Synthesis of Cyclic Peptides

Synthesis of Cyclopeptides Analogues of Natural Products and Evaluation as Herbicides and Inhibitors of Cyanobacteria

Natural products derived from plants or microorganisms have been considered as eco-friendly herbicides with application in crop protection. Several natural cyclopeptides have been reported as herbicides, while others have been identified as inhibitors of cyanobacteria. In this work, the syntheses of cyclotetrapeptides and cyclopentapeptides analogues of natural products were successfully performed by solid-phase peptide synthesis of their linear precursor and solution-phase macrolactamization. Four of the obtained peptides and cyclopeptides present phytotoxicity with more than 70% of radicle growth inhibition at 67 μg/mL. In addition, evaluation of 20 peptides and cyclopeptides, as inhibitors of cyanobacteria, rendered five active compounds that reduced the concentration of microcystins in the culture medium.

Total and chemoenzymatic synthesis of the lipodepsipeptide rhizomide A

Rhizomides are a family of depsipeptide macrolactones synthesized by a non-ribosomal peptide synthetase (NRPS) encoded in the genome of Paraburkholderia rhizoxinica str. HKI 454. In this study, the total and chemoenzymatic synthesis of the depsipeptide rhizomide A is described. Rhizomide A was generated through macrolactamization while thelinear C-terminal N-acetylcysteamine (SNAC) thioester substrate was synthesized through a C-terminal thioesterification strategy. It was shown that the rhizomide A thioesterase (RzmA-TE) is an active macrocyclization catalyst, allowing the chemoenzymatic synthesis of rhizomide A.This work further showcases the biocatalytic power of TEs in accessing complex macrocyclic natural products.

Total Synthesis and Antimalarial Activity of Dominicin, a Cyclic Octapeptide from a Marine Sponge

Dominicin, a macrocyclic peptide isolated from the marine sponge Eurypon laughlini, has been synthesized for the first time by solid-phase peptide synthesis. The strategy uses oxime resin and takes advantage of the nucleophile susceptibility of the oxime ester bond. The synthesis relies on the preparation of a linear precursor followed by on-resin head-to-tail concomitant cyclization-cleavage. This is the first report of the use of a Boc/O^tBu biorthogonal protection strategy on oxime resin to facilitate concomitant N-terminal and side-chain tert-butyl ether deprotection cyclization of unprotected peptides. Also, we report the first antimalarial investigation of dominicin. Interestingly, the natural macrocyclic peptide demonstrates effective low micromolar activity (1.8 μM) against the chloroquine-mefloquine-pyrimethamine-resistant Dd2 strain of Plasmodium falciparum.

Cyclic Tetrapeptides from Nature and Design: A Review of Synthetic Methodologies, Structure, and Function

Small cyclic peptides possess a wide range of biological properties and unique structures that make them attractive to scientists working in a range of areas from medicinal to materials chemistry. However, cyclic tetrapeptides (CTPs), which are important members of this family, are notoriously difficult to synthesize. Various synthetic methodologies have been developed that enable access to natural product CTPs and their rationally designed synthetic analogues having novel molecular structures. These methodologies include the use of reversible protecting groups such as pseudoprolines that restrict conformational freedom, ring contraction strategies, on-resin cyclization approaches, and optimization of coupling reagents and reaction conditions such as temperature and dilution factors. Several fundamental studies have documented the impacts of amino acid configurations, N-alkylation, and steric bulk on both synthetic success and ensuing conformations. Carefully executed retrosynthetic ring dissection and the unique structural features of the linear precursor sequences that result from the ring dissection are crucial for the success of the cyclization step. Other factors that influence the outcome of the cyclization step include reaction temperature, solvent, reagents used as well as dilution levels. The purpose of this review is to highlight the current state of affairs on naturally occurring and rationally designed cyclic tetrapeptides, including strategies investigated for their syntheses in the literature, the conformations adopted by these molecules, and specific examples of their function. Using selected examples from the literature, an in-depth discussion of the synthetic techniques and reaction parameters applied for the successful syntheses of 12-, 13-, and 14-membered natural product CTPs and their novel analogues are presented, with particular focus on the cyclization step. Selected examples of the three-dimensional structures of cyclic tetrapeptides studied by NMR, and X-ray crystallography are also included.

