A valid model for the mechanism of oxidation of tryptophan to formylkynurenine-25 years later

Photosensitized Oxidation of Free and Peptide Tryptophan to N-Formylkynurenine

The oxidation of proteins and, in particular, of tryptophan (Trp) residues leads to chemical modifications that can affect the structure and function. The oxidative damage to proteins in photochemical processes is relevant in the skin and eyes and is related to a series of pathologies triggered by exposure to electromagnetic radiation. In this work, we studied the photosensitized formation of N-formylkynurenine (NFKyn) from Trp in different reaction systems. We used two substrates: free Trp and a peptide of nine amino acid residues, with Trp being the only oxidizable residue. Two different photosensitizers were employed: Rose Bengal (RB) and pterin (Ptr). The former is a typical type II photosensitizer [acts by producing singlet oxygen (1O2)]. Ptr is the parent compound of oxidized or aromatic pterins, natural photosensitizers that accumulate in human skin under certain pathological conditions and act mainly through type I mechanisms (generation of radicals). Experimental data were collected in steady photolysis, and the irradiated solutions were analyzed by chromatography (HPLC). Results indicate that the reaction of Trp with 1O2 initiates the process leading to NFKyn, but different competitive pathways take place depending on the photosensitizer and the substrate. In Ptr-photosensitization, a type I mechanism is involved in secondary reactions accelerating the formation of NFKyn when free Trp is the substrate.

Revisiting carotenoids as dietary antioxidants for human health and disease prevention

Humans are unique indiscriminate carotenoid accumulators, so the human body accumulates a wide range of dietary carotenoids of different types and to varying concentrations. Carotenoids were once recognized as physiological antioxidants because of their ability to quench singlet molecular oxygen (1O2). In the 1990s, large-scale intervention studies failed to demonstrate that supplementary β-carotene intake reduces the incidence of lung cancer, although its antioxidant activity was supposed to contribute to the prevention of oxidative stress-induced carcinogenesis. Nevertheless, the antioxidant activity of carotenoids has attracted renewed attention as the pathophysiological role of 1O2 has emerged, and as the ability of dietary carotenoids to induce antioxidant enzymes has been revealed. This review focuses on six major carotenoids from fruit and vegetables and revisits their physiological functions as biological antioxidants from the standpoint of health promotion and disease prevention. β-Carotene 9',10'-oxygenase-derived oxidative metabolites trigger increases in the activities of antioxidant enzymes. Lutein and zeaxanthin selectively accumulate in human macular cells to protect against light-induced macular impairment by acting as antioxidants. Lycopene accumulates exclusively and to high concentrations in the testis, where its antioxidant activity may help to eliminate oxidative damage. Dietary carotenoids appear to exert their antioxidant activity in photo-irradiated skin after their persistent deposition in the skin. An acceptable level of dietary carotenoids for disease prevention should be established because they can have deleterious effects as prooxidants if they accumulate to excess levels. Finally, it is expected that the reason why humans are indiscriminate carotenoid accumulators will be understood soon.

Strategies for total synthesis of bispyrrolidinoindoline alkaloids

Covering up to 2021Complex cyclotryptamine alkaloids with a bispyrrolidino[2,3-b]indoline (BPI) skeleton are an intriguing family of natural products, exhibiting wide systematic occurrences, large structural diversity, and multiple biological activities. Based on their structural characteristics, BPI alkaloids can be classified into chimonanthine-type BPI alkaloids, BPI diketopiperazines, and BPI epipolythiodiketopiperazines. These intricate molecules have captivated great attention soon after their isolation and identification in the 1960s. Due to the structural complexity, the total synthesis of these cyclotryptamine alkaloids is challenging. Nevertheless, remarkable progress has been achieved in the last six decades; in particular, several methods have been successfully established for the construction of vicinal all-carbon quaternary stereocenters. In this review, the structural diversity and chemical synthesis of these BPI alkaloids were summarized. BPI alkaloids are mainly synthesized by the methods of oxidative dimerization, reductive dimerization, and alkylation of bisoxindole. The purpose of this review is to present overall strategies for assembling the BPI skeleton and efforts towards controlling the stereocenters.

Two-colour single-molecule photoinduced electron transfer fluorescence imaging microscopy of chaperone dynamics

Many proteins are molecular machines, whose function is dependent on multiple conformational changes that are initiated and tightly controlled through biochemical stimuli. Their mechanistic understanding calls for spectroscopy that can probe simultaneously such structural coordinates. Here we present two-colour fluorescence microscopy in combination with photoinduced electron transfer (PET) probes as a method that simultaneously detects two structural coordinates in single protein molecules, one colour per coordinate. This contrasts with the commonly applied resonance energy transfer (FRET) technique that requires two colours per coordinate. We demonstrate the technique by directly and simultaneously observing three critical structural changes within the Hsp90 molecular chaperone machinery. Our results reveal synchronicity of conformational motions at remote sites during ATPase-driven closure of the Hsp90 molecular clamp, providing evidence for a cooperativity mechanism in the chaperone’s catalytic cycle. Single-molecule PET fluorescence microscopy opens up avenues in the multi-dimensional exploration of protein dynamics and allosteric mechanisms.

