Epimerisation in Peptide Synthesis

Epimerisation is basically a chemical conversion that includes the transformation of an epimer into another epimer or its chiral partner. Epimerisation of amino acid is a side reaction that sometimes happens during peptide synthesis. It became the most avoided reaction because the process affects the overall conformation of the molecule, eventually even altering the bioactivity of the peptide. Epimerised products have a high similarity of physical characteristics, thus making it difficult for them to be purified. In regards to amino acids, epimerisation is very important in keeping the chirality of the assembled amino acids unchanged during the peptide synthesis and obtaining the desirable product without any problematic purification. In this review, we report several factors that induce epimerisation during peptide synthesis, including how to characterise and affect the bioactivities. To avoid undesirable epimerisation, we also describe several methods of suppressing the process.

Synthesis of a Cyclooctapeptide, Cyclopurpuracin, and Evaluation of Its Antimicrobial Activity

Cyclopurpuracin is a cyclooctapeptide isolated from the methanol extract of Annona purpurea seeds with a sequence of cyclo-Gly-Phe-Ile-Gly-Ser-Pro-Val-Pro. In our previous study, the cyclisation of linear cyclopurpuracin was problematic; however, the reversed version was successfully cyclised even though the NMR spectra revealed the presence of a mixture of conformers. Herein, we report the successful synthesis of cyclopurpuracin using a combination of solid- and solution-phase synthetic methods. Initially, two precursors of cyclopurpuracin were prepared, precursor linear A (NH₂-Gly-Phe-Ile-Gly-Ser(t-Bu)-Pro-Val-Pro-OH) and precursor linear B (NH-Pro-Gly-Phe-Ile-Gly-Ser(t-Bu)-Pro-Val-OH, and various coupling reagents and solvents were trialled to achieve successful synthesis. The final product was obtained when precursors A and B were cyclised using the PyBOP/NaCl method, resulting in a cyclic product with overall yields of 3.2% and 3.6%, respectively. The synthetic products were characterised by HR-ToF-MS, ¹H-NMR, and ¹³C-NMR, showing similar NMR profiles to the isolated product from nature and no conformer mixture. The antimicrobial activity of cyclopurpuracin was also evaluated for the first time against S. aureus, E. coli, and C. albicans, showing weak activity with MIC values of 1000 µg/mL for both synthetic products, whereas the reversed cyclopurpuracin was more effective with an MIC of 500 µg/mL.

Proximity effects in the electron ionisation mass spectra of substituted cinnamamides

The electron ionisation mass spectra of an extensive set of 53 ionised monosubstituted and disubstituted cinnamamides [XC₆H₄CH=CHCONH₂, X = H, F, Cl, Br, I, CH₃, CH₃O, CF₃, NO₂, CH₃CH₂, (CH₃)₂CH and (CH₃)₃C; and XYC₆H₃CH=CHCONH₂, X = Y = Cl; and X, Y = F, Cl or Br] are reported and discussed. Particular attention is paid to the significance of loss of the substituent, X, from the 2-position, via a rearrangement that is sometimes known as a proximity effect, which has been reported for a range of radical-cations, but is shown in this work to be especially important for ionised cinnamamides. When X is in the 2-position of the aromatic ring, [M - X]⁺ is formed to a far greater extent than [M - H]⁺; in contrast, when X is in the 3-position or 4-position, [M - H]⁺ is generally much more important than [M - X]⁺. Parallel trends are found in the spectra of XYC₆H₃CH=CHCONH₂: the signal for [M - X]⁺ dominates that for [M - Y]⁺ when X is in the 2-position and Y in the 4-position or 5-position, irrespective of the nature of X and Y. Further insight is obtained by studying the competition between expulsion of X^· and alternative fragmentations that may be described as simple cleavages. Loss of ^·NH₂ results in the formation of a substituted cinnamoyl cation, [XC₆H₄CH=CHCO]⁺ or [XYC₆H₃CH=CHCO]⁺; this process competes far less effectively with the proximity effect when X is in the 2-position than when it is in the 3-position or 4-position. Additional information has been obtained by investigating the competition between formation of [M - H]⁺ by the proximity effect and loss of CH₃^· by cleavage of a 4-alkyl group to give a benzylic cation, [R¹R²CC₆H₄CH=CHCONH₂]⁺ (R¹, R² = H, CH₃).

