Solid-phase Peptide Synthesis Research Articles

Synthesis, antiproliferative and antimicrobial activities of (KLAKLAK)2-NH2 analogue containing nor-Leu and its conjugates with a second pharmacophore

Peptides are a promising alternative of conventional medical drugs for the treatment of different diseases because they have no or have very few side effects owing to the natural mechanisms for their elimination. There are a lot of examples of drugs on the pharmaceutical market based on modified amino acids and peptides. Herein, we report the synthesis and studies on the antimicrobial peptide (KLAKLAK)2-NH2 where Leu is replaced by the unnatural amino acid nor-Leu. In addition, a second pharmacophore with well proven anticancer properties is introduced to the peptide moiety. All structures were synthesized by conventional solid phase peptide synthesis. The antiproliferative and antimicrobial activities were studied using MTT-dye reduction assay and disk-diffusion test, respectively. Biological activity assays showed that the introduction of nor-Leu in the primary structure of the parent compound does not lead to an increase in the antiproliferative activity. However, the combination with the second pharmacophore 1,8-naphtalimide in a hybrid structure 1,8-NphtG-(KNleAKNleAK)2-NH2 leads to a significant increase in the antiproliferative properties. The antimicrobial tests showed that all tested compounds exhibit antimicrobial activity. The peptide and the second pharmacophore had a synergistic effect. In combination with complete hydrolytic stability for 72 h in model systems, the compound 1,8-NphtG-(KNleAKNleAK)2-NH2 is the best candidate for a medical drug in the treatment of mammary gland type A adenocarcinoma (MCF-7) in combination with antimicrobial properties.

Fmoc-SPPS-compatible p-methoxyphenacyl-modified glutamic for the synthesis of photocaged peptides

The development of photocaged glutamic acid (Glu) contributes to the time-resolved control of peptide and protein activities. Here, we efficiently synthesized the Glu with the side chain modified by photosensitive p-methoxyphenacyl group. This photocaged Glu can be introduced into peptide through standard 9‑fluorenylmethoxycarbonyl (Fmoc) solid phase peptide synthesis (SPPS), and can be re-exposed the Glu side-chain carboxy group by removing the photosensitive group under light irradiation. We prepared caged Endothelin-1 (ET-1) analogues with p-methoxyphenacyl-modified Glu and successfully achieved decaging.

Development of a nitrogen-bound hydrophobic auxiliary: application to solid/hydrophobic-tag relay synthesis of calpinactam.

In the last couple of decades, technologies and strategies for peptide synthesis have advanced rapidly. Although solid-phase peptide synthesis (SPPS) and liquid-phase peptide synthesis (LPPS) have contributed significantly to the development of the field, there have been remaining challenges for C-terminal modifications of peptide compounds in SPPS and LPPS. Orthogonal to the current standard approach that relies on installation of a carrier molecule at the C-terminus of amino acids, we developed a new hydrophobic-tag carbonate reagent which facilitated robust preparation of nitrogen-tag-supported peptide compounds. This auxiliary was easily installed on a variety of amino acids including oligopeptides that have a broad range of noncanonical residues, allowing simple purification of the products by crystallization and filtration. We demonstrated a de novo solid/hydrophobic-tag relay synthesis (STRS) strategy using the nitrogen-bound auxiliary for total synthesis of calpinactam.

Abstract 2193: Synthesis of the Transmembrane Domain of the Spike Protein from SARS-CoV-2 Using Solid Phase Peptide Synthesis and Determination of Its Oligomerization State

Abstract 2193: Synthesis of the Transmembrane Domain of the Spike Protein from SARS-CoV-2 Using Solid Phase Peptide Synthesis and Determination of Its Oligomerization State

Synthesis of multi-module low density lipoprotein receptor class A domains with acid labile cyanopyridiniumylides (CyPY) as aspartic acid masking groups.

Low-density lipoprotein receptor class A domains (LA modules) are common ligand-binding domains of transmembrane receptors of approximately 40 amino acids that are involved in several cellular processes including endocytosis of extracellular targets. Due to their wide-ranging function and distribution among different transmembrane receptors, LA modules are of high interest for therapeutic applications. However, the efficient chemical synthesis of LA modules and derivatives is hindered by complications, many arising from the high abundance of aspartic acid and consequent aspartimide formation. Here, we report a robust, efficient and general applicable chemical synthesis route for accessing such LA modules, demonstrated by the synthesis and folding of the LA3 and LA4 modules of the low-density lipoprotein receptor, as well as a heterodimeric LA3-LA4 constructed by chemical ligation. The synthesis of the aspartic acid-rich LA domain peptides is made possible by the use of cyanopyridiniumylides (CyPY) - reported here for the first time - as a masking group for carboxylic acids. We show that cyanopyridiniumylide masked aspartic acid monomers are readily available building blocks for solid phase peptide synthesis and successfully suppress aspartimide formation. Unlike previously reported ylide-based carboxylic acid protecting groups, CyPY protected aspartic acids are converted to the free carboxylic acid by acidic hydrolysis and are compatible with all common residues and protecting groups. The chemical synthesis of Cys- and Asp-rich LA modules enables new access to a class of difficult to provide, but promising protein domains.

