Microwave Heating for Solid-Phase Peptide Synthesis: General Evaluation and Application to 15-mer Phosphopeptides

Multiphosphorylation-Dependent Recognition of Anti-pS2 Antibodies against RNA Polymerase II C-Terminal Domain Revealed by Chemical Synthesis

Phosphorylation is a major constituent of the CTD code, which describes the set of post-translational modifications on 52 repeats of a YSPTSPS consensus heptad that orchestrates the binding of regulatory proteins to the C-terminal domain (CTD) of RNA polymerase II. Phospho-specific antibodies are used to detect CTD phosphorylation patterns. However, their recognition repertoire is underexplored due to limitations in the synthesis of long multiphosphorylated peptides. Herein, we describe the development of a synthesis strategy that provides access to multiphosphorylated CTD peptides in high purity without HPLC purification for immobilization onto microtiter plates. Native chemical ligation was used to assemble 12 heptad repeats in various phosphoforms. The synthesis of >60 CTD peptides, 48-90 amino acids in length and containing up to 6 phosphosites, enabled a detailed and rapid analysis of the binding characteristics of different anti-pSer2 antibodies. The three antibodies tested showed positional selectivity with marked differences in the affinity of the antibodies for pSer2-containing peptides. Furthermore, the length of the phosphopeptides allowed a systematic analysis of the multivalent chelate-type interactions. The absence of multivalency-induced binding enhancements is probably due to the high flexibility of the CTD scaffold. The effect of clustered phosphorylation proved to be more complex. Recognition of pSer2 by anti-pSer2-antibodies can be prevented and, perhaps surprisingly, enhanced by the phosphorylation of "bystander" amino acids in the vicinity. The results have relevance for functional analysis of the CTD in cell biological experiments.

Dissecting the role of protein phosphorylation: a chemical biology toolbox

Protein phosphorylation is a crucial regulator of protein and cellular function, yet, despite identifying an enormous number of phosphorylation sites, the role of most is still unclear. Each phosphoform, the particular combination of phosphorylations, of a protein has distinct and diverse biological consequences. Aberrant phosphorylation is implicated in the development of many diseases. To investigate their function, access to defined protein phosphoforms is essential. Materials obtained from cells often are complex mixtures. Recombinant methods can provide access to defined phosphoforms if site-specifically acting kinases are known, but the methods fail to provide homogenous material when several amino acid side chains compete for phosphorylation. Chemical and chemoenzymatic synthesis has provided an invaluable toolbox to enable access to previously unreachable phosphoforms of proteins. In this review, we selected important tools that enable access to homogeneously phosphorylated protein and discuss examples that demonstrate how they can be applied. Firstly, we discuss the synthesis of phosphopeptides and proteins through chemical and enzymatic means and their advantages and limitations. Secondly, we showcase illustrative examples that applied these tools to answer biological questions pertaining to proteins involved in signal transduction, control of transcription, neurodegenerative diseases and aggregation, apoptosis and autophagy, and transmembrane proteins. We discuss the opportunities and challenges in the field.

Determining the structure and binding mechanism of oxytocin-Cu2+ complex using paramagnetic relaxation enhancement NMR analysis

Oxytocin is a neuropeptide that binds copper ions in nature. The structure of oxytocin in interaction with Cu²⁺ was determined here by NMR, showing which atoms of the peptide are involved in binding. Paramagnetic relaxation enhancement NMR analyses indicated a binding mechanism where the amino terminus was required for binding and subsequently Tyr2, Ile3 and Gln4 bound in that order. The aromatic ring of Tyr2 formed a π-cation interaction with Cu²⁺. Oxytocin copper complex structure revealed by paramagnetic relaxation enhancement NMR analyses.

Multiphosphorylated peptides: importance, synthetic strategies, and applications for studying biological mechanisms

Advances in the synthesis of multiphosphorylated peptides and peptide libraries: tools for studying the effects of phosphorylation patterns on protein function and regulation.

A targeted approach for the synthesis of multi-phosphorylated peptides: a tool for studying the role of phosphorylation patterns in proteins

Protein phosphorylation barcodes, clusters of several phosphorylation sites within a short unfolded region, control many cellular processes. Existing biochemical methods used to study the roles of these barcodes suffer from low selectivity and provide only qualitative data. Chemically synthesized multiphosphopeptide libraries are selective and specific, but their synthesis is extremely difficult using the current peptide synthesis methods. Here we describe a new microwave assisted approach for synthesizing a library of multiphosphopeptides, using the C-terminus of rhodopsin as a proof of concept. Our approach utilizes multiple protocols for synthesizing libraries of multiphosphopeptides instead of the inefficient single protocol methods currently used. Using our approach we demonstrated the synthesis with up to seven phosphorylated amino acids, sometimes next to each other, an accomplishment that was impractical before. Synthesizing the Rhodopsin derived multiphosphopeptide library enabled dissecting the precise phosphorylation barcode required for the recruitment, activation and modulation of the conformation of Arrestin. Since phosphorylation barcodes modulate the activity of hundreds of GPCRs, synthesizing libraries of multiphosphopeptides is the method of choice for studying their molecular mechanisms of action. Our approach provides an invaluable tool for evaluating how protein phosphorylation barcodes regulate their activity.

