Bioorganometallic Chemistry - Transition Metal Complexes with α-Amino Acids and Peptides

A new, interdisciplinary research area has emerged known as bioorganometallic chemistry. It focuses on the introduction of organometallic fragments into biomolecules (see, for example, structure on the right). “Classical” α-amino acid and peptide ligands have proven particularly versatile, and provide access to compounds that display interesting stereochemistry. α-Amino acids and peptides can be synthesized, labeled, stabilized, or activated by organometallic fragments.     

Photoionisation mass spectra of volatile derivatives of short peptides and appearance potentials of their characteristic ions

Mass spectra of the volatile derivatives of short peptides were studied by the photoionisation method with the use of monochromatic photons. The dependence of the intensity of the main peaks on the photon energy was analysed from 7·5 to 13·0 eV. The data obtain reveal the influence of the chemical structure of amino acid residues on the relative probability of the decomposition of peptide molecular ions at the CH? CO and CO? NH bonds, resulting in the formation of positively charged aldimine and amino acid N-terminal fragments, respectively. These data may be used as a basis for the application of the photoionisation technique to mass spectrometric sequential studies in peptides. In peptides containing residues of aliphatic amino acid the decomposition results mainly in the formation of aldimine ions, the stability of which increase with the increase of the alkyl chain size. In peptides containing residues of aromatic amino acids the decomposition is usually observed leading to formation of the amino acid ions. Ionisation potentials, as well as photoionisation efficiency curves and appearance potentials were determined for characteristic ions. Comparison was made of the values of the appearance potentials of different fragments formed upon decomposition of molecular ions. It has been shown that for peptides containing aliphatic amino acid moieties the appearance potentials of aldimine fragments are always lower than those inherent to peptides containing aromatic amino acid residues. The larger the size of an aliphatic chain, the lower is the energy of formation of these fragments. For all the compounds studied, including the peptides containing aromatic amino acid residues, the appearance potentials of the aldimine ions did not exceed those of the amino acid ions. These data indicate that, contrary to the experiments with electron-impact with energy of about 70 eV, upon ionisation with photons with energy from 7·5 to 13·0 eV, the aldimine fragments appear directly due to primary decomposition of molecular ions, independent of the formation of the amino acid fragments. The photoionisation efficiency curves for peptides containing different types of amino acid residues facilitate the choice of an optimal photon energy providing unequivocal information on the amino acid sequence in the peptide under study.     

Antiviral Peptides (AVPs) of Marine Origin as Propitious Therapeutic Drug Candidates for the Treatment of Human Viruses

The marine environment presents a favorable avenue for potential therapeutic agents as a reservoir of new bioactive natural products. Due to their numerous potential pharmacological effects, marine-derived natural products—particularly marine peptides—have gained considerable attention. These peptides have shown a broad spectrum of biological functions, such as antimicrobial, antiviral, cytotoxic, immunomodulatory, and analgesic effects. The emergence of new virus strains and viral resistance leads to continuing efforts to develop more effective antiviral drugs. Interestingly, antimicrobial peptides (AMPs) that possess antiviral properties and are alternatively regarded as antiviral peptides (AVPs) demonstrate vast potential as alternative peptide-based drug candidates available for viral infection treatments. Hence, AVPs obtained from various marine organisms have been evaluated. This brief review features recent updates of marine-derived AVPs from 2011 to 2021. Moreover, the biosynthesis of this class of compounds and their possible mechanisms of action are also discussed. Selected peptides from various marine organisms possessing antiviral activities against important human viruses—such as human immunodeficiency viruses, herpes simplex viruses, influenza viruses, hepatitis C virus, and coronaviruses—are highlighted herein.     

Antioxidant and Antimicrobial Peptides Derived from Food Proteins

Recently, the demand for food proteins in the market has increased due to a rise in degenerative illnesses that are associated with the excessive production of free radicals and the unwanted side effects of various drugs, for which researchers have suggested diets rich in bioactive compounds. Some of the functional compounds present in foods are antioxidant and antimicrobial peptides, which are used to produce foods that promote health and to reduce the consumption of antibiotics. These peptides have been obtained from various sources of proteins, such as foods and agri-food by-products, via enzymatic hydrolysis and microbial fermentation. Peptides with antioxidant properties exert effective metal ion (Fe²⁺/Cu²⁺) chelating activity and lipid peroxidation inhibition, which may lead to notably beneficial effects in promoting human health and food processing. Antimicrobial peptides are small oligo-peptides generally containing from 10 to 100 amino acids, with a net positive charge and an amphipathic structure; they are the most important components of the antibacterial defense of organisms at almost all levels of life—bacteria, fungi, plants, amphibians, insects, birds and mammals—and have been suggested as natural compounds that neutralize the toxicity of reactive oxygen species generated by antibiotics and the stress generated by various exogenous sources. This review discusses what antioxidant and antimicrobial peptides are, their source, production, some bioinformatics tools used for their obtainment, emerging technologies, and health benefits.     

