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

Stability of Protein Pharmaceuticals: Recent Advances

There have been significant advances in the formulation and stabilization of proteins in the liquid state over the past years since our previous review. Our mechanistic understanding of protein-excipient interactions has increased, allowing one to develop formulations in a more rational fashion. The field has moved towards more complex and challenging formulations, such as high concentration formulations to allow for subcutaneous administration and co-formulation. While much of the published work has focused on mAbs, the principles appear to apply to any therapeutic protein, although mAbs clearly have some distinctive features. In this review, we first discuss chemical degradation reactions. This is followed by a section on physical instability issues. Then, more specific topics are addressed: instability induced by interactions with interfaces, predictive methods for physical stability and interplay between chemical and physical instability. The final parts are devoted to discussions how all the above impacts (co-)formulation strategies, in particular for high protein concentration solutions.'

Multienzyme Mimicking Cascade Mn3O4 Catalyst to Augment Reactive Oxygen Species Elimination and Colorimetric Detection: A Study of Phase Variation upon Calcination Temperature

Over decades, nanozyme has served as a better replacement of bioenzymes and fulfills most of the shortcomings and intrinsic disadvantages of bioenzymes. Recently, manganese-based nanomaterials have been highly noticed for redox-modulated multienzyme mimicking activity and wide applications in biosensing and biomedical science. The redox-modulated multienzyme mimicking activity was highly in tune with their size, surface functionalization, and charge on the surface and phases. On the subject of calcination temperature to Mn3O4 nanoparticles (NPs), its phase has been transformed to Mn2O3 NPs and Mn5O8 NPs upon different calcination temperatures. Assigning precise structure-property connections is made easier by preparing the various manganese oxides in a single step. The present study has focused on the variation of multienzyme mimicking activity with different phases of Mn3O4 NPs, so that they can be equipped for multifunctional activity with greater potential. Herein, spherical Mn3O4 NPs have been synthesized via a one-step coprecipitation method, and other phases are obtained by direct calcination. The calcination temperature varies to 100, 200, 400, and 600 °C and the corresponding manganese oxide NPs are named M-100, M-200, M-400, and M-600, respectively. The phase transformation and crystalline structure are evaluated by powder X-ray diffraction and selected-area electron diffraction analysis. The different surface morphologies are easily navigated by Fourier transform infrared, field-emission scanning electron microscopy, and high-resolution transmission electron microscopy analysis. Fortunately, for the mixed valence state of Mn3O4 NPs, all phases of manganese oxide NPs showed multienzyme mimicking activity including superoxide dismutase (SOD), catalase, oxidase (OD), and peroxidase; therefore, it offers a synergistic antioxidant ability to overexpose reactive oxygen species. Mn3O4 NPs exhibited good SOD-like enzyme activity, which allowed it to effectively remove the active oxygen (O2•-) from cigarette smoke. A sensitive colorimetric sensor with a low detection limit and a promising linear range has been designed to detect two isomeric phenolic pollutants, hydroquinone (H2Q) and catechol (CA), by utilizing optimized OD activity. The current probe has outstanding sensitivity and selectivity as well as the ability to visually detect two isomers with the unaided eye.

Photoinactivation of microorganisms using bacteriochlorins as photosensitizers

In recent years, some microorganisms have shown resistance to conventional treatments. Considering this increase in resistant pathogens, treatment alternatives are needed to promote greater treatment efficiency. In this sense, antimicrobial photodynamic therapy (aPDT) has been an alternative treatment. This technique uses a photosensitizer that is activated by light with a specific wavelength producing reactive species, leading to the death of pathogenic microorganisms. In this study, bacteriochlorophyll derivatives such as bacteriochlorin metoxi (Bchl-M) and bacteriochlorin trizma (Bchl-T) obtained from purple bacterium (Rhodopseudomonas faecalis), were evaluated as photosensitizers in the aPDT. Photodynamic inactivation (PDI) of the microorganisms Staphylococcus aureus, Micrococcus luteus, Candida albicans and Pseudomonas aeruginosa was investigated with both bacteriochlorins (Bchl-M and Bchl-T) at different concentrations (1, 15 and 30 µM for S. aureus; 1, 15, 30, 45, 60 and 75 µM for M. luteus; 30, 60, 90, 105, 120 and 150 µM for C. albicans; and 200 µM for P. aeruginosa) and different doses of light (20 and 30 J/cm2 for S. aureus and M. luteus; 30 and 45 J/cm2 for C. albicans; and 45 J/cm2 for P. aeruginosa) to inactivate them. Both photosensitizers showed good activation against S. aureus and for M. luteus, we observed the inactivation of these microorganisms at approximately 3 log, showing to be a good photosensitizers for these microorganisms.