Convenient Synthesis of N-Heterocycle-Fused Tetrahydro-1,4-diazepinones

A general approach towards the synthesis of tetrahydro-4H-pyrazolo[1,5-a][1,4]diazepin-4-one, tetrahydro[1,4]diazepino[1,2-a]indol-1-one and tetrahydro-1H-benzo[4,5]imidazo[1,2-a][1,4]diazepin-1-one derivatives was introduced. A regioselective strategy was developed for synthesizing ethyl 1-(oxiran-2-ylmethyl)-1H-pyrazole-5-carboxylates from easily accessible 3(5)-aryl- or methyl-1H-pyrazole-5(3)-carboxylates. Obtained intermediates were further treated with amines resulting in oxirane ring-opening and direct cyclisation-yielding target pyrazolo[1,5-a][1,4]diazepin-4-ones. A straightforward two-step synthetic approach was applied to expand the current study and successfully functionalize ethyl 1H-indole- and ethyl 1H-benzo[d]imidazole-2-carboxylates. The structures of fused heterocyclic compounds were confirmed by ¹H, ¹³C, and ¹⁵N-NMR spectroscopy and HRMS investigation.

Dual Activation of Unsaturated Amides with Schwartz's Reagent: A Diastereoselective Access to Cyclopentanols and N,O-Dimethylcyclopentylhydroxylamines

The diastereoselective access to cyclopentanols and N,O-dimethylcyclopentylhydroxylamines from 4-pentenoic acid-derived Weinreb amides is described. Based on the concomitant generation of both the nucleophilic and the electrophilic poles by hydrozirconation of the amide and the C=C double bond, the cyclisation may be tuned towards cyclopentanols or N,O-dimethylcyclopentylhydroxylamines depending on the ring-closure promotor. An extension to cis 3-substituted N,O-dimethylcyclohexylhydroxylamines is also presented.

Indium-Catalysed Transfer Hydrogenation for the Reductive Cyclisation of 2-Alkynyl Enones towards Trisubstituted Furans

Indium tribromide catalysed the transfer hydrogenation from dihydroaromatic compounds, such as the commercially available γ-terpinene, to enones, which resulted in the cyclisation to trisubstituted furan derivatives. The reaction was initiated by a Michael addition of a hydride nucleophile to the enone subunit followed by a Lewis-acid-assisted cyclisation and the formation of a furan-indium intermediate and a Wheland intermediate derived from the dihydroaromatic starting material. The product was formed by protonation from the Wheland complex and replaced the indium tribromide substituent. In addition, a site-specific deuterium labelling of the dihydroaromatic HD surrogates resulted in site specific labelling of the products and gave useful insights into the reaction mechanism by H-D scrambling.

Preparation of Tetrabenzo[4.4.2]undecastarphene by On-Surface Synthesis

A large dissymmetric starphene molecule, the tetrabenzo[a,c,u,w]naphtho[2,3-l]nonaphene, was obtained by first preparing a soluble precursor which was then sublimated on a Au(111) surface in an ultra-high vacuum. In a second step, controlled annealings from 200 °C to 275 °C initiated two successive cyclodehydrogenation steps with the formation of 3 new carbon-carbon bonds. A second conformer was also stable enough during the annealing step to give another compound in similar yield, the benzodibenzo[7,8,9,10]naphthaceno[2,1-h]phenanthro[9,10-p]hexaphene. The formation of this more-hindered species stresses the importance of strong molecule-surface interactions during the cyclodehydrogenations steps of these large polyaromatic hydrocarbons.

