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Orthogonal ring-closing alkyne and olefin metathesis for the synthesis of small GTPase-targeting bicyclic peptides.

Cromm PM, Schaubach S, Spiegel J, Fürstner A, Grossmann TN, Waldmann H - Nat Commun (2016)

Bottom Line: The orthogonal RCM/RCAM system was successfully used to evolve a monocyclic peptide inhibitor of the small GTPase Rab8 into a bicyclic ligand.This modified peptide shows the highest affinity for an activated Rab GTPase that has been reported so far.The RCM/RCAM-based formation of bicyclic peptides provides novel opportunities for the design of bioactive scaffolds suitable for the modulation of challenging protein targets.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany.

ABSTRACT
Bicyclic peptides are promising scaffolds for the development of inhibitors of biological targets that proved intractable by typical small molecules. So far, access to bioactive bicyclic peptide architectures is limited due to a lack of appropriate orthogonal ring-closing reactions. Here, we report chemically orthogonal ring-closing olefin (RCM) and alkyne metathesis (RCAM), which enable an efficient chemo- and regioselective synthesis of complex bicyclic peptide scaffolds with variable macrocycle geometries. We also demonstrate that the formed alkyne macrocycle can be functionalized subsequently. The orthogonal RCM/RCAM system was successfully used to evolve a monocyclic peptide inhibitor of the small GTPase Rab8 into a bicyclic ligand. This modified peptide shows the highest affinity for an activated Rab GTPase that has been reported so far. The RCM/RCAM-based formation of bicyclic peptides provides novel opportunities for the design of bioactive scaffolds suitable for the modulation of challenging protein targets.

No MeSH data available.


Alkyne macrocyclization.(a) The linear peptide is assembled via SPPS including the incorporation of two α-methylated-α-alkynylated building blocks (1–4). The C-terminal building block is always (S)-configured, the configuration of the N-terminal building block varies between the different architectures. Complex 5 is used to perform the RCAM reaction. (i=2, 3, 6, number of amino acids between non-natural building blocks; j=3, 6; m=1, 2, 4; n=1, 2; R=side chain of a proteinogenic amino acid) (b) Fluorenylmethoxycarbonyl (Fmoc) protected non-natural amino acids incorporated into the peptide sequence (alkyne: 1–4, olefin: 6). The alkyne building blocks 1–4 are either used in the (S)- or (R)-configuration depending on the macrocycle architecture. Mo-complex (5) used for RCAM.
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f1: Alkyne macrocyclization.(a) The linear peptide is assembled via SPPS including the incorporation of two α-methylated-α-alkynylated building blocks (1–4). The C-terminal building block is always (S)-configured, the configuration of the N-terminal building block varies between the different architectures. Complex 5 is used to perform the RCAM reaction. (i=2, 3, 6, number of amino acids between non-natural building blocks; j=3, 6; m=1, 2, 4; n=1, 2; R=side chain of a proteinogenic amino acid) (b) Fluorenylmethoxycarbonyl (Fmoc) protected non-natural amino acids incorporated into the peptide sequence (alkyne: 1–4, olefin: 6). The alkyne building blocks 1–4 are either used in the (S)- or (R)-configuration depending on the macrocycle architecture. Mo-complex (5) used for RCAM.

Mentions: To explore RCAM-based macrocyclization of peptides on solid support (Fig. 1a), two α-methyl-α-alkynyl building blocks (1–4) of varying linker length and configuration (Fig. 1b) were introduced into model peptides using Fmoc-based SPPS. Peptide sequences, architectures and relative spacing of non-natural amino acids (i,i+3, i,i+4 and i,i+7) were selected by analogy to previously explored RCM-based peptide macrocyclizations33. As proof-of-concept and to test the robustness of the reaction, we designed model peptides that contain all functionalities present among the 20 proteinogenic amino acids and yield macrocyclic peptides 7–9 after RCAM (Fig. 2a). Investigation of various RCAM conditions including the latest generation of stable Mo-complexes4546 (Supplementary Table 1) revealed efficient conversions after 3 h at 40 °C in toluene if Tentagel rink amide resin and complex 5 (Fig. 1a) were used (Supplementary Figs 2–5, Supplementary Table 2). Under these conditions, macrocycles were formed for all three architectures (7–9) with the best results obtained for an i,i+4 geometry and a final crosslink of nine carbon atoms (8). Shortening the hydrocarbon bridge from nine to eight carbon atoms reduces the efficiency of the reaction presumably due to increased ring strain (Supplementary Fig. 4).