The Use of Photoactive Polymeric Nanoparticles and Nanofibers to Generate a Photodynamic-Mediated Antimicrobial Effect, with a Special Emphasis on Chronic Wounds

This review is concerned with chronic wounds, with an emphasis on biofilm and its complicated management process. The basics of antimicrobial photodynamic therapy (PDT) and its underlying mechanisms for microbial eradication are presented. Intrinsically active nanocarriers (polydopamine NPs, chitosan NPs, and polymeric micelles) that can further potentiate the antimicrobial photodynamic effect are discussed. This review also delves into the role of photoactive electrospun nanofibers, either in their eluting or non-eluting mode of action, in microbial eradication and accelerating the healing of wounds. Synergic strategies to augment the PDT-mediated effect of photoactive nanofibers are reviewed.

Water-Soluble Star Polymer as a Potential Photoactivated Nanotool for Lysozyme Degradation

The development of nanotools for chemical sensing and macromolecular modifications is a new challenge in the biomedical field, with emphasis on artificial peptidases designed to cleave peptide bonds at specific sites. In this landscape, metal porphyrins are attractive due to their ability to form stable complexes with amino acids and to generate reactive oxygen species when irradiated by light of appropriate wavelengths. The issues of hydrophobic behavior and aggregation in aqueous environments of porphyrins can be solved by using its PEGylated derivatives. This work proposes the design of an artificial photo-protease agent based on a PEGylated mercury porphyrin, able to form a stable complex with l-Tryptophan, an amino acid present also in the lysozyme structure (a well-known protein model). The sensing and photodegradation features of PEGylated mercury porphyrin were exploited to detect and degrade both l-Trp and lysozyme using ROS, generated under green (532 nm) and red (650 nm) light lasers. The obtained system (Star3600_Hg) and its behavior as a photo-protease agent were studied by means of several spectroscopies (UV-Vis, fluorescence and circular dichroism), and MALDI-TOF mass spectrometry, showing the cleavage of lysozyme and the appearance of several short-chain residues. The approach of this study paves the way for potential applications in theranostics and targeted bio-medical therapies.

On-site airborne pathogen detection for infection risk mitigation

Human-infecting pathogens that transmit through the air pose a significant threat to public health. As a prominent instance, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that caused the COVID-19 pandemic has affected the world in an unprecedented manner over the past few years. Despite the dissipating pandemic gloom, the lessons we have learned in dealing with pathogen-laden aerosols should be thoroughly reviewed because the airborne transmission risk may have been grossly underestimated. From a bioanalytical chemistry perspective, on-site airborne pathogen detection can be an effective non-pharmaceutic intervention (NPI) strategy, with on-site airborne pathogen detection and early-stage infection risk evaluation reducing the spread of disease and enabling life-saving decisions to be made. In light of this, we summarize the recent advances in highly efficient pathogen-laden aerosol sampling approaches, bioanalytical sensing technologies, and the prospects for airborne pathogen exposure measurement and evidence-based transmission interventions. We also discuss open challenges facing general bioaerosols detection, such as handling complex aerosol samples, improving sensitivity for airborne pathogen quantification, and establishing a risk assessment system with high spatiotemporal resolution for mitigating airborne transmission risks. This review provides a multidisciplinary outlook for future opportunities to improve the on-site airborne pathogen detection techniques, thereby enhancing the preparedness for more on-site bioaerosols measurement scenarios, such as monitoring high-risk pathogens on airplanes, weaponized pathogen aerosols, influenza variants at the workplace, and pollutant correlated with sick building syndromes.

The Role of Polyphenolic Antioxidants from Tea and Rosemary in the Hydroxyl Radical Oxidation of N-Acetyl Alanine

In dead biological tissues such as human hair, the ability of antioxidants to minimise autoxidation is determined by their chemical reactions with reactive oxygen species. In order to improve our understanding of factors determining such antioxidant properties, the mechanistic chemistry of four phenolic antioxidants found in tea and rosemary extracts (epicatechin, epigallocatechin gallate, rosmarinic and carnosic acids) has been investigated. The degradation of N-acetyl alanine by photochemically generated hydroxyl radicals was used as a model system. A relatively high concentration of the antioxidants (0.1 equivalent with respect to the substrate) tested the ability of the antioxidants to intercept both initiating hydroxyl radicals (preventive action) and propagating peroxyl radicals (chain-breaking action). LC-MS data showed the formation of hydroxylated derivatives, quinones and hydroperoxides of the antioxidants. The structure of the assignment was aided by deuterium exchange experiments. Tea polyphenolics (epicatechin and epigallocatechin gallate) outperformed the rosemary compounds in preventing substrate degradation and were particularly effective in capturing the initiating radicals. Carnosic acid was suggested to act mostly as a chain-breaking antioxidant. All of the antioxidants except for rosmarinic acid generated hydroperoxides which was tentatively ascribed to the insufficient lability of the benzylic C-H bond of rosmarinic acid.

