PotM: About the Impact of Fluorinated Building Blocks

PotM: About the Impact of Fluorinated Building Blocks

Published on 14.05.2024

Clever Move - Add positive effects to your molecule by introducing the most electronegative element. Discover fluorinated building blocks as game changer for your lead development. 

While elemental fluorine is a rather reactive fellow and its handling requires special precautions due to its dangerous nature and toxicity, fluorinated amino acids in contrast are very tame and offer exciting opportunities to control and improve the properties of synthetic molecules.

Fluorine is the element with highest electronegativity and, compared with the C-H bond, C-F has a very high and reversed polarity and is less polarizable. Fluorine is frequently considered bioisosteric to hydrogen, as both have similar van-der-Waals radii (135 nm vs. 120 nm). C-F bonds are significantly longer than C-H bonds (~140 nm vs. ~100 nm), and -CF3 groups have about the same spatial requirements as ethyl (-CH2-CH3) or even isopropyl (-CH2-(CH3)2) residues. Consequently, in small molecules and peptides, hydrogen often may be substituted for fluorine without abolishing binding to proteins and enzymes. Thus, one can exploit the potential of fluorine containing substituents to improve or fine-tune the desired properties of a pharmaceutic molecule or peptide, or to characterize and understand a biological system.

Once incorporated into a building block, fluorine won’t react any further (in fact, fluorinated residues are quite inert). Currently, more than 20% of medications contain at least one fluorine atom. As versatile bioisostere, fluorine has been used to substitute several functional groups, e.g., carbonyl, amine, nitrile, nitro, thiol, hydroxy or hydrogen.

Functional groups which might be replaced by fluorine.


Adding trifluoromethyl (-CF3) and thiotrifluoromethyl (-SCF3) moiety (or replacing methyl groups with them) can dramatically increase the lipophilicity of a molecule or synthetic peptide and increase its stability against thermal or chemical denaturation and against proteolytic degradation. This is especially the case for the highly fluorinated analogs of hydrophobic amino acids (Leu, Ile, Val, Phe). Multiple -CF3 groups on one molecule can convey properties which are similar to those of a longer perfluoroalkyl chain and can modulate stability and self-organization of folding motifs.

The fluorination of peptides is achieved either by chemical synthesis from suitably protected building blocks or in vitro with the help of auxotrophic bacterial strains which are supplied with engineered tRNA-synthetases to translate a dedicated codon into the non-canonical amino acid.

On top of that, the fluorine isotope 19F is a very useful probe for NMR spectroscopy, due to its nuclear spin of ½ and a high gyromagnetic ratio. As 19F comprises nearly 100% of the naturally occurring element, fluorinated amino acids are an excellent sensitive and non-perturbing tool for studying the local protein environment and protein dynamics as well.

At Iris Biotech, we offer an extensive selection of α-trifluoromethyl-, trifluoromethyl-, trifluoromethylthio-, and γ,γ-difluoro amino acids.

→ For more information, download our flyer about fluorinated building blocks! 

→ You are interested in -SCF3? Read our recent blog

Register for our online workshop “All FluorINE – About SCF3 and other fluorinated amino acids” featuring Prof. Thierry Brigaud!


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Small, but powerful and attractive: 19F in biomolecular NMR; A. M. Gronenborn; Structure 2022; 30(1): 6–14. https://doi.org/10.1016%2Fj.str.2021.09.009

Deciphering the Fluorine Code - The Many Hats Fluorine Wears in a Protein Environment; A. Berger, J.-S. Völler, N. Budisa, B. Koksch; Accounts Chem Res. 2017; 50: 2093-2103. https://doi.org/10.1021/acs.accounts.7b00226

Fluorinated peptide biomaterials; J. N. Sloand, M. A. Miller, S. H. Medina; Pept Sci (Hoboken) 2021; 113(2): e24184. https://doi.org/10.1002/pep2.24184

Fluorinated Protein and Peptide Materials for Biomedical Applications; J. M. Monkovic, H. Gibson, J. W. Sun, J. K. Montclare; Pharmaceuticals 2022; 15: 1201-1237. https://doi.org/10.3390/ph15101201

Perfluorocarbons in Chemical Biology; M. A. Miller, E. M. Sletten; Chembiochem 2020; 21(24): 3451-3462. https://doi.org/10.1002%2Fcbic.202000297

Trifluoromethylthiolation of Tryptophan and Tyrosine Derivatives: A Tool for Enhancing the Local Hydrophobicity of Peptides; J. Gregorc, N. Lensen, G. Chaume, J. Iskra, T. Brigaud; J Org Chem 2023; 88: 13169-13177. https://doi.org/10.1021/acs.joc.3c01373

Probing the Outstanding Local Hydrophobicity Increases in Peptide Sequences Induced by Incorporation of Trifluoromethylated Amino Acids; C. Gadais, E. Devillers, V. Gasparik, E. Chelain, J. Pytkowicz, T. Brigaud; Chembiochem 2018; 19: 1026-1030. https://doi.org/10.1002/cbic.201800088