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Veronese E, Metrangolo P, Dichiarante V. Engineering Amino Acid and Peptide Supramolecular Architectures through Fluorination. Chemistry 2024; 30:e202400617. [PMID: 38634399 DOI: 10.1002/chem.202400617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/26/2024] [Accepted: 04/17/2024] [Indexed: 04/19/2024]
Abstract
Fluorinated non-natural amino acids are attracting considerable research interest, especially in the biomedical field and in materials science, thanks to their ability to self-assemble into peculiar supramolecular structures. The conformational changes induced by the presence of fluorine atoms obviously affect their functions, as well as the biological activity of the deriving peptides and proteins. Here, we will briefly describe the main effects of fluorination on the aggregation behavior of such building blocks, focusing in particular on their improved tendency to form fibrils, and gels therefrom. Our aim is to underline the promising potential of fluorination as a tool to affect the self-assembly features of amino acids, both when used alone and when inserted into polypeptide sequences. The ability of fluorine to influence physical, chemical, and structural properties of these substrates offers the possibility to engineer bioinspired materials with specific and tunable functions.
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Affiliation(s)
- Eleonora Veronese
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, via L. Mancinelli 7, 20131, Milan, Italy
| | - Pierangelo Metrangolo
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, via L. Mancinelli 7, 20131, Milan, Italy
| | - Valentina Dichiarante
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, via L. Mancinelli 7, 20131, Milan, Italy
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2
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Goettig P, Koch NG, Budisa N. Non-Canonical Amino Acids in Analyses of Protease Structure and Function. Int J Mol Sci 2023; 24:14035. [PMID: 37762340 PMCID: PMC10531186 DOI: 10.3390/ijms241814035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/18/2023] [Accepted: 08/20/2023] [Indexed: 09/29/2023] Open
Abstract
All known organisms encode 20 canonical amino acids by base triplets in the genetic code. The cellular translational machinery produces proteins consisting mainly of these amino acids. Several hundred natural amino acids serve important functions in metabolism, as scaffold molecules, and in signal transduction. New side chains are generated mainly by post-translational modifications, while others have altered backbones, such as the β- or γ-amino acids, or they undergo stereochemical inversion, e.g., in the case of D-amino acids. In addition, the number of non-canonical amino acids has further increased by chemical syntheses. Since many of these non-canonical amino acids confer resistance to proteolytic degradation, they are potential protease inhibitors and tools for specificity profiling studies in substrate optimization and enzyme inhibition. Other applications include in vitro and in vivo studies of enzyme kinetics, molecular interactions and bioimaging, to name a few. Amino acids with bio-orthogonal labels are particularly attractive, enabling various cross-link and click reactions for structure-functional studies. Here, we cover the latest developments in protease research with non-canonical amino acids, which opens up a great potential, e.g., for novel prodrugs activated by proteases or for other pharmaceutical compounds, some of which have already reached the clinical trial stage.
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Affiliation(s)
- Peter Goettig
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, Strubergasse 21, 5020 Salzburg, Austria
| | - Nikolaj G. Koch
- Biocatalysis Group, Technische Universität Berlin, 10623 Berlin, Germany;
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany;
| | - Nediljko Budisa
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany;
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Miles SA, Nillama JA, Hunter L. Tinker, Tailor, Soldier, Spy: The Diverse Roles That Fluorine Can Play within Amino Acid Side Chains. Molecules 2023; 28:6192. [PMID: 37687021 PMCID: PMC10489206 DOI: 10.3390/molecules28176192] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023] Open
Abstract
Side chain-fluorinated amino acids are useful tools in medicinal chemistry and protein science. In this review, we outline some general strategies for incorporating fluorine atom(s) into amino acid side chains and for elaborating such building blocks into more complex fluorinated peptides and proteins. We then describe the diverse benefits that fluorine can offer when located within amino acid side chains, including enabling 19F NMR and 18F PET imaging applications, enhancing pharmacokinetic properties, controlling molecular conformation, and optimizing target-binding.
