New TFA-Free Cleavage and Final Deprotection in Fmoc Solid-Phase Peptide Synthesis: Dilute HCl in Fluoro Alcohol

Brønsted Acid-Lewis Acid (BA-LA) Induced Final Deprotection/Peptide Resin Cleavage in Fmoc/t-Bu Solid-Phase Peptide Synthesis: HCl/FeCl3 and AcOH/FeCl3 as Viable PFAS-Free Alternatives for TFA

The widely used Fmoc/t-Bu solid-phase peptide synthesis (SPPS) is hampered by relying on corrosive, per/polyfluoroalkyl substance (PFAS) classified trifluoroacetic acid (TFA) as a universal protecting group (PG) removal/resin cleavage reagent. We report that suitable combinations of Brønsted acids (BAs) and Lewis acids (LAs) such as HCl/FeCl3 and AcOH/FeCl3 constitute viable alternatives for TFA as PFAS-free cleavage agents. Using water miscible dimethyl carbonate (DMC) and acetonitrile (MeCN) as solvents enabled diluting cleavage mixtures with suitable aqueous solutions, allowing for direct use in purification in which removal of >99.99% iron from an HCl/FeCl3 induced cleavage was demonstrated.

Self-assembly of spin-labeled antimicrobial peptides magainin 2 and PGLa in lipid bilayers

The cationic antimicrobial peptides PGLa and magainin 2 (Mag2) are known for their antimicrobial activity and synergistic enhancement in antimicrobial and membrane leakage assays. Further use of peptides in combinatory therapy requires knowledge of the mechanisms of action of both individual peptides and their mixtures. Here, electron paramagnetic resonance (EPR), double electron-electron resonance (DEER, also known as PELDOR) and electron spin echo envelope modulation (ESEEM) spectroscopies were applied to study self-assembly and localization of spin-labeled PGLa and Mag2 in POPE/POPG membranes with a wide range of peptide/lipid ratios (P/L) from ∼1/1500 to 1/50. EPR and DEER data showed that both peptides tend to organize in clusters, which occurs already at the lowest peptide/lipid molar ratio of 1/1500 (0.067 mol%). For individual peptides, these clusters are quite dense with intermolecular distances of the order of ∼2 nm. In the presence of a synergistic peptide partner, these homo-clusters are transformed into lipid-diluted hetero-clusters. These clusters are characterized by a local surface density that is several times higher than expected from a random distribution. ESEEM data indicate a slightly different insertion depth of peptides in hetero-clusters when compared to homo-clusters.

Templated Total Synthesis of Cu(I)-Methanobactin OB3b

Methanobactin OB3b (Mbn-OB3b) is a unique natural product with stunning affinity for copper ions (Ka ≈Cu(I) 1034 ). Here, we report the first total synthesis of Cu(I)-bound methanobactin OB3b featuring as key transformations a cyclodehydration-thioacylation sequence, to generate the conjugated heterocyclic systems, and a copper-templated cyclization, to complete the caged structure of the very sensitive target compound.

HFIP in Organic Synthesis

1,1,1,3,3,3-Hexafluoroisopropanol (HFIP) is a polar, strongly hydrogen bond-donating solvent that has found numerous uses in organic synthesis due to its ability to stabilize ionic species, transfer protons, and engage in a range of other intermolecular interactions. The use of this solvent has exponentially increased in the past decade and has become a solvent of choice in some areas, such as C-H functionalization chemistry. In this review, following a brief history of HFIP in organic synthesis and an overview of its physical properties, literature examples of organic reactions using HFIP as a solvent or an additive are presented, emphasizing the effect of solvent of each reaction.