Macrocyclization strategies for the total synthesis of cyclic depsipeptides.

Cyclic depsipeptides are an important class of peptide natural products that are defined by the presence of ester and amide bonds within the macrocycle. The structural diversity of depsipeptides has required the development of a broad range of synthetic strategies to access these biologically active compounds. Solid phase peptide synthesis (SPPS) strategies have been an invaluable tool in their synthesis. The key aspect of their synthesis is the macrocyclization strategy. Three main strategies are used, solution phase macrolactamization of acyclic ester containing peptide, on-resin macrolactamization of a sidechain-anchored peptide, and the solution phase macrolactonization of a linear peptide. Additionally, biocatalysts have been used to produce these compounds in a regio- and chemo-selective manner. Each compound offers unique challenges, requiring careful synthetic design to avoid undesirable side reactivity or unwanted epimerization during the esterification and macrocyclizing steps. This focused review analyzes these three strategies for cyclic depsipeptide natural product total synthesis with selected examples from the literature between 2001-2023.

A novel series of dipeptide derivatives containing indole-3-carboxylic acid conjugates as potential antimicrobial agents: the design, solid phase peptide synthesis, in vitro biological evaluation, and molecular docking study.

A new library of peptide-heterocycle hybrids consisting of an indole-3-carboxylic acid constituent conjugated with short dipeptide motifs was designed and synthesized by using the solid phase peptide synthesis methodology. All the synthesized compounds were characterized by spectroscopic techniques. Additionally, the synthesized compounds were subjected to in vitro antimicrobial activities. Two Gram-negative bacteria (Escherichia coli and Pseudomonas aeruginosa) and two Gram-positive (Streptococcus pyogenes and Staphylococcus aureus) were used for the evaluation of the antibacterial activity of the targeted dipeptide derivatives. Good antibacterial activity was observed for the screened analogues by comparing their activities with that of ciprofloxacin, the standard drug. Also, two fungi (Aspergillus niger and Candida albicans) were employed for the evaluation of the antifungal activity of the synthesized compounds. When compared to the standard drug Fluconazole, it was observed that the screened analogues exhibited good antifungal activity. In continuation, all the synthesized derivatives were subjected to integrated molecular docking studies and molecular dynamics simulations to investigate binding affinities, intermolecular interaction networks, and conformational flexibilities with deoxyribonucleic acid (DNA) gyrase and lanosterol-14-alpha demethylase. The molecular docking studies revealed that indole-3-carboxylic acid conjugates exhibited encouraging binding interaction networks and binding affinity with DNA gyrase and lanosterol-14 alpha demethylase to show antibacterial and antifungal activity, respectively. Such synthesis, biological activity, molecular dynamics simulations, and molecular docking studies of short peptides with an indole conjugate unlock the door for the near future advancement of novel medicines containing peptide-heterocycle hybrids with the ability to be effective as antimicrobial agents.

Computer vision as a new paradigm for monitoring of solution and solid phase peptide synthesis.

We report a strategy for the camera-enabled non-contact colourimetric reaction monitoring and optimisation of amide bond formation, mediated by coupling reagents. For amide bond formation in solution phase, investigation of reactions mediated by HATU, PyAOP, and DIC/Oxyma evidenced correlations between colour parameters extracted from video data and conversion to amide product measured by off-line HPLC analysis of concentration. These correlations, supported by mutual information analysis, were further investigated using video recordings of solid phase peptide synthesis (SPPS), co-analysed by off-line HPLC to track remaining unreacted substrate in solution. An optimisation method of coupling time in SPPS was derived from ΔE (a measurement of colour contrast), giving comparable isolated peptide yield and purity at 65-95% reduced overall reaction time. The same colour data enabled data-rich monitoring of reaction rate attenuation, consisted with computationally-derived measures of amino acid steric bulk. These findings provide a foundation for exploring the use of camera technology and computer vision towards automated and online mechanistic profiling of SPPS.

