Synthesis Of Cyclic Peptides Research Articles

Constructing Cyclic Peptides Using an On-Tether Sulfonium Center

In recent years, cyclic peptides have attracted increasing attention in the field of drug discovery due to their excellent biological activities, and, as a consequence, they are now used clinically. It is, therefore, critical to seek effective strategies for synthesizing cyclic peptides to promote their application in the field of drug discovery. This paper reports a detailed protocol for the efficient synthesis of cyclic peptides using on-resin or intramolecular (intermolecular) bisalkylation. Using this protocol, linear peptides were synthesized by taking advantage of solid-phase peptide synthesis with cysteine (Cys) and methionine (Met) coupled simultaneously on the resin. Further, cyclic peptides were synthesized via bisalkylation between Met and Cys using a tunable tether and an on-tether sulfonium center. The whole synthetic route can be divided into three major processes: the deprotection of Cys on the resin, the coupling of the linker, and the cyclization between Cys and Met in a trifluoroacetic acid (TFA) cleavage solution. Furthermore, inspired by the reactivity of the sulfonium center, a propargyl group was attached to the Met to trigger thiol-yne addition and form a cyclic peptide. After that, the crude peptides were dried and dissolved in acetonitrile, separated, and then purified by high-performance liquid chromatography (HPLC). The molecular weight of the cyclic peptide was confirmed by liquid chromatography-mass spectrometry (LC-MS), and the stability of the cyclic peptide combination with the reductant was further confirmed using HPLC. In addition, the chemical shift in the cyclic peptide was analyzed by 1H nuclear magnetic resonance (1H NMR) spectra. Overall, this protocol aimed to establish an effective strategy for synthesizing cyclic peptides.

Synthetic Tools that Enable Synthesis and Understanding of Bioactive Macrocycles

AbstractThis article aims to summarizing the evolution of my lab’s research efforts in making and understanding peptide macrocycles. What started as a curiosity-driven investigation of amphoteric structures in multicomponent reactions, has turned into a sustained exploration of complex macrocyclic peptides. As part of this journey, my students and I have introduced new tools that enable chemical synthesis and property-driven optimization of cyclic peptides. These contributions are expected to be relevant in the areas of drug discovery and biological probe design.

Synthesis of Cyclic Peptides in SPPS with Npb-OH Photolabile Protecting Group.

Significant efforts have been made in recent years to identify more environmentally benign and safe alternatives to side-chain protection and deprotection in solid-phase peptide synthesis (SPPS). Several protecting groups have been endorsed as suitable candidates, but finding a greener protecting group in SPPS has been challenging. Here, based on the 2-(o-nitrophenyl) propan-1-ol (Npp-OH) photolabile protecting group, a structural modification was carried out to synthesize a series of derivatives. Through experimental verification, we found that 3-(o-Nitrophenyl) butan-2-ol (Npb-OH) had a high photo-release rate, high tolerance to the key conditions of Fmoc-SPPS (20% piperidine DMF alkaline solution, and pure TFA acidic solution), and applicability as a carboxyl-protective group in aliphatic and aromatic carboxyl groups. Finally, Npb-OH was successfully applied to the synthesis of head–tail cyclic peptides and side-chain–tail cyclic peptides. Moreover, we found that Npb-OH could effectively resist diketopiperazines (DKP). The α-H of Npb-OH was found to be necessary for its photosensitivity in comparison to 3-(o-Nitrophenyl)but-3-en-2-ol (Npbe-OH) during photolysis-rate verification.

Solid‐Phase Synthesis of Macrocyclic Peptides via Side‐Chain Anchoring of the Ornithine δ‐Amine

AbstractCyclic peptides represent a popular class of macrocyclic drug candidates and therefore their solid phase synthesis has attracted much attention. In this contribution we present an efficient method of side‐chain anchoring for ornithine and lysine residues to be used in the standard Fmoc‐based synthesis of cyclic peptides via on‐resin cyclization. We demonstrate that the side chain of ornithine and lysine protected with N‐Boc‐group can efficiently be converted to the isocyanate which is then immobilized on Wang‐type resin in almost quantitative yield. We further show the synthesis of four biologically active cyclic peptides employing the side chain ornithine anchoring. Our method is at least on a par with the previously reported methodologies in terms of yield and the purity of the final products and is arguably operationally more straightforward.