The Influence of Cadmium on Fountain Grass Performance Correlates Closely with Metabolite Profiles

The relationship between metabolite changes and biological endpoints in response to cadmium (Cd) stress remains unclear. Fountain grass has good Cd enrichment and tolerance abilities and is widely used in agriculture and landscaping. We analyzed the metabolic responses by detecting the metabolites through UPLC-MS and examined the relationships between metabolite changes and the characteristics of morphology and physiology to different Cd stress in fountain grass. Our results showed that under Cd stress, 102 differential metabolites in roots and 48 differential metabolites in leaves were detected, with 20 shared metabolites. Under Cd stress, most of the carbohydrates in leaves and roots decreased, which contributed to the lowered leaf/root length and fresh weight. In comparison, most of the differential amino acids and lipids decreased in the leaves but increased in the roots. Almost all the differential amino acids in the roots were negatively correlated with root length and root fresh weight, while they were positively correlated with malondialdehyde content. However, most of the differential amino acids in the leaves were positively correlated with leaf length and leaf fresh weight but negatively correlated with malondialdehyde content. Metabolic pathway analysis showed that Cd significantly affects seven and eight metabolic pathways in the leaves and roots, respectively, with only purine metabolism co-existing in the roots and leaves. Our study is the first statement on metabolic responses to Cd stress and the relationships between differential metabolites and biological endpoints in fountain grass. The coordination between various metabolic pathways in fountain grass enables plants to adapt to Cd stress. This study provides a comprehensive framework by explaining the metabolic plasticity and Cd tolerance mechanisms of plants.

Dynamic photodamage of red blood cell induced by CisDiMPyP porphyrin

It is well-known that oxidative damage in red blood cell (RBC) usually causes morphological changes and increased membrane rigidity. Although many studies have focused on investigating how RBC responds to a photodynamic stimulus, the intermediate steps between membrane damage and hemolysis are not reported. To give a comprehensive insight into changes of RBC membrane property under different oxidative damage levels, we employed the photoactivation of CisDiMPyP porphyrin that primarily generates singlet oxygen ¹O₂ as oxidant species. We found that there were distinguishable characteristic damages depending on the ¹O₂ flux over the membrane, in a way that each impact of photooxidative damage was categorized under three damage levels: mild (maintaining the membrane morphology and elasticity), moderate (membrane elongation and increased membrane elasticity) and severe (wrinkle-like deformation and hemolysis). When sodium azide (NaN₃) was used as a singlet oxygen quencher, delayed cell membrane alterations and hemolysis were detected. The delay times showed that ¹O₂ indeed plays a key role that causes RBC photooxidation by CisDiMPyP. We suggest that the sequence of morphological changes (RBC discoid area expansion, wrinkle-like patterns, and hemolysis) under photooxidative damage occurs due to damage to the lipid membrane and cytoskeletal network proteins.

Intrinsic Light-Activated Oxidase Mimicking Activity of Conductive Polyaniline Nanofibers: A Class of Metal-Free Nanozyme

In recent decades, studies have focused on inorganic nanozymes to overcome the intrinsic drawbacks of bioenzymes due to the demands of improving the reaction conditions and lack of robustness to harsh environmental factors. Many biochemical reactions catalyzed by enzymes require light activation. Light-activated nanozymes have distinct advantages, including being regulated by light stimuli, activating the molecular oxygen to produce reactive oxygen species (ROS) without interfering supplementary oxidants, and often showing a synergistic effect to catalyze some challenging reactions. Only a few studies have been done on this connection. Therefore, it is still a big challenge to develop a nanozyme regulated by light activation. Herein, we uncovered the light-activated oxidase mimicking activity of a conducting polymer polyaniline nanofibers (PANI-NFs). PANI-NFs exhibit intrinsic light-activated brilliant oxidase-like activity, can catalyze the colorless tetramethyl benzidine (TMB) to produce a blue product TMBox, and have a distinct K_m = 0.087 mM and a high V_max = 2.32 μM min^-1 value, measured by using Hanes-Woolf kinetics. We also report the light-activated oxidase activity of some other renowned carbocatalysts graphene oxide and graphitic carbon nitride and compare them with PANI-NFs. This type of property shown by the conductive polymer is amazing. The density functional theory is used to verify the stability and the mode of adsorption of the PANI NFs-TMB composite, which corroborates the experimental results. Furthermore, the current nanozyme demonstrated a significant ability to kill both Gram-negative and Gram-positive bacteria as well as effectively destroy biofilms under physiological conditions. We believe that this work provides the motivation to create a link between optoelectronics and biological activity in the near future.