Sustainable Access to 5-Amino-Oxazoles and Thiazoles via Calcium-Catalyzed Elimination-Cyclization with Isocyanides

Herein, we report a sustainable, modular, rapid and high-yielding transformation to afford densely functionalized 5-aminooxazoles and thiazoles. The reaction is tolerant to a wide range of functional groups and is typically complete in under 30 min. Furthermore, the described transformation is inherently green in relation to the catalyst and solvent choice as well as producing environmentally benign alcoholic by-products.

Thiyl Radicals: Versatile Reactive Intermediates for Cyclization of Unsaturated Substrates

Sulfur centered radicals are widely employed in chemical synthesis, in particular for alkene and alkyne hydrothiolation towards thioether bioconjugates. The steadfast radical chain process that enables efficient hydrothiolation has been explored in the context of cascade reactions to furnish complex molecular architectures. The use of thiyl radicals offers a much cheaper and less toxic alternative to the archetypal organotin-based radical methods. This review outlines the development of thiyl radicals as reactive intermediates for initiating carbocyclization cascades. Key developments in cascade cyclization methodology are presented and applications for natural product synthesis are discussed. The review provides a chronological account of the field, beginning in the early seventies up to very recent examples; a span of almost 50 years.

Lithium-Bromide Exchange versus Nucleophilic Addition of Schiff's base: Unprecedented Tandem Cyclisation Pathways

By exploring lithium-bromide exchange reactivity of aromatic Schiff's bases with tert-butyllithium (tBuLi), we have revealed unprecedented competitive intermolecular and intramolecular cascade annulation pathways, leading to valuable compounds, such as iso-indolinones and N-substituted anthracene derivatives. A series of reaction parameters were probed, including solvent, stoichiometry, sterics and organolithium reagent choice, in order to understand the influences that limit such ring-closing pathways. With two viable reactivity options for the organolithium on the imine; namely, nucleophilic addition or lithium-bromide exchange, a surprising competitive nature was observed, where nucleophilic addition dominated, even under cryogenic conditions. Considering the most commonly used solvents for lithium-bromide exchange, tetrahydrofuran (THF) and diethyl ether (Et₂ O), contrasting reactivity outcomes were revealed with nucleophilic addition promoted in THF, while Et₂ O yielded almost double the conversion of cyclic products than in THF.

Synthesis of the Core Framework of the Cornexistins by Intramolecular Nozaki-Hiyama-Kishi Coupling

A new and direct approach to the construction of the core framework of the herbicidal natural products cornexistin and hydroxycornexistin has been developed. Formation of the nine-membered carbocycle found in the natural products has been accomplished by an intramolecular Nozaki-Hiyama-Kishi reaction between a vinylic iodide and an aldehyde. Good yields of carbocyclic products were obtained from the reaction, but diastereomeric mixtures of allylic alcohols were produced. The cyclisation reaction was successful irrespective of the relative configuration of the stereogenic centres in the cyclisation precursor.

A Gold Carbene Manifold to Prepare Fused γ-Lactams by Oxidative Cyclisation of Ynamides

Gold-catalysed oxidative cyclisation reactions of ynamides offer great promise in γ-lactam synthesis but are limited by preferential over-oxidation to form α-keto imides. Evaluating the factors that might limit N-cyclisation pathways led to effective gold-catalysed conditions that allow access to different fused γ-lactams on changing the ynamide N-substituent and accommodate previously incompatible substitution patterns. New and efficient methods for the synthesis of functionalised 3-aryl indoles and cyclohepta[c]pyrrol-1-one derivatives are presented. These conditions illustrate the complementarity of gold catalysis to other metals.