Antinociceptive activity of thiazole-containing cyclized DAMGO and Leu-(Met) enkephalin analogs

Numerous studies demonstrate the promise of opioid peptides as analgesics, but poor oral bioavailability has limited their therapeutic development. This study sought to increase the oral bioavailability of opioid peptides by cyclization, using Hantzsch-based macrocyclization strategies to produce two new series of cyclized DAMGO and Leu/Met-enkephalin analogs. Opioid receptor affinity and selectivity for compounds in each series were assessed in vitro with radioligand competition binding assays. Compounds demonstrated modest affinity but high selectivity for the mu, delta, and kappa opioid receptors (MOR, DOR and KOR), while selectivity for mu opioid receptors varied by structure. Antinociceptive activity of each compound was initially screened in vivo following intracerebroventricular (i.c.v.) administration and testing in the mouse 55 °C warm-water tail-withdrawal test. The four most active compounds were then evaluated for dose- and time-dependent antinociception, and opioid receptor selectivity in vivo. Cyclic compounds 1924-10, 1936-1, 1936-7, and 1936-9 produced robust and long- lasting antinociception with ED₅₀ values ranging from 0.32-0.75 nmol following i.c.v. administration mediated primarily by mu- and delta-opioid receptor agonism. Compounds 1924-10, 1936-1 and 1936-9 further displayed significant time-dependent antinociception after oral (10 mg kg^-1, p.o.) administration. A higher oral dose (30 mg kg^-1. p.o.) of all four cyclic peptides also reduced centrally-mediated respiration, suggesting successful penitration into the CNS. Overall, these data suggest cyclized opioid peptides synthesized by a Hantzsch-based macrocyclization strategy can retain opioid agonist activity to produce potent antinociception in vivo while conveying improved bioavailability following oral administration.

Photocyclization of Tetra- and Pentapeptides Containing Adamantylphthalimide and Phenylalanines: Reaction Efficiency and Diastereoselectivity

A series of tetrapeptides and pentapeptides was synthesized bearing a phthalimide chromophore at the N-terminus. The C-terminus of the peptides was strategically substituted with an amino acid, Phe, Phe(OMe), or Phe(OMe)₂ characterized by different oxidation potentials. The photochemical reactivity of the peptides was investigated by preparative irradiation and isolation of photoproducts, as well as with laser flash photolysis. Upon photoexcitation, the peptides undergo photoinduced electron transfer (PET) and decarboxylation, followed by diastereoselective cyclization with the retention of configuration for tetrapeptides or inversion of configuration for pentapeptides. Molecular dynamics (MD) simulations and NOE experiments enabled assignment of the stereochemistry of the cyclic peptides. MD simulations of the linear peptides disclosed conformational reasons for the observed diastereoselectivity, being due to the peptide backbone spatial orientation imposed by the Phe amino acids. The photochemical efficiency for the decarboxylation and cyclization is not dependent on the peptide length, but it depends on the oxidation potential of the amino acid at the C-terminus. The results described herein are particularly important for the rational design of efficient photochemical reactions for the preparation of cyclic peptides with the desired selectivity.

Recent Reports of Solid-Phase Cyclohexapeptide Synthesis and Applications

Macrocyclic peptides are privileged scaffolds for drug development and constitute a significant portion of macrocyclic drugs on the market today in fields spanning from infectious disease to oncology. Developing orally bioavailable peptide-based drugs remains a challenging task; however, macrocyclization of linear peptides can be an effective strategy to improve membrane permeability, proteolytic stability, oral bioavailability, and overall drug-like characteristics for this class. Significant advances in solid-phase peptide synthesis (SPPS) have enabled the efficient construction of macrocyclic peptide and peptidomimetic libraries with macrolactamization being performed on-resin or in solution phase. The primary goal of this review is to summarize solid-phase cyclohexapeptide synthesis using the on-resin and solution-phase macrocyclization methodologies published since 2013. We also highlight their broad applications ranging from natural product total synthesis, synthetic methodology development, and medicinal chemistry, to drug development and analyses of conformational and physiochemical properties.