An Optimized Protocol for the Synthesis of Peptides Containing trans-Cyclooctene and Bicyclononyne Dienophiles as Useful Multifunctional Bioorthogonal Probes

Despite the great advances in solid-phase peptide synthesis (SPPS), the incorporation of certain functional groups into peptide sequences is restricted by the compatibility of the building blocks with conditions used during SPPS. In particular, the introduction of highly reactive groups used in modern bioorthogonal reactions into peptides remains elusive. Here, we present an optimized synthetic protocol enabling installation of two strained dienophiles, trans-cyclooctene (TCO) and bicyclononyne (BCN), into different peptide sequences. The two groups enable fast and modular post-synthetic functionalization of peptides, as we demonstrate in preparation of peptide-peptide and peptide-drug conjugates. Due to the excellent biocompatibility, the click-functionalization of the peptides can be performed directly in live cells. We further show that the introduction of both clickable groups into peptides enables construction of smart, multifunctional probes that can streamline complex chemical biology experiments such as visualization and pull-down of metabolically labeled glycoconjugates. The presented strategy will find utility in construction of peptides for diverse applications, where high reactivity, efficiency and biocompatibility of the modification step is critical.     

Porous Aerogels and Adsorption of Pollutants from Water and Air: A Review

Aerogels are open, three-dimensional, porous materials characterized by outstanding properties, such as low density, high porosity, and high surface area. They have been used in various fields as adsorbents, catalysts, materials for thermal insulation, or matrices for drug delivery. Aerogels have been successfully used for environmental applications to eliminate toxic and harmful substances—such as metal ions or organic dyes—contained in wastewater, and pollutants—including aromatic or oxygenated volatile organic compounds (VOCs)—contained in the air. This updated review on the use of different aerogels—for instance, graphene oxide-, cellulose-, chitosan-, and silica-based aerogels—provides information on their various applications in removing pollutants, the results obtained, and potential future developments.     

Advantages of derivatization by osmium tetroxide and 2,2'-bipyridine for matrix-assisted laser desorption/ionization post-source decay fragment ion analysis of peptides

Matrix-assisted laser desorption/ionization--post-source decay (MALDI-PSD) fragment ion analysis is frequently used for peptide sequence determination. PSD fragmentation is often changed or improved in terms of, e.g., sequence coverage, after derivatization. In this work, the influence of modification by an osmium tetroxide-bipyridine reagent (Os,bipy) on the MALDI-PSD behaviour of peptides is studied. The reagent modifies peptides specifically at tryptophan residues and oxidizes methionine to methionine sulfone and cysteine to cysteic acid. As a result the masses of some of the fragments are specifically shifted in case of peptides containing a methionine by +32 Da and, in cases of peptides containing a cysteine residue, by +48 Da. In addition, due to the change in protonation properties of a peptide after oxidation, fragments containing cysteic acid are in most cases totally suppressed. This effect significantly facilitates peptide sequence determination. Improvement of MALDI-TOFMS and PSD analysis after the reaction with Os,bipy is demonstrated for examples involving derivatives of humanin, a novel neuroprotective peptide.     

Modification of silicon-substituted polynorbornenes by epoxidation of main chain double bonds

Postpolymerization modification of metathesis Si-containing polynorbornenes by epoxidation of double bonds of the main chain was carried out for the first time. New polynorbornenes containing one or two side Me₃Si substituents in a monomer unit and oxirane fragments in the main chain were obtained and characterized. Some features of epoxidation of polynorbornenes by 1.1-dimethyldioxirane (formed in situ) or m-chloroperbenzoic acid were studied. It was shown that m-chloroperbenzoic acid was an effective epoxidation agent, which did not affect Si?C bonds in polynorbornenes. It was found that the preparation of high-molecular-weight epoxidated polynorbornenes required one to introduce an oxidation inhibitor into the reaction mixture and to perform the reaction in toluene. Chlorine-containing solvents, such as chloroform and chlorobenzene, promoted the destruction of polynorbornenes. It was shown that the introduction of oxirane fragments into the polynorbornene main chain increased its T _g by 15?40°C.     

