Mucosal-associated invariant T cells (MAIT cells) are innate-like immune cells (T lymphocytes) that protect against bacterial infections. They are potently activated by the microbial metabolite 5-(2-oxopropylideneamino)-d-ribitylaminouracil (5-OP-RU), which bonds covalently to an amine of a specific lysine residue of the antigen-presenting protein MR1 to form an imine (Schiff base). However, 5-OP-RU undergoes rapid degradative intramolecular cyclisation in water, and more robust analogues are needed for therapeutic applications. Here, inspired by the structural similarities between 5-OP-RU and 6-formylpterin, a water-stable covalent MR1 ligand that does not activate MAIT cells, we describe the design and synthesis of a novel isopterin analogue of this microbial natural product, and show that it is both water-stable and activates reporter cells expressing the MAIT T cell receptor. Further, we present a protein-bound crystal structure and molecular dynamics simulations of this stable analogue to show that it mimics the MR1-bound conformation of 5-OP-RU. This study demonstrates the potential of this bicyclic scaffold for stabilising 5-OP-RU mimetics, advances our understanding of the molecular requirements for MR1 binding and MAIT cell activation, and informs the design and synthesis of future MAIT cell antigens as potential immunotherapeutics.

Gene duplication followed by adaptation to new selection pressures has been proposed to be of central importance in the evolution of venom toxins. Coupling high-quality genome data with quantitative bioactivity readouts can be used to understand how venom toxins evolved, but such studies are rare. Here, we report a near chromosomal-level genome assembly for Doratifera vulnerans (Lepidoptera: Limacodidae), which is venomous in the larval stage. We identify 115 gene loci that produce the polypeptide toxins in venom, including numerous multigene families as well as single-copy genes. Previously described membrane-permeabilizing peptides that cause pain are shown to be encoded by a gene cluster on chromosome 7 that also encodes multiple members of the cecropin family, which are insect innate immunity peptides. These data reveal the origin of defensive toxins from immune peptides followed by strong sequence divergence driven by positive selection pressures. Dv13, which is present as a trace component in the venom, and which has sequence features conserved with canonical cecropin A, potently inhibited the growth of Gram-negative bacteria and fungi, but only weakly permeabilized the membranes of mammalian neurons with EC 50 values >100 µM. In contrast, peptides Dv11 and Dv12 are abundant in the venom, have sequence features divergent from Dv13, and potently disrupt mammalian neuronal membranes with EC 50 values as low as 190 nM, but have reduced antimicrobial activity. These data provide evidence for the adaptation of innate immune peptides as specialized defensive venom toxins and provide a natural experiment informing the structure–activity relationships of cecropin family peptides.

N-methylation of cyclic peptides is a widely used strategy to enhance membrane permeability; however, it can also influence metabolic stability. In celebration of Professor David Craik's scientific achievements - particularly in the field of peptide research - we were fortunate to gain access to a series of his cyclic peptides to investigate their liver microsomal stability. Our study revealed that the liver microsome stability of a series of 14 cyclic hexapeptides is highly variable, despite minimal differences in sequence, molecular weight and cLogP. Notably, all compounds containing cis-amide bonds exhibited very poor rat liver microsomal stability, with half-lives of less than 3 min. This work highlights a potential metabolic liability that should be taken into account when designing cyclic peptides as potential drug candidates.

Bacterial synthesis of vitamin B2 generates a by-product, 5-(2-oxopropylideneamino)- d -ribityl-aminouracil (5-OP-RU), with potent immunological properties in mammals, but it is rapidly degraded in water. This natural product covalently bonds to the key immunological protein MR1 in the endoplasmic reticulum of antigen presenting cells (APCs), enabling MR1 refolding and trafficking to the cell surface, where it interacts with T cell receptors (TCRs) on mucosal associated invariant T lymphocytes (MAIT cells), activating their immunological and antimicrobial properties. Here, we strategically modify this natural product to understand the molecular basis of its recognition by MR1. This culminated in the discovery of new water-stable compounds with extremely powerful and distinctive immunological functions. We report their capacity to bind MR1 inside APCs, triggering its expression on the cell surface (EC 50 17 nM), and their potent activation (EC 50 56 pM) or inhibition (IC 50 80 nM) of interacting MAIT cells. We further derivatize compounds with diazirine-alkyne, biotin, or fluorophore (Cy5 or AF647) labels for detecting, monitoring, and studying cellular MR1. Computer modeling casts new light on the molecular mechanism of activation, revealing that potent activators are first captured in a tyrosine- and serine-lined cleft in MR1 via specific pi-interactions and H-bonds, before more tightly attaching via a covalent bond to Lys43 in MR1. This chemical study advances our molecular understanding of how bacterial metabolites are captured by MR1, influence cell surface expression of MR1, interact with T cells to induce immunity, and offers novel clues for developing new vaccine adjuvants, immunotherapeutics, and anticancer drugs.

