Chemical synthesis and biological activity of peptides incorporating an ether bridge as a surrogate for a disulfide bond

Disulfide bridges contribute to the definition and rigidity of polypeptides, but they are inherently unstable in reducing environments and in the presence of isomerases and nucleophiles. Strategies to address these deficiencies, ideally without significantly perturbing the structure of the polypeptide, would be of great interest. One possible surrogate for the disulfide bridge is a simple thioether, but these are susceptible to oxidation. We report the introduction of an ether linkage into the biologically active, disulfide-rich peptides oxytocin, tachyplesin I, and conotoxin α-ImI, using an ether-containing diaminodiacid as the key building block, obtained by the stereoselective ring-opening addition reaction of an aziridine skeleton with a hydroxy group. NMR studies indicated that the derivatives with an ether surrogate bridge exhibited very small change of their three-dimensional structures. The analogs obtained using this novel substitution strategy were found to be more stable than the original peptide in oxidative and reductive conditions; without a loss of bioactivity. This strategy is therefore proposed as a practical and versatile solution to the stability problems associated with cysteine-rich peptides.

We report the first introduction of an ether linkage as surrogate into the disulfide-rich peptides using ether-containing diaminodiacid.     

Cyclodepsipeptide alveolaride C: total synthesis and structural assignment

First stereoselective total synthesis of naturally occurring bioactive cyclodepsipeptide alveolaride C has been achieved using a convergent approach. This synthetic study enabled us to establish unambiguously the stereochemistry of three unassigned chiral centres embedded in the nonpeptidic segment as well as revised the stereochemistry of the proposed β-phenylalanine counterpart of the molecule. The key strategic features of this synthesis include Sharpless asymmetric dihydroxylation for installing the vicinal diol moiety, Julia–Kocienski olefination for constructing the aliphatic side chain, the Shiina protocol for intermolecular esterification, amide coupling and macrolactamization for the ring formation.

First total synthesis of natural cyclodepsipeptide alveolaride C has been accomplished with an unambiguous solution to its structural riddle.     

Total synthesis of crotophorbolone

As a natural diterpenoid, crotophorbolone possesses a challenging trans,trans-5/7/6 framework decorated with six contiguous stereogenic centers and is structurally and biogenetically related to tigliane-type diterpenoids with intriguing bioactivities such as phorbol and prostratin. Based on the convergent strategy, we completed an eighteen-step total synthesis of crotophorbolone starting from (−)-carvone and (+)-dimethyl-2,3-O-isopropylidene-l-tartrate. The key elements of the synthesis involve expedient installation of the six-membered ring and the five-membered ring with multiple functional groups at an early stage, cyclization of the seven-membered ring through alkenylation of the ketone between the five-membered ring and the six-membered ring, functional group-sensitive ring-closing metathesis and final selective introduction of hydroxyls at C₂₀ and C₄.

Convergent total synthesis of crotophorbolone was accomplished in 18 longest linear steps. Observation of unexpected thermodynamic stability of a cis,trans-5/7/6 tricycle would benefit synthetic design of tigliane- and daphnane-related diterpenoids.     

Salient features of the aza-Wacker cyclization reaction

The intramolecular aza-Wacker reaction has unparalleled potential for the site-selective amination of olefins, but it is perhaps underappreciated relative to other alkene oxidations. The first part of this review makes the distinction between classical and tethered aza-Wacker cyclization reactions and summarizes examples of the latter. The second portion focuses on developments in asymmetric aza-Wacker cyclization technology. The final part of the review summarizes applications of all classes of aza-Wacker cyclization reactions to natural product assembly.

The aza-Wacker cyclization reaction is a powerful strategy for alkene amination.     

Designed alpha-helical barrels for charge-selective peptide translocation

Synthetic alpha-helix based pores for selective sensing of peptides have not been characterized previously. Here, we report large transmembrane pores, pPorA formed from short synthetic alpha-helical peptides of tunable conductance and selectivity for single-molecule sensing of peptides. We quantified the selective translocation kinetics of differently charged cationic and anionic peptides through these synthetic pores at single-molecule resolution. The charged peptides are electrophoretically pulled into the pores resulting in an increase in the dissociation rate with the voltage indicating successful translocation of peptides. More specifically, we elucidated the charge pattern lining the pore lumen and the orientation of the pores in the membrane based on the asymmetry in the peptide-binding kinetics. The salt and pH-dependent measurements confirm the electrostatic dominance and charge selectivity in controlling target peptide interaction with the pores. Remarkably, we tuned the selectivity of the pores to charged peptides by modifying the charge composition of the pores, thus establishing the molecular and electrostatic basis of peptide translocation. We suggest that these synthetic pores that selectively conduct specific ions and biomolecules are advantageous for nanopore proteomics analysis and synthetic nanobiotechnology applications.