Marine Cyclic Peptides: Antimicrobial Activity and Synthetic Strategies

Oceans are a rich source of structurally unique bioactive compounds from the perspective of potential therapeutic agents. Marine peptides are a particularly interesting group of secondary metabolites because of their chemistry and wide range of biological activities. Among them, cyclic peptides exhibit a broad spectrum of antimicrobial activities, including against bacteria, protozoa, fungi, and viruses. Moreover, there are several examples of marine cyclic peptides revealing interesting antimicrobial activities against numerous drug-resistant bacteria and fungi, making these compounds a very promising resource in the search for novel antimicrobial agents to revert multidrug-resistance. This review summarizes 174 marine cyclic peptides with antibacterial, antifungal, antiparasitic, or antiviral properties. These natural products were categorized according to their sources—sponges, mollusks, crustaceans, crabs, marine bacteria, and fungi—and chemical structure—cyclic peptides and depsipeptides. The antimicrobial activities, including against drug-resistant microorganisms, unusual structural characteristics, and hits more advanced in (pre)clinical studies, are highlighted. Nocathiacins I–III (91–93), unnarmicins A (114) and C (115), sclerotides A (160) and B (161), and plitidepsin (174) can be highlighted considering not only their high antimicrobial potency in vitro, but also for their promising in vivo results. Marine cyclic peptides are also interesting models for molecular modifications and/or total synthesis to obtain more potent compounds, with improved properties and in higher quantity. Solid-phase Fmoc- and Boc-protection chemistry is the major synthetic strategy to obtain marine cyclic peptides with antimicrobial properties, and key examples are presented guiding microbiologist and medicinal chemists to the discovery of new antimicrobial drug candidates from marine sources.

Total Synthesis and Structure Correction of the Cyclic Lipodepsipeptide Orfamide A

A total synthesis of the cyclic lipodepsipeptide natural product orfamide A was achieved. By developing a synthesis format using an aminoacid ester building block and SPPS protocol adaptation, a focused library of target compounds was obtained, in high yield and purity. Spectral and LC-HRMS data of all library members with the isolated natural product identified the 5 Leu residue to be d- and the 3'-OH group to be R-configured. The structural correction of orfamide A by chemical synthesis and analysis was confirmed by biological activity comparison in Chlamydomonas reinhardtii, which indicated compound configuration to be important for bioactivity. Acute toxicity was also found against Trypanosoma brucei, the parasite causing African sleeping sickness.

Greening the synthesis of peptide therapeutics: an industrial perspective

Solid-phase peptide synthesis (SPPS) is generally the method of choice for the chemical synthesis of peptides, allowing routine synthesis of virtually any type of peptide sequence, including complex or cyclic peptide products. Importantly, SPPS can be automated and is scalable, which has led to its widespread adoption in the pharmaceutical industry, and a variety of marketed peptide-based drugs are now manufactured using this approach. However, SPPS-based synthetic strategies suffer from a negative environmental footprint mainly due to extensive solvent use. Moreover, most of the solvents used in peptide chemistry are classified as problematic by environmental agencies around the world and will soon need to be replaced, which in recent years has spurred a movement in academia and industry to make peptide synthesis greener. These efforts have been centred around solvent substitution, recycling and reduction, as well as exploring alternative synthetic methods. In this review, we focus on methods pertaining to solvent substitution and reduction with large-scale industrial production in mind, and further outline emerging technologies for peptide synthesis. Specifically, the technical requirements for large-scale manufacturing of peptide therapeutics are addressed.

Sequence-defined positioning of amine and amide residues to control catechol driven wet adhesion

Catechol and amine residues, both abundantly present in mussel adhesion proteins, are known to act cooperatively by displacing hydration barriers before binding to mineral surfaces. In spite of synthetic efforts toward mussel-inspired adhesives, the effect of positioning of the involved functional groups along a polymer chain is not well understood. By using sequence-defined oligomers grafted to soft hydrogel particles as adhesion probes, we study the effect of catechol-amine spacing, as well as positioning relative to the oligomer terminus. We demonstrate that the catechol-amine spacing has a significant effect on adhesion, while shifting their position has a small effect. Notably, combinations of non-charged amides and catechols can achieve similar cooperative effects on adhesion when compared to amine and catechol residues. Thus, these findings provide a blueprint for the design of next generation mussel-inspired adhesives.

1,4-Benzenedimethanethiol (1,4-BDMT) as a scavenger for greener peptide resin cleavages

Aiming at elevating the environmental profile of the solid-phase peptide synthesis (SPPS) methodology by improving the quality of crude peptides that SPPS provides we assessed a series of benzylthiols (BTs) as scavengers for global deprotection/TFA cleavage of exenatide peptide resin accessed by Fmoc SPPS. In these studies we identified 1,4-BDMT as a scavenger that affords the peptide in higher quality than the standard aliphatic thiol reagents, not least in terms of the content of critical peptide impurities in the crude material. Further, 1,4-BDMT exhibited favorable UV detectability as well as stability and solubility in TFA. Finally, based on the MS assessment of the crude exenatide products herein we propose that thiol scavengers in the cleavage of Trp containing peptide resins do not minimize the content of Trp oxidants by means of inhibiting Trp oxidation but rather by forming a peptide–thiol adduct via a mechanism involving an attack of a thiol on an oxindolylalanine (Oia) impurity present in the crude material.