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Inhibitors of histone deacetylases (HDACs) have received special attention as novel anticancer agents. Among various types of synthetic inhibitors, benzamides constitute an important class, and one is an approved drug (chidamide). Here, we present a novel class of HDAC inhibitors containing the N-(2-aminophenyl)-benzamide functionality as the zinc-binding group linked to various cap groups, including the amino acids pyroglutamic acid and proline. We have identified benzamides that inhibit HADC1 and HDAC2 at nanomolar concentrations, with antiproliferative activity at micromolar concentrations against A549 and SF268 cancer cell lines. Docking studies shed light on the mode of binding of benzamide inhibitors to HDAC1, whereas cellular analysis revealed downregulated expression of EGFR mRNA and protein. Two benzamides were investigated in a mouse model of bleomycin-induced pulmonary fibrosis, and both showed efficacy on a preventative dosing schedule. N-(2-Aminophenyl)-benzamide inhibitors of class I HDACs might lead to new approaches for treating fibrotic disorders.

Application of a miniaturized 24-well plate system for cultivation profiling (MATRIX) permitted optimization of the cultivation conditions for the marine-derived fungus Talaromyces sp. CMB-TU011, facilitating access to the rare cycloheptapeptide talarolide A (1) along with three new analogues, B–D (2–4). Detailed spectroscopic analysis supported by Marfey’s analysis methodology was refined to resolve N-Me-l-Ala from N-Me-d-Ala, l-allo-Ile from l-Ile and l-Leu, and partial and total syntheses of 2, and permitted unambiguous assignment of structures for 1 (revised) and 2–4. Consideration of diagnostic ROESY correlations for the hydroxamates 1 and 3–4, and a calculated solution structure for 1, revealed how cross-ring H-bonding to the hydroxamate moiety influences (defines/stabilizes) the cyclic peptide conformation. Such knowledge draws attention to the prospect that hydroxamates may be used as molecular bridges to access new cyclic peptide conformations, offering the prospect of new biological properties, including enhanced oral bioavailability.

Abstract Aromatic groups are key mediators of protein–membrane association at cell surfaces, contributing to hydrophobic effects and π‐membrane interactions. Here we show electrostatic and hydrophobic influences of aromatic ring substituents on membrane affinity and cell uptake of helical, cyclic and cell penetrating peptides. Hydrophobicity is important, but subtle changes in electrostatic surface potential, dipoles and polarizability also enhance association with phospholipid membranes and cell uptake. A combination of fluorine and sulfur substituents on an aromatic ring induces microdipoles that enhance cell uptake of 12‐residue peptide inhibitors of p53‐HDM2 interaction and of cell‐penetrating cyclic peptides. These aromatic motifs can be readily inserted into peptide sidechains to enhance their cell uptake.

Cyclic peptides that modulate protein-protein interactions can be valuable therapeutic candidates if they can be delivered intact to their target proteins in cells. Here we systematically compare the effects of different helix-inducing cyclization constraints on the capacity of a macrocyclic peptide component to confer α-helicity, protein-binding affinity, resistance to degradative proteases and cell uptake to a 12-residue peptide fragment of tumor suppressor protein p53. We varied the helix-inducing constraint (hydrocarbon, lactam, aliphatic or aromatic thioether, etc.) and the position of the cyclization linker (i to i + 4 or i to i + 7 bridges) in order to sculpt the macrocyclic size, stabilize its structure, and promote cell uptake. We find that rigidifying the macrocycle leads to higher alpha helicity, target affinity and proteolytic stability to different extents, whereas cell uptake of compounds shown here is mostly driven by hydrophobicity and aromaticity of the macrocycle.

An alpha helical turn can be reproduced in a cyclic pentapeptide if the first and fifth amino acid sidechains are correctly joined. Here structural studies (CD, NMR, in silico) reveal why N-methylation at positions not involved in hydrogen bonds disrupts helicity whereas ester bonds can maintain helicity and promote greater cell uptake.

N- or C-methylation in natural and synthetic cyclic peptides can increase membrane permeability, but it remains unclear why this happens in some cases but not others. Here we compare three-dimensional structures for cyclic peptides from six families, including isomers differing only in the location of an N- or Cα-methyl substituent. We show that a single methyl group only increases membrane permeability when it connects or expands hydrophobic surface patches. Positional isomers, with the same molecular weight, hydrogen bond donors/acceptors, rotatable bonds, calculated LogP, topological polar surface area, and total hydrophobic surface area, can have different membrane permeabilities that correlate with the size of the largest continuous hydrophobic surface patch. These results illuminate a key local molecular determinant of membrane permeability.