Revealing mechanisms of complex protein machines requires simultaneous exploration of multiple structural coordinates. Here the authors report two-colour fluorescence microscopy combined with photoinduced electron transfer probes to simultaneously detect two structural coordinates in single protein molecules.

The Effects of Ionising and Non-Ionising Electromagnetic Radiation on Extracellular Matrix Proteins

Exposure to sub-lethal doses of ionising and non-ionising electromagnetic radiation can impact human health and well-being as a consequence of, for example, the side effects of radiotherapy (therapeutic X-ray exposure) and accelerated skin ageing (chronic exposure to ultraviolet radiation: UVR). Whilst attention has focused primarily on the interaction of electromagnetic radiation with cells and cellular components, radiation-induced damage to long-lived extracellular matrix (ECM) proteins has the potential to profoundly affect tissue structure, composition and function. This review focuses on the current understanding of the biological effects of ionising and non-ionising radiation on the ECM of breast stroma and skin dermis, respectively. Although there is some experimental evidence for radiation-induced damage to ECM proteins, compared with the well-characterised impact of radiation exposure on cell biology, the structural, functional, and ultimately clinical consequences of ECM irradiation remain poorly defined.

Visible-Light-Mediated Modification and Manipulation of Biomacromolecules

Chemically modified biomacromolecules-i.e., proteins, nucleic acids, glycans, and lipids-have become crucial tools in chemical biology. They are extensively used not only to elucidate cellular processes but also in industrial applications, particularly in the context of biopharmaceuticals. In order to enable maximum scope for optimization, it is pivotal to have a diverse array of biomacromolecule modification methods at one's disposal. Chemistry has driven many significant advances in this area, and especially recently, numerous novel visible-light-induced photochemical approaches have emerged. In these reactions, light serves as an external source of energy, enabling access to highly reactive intermediates under exceedingly mild conditions and with exquisite spatiotemporal control. While UV-induced transformations on biomacromolecules date back decades, visible light has the unmistakable advantage of being considerably more biocompatible, and a spectrum of visible-light-driven methods is now available, chiefly for proteins and nucleic acids. This review will discuss modifications of native functional groups (FGs), including functionalization, labeling, and cross-linking techniques as well as the utility of oxidative degradation mediated by photochemically generated reactive oxygen species. Furthermore, transformations at non-native, bioorthogonal FGs on biomacromolecules will be addressed, including photoclick chemistry and DNA-encoded library synthesis as well as methods that allow manipulation of the activity of a biomacromolecule.

Inactivation and Site-specific Oxidation of Aquatic Extracellular Bacterial Leucine Aminopeptidase by Singlet Oxygen

Extracellular enzymes are master recyclers of organic matter, and to predict their functional lifetime, we need to understand their environmental transformation processes. In surface waters, direct and indirect photochemical transformation is a known driver of inactivation. We investigated molecular changes that occur along with inactivation in aminopeptidase, an abundant class of extracellular enzymes. We studied the inactivation kinetics and localized oxidation caused by singlet oxygen, ¹O₂, a major photochemically derived oxidant toward amino acids. Aminopeptidase showed second-order inactivation rate constants with ¹O₂ comparable to those of free amino acids. We then visualized site-specific oxidation kinetics within the three-dimensional protein and demonstrated that fastest oxidation occurred around the active site and at other reactive amino acids. However, second-order oxidation rate constants did not correlate strictly with the ¹O₂-accessible surface areas of those amino acids. We inspected site-specific processes by a comprehensive suspect screening for 723,288 possible transformation products. We concluded that histidine involved in zinc coordination at the active site reacted slower than what was expected by its accessibility, and we differentiated between two competing reaction pathways of ¹O₂ with tryptophan residues. This systematic analysis can be directly applied to other proteins and transformation reactions.

Identification and Quantification of Oxidation Products in Full-Length Biotherapeutic Antibodies by NMR Spectroscopy

Therapeutic proteins are an indispensable class of drugs and often therapeutics of last resort. They are sensitive to oxidation, which is of critical concern, because it can affect drug safety and efficacy. Protein oxidation, with methionine and tryptophan as the most susceptible moieties, is mainly monitored by HPLC–MS techniques. However, since several oxidation products display the same mass difference, their identification by MS is often ambiguous. Therefore, an alternative analytical method able to unambiguously identify and, ideally, also quantify oxidation species in proteins is highly desired. Here, we present an NMR-based approach to monitor oxidation in full-length proteins under denaturing conditions, as demonstrated on two biotherapeutic monoclonal antibodies (mAbs). We show that methionine sulfoxide, methionine sulfone, N-formylkynurenine, kynurenine, oxindolylalanine, hydroxypyrroloindole, and 5-hydroxytryptophan result in characteristic chemical shift correlations suited for their identification and quantification. We identified the five most abundant oxidation products in forced degradation studies of two full-length therapeutic mAbs and can also unambiguously distinguish oxindolylalanine from 5-hydroxytryptophan, which are undistinguishable by MS due to the same mass shift. Quantification of the abundant methionine sulfoxide by NMR and MS gave highly comparable values. These results underline the suitability of NMR spectroscopy for the identification and quantification of critical quality attributes of biotherapeutics.

