both solution-phase (13% yield) and solid-phase (81% yield) techniques. Monolayers on gold derived from 5 have been analyzed by ellipsometry and FTIR. The monolayers exhibit thicknesses similar to monolayers derived from 1 and possess H-bonded amide functionality.