Orthogonal ring-closing alkyne and olefin metathesis for the synthesis of small GTPase-targeting bicyclic peptides.

Cromm PM, Schaubach S, Spiegel J, Fürstner A, Grossmann TN, Waldmann H - Nat Commun (2016)

Alkyne macrocyclization.(a) The linear peptide is assembled via SPPS including the incorporation of two α-methylated-α-alkynylated building blocks (1–4). The C-terminal building block is always (S)-configured, the configuration of the N-terminal building block varies between the different architectures. Complex 5 is used to perform the RCAM reaction. (i=2, 3, 6, number of amino acids between non-natural building blocks; j=3, 6; m=1, 2, 4; n=1, 2; R=side chain of a proteinogenic amino acid) (b) Fluorenylmethoxycarbonyl (Fmoc) protected non-natural amino acids incorporated into the peptide sequence (alkyne: 1–4, olefin: 6). The alkyne building blocks 1–4 are either used in the (S)- or (R)-configuration depending on the macrocycle architecture. Mo-complex (5) used for RCAM.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4834642&req=5

f1: Alkyne macrocyclization.(a) The linear peptide is assembled via SPPS including the incorporation of two α-methylated-α-alkynylated building blocks (1–4). The C-terminal building block is always (S)-configured, the configuration of the N-terminal building block varies between the different architectures. Complex 5 is used to perform the RCAM reaction. (i=2, 3, 6, number of amino acids between non-natural building blocks; j=3, 6; m=1, 2, 4; n=1, 2; R=side chain of a proteinogenic amino acid) (b) Fluorenylmethoxycarbonyl (Fmoc) protected non-natural amino acids incorporated into the peptide sequence (alkyne: 1–4, olefin: 6). The alkyne building blocks 1–4 are either used in the (S)- or (R)-configuration depending on the macrocycle architecture. Mo-complex (5) used for RCAM.
Mentions: To explore RCAM-based macrocyclization of peptides on solid support (Fig. 1a), two α-methyl-α-alkynyl building blocks (1–4) of varying linker length and configuration (Fig. 1b) were introduced into model peptides using Fmoc-based SPPS. Peptide sequences, architectures and relative spacing of non-natural amino acids (i,i+3, i,i+4 and i,i+7) were selected by analogy to previously explored RCM-based peptide macrocyclizations33. As proof-of-concept and to test the robustness of the reaction, we designed model peptides that contain all functionalities present among the 20 proteinogenic amino acids and yield macrocyclic peptides 7–9 after RCAM (Fig. 2a). Investigation of various RCAM conditions including the latest generation of stable Mo-complexes4546 (Supplementary Table 1) revealed efficient conversions after 3 h at 40 °C in toluene if Tentagel rink amide resin and complex 5 (Fig. 1a) were used (Supplementary Figs 2–5, Supplementary Table 2). Under these conditions, macrocycles were formed for all three architectures (7–9) with the best results obtained for an i,i+4 geometry and a final crosslink of nine carbon atoms (8). Shortening the hydrocarbon bridge from nine to eight carbon atoms reduces the efficiency of the reaction presumably due to increased ring strain (Supplementary Fig. 4).

Bottom Line: The orthogonal RCM/RCAM system was successfully used to evolve a monocyclic peptide inhibitor of the small GTPase Rab8 into a bicyclic ligand.This modified peptide shows the highest affinity for an activated Rab GTPase that has been reported so far.The RCM/RCAM-based formation of bicyclic peptides provides novel opportunities for the design of bioactive scaffolds suitable for the modulation of challenging protein targets.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany.

ABSTRACT
Bicyclic peptides are promising scaffolds for the development of inhibitors of biological targets that proved intractable by typical small molecules. So far, access to bioactive bicyclic peptide architectures is limited due to a lack of appropriate orthogonal ring-closing reactions. Here, we report chemically orthogonal ring-closing olefin (RCM) and alkyne metathesis (RCAM), which enable an efficient chemo- and regioselective synthesis of complex bicyclic peptide scaffolds with variable macrocycle geometries. We also demonstrate that the formed alkyne macrocycle can be functionalized subsequently. The orthogonal RCM/RCAM system was successfully used to evolve a monocyclic peptide inhibitor of the small GTPase Rab8 into a bicyclic ligand. This modified peptide shows the highest affinity for an activated Rab GTPase that has been reported so far. The RCM/RCAM-based formation of bicyclic peptides provides novel opportunities for the design of bioactive scaffolds suitable for the modulation of challenging protein targets.

No MeSH data available.