Development and Characterization of Novel FAP-Targeted Theranostic Pairs: A Bench-to-Bedside Study.

Fibroblast activation protein (FAP) is among the most popular targets in nuclear medicine imaging and cancer theranostics. Several small-molecule moieties (FAPI-04, FAPI-46, etc.) are used for developing FAP-targeted theranostic agents. Nonetheless, the circulation time of FAP inhibitors is relatively short, resulting in rapid clearance via kidneys, low tumor uptake, and associated unsatisfactory treatment efficacy. To address the existing drawbacks, we engineered 3 peptides named FD1, FD2, and FD3 with different circulation times through solid-phase peptide synthesis. All the 3 reported peptides bind to human and murine FAP with single-digit nanomolar affinity measured by surface plasmon resonance. The diagnostic and therapeutic potential of the agents labeled with 68Ga and 177Lu was assessed in several tumor models exhibiting different levels of FAP expression. While radiolabeled FD1 was rapidly excreted from kidneys, radiolabeled FD2/FD3 have significantly prolonged circulation, increased tumor uptake, and decreased kidney accumulation. Our findings indicated that [68Ga]Ga-DOTA-FD1 positron emission tomography (PET) effectively detected FAP dynamics, whereas [177Lu]Lu-DOTA-FD2 and [177Lu]Lu-DOTA-FD3 exhibited remarkable therapeutic efficacy in FAP-overexpressing tumor models, including pancreatic cancer cell models characterized by abundant stroma. Moreover, a pilot translational investigation demonstrated that [68Ga]Ga-DOTA-FD1 had the capability to identify both primary and metastatic tumors with precision and distinction. In summary, we developed [68Ga]Ga-DOTA-FD1 for same-day PET imaging of FAP dynamics and [177Lu]Lu-DOTA-FD2 and [177Lu]Lu-DOTA-FD3 for effective radioligand therapy of FAP-overexpressing tumors.

Synthesis of Peptides and Proteins with Site-Specific Glutamate Arginylation.

Solid-phase peptide synthesis and protein semi-synthesis are powerful methods for site-specific modification of peptides and proteins. We describe protocols using these techniques for the syntheses of peptides and proteins bearing glutamate arginylation (EArg) at specific sites. These methods overcome challenges posed by enzymatic arginylation methods and allow for a comprehensive study of the effects of EArg on protein folding and interactions. Potential applications include biophysical analyses, cell-based microscopic studies, and profiling of EArg levels and interactomes in human tissue samples.

An identification method to distinguish monomeric sugar isomers on glycopeptides.

A one-step protocol for the automated flow synthesis of protected glycosylated amino acids is described using pumps with open-source controls in overall yields of 21-50%. The resulting glycosylated amino acids could be used directly in solid-phase peptide synthesis (SPPS) protocols to quickly produce glycopeptide standards. Access to a variety of stereoisomers of the sugar enabled the development of an LC-MS/MS protocol that can distinguish between peptides modified with carbohydrates having the same exact mass. This method could definitively identify fucose in an O-glycosylation site on the transmembrane protein, Notch1.

Transport phenomena in solid phase synthesis supported by cross-linked polymer beads

Transport phenomena in solid phase synthesis.

Towards the use of an amino acid cleavable linker for solid-phase chemical synthesis of peptides and proteins.

The synthesis of proteins by solid-phase chemical ligation (SPCL) suffers from the paucity of linkers that can be cleaved under mild conditions. Here, we deployed a spontaneous nickel-assisted cleavage (SNAC) tag, known to undergo spontaneous cleavage in the presence of nickel(II), as a linker for C-to-N SPCL.

Delivery of siRNA using cationic rosette nanotubes for gene silencing.

The quest for new therapeutic treatments for hereditary diseases has led to many advances in RNA interference (RNAi) and gene silencing. While this technique has the potential to address many problems, the key to its continued use is the development of effective delivery strategies that would reduce cellular toxicity and increase silencing efficiency. Rosette nanotubes (RNTs) are biomimetic supramolecular nanostructures formed through the self-assembly of hybrid guanine-cytosine (G∧C) DNA bases. Here, we used bioactive RNTs for siRNA delivery and gene silencing. Fifteen lysine-functionalized twin-G∧C motifs (KnT, n = 1 to 15) were synthesized using solid phase peptide synthesis to produce building blocks that self-assembled to produce cationic RNTs under physiological conditions. The intracellular uptake of siRNA delivered by the oligo-L-lysine RNTs was examined and it was found that the complexation of siRNA was affected by the cationic charges from the lysine residues and the length of RNTs formed, with the higher charged KnT RNTs delivering siRNA to the cells at a faster rate. In addition, by protecting siRNA from serum degradation, KnT RNTs were shown to deliver their cargo to the cells effectively via the endocytic pathway. A reduction in the expression (∼70%) of the target stat3 protein was observed during gene expression analysis in HCT116 and A549 cell lines.