UV-A induced damage to lysozyme via Type I photochemical reactions sensitized by kynurenic acid

In this work we studied the mechanisms of Type I photodamage to a model protein, hen egg white lysozyme (HEWL), sensitized by kynurenic acid (KNA) - one of the most efficient photosensitizers of the human eye lens present in trace amounts within tissue. The kynurenic acid radical, KNA^•-, formed in the quenching of triplet KNA by HEWL, can be readily oxidized by molecular oxygen with the formation of superoxide anion radical O₂^•-. This leads to two ways of damage to proteins: either via the direct reactions between KNA^•- and HEWL^• radicals (Type Ia) or via the reactions between superoxide anion O₂^•- and HEWL^• radicals (Type Ib). Our results demonstrate significant degradation of the protein during Type Ia photolysis with the formation of various oligomeric and oxygenated forms of HEWL and several deoxygenated products of KNA. Liquid chromatography-mass spectrometry analysis revealed the cross-linking of HEWL via tryptophan (Trp⁶²) and tyrosine (Tyr²³) residues and, for the first time, the covalent binding of KNA to protein via tryptophan (Trp⁶² and Trp¹²³) residues. It was found that Type Ib reactions lead to substantially smaller damage to HEWL; the degradation quantum yields (Φ_deg) of HEWL are 1.3 ± 0.3% and 0.12 ± 0.03% for Type Ia and Ib photolyses, respectively. Low Φ_deg values for both types of photolysis indicate the Back Electron Transfer (BET) with the restoration of initial reagents as the main radical decay path with significantly higher BET efficiency in the case of Type Ib reactions. Therefore, in essentially oxygen-free tissues like the eye lens, the direct radical reactions via Type Ia mechanism could induce significantly larger damage to proteins, leading to their cross-linking and oxidation. The accumulation of these modifications can cause the development of various diseases, in particular, cataracts in the eye lens.

Environmental fate processes of antimicrobial peptides daptomycin, bacitracins, and polymyxins

Antimicrobial peptides (AMPs) are increasingly important as a last resort against multi-drug resistant bacteria due to resistance formation towards conventional antibiotics. However, many AMPs were introduced to the market before environmental risk assessment was required, e.g., by the European Medicines Agency (EMA) since 1998. While AMPs have been administered as antibiotics and growth promotors in feedstock since the 1960s and were reconsidered for human medicine by the EMA in 2013, details about their mobility and persistence in the environment remain unknown. This study investigated the environmental fate of three commonly used AMPs: bacitracins, daptomycin, and polymyxins B and E (Colistin). We observed moderate sorption affinity of daptomycin to standard European soils (K_d = 20.6-48.6), while polymyxins adsorbed irreversibly. Bacitracin variants sorbed slightly to sandy soil (K_d = 5.8-8) and significantly to clayey soil (K_d = 169-250). We further investigated photochemical and microbial transformation processes relevant in surface waters. We demonstrated that phototransformation of all AMPs was enhanced in the presence of dissolved organic matter and fast bimolecular reaction rate constant with singlet oxygen contributed largely to indirect phototransformation (15-41%). Phototransformation product analysis for daptomycin was consistent with expected modifications of the tryptophan and kynurenine moieties. Moreover, riverine biofilm communities demonstrated biotransformation potential for all AMPs. Our findings of sorption behaviour, photo- and biotransformation suggest that these processes play a critical role in the fate of bacitracins, daptomycin, and polymyxins in environmental systems.

Susceptibility of protein therapeutics to spontaneous chemical modifications by oxidation, cyclization, and elimination reactions

Peptides and proteins are preponderantly emerging in the drug market, as shown by the increasing number of biopharmaceutics already approved or under development. Biomolecules like recombinant monoclonal antibodies have high therapeutic efficacy and offer a valuable alternative to small-molecule drugs. However, due to their complex three-dimensional structure and the presence of many functional groups, the occurrence of spontaneous conformational and chemical changes is much higher for peptides and proteins than for small molecules. The characterization of biotherapeutics with modern and sophisticated analytical methods has revealed the presence of contaminants that mainly arise from oxidation- and elimination-prone amino-acid side chains. This review focuses on protein chemical modifications that may take place during storage due to (1) oxidation (methionine, cysteine, histidine, tyrosine, tryptophan, and phenylalanine), (2) intra- and inter-residue cyclization (aspartic and glutamic acid, asparagine, glutamine, N-terminal dipeptidyl motifs), and (3) β-elimination (serine, threonine, cysteine, cystine) reactions. It also includes some examples of the impact of such modifications on protein structure and function.

Identification of Products from Thermal Degradation of Tryptophan Containing Pentapeptides: Oxidation and Decarboxylation

In this contribution, we investigate the thermal decomposition of four pentapeptides containing a tryptophan moiety. Pentapeptides were heated at 220 °C, and the resulting reaction mixtures were investigated by HPLC coupled to high-resolution mass spectrometry and tandem mass spectrometry. A total of 95 thermal decomposition products could be observed and resolved by chromatography. In detail, we report on the structure assignment of two types of reaction products common to investigated peptides and introduce two decomposition mechanisms. Pentapeptides react with oxygen to produce hydroxyl-tryptophan derivatives. In addition, we observe the C-terminal decarboxylation of two peptides to form N-acyl tryptamine derivatives.

