Author: Oleg Melnyk

The synthesis of peptide hydrazides on hydrazine 2CT and hydrazone resin was optimized using CMR-free reagents and solvents. The suggested protocols allow for reduced reagent consumption and the avoidance of DMF and DCM. The obtained results can simplify the synthesis of peptide building blocks for native chemical ligation.

ABSTRACT

Peptide hydrazides are widely applied as precursors of peptide thioesters, valuable building blocks for the synthesis of proteins by native chemical ligation. In addition, they can be applied for the selective modification of cargo or carrier molecules using hydrazone ligation technique. In this work, we describe key aspects of solid phase synthesis of peptide hydrazides on hydrazine 2CT and hydrazone resin. Special attention is paid to the optimization of synthetic procedures using “preferred” and “usable” organic solvents. Thus, optimization of 2-CTC resin loading with Fmoc-hydrazine permits to reduce reagents consumption and avoid DMF and DCM application. The final products can be released from the polymer support with simultaneous BOC removal with 5% HCl (aq) in acetone. Although this protocol demands subsequent peptide deprotection to remove other protecting groups, it benefits of significantly reduced TFA consumption. Because of improved stability in acidic conditions and the possibility of selective Mtt removal and peptide cleavage in green solvents, hydrazone resin can be considered as a useful alternative for peptide hydrazides synthesis. Obtained results can simplify the synthesis of peptide building blocks for native chemical ligation using CMR-free reagents and solvents.

We have attached a wide range of blocking groups to glucagon with the intention of interfering with the quaternary interactions that drive self-association. In so doing, we have identified multiple groups that are able to significantly block fibril formation.

ABSTRACT

Protein self-interaction leading to aggregation is a major challenge facing protein pharmaceuticals. It leads to a range of problems, including increases in immunogenicity and loss of activity. In this work, we describe an approach for blocking or antagonizing the quaternary interactions that drive self-association. We applied the approach to glucagon, a therapeutic peptide known for its propensity to form fibrils due to self-interaction. We synthesized a regio-pure common feedstock that allowed easy modification with potential blocking peptides that represented a range of chemical types (anionic, cationic, polar, and nonpolar). From these synthesized materials, we identified two modified glucagons that showed significant stabilization against fibril formation compared with unmodified glucagon. This was confirmed by three complementary biophysical techniques. Both successful modifications introduced excess net charge to glucagon, consistent with overall electrostatic repulsion being at the root of the observed fibrillation resistance. This approach can potentially be applied to other therapeutic proteins that suffer from the problems associated with self-association.

No abstract is available for this article.

A novel GAPDH-derived peptide JFP-2826, which showed selective antimicrobial activity against marine-specific Vibrio bacteria, was identified from the transcriptome of Rhopilema esculentum. Jellyfish GAPDH may have a newly discovered antimicrobial-related function conducted by releasing JFP-2826-like cryptic peptides.

ABSTRACT

Marine organisms serve as a rich source of bioactive natural compounds, including antimicrobial agents. Jellyfish, which are ancient marine invertebrates with hundreds of millions of years of evolutionary history, have been in continuous contact with a diverse array of pathogenic microorganisms from seawater, which may give rise to a distinctive innate immune system and related defensive molecules. However, it is difficult and inefficient to isolate active ingredients directly from jellyfish for enrichment, though few jellyfish-sourced antimicrobial peptides (AMPs) have been reported. In this study, we utilized transcriptomic big data with bioinformatic tools to dig deeper into potential antimicrobial components in jellyfish, and identified a new AMP JFP-2826 from Rhopilema esculentum. The 20-mer peptide exhibited an alpha-helix structure and showed antimicrobial activity against selected bacterial strains; more importantly, JFP-2826 demonstrated good selectivity for marine-specific Vibrio including Vibrio vulnificus. Sequence analysis of the full-length protein of JFP-2826 revealed that it is derived from the housekeeping gene glyceraldehyde-3-phosphate dehydrogenase (GAPDH), which is probably produced through enzymatic cleavage of the N-terminal fragment. This suggests that GAPDH of jellyfish might have a newly discovered antimicrobial-related function that is conducted by releasing JFP-2826-like cryptic peptides. JFP-2826 can be subjected to further structural modifications and optimizations to potentially become a potent lead peptide for the development of novel antimicrobial drugs treating infections of marine pathogens.