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Affiliation(s)
| | | | - Luke Hunter
- School of Chemistry, The University of New South Wales (UNSW), Sydney 2052, Australia
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Chowdhary S, Pelzer T, Saathoff M, Quaas E, Pendl J, Fulde M, Koksch B. Fine‐tuning the antimicrobial activity of β‐hairpin peptides with fluorinated amino acids. Pept Sci (Hoboken) 2023. [DOI: 10.1002/pep2.24306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Affiliation(s)
- Suvrat Chowdhary
- Institute of Chemistry and Biochemistry Freie Universität Berlin Berlin Germany
| | - Tim Pelzer
- Institute of Chemistry and Biochemistry Freie Universität Berlin Berlin Germany
| | - Mareike Saathoff
- Institute of Microbiology and Epizootics, Centre of Infection Medicine Freie Universität Berlin Berlin Germany
| | - Elisa Quaas
- Institute of Chemistry and Biochemistry, Core Facility SupraFAB Freie Universität Berlin Berlin Germany
| | - Johanna Pendl
- Institute of Veterinary Anatomy Freie Universität Berlin Berlin Germany
| | - Marcus Fulde
- Institute of Microbiology and Epizootics, Centre of Infection Medicine Freie Universität Berlin Berlin Germany
- Veterinary Centre for Resistance Research (TZR) Freie Universität Berlin Berlin Germany
| | - Beate Koksch
- Institute of Chemistry and Biochemistry Freie Universität Berlin Berlin Germany
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Hohmann T, Chowdhary S, Ataka K, Er J, Dreyhsig GH, Heberle J, Koksch B. Introducing Aliphatic Fluoropeptides: Perspectives on Folding Properties, Membrane Partition and Proteolytic Stability. Chemistry 2023; 29:e202203860. [PMID: 36722398 DOI: 10.1002/chem.202203860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/02/2023]
Abstract
A de novo designed class of peptide-based fluoropolymers composed of fluorinated aliphatic amino acids as main components is reported. Structural characterization provided insights into fluorine-induced alterations on β-strand to α-helix transition upon an increase in SDS content and revealed the unique formation of PPII structures for trifluorinated fluoropeptides. A combination of circular dichroism, fluorescence-based leaking assays and surface enhanced infrared absorption spectroscopy served to examine the insertion and folding processes into unilamellar vesicles. While partitioning into lipid bilayers, the degree of fluorination conducts a decrease in α-helical content. Furthermore, this study comprises a report on the proteolytic stability of peptides exclusively built up by fluorinated amino acids and proved all sequences to be enzymatically degradable despite the degree of fluorination. Herein presented fluoropeptides as well as the distinctive properties of these artificial and polyfluorinated foldamers with enzyme-degradable features will play a crucial role in the future development of fluorinated peptide-based biomaterials.
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Affiliation(s)
- Thomas Hohmann
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195, Berlin, Germany
| | - Suvrat Chowdhary
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195, Berlin, Germany
| | - Kenichi Ataka
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Jasmin Er
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195, Berlin, Germany
| | - Gesa Heather Dreyhsig
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195, Berlin, Germany
| | - Joachim Heberle
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Beate Koksch
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195, Berlin, Germany
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Wehrhan L, Leppkes J, Dimos N, Loll B, Koksch B, Keller BG. Water Network in the Binding Pocket of Fluorinated BPTI-Trypsin Complexes─Insights from Simulation and Experiment. J Phys Chem B 2022; 126:9985-9999. [PMID: 36409613 DOI: 10.1021/acs.jpcb.2c05496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Structural waters in the S1 binding pocket of β-trypsin are critical for the stabilization of the complex of β-trypsin with its inhibitor bovine pancreatic trypsin inhibitor (BPTI). The inhibitor strength of BPTI can be modulated by replacing the critical lysine residue at the P1 position by non-natural amino acids. We study BPTI variants in which the critical Lys15 in BPTI has been replaced by α-aminobutyric acid (Abu) and its fluorinated derivatives monofluoroethylglycine (MfeGly), difluoroethylglycine (DfeGly), and trifluoroethylglycine (TfeGly). We investigate the hypothesis that additional water molecules in the binding pocket can form specific noncovalent interactions with the fluorinated side chains and thereby act as an extension of the inhibitors. We report potentials of mean force (PMF) of the unbinding process for all four complexes and enzyme activity inhibition assays. Additionally, we report the protein crystal structure of the Lys15MfeGly-BPTI-β-trypsin complex (pdb: 7PH1). Both experimental and computational data show a stepwise increase in inhibitor strength with increasing fluorination of the Abu side chain. The PMF additionally shows a minimum for the encounter complex and an intermediate state just before the bound state. In the bound state, the computational analysis of the structure and dynamics of the water molecules in the S1 pocket shows a highly dynamic network of water molecules that does not indicate a rigidification or stabilizing trend in regard to energetic properties that could explain the increase in inhibitor strength. The analysis of the energy and the entropy of the water molecules in the S1 binding pocket using grid inhomogeneous solvation theory confirms this result. Overall, fluorination systematically changes the binding affinity, but the effect cannot be explained by a persistent water network in the binding pocket. Other effects, such as the hydrophobicity of fluorinated amino acids and the stability of the encounter complex as well as the additional minimum in the potential of mean force in the bound state, likely influence the affinity more directly.