1,4-BDMT is a benign, non-odorous scavenger for peptide resin cleavages which provides crude peptides in higher quality than the aliphatic thiols used for this purpose.

Rapid and Quantitative De-tert-butylation for Poly(acrylic acid) Block Copolymers and Influence on Relaxation of Thermoassociated Transient Networks

The synthesis of charged polymers often requires the polymerization of protected monomers, followed by a polymer-analogous reaction to the polyelectrolyte product. We present a mild, facile method to cleave tert-butyl groups from poly(tert-butyl acrylate) blocks that yields poly(acrylic acid) (pAA) blocks free of traces of the ester. The reaction utilizes a slight excess of HCl in hexafluoroisopropanol (HFIP) at room temperature and runs to completion within 4 h. We compare deprotection in HFIP with the common TFA/DCM method and show that the latter does not yield clean pAA. We show the effect of complete tert-butyl cleavage on a ABA triblock copolymer, where poly(N-isopropylacrylamide) (pNIPAM) is A and pAA is B, by means of viscosimetry, DLS, and SAXS on solutions above overlap. The pNIPAM blocks dehydrate, and their increased self-affinity above the lower critical solution temperature (LCST) results in network formation by the triblocks. This manifests itself as an increase in viscosity and a slowing down of the first-order correlation function in light scattering. However, this stickering effect manifests itself exclusively when the pAA block is tert-butyl-free. Additionally, SAXS shows that the conformational properties of tert-butyl-free pAA copolymers are markedly different from those with residual esters. Thus, we illustrate a surprising effect of hydrophobic impurities that act across blocks and assert the usefulness of HCl/HFIP in pAA synthesis.

Synthesis and evaluation of aryliden- and hetarylidenfuranone derivatives of usnic acid as highly potent Tdp1 inhibitors

Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a repair enzyme for stalled DNA-topoisomerase 1 (Top 1) cleavage complexes and other 3'-end DNA lesions. Tdp1 is a promising target for anticancer therapy, since it can repair DNA lesions caused by Top1 inhibitors leading to drug resistance. Hence, Tdp1 inhibition should result in synergistic effect with Top1 inhibitors. Twenty nine derivatives of (+)-usnic acid were tested for in vitro Tdp1 inhibitory activity using a fluorescent-based assay. Excellent activity was obtained, with derivative 6m demonstrating the lowest IC₅₀ value of 25 nM. The established efficacy was verified using a gel-based assay, which gave close results to that of the fluorescent assay. In addition, molecular modeling in the Tdp1 substrate binding pocket suggested plausible binding modes for the active analogues. The synergistic effect of the Tdp1 inhibitors with topotecan, a Top1 poison in clinical use, was tested in two human cell lines, A-549 and HEK-293. Compounds 6k and 6x gave very promising results. In particular, 6x has a low cytotoxicity and an IC₅₀ value of 63 nM, making it a valuable lead compound for the development of potent Tdp1 inhibitors for clinical use.

O-GlcNAcase Fragment Discovery with Fluorescence Polarimetry

The attachment of the sugar N-acetyl-D-glucosamine (GlcNAc) to specific serine and threonine residues on proteins is referred to as protein O-GlcNAcylation. O-GlcNAc transferase (OGT) is the enzyme responsible for carrying out the modification, while O-GlcNAcase (OGA) reverses it. Protein O-GlcNAcylation has been implicated in a wide range of cellular processes including transcription, proteostasis, and stress response. Dysregulation of O-GlcNAc has been linked to diabetes, cancer, and neurodegenerative and cardiovascular disease. OGA has been proposed to be a drug target for the treatment of Alzheimer's and cardiovascular disease given that increased O-GlcNAc levels appear to exert a protective effect. The search for specific, potent, and drug-like OGA inhibitors with bioavailability in the brain is therefore a field of active research, requiring orthogonal high-throughput assay platforms. Here, we describe the synthesis of a novel probe for use in a fluorescence polarization based assay for the discovery of inhibitors of OGA. We show that the probe is suitable for use with both human OGA, as well as the orthologous bacterial counterpart from Clostridium perfringens, CpOGA, and the lysosomal hexosaminidases HexA/B. We structurally characterize CpOGA in complex with a ligand identified from a fragment library screen using this assay. The versatile synthesis procedure could be adapted for making fluorescent probes for the assay of other glycoside hydrolases.