Microwave-assisted synthesis of cyclic phosphopeptide on solid support

Phosphopeptides are important tools for studying intracellular signal transduction events in vitro and in vivo and are also potential drugs due to their direct competition with phosphoprotein recognition elements. Cyclization has been demonstrated to improve peptide selectivity, metabolic stability, and bioavailability. However, cyclic phosphopeptide synthesis may not be straightforward due to the sterically hindered phosphorylated side-chain amino acid derivatives. One option to overcome this hurdle is to use microwave-assisted synthesis, which has been shown to increase efficiency and reduce synthesis time. Herein, a detailed protocol is provided for synthesizing cyclic phosphopeptides using automated microwave. The overall synthesis duration was reduced and yields increased compared with a manual conventional method. This method provides a general, fast and facile way to synthesize cyclic peptides, demonstrating the synthesis of cyclic phosphorylated peptides which are known to be among the most challenging to produce.

Killing of Mycobacterium avium by lactoferricin peptides: improved activity of arginine- and D-amino-acid-containing molecules

Mycobacterium avium causes respiratory disease in susceptible individuals, as well as disseminated infections in immunocompromised hosts, being an important cause of morbidity and mortality among these populations. Current therapies consist of a combination of antibiotics taken for at least 6 months, with no more than 60% overall clinical success. Furthermore, mycobacterial antibiotic resistance is increasing worldwide, urging the need to develop novel classes of antimicrobial drugs. One potential and interesting alternative strategy is the use of antimicrobial peptides (AMP). These are present in almost all living organisms as part of their immune system, acting as a first barrier against invading pathogens. In this context, we investigated the effect of several lactoferrin-derived AMP against M. avium. Short peptide sequences from both human and bovine lactoferricins, namely, hLFcin1-11 and LFcin17-30, as well as variants obtained by specific amino acid substitutions, were evaluated. All tested peptides significantly inhibited the axenic growth of M. avium, the bovine peptides being more active than the human. Arginine residues were found to be crucial for the display of antimycobacterial activity, whereas the all-d-amino-acid analogue of the bovine sequence displayed the highest mycobactericidal activity. These findings reveal the promising potential of lactoferricins against mycobacteria, thus opening the way for further research on their development and use as a new weapon against mycobacterial infections.

Backbone amide linker strategy: protocols for the synthesis of C-terminal peptide aldehydes

In the backbone amide linker (BAL) strategy, the peptide is anchored not at the C-terminus but through a backbone amide, which leaves the C-terminal available for various modifications. This is thus a very general strategy for the introduction of C-terminal modifications. The BAL strategy was originally developed using a trisalkoxybenzyl linker, but since then range linkers (handles) with different properties have also been developed. The BAL anchoring is established by anchoring an aromatic aldehyde, typically a trisalkoxybenzaldehyde, to the solid support, followed by attachment of the first amino acid residue by reductive amination. This can be used as a general approach for the introduction of other C-terminal modifications as well as functionalities, such as fluorophors. The second step is an acylation of a secondary amine, followed by standard Fmoc-based solid-phase synthesis to assemble the final peptide. One useful application of this strategy is in the synthesis of C-terminal peptide aldehydes. The C-terminal aldehyde is masked as an acetal during synthesis and then conveniently demasked in the final cleavage step to generate the free aldehyde. Another application is in the synthesis of peptide thioesters with a C-terminal glycine.

Microwave-assisted solid-phase peptide synthesis using the biotage Syro Wave™

Fast and precise heating by microwave irradiation during solid-phase peptide synthesis (SPPS) can reduce reaction times as well as provide better purities and greater yields for the synthesis of difficult peptides. Microwave- assisted SPPS has proven to be a useful and reliable tool for the synthesis of peptides as well as small proteins. It is particularly well suited for sequences with a high propensity to form β-sheet-type structures and for sterically difficult couplings. In this protocol, conditions and detailed procedures are described for performing microwave-assisted SPPS using the Syro Wave™. Here we describe the synthesis of two difficult peptide sequences: the first is derived from the C-terminus of the MuLV CTL epitope, the second is a de novo designed peptide with a C-terminal alkyne.

Peptide release, side-chain deprotection, work-up, and isolation

After having successfully synthesized a peptide, it has to be released from the solid support, unless it is being used for on-resin display. The linker and, in some cases, the cleavage mixture determine the C-terminal functionality of the released peptide. In most cases, the peptide is released with concomitant removal of side-chain protecting groups. However, some combinations of linkers and side-chain protecting groups enable a two-stage procedure, either using orthogonal chemistry or graduated labilities. Herein, we describe protocols for the release of peptides from the most commonly used linker types providing a variety of different C-terminal functionalities, including acids, amides, amines, and aldehydes. Moreover, suggestions for determination of peptide purity and for storage conditions are provided.