Selective thiazoline peptide cyclisation compatible with mRNA display and efficient synthesis.

Peptide display technologies are a powerful method for discovery of new bioactive sequences, but linear sequences are often very unstable in a biological setting. Macrocyclisation of such peptides is beneficial for target affinity, selectivity, stability, and cell permeability. However, macrocyclisation of a linear hit is unreliable and requires extensive structural knowledge. Genetically encoding macrocyclisation during the discovery process is a better approach, and so there is a need for diverse cyclisation options that can be deployed in the context of peptide display techniques such as mRNA display. In this work we show that meta-cyanopyridylalanine (mCNP) can be ribosomally incorporated into peptides, forming a macrocycle in a spontaneous and selective reaction with an N-terminal cysteine generated from bypassing the initiation codon in translation. This reactive amino acid can also be easily incorporated into peptides during standard Fmoc solid phase peptide synthesis, which can otherwise be a bottleneck in transferring from peptide discovery to peptide testing and application. We demonstrate the potential of this new method by discovery of macrocyclic peptides targeting influenza haemagglutinin, and molecular dynamics simulation indicates the mCNP cross-link stabilises a beta sheet structure in a representative of the most abundant cluster of active hits. Cyclisation by mCNP is also shown to be compatible with thioether macrocyclisation at a second cysteine to form bicycles of different architectures, provided that cysteine placement reinforces selectivity, with this bicyclisation happening spontaneously and in a controlled manner during peptide translation. Our new approach generates macrocycles with a more rigid cross-link and with better control of regiochemistry when additional cysteines are present, opening these up for further exploitation in chemical modification of in vitro translated peptides, and so is a valuable addition to the peptide discovery toolbox.

Metal-protein solution interactions investigated using model systems: Thermodynamic and spectroscopic methods.

The first-row D-block metal ions are essential for the physiology of living organisms, functioning as cofactors in metalloproteins or structural components for enzymes: almost half of all proteins require metals to perform the biological function. Understanding metal-protein interactions is crucial to unravel the mysteries behind molecular biology, understanding the effects of metal imbalance and toxicity or the diseases due to disorders in metal homeostasis. Metal-protein interactions are dynamic: they are noncovalent and affected by the environment to which the system is exposed. To reach a complete comprehension of the system, different conditions must be considered for the experimental investigation, in order to get information on the species distribution, the ligand coordination modes, complex stoichiometry and geometry. Thinking about the whole environment where a protein acts, investigations are often challenging, and simplifications are required to study in detail the mechanisms of metal interaction. This chapter is intended to help researchers addressing the problem of the complexity of metal-protein interactions, with particular emphasis on the use of peptides as model systems for the metal coordination site. The thermodynamic and spectroscopic methods most widely employed to investigate the interaction between metal ions and peptides in solution are here covered. These include solid-phase peptide synthesis, potentiometric titrations, calorimetry, electrospray ionization mass spectrometry, UV-Vis spectrophotometry, circular dichroism (CD), nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR). Additional experimental methods, which can be employed to study metal complexes with peptides, are also briefly mentioned. A case-study is finally reported providing a practical example of the investigation of metal-protein interaction by means of thermodynamic and spectroscopic methods applied to peptide model systems.

Discovery and optimisation of conotoxin Vc1.1 and analogues with analgesic properties

A specimen of the marine cone snail Conus victoriae collected from a beach in Broome, Western Australia, by a group from The University of Melbourne led to the discovery of the α-conotoxin Vc1.1, which was found to have analgesic activity in rodents. The discovery of this venom-derived peptide led to a series of structural, mechanistic and pharmacological studies directed towards the development of a new analgesic for neuropathic pain by groups in Australia and internationally. Solid-phase peptide synthesis played an important role in developing structure–activity relationships. Studies in a rat model of neuropathic pain showed that a cyclic analogue of the peptide, cVc1.1, had comparable analgesic activity with that of gabapentin, one of the foremost clinically used drugs for neuropathic pain, with cVc1.1 delivered orally at a 120-fold lower dose than gabapentin. Originally, Vc1.1 was believed to act primarily through nicotinic acetylcholine receptors, but evidence for a mechanism mediated through γ-aminobutyric acid B (GABAB) receptors later emerged. Efforts to optimise the binding and pharmacological properties of analogues of Vc1.1 revealed that the affinity towards either receptor can be modulated by sequence mutations, disulfide bond modifications and backbone cyclisation. This Account describes the discovery, structure, chemistry and pharmacology of Vc1.1, with a focus on studies carried out in Australian laboratories.