The integration of a polyarginine cell penetrating peptide with a GRP78-targeting peptide provides selective and effective peptide-based siRNA transfection directly within the GRP78 overexpressing prostate cancer (DU145) cells.

ABSTRACT

This study investigated a peptide-based GRP78-targeting strategy for short-interfering (si) RNA delivery in cancer cells. Synthetic fluorescein-labeled amphiphilic peptides composed of the hydrophobic cell surface (cs) GRP78-targeting and hydrophilic, polycationic arginine-rich cell penetrating peptides demonstrated GRP78-dependent cell uptake in the DU145 prostate cancer cells, and to a lesser extent in the non-cancerous human lung fibroblast WI-38 cell line. Mechanistic studies revealed energy-dependent GRP78 receptor-mediated endocytosis of the GRP78-targeting peptide with polyarginine (W1-R9). The cytosolic accumulation of this peptide underscored its potential utility in siRNA delivery. Peptide:siRNA complexes formed stably condensed nanoparticles, with calcium functioning as an ionic stabilizer and additive promoting endosomal siRNA escape for RNA interference (RNAi) activity. Preliminary peptide-based siRNA transfections in the DU145 cells demonstrated that GRP78 knockdown led to an interplay in between pro-survival and cell death outcomes under ER stress induction. Thus, the GRP78-targeting polyarginine peptides enables efficient cell uptake for specific siRNA delivery in the DU145 cells. This class of bio-active synthetic peptides is important for the investigation of cancer biology, leading to the innovation of cancer-targeted gene delivery and therapy approaches.

Interaction analysis of the antibody mimetic peptide H1H3s with its target protein through cross-linking mass spectrometry confirmed the proposed binding site. Binding and virus neutralizing properties were preserved in a proteolytically stable D-amino acid peptide variant. K➔D exchanges yielded a peptide that assembles into nanofibrils and enhances retroviral infection.

ABSTRACT

Antibody mimetic peptides have evolved as versatile tools for biomedical applications, based on their ability to interfere with protein–protein interactions. We had previously designed a functional mimic of the broadly neutralizing HIV-1 antibody b12 that recognizes the CD4 binding site of the HIV-1 envelope glycoprotein gp120. The molecular details of the interaction of a linear variant of this peptide (H1H3s) with gp120 have now been characterized through cross-linking mass spectrometry, confirming the proposed involvement of the CD4 binding site of gp120 in the interaction. In addition, a variant of the b12 mimetic peptide composed mostly of D-amino acids was shown to be stable towards proteolytic degradation, while the binding and HIV-1 neutralizing properties were largely preserved. Furthermore, a peptide variant in which aspartate residues were replaced with lysine was shown to strongly enhance infection of cells with HIV-1 and GALV glycoprotein pseudotyped viral vectors, respectively, introducing this peptide as a tool to facilitate retroviral gene transfer. Collectively, the presented results highlight the versatile potential therapeutic and gene transfer applications of H1H3s and its variants in particular, as well as antibody mimetic peptides in general.

The Insect Antimicrobial Peptide Database (IAMPDB) represents a specialized database of insect-derived antimicrobial peptides (IAMPs). The data are sourced from UniProt and its associated literature from PubMed. Currently, the database holds 438 entries of IAMPs from 148 insects across 10 taxonomical insect orders. The data can be used to target 181 microorganisms and study 33 activities. Researchers, scientists, and pharmaceutical industries can utilize this database for drug development, disease-resistant crop development, and more.

ABSTRACT

Insects, a majority of animal species, rely on innate immunity and antimicrobial peptides (AMPs), which are a part of their innate immunity, to combat diverse parasites and pathogens. These peptides have applications ranging from agriculture to antimicrobial resistance (AMR). However, there is a lack of a specialized database, prompting the development of the Insect Antimicrobial Peptide Database (IAMPDB) as a pioneering comprehensive Knowledgebase dedicated to

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nsect-derived antimicrobial peptides (IAMPs), serving as a resource for researchers and industry professionals. Curated from UniProt and associated literature(s), IAMPDB currently houses 438 curated entries of IAMPs from various insect species, spanning 10 taxonomical orders of insects. Each entry is meticulously annotated with details on peptide sequence, source organism, activities, physicochemical properties, and more. IAMPDB offers a user-friendly interface with diverse search options, interactive visualizations, and links to external databases; advanced tools, including a peptide sequence alignment toolbox and a peptide feature calculation toolbox, facilitating sequence alignment, physicochemical property calculation, and in-depth analysis. The knowledgebase is accessible online (at URL https://bblserver.org.in/iampdb/).