Oxidative degradation pathways of beclabuvir hydrochloride mediated by hydrogen peroxide and UV/Vis light

Beclabuvir hydrochloride (BCV) is a marketed product for the treatment of hepatitis C viral infection. It contains functional groups such as indole, tertiary amine and amides. Forced degradation studies of BCV revealed different degradation profiles under photo and hydrogen peroxide oxidative conditions. Under the photo-oxidative degradation conditions, the tertiary amine on the piperazine ring was oxidized to form the degradants as the hydroxyl and des-methyl analogs of beclabuvir. However, under the oxidative condition using hydrogen peroxide, the indole ring was oxidized to form a typical kynuric degradant and two unexpected cyclohexyl rearranged diastereomeric degradants. The plausible mechanisms for the photo and hydrogen peroxide mediated oxidative degradation of beclabuvir hydrochloride are proposed.

Bioactive Rearrangement Products from Aqueous Photolysis of Pharmaceutical Steroids

In an ongoing effort to study the environmental fate of endocrine-active steroid hormones, we report the formation of phenolic rearrangement products (3 and 4) with a novel 6,5,8,5-ring system following aqueous photolysis of dienogest (1) and methyldienolone (2). The structures were established by analysis of 2D NMR and HRMS data, and that of 3 was confirmed by X-ray diffraction analysis. These photoproducts exhibit progestogenic and androgenic activity, albeit with less potency than their parent compounds.

Riboflavin-induced Type 1 photo-oxidation of tryptophan using a high intensity 365 nm light emitting diode

The mechanism of photo-oxidation of tryptophan (Trp) sensitized by riboflavin (RF) was examined employing high concentrations of Trp and RF, with a high intensity 365 nm light emitting diode (LED) source under N₂, 20% and 100% O₂ atmospheres. Dimerization of Trp was a major pathway under the N₂ atmosphere, though this occurred with a low yield (^Dφ_Trp = 5.9 × 10^-3), probably as a result of extensive back electron transfer reactions between RF^•- and Trp(H)^•+. The presence of O₂ decreased the extent of this back electron transfer reaction, and the extent of Trp dimerization. This difference is attributed to the formation of O₂^•- (generated via electron transfer from RF^•- to O₂) which reacts rapidly with Trp^• leading to extensive consumption of the parent amino acid and formation of peroxides and multiple other oxygenated products (N-formylkynurenine, alcohols, diols) of Trp, as detected by LC-MS. Thus, it appears that the first step of the Type 1 mechanism of Trp photo-oxidation, induced by this high intensity 365 nm light source, is an electron transfer reaction between the amino acid and ³RF, with the presence of O₂ modulating the subsequent reactions and the products formed, as a result of O₂^•- formation. These data have potential biological significance as LED systems and RF-based treatments have been proposed for the treatment of pathological myopia and keratitis.

Superoxide radicals react with peptide-derived tryptophan radicals with very high rate constants to give hydroperoxides as major products

Oxidative damage is a common process in many biological systems and proteins are major targets for damage due to their high abundance and very high rate constants for reaction with many oxidants (both radicals and two-electron species). Tryptophan (Trp) residues on peptides and proteins are a major sink for a large range of biological oxidants as these side-chains have low radical reduction potentials. The resulting Trp-derived indolyl radicals (Trp^•) have long lifetimes in some circumstances due to their delocalized structures, and undergo only slow reaction with molecular oxygen, unlike most other biological radicals. In contrast, we have shown previously that Trp^• undergo rapid dimerization. In the current study, we show that Trp^• also undergo very fast reaction with superoxide radicals, O₂^•-, with k 1-2 × 10⁹ M^-1 s^-1. These values do not alter dramatically with peptide structure, but the values of k correlate with overall peptide positive charge, consistent with positive electrostatic interactions. These reactions compete favourably with Trp^• dimerization and O₂ addition, indicating that this may be a major fate in some circumstances. The Trp^• + O₂^•- reactions occur primarily by addition, rather than electron transfer, with this resulting in high yields of Trp-derived hydroperoxides. Subsequent degradation of these species, both stimulated and native decay, gives rise to N-formylkynurenine, kynurenine, alcohols and diols. These data indicate that reaction of O₂^•- with Trp^• should be considered as a major pathway to Trp degradation on peptides and proteins subjected to oxidative damage.