A Study of peptide-peptide interaction by matrix-assisted laser desorption/ionization

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry was used to study peptide-peptide interaction. The interaction was seen when 6-aza-2-thiothymine was used as a matrix (pH 5.4), but was disrupted with a more acidic matrix, alpha-cyano-4-hydroxycinnamic acid (pH 2.0). In the present study, we show that dynorphin, an opioid peptide, and five of its fragments that contain two adjacent basic residues (Arg6-Arg7), all interact noncovalently with peptides that contain two to five adjacent acidic residues (Asp or Glu). Two other nonrelated peptides containing two (Arg6-Arg7) or three (Arg1-Lys2-Arg3) adjacent basic amino acid residues were studied and exhibited the same behavior. However, peptides containing adjacent Lys or His did not form noncovalent complexes with acidic peptides. The noncovalent bonding was sufficiently stable that digestion with trypsin only cleaved Arg and Lys residues that were not involved in hydrogen bonding with the acidic residues. In an equimolar mixture of dynorphin, dynorphin fragments (containing the motif RR), and an acidic peptide (minigastrin), the acidic peptide preferentially complexed with dynorphin. If the concentration of minigastrin was increased 10 fold, noncovalent interaction was seen with dynorphin and all its fragments containing the motif RR. In the absence of dynorphin, minigastrin formed noncovalent complexes with all dynorphin fragments. These findings suggest that conformation, equilibrium, and concentration do play a role in the occurrence of peptide-peptide interaction. Observations from this study include: (1) ionic bonds were not disrupted by enzymatic digests, (2) conformation and concentration influenced complex formation, and (3) the complex did not form with fragments of dynorphin or unrelated peptides that did not contain the motifs RR or RKR, nor with a fragment of dynorphin where Arg7 was mutated to a phenylalanine residue. These findings strongly suggest that peptide-peptide interaction does occur, and can be studied by MALDI if near physiologic pH is maintained.     

Snake Venom Components: Tools and Cures to Target Cardiovascular Diseases

Cardiovascular diseases (CVDs) are considered as a major cause of death worldwide. Therefore, identifying and developing therapeutic strategies to treat and reduce the prevalence of CVDs is a major medical challenge. Several drugs used for the treatment of CVDs, such as captopril, emerged from natural products, namely snake venoms. These venoms are complex mixtures of bioactive molecules, which, among other physiological networks, target the cardiovascular system, leading to them being considered in the development and design of new drugs. In this review, we describe some snake venom molecules targeting the cardiovascular system such as phospholipase A2 (PLA2), natriuretic peptides (NPs), bradykinin-potentiating peptides (BPPs), cysteine-rich secretory proteins (CRISPs), disintegrins, fibrinolytic enzymes, and three-finger toxins (3FTXs). In addition, their molecular targets, and mechanisms of action—vasorelaxation, inhibition of platelet aggregation, cardioprotective activities—are discussed. The dissection of their biological effects at the molecular scale give insights for the development of future snake venom-derived drugs.     

Synthesis of iodinated meta-carboranecarboxylic acids

A new method for introduction of one and two iodine atoms into the meta-carborane fragments containing carboxy groups at the core carbon atoms C¹/C² was developed. Reaction proceeded in acetic acid at heating in the presence of concentrated nitric and sulfuric acids.     

Amino acid bromides: their utilization for difficult couplings in solid-phase peptide synthesis

Use of N-protected-α-amino acid bromides for facile solid-phase synthesis of peptides (SPPS) containing extremely sterically hindered non-proteinogenic amino acids is presented. Amino acid bromides (Aaa-Br), generated in situ, were used for the synthesis of long chain homopeptides containing up to eight successive α-MeVal or Aib residues. SPPS of a heteropeptide containing a very bulky amino acid building block is also described. The choice of suitable N-protections is discussed.     