An Efficient Approach for the Design and Synthesis of Antimicrobial Peptide-Peptide Nucleic Acid Conjugates.

Peptide-Peptide Nucleic Acid (PNA) conjugates targeting essential bacterial genes have shown significant potential in developing novel antisense antimicrobials. The majority of efforts in this area are focused on identifying different PNA targets and the selection of peptides to deliver the peptide-PNA conjugates to Gram-negative bacteria. Notably, the selection of a linkage strategy to form peptide-PNA conjugate plays an important role in the effective delivery of PNAs. Recently, a unique Cysteine- 2-Cyanoisonicotinamide (Cys-CINA) click chemistry has been employed for the synthesis of cyclic peptides. Considering the high selectivity of this chemistry, we investigated the efficiency of Cys-CINA conjugation to synthesize novel antimicrobial peptide-PNA conjugates. The PNA targeting acyl carrier protein gene (acpP), when conjugated to the membrane-active antimicrobial peptides (polymyxin), showed improvement in antimicrobial activity against multidrug-resistant Gram-negative Acinetobacter baumannii. Thus, indicating that the Cys-CINA conjugation is an effective strategy to link the antisense oligonucleotides with antimicrobial peptides. Therefore, the Cys-CINA conjugation opens an exciting prospect for antimicrobial drug development.

Development of a general bioluminescent activity assay for peptide ligases.

In recent years, some peptide ligases have been identified, such as bacterial sortases and certain plant asparaginyl or prolyl endopeptidases. Peptide ligases have wide applications in protein labelling and cyclic peptide synthesis. To characterize various known peptide ligases or identify new ones, we propose a general bioluminescent activity assay via the genetic fusion of a recognition motif of peptide ligase(s) to the C-terminus of an inactive large NanoLuc fragment (LgBiT) and the chemical introduction of a nucleophilic motif preferred by the peptide ligase(s) to the N-terminus of the low-affinity SmBiT complementation tag. After the inactive ligation version LgBiT protein was ligated with the low-affinity ligation version SmBiT tag by the expected peptide ligase(s), its luciferase activity would be restored and could be quantified sensitively according to the measured bioluminescence. In the present study, we first validated the bioluminescent activity assay using bacterial sortase A and plant-derived butelase-1. Subsequently, we screened novel peptide ligases from crude extracts of selected plants using two LgBiT-SmBiT ligation pairs. Among 80 common higher plants, we identified that five of them likely express asparaginyl endopeptidase-type peptide ligase and four of them likely express prolyl endopeptidase-type peptide ligase, suggesting that peptide ligases are not so rare in higher plants and more of them await discovery. The present bioluminescent activity assay is ultrasensitive, convenient for use, and resistant to protease interference, and thus would have wide applications for characterizing known peptide ligases or screening new ones from various sources in future studies.

Gold(I)-Mediated Rapid Cyclization of Propargylated Peptides via Imine Formation.

In fundamental research and drug discovery, there is still a need for effective and straightforward chemical approaches for generating cyclic peptides. The divergent synthesis of cyclic peptides remains a challenge, in particular when cyclization is carried out in the presence of unprotected side chains and a nonpeptidic component within the cycle is needed. Herein, we describe a novel and efficient strategy based on Au(I)-mediated cyclization of unprotected peptides through rapid (30–60 min) amine addition on a propargyl group to generate an imine linkage. Mechanistic insights reveal that the reaction proceeds via regioselective Markovnikov’s addition of the amine on the Au(I)-activated propargyl. This strategy was successfully applied to prepare efficiently (56–94%) over 35 diverse cyclic peptides having different sequences and lengths. We have also achieved stereoselective reduction of cyclic imines employing chiral ligands. The practicality of our method was extended for the synthesis of cyclic peptides that bind Lys48-linked di-ubiquitin chains with high affinity, leading to apoptosis of cancer cells.

