Total synthesis of the peptaibols hypomurocin A3 and hypomurocin A5, and their conformation analysis

Peptaibiotics: Harnessing the potential of microbial secondary metabolites for mitigation of plant pathogens

Agricultural systems are in need of low-cost, safe antibiotics to protect crops from pests and diseases. Peptaibiotics, a family of linear, membrane-active, amphipathic polypeptides, have been shown to exhibit antibacterial, antifungal, and antiviral activity, and to be inducers of plant resistance against a wide range of phytopathogens. Peptaibiotics belong to the new generation of alternatives to agrochemicals, aligned with the United Nations Sustainable Development Goals and the One Health approach toward ensuring global food security and safety. Despite that, these fungi-derived, non-ribosomal peptides remain surprisingly understudied, especially in agriculture, where only a small number has been tested against a reduced number of phytopathogens. This lack of adoption stems from peptaibiotics' poor water solubility and the difficulty to synthesize and purify them in vitro, which compromises their delivery and inclusion in formulations. In this review, we offer a comprehensive analysis of peptaibiotics' classification, biosynthesis, relevance to plant protection, and mode of action against phytopathogens, along with the techniques enabling researchers to extract, purify, and elucidate their structure, and the databases holding such valuable data. It is also discussed how chemical synthesis and ionic liquids could increase their solubility, how genetic engineering and epigenetics could boost in vitro production, and how omics can reduce screenings' workload through in silico selection of the best candidates. These strategies could turn peptaibiotics into effective, ultra-specific, biodegradable tools for phytopathogen control.

Synthesis and Solid State Conformation of Tetrapeptide Amides Containing two Aib and two (αMe)Phe Residues - Use of Enantiomerically Pure 2-Benzyl-2-methyl-2H-azirin-3-amines as (αMe)Phe-Synthons

A series of tetrapeptide amides containing two aminoisobutyric acids (Aib) and two α-methylphenylalanine ((αMe)Phe) units were prepared through the 'azirine/oxazolone method'. New 2-benzyl-2-methyl-2H-azirin-3-amines have been used for the selective introduction of (S)- and (R)-(αMe)Phe, respectively. The solid-state conformations of five tetrapeptide amides were determined by X-ray crystallography. In all cases, two β-turns stabilize 3₁₀ -helical conformations and it was confirmed that, in contrast to proteinogenic amino acids, the configuration of (αMe)Phe does not determine the screw sense of the helix.

Diversity of Linear Non-Ribosomal Peptide in Biocontrol Fungi

Biocontrol fungi (BFs) play a key role in regulation of pest populations. BFs produce multiple non-ribosomal peptides (NRPs) and other secondary metabolites that interact with pests, plants and microorganisms. NRPs-including linear and cyclic peptides (L-NRPs and C-NRPs)-are small peptides frequently containing special amino acids and other organic acids. They are biosynthesized in fungi through non-ribosomal peptide synthases (NRPSs). Compared with C-NRPs, L-NRPs have simpler structures, with only a linear chain and biosynthesis without cyclization. BFs mainly include entomopathogenic and mycoparasitic fungi, that are used to control insect pests and phytopathogens in fields, respectively. NRPs play an important role of in the interactions of BFs with insects or phytopathogens. On the other hand, the residues of NRPs may contaminate food through BFs activities in the environment. In recent decades, C-NRPs in BFs have been thoroughly reviewed. However, L-NRPs are rarely investigated. In order to better understand the species and potential problems of L-NRPs in BFs, this review lists the L-NRPs from entomopathogenic and mycoparasitic fungi, summarizes their sources, structures, activities and biosynthesis, and details risks and utilization prospects.

Solid-state conformations of linear depsipeptide amides with an alternating sequence of α,α-disubstituted α-amino acid and α-hydroxy acid

Depsipeptides and cyclodepsipeptides are analogues of the corresponding peptides in which one or more amide groups are replaced by ester functions. Reports of crystal structures of linear depsipeptides are rare. The crystal structures and conformational analyses of four depsipeptides with an alternating sequence of an α,α-disubstituted α-amino acid and an α-hydroxy acid are reported. The molecules in the linear hexadepsipeptide amide in (S)-Pms-Acp-(S)-Pms-Acp-(S)-Pms-Acp-NMe₂ acetonitrile solvate, C₄₇H₅₈N₄O₉·C₂H₃N, (3b), as well as in the related linear tetradepsipeptide amide (S)-Pms-Aib-(S)-Pms-Aib-NMe₂, C₂₈H₃₇N₃O₆, (5a), the diastereoisomeric mixture (S,R)-Pms-Acp-(R,S)-Pms-Acp-NMe₂/(R,S)-Pms-Acp-(R,S)-Pms-Acp-NMe₂ (1:1), C₃₂H₄₁N₃O₆, (5b), and (R,S)-Mns-Acp-(S,R)-Mns-Acp-NMe₂, C₃₀H₃₇N₃O₆, (5c) (Pms is phenyllactic acid, Acp is 1-aminocyclopentanecarboxylic acid and Mns is mandelic acid), generally adopt a β-turn conformation in the solid state, which is stabilized by intramolecular N-H...O hydrogen bonds. Whereas β-turns of type I (or I') are formed in the cases of (3b), (5a) and (5b), which contain phenyllactic acid, the torsion angles for (5c), which incorporates mandelic acid, indicate a β-turn in between type I and type III. Intermolecular N-H...O and O-H...O hydrogen bonds link the molecules of (3a) and (5b) into extended chains, and those of (5a) and (5c) into two-dimensional networks.