Total Synthesis of Ecumicin

The first total synthesis of the potent anti-mycobacterial cyclic depsipeptide natural product ecumicin is described. Synthesis was achieved via a solid-phase strategy, incorporating the synthetic non-proteinogenic amino acids N-methyl-4-methoxy-l-tryptophan and threo-β-hydroxy-l-phenylalanine into the growing linear peptide chain. The synthesis employed key on-resin esterification and dimethylation steps as well as a final macrolactamization between the unusual N-methyl-4-methoxy-l-tryptophan unit and a bulky N-methyl-l-valine residue. The synthetic natural product possessed potent antimycobacterial activity against the virulent H37Rv strain of Mycobacterium tuberculosis (MIC₉₀ = 312 nM).

A Low-Molecular-Weight Gelator Composed of Pyrene and Fluorene Moieties for Effective Charge Transfer in Supramolecular Ambidextrous Gel

Charge-transfer (CT) gel materials obtained from low-molecular-weight (LMW) compounds through a supramolecular self-assembly approach have received fascinating attention by many researchers because of their interesting material property and potential applications. However, most of the CT gel materials constructed were of organogels while the construction of CT gels in the form of a hydrogel is a challenge because of the solubility issue in water, which considerably limits the use of CT hydrogels. Herein, for the first time, we report a new LMW gelator [N^α-(fluorenylmethoxycarbonyl)-N^ε-(δ-butyric-1-pyrenyl)-l-lysine, (FmKPy)], composed of two functional moieties such as fluorenylmethoxycarbonyl and pyrene, which not only parade both hydro and organo (ambidextrous) supramolecular gel formation but also exhibit CT ambidextrous gels when mixed with an electron acceptor such as 2,4,7-trinitro-9-fluorenone (TNF). This finding is significant as the established CT organogelator in the literature did not form an organogel in the absence of an electron acceptor or lose their gelation property upon the addition of the acceptor. CT between pyrene and TNF was confirmed by the color change as well as the appearance of the CT band in the visible region of the absorption spectrum. CT between FmKPy and TNF was supported by the solvent dilution method using tetrahydrofuran as the gel breaker and pyrene fluorescence quenching in the case compound containing pyrene and TNF. The morphology of FmKPy ambidextrous gels indicates the fibrous nature while the self-assembled structure is primarily stabilized by π-π stacking among fluorenyl and pyrenyl moieties and hydrogen bonding between amide groups. The FmKPy-TNF CT ambidextrous gel retains the fibrous nature; however, the size of the fibers changed. In FmKPy-TNF CT gels, TNF is intercalated between pyrene moieties in the self-assembled structure as confirmed by fluorescence quenching and powder X-ray diffraction. The FmKPy ambidextrous gel exhibits significant properties such as low minimum gelation concentration (MGC), thixotropic nature, pH stimuli response, and high thermal stability. Upon the addition of TNF, the FmKPy-TNF CT ambidextrous gel maintains all these properties except MGC which increased for FmKPy-TNF. Because pyrene-based LMW organogels have been developed widely for many applications while their hydrogels were limited, the current finding of the pyrene-based ambidextrous fluorescent gel with the CT property provides a wide opportunity to use FmKPy as a soft material maker and also for potential applications in fields like surface coating, three-dimensional printing, and so forth.

Understanding Tetrahydropyranyl as a Protecting Group in Peptide Chemistry

Tetrahydropyranyl (Thp) is recognized as a useful protecting group for alcohols in organic synthesis. It has several advantages, including low cost, ease of introduction, general stability to most non-acidic reagents, it confers good solubility, and the ease with which it can be removed if the functional group it protects requires manipulation. However, little attention has been paid to Thp in peptide chemistry. Provided here is a concise analysis of the Thp protection of various amino acid functionalities (OH, SH, NH and COOH) and its application to peptide synthesis. Thp is a useful moiety for the side-chain protection of serine, threonine and cysteine and is suitable for the Fmoc/tBu solid-phase peptide synthesis strategy. The immobilized version of 3,4-dihydro-2H-pyran, the so-called Ellman resin, is also discussed as a useful solid support for anchoring the side chains of serine, threonine and tryptophan residues.