Implications of differential peroxyl radical-induced inactivation of glucose 6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase for the pentose phosphate pathway

Escherichia coli glucose-6-phosphate dehydrogenase (G6PDH) and 6-phosphogluconate dehydrogenase (6PGDH) are key enzymes of the pentose phosphate pathway, responsible for the NADPH production in cells. We investigated modification of both enzymes mediated by peroxyl radicals (ROO^·) to determine their respective susceptibilities to and mechanisms of oxidation. G6PDH and 6PGDH were incubated with AAPH (2,2'-azobis(2-methylpropionamidine)dihydrochloride), which was employed as ROO^· source. The enzymatic activities of both enzymes were determined by NADPH release, with oxidative modifications examined by electrophoresis and liquid chromatography (LC) with fluorescence and mass (MS) detection. The activity of G6PDH decreased up to 62.0 ± 15.0% after 180 min incubation with 100 mM AAPH, whilst almost total inactivation of 6PGDH was determined under the same conditions. Although both proteins contain abundant Tyr (particularly 6PGDH), these residues were minimally affected by ROO^·, with Trp and Met being major targets. LC-MS and in silico analysis showed that the modification sites of G6PDH are distant to the active site, consistent with a dispersed distribution of modifications, and inactivation resulting from oxidation of multiple Trp and Met residues. In contrast, the sites of oxidation detected on 6PGDH are located close to its catalytic site indicating a more localized oxidation, and a consequent high susceptibility to ROO^·-mediated inactivation.

PDTAC: Targeted Photodegradation of GPX4 Triggers Ferroptosis and Potent Antitumor Immunity

Targeted degradation of proteins, especially those regarded as undruggable or difficult to drug, attracts wide attention to develop novel therapeutic strategies. Glutathione peroxidase 4 (GPX4), the key enzyme regulating ferroptosis, is currently a target with just covalent inhibitors. Here, we developed a targeted photolysis approach and achieved efficient degradation of GPX4. The photodegradation-targeting chimeras (PDTACs) were synthesized by conjugating a clinically approved photosensitizer (verteporfin) to noninhibitory GPX4-targeting peptides. These chimeras selectively degraded the target protein in both cell lysates and living cells upon red-light irradiation. The targeted photolysis of GPX4 resulted in dominant ferroptotic cell death in malignant cancer cells. Moreover, the dying cells resulting from the PDTACs exhibited potent immunogenicity in vitro and efficiently elicited antitumor immunity in vivo. Our approach therefore provides a novel method to induce GPX4 dysfunction based on noncovalent binding and specifically trigger immunogenic ferroptosis, which may boost the application of ferroptosis in cancer immunotherapy.

Role of amino acid oxidation and protein unfolding in peroxyl radical and peroxynitrite-induced inactivation of glucose-6-phosphate dehydrogenase from Leuconostoc mesenteroides

The mechanisms underlying the inactivation of Leuconostoc mesenteroides glucose 6-phosphate dehydrogenase (G6PDH) induced by peroxyl radicals (ROO^●) and peroxynitrite (ONOO^-), were explored. G6PDH was incubated with AAPH (2,2' -azobis(2-methylpropionamidine)dihydrochloride), used as ROO^● source, and ONOO^-. Enzymatic activity was assessed by NADPH generation, while oxidative modifications were analyzed by gel electrophoresis and liquid chromatography (LC) with fluorescence and mass detection. Changes in protein conformation were studied by circular dichroism (CD) and binding of the fluorescent dye ANS (1-anilinonaphthalene-8-sulfonic acid). Incubation of G6PDH (54.4 μM) with 60 mM AAPH showed an initial phase without significant changes in enzymatic activity, followed by a secondary time-dependent continuous decrease in activity to ∼59% of the initial level after 90 min. ONOO^- induced a significant and concentration-dependent loss of G6PDH activity with ∼46% of the initial activity lost on treatment with 1.5 mM ONOO^-. CD and ANS fluorescence indicated changes in G6PDH secondary structure with exposure of hydrophobic sites on exposure to ROO^●, but not ONOO^-. LC-MS analysis provided evidence for ONOO^--mediated oxidation of Tyr, Met and Trp residues, with damage to critical Met and Tyr residues underlying enzyme inactivation, but without effects on the native (dimeric) state of the protein. In contrast, studies using chloramine T, a specific oxidant of Met, provided evidence that oxidation of specific Met and Trp residues and concomitant protein unfolding, loss of dimer structure and protein aggregation are involved in G6PDH inactivation by ROO^●. These two oxidant systems therefore have markedly different effects on G6PDH structure and activity.