Characterizing the structural and folding properties of long-sequence hypomurocin B peptides and their analogs

We studied the folding processes of long-sequence hypomurocin (HM) peptides and their analogs by means of molecular dynamics methods, focusing on the formation of various helical structures and intramolecular H-bonds. The evolution of different helical conformations, such as the 310 -, α-, and left-handed α-helices, was examined, taking into account the entire sequence and each amino acid of peptides. The results indicated that the HM peptides and their analogs possessed a propensity to adopt helical conformations, and they showed a preference for the 310 -helical structure over the α-helical one. The evolution of a variety of the intramolecular H-bonds, including local and non-local interactions, was also investigated. The results pointed out that on the one hand, the appearance of local, helix-stabilizing H-bonds correlated with the presence of helical conformations, and on the other hand, the non-local H-bonds did not affect significantly the formation of helical structures. Additionally, comparing the structural and folding features of HM peptides and their analogs, our study led to the observation that the L-D isomerism of isovaline amino acid induced effects on the folding processes of these long-sequence peptaibol molecules. Accordingly, the HM peptides and their analogs could be characterized by typical structural and folding properties. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 645-657, 2016.

In silico conformational analysis of the short-sequence hypomurocin a peptides

In this theoretical study, a conformational analysis was performed on short-sequence hypomurocin A peptides, in order to identify their characteristic structural properties. For each hypomurocin A molecule, not only the backbone conformations, but also the side-chain conformations were examined. The results indicated that certain tetrapeptide units could be characterized by types I and III β-turn structures, and considering the helical conformations, it could be concluded that the hypomurocin A peptides showed a preference for the 3₁₀-helical structure over the α-helical structure. Beside the backbone conformations, the side-chain conformations were investigated, and the preferred rotamer states of the side-chains of amino acids were determined. Furthermore, the occurrence of i ← i + 3 and i ← i + 4 intramolecular H-bonds was studied, which could play a role in the structural stabilization of β-turns and helical conformations. On the whole, our theoretical study supplied a comprehensive characterization of the three-dimensional structure of short-sequence hypomurocin A peptides.

(S)-N-[(4-{(S)-1-[2-(4-Meth-oxy-benz-amido)-2-methyl-propano-yl]pyrrolidine-2-carboxamido}-3,4,5,6-tetra-hydro-2H-pyran-4-yl)carbon-yl]proline dimethyl sulfoxide monosolvate (4-MeBz-Aib-Pro-Thp-Pro-OH)

The asymmetric unit of the title compound, C28H38N4O8·C2H6OS, contains one tetra-peptide and one disordered dimethyl sulfoxide (DMSO) mol-ecule. The central five-membered ring (Pro(2)) of the peptide mol-ecule has a disordered envelope conformation [occupancy ratio 0.879 (2):0.121 (2)] with the envelope flap atom, the central C atom of the three ring methylene groups, lying on alternate sides of the mean ring plane. The terminal five-membered ring (Pro(4)) also adopts an envelope conformation with the C atom of the methylene group closest to the carboxylic acid function as the envelope flap, and the six-membered tetra-hydro-pyrane ring shows a chair conformation. The tetra-peptide exists in a helical conformation, stabilized by an intra-molecular hydrogen bond between the amide N-H group of the heterocyclic α-amino acid Thp and the amide O atom of the 4-meth-oxy-benzoyl group. This inter-action has a graph set motif of S(10) and serves to maintain a fairly rigid β-turn structure. In the crystal, the terminal hy-droxy group forms a hydrogen bond with the amide O atom of Thp of a neighbouring mol-ecule, and the amide N-H group at the opposite end of the mol-ecule forms a hydrogen bond with the amide O atom of Thp of another neighbouring mol-ecule. The combination of both inter-molecular inter-actions links the mol-ecules into an extended three-dimensional framework.