Stepwise O-Atom Transfer in Heme-Based Tryptophan Dioxygenase: Role of Substrate Ammonium in Epoxide Ring Opening

Heme-based tryptophan dioxygenases are established immunosuppressive metalloproteins with significant biomedical interest. Here, we synthesized two mechanistic probes to specifically test if the α-amino group of the substrate directly participates in a critical step of the O atom transfer during catalysis in human tryptophan 2,3-dioxygenase (TDO). Substitution of the nitrogen atom of the substrate to a carbon (probe 1) or oxygen (probe 2) slowed the catalytic step following the first O atom transfer such that transferring the second O atom becomes less likely to occur, although the dioxygenated products were observed with both probes. A monooxygenated product was also produced from probe 2 in a significant quantity. Analysis of this new product by HPLC coupled UV-vis spectroscopy, high-resolution mass spectrometry, 1H NMR, 13C NMR, HSQC, HMBC, and infrared (IR) spectroscopies concluded that this monooxygenated product is a furoindoline compound derived from an unstable epoxyindole intermediate. These results prove that small molecules can manipulate the stepwise O atom transfer reaction of TDO and provide a showcase for a tunable mechanism by synthetic compounds. The product analysis results corroborate the presence of a substrate-based epoxyindole intermediate during catalysis and provide the first substantial experimental evidence for the involvement of the substrate α-amino group in the epoxide ring-opening step during catalysis. This combined synthetic, biochemical, and biophysical study establishes the catalytic role of the α-amino group of the substrate during the O atom transfer reactions and thus represents a substantial advance to the mechanistic comprehension of the heme-based tryptophan dioxygenases.

Formation and detection of oxidant-generated tryptophan dimers in peptides and proteins

Free radicals are produced during physiological processes including metabolism and the immune response, as well as on exposure to multiple external stimuli. Many radicals react rapidly with proteins resulting in side-chain modification, backbone fragmentation, aggregation, and changes in structure and function. Due to its low oxidation potential, the indole ring of tryptophan (Trp) is a major target, with this resulting in the formation of indolyl radicals (Trp^•). These undergo multiple reactions including ring opening and dimerization which can result in protein aggregation. The factors that govern Trp^• dimerization, the rate constants for these reactions and the exact nature of the products are not fully elucidated. In this study, second-order rate constants were determined for Trp^• dimerization in Trp-containing peptides to be 2-6 × 10⁸M^-1s^-1 by pulse radiolysis. Peptide charge and molecular mass correlated negatively with these rate constants. Exposure of Trp-containing peptides to steady-state radiolysis in the presence of NaN₃ resulted in consumption of the parent peptide, and detection by LC-MS of up to 4 different isomeric Trp-Trp cross-links. Similar species were detected with other oxidants, including CO₃^•- (from the HCO₃^- -dependent peroxidase activity of bovine superoxide dismutase) and peroxynitrous acid (ONOOH) in the presence or absence of HCO₃^-. Trp-Trp species were also isolated and detected after alkaline hydrolysis of the oxidized peptides and proteins. These studies demonstrate that Trp^• formed on peptides and proteins undergo rapid recombination reactions to form Trp-Trp cross-linked species. These products may serve as markers of radical-mediated protein damage, and represent an additional pathway to protein aggregation in cellular dysfunction and disease.

Lysozyme oxidation by singlet molecular oxygen: Peptide characterization using [18 O]-labeling oxygen and nLC-MS/MS

Singlet molecular oxygen (¹ O₂ ) is generated in biological systems and reacts with different biomolecules. Proteins are a major target for ¹ O₂ , and His, Tyr, Met, Cys, and Trp are oxidized at physiological pH. In the present study, the modification of lysozyme protein by ¹ O₂ was investigated using mass spectrometry approaches. The experimental findings showed methionine, histidine, and tryptophan oxidation. The experiments were achieved using [¹⁸ O]-labeled ¹ O₂ released from thermolabile endoperoxides in association with nano-scale liquid chromatography coupled to electrospray ionization mass spectrometry. The structural characterization by nLC-MS/MS of the amino acids in the tryptic peptides of the proteins showed addition of [¹⁸ O]-labeling atoms in different amino acids.

On the prevalence of bridged macrocyclic pyrroloindolines formed in regiodivergent alkylations of tryptophan

A Friedel-Crafts alkylation is described that efficiently transforms tryptophan-containing peptides into macrocycles of varying ring connectivity. Factors are surveyed that influence the distribution of regioisomers, with a focus on indole C3-alkylations leading to bridged endo-pyrroloindolines. We probe the stability and stereochemistry of these pyrroloindolines, study their rearrangement to C2-linked indolic macrocycles, and demonstrate a scalable, stereoselective synthesis of this compound class. Placing the macrocyclization in sequence with further template-initiated annulation leads to extraordinary polycyclic products and further demonstrates the potential for this chemistry to drive novel peptidomimetic lead discovery programs.

Ab-initio HF and density functional theory investigations on the synthesis mechanism, conformational stability, molecular structure and UV spectrum of N’-Formylkynurenine

Tryptophan methyl ester (Trp-ME) degrades with singlet oxygen and produce compounds which are photosensitizers and may react to form other derivatives such as N’-Formylkynurénine (NFK) and kynurenine, which are the final products of this oxidation. In order to study and optimize the molecular structure of NFK and determine its different thermodynamic properties, we performed a conformational analysis by DFT/B3LYP method with 3-21G basis set. Six most stable conformations were observed through the analysis of the potential energy surfaces, obtained by a relaxed scan of the dihedral angles.