Synthetic alpha-helix based pores for selective sensing of peptides have not been characterized previously.     

Enantioselective total synthesis of (−)-myrifabral A and B

A catalytic enantioselective approach to the Myrioneuron alkaloids (−)-myrifabral A and (−)-myrifabral B is described. The synthesis was enabled by a palladium-catalyzed enantioselective allylic alkylation, that generates the C(10) all-carbon quaternary center. A key N-acyl iminium ion cyclization forged the cyclohexane fused tricyclic core, while vinyl boronate cross metathesis and oxidation afforded the lactol ring of (−)-myrifabral A. Adaptation of previously reported conditions allowed for the conversion of (−)-myrifabral A to (−)-myrifabral B.

A catalytic enantioselective approach to the Myrioneuron alkaloids (−)-myrifabral A and (−)-myrifabral B is described.     

Rh(i)-catalyzed stereoselective desymmetrization of prochiral cyclohexadienones via highly exo-selective Huisgen-type [3 + 2] cycloaddition

A Rh(i)-catalyzed highly stereoselective desymmetrization of 2-alkynylbenzaldehyde-tethered cyclohexadienones triggered by intramolecular Huisgen-type [3 + 2] cycloaddition has been developed. This method enables convergent construction of complex epoxy-bridged polycyclic ring systems with five contiguous stereocenters with excellent exo-selectivity and broad substrate scope. The highly atom-economical process involves 6-endo-dig cyclization of carbonyl oxygen onto an activated alkyne resulting in a highly reactive metal–benzopyrylium intermediate, which readily undergoes intramolecular [3 + 2] annulation/hydration. Asymmetric induction is also achieved for the first time in Rh(i)-catalyzed 1,3-dipolar cycloaddition using an easily accessible chiral diene as the ligand.

A Rh(i)-catalyzed highly stereoselective desymmetrization of 2-alkynylbenzaldehyde-tethered cyclohexadienones triggered by intramolecular Huisgen-type [3 + 2] cycloaddition has been developed.     

Cyclization of interlocked fumaramides into β-lactams: experimental and computational mechanistic assessment of the key intercomponent proton transfer and the stereocontrolling active pocket

A detailed mechanistic study of the diastereoselective CsOH-promoted cyclization of interlocked fumaramides to give β-lactams is described. The mechanistic analysis comprises the experimental evaluation of the structure-reactivity relationship for a wide range of fumaramides [2]rotaxanes (Hammet-plots), KIE studies with deuterium-labelled interlocked fumaramides and computational analysis of two alternative mechanistic pathways for the cyclization process. The obtained results confirm that: (a) the rate-determining step is the deprotonation of the N-benzyl group of the thread by the amidate group of the macrocycle generated by the external base, (b) the polyamide macrocycle plays an important role not only as activating element but also as the stereodifferenciating factor responsible for the observed diastereoselection and (c) the higher flexibility of the adamantyl core speeds up the cyclization process in diadamantyl-derived rotaxanes.

A mechanistic study of the diastereoselective cyclization of interlocked fumaramides to give β-lactams unveils the key factors for successfully taming the process.     

Investigation of cytolysin variants by peptide mapping: enhanced protein characterization using complementary ionization and mass spectrometric techniques

Matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) have been used in conjunction with time-of-flight (TOF) and quadrupole ion trap (IT) mass spectrometry, respectively, to analyze various cytolysin proteins isolated from the sea anemone Stichodactyla helianthus and digested by the protease trypsin. By employing different ionization methods, the subsequent changes in ionization selectivity for the peptides in the digested protein samples resulted in ion abundance variation reflected in the mass spectra. Upon investigation of this variation generated by the two ionization processes, it has been shown in this study that enhanced protein coverage (e.g., >95% for cytolysin III) can be achieved. Additionally, capillary and microbore reversed-phase high-performance liquid chromatography (RP-HPLC) coupled with ESI mass spectrometry (MS) as well as flow injection analysis by nanoflow ESI-MS afforded the necessary limit of detection (LOD) for detailed structural information of the cytolysin proteins by tandem mass spectrometry (MS/MS) methods. It can be concluded that cytolysins II and III correspond to sticholysins I and II, that "cytolysin I" is a mixture of modified forms of cytolysins II and III, and that "cytolysin IV" is an incompletely processed precursor of cytolysin III.     

