Welcome to the Biotage Peptide Synthesis Blogs.

      How to use the isolectric point to inform your peptide purification mobile phase pH

      Jul 22, 2020 2:20:22 PM / by Elizabeth Denton posted in Reversed-phase, Alstra, Peptide Purification, Method development

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      The isolectric point (pI) is a physical property of every peptide (and any other compound for that matter) that can be the root cause for many of the issues experienced when handling these compounds. Often times a quick check of the pI can help inform which conditions will increase or decrease aggregation potential, or lead to better solubility and generally easier handling.  

      In today's discussion, I'll demonstrate how you can use the pI to guide your purification method development for peptides.

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      Peptide Workflow in action at Red Glead Discovery

      May 28, 2020 3:33:10 PM / by Amit Mehrotra posted in Peptides, Workflow, Alstra

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      Red Glead Discovery (RGD) is a pre-clinical drug discovery CRO offering a broad range of services to Life Science clients. With a focus on small molecules and peptides, their drug discovery platform ranges from medicinal chemistry and synthesis to ADME and biology. In addition to the CRO business, they also perform research collaborations with various biotech and academic partners.

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      Cyclic Peptides Webinar Recap

      Apr 15, 2020 2:40:31 PM / by Elizabeth Denton posted in Peptides, Troubleshooting and Optimization, Webinar, Automation, Alstra

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      Peptides, while exhibiting potential for unique specificity and affinity, still suffer from stability issues when introduced to a biological system.  One strategy to overcome these stability issues is include a covalent bond, creating a peptide macrocycle.  

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      Disulfide Rich Peptides - which order should the disulfide bonds be formed?

      Apr 15, 2020 2:38:56 PM / by Elizabeth Denton posted in Peptides, Troubleshooting and Optimization, Synthesis, Alstra

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      Disulfide rich peptides are being identified in species of both plants and animals at increasing rates. As new molecules are discovered and disulfide bonding patterns characterized, the need for simplified chemical synthesis strategies is also increasing.

      I have previously written about optimizing removal of several orthogonal side chain protecting groups including allyl, alloc, ivDde and acetamidomethyl (Acm) groups. The question that I’ll address today, though, is does the order in which the disulfide bonds are formed matter for cleaning up reactions to produce chemically synthesized disulfide rich peptides?

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      Using microwave heating for your stapled peptide synthesis

      Jan 24, 2020 10:27:08 PM / by Elizabeth Denton posted in Peptides, Synthesis, Alstra

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      Hydrocarbon stapling as a strategy to stabilize secondary structures of peptides, while introduced by Miller, Blackwell and Grubbs in the mid 1990s, really grew to the forefront with seminal work by Schaffmeister and Verdine in early 2000s.  Protocols have been developed that enable this post-synthesis modification while the peptide is still on resin, but often these metathesis reactions are performed manually, and at room temperature.

      In today's post, I'll compare several different sets of reaction conditions using microwave heating with the goal of expediting the olefin metathesis reaction, without compromising reaction efficiency, and towards automating the entire synthesis.

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      Optimizing the removal of an ACM protecting group

      Nov 14, 2019 3:40:28 PM / by Elizabeth Denton posted in Peptides, Troubleshooting and Optimization, Synthesis, Alstra

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      Disulfide rich peptides have gained significant attention recently due to their incredible biological stability and tolerance to epitope grafting.  This class of peptides is often folded in solution, assuming the desired disulfide bond pattern correlates with the most thermodynamically stable structure.  Sometimes though, especially for chemically synthesized cysteine rich peptides, this is not the case.  The result is a complex mixture of peptides with varying disulfide bonding patterns and identical mass.

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      Does amino acid concentration really matter during peptide synthesis?

      Nov 8, 2019 4:15:44 PM / by Elizabeth Denton posted in Peptides, Troubleshooting and Optimization, Media and Resin, Automation, Alstra

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      When it comes to synthesizing a peptide, the first thing that comes to mind is the number of stoichiometric equivalents to use.  Sometimes that number is as few as 1.5, sometimes it’s as high as 20!

      But have you ever thought about the liquid volume that contains those molecules and how that might affect the success of your coupling reaction?  In this post I will discuss the impact of amino acid concentration in the overall success of solid phase peptide synthesis.

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      How do I choose my resin for peptide synthesis? {Part 1}

      Nov 8, 2019 4:13:33 PM / by Elizabeth Denton posted in Peptides, Synthesis, Media and Resin, Alstra

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      It used to be easy with only polystyrene based resin types, but nowadays there is a broad choice of types to choose from, including everything from the C-terminal functionality (Rink vs Wang) to the polymer from which the resin itself is synthesized.