The most stable form of NFK has been registered for D[Formula: see text], D[Formula: see text], D[Formula: see text], D[Formula: see text], D[Formula: see text], and D[Formula: see text]. The study was conducted by HF and DFT/B3LYP with 6-31G(d,p), 6-3[Formula: see text](d,p) and 6-31[Formula: see text](d,p) basis sets, on the optimized geometry of the most stable conformation and its thermodynamic and orbital properties. Two absorption bands were recorded at [Formula: see text][Formula: see text]nm and at [Formula: see text][Formula: see text]nm and were also determined by TD-DFT method. They showed good agreement with the UV experimental spectrum which confirms that it is a powerful tool to determine the dynamic and static properties of molecules. The surface of the electrostatic potential (ESP) of the NFK was also analyzed.

The mechanism of formation of N-formylkynurenine by heme dioxygenases

Heme dioxygenases catalyze the oxidation of L-tryptophan to N-formylkynurenine (NFK), the first and rate-limiting step in tryptophan catabolism. Although recent progress has been made on early stages in the mechanism, there is currently no experimental data on the mechanism of product (NFK) formation. In this work, we have used mass spectrometry to examine product formation in a number of dioxygenases. In addition to NFK formation (m/z = 237), the data identify a species (m/z = 221) that is consistent with insertion of a single atom of oxygen into the substrate during O(2)-driven turnover. The fragmentation pattern for this m/z = 221 species is consistent with a cyclic amino acetal structure; independent chemical synthesis of the 3a-hydroxypyrroloindole-2-carboxylic acid compound is in agreement with this assignment. Labeling experiments with (18)O(2) confirm the origin of the oxygen atom as arising from O(2)-dependent turnover. These data suggest that the dioxygenases use a ring-opening mechanism during NFK formation, rather than Criegee or dioxetane mechanisms as previously proposed.

Photo-oxidation of proteins

Photo-induced damage to proteins occurs via multiple pathways. Direct damage induced by UVB (λ 280-320 nm) and UVA radiation (λ 320-400 nm) is limited to a small number of amino acid residues, principally tryptophan (Trp), tyrosine (Tyr), histidine (His) and disulfide (cystine) residues, with this occurring via both excited state species and radicals. Indirect protein damage can occur via singlet oxygen ((1)O(2)(1)Δ(g)), with this resulting in damage to Trp, Tyr, His, cystine, cysteine (Cys) and methionine (Met) residues. Although initial damage is limited to these residues multiple secondary processes, that occur both during and after radiation exposure, can result in damage to other intra- and inter-molecular sites. Secondary damage can arise via radicals (e.g. Trp, Tyr and Cys radicals), from reactive intermediates generated by (1)O(2) (e.g. Trp, Tyr and His peroxides) and via molecular reactions of photo-products (e.g. reactive carbonyls). These processes can result in protein fragmentation, aggregation, altered physical and chemical properties (e.g. hydrophobicity and charge) and modulated biological turnover. Accumulating evidence implicates these events in cellular and tissue dysfunction (e.g. apoptosis, necrosis and altered cell signaling), and multiple human pathologies.

HIC resolution of an IgG1 with an oxidized Trp in a complementarity determining region

Susceptibility of tryptophan (Trp) in a complementarity-determining region (CDR) to oxidation is a significant issue for recombinant monoclonal antibody (mAb) therapeutics due to the clinical efficacy and stability concerns. Here we present a case study using hydrophobic interaction chromatography (HIC) to separate an oxidized Trp containing population of an IgG1. The best separation was achieved using dual Dionex ProPac HIC-10 columns, and the oxidized Trp population was isolated as a separated pre-peak. Peptide map analysis revealed that the oxidized Trp is located in a heavy chain CDR. In addition, the HIC method was capable of monitoring the oxidation status of the CDR Trp, as the oxidation rate of the CDR Trp measured by HIC directly correlated with the results of the peptide maps. The same method conditions were also capable of separating oxidized methionine (Met) and isomerization/deamidation products, which co-elute as another pre-peak at a different retention time from the oxidized Trp species. These observations indicate that the HIC procedure can be utilized to monitor the oxidative status of the CDR Trp in the IgG1.

Singlet-oxygen-mediated amino acid and protein oxidation: formation of tryptophan peroxides and decomposition products

Proteins are major biological targets for oxidative damage within cells owing to their high abundance and rapid rates of reaction with radicals and excited-state species, including singlet oxygen. Reaction of Tyr, Trp, and His residues, both free and on proteins, with singlet oxygen generates peroxides in high yield. Peroxides have also been detected on proteins within intact cells on exposure to visible light in the presence of a photosensitizer. The structures of some of these materials have been elucidated for free amino acids, but less is known about peptide- and protein-bound species. In this study we have characterized Trp-derived peroxides, radicals, and breakdown products generated on free Trp and Trp residues in peptides and proteins, using LC/MS/MS. With free Trp, seven major photoproducts were characterized, including two isomeric hydroperoxides, two alcohols, two diols, and N-formylkynurenine, consistent with singlet oxygen-mediated reactions. The hydroperoxides decompose rapidly at elevated temperatures and in the presence of reductants to the corresponding alcohols. Some of these materials were detected on proteins after complete enzymatic (Pronase) hydrolysis and LC/MS/MS quantification, providing direct evidence for peroxide formation on proteins. This approach may allow the quantification of protein modification in intact cells arising from singlet oxygen formation.