Similarity between condensed phase and gas phase chemistry: Fragmentation of peptides containing oxidized cysteine residues and its implications for proteomics

Amino acid residues containing thioethers are easily oxidized during protein purification, derivatization, and/or digestion. For instance, oxidation of methionine residues in proteins during SDS-PAGE is commonly observed. Under low energy collision induced dissociation this gives rise to a second series of fragment ion of lower abundance that are shifted by -64 Da when compared to the oxidized methionine-containing fragments. We report here that alkylated cysteine residues can be found in their oxidized form too, indicating that the oxidation of thioethers can occur during and following protein digestion and not only during SDS-PAGE or reduction and alkylation. Collision induced dissociation experiments on the singly- and multiply-charged species reveals that these peptides preferentially undergo elimination reactions that forms a dehydroalanine from the oxidized, alkylated cysteine residue. This contrasts to the less abundant elimination reaction of peptides containing oxidized methionines which cannot form an alpha,beta-unsaturated compound, but parallels the condensed phased chemistry of sulfoxides. The masses of both precursor and product ions are shifted such that these peptides cannot be identified in database searches with current algorithms. Incorporation of this fragmentation pattern is important for the isotope-coded affinity tag approach since this method is based on peptides containing cysteine residues.     

有机分子中引入二氟亚甲基方法的最新进展

本综述从直接氟化法和间接氟化法两个方面就近些年来在有机化合物中引入二氟亚甲基的方法进行了概括。直接氟化法中，主要介绍了利用亲核和亲电两类氟化试剂在分子中导入-CF~2-的一些最新进展；间接氟化法则主要介绍了一些新的含-CF~2-的合成砌块在合成二氟亚甲基化合物中的应用。     

Modelling of the gas-phase phosphate group loss and rearrangement in phosphorylated peptides

The gas-phase dissociation of phosphorylated peptides was modelled using a combination of quantum mechanics and the Rice-Ramsperger-Kassel-Marcus theory. Potential energy surfaces and unimolecular reaction rates for several low-energy fragmentation and rearrangement pathways were estimated, and a general mechanism was proposed. The neutral loss of the phosphoric acid was mainly an outcome of the intramolecular nucleophilic substitution mechanism. The mechanism involves a nucleophilic attack of the phosphorylated amino acid N-terminal carbonyl oxygen on β-carbon, yielding a cyclic five-membered oxazoline product ion. Regardless of the proton mobility, the pathway was charge directed either by a mobile proton or by a positively charged side chain of some basic residue. Although the mechanistic aspects of the phosphate loss are not influenced by the proton mobility environment, it does affect ion abundances. Results suggest that under the mobile proton environment, the interplay between phosphoric acid neutral loss product ion and backbone cleavage fragments should occur. On the other hand, when proton mobility is limited, neutral loss product ion may predominate. The fragmentation dynamics of phosphoserine versus phosphothreonine containing peptides suggests that H(3)PO(4) neutral loss from phosphothreonine containing peptides is less abundant than that from their phosphoserine containing analogs. During the low-energy CID of phosphorylated peptides in the millisecond time range, typical for ion trap instruments, a phosphate group rearrangement may happen, resulting in an interchange between the phosphorylated and the hydroxylated residues. Unimolecular dissociation rate constants imply the low abundance of such scrambled product ions.     

Redox Imbalance and Mitochondrial Release of Apoptogenic Factors at the Forefront of the Antitumor Action of Mango Peel Extract

Today, an improved understanding of cancer cell response to cellular stress has become more necessary. Indeed, targeting the intracellular pro-oxidant/antioxidant balance triggering the tumor commitment to cell demise could represent an advantageous strategy to develop cancer-tailored therapies. In this scenario, the present study shows how the peel extract of mango—a tropical fruit rich in phytochemicals with nutraceutical properties—can affect the cell viability of three colon cancer cell lines (HT29, Caco-2 and HCT116), inducing an imbalance of cellular redox responses. By using hydro-alcoholic mango peel extract (MPE), we observed a consistent decline in thiol group content, which was accompanied by upregulation of MnSOD—a mitochondrial scavenger enzyme that modulates the cellular response against oxidative damage. Such an effect was the consequence of an early production of mitochondrial superoxide anions that appeared after just 30 min of exposure of colon cancer cells to MPE. The effect was accompanied by mitochondrial injury, consisting of the dissipation of mitochondrial membrane potential and a decrease in the level of proteins localized in the mitochondrial membrane—such as voltage-dependent anion-selective channel (VDAC1), mitofilin, and some members of Bcl-2 family proteins (Mcl-1, Bcl-2 and Bcl-X_L)—with the mitochondrial release of apoptogenic factors (cytochrome C and AIF). The analysis of the cytotoxic effects exerted by the different constituents of MPE (gallic acid, mangiferin, citric acid, quinic acid, pentagalloyl glucose, and methyl gallate) allowed us to identify those phytochemicals responsible for the observed anticancer effects, sustaining their future employment as chemopreventive or therapeutic agents.     