Guidelines from regulatory agencies support the analysis and quality control of peptide and protein drugs. Key aspects of the analysis process are summarized here.

ABSTRACT

Peptides and proteins have become increasingly important in the treatment of various diseases, including infections, metabolic disorders, and cancers. Over the past decades, the number of approved peptide- and protein-based drugs has grown significantly, now accounting for about 25% of the global pharmaceutical market. This increase has been recorded since the introduction of the first therapeutic peptide, insulin, in 1921. Therapeutic peptides and proteins offer several advantages over small molecule drugs, including high specificity, potency, and safety; however, they also face challenges related to instability in liquid formulations. To address this issue, numerous formulation techniques have been developed to enhance their stability. In either state, physical and chemical characterization of the peptide or protein of interest is crucial for ensuring the identity, purity, and activity of these therapeutic agents. Regulatory bodies such as the FDA, ICH, and EMA have established guidelines for the analysis, stability testing, and quality control of peptides and biologics to ensure the safety and effectiveness of these drugs. In the present review, these guidelines and the consequences thereof are summarized and provided to support the notion of developing tailored bioanalytical workflows for each peptide or protein drug.

A divergent synthesis strategy was developed for producing various anabaenopeptins (AP) for harmful algal bloom monitoring. The synthesis involved on-resin stepwise pentapeptide assembly on a MeDbz linker, then N-α-ureido amino acid attachment and cyclization. This approach proved effective as a general platform for anabaenopeptin synthesis, allowing rapid access to anabaenopeptins A, B, F, and oscillamide Y.

ABSTRACT

A divergent synthesis strategy was developed for producing various anabaenopeptins (AP) for harmful algal bloom monitoring. The synthesis involved on-resin stepwise pentapeptide assembly on a MeDbz linker then N-α-ureido amino acid attachment and cyclization. To manage N-methylated amino acids, modified coupling conditions were employed. Lysine’s ε-amino group reacted with the activated MeDbz linker in a self-cleaving head-to-side chain cyclization. Cyclization conditions were optimized by screening different pH levels to control lysine α-amine cyclization and prevent hydrolysis. Global cleavage and purification afforded the pure anabaenopeptins. This approach proved effective as a general platform for anabaenopeptin synthesis, allowing rapid access to anabaenopeptins A, B, F, and oscillamide Y.

The self-assembly and bioactivity of the lipopeptide lipoyl-KTTKS which comprises lipoic acid conjugated to a collagen-stimulating pentapeptide are examined. Self-assembly into curly fibrils (wormlike micelles) is observed, these structures being dissociated in the presence of a chemical reductant. The lipopeptide also undergoes photo-degradation in the presence of UV radiation. Lipoyl-KTTKS has excellent cytocompatibility, stimulates collagen production and enhances the rate of cell repopulation in a simple in vitro scratch assay.

ABSTRACT

Lipoic acid is a biocompatible compound with antioxidant activity that is of considerable interest in cosmetic formulations, and the disulfide group in the N-terminal ring confers redox activity. Here, we study the self-assembly and aspects of the bioactivity of a lipopeptide (peptide amphiphile) comprising the KTTKS collagen-stimulating pentapeptide sequence conjugated to an N-terminal lipoic acid chain, lipoyl-KTTKS. Using SAXS, SANS and cryo-TEM, lipoyl-KTTKS is found to form a population of curly fibrils (wormlike micelles) above a critical aggregation concentration. Upon chemical reduction, the fibrils (and β-sheet structure) are disrupted because of the breaking of the disulfide bond, which produces dihydrolipoic acid. Lipoyl-KTTKS also undergoes photo-degradation in the presence of UV radiation. Through cell assays using fibroblasts, we found that lipoyl-KTTKS has excellent cytocompatibility across a wide concentration range, stimulates collagen production, and enhances the rate of cell coverage in a simple in vitro scratch assay of ‘wound healing’. Lipoyl-KTTKS thus has several notable properties that may be useful for the development of cosmetics, cell scaffolds or tissue engineering materials.

A post-docking analysis was used to explore the binding modes formed between 44 peptides identified by phage display and nine proteins overexpressed in HeLa and MDA-MB-231 cell lines, facilitating the selection of the best peptide candidates.