Mammalian heme peroxidases: from molecular mechanisms to health implications

A marked increase in interest has occurred over the last few years in the role that mammalian heme peroxidase enzymes, primarily myeloperoxidase, eosinophil peroxidase, and lactoperoxidase, may play in both disease prevention and human pathologies. This increased interest has been sparked by developments in our understanding of polymorphisms that control the levels of these enzymes, a greater understanding of the basic chemistry and biochemistry of the oxidants formed by these species, the development of specific biomarkers that can be used in vivo to detect damage induced by these oxidants, the detection of active forms of these peroxidases at most, if not all, sites of inflammation, and a correlation between the levels of these enzymes and a number of major human pathologies. This article reviews recent developments in our understanding of the enzymology, chemistry, biochemistry and biologic roles of mammalian peroxidases and the oxidants that they generate, the potential role of these oxidants in human disease, and the use of the levels of these enzymes in disease prognosis.

Oxidative modification of cytochrome c by singlet oxygen

Singlet oxygen ((1)O(2)) is a reactive oxygen species that may be generated in biological systems. Photodynamic therapy generates (1)O(2) by photoexcitation of sensitizers resulting in intracellular oxidative stress and induction of apoptosis. (1)O(2) oxidizes amino acid side chains of proteins and inactivates enzymes when generated in vitro. Among proteogenic amino acids, His, Tyr, Met, Cys, and Trp are known to be oxidized by (1)O(2) at physiological pH. However, there is a lack of direct evidence of oxidation of proteins by (1)O(2). Because (1)O(2) is difficult to detect in cells, identifying oxidized cellular products uniquely derived from (1)O(2) could serve as a marker of its presence. In the present study, (1)O(2) reactions with model peptides analyzed by tandem mass spectrometry provide insight into the mass of prominent adducts formed with the reactive amino acids. Analysis by MALDI-TOF and tandem mass spectrometry of peptides of cytochrome c exposed to (1)O(2) generated by photoexcitation of the phthalocyanine Pc 4 showed unique oxidation products, which might be used as markers of the presence of (1)O(2) in the mitochondrial intermembrane space. Differences in the elemental composition of the oxidized amino acid residues observed with cytochrome c and the model peptides suggest that the protein environment can affect the oxidation pathway.

The second enzyme in pyrrolnitrin biosynthetic pathway is related to the heme-dependent dioxygenase superfamily

Pyrrolnitrin is a commonly used and clinically effective treatment for fungal infections and provides the structural basis for the more widely used fludioxinil. The pyrrolnitrin biosynthetic pathway consists of four chemical steps, the second of which is the rearrangement of 7-chloro-tryptophan by the enzyme PrnB, a reaction that is so far unprecedented in biochemistry. When expressed in Pseudomonas fluorescens, PrnB is red in color due to the fact that it contains 1 mol of heme b per mole of protein. The crystal structure unexpectedly establishes PrnB as a member of the heme-dependent dioxygenase superfamily with significant structural but not sequence homology to the two-domain indoleamine 2,3-dioxygenase enzyme (IDO). The heme-binding domain is also structurally similar to that of tryptophan 2,3-dioxygenase (TDO). Here we report the binary complex structures of PrnB with d- and l-tryptophan and d- and l-7-chloro-tryptophan. The structures identify a common hydrophobic pocket for the indole ring but exhibit unusual heme ligation and substrate binding when compared with that observed in the TDO crystal structures. Our solution studies support the heme ligation observed in the crystal structures. Purification of the hexahistidine-tagged PrnB yields homogeneous protein that only displays in vitro activity with 7-chloro-l-tryptophan after reactivation with crude extract from the host strain, suggesting that an as yet unknown cofactor is required for activity. Mutation of the proximal heme ligand results, not surprisingly, in inactive enzyme. Redox titrations show that PrnB displays a significantly different reduction potential to that of IDO or TDO, indicating possible differences in the PrnB catalytic cycle. This is confirmed by the absence of tryptophan dioxygenase activity in PrnB, although a stable oxyferrous adduct (which is the first intermediate in the TDO/IDO catalytic cycle) can be generated. We propose that PrnB shares a key catalytic step with TDO and IDO, generation of a tryptophan hydroperoxide intermediate, although this species suffers a different fate in PrnB, leading to the eventual formation of the product, monodechloroaminopyrrolnitrin.

Photoreactivity of Amino Acids: Tryptophan-induced Photochemical Events via Reactive Oxygen Species Generation

Tryptophan (Trp), an aromatic amino acid, is a constituent of peptides/proteins and is also a precursor of serotonin, kynurenine derivatives, and nicotinamide adenine dinucleotides. There have been a number of reports on photochemical reactions involving peptides/proteins which contain Trp that showed significant photodegradation, dimerization, and photoionization. The photochemical properties of Trp have not been fully elucidated, and this would provide novel insight into the handling of Trp-containing peptides/proteins. Consequently, we have been trying to evaluate the photochemical properties of Trp, as well as other essential amino acids, focusing on their photosensitivity, photodegradation, and their ability to induce lipid peroxidation. Among all the essential amino acids tested, Trp exhibited the maximal level of superoxide anion generation under 18 h of light exposure (30000 lux). UV spectral analysis of Trp suggested the absorbability of UVA/B light, and exposure of Trp, in both solid and solution states, to UVA/B light resulted in significant photodegradation (t(0.5): 18 h) and gradual color changes. In addition, photoirradiated Trp generated lipoperoxidant, a causative agent of photoirritation, and this might be associated with ROS generation.