Optimum concentration of trifluoroacetic acid for reversed-phase liquid chromatography of peptides revisited

Trifluoroacetic acid (TFA) remains the dominant mobile phase additive for reversed-phase high-performance liquid chromatography (RP-HPLC) of peptides after more than two decades since its introduction to this field. Generally, TFA has been employed in a concentration range of 0.05-0.1% (6.5-13 mM) for the majority of peptide separations. In order to revisit the question as to whether such a concentration range is optimum for separations of peptide mixtures containing peptides of varying net positive charge, the present study examined the effect of varying TFA concentration on RP-HPLC at 25 and 70 degrees C of three groups of synthetic 10-residue synthetic peptides containing either one (+1) or multiple (+3, +5) positively charged groups. The results show that the traditional range of TFA concentrations employed for peptide studies is not optimum for many, perhaps the majority, of peptide applications. For efficient resolution of peptide mixtures, particularly those containing peptides with multiple positive charges, our results show that 0.2-0.25% TFA in the mobile phase will achieve optimum resolution. In addition, the use of high temperature as a complement to such TFA concentration levels is also effective in maximizing peptide resolution.     

Design and synthesis of a multi-detachable benzhydrylamine-resin for solid phase peptide synthesis

Peptides with C-terminal α-carboxamides were synthesized from a multi-detachable benzhydrylamine-resin containing a Boc-(4-acetoxy)benzhydryl-amine handle of unambiguous origin. The peptides bound to the new resin are stable to trifluoroacetic acid, but are cleavable by hydrogen fluoride, base and nucleophiles to give unprotected or protected peptide fragments.     

1-Ethoxyethylidene, a new group for the stepwise SPPS of aminooxyacetic acid containing peptides

For more than a decade, the oxime ether ligation has proven to be one of the most efficient technique for the preparation of various peptide conjugates. However, despite numerous reports, the preparation of aminooxy-containing peptides is still hampered by N-overacylation of the NH-O function either during its incorporation or through the peptide-chain elongation. This restricts the introduction of protected-NH-O function at the last acylation step and prevents the use of standard solid-phase peptide synthesis (SPPS) procedures for the preparation of more complex aminooxy-peptides. We have studied the coupling of modified Fmoc-lysine containing either N-Boc- or N,N'-bis-Boc-protected aminooxyacetic acids (Aoa) during the elongation of the peptide chain and found that none of them is adequate. To circumvent this limitation, we propose to protect the Aoa moiety with a 1-ethoxyethylidene group (Eei) to provide 2-(1-ethoxyethylideneaminooxy)acetic acid building block. We showed that the Eei group is fully compatible with standard SPPS conditions and safely allows the multiple incorporation of the aminooxy functionality into the growing peptide. Since Eei-protected Aoa remains as flexible as normal amino acids in peptide synthesis, it may become the rule for the straightforward preparation of aminooxy peptides.     

Phytoecdysteroids from Serratula coronata L. for Psoriatic Skincare

Phytoecdysones from Serratula coronata seem to be promising agents for skincare in patients with psoriasis. The aim of the study was to determine the effects of creams containing the extract of S. coronata on psoriatic lesions. Creams with different formulas were prepared: 0-Lekobaza^®, 1-Lekobaza^®, S. coronata, 2-Lekobaza^®, Salicylic acid, 3-Lekobaza^®, S. coronata, Salicylic acid. After examination of skin penetration and biosafety, the designated cream was applied twice daily for 6 weeks on 72 psoriatic plaques located on elbows or knees. The lesions were assessed at baseline and follow-up of 6 weeks. The lesions area was measured, and severity of scaling, erythema, and infiltration was assessed using a 5-point scale (from 0—none to 4—very severe). Skin hydration and structure, pH, transepidermal water loss, erythema, and melanin index were analyzed instrumentally. Creams 1, 2, and 3 significantly reduced the area of psoriatic plaques. Improvement in erythema and infiltration was observed for creams 1 and 3. Creams 1–3 reduced scaling. Our study confirmed a beneficial effect of creams containing S. coronata extract on psoriatic lesions.