Target-templated de novo design of macrocyclic d-/l-peptides: discovery of drug-like inhibitors of PD-1

Peptides are a rapidly growing class of therapeutics with various advantages over traditional small molecules, especially for targeting difficult protein–protein interactions. However, current structure-based methods are largely limited to natural peptides and are not suitable for designing bioactive cyclic topologies that go beyond natural l-amino acids. Here, we report a generalizable framework that exploits the computational power of Rosetta, in terms of large-scale backbone sampling, side-chain composition and energy scoring, to design heterochiral cyclic peptides that bind to a protein surface of interest. To showcase the applicability of our approach, we developed two new inhibitors (PD-i3 and PD-i6) of programmed cell death 1 (PD-1), a key immune checkpoint in oncology. A comprehensive biophysical evaluation was performed to assess their binding to PD-1 as well as their blocking effect on the endogenous PD-1/PD-L1 interaction. Finally, NMR elucidation of their in-solution structures confirmed our de novo design approach.

In silico design of heterochiral cyclic peptides that bind to a specific surface patch on the target protein (PD-1, in this case) and disrupt protein–protein interactions.     

Hydantoin-bridged medium ring scaffolds by migratory insertion of urea-tethered nitrile anions into aromatic C–N bonds

Bicyclic or tricyclic nitrogen-containing heterocyclic scaffolds were constructed rapidly by intramolecular nucleophilic aromatic substitution of metallated nitriles tethered by a urea linkage to a series of electronically unactivated heterocyclic precursors. The substitution reaction constitutes a ring expansion, enabled by the conformationally constrained tether between the nitrile and the heterocycle. Attack of the metallated urea leaving group on the nitrile generates a hydantoin that bridges the polycyclic products. X-ray crystallography reveals ring-dependant strain within the hydantoin.

Bicyclic or tricyclic nitrogen-containing heterocyclic scaffolds were constructed rapidly by ring expanding intramolecular S_NAr on a series of electronically unactivated heterocyclic precursors.     

SyntaLinker: automatic fragment linking with deep conditional transformer neural networks

Linking fragments to generate a focused compound library for a specific drug target is one of the challenges in fragment-based drug design (FBDD). Hereby, we propose a new program named SyntaLinker, which is based on a syntactic pattern recognition approach using deep conditional transformer neural networks. This state-of-the-art transformer can link molecular fragments automatically by learning from the knowledge of structures in medicinal chemistry databases (e.g. ChEMBL database). Conventionally, linking molecular fragments was viewed as connecting substructures that were predefined by empirical rules. In SyntaLinker, however, the rules of linking fragments can be learned implicitly from known chemical structures by recognizing syntactic patterns embedded in SMILES notations. With deep conditional transformer neural networks, SyntaLinker can generate molecular structures based on a given pair of fragments and additional restrictions. Case studies have demonstrated the advantages and usefulness of SyntaLinker in FBDD.

Linking fragments to generate a focused compound library for a specific drug target is one of the challenges in fragment-based drug design (FBDD).     

Unequivocal structure confirmation of a breitfussin analog by anisotropic NMR measurements

Structural features of proton-deficient heteroaromatic natural products, such as the breitfussins, can severely complicate their characterization by NMR spectroscopy. For the breitfussins in particular, the constitution of the five-membered oxazole central ring cannot be unequivocally established via conventional NMR methods when the 4′-position is halogenated. The level of difficulty is exacerbated by 4′-iodination, as the accuracy with which theoretical NMR parameters are determined relies extensively on computational treatment of the relativistic effects of the iodine atom. It is demonstrated in the present study, that the structure of a 4′-iodo breitfussin analog can be unequivocally established by anisotropic NMR methods, by adopting a reduced singular value decomposition (SVD) protocol that leverages the planar structures exhibited by its conformers.

Structural features of proton-deficient heteroaromatic natural products, such as the breitfussins, can severely complicate their characterization by NMR spectroscopy.     

Rhodium catalysed C-3/5 methylation of pyridines using temporary dearomatisation

Pyridines are ubiquitous aromatic rings used in organic chemistry and are crucial elements of the drug discovery process. Herein we describe a new catalytic method that directly introduces a methyl group onto the aromatic ring; this new reaction is related to hydrogen borrowing, and is notable for its use of the feedstock chemicals methanol and formaldehyde as the key reagents. Conceptually, the C-3/5 methylation of pyridines was accomplished by exploiting the interface between aromatic and non-aromatic compounds, and this allows an oscillating reactivity pattern to emerge whereby normally electrophilic aromatic compounds become nucleophilic in the reaction after activation by reduction. Thus, a set of C-4 functionalised pyridines can be mono or doubly methylated at the C-3/5 positions.

Electron poor pyridines can be activated by reduction and then methylated at C3/5 using formaldehyde.     