Fluorocyclisation via I(I)/I(III) catalysis: a concise route to fluorinated oxazolines

Herein, we describe a catalytic fluorooxygenation of readily accessible N-allylcarboxamides via an I(I)/I(III) manifold to generate 2-oxazolines containing a fluoromethyl group. Catalysis is conditional on the oxidation competence of Selectfluor®, whilst HF serves as both a fluoride source and Brønsted acid activator. The C(sp3)-F bond of the mono-fluoromethyl unit and the C(sp3)-O bond of the ring are aligned in a synclinal relationship thereby engaging in stabilising hyperconjugative interactions with vicinal, electron-rich σ-bonds (σC-C→σ*C-F and σC-H→σ*C-O). This manifestation of the stereoelectronic gauche effect was established by X-ray crystallographic analysis of a representative example. Given the importance of fluorine in drug discovery, its ability to modulate conformation, and the prevalence of the 2-oxazoline scaffold in Nature, this strategy provides a rapid entry into an important bioisostere class.

Synthesis and Antiproliferative Activity of Minor Hops Prenylflavonoids and New Insights on Prenyl Group Cyclization

Synthesis of minor prenylflavonoids found in hops and their non-natural derivatives were performed. The antiproliferative activity of the obtained compounds against some human cancer cell lines was investigated. Using xanthohumol isolated from spent hops as a lead compound, a series of minor hop prenylflavonoids and synthetic derivatives were obtained by isomerization, cyclisation, oxidative-cyclisation, oxidation, reduction and demethylation reactions. Three human cancer cell lines-breast (MCF-7), prostate (PC-3) and colon (HT-29)-were used in antiproliferative assays, with cisplatin as a control compound. Five minor hop prenyl flavonoids and nine non-natural derivatives of xanthohumol have been synthetized. Syntheses of xanthohumol K, its dihydro- and tetrahydro-derivatives and 1″,2″,α,β-tetrahydroxanthohumol C were described for the first time. All of the minor hops prenyl flavonoids exhibited strong to moderate antiproliferative activity in vitro. The minor hops flavonoids xanthohumol C and 1″,2″-dihydroxanthohumol K and non-natural 2,3-dehydroisoxanthohumol exhibited the activity comparable to cisplatin. Results described in the article suggest that flavonoids containing chromane- and chromene-like moieties, especially chalcones, are potent antiproliferative agents. The developed new efficient, regioselective cyclisation reaction of the xanthohumol prenyl group to 1″,2″-dihydroxantohumol K may be used in the synthesis of other compounds with the chromane moiety.

A Thiolactone Strategy for Straightforward Synthesis of Disulfide-Linked Side-Chain-to-Tail Cyclic Peptides Featuring an N-Terminal Modification Handle

The development of straightforward and versatile peptide cyclisation methods is highly desired to meet the demand for more stable peptide-based drugs. Herein, a new method for the synthesis of side-chain-to-tail cyclic peptides with the simultaneous introduction of an N-terminal handle, based on the introduction of an N-terminal thiolactone building block, is described. A primary amine liberates a homocysteine analogue from the thiolactone building block, which further enables cyclisation of the peptide through disulfide-bond formation with a C-terminal cysteamine. Postcyclisation modification can be achieved by using small bifunctional amines. Alternatively, the synthesis of lipopeptides is demonstrated through direct thiolactone opening with long-chain alkyl amines.

Practical synthetic strategies towards lipophilic 6-iodotetrahydroquinolines and -dihydroquinolines

The synthesis of novel tetrahydroquinolines (THQ) and dihydroquinolines (DHQ) are reported using three practical, scalable synthetic approaches to access highly lipophilic analogues bearing a 6-iodo substituent, each with a different means of cyclisation. A versatile and stable quinolin-2-one intermediate was identified, which could be reduced to the corresponding THQ with borane reagents, or to the DHQ with diisobutylaluminium hydride via a novel elimination that is more favourable at higher temperatures. Coupling these strongly electron-donating scaffolds to electron-accepting moieties caused the resulting structures to exhibit strong fluorescence.