Comparative conformational analyses and molecular dynamics studies of glycylglycine methyl ester and glycylglycine N-methylamide

Amide–ester substitution and water models significantly alter conformational and solvation properties of glycine–glycine dipeptides.

The Pseudoproline Approach to Peptide Cyclization

The development of efficient methods for the synthesis of cyclic peptides is of interest because of the many potential applications of this class of molecule. Pseudoprolines are derived from serine, threonine, and cysteine and can be used as traceless turn-inducers to facilitate the cyclization of a wide range of linear peptide precursors. The incorporation of a pseudoproline into the peptide to be cyclized generally results in a cyclization reaction that proceeds more quickly and with higher yield than that of an analogous sequence without the pseudoproline. Installation of a pseudoproline at the C-terminal position of a linear peptide sequence has also been shown to eliminate any epimerization of this residue during the reaction. Following pseudoproline-mediated cyclization, these turn-inducers can be removed on treatment with acid in a similar manner to other protecting groups to provide the native peptide sequence, and in the case of cysteine-derived pseudoprolines, the resulting cysteine can be readily converted into alanine through desulfurization. These traceless turn-inducers have been successfully used in the synthesis of cyclic peptides containing either serine, threonine, cysteine or alanine residues.

Isolation of a Cyclic Depsipetide, Aspergillicin F, and Synthesis of Aspergillicins with Innate Immune-Modulating Activity

Innate immunity is the front line of self-defense against microbial infection. After searching for natural compounds that regulate innate immunity using an ex vivo Drosophila culture system, we identified a new cyclic depsipeptide, aspergillicin F, from the fungus Aspergillus sp., as an innate immune suppressor. The total synthesis and biological evaluation of the aspergillicin family, including aspergillicin F, were performed, revealing that slight structural differences in the side chains of amino acid residues alter innate immunity-regulating activity.

Serine/threonine ligation for natural cyclic peptide syntheses

The effectiveness of Ser/Thr ligation-mediated peptide cyclization has been demonstrated by the synthesis of cyclic peptide natural products, such as daptomycin, cyclomontanin B, yunnanin C and mahafacyclin B.

Synthesis of trifunctional thiazolyl amino acids and their use for the solid-phase synthesis of small molecule compounds and cyclic peptidomimetics

Chiral thiazolyl amino acid building blocks for the solid-phase synthesis of small molecules, peptides, and cyclic peptides have been designed and synthesized starting from Fmoc protected asparagine and glutamine. In efforts to demonstrate the usefulness and validity of such building blocks, a small library of 16 new thiazole containing small molecules has been prepared and characterized. Additionally, we report the use of the newly prepared trifunctional thiazolyl glutamine for the on-resin, head-to-tail synthesis of cyclic peptides.

Flexible or fixed: a comparative review of linear and cyclic cancer-targeting peptides

Peptides can serve as versatile cancer-targeting ligands and have been used for clinically relevant applications such as cancer imaging and therapy. A current and long-standing focus within peptide research is the creation of structurally constrained peptides generated through cyclization. Cyclization is envisioned to enhance the selective binding, uptake, potency and stability of linear precursors. This review compares closely related linear and cyclic peptides in these respects. Peptide cyclization generally improves the selective binding and stability of linear precursors; however, not all cyclization strategies and constrained geometries enhance these properties to the same extent. In some instances, linear analogues actually have better cancer-targeting properties compared with their cyclic counterparts. Although cyclization does not necessarily improve the cancer-targeting properties of linear analogues, cyclic peptides may obtain properties that allow them to be used for additional applications. This review aims to convey the advantages and limitations of cyclic cancer-targeting peptides.