ABSTRACT

Peptides binding overexpressed breast and cervical cancer cell surface proteins can be isolated by phage display technology, and their affinity to their potential receptors can be assessed by molecular docking. We isolated 44 phage clones displaying dodecapeptides with high affinity to HeLa cervical cancer and MDA-MB-231 (MDA) breast cancer cells by repeated biopanning of an MK13 phage library and explored their affinity to specific proteins by molecular docking. Six peptides appeared repeatedly during biopanning: two with affinity to HeLa (H5/H21), and four with affinity to MDA cells (M3/M7/M15/M17). Peptide pairs M3/H5 and H1/M17 had affinity to both cell lines. A systematic review identified Annexin A2, EGFR, CD44, CD146, and Integrin alpha V as potential protein targets in HeLa cells, and Vimentin, Galectin-1, and Annexins A1 and A5 in MDA cells. Via virtual screening, we selected six peptides with the highest total docking scores: H1 (−916.32), H6 (−979.21), H19 (−1093.24), M6 (−732.21), M16 (−745.5), and M19 (−739.64), and identified that docking scores were strengthened by the protein type, the interacting amino acid side chains, and the polarity of peptides. This approach facilitates the selection of relevant peptides that could be further explored for active targeting in cancer diagnosis and treatment.

L’article Peptide mimetics, peptoids and peptide nucleic acids est apparu en premier sur Groupe Français des Peptides et Protéines.

YdgR transporter from E. coli selectively transports the fluorescence reporter substrate β-Ala-Lys(AMCA), but modifications such as reducing the lysine chain or substituting or altering the AMCA fluorophore block transport.

ABSTRACT

Fluorescent probes are widely used in cellular imaging and disease diagnosis. Acting as substitute carriers, fluorescent probes can also be used to help transport drugs within cells. In this study, commonly used fluorophores, TAMRA (5-carboxytetramethylrhodamine), PBA (1-pyrenebutyric acid), NBD (nitrobenzoxadiazole), OG (Oregon Green), and CF (5-carboxyfluorescein) were conjugated with the dipeptide β-Ala-Lys, the peptide moiety of the well-established peptide transporter substrate β-Ala-Lys(AMCA) (AMCA: 7-amino-4-methyl-coumarin-3-acetic acid) by modifying it with respect to side-chain length and functional end groups. The analogs were tested for transport through or inhibition of YdgR, a prototypical peptide transporter from E. coli and apparently homologous to the human PEPT1. Strikingly, none of the dipeptide-fluorophore conjugates nor minor modifications in the reporter substrate were tolerated by YdgR, indicating discrepancies to PEPT1. These findings underscore intricate substrate recognition mechanisms governing substrate recognition by YdgR.

Multiepitope DNA constructs harboring the immunogenic and conserved epitopes of the L1, L2 and E7 proteins of HPV16/18 were delivered using KALA and REV cell-penetrating peptides. The stability of the REV/DNA and KALA/DNA complexes against DNase I and serum protease was investigated and their entry into HEK-293T eukaryotic cells was analyzed qualitatively and quantitatively. The anti-tumor effects of the peptide/DNA complexes were investigated in the C57BL/6 mouse model.

ABSTRACT

Developing human papillomavirus (HPV) therapeutic DNA vaccines requires an effective delivery system, such as cell-penetrating peptides (CPPs). In the current study, the multiepitope DNA constructs harboring the immunogenic and conserved epitopes of the L1, L2, and E7 proteins of HPV16/18 (pcDNA-L1-L2-E7 and pEGFP-L1-L2-E7) were delivered using KALA and REV CPPs with different properties in vitro and in vivo. Herein, after confirmation of the REV/DNA and KALA/DNA complexes, their stability was investigated against DNase I and serum protease. Then, their entry into HEK-293T eukaryotic cells was analyzed by qualitative and quantitative methods. Finally, anti-tumor effects of the peptide/DNA complexes were investigated in the C57BL/6 mouse model. Based on the obtained data, the REV/DNA and KALA/DNA complexes at the N/P ratio of 5:1 demonstrated successful penetration into HEK-293T cells. Furthermore, in vivo studies represented that the REV/DNA (survival rate: 75%) and KALA/DNA (survival rate: 50%) complexes provided significant protection against C3 tumors in mice. Indeed, REV CPP exhibited a higher survival rate and lower tumor volume than KALA CPP, 50 days after the C3 challenge. These findings represented the potential of KALA and REV CPPs, especially REV, as promising gene delivery systems for developing HPV therapeutic DNA vaccine candidates.