Chemical Synthesis and Cell-Free Expression of Thiazoline Ring-Bridged Cyclic Peptides and Their Properties on Biomembrane Permeability

Abstract Cyclic peptides that exhibit biomembrane permeability provide a useful platform in the development of peptide drugs. Here, the reaction characteristics and versatility of a novel type of cyclic peptide having a thiazoline ring structure in the main chain were investigated. The thiazoline ring-bridged cyclic peptides were chemically synthesized by the intramolecular cyclization of linear peptides composed of N-terminal Cys and a non-natural amino acid having a cyano group on the side chain. The thiazoline ring-bridged cyclic peptides had higher model membrane permeability than amide- and thioether-bridged cyclic peptides with similar amino acid sequences. By comparing the solution structures, the factors that contribute to the higher membrane permeability were examined. In addition, the present peptide cyclization was applied to a cell-free translation system. The expression of peptides having the cyanated non-natural amino acids and subsequent spontaneous cyclization were successfully achieved.

Head-to-tail cyclization for the synthesis of naturally occurring cyclic peptides on organophosphorus small-molecular supports

4,4′-bis(diphenylphosphinyloxyl) diphenyl ketoxime and 4-diphenyl phospholoxy benzyl alcohol were designed and prepared as supports for peptide synthesis. The total synthesis of cyclic peptides in a resin-free manner was successfully demonstrated.

Macrocylases as synthetic tools for ligand synthesis: enzymatic synthesis of cyclic peptides containing metal-binding amino acids.

Improving the sustainability of synthesis is a major goal in green chemistry, which has been greatly aided by the development of asymmetric transition metal catalysis. Recent advances in asymmetric catalysis show that the ability to control the coordination sphere of substrates can lead to improvements in enantioselectivity and activity, in a manner resembling the operation of enzymes. Peptides can be used to mimic enzyme structures and their secondary interactions and they are easily accessible through solid-phase peptide synthesis. Despite this, cyclic peptides remain underexplored as chiral ligands for catalysis due to synthetic complications upon macrocyclization. Here, we show that the solid-phase synthesis of peptides containing metal-binding amino acids, bipyridylalanine (1), phenyl pyridylalanine (2) and N,N-dimethylhistidine (3) can be combined with peptide macrocylization using peptide cyclase 1 (PCY1) to yield cyclic peptides under mild conditions. High conversions of the linear peptides were observed (approx. 90%) and the Cu-bound cyclo(FSAS(1)SSKP) was shown to be a competent catalyst in the Friedel-Crafts/conjugate addition of indole. This study shows that PCY1 can tolerate peptides containing amino acids with classic inorganic and organometallic ligands as side chains, opening the door to the streamlined and efficient development of cyclic peptides as metal ligands.

Three Methods for the Solution Phase Synthesis of Cyclic Peptides.

Cyclic peptides, which often exhibit interesting biological properties, can be obtained by macrolactamization of adequately protected linear peptide chains. Because of the remarkable biological properties, methods for the efficient cyclization of peptides are of high interest. We herein describe threedifferent protocols for the cyclization of peptides and depsipeptides via amide bond formation. These methods can, in principal, be applied to any linear peptide chain.

Nγ -Hydroxyasparagine: A Multifunctional Unnatural Amino Acid That is a Good P1 Substrate of Asparaginyl Peptide Ligases.

