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Matabaro E, Witte L, Gherlone F, Vogt E, Kaspar H, Künzler M. Promiscuity of Omphalotin A Biosynthetic Enzymes Allows de novo Production of Non-Natural Multiply Backbone N-Methylated Peptide Macrocycles in Yeast. Chembiochem 2024; 25:e202300626. [PMID: 38059521 DOI: 10.1002/cbic.202300626] [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: 09/12/2023] [Revised: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 12/08/2023]
Abstract
Multiple backbone N-methylation and macrocyclization improve the proteolytic stability and oral availability of therapeutic peptides. Chemical synthesis of such peptides is challenging, in particular for the generation of peptide libraries for screening purposes. Enzymatic backbone N-methylation and macrocyclization occur as part of both non-ribosomal and ribosomal peptide biosynthesis, exemplified by the fungal natural products cyclosporin A and omphalotin A, respectively. Omphalotin A, a 9fold backbone N-methylated dodecamer isolated from the agaricomycete Omphalotus olearius, can be produced in Pichia pastoris by coexpression of the ophMA and ophP genes coding for the peptide precursor protein harbouring an autocatalytic peptide α-N-methyltransferase domain, and a peptide macrocyclase, respectively. Since both OphMA and OphP were previously shown to be relatively promiscuous in terms of peptide substrates, we expressed mutant versions of ophMA, encoding OphMA variants with altered core peptide sequences, along with wildtype ophP and assessed the production of the respective peptide macrocycles by the platform by high-performance liquid chromatography, coupled with tandem mass spectrometry (HPLC-MS/MS). Our results demonstrate the successful production of fifteen non-natural omphalotin-derived macrocycles, containing polar, aromatic and charged residues, and, thus, suggest that the system may be used as biotechnological platform to generate libraries of non-natural multiply backbone N-methylated peptide macrocycles.
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Affiliation(s)
- Emmanuel Matabaro
- Institute of Microbiology, Department of Biology, ETH Zürich, Vladimir-Prelog Weg 4, HCI F423, 8093, Zürich, Switzerland
| | - Luca Witte
- Institute of Microbiology, Department of Biology, ETH Zürich, Vladimir-Prelog Weg 4, HCI F423, 8093, Zürich, Switzerland
| | - Fabio Gherlone
- Institute of Microbiology, Department of Biology, ETH Zürich, Vladimir-Prelog Weg 4, HCI F423, 8093, Zürich, Switzerland
| | - Eva Vogt
- Institute of Microbiology, Department of Biology, ETH Zürich, Vladimir-Prelog Weg 4, HCI F423, 8093, Zürich, Switzerland
| | - Hannelore Kaspar
- Institute of Microbiology, Department of Biology, ETH Zürich, Vladimir-Prelog Weg 4, HCI F423, 8093, Zürich, Switzerland
| | - Markus Künzler
- Institute of Microbiology, Department of Biology, ETH Zürich, Vladimir-Prelog Weg 4, HCI F423, 8093, Zürich, Switzerland
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Rüdisser SH, Matabaro E, Sonderegger L, Güntert P, Künzler M, Gossert AD. Conformations of Macrocyclic Peptides Sampled by Nuclear Magnetic Resonance: Models for Cell-Permeability. J Am Chem Soc 2023; 145:27601-27615. [PMID: 38062770 PMCID: PMC10739998 DOI: 10.1021/jacs.3c09367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/21/2023]
Abstract
The biological activities and pharmacological properties of peptides and peptide mimetics are determined by their conformational states. Therefore, a detailed understanding of the conformational landscape is crucial for rational drug design. Nuclear magnetic resonance (NMR) is the only method for structure determination in solution. However, it remains challenging to determine the structures of peptides using NMR because of very weak nuclear Overhauser effects (NOEs), the semiquantitative nature of the rotating frame Overhauser effect (ROE), and the low number of NOEs/ROEs in N-methylated peptides. In this study, we introduce a new approach to investigating the structures of modified macrocyclic peptides. We utilize exact NOEs (eNOEs) in viscous solvent mixtures to replicate various cellular environments. eNOEs provide detailed structural information for highly dynamic modified peptides. Structures of high precision were obtained for cyclosporin A, with a backbone atom rmsd of 0.10 Å. Distinct conformational states in different environments were identified for omphalotin A (OmphA), a fungal nematotoxic and multiple backbone N-methylated macrocyclic peptides. A model for cell-permeation is presented for OmphA, based on its structures in polar, apolar, and mixed polarity solvents. During the transition from a polar to an apolar environment, OmphA undergoes a rearrangement of its H-bonding network, accompanied by a cis to trans isomerization of the ω torsion angle within a type VIa β-turn. We hypothesize that the kinetics of these conformational transitions play a crucial role in determining the membrane-permeation capabilities of OmphA.
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Affiliation(s)
| | | | | | - Peter Güntert
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Zürich 8093, Switzerland
- Institute
of Biophysical Chemistry, Goethe University, Frankfurt am Main 60438, Germany
- Department
of Chemistry, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Markus Künzler
- Department
of Biology, ETH Zürich, Zürich 8093, Switzerland
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