      All resins have one thing in common, and that’s the reactive site loading level. In this post, I will share my experiences with how this important factor impacts the success of peptide synthesis.

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      Five Tips and Tricks for Success in Solid Phase Peptide Synthesis

      Sep 27, 2019 3:26:17 PM / by Elizabeth Denton posted in Peptides, Troubleshooting and Optimization, Synthesis, Alstra

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      In my role as a peptide application scientist, I have had the pleasure of working with many groups that are venturing into the world of peptides for the first time.  Although it seems rather  straightforward to experienced synthetic chemists, producing acceptable yield and purity certainly comes with unique challenges in solid phase peptide synthesis .

      In this post I would like to present some of the tips and tricks that I have picked up along the way.

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      Peptides containing cysteine: the role of scavengers in cleavage cocktail

      Sep 11, 2019 10:48:03 PM / by Elizabeth Denton posted in Peptides, Synthesis, Alstra

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      Since the development of Fmoc-based solid phase peptide synthesis, a wide variety of cleavage cocktails have emerged.  Each cleavage cocktail contains a unique combination of scavengers designed to prevent either side reactions mediated by the released protecting groups or the side chains themselves, or both during the peptide cleavage reaction.  As the number of scientists performing peptide synthesis grows, the question “which cleavage cocktail should I use?” comes up more often than not.

      In today’s post, I’ll highlight the role of of scavengers for peptides containing cysteine residues.

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      Room temperature allyl ester and alloc deprotections - what is the lifetime of palladium?

      Jun 11, 2019 8:30:33 PM / by Elizabeth Denton posted in Peptides, Synthesis, Alstra

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      In a previous post, I did some work evaluating the efficiency of alloc removal with tetrakis palladium using microwave assistance and atmospheric conditions, which worked beautifully.  Given the known sensitivity of palladium catalysts (see Derek Lowe's post for a humorous dialogue), I sought to further explore the sensitivity of palladium towards the alloc removal in the context of a peptide.

      In this post, I'll explore a variety of atmospheric, room temperature alloc deprotection conditions aimed at evaluating the catalytic lifetime of palladium tetrakis for effective alloc removal. 

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      Using microwave heating to expedite your allyl ester or alloc deprotection

      Jun 11, 2019 8:28:51 PM / by Elizabeth Denton posted in Peptides, Troubleshooting and Optimization, Synthesis, Alstra

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      Orthogonal amino acid protecting groups effectively expand the chemical tool kit available to peptide chemists allowing for synthesis of much more complex molecules.  Often times, orthogonal protecting groups are used in Fmoc-based chemistry to facilitate post-synthesis modifications of peptides, like the addition of small molecule fluorophores and more commonly now, peptide cyclization efforts.

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      Using double coupling to improve your peptide synthesis

      Apr 29, 2019 6:06:48 PM / by Elizabeth Denton posted in Peptides, Troubleshooting and Optimization, Synthesis, Alstra

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      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.

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      How to quantify your first amino acid loading onto Wang resins

      Apr 29, 2019 6:04:33 PM / by Elizabeth Denton posted in Peptides, Synthesis, Media and Resin, Alstra

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      While many of the standard amino acids can be purchased pre-loaded onto Wang type resins, there are still cases where coupling the first amino acid onto Wang resin manually is necessary.  In my case, an unnatural amino acid was required on the C-terminus so there was not a commercially available source.

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      How to handle peptides that contain methionine

      Mar 28, 2019 2:24:34 PM / by Elizabeth Denton posted in Peptides, Troubleshooting and Optimization, Synthesis, Automation, Alstra

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      The diversity of amino acid side chain functionalities, coupled with secondary structure, gives peptides and proteins their unique properties and activities. However, when it comes to chemically synthesizing peptides or even small proteins, the side chain functionalities can do more harm than good.

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      Webinar: Synthesizing Disulfide-rich Peptides

      Feb 1, 2019 4:46:25 PM / by Elizabeth Denton posted in Peptides, Troubleshooting and Optimization, Synthesis, Webinar, Alstra

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      Elizabeth Denton, PhD, Senior Scientist Peptide Chemistry, recorded a webinar titled Disulfide Rich Peptides: Optimizing and Automating Syntheses with Regioselective Formation of Disulfide Bonds. To learn more, read the description below as well as watch the recording!

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