Cyclisation mechanisms in the biosynthesis of ribosomally synthesised and post-translationally modified peptides

Ribosomally synthesised and post-translationally modified peptides (RiPPs) are a large class of natural products that are remarkably chemically diverse given an intrinsic requirement to be assembled from proteinogenic amino acids. The vast chemical space occupied by RiPPs means that they possess a wide variety of biological activities, and the class includes antibiotics, co-factors, signalling molecules, anticancer and anti-HIV compounds, and toxins. A considerable amount of RiPP chemical diversity is generated from cyclisation reactions, and the current mechanistic understanding of these reactions will be discussed here. These cyclisations involve a diverse array of chemical reactions, including 1,4-nucleophilic additions, [4 + 2] cycloadditions, ATP-dependent heterocyclisation to form thiazolines or oxazolines, and radical-mediated reactions between unactivated carbons. Future prospects for RiPP pathway discovery and characterisation will also be highlighted.

The reactions of 2-ethoxymethylidene-3-oxo esters and their analogues with 5-aminotetrazole as a way to novel azaheterocycles

The interaction of 2-ethoxymethylidene-3-oxo esters and their analogues with 5-aminotetrazole is an efficient synthetic approach to novel azaheterocycles. 2-Ethoxymethylidene-3-oxo esters bearing alkyl substituents react with 5-aminotetrazole to form ethyl 2-azido-4-alkylpyrimidine-5-carboxylates which are capable of subsequent nucleophilic substitution. The use of diethyl 2-ethoxymethylidenemalonate in this reaction resulted in ethyl 7-hydroxytetrazolo[1,5-a]pyrimidine-6-carboxylate, while ethyl 2-ethoxymethylidenecyanoacetate yielded 5-[2,6-diamino-3,5-bis(ethoxycarbonyl)pyridinium-1-yl]tetrazol-1-ide through an alternative pathway. Ethyl 2-benzoyl-3-ethoxyprop-2-enoate reacted with 5-aminotetrazole by two reaction routes to form ethyl 2-benzoyl-3-(1H-tetrazol-5-ylamino)prop-2-enoate and ethyl 7-(1-ethoxy-1,3-dioxo-3-phenylpropan-2-yl)-5-phenyl-4,7-dihydrotetrazolo[1,5-a]pyrimidine-6-carboxylate.

Electrochemical selenium- and iodonium-initiated cyclisation of hydroxy-functionalised 1,4-dienes

The cobalt(I)-catalysed 1,4-hydrovinylation reaction of allyloxytrimethylsilane and allyl alcohol with substituted 1,3-dienes leads to hydroxy-functionalised 1,4-dienes in excellent regio- and diastereoselective fashion. Those 1,4-dienols can be converted into tetrahydrofuran and pyran derivatives under indirect electrochemical conditions generating selenium or iodonium cations. The reactions proceed in good yields and regioselectivities for the formation of single diastereomers.

Development of an additive-controlled, SmI2-mediated stereoselective sequence: Telescoped spirocyclisation, lactone reduction and Peterson elimination

Studies on SmI₂-mediated spirocyclisation and lactone reduction culminate in a telescoped sequence in which additives are used to “switch on” individual steps mediated by the electron transfer reagent. The sequence involves the use of two activated SmI₂ reagent systems and a silicon stereocontrol element that exerts complete diastereocontrol over the cyclisation and is removed during the final stage of the sequence by Peterson elimination. The approach allows functionalised cyclopentanols containing two vicinal quaternary stereocentres to be conveniently prepared from simple starting materials.

Interplay of ortho- with spiro-cyclisation during iminyl radical closures onto arenes and heteroarenes

Sensitised photolyses of ethoxycarbonyl oximes of aromatic and heteroaromatic ketones yielded iminyl radicals, which were characterised by EPR spectroscopy. Iminyls with suitably placed arene or heteroarene acceptors underwent cyclisations yielding phenanthridine-type products from ortho-additions. For benzofuran and benzothiophene acceptors, spiro-cyclisation predominated at low temperatures, but thermodynamic control ensured ortho-products, benzofuro- or benzothieno-isoquinolines, formed at higher temperatures. Estimates by steady-state kinetic EPR established that iminyl radical cyclisations onto aromatics took place about an order of magnitude more slowly than prototypical C-centred radicals. The cyclisation energetics were investigated by DFT computations, which gave insights into factors influencing the two cyclisation modes.

