First-hand experience with Pickapep, a new analysis and visualization tool for chemically modified peptides

Peptides, consisting of natural amino acids, have been an integral part in drug discovery, especially since their chemical accessibility through solid phase peptide synthesis (SPPS) in 1963 by Robert Bruce Merrifield. We have seen successful drugs like Fuzeon on the market, that consisted exclusively of natural amino acids, but there certainly are limitations. Canonical amino acid sequences are substrates to enzymes that prematurely digest the peptide, prior to their ability to unleash their purpose as a drug. Moreover, during the design of a drug, one must rely on the given building blocks of canonical amino acids, which often results in insufficient pharmacological impact.

Over the decades, peptide chemists have developed ways, to significantly enhance pharmacological properties like metabolic stability and bioavailability of peptides through divers chemical alterations, fusing the world of small molecule-based organic synthesis and the endless flexibility thereof with biomolecule conjugation and peptide chemistry, which in result leads to endless opportunities for peptide chemists to tune their desired drugs from fragile natural components into stable and powerful drugs.

A common modification to enhance for instance the stability of peptides is lipidation. As an example, GLP-1 has a half-life of about 1-2 minutes, before degradation in the human body. The lapidated GLP-1 analogue Semaglutide instead has a half-life of 165 hours, as the fatty acid chain binds to human serum albumin HSA in the blood stream. This trick allowed the generation of some of the biggest blockbuster drugs that were ever created, such as Ozempic (Semaglutide) by 诺和诺德 or Mounjaro (Tirzepatide) by 礼来

Peptide cyclization is another tool to effectively stabilize peptides and enhance their rigidity to improve pharmacologic properties. Natural peptide cyclization takes place through disulfide-bond formation, but the formation of disulfides is reversible through reductive substances, such as glutathione as cellular reductive agent. Therefore, peptide cyclization by chemical means became very popular, employing head-to-tail cyclizations or irreversible peptide stapling with e.g. benzyl bromide scaffolds that connect thiols from cysteine residues through an organic molecule.

Numerous other chemical modifications are commonly applied, such as the use of D-amino acids, the creation of peptide conjugates with other biomolecules like carbohydrates or antibodies and many more. It can be assumed, that more than 50% of the peptide-based drugs in current development are therefore chemically modified, providing the means to enhance properties like their polarity, flexibility, stability, solubility, membrane permeability, protein resistance and target affinity.

There were a couple of online tools available, that provide access to various peptide parameters, such as molecular weight and polarity. However, the set of non-canonical amino acids and chemical alterations in the peptide sequences that can be added are fairly limited, while also peptides have to be processed in these tools in a one-by-one fashion.

Christian Steuer and colleagues from the ETH Zurich recently published a new open-source tool called PICKAPEP, which facilitates the virtual construction of peptidomimetics with various types chemical modifications and cyclizations and allows parallel processing of peptide sets at once. This tool is intended to support peptide researchers to gather information about chemically modified peptides and improve thus the efficiency in the drug discovery process.

The key features of their new tool are:

1)???? The virtual construction and visualization of peptidomimetics

2)???? Parameter calculation

a.????? molecular weight

b.????? topological surface area

c.????? logP

d.????? rotatable bonds

e.????? SMILES codes

3)???? Custom amino acids

4)???? Batch processing

On the entry-interface of PICKAPEP, one can enter a peptide sequence, that can then be further processed with cyclization or modifications. In a simple example, one can add a peptide, with two cysteines and process it further for cyclization. As an example, Linaclotide can be generated by adding the sequence CCEYCCNPACTGCY into the mask, while the button is checked for further cyclization and modification.

The peptide is being displayed already with the corresponding properties. One can now go ahead and by easy means connect the corresponding disulfides to create Linaclotide.

The software can directly export files for processing with PyMOL, to further visualize the molecules.

One has multiple options to cyclize peptides in different ways and insert chemical modifications. A selection of non-canonical amino acids and chemical modifications is provided in the supporting information of the paper.

To further allow the generation of unique peptide hybrids with organic molecules and unnatural amino acids of every kind, on can easily create SMILE codes for an individual amino acid or building block on e.g. https://www.cheminfo.org/flavor/malaria/Utilities/SMILES_generator___checker/index.html or other online tools and save those into the PICKAPEP software.

As a special feature, the software can process multiple peptides at once from .xlsx or .csv files and of note, as the software is on your computer, you may process confidential sequences through it.

In sum, the new PICKAPEP software is a new and very versatile and useful tool to obtain rapid information and visualization of chemically modified peptides and accompanies well the trend of chemically modified peptides in drug development.

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At Intavis Peptide Services, we are experts in generating complex and chemically modified peptides for your R&D. Please contact us for further information and requests: [email protected]