Solid-phase synthesis of phosphopeptides

Phosphopeptides are generally prepared by incorporation of suitable, protected phosphoamino acid derivatives during peptide synthesis using routine coupling protocols. The feasibility of chemical synthesis of phosphorylated peptides by Fmoc-SPPS was greatly enhanced by the introduction of the monobenzyl protecting group for the phosphate group. This minimized β-elimination of the phosphate group and made Fmoc-based synthesis of phosphopeptides the preferred synthesis strategy. Described here is our strategy for the synthesis of phosphopeptides attached to the solid support PEGA via a backbone amide linker type. This linker allows removal of side-chain protection groups without releasing the phosphopeptide from the solid support, thus enabling solid-phase-based pull-down reactions and peptide-protein interaction studies.

Optimization of the solid-phase synthesis of [18F] radiolabeled peptides for positron emission tomography

Establishing improved methods for the radiolabeling of peptides with fluorine-18 via solid-phase peptide synthesis (SPPS) is desirable for the efficient synthesis of peptide-based molecular imaging agents. This work focuses on the development of a standardized platform to facilitate the reliable and efficient synthesis of high-purity fluorine-18 radiolabeled peptides for in vivo imaging with positron emission tomography (PET). Seven commercially available resins were selected for solid-phase radiolabeling of the model peptide VQAAIDYING with 4-[(18)F]fluorobenzoic acid ([(18)F]FBA). A wide range of radiochemical yields (18.8 ± 1.5% to 41.2 ± 5.3%) was obtained using standard conditions (coupling: 3 eq amino acid, 3 eq HATU, 6 eq DIPEA, 1.5 h, r.t.; cleavage: 94% TFA, 3 h, r.t.). After modification of coupling reagents and employing heated reactions to 37°C, radiochemical yields were improved by as much as 35.3% over standard conditions. When the optimized conditions were applied to the synthesis of [(18)F]FBA-PEG(28)-A20FMDV2, which targets the α(v)β(6) integrin in vivo, radiochemical yields improved by as much as 73.4% over those obtained using standard coupling and cleavage conditions. This platform can be utilized to improve the synthesis of peptide-based molecular probes for molecular imaging with PET.

Semi-automated microwave-assisted SPPS: Optimization of protocols and synthesis of difficult sequences

Precise microwave heating has emerged as a valuable addition to solid-phase peptide synthesis. New methods and protocols are required to utilize this potential and make it a reliable technique. Here, we describe a new semi-automated instrument for solid-phase peptide synthesis with microwave heating and report protocols for its reliable use. The instrument features a flow-through reaction vessel that is placed in the microwave instrument throughout the synthesis. Bubbling with N(2) gas during the microwave irradiation proved important for temperature control. Washing and Fmoc removal steps were automated, while activated Fmoc-amino acids were added manually. Several linkers and resins were evaluated and protocols for synthesis of difficult sequences were developed. These included on-resin reductive amination of BAL handles under microwave heating. We believe that the instrument, as well as the protocols for its use, will be useful tools for peptide chemists.

Microwave-assisted solid-phase peptide synthesis at 60 degrees C: alternative conditions with low enantiomerization

Several conditions have been used in the coupling reaction of stepwise SPPS at elevated temperature (SPPS-ET), but we have elected the following as our first choice: 2.5-fold molar excess of 0.04-0.08 M Boc or Fmoc-amino acid derivative, equimolar amount of DIC/HOBt (1:1) or TBTU/DIPEA (1:3), 25% DMSO/toluene, 60 degrees C, conventional heating. In this study, aimed to further examine enantiomerization under such condition and study the applicability of our protocols to microwave-SPPS, peptides containing L-Ser, L-His, L-Cys and/or L-Met were manually synthesized traditionally, at 60 degrees C using conventional heating and at 60 degrees C using microwave heating. Detailed assessment of all crude peptides (in their intact and/or fully hydrolyzed forms) revealed that, except for the microwave-assisted coupling of L-Cys, all other reactions occurred with low levels of amino acid enantiomerization (<2%). Therefore, herein we (i) provide new evidences that our protocols for SPPS at 60 degrees C using conventional heating are suitable for routine use, (ii) demonstrate their appropriateness for microwave-assisted SPPS by Boc and Fmoc chemistries, (iii) disclose advantages and limitations of the three synthetic approaches employed. Thus, this study complements our past research on SPPS-ET and suggests alternative conditions for microwave-assisted SPPS.

Enhanced microwave-assisted method for on-bead disulfide bond formation: synthesis of alpha-conotoxin MII

A novel enhanced microwave-assisted disulfide bridge formation method has been developed. To optimize the synthesis of the biologically important bicyclic peptide alpha-conotoxin MII (alpha-CtxMII), several cyclization methods have been tested and are discussed herein. By using m.w.-assisted heating, we achieved high yields for the first loop cyclization of alpha-CtxMII on-bead. This method has the advantage of avoiding intermolecular by-products during the cyclization step. Furthermore, the method gives higher yields compared with the common on-bead cyclization methods. The second disulfide bridge of alpha-CtxMII was formed using a simple oxidation method after the cleavage of the intermediate monocyclic peptide from the resin. This method has the potential to be efficient for the synthesis of other disulfide rich biologically important peptides.