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Affiliation(s)
- Leon Wehrhan
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry, Arnimallee 22, Berlin14195, Germany
| | - Jakob Leppkes
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry, Arnimallee 20, Berlin14195, Germany
| | - Nicole Dimos
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 6, Berlin14195, Germany
| | - Bernhard Loll
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 6, Berlin14195, Germany
| | - Beate Koksch
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry, Arnimallee 20, Berlin14195, Germany
| | - Bettina G Keller
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry, Arnimallee 22, Berlin14195, Germany
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Chowdhary S, Schmidt RF, Sahoo AK, Tom Dieck T, Hohmann T, Schade B, Brademann-Jock K, Thünemann AF, Netz RR, Gradzielski M, Koksch B. Rational design of amphiphilic fluorinated peptides: evaluation of self-assembly properties and hydrogel formation. NANOSCALE 2022; 14:10176-10189. [PMID: 35796261 DOI: 10.1039/d2nr01648f] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Advanced peptide-based nanomaterials composed of self-assembling peptides (SAPs) are of emerging interest in pharmaceutical and biomedical applications. The introduction of fluorine into peptides, in fact, offers unique opportunities to tune their biophysical properties and intermolecular interactions. In particular, the degree of fluorination plays a crucial role in peptide engineering as it can be used to control the characteristics of fluorine-specific interactions and, thus, peptide conformation and self-assembly. Here, we designed and explored a series of amphipathic peptides by incorporating the fluorinated amino acids (2S)-4-monofluoroethylglycine (MfeGly), (2S)-4,4-difluoroethylglycine (DfeGly) and (2S)-4,4,4-trifluoroethylglycine (TfeGly) as hydrophobic components. This approach enabled studying the impact of fluorination on secondary structure formation and peptide self-assembly on a systematic basis. We show that the interplay between polarity and hydrophobicity, both induced differentially by varying degrees of side chain fluorination, does affect peptide folding significantly. A greater degree of fluorination promotes peptide fibrillation and subsequent formation of physical hydrogels in physiological conditions. Molecular simulations revealed the key role played by electrostatically driven intra-chain and inter-chain contact pairs that are modulated by side chain fluorination and give insights into the different self-organization behaviour of selected peptides. Our study provides a systematic report about the distinct features of fluorinated oligomeric peptides with potential applications as peptide-based biomaterials.
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Affiliation(s)
- Suvrat Chowdhary
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195 Berlin, Germany.
| | - Robert Franz Schmidt
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Anil Kumar Sahoo
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Tiemo Tom Dieck
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195 Berlin, Germany.
| | - Thomas Hohmann
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195 Berlin, Germany.
| | - Boris Schade
- Institute of Chemistry and Biochemistry and Core Facility BioSupraMol, Freie Universität Berlin, Fabeckstraße 36a, 14195 Berlin, Germany
| | - Kerstin Brademann-Jock
- Federal Institute for Materials Research and Testing (BAM), Unter den Eichen 87, 12205 Berlin, Germany
| | - Andreas F Thünemann
- Federal Institute for Materials Research and Testing (BAM), Unter den Eichen 87, 12205 Berlin, Germany
| | - Roland R Netz
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Michael Gradzielski
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Beate Koksch
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195 Berlin, Germany.
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