Peptidyl asparaginyl ligases (PALs) are powerful tools for peptide macrocyclization. Herein, we report that a derivative of Asn, namely Nγ -hydroxyasparagine or Asn(OH), is an unnatural P1 substrate of PALs. By Asn(OH)-mediated cyclization, we prepared cyclic peptides as new matrix metalloproteinase 2 (MMP2) inhibitors displaying the hydroxamic acid moiety of Asn(OH) as the key pharmacophore. The most potent cyclic peptide (Ki =2.8±0.5 nM) was built on the hyperstable tetracyclic scaffold of rhesus theta defensin-1. The Asn(OH) residue in the cyclized peptides can also be readily oxidized to Asp. By this approach, we synthesized several bioactive Asp-containing cyclic peptides (MCoTI-II, kB2, SFTI, and integrin-targeting RGD peptides) that are otherwise difficult targets for PAL-catalyzed cyclization owing to unfavorable kinetics of the P1-Asp substrates. This study demonstrates that substrate engineering is a useful strategy to expand the application of PAL ligation in the synthesis of therapeutic cyclic peptides.

Nγ‐Hydroxyasparagine: A Multifunctional Unnatural Amino Acid That is a Good P1 Substrate of Asparaginyl Peptide Ligases

AbstractPeptidyl asparaginyl ligases (PALs) are powerful tools for peptide macrocyclization. Herein, we report that a derivative of Asn, namely Nγ‐hydroxyasparagine or Asn(OH), is an unnatural P1 substrate of PALs. By Asn(OH)‐mediated cyclization, we prepared cyclic peptides as new matrix metalloproteinase 2 (MMP2) inhibitors displaying the hydroxamic acid moiety of Asn(OH) as the key pharmacophore. The most potent cyclic peptide (Ki=2.8±0.5 nM) was built on the hyperstable tetracyclic scaffold of rhesus theta defensin‐1. The Asn(OH) residue in the cyclized peptides can also be readily oxidized to Asp. By this approach, we synthesized several bioactive Asp‐containing cyclic peptides (MCoTI‐II, kB2, SFTI, and integrin‐targeting RGD peptides) that are otherwise difficult targets for PAL‐catalyzed cyclization owing to unfavorable kinetics of the P1‐Asp substrates. This study demonstrates that substrate engineering is a useful strategy to expand the application of PAL ligation in the synthesis of therapeutic cyclic peptides.

Fast and Selective Reaction of 2-Benzylacrylaldehyde with 1,2-Aminothiol for Stable N-Terminal Cysteine Modification and Peptide Cyclization.

N-terminal cysteine (Cys)-specific reactions have been exploited for protein and peptide modifications. However, existing reactions for N-terminal Cys suffer from low reaction rate, unavoidable side reactions, or poor stability for reagents or products. Herein we report a fast, efficient, and selective conjugation between 2-benzylacrylaldehyde (BAA) and 1,2-aminothiol, which involves multistep reactions including aldimine condensation, Michael addition, and reduction of imine by NaBH3CN. This conjugation proceeds with a rate constant of ∼2700 M-1 s-1 under neutral condition at room temperature to produce a pair of seven-membered ring diastereoisomers, which are stable under neutral and acidic conditions. This method enables the selective modifications of the N-terminal Cys residue without interference from the internal Cys and lysine residues, providing a useful alternative to existing approaches for site-specific peptide or protein modifications and synthesis of cyclic peptides.

Use of a Removable Backbone Modification Strategy to Prevent Aspartimide Formation in the Synthesis of Asp Lactam Cyclic Peptides†

Main observation and conclusionThe synthesis of an Asp lactam derivative of A‐183, a selective inhibitor of Factor 7a with good anticoagulant and antithrombotic activity, is described. Our synthesis depends on the use of a removable backbone modification (RBM) strategy to prevent aspartimide formation, which thwarted all attempts to synthesize this target using direct solid‐phase peptide synthesis. Validation of the RBM strategy in the synthesis of a second Asp lactam derivative was also accomplished. The RBM strategy is therefore proposed as a general method for the synthesis of Asp lactam cyclic peptides.