No abstract is available for this article.

The natural Short Neuropeptide F (sNPF) from the pea aphid (Acyrthosiphon pisum) was used as lead compound to design five novel sNPF analogs, altering the N-terminal amino acid to Ser, Thr, Tyr, Leu, or Gln. Aphid bioassays showed that the analog I-3 was more active than the natural Acypi-sNPF-1 and pymetrozine. I-3 can be utilized as a selective and environmentally friendly insecticide to manage pea aphids.

ABSTRACT

Short neuropeptide F (sNPF) is an insect-specific neuropeptide named for its C-terminal phenylalanine. It consists of 6–19 amino acids with a conserved RLRFa structure, regulating feeding, growth, circadian rhythms, and water-salt balance in insects. Its receptor belongs to GPCR-As and binds sNPF to regulate the insect nervous system. Many research groups are evaluating sNPF for plant protection and pest control. In this study, the natural sNPF from the pea aphid (Acyrthosiphon pisum) was used as a lead compound. Five novel sNPF analogs were designed and synthesized through molecular docking and peptidomimetics, altering the N-terminal amino acid to Ser, Thr, Tyr, Leu, or Gln. Aphid bioassays showed that the analog I-3 (YLRLRFa, LC₅₀ = 1.820 mg/L) was more active than the natural Acypi-sNPF-1 and pymetrozine. The structure–activity relationship analysis indicated that N-terminal tyrosine incorporation, combined with increased ClogP and TPSA, enhanced aphidicidal activity. Furthermore, Toxtree’s toxicity predictions suggest a low risk for all compounds, and a toxicity assay conducted on the honeybee (Apis mellifera) for I-3, which exhibits high aphidicidal activity, indicates that I-3 does not pose a toxicity risk to non-target organisms. Thus, I-3 can be utilized as a selective and environmentally friendly insecticide to manage pea aphids.

L’article test-FH est apparu en premier sur Groupe Français des Peptides et Protéines.

PepFuNN is a new open-source version of the PepFun package with functions to study the chemical space of peptide libraries and perform structure–activity relationship analyses. It is a Python package comprising five modules to study peptides with natural amino acids and, in some cases, sequences with non-natural amino acids based on the availability of a public monomer dictionary.

ABSTRACT

We present PepFuNN, a new open-source version of the PepFun package with functions to study the chemical space of peptide libraries and perform structure–activity relationship analyses. PepFuNN is a Python package comprising five modules to study peptides with natural amino acids and, in some cases, sequences with non-natural amino acids based on the availability of a public monomer dictionary. The modules allow calculating physicochemical properties, performing similarity analysis using different peptide representations, clustering peptides using molecular fingerprints or calculated descriptors, designing peptide libraries based on specific requirements, and a module dedicated to extracting matched pairs from experimental campaigns to guide the selection of the most relevant mutations in design new rounds. The code and tutorials are available at https://github.com/novonordisk-research/pepfunn.

Peptides were comprehensively summarized in the aspects of sources, function, the use of peptides in cosmetics and skin care, and indications for the delivery of cosmetic peptides. Attention was also given to the development of cosmetic peptides in the future.

ABSTRACT

Peptides are molecules that consist of at least two amino acids linked by peptide bonds. The difference between peptides and proteins is primarily based on size and structure. Typically, oligopeptides consist of fewer than about 10–20 amino acids, and polypeptides consist of more than 20 amino acids, whereas proteins usually are made up more than 50 amino acids and often contain multiple peptide subunits as stated in the International Union of Pure and Applied Chemistry rules. Beyond the nutritional properties, peptides are also structural components of hormones, enzymes, toxins, and antibiotics and play several fundamental physiological roles in the body. Since the introduction of the first commercial peptide drug, insulin, peptide-based drugs have gained increased interest. So far, more than 80 peptide-based drugs have reached the market for a wide range of conditions, such as diabetes, cardiovascular diseases, and urological disorders. Meanwhile, peptides have also gained significant attention in the cosmetic industry because of their potential in boosting skin health. In this review, peptides were comprehensively summarized in the aspects of sources, function, the use of peptides in cosmetics and skin care, and indications for the delivery of cosmetic peptides.

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