Total synthesis, structure elucidation and expanded bioactivity of icosalide A: effect of lipophilicity and ester to amide substitution on its bioactivity.

The first total synthesis of icosalide A, an antibacterial depsipeptide that is unique in that it contains two lipophilic beta-hydroxy acids, has been achieved by following Fmoc solid-phase peptide synthesis in combination with solution-phase synthesis. The ambiguity in the absolute stereochemistry of icosalide A has been resolved by synthesizing the reported structures and other relevant diastereomers of icosalides and comparing their NMR data. NMR-based structure elucidation of icosalide A revealed a well-folded structure with cross-strand hydrogen bonds similar to the anti-parallel beta-sheet conformation in peptides and displayed a synergistic juxtaposition of the aliphatic sidechains. 12 analogues of icosalide A were synthesized by varying the constituent lipophilic beta-hydroxy acid residues, and their biological activities against Bacillus thuringiensis and Paenibacillus dendritiformis were explored. Most of these icosalide analogues showed an MIC of 12.5 μg mL-1 against both bacteria. Swarming inhibition by icosalides was least in B. thuringiensis (8.3%) compared to that in P. dendritiformis (33%). Furthermore, this is the first report of icosalides showing assured inhibitory action (MIC between 2 and 10 μg mL-1) against the active stage of Mycobacterium tuberculosis and cancer cell lines such as HeLa and ThP1. This study could help optimize icosalides for anti-TB, antibacterial, and anti-cancer activities.

Modular Synthesis of Unnatural Peptides via Rh(III)-Catalyzed Diastereoselective Three-Component Carboamidation Reaction.

Herein we report a modular peptide ligation methodology that couples dioxazolones, arylboronic acids, and acrylamides to construct amide bonds in a diastereoselective manner under mild conditions, facilitated by Rh(III) catalysis. By converting the C-terminus of one peptide into a dioxazolone and the N-terminus of a second peptide into an acrylamide, the two pieces can be bridged by an arylboronic acid to construct unnatural phenylalanine, tyrosine, and tryptophan residues at the junction point with diastereoselectivity for their corresponding d-stereocenters. The reaction exhibits excellent functional group tolerance with a large substrate scope and is compatible with a wide array of protected amino acid residues that are utilized in Fmoc solid phase peptide synthesis. The methodology is applied to the synthesis of six diastereomeric proteasome inhibitor analogs, as well as the ligation of two 10-mer oligopeptides to construct a 21-mer polypeptide with an unnatural phenylalanine residue at the center.

Synthesizing Cylic Peptides with Antioxidant Properties using Solid Phase Peptide Synthesis as an Alternative to Natural Product Isolation from Pork

Tetrapeptides Ser-Leu-Tyr-Ala and Tyr-Leu-Tyr-Ala are two derivates that have been successfully isolated from the pork and synthesized using Solid Phase Peptide Synthesis (SPPS) method. Tetrapeptide Gly-Ala-Trp-Ala has also been successfully isolated from the Sardinella aurita fish found in Atlantic Ocean using SPPS. This study aims to synthesize tetrapeptide Ser-Leu-Tyr-Ala, Tyr-Leu-Tyr-Ala and Gly-Ala-Trp-Leu using the SPPS method, and to find the antioxidant properties of the synthesized tetrapeptides using DPPH test. The three tetrapeptides have been synthesized using 2-chlorotritilchloride resin as solid phase, Fmoc group protection, and coupling reagent HBTU/HOBt. HR-TOF-MS with m/z was [M+H]+ 453,23 and [2M+H]+ 905,49 for Ser- Leu-Tyr-Ala, [M+H]+114,61 for Tyr-Leu-Tyr-Ala and [M+H]+ 446,23 for Gly-Ala-Trp-Leu. The antioxidant properties of Ser-Leu-Tyr- Ala had an IC50 value of 11130,04 mg/ml, while the antioxidant properties of Tyr-Leu-Tyr-Ala had an IC50 value of 4319,522 mg/ml.
 Keywords: solid phase peptide synthesis, antioxidant