Alkyne hydroarylation with Au N-heterocyclic carbene catalysts

Mono- and dinuclear gold complexes with N-heterocyclic carbene (NHC) ligands have been employed as catalysts in the intermolecular hydroarylation of alkynes with simple unfunctionalised arenes. Both mono- and dinuclear gold(III) complexes were able to catalyze the reaction; however, the best results were obtained with the mononuclear gold(I) complex IPrAuCl. This complex, activated with one equivalent of silver tetrafluoroborate, exhibited under acidic conditions at room temperature much higher catalytic activity and selectivity compared to more commonly employed palladium(II) catalysts. Moreover, the complex was active, albeit to a minor extent, even under neutral conditions, and exhibited lower activity but higher selectivity compared to the previously published complex AuCl(PPh(3)). Preliminary results on intramolecular hydroarylations using this catalytic system indicate, however, that alkyne hydration by traces of water may become a serious competing reaction.

Cyclisation increases the stability of the sea anemone peptide APETx2 but decreases its activity at acid-sensing ion channel 3

APETx2 is a peptide isolated from the sea anemone Anthopleura elegantissima. It is the most potent and selective inhibitor of acid-sensing ion channel 3 (ASIC3) and it is currently in preclinical studies as a novel analgesic for the treatment of chronic inflammatory pain. As a peptide it faces many challenges in the drug development process, including the potential lack of stability often associated with therapeutic peptides. In this study we determined the susceptibility of wild-type APETx2 to trypsin and pepsin and tested the applicability of backbone cyclisation as a strategy to improve its resistance to enzymatic degradation. Cyclisation with either a six-, seven- or eight-residue linker vastly improved the protease resistance of APETx2 but substantially decreased its potency against ASIC3. This suggests that either the N- or C-terminus of APETx2 is involved in its interaction with the channel, which we confirmed by making N- and C-terminal truncations. Truncation of either terminus, but especially the N-terminus, has detrimental effects on the ability of APETx2 to inhibit ASIC3. The current work indicates that cyclisation is unlikely to be a suitable strategy for stabilising APETx2, unless linkers can be engineered that do not interfere with binding to ASIC3.

Fused bicyclic piperidines and dihydropyridines by dearomatising cyclisation of the enolates of nicotinyl-substituted esters and ketones

The silyl enol ether derivatives of ketones or esters tethered by a hydrocarbon or ether linkage to the 3-position of a pyridine ring undergo dearomatising nucleophilic attack on the ring once it is activated (as an acylpyridinium species) by the addition of methyl chloroformate. The bicyclic dihydropyridine products are in some cases unstable, but may be isolated after hydrogenation as fused bicyclic piperidines.

Cyclotides: macrocyclic peptides with applications in drug design and agriculture

Cyclotides are disulfide-rich peptides from plants that are exceptionally stable as a result of their unique cyclic cystine knot structural motif. Their natural role is thought to be as plant defence agents, most notably against insect pests, but they also have potential applications in drug design and agriculture. This article identifies gaps in current knowledge on cyclotides and suggests future directions for research into this fascinating family of ultra-stable mini-proteins.

Synthesis of chiral cyclohexanes and carbasugars by 6-exo-dig radical cyclisation reactions

Treatment of 5-(tert-butyldimethylsilyl)-2,3-O-isopropylidene-D-ribose with lithium acetylides gave mixtures of syn- and anti-alkynols 2a–2c which were separated following protection as methoxymethyl ethers. These were converted to the corresponding iodides which underwent 6-exo-dig radical cyclisation to afford chiral cyclohexanes and carbasugars. Oxidation of the primary alcohols 6a–b gave the corresponding aldehydes which on treatment with Grignard reagents afforded a mixture of alcohols. The corresponding iodides underwent similar 6-exo-dig cyclisation to give fully functionalised cyclohexanes.