Solid-phase peptide head-to-side chain cyclodimerization: discovery of C(2)-symmetric cyclic lactam hybrid α-melanocyte-stimulating hormone (MSH)/agouti-signaling protein (ASIP) analogues with potent activities at the human melanocortin receptors

A novel hybrid melanocortin pharmacophore was designed based on the pharmacophores of the agouti-signaling protein (ASIP), an endogenous melanocortin antagonist, and α-melanocyte-stimulating hormone (α-MSH), an endogenous melanocortin agonist. The designed hybrid ASIP/MSH pharmacophore was explored in monomeric cyclic, and cyclodimeric templates. The monomeric cyclic disulfide series yielded peptides with hMC3R-selective non-competitive binding affinities. The direct on-resin peptide lactam cyclodimerization yielded nanomolar range (25-120 nM) hMC1R-selective full and partial agonists in the cyclodimeric lactam series which demonstrates an improvement over the previous attempts at hybridization of MSH and agouti protein sequences. The secondary structure-oriented pharmacophore hybridization strategy will prove useful in development of unique allosteric and orthosteric melanocortin receptor modulators. This report also illustrates the utility of peptide cyclodimerization for the development of novel GPCR peptide ligands.

Depsipeptide synthesis

Naturally occurring cyclic depsipeptides, peptides that contain one or more ester bonds in addition to the amide bonds, have emerged as an important source of pharmacologically active compounds or promising lead structures for the development of novel synthetically derived drugs. This class of natural products has been found in many organisms, such as fungi, bacteria, and marine organisms. It is very well known that cyclic depsipeptides and their derivatives exhibit a diverse spectrum of biological activities, including insecticidal, antiviral, antimicrobial, antitumor, tumor-promotive, anti-inflammatory, and immunosuppressive actions. However, they have shown the greatest therapeutic potential as anticancer and particularly antimicrobial agents. Difficulties associated with isolation and purification of larger quantities of this class of natural products and, particularly, unlimited access to their synthetic analogs significantly hampered cyclic depsipeptides exploitation as lead compounds for development of new drugs. As an alternative, total solution or solid-phase peptide synthesis of these important natural products and combinatorial chemistry approaches can be employed to elucidate structure-activity relationships and to find new potent compounds of this class. In this chapter, methods for formation of depsipeptide ester bonds, hydroxyl group protection, and solid-phase reaction monitoring are described.

Total solid-phase synthesis of marine cyclodepsipeptide IB-01212

A suitable combination of synthetic design, orthogonal protecting groups and coupling reagents was used to complete the first known synthesis of the natural marine cyclodepsipeptide IB-01212. The cyclic, symmetric octapeptide contains two of each of the following residues: L-N,N-Me2Leu, L-Ser, L-N-MeLeu and L-N-MePhe. IB-01212 also features two symmetric ester bonds between the hydroxyl group of Ser and the carboxyl function of the N-MePhe. Total solid-phase syntheses of the product was performed in parallel via three distinct routes: dimerization of heterodetic fragments, linear synthesis, and convergent synthesis. The convergent strategy gave the best results in terms of product yield and purity and is particularly suitable for the large-scale synthesis of IB-01212 and similar peptides.

N,O-Isopropylidenated Threonines as Tools for Peptide Cyclization: Application to the Synthesis of Mahafacyclin B

[structure: see text] The influence of a single N,O-isopropylidenated threonine turn-inducer on the cyclization of a linear heptapeptide precursor to mahafacyclin B has been investigated. Incorporation of an N,O-isopropylidenated threonine more than doubles the head-to-tail cyclization yield. The N,O-isopropylidene grouping is then readily disassembled to give the antimalarial cyclic peptide in high yield.

Pseudoprolines as Removable Turn Inducers: Tools for the Cyclization of Small Peptides

The cyclization of small peptides which do not incorporate turn inducers is often difficult. We have developed a method involving the use of removable turn inducers, in the form of pseudoprolines, for the cyclization of difficult peptide sequences. The pseudoprolines induce a cisoid amide bond in the peptide backbone which facilitates cyclization. They are then readily removed to yield a cyclic peptide that does not contain any turn inducers.