Enantioselective Total Synthesis of Avrainvillamide and the Stephacidins

In this article, full details regarding our total synthesis of avrainvillamide and the stephacidins are presented. After an introduction and summary of prior synthetic studies in this family of structurally complex anticancer natural products, the evolution of a final synthetic approach is described. Thus, a thorough description of three separate model studies is provided for construction of the characteristic bicyclo[2.2.2]diazaoctane ring system common to these alkaloids. The first and second approaches sought to build the core using formal Diels-Alder and vinyl radical pathways, respectively. Although these strategies failed in their primary objective, they fostered the development of a new and mechanistically intriguing method for the synthesis of indolic enamides such as those found in numerous bioactive natural products. The scope and generality of this simple method for the direct dehydrogenation of tryptophan derivatives is described. Finally, details of a third and successful route to the core of these alkaloids are described which features oxidative C-C bond formation. Specifically, the first heterocoupling of two different types of carbonyl species (ester and amide) is accomplished in good yield, on a preparative scale, and with complete stereocontrol. The information gained in these model studies enabled an enantioselective total synthesis of stephacidin A. The absolute configuration of these alkaloids was firmly established in collaboration with Professor William Fenical. A full account of our successful efforts to convert stephacidin A into stephacidin B via avrainvillamide is presented. Finally, the first analogues of these natural products have been prepared and evaluated for anticancer activity.

Sensitizer-mediated photooxidation of histidine residues: evidence for the formation of reactive side-chain peroxides

Exposure of proteins to visible light in the presence of a sensitizer results in the oxidation of Met, Trp, Tyr, Cys, and His side chains. These reactions are only partially understood, particularly with His. In this study, the oxidation of free His, His derivatives, and His-containing peptides has been examined using visible light and a range of sensitizers. It is shown that photooxidation gives rise to unstable peroxides, in a light-, illumination time-, and sensitizer-dependent manner. The yield of these materials is increased when reactions are carried out in solutions prepared with D2O, which prolongs the lifetime of 1O2, and decreased in the presence of the potent 1O2 scavenger azide, consistent with the involvement of this excited state. These peroxides have half-lives of hours, though the rate of decomposition is enhanced by elevated temperatures, reductants, and metal ions. Reducing metal ions catalyze the formation of radicals, which have been detected by EPR spin trapping. Structural analysis of His photo-products using NMR spectroscopy has provided evidence for the formation of oxygenated and cyclized compounds (e.g., 6a-hydroxy-2-oxo-octahydro-pyrollo[2,3-d]imidazole-5-carboxylic acid) and cross-linked materials. The latter materials may be partly responsible for the high yield of aggregated materials detected on photooxidation of His-containing proteins.

Actions of ultraviolet light on cellular structures

Solar radiation is the primary source of human exposure to ultraviolet (UV) radiation. Overexposure without suitable protection (i.e., sunscreen and clothing) has been implicated in mutagenesis and the onset of skin cancer. These effects are believed to be initiated by UV-mediated cellular damage, with proteins and DNA as primary targets due to a combination of their UV absorption characteristics and their abundance in cells. UV radiation can mediate damage via two different mechanisms: (a) direct absorption of the incident light by the cellular components, resulting in excited state formation and subsequent chemical reaction, and (b) photosensitization mechanisms, where the light is absorbed by endogenous (or exogenous) sensitizers that are excited to their triplet states. The excited photosensitizers can induce cellular damage by two mechanisms: (a) electron transfer and hydrogen abstraction processes to yield free radicals (Type I); or (b) energy transfer with O2 to yield the reactive excited state, singlet oxygen (Type II). Direct UV absorption by DNA leads to dimers of nucleic acid bases including cyclobutane pyrimidine species and pyrimidine (6-4) pyrimidone compounds, together with their Dewar isomers. These three classes of dimers are implicated in the mutagenicity of UV radiation, which is typified by a high level of CC-->TT and C-->T transversions. Single base modifications can also occur via sensitized reactions including Type 1 and Type II processes. The main DNA product generated by (1)O2 is 8-oxo-Gua; this is a common lesion in DNA and is formed by a range of other oxidants in addition to UV. The majority of UV-induced protein damage appears to be mediated by (1)O2, which reacts preferentially with Trp, His, Tyr, Met, Cys and cystine side chains. Direct photo-oxidation reactions (particularly with short-wavelength UV) and radicals can also be formed via triplet excited states of some of these side chains. The initial products of (1)O2-mediated reactions are endoperoxides with the aromatic residues, and zwitterions with the sulfur-containing residues. These intermediates undergo a variety of further reactions, which can result in radical formation and ring-opening reactions; these result in significant yields of protein cross-links and aggregates, but little protein fragmentation. This review discusses the formation of these UV-induced modifications and their downstream consequences with particular reference to mutagenesis and alterations in protein structure and function.