Optimizing the removal of an ivDde protecting group

As the complexity of peptides continues to grow, so does the use of amino acids with side chain protecting groups that can be selectively removed, leaving the peptide on resin and the remaining side chain protecting groups intact.  While there are  protocols to be found in the literature,  they may not work to the highest level of efficiency every single time.  This can lead to disasterous results for any subsequent chemistry.

In today’s post, I’ll evaluate a variety of conditions for removing an ivDde protecting group.

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Can you use normal-phase chromatography to purify protected peptides?

Chemical synthesis of peptides, and even proteins, offers the possibility to expand the functionality and stability imbued by nature.  However, chemical synthesis of very long peptides and small proteins remains today an exceedingly difficult task.  Several ligation strategies have been developed that help to alleviate this challenge.  These strategies though, require a purified, yet fully protected peptide fragment.

Purification of a fully protected peptide species can be challenging by standard reversed-phase techniques, primarily due to the limited solubility of protected peptides in aqueous solutions.  In today’s post, I will discuss using normal-phase chromatography for purification of protected peptides.

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Synthesizing hydrophobic peptides – choosing the right solvent

Every now and again I hear the question “which solvent do you recommend for my solid phase peptide synthesis?”  Historically, dichloromethane (DCM) was used as a solvent for solid phase synthesis as the kinetics of amino acid activation and amine coupling were much more favorable.  However, solubility concerns, particularly for Fmoc-protected amino acids limited the utility of the solvent.  Nowadays, DMF and NMP are the two principle solvents for both microwave assisted and room temperature solid phase peptide synthesis.  But the question remains, which one is better?

In today’s post, I will compare how the choice of dimethylformamide (DMF) or N-methylpyrolidone (NMP) effects the synthesis of a short yet very hydrophobic peptide.

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Green solvents for solid phase peptide synthesis?

As peptide therapeutics continue to gain interest from the medical community and pharmaceutical companies, concerns regarding the cost of manufacturing also grow.  Cost  includes the expense of reagents and solvents, including DMF and NMP, used in the synthesis but also subsequent disposal.  Combining this fact along with growing conversations about strategies to make chemistry green(er) and more of interest to this blog, greener solvents in peptide chemistry.

The looming question is, what replacement solvents should we use and is Fmoc-based solid phase peptide synthesis still efficient?  In this post, I will highlight a few solvents mentioned during a green chemistry presentation at TIDES 2017, a conference specifically geared towards peptide and oligonucleotide therapeutic development Continue reading Green solvents for solid phase peptide synthesis?

Which stationary phase should I chose for my peptide purification?

Almost all the peptides I have synthesized were subsequently purified using a reversed-phase C18 column.  Sometimes this worked, but sometimes it didn’t work so well.  When my C18 purifications failed, I questioned whether or not I could have predicted this outcome prior to extensive HPLC efforts.  Since then, I have learned that the amino acid composition of the peptide may give some clues to the peptide’s chromatographic behavior.

While there are numerous stationary phase functionalizations for reversed-phase chromatography, in today’s post I will describe some differences I have observed when purifying peptides using C18 or C4 functionalized stationary phases for peptide purifications.

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Why won’t my peptide stick to my column?

Conversations are routinely held regarding handling hydrophobic peptides, but hydrophilic peptides offer their own challenges when it comes to purification.  In a previous post, I synthesized Octa-Arg, an extremely hydrophilic peptide. I used  ion pairing reagents to increase the peptide’s overall retention by the stationary phase, but choosing the solvent should to use for solubilizing the peptide for purification by flash column chromatography was no easy task.

In today’s post, I’ll investigate several solvents commonly used to inject peptide samples for purification and evaluate their impact in peptide retention by the stationary phase.

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How to purify hydrophilic peptides with flash column chromatography

Synthesizing hydrophilic peptides can be relatively straightforward, especially when compared to the trials and tribulations encountered when synthesizing hydrophobic peptides.  However, purifying hydrophilic peptides using standard reversed-phase chromatography can be a challenge.    In a previous post, I encountered this problem during my analytical HPLC analysis of crude peptide mixtures.

In this post, I will discuss the use of ion pairing agents to increase the perceived hydrophobicity of your peptide, increasing the column retention and enabling a smooth purification of your hydrophilic peptide.

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Microwave heating – a route to better quality crude peptides

Historically, solid phase peptide synthesis has been conducted at room temperature, demanding long reaction times and often double coupling to ensure a quality crude peptide product.  More recently however, different strategies have been identified to heat the reactor vial, increasing the overall reaction rate and potentially the crude purity of your peptide.

In today’s post I will demonstrate that microwave heating can improve the crude purity of your desired peptide.

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How long are amino acids stable in solution?

In previous posts I have described using high concentrations of amino acids to improve your peptide synthesis among some other tips and tricks.  But there is a particularly handy tip that was left off the list.

Weighing out and dissolving the amino acids and coupling reagents requires the greatest amount of manual effort when setting up a peptide synthesis, particularly for automated instruments. One way to alleviate some of this time investment is to generate stock solutions of your amino acids for use over the course of several syntheses.  You’re probably asking yourself though: “how long are those amino acid solutions actually stable?”

In today’s post I’ll answer that question by comparing the crude purity of peptides synthesized using amino acid stock solutions or freshly dissolved amino acids.

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Using double coupling to improve your peptide synthesis

There are several strategies employed when a peptide synthesis requires optimization.  Typically, the first thing considered is whether or not to double couple specific amino acids within the sequence.  This is somewhat of a change in mentality from traditional room temperature synthesis strategies where double coupling is frequently used for the entire peptide sequence.

In a previous post, I briefly described several scenarios in which doubling coupling can be used in conjunction with microwave heating to improve the overall crude peptide purity.  In today’s post, I will delve more deeply into the question of whether or not double coupling is necessary to improve your peptide synthesis.

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