High yield synthesis of tentoxin, a cyclic tetrapeptide

Tentoxin is a naturally occurring phytotoxic cyclic tetrapeptide excreted by fungi of the Alternaria alternata family. The four total syntheses of tentoxin published to date give poor total yields, mainly owing to two difficulties, the introduction of the dehydro amino acid and more especially the cyclization step. Here we describe a method that stereospecifically introduces Z-dehydrophenylalanine (deltaZPhe) by a modified Erlenmeyer aldolization reaction. The linear tetrapeptide, Boc-R1Ala-Leu-R2deltaZPhe-G1y-OMe (R1, R2: CH3, 14CH3), the precursor of tentoxin, was obtained in a 72% yield from Boc-Leu-Gly-OH. This linear tetrapeptide, labelled with carbon-14, was used for a comparative study of four cyclization reagents DPPA, DCC-PfpOH, HBTU and HATU. This last was the most effective and gave tentoxin in a 81% cyclization yield. The activated ester formed with this reagent displayed an enhanced capacity for cyclization, permitting cyclization in concentrated medium (10 mM). This new synthetic route gave tentoxin in a 60% yield from Boc-Leu-Gly-OH and offers a means of achieving the synthesis of hitherto elusive analogues.

Probing host-selective phytotoxicity: synthesis of destruxin B and several natural analogues

The syntheses of the host-selective phytotoxin destruxin B [cyclo(betaAla-Hmp-Pro-Ile-MeVal-MeAla), Hmp = (2R)-2-hydroxy-4-methylpentanoic acid], and the closely related natural analogues homodestruxin B (MeVal-->MeIle), desmethyldestruxin B (MeVal-->Val), hydroxydestruxin B (Hmp-->Dhmp, Dhmp = (2R)-2,4-dihydroxy-4-methylpentanoic acid), and hydroxyhomodestruxin B (MeVal-->MeIle, Hmp-->Dhmp) are described. In each case, the MeAla-betaAla linkage was formed by cyclization and the precursor linear hexadepsipeptides were formed by condensing two three-residue fragments. Radiolabeled samples of destruxin B, homodestruxin B, and hydroxydestruxin B were prepared by coupling [3-(14)C]-beta-alanine to the appropriate pentadepsipeptide followed by cyclization. A noteworthy feature of the synthesis involves the novel use of a Boc-hydrazide protecting group on dipeptides with a C-terminal N-methylalanine residue to inhibit the otherwise facile dioxopiperazine formation during peptide coupling.

A thioester ligation approach to amphipathic bicyclic peptide library

An efficient approach to synthesize an amphipathic bicyclic peptide library from unprotected peptides is demonstrated through an on-resin intramolecular thioester ligation and an off-resin DMSO-mediated disulfide formation.

Design, synthesis, and biological activity of a cyclic peptide: an inhibitor of HIV-1 tat-TAR interactions in human cells

Replication of human immunodeficiency virus type 1 (HIV-1) requires specific interactions of Tat protein with the transactivation responsive region (TAR) RNA, a 59-base stem-loop structure located at the 5'-end of all HIV mRNAs. A number of cyclic peptides are known to possess antibiotic activity and increased biological stability. Here we report the design, synthesis, and biological activity of a cyclic peptide (2), which inhibits transcriptional activation by Tat protein in human cells with an IC50 of approximately 40 nM. Cyclic peptides that can target specific RNA structures provide a new class of small molecules that can be used to control cellular processes involving RNA-protein interactions in vivo.

Probing Host-Selective Phytotoxicity: Synthesis and Biological Activity of Phomalide, Isophomalide, and Dihydrophomalide