First total synthesis of WLIP: on the importance of correct protecting group choice

Cyclic lipodepsipeptides (CLPs) are a group of metabolites produced by Pseudomonas bacteria, involved in various biological functions and displaying a wide range of properties, including antibacterial and antifungal activities. The white line-inducing principle (WLIP) is a member of the viscosin group featuring a Glu2 amino acid. Recently, a total synthesis of pseudodesmin A - the Gln2 counterpart of WLIP - was described, and we here expand this route to Glu2 containing CLPs. We report the first total synthesis of WLIP and at the same time establish that the Gln2 to Glu2 substitution has an adverse impact on the crude purity and overall yield. A comparative study of different CLP analogues reveals the importance of the nature of the Glx2 protecting group in determining these outcomes. Replacement of the conventional tBu protecting group by the larger benzyl group for the Glu residue in our synthesis strategy indeed resulted in an improved conversion. Next to achieving the first WLIP total synthesis, we thus show the importance of a careful choice of protecting groups for the success of this type of solid-phase synthesis approaches towards CLPs.

Chemoselective Cleavage of p-Methoxybenzyl and 2-Naphthylmethyl Ethers Using a Catalytic Amount of HCl in Hexafluoro-2-propanol

A new, fast, mild and chemoselective deprotection method to cleave p-methoxybenzyl and 2-naphthylmethyl ethers using catalytic amounts of hydrochloric acid in a 1:1 mixture of hexafluoro-2-propanol (HFIP) and methylene chloride (DCM) is described. The scope of the methodology becomes apparent from 14 examples of orthogonally protected monosaccharides that are subjected to HCl/HFIP treatment. The applicability of the HCl/HFIP method is illustrated by the synthesis of a sulfated β-mannuronic acid disaccharide.

Tetrahydropyranyl, a nonaromatic acid-labile Cys protecting group for Fmoc peptide chemistry

Tetrahydropyranyl (Thp), which exploits the concept of being an S,O-acetal nonaromatic protecting group for cysteine, has been shown to be superior to Trt, Dpm, Acm, and StBu in solid-phase peptide synthesis using the Fmoc/tBu strategy. Thus, Cys racemization and C-terminal 3-(1-piperidinyl)alanine formation were minimized when the Cys was protected with Thp. This nonaromatic protecting group also improved the solubility of Cys-containing protected peptides.

Chemical synthesis of proteins using peptide hydrazides as thioester surrogates

This protocol provides a detailed procedure for the chemical synthesis of proteins through native chemical ligation of peptide hydrazides. The two crucial stages of this protocol are (i) the solid-phase synthesis of peptide hydrazides via Fmoc chemistry and (ii) the native chemical ligation of peptide hydrazides through in situ NaNO2 activation and thiolysis. This protocol may be of help in the synthesis of proteins that are not easily produced by recombinant technology and that include acid-sensitive modifications; it also does not involve the use of hazardous HF. The utility of the protocol is shown for the total synthesis of 140-aa-long α-synuclein, a protein that has an important role in the development of Parkinson's disease. The whole synthesis of the target protein α-synuclein in milligram scale takes ~30 working days.

Overcoming product inhibition in catalysis of the intramolecular Schmidt reaction

A method for carrying out the intramolecular Schmidt reaction of alkyl azides and ketones using a substoichiometric amount of catalyst is reported. Following extensive screening, the use of the strong hydrogen-bond-donating solvent hexafluoro-2-propanol was found to be consistent with low catalyst loadings, which ranged from 2.5 mol % for favorable substrates to 25 mol % for more difficult cases. Reaction optimization, broad substrate scope, and preliminary mechanistic studies of this improved version of the reaction are described.

Stereoselective ribosylation of amino acids

The glycosylation properties of ribofuranosyl N-phenyltrifluoroacetimidates toward carboxamide side chains of asparagine and glutamine were investigated. Conditions were found that promote nearly exclusive formation of the α-anomerically configured N-glycosides. The strategy allows for the synthesis of Fmoc-amino acids suitably modified for the preparation of ADP-ribosylated peptides. Furthermore, ribosylation of serine with these donors proved to be completely α-selective, and for the first time, α-ribosylated glutamic and aspartic acid, the naturally occurring sites for poly-ADP-ribosylation, were synthesized.