Correction for ‘Twists or turns: stabilising alpha vs. beta turns in tetrapeptides’ by Huy N. Hoang et al., Chem. Sci., 2019, 10, 10595–10600, DOI: 10.1039/C9SC04153B.

The cyclic heptapeptide derivative, sanguinamide A, is a model scaffold for studying how component amino acids, heterocycles, and N-methylation influence membrane permeability and oral bioavailability. Membrane permeable sanguinamide A analogues have been reported, but there is limited data on their pharmacokinetic properties in vivo. Here we report pharmacokinetic properties for highly cell and membrane permeable sanguinamideAanalogues in rats and find that there is no correlation between reported permeability in vitro and oral bioavailability in vivo. We show that N-methylation of sanguinamide A analogues gives compounds with greater flexibility, greater susceptibility to degradation by rat liver microsomes, and lower oral bioavailability in rats.

AbstractThe introduction of an amide bond linking side chains of the first and fifth amino acids forms a cyclic pentapeptide that optimally stabilizes the smallest known α‐helix in water. The origin of the stabilization is unclear. The observed dependence of α‐helicity on the solvent and cyclization linker led us to discover a novel long‐range n to π* interaction between a main‐chain amide oxygen and a uniquely positioned carbonyl group in the linker of cyclic pentapeptides. CD and NMR spectra, NMR and X‐ray structures, modelling, and MD simulations reveal that this first example of a synthetically incorporated long‐range n to π* CO⋅⋅⋅Cγ=Ο interaction uniquely enforces an almost perfect and remarkably stable peptide α‐helix in water but not in DMSO. This unusual interaction with a covalent amide bond outside the helical backbone suggests new approaches to synthetically stabilize peptide structures in water.

Rule-of-five parameters and membrane permeabilities have been routinely used to guide development of orally bioavailabile drugs. Here we compare enantiomeric pairs of cyclic hexapeptides with identical rule-of-five parameters and membrane permeabilities. For each enantiomeric pair, the isomer with more l- than d-amino acids is much more orally bioavailable in rats, more metabolically stable to rat liver microsomes, and cleared more slowly in vivo.

Wollamides are cyclic hexapeptides, recently isolated from an Australian soil Streptomyces isolate, that exhibit promising in vitro antimycobacterial activity against Mycobacterium bovis Bacille Calmette Guérin without displaying cytotoxicity against a panel of mammalian cells. Here, we report the synthesis and antimycobacterial activity of 36 new synthetic wollamides, collated with all known synthetic and natural wollamides, to reveal structure characteristics responsible for in vitro growth-inhibitory activity against Mycobacterium tuberculosis (H37Rv, H37Ra, CDC1551, HN878, and HN353).

Most protein-protein interactions occur inside cells. Peptides can inhibit protein-protein interactions but tend not to enter cells. We systematically compare cell permeability for 8-12 residue model peptides with helix-inducing lactam/hydrocarbon linkers between amino acid sidechains. Cell uptake increases when hydrophobic residues and lactam linkers (i, i + 4) form a contiguous hydrophobic surface patch. Uptake increases further when both hydrophobic and positively charged (but not neutral or negative) residues are clustered into like surface patches. Amphipathicity alone is however insufficient for cell uptake of acyclic sequences. Changing the linker from lactam to hydrocarbon further increases uptake, but also promotes cell lysis. Helicity, positive charge and amphipathicity together promote cell permeability. Most known bioactive helical peptides do not optimally cluster residues for amphipathicity and so are likely unoptimised for cell uptake.

A new strategy is demonstrated for making peptides helical, using a carbohydrate to bridge between sidechains at each end of a pentapeptide. CD and NMR spectra establish that both an α-helix and a 310-helix structure can form depending upon the bridge.

Glucagon-like peptide (GLP-1) is an endogenous hormone that induces insulin secretion from pancreatic islets and modified forms are used to treat diabetes mellitus type 2. Understanding how GLP-1 interacts with its receptor (GLP-1R) can potentially lead to more effective drugs. Modeling and NMR studies of the N-terminus of GLP-1 suggest a β-turn between residues Glu9-Phe12 and a kinked alpha helix between Val16-Gly37. N-terminal turn constraints attenuated binding affinity and activity (compounds 1–8). Lys-Asp (i, i+4) crosslinks in the middle and at the C-terminus increased alpha helicity and cAMP stimulation without much effect on binding affinity or beta-arrestin 2 recruitment (compounds 9–18). Strategic positioning of helix-inducing constraints and amino acid substitutions (Tyr16, Ala22) increased peptide helicity and produced ten-fold higher cAMP potency (compounds 19–28) over GLP-1(7–37)-NH2. The most potent cAMP activator (compound 23) was also the most potent inducer of insulin secretion.