The cyclic depsipeptide phomalide [cyclo(Val-(E)-Aba-Hpp-Hmp-(R)-Leu); Aba = 2-amino-2-butenoic acid, Hpp = (2S)-2-hydroxy-3-phenylpropanoic acid, Hmp = (2S)-2-hydroxy-4-methylpentanoic acid] is the host-selective phytotoxin produced by the fungus [Leptosphaeria maculans (Desm.) Ces. et de Not., asexual stage Phoma lingam (Tode ex Fr.) Desm.] which causes blackleg disease (a devastating disease of several economically important brassica crops). Efficient total syntheses of phomalide, its (Z)-isomer isophomalide, and the two dihydro analogues [(R)-dihydrophomalide and (S)-dihydrophomalide] are described. A [2 + 3] fragment coupling of Cbz-Val-(Z)-Aba with Hpp-Hmp-D-Leu-OBn followed by deprotection and cyclization gave isophomalide which was diastereoselectively isomerized to phomalide by conjugate addition of PhSeH followed by elimination of the corresponding selenoxide. The dihydro analogues were prepared similarly using Cbz-Val-(R)-Abu or Cbz-Val-(S)-Abu (Abu = 2-aminobutanoic acid) in place of Cbz-Val-(Z)-Aba. Biological evaluations of phomalide, isophomalide, and the dihydrophomalides revealed that only phomalide (10(-)(5) M) caused necrotic, chlorotic, and reddish lesions on canola (Brassica napus and Brassica rapa; susceptible to blackleg) leaves whereas no damage was observed on brown mustard (Brassica juncea; resistant to blackleg) or white mustard (Sinapis alba; resistant to blackleg) leaves, even at significantly higher concentrations (10(-)(4) M). Thus, both the presence and configuration of the double bond is crucial for selective phytotoxicity. This is the first reported synthesis of an (E)-Aba-containing natural product, and importantly, the (Z) --> (E) isomerization approach should be applicable to other (depsi)peptide targets thereby allowing investigation of the effect of the double-bond configuration on various properties.

The design, synthesis, and biological evaluation of analogues of the serine-threonine protein phosphatase 1 and 2A selective inhibitor microcystin LA: rational modifications imparting PP1 selectivity

Based on the results from previously reported molecular modeling analyses of the interactions between the inhibitor microcystin and the serine-threonine protein phosphatases 1 and 2A, we have designed analogues of microcystin LA with structural modifications intended to impart PP1 selectivity. The synthesis of several first generation analogues followed by inhibition assays revealed that all three are PP1-selective, as predicted. Although the observed selectivities are modest, one of the designed analogues is more selective for PP1 than any known small molecule inhibitor.

Synthesis of a Trisubstituted 1,4-Diazepin-3-one-Based Dipeptidomimetic as a Novel Molecular Scaffold

We describe two routes for the synthesis of a trisubstituted 1,2,5-hexahydro-3-oxo-1H-1,4-diazepine ring (DAP), a novel, conformationally constrained, seven-membered dipeptidomimetic ring system. The linear precursor for the model DAPs, targeted for conformational analysis studies, was obtained by reductive alkylation of tert-butyl alaninate or phenylalaninate by N-Boc-alpha-amino-gamma-oxo-N,N-dimethylbutyramide. Acetylation of the newly formed secondary amine followed by acidolytic deprotection of the amino and carboxyl terminal protecting groups and subsequent diphenylphosphorazidate-mediated ring formation yielded the blocked model DAPs. The synthesis of the DAP synthon started with 1-tert-butyl hydrogen N-(benzyloxycarbonyl)aspartate. The aldehyde obtained from the beta-carboxyl was used to reductively alkylate benzyl phenylalaninate, generating a secondary amine. Hydrogenolytic deprotection of the end-groups yielded the linear precursor which was cyclized via lactam formation mediated by 1-hydroxy-7-azabenzotriazolyl-N,N,N',N'-tetramethyluronium hexafluorophosphate. This route yielded the reversibly protected hexahydro-1H-3-oxo-2(S)-benzyl-5(S)-(tert-butyloxycarbonyl)-1,4-diazepine. This synthon unit can be subsequently elaborated by substituting the functional groups (secondary amine and carboxyl). Therefore, the DAPs may serve as novel molecular scaffolds to reproduce a biologically relevant topology or as a dipeptido-conformation-mimetic that can be incorporated into bioactive peptides. In addition, these synthetic routes will allow the introduction of different chiralities at positions 2 and 5 as well as the diversification of the side chains at position 2. Furthermore, the synthetic routes described here can be easily modified to obtain larger ring systems with variable degrees of conformational flexibility.