Organometallic AlaM reagents for umpolung peptide diversification

Selective modifications of peptides and proteins have emerged as a promising strategy to develop novel mechanistic probes and prepare compounds with translational potentials. Here, we report alanine carbastannatranes AlaSn as a universal synthon in various C-C and C-heteroatom bond-forming reactions. These reagents are compatible with peptide manipulation techniques and can undergo chemoselective conjugation in minutes when promoted by Pd(0). Despite their increased nucleophilicity and propensity to transfer the alkyl group, C(sp3)-C(sp2) coupling with AlaSn can be accomplished at room temperature under buffered conditions (pH 6.5-8.5). We also show that AlaSn can be easily transformed into several canonical L- and D-amino acids in arylation, acylation, and etherification reactions. Furthermore, AlaSn can partake in macrocyclizations exemplified by the synthesis of medium size cyclic peptides with various topologies. Taken together, metalated alanine AlaSn demonstrates unparalleled scope and represents a new type of umpolung reagents suitable for structure-activity relationship studies and peptide diversification.

Total Synthesis of Hytramycin V, an Antibiotic Cyclopeptide

Abstract The total synthesis of the piperazic acid-containing antibiotic cyclic peptide, hytramycin V, has been achieved. Unexpected cleavage of the peptide bond was observed during the synthesis of a pentapeptide, we then successfully found that the addition of 2,6-di-tert-butylpyridine (2,6-DTBP) was effective to prevent the cleavage upon acylation with AgCN, leading to a pentapeptide in excellent yield. The synthesis of a hexapeptide, followed by global deprotection of the protecting groups provided a cyclization precursor. Finally, macrolactamization of the precursor using T3P® under high-dilution conditions furnished the desired natural product, hytramycin V. The synthesis of the enantiomer of hytramycin V was also achieved, and no difference between the enantiomers was observed in the evaluation of their antibacterial activity against Mycobacterium strains, revealing the fact that the potency of the activity was not dependent on the chirality of the cyclopeptide backbone.

Natural Thiazoline-Based Cyclodepsipeptides from Marine Cyanobacteria: Chemistry, Bioefficiency and Clinical Aspects.

Peptides and peptide-based therapeutics are biomolecules that demarcate a significant chemical space to bridge small molecules with biological therapeutics, such as antibodies, recombinant proteins, and protein domains. Cyclooligopeptides and depsipeptides, particularly cyanobacteria-derived thiazoline-based polypeptides (CTBCs), exhibit a wide array of pharmacological activities due to their unique structural features and interesting bioactions, which furnish them as promising leads for drug discovery. In the present study, we comprehensively review the natural sources, distinguishing chemistries, and pertinent bioprofiles of CTBCs. We analyze their structural peculiarities counting the mode of actions for biological portrayals which render CTBCs as indispensable sources for emergence of prospective peptide-based therapeutics. In this milieu, metal organic frameworks and their biomedical applications are also briefly discussed. To boot, the challenges, approaches, and clinical status of peptide-based therapeutics are conferred. Based on these analyses, CTBCs can be appraised as ideal drug targets that have always remained a challenge for traditional small molecules, like those involved in protein- protein interactions or to be developed as potential cancer-targeting nanomaterials. Cyclization-induced reduced conformational freedom of these cyclooligopeptides contribute to improved metabolic stability and binding affinity to their molecular targets. Clinical success of several cyclic peptides provokes the large library-screening and synthesis of natural product-like cyclic peptides to address the unmet medical needs. CTBCs can be considered as the most promising lead compounds for drug discovery. Adopting the amalgamation of advanced biological and biopharmaceutical strategies might endure these cyclopeptides to be prospective biomolecules for futuristic therapeutic applications in the coming times.

Synthesis of Cyclic Peptides by Cooperative Stapling of Native Peptides at Lysine and Tyrosine or Arginine

Synthesis of Cyclic Peptides by Cooperative Stapling of Native Peptides at Lysine and Tyrosine or Arginine

Silver-Promoted Synthesis of Cyclic Peptides by Ring Expansion

Key words silver catalysis - thiolactams - ring expansion - cyclic peptides