Asymmetric systematic synthesis,structures, and (chir)optical properties of a series of dihetero[8]helicenes

A series of dihetero[8]helicenes have been systematically synthesized in enantiomerically enriched forms by utilizing the characteristic transformations of the organosulfur functionality. The synthetic route begins with assembling a ternaphthyl common synthetic intermediate from 2-naphthol and bissulfinylnaphthalene through an extended Pummerer reaction followed by facile multi-gram-scale resolution. The subsequent cyclization reactions into dioxa- and dithia[8]helicenes take place with excellent axial-to-helical chirality conversion. Dithia[8]helicene is further transformed into the nitrogen and the carbon analogs by replacing the two endocyclic sulfur atoms via S_NAr-based skeletal reconstruction. The efficient systematic synthesis has enabled comprehensive evaluation of physical properties, which has clarified the effect of the endocyclic atoms on their structures and (chir)optical properties as well as the unexpected conformational stability of the common helical framework.

A series of dihetero[8]helicenes have been synthesized in a stereoselective manner through an organosulfur-based synthetic strategy, which has enabled clarifying the effect of the endocyclic atoms on physical properties.     

Cu-catalyzed hydroxycyclopropanol ring-opening cyclization to tetrahydrofurans and tetrahydropyrans: short total syntheses of hyperiones

Tetrahydrofurans (THFs) and tetrahydropyrans (THPs) are important core scaffolds frequently found in many molecules of medicinal importance. Herein, we report a novel copper-catalyzed hydroxycyclopropanol ring-opening cyclization methodology to synthesize di- or tri-substituted THFs and THPs. In this reaction, a strained C–C bond was cleaved and a new Csp³–O bond was formed to produce the aforementioned O-heterocycles. The new THF synthesis features a broad substrate scope, scalability, and good functional-group tolerability. It enabled us to complete the shortest enantioselective syntheses of hyperiones A and B (3 and 4 steps, respectively), which is significantly shorter than the previously reported two total syntheses (≥10 steps).

A novel Cu-catalyzed hydroxycyclopropanol ring-opening cyclization was developed to synthesize substituted tetrahydrofuran/tetrahydropyran molecules including two norlignan natural products hyperiones A and B.     

A β-hairpin epitope as novel structural requirement for protein arginine rhamnosylation

For canonical asparagine glycosylation, the primary amino acid sequence that directs glycosylation at specific asparagine residues is well-established. Here we reveal that a recently discovered bacterial enzyme EarP, that transfers rhamnose to a specific arginine residue in its acceptor protein EF-P, specifically recognizes a β-hairpin loop. Notably, while the in vitro rhamnosyltransferase activity of EarP is abolished when presented with linear substrate peptide sequences derived from EF-P, the enzyme readily glycosylates the same sequence in a cyclized β-hairpin mimic. Additional studies with other substrate-mimicking cyclic peptides revealed that EarP activity is sensitive to the method used to induce cyclization and in some cases is tolerant to amino acid sequence variation. Using detailed NMR approaches, we established that the active peptide substrates all share some degree of β-hairpin formation, and therefore conclude that the β-hairpin epitope is the major determinant of arginine-rhamnosylation by EarP. Our findings add a novel recognition motif to the existing knowledge on substrate specificity of protein glycosylation, and are expected to guide future identifications of rhamnosylation sites in other protein substrates.

For bacterial arginine rhamnosylation, the rhamnosyltransferase EarP specifically recognizes a β-hairpin structure in the acceptor substrate.     

Total synthesis and complete configurational assignment of amphirionin-2

Amphirionin-2 is a linear polyketide metabolite that exhibits potent and selective cytotoxic activity against certain human cancer cell lines. We disclose herein the first total synthesis of amphirionin-2 and determination of its absolute configuration. Our synthesis featured an extensive use of cobalt-catalyzed Mukaiyama-type cyclization of γ-hydroxy olefins for stereoselective formation of all the tetrahydrofuran rings found in the natural product, and a late-stage Stille-type coupling for convergent assembly of the entire carbon backbone. Four candidate diastereomers of amphirionin-2 were synthesized in a unified, convergent manner, and their spectroscopic/chromatographic properties were compared with those of the authentic material. The present study culminated in the reassignment of the C5/C7 relative configuration, assignment of the C12/C18 relative configuration, and determination of the absolute configuration of amphirionin-2.

An extensive application of cobalt-catalyzed Mukaiyama-type cyclization of γ-hydroxy olefins and a late-stage Stille-type reaction enabled syntheses of four diastereomers of amphirionin-2 to establish its absolute configuration.     

A happy medium: the synthesis of medicinally important medium-sized rings via ring expansion

Medium-sized rings have much promise in medicinal chemistry, but are difficult to make using direct cyclisation methods. In this minireview, we highlight the value of ring expansion strategies to address this long-standing synthetic challenge. We have drawn on recent progress (post 2013) to highlight the key reaction design features that enable successful ‘normal-to-medium’ ring expansion for the synthesis of these medicinally important molecular frameworks, that are currently under-represented in compound screening collections and marketed drugs in view of their challenging syntheses.

Ring expansion strategies are ideally suited to make synthetically challenging, medium-sized rings with much potential in medicinal chemistry.