Peracetic acid integrated catalytic ceramic membrane filtration for enhanced membrane fouling control: Performance evaluation and mechanism analysis

Endowing ceramic membrane (CM) catalytic reactivity can enhance membrane fouling control in the aid of in situ oxidation process. Peracetic acid (PAA) oxidant holds great prospect to integrate with CM for membrane fouling control, owing to the prominent advantages of high oxidation efficacy and easy activation. Herein, this study, for the first time, presented a PAA/CM catalytic filtration system achieving highly-efficient protein fouling alleviation. A FeOCl functionalized CM (FeOCl-CM) was synthesized, possessing high hydrophilicity, low surface roughness, and highly-efficient activation towards PAA oxidation. Using bovine serum albumin (BSA) as the model protein foulant, the PAA/FeOCl-CM catalytic filtration notably alleviated fouling occurring in both membrane pores and surface, and halved the flux reduction degree as compared with the conventional CM filtration. The PAA/FeOCl-CM catalytic oxidation allows quick and complete disintegration of BSA particles, via the breakage of the amide I and II bands and the ring opening of the aromatic amino acids (e.g., Tryptophan, Tyrosine). In-depth investigation revealed that the in situ generated ^•OH and ¹O₂ were the key reactive species towards BSA degradation during catalytic filtration, while the organic radical oxidation and the direct electron transfer pathway from BSA to PAA via FeOCl-CM played minor roles. Overall, our findings highlight a new PAA/CM catalytic filtration strategy for achieving highly-efficient membrane fouling control and provide an understanding of the integrated PAA catalytic oxidation - membrane filtration behaviors.

Novel "Turn-On" Luminescent Chemosensor for Arginine by Using a Lanthanide Metal-Organic Framework Photosensitizer

Arginine is considered as a biomarker of cystinuria and other diseases, and thus, it is of urgency to develop a simple and rapid method with high sensitivity and selectivity for arginine detection to meet the demand of on-site analysis and bedside diagnosis. In this work, a lanthanide metal-organic framework, La(TATB), was prepared using a triazine-based planar ligand, 4,4',4″-s-triazine-2,4,6-triyltribenzoate (H₃TATB), and lanthanide ion (La³⁺). La(TATB) can be used as a highly photosensitive agent to activate molecular oxygen to ¹O₂ to achieve efficient photosensitive oxidation of arginine accompanied by strong blue fluorescence emission under 302 nm UV irradiation. Due to the porous structure and high specific surface area of La(TATB), short-life ¹O₂ can effectively approach and react with amino acid substrate molecules, thus leading to higher sensitivity than other systems. Therefore, the "turn-on" fluorescence sensing of trace arginine can be realized, with a measured linear response range of 10-20,000 nM and a limit of detection as low as 7 nM. This method can be used for the detection of trace arginine in urine, which is conducive to the bedside diagnosis and rapid screening of cystinuria and other diseases. The proposed method not only expands the application scope of Ln-MOFs but also provides a new construction strategy for "turn-on" luminescence sensors.

Oxidant-mediated modification and cross-linking of beta-2-microglobulin

Beta-2-microglobulin (B2M) is synthesized by all nucleated cells and forms part of the major histocompatibility complex (MHC) class-1 present on cell surfaces, which presents peptide fragments to cytotoxic CD8⁺ T-lymphocytes, or by association with CD1, antigenic lipids to natural killer T-cells. Knockout of B2M results in loss of these functions and severe combined immunodeficiency. Plasma levels of this protein are low in healthy serum, but are elevated up to 50-fold in some pathologies including chronic kidney disease and multiple myeloma, where it has both diagnostic and prognostic value. High levels of the protein are associated with amyloid formation, with such deposits containing significant levels of modified or truncated protein. In the current study we examine the chemical and structural changes induced of B2M generated by both inflammatory oxidants (HOCl and ONOOH), and photo-oxidation (¹O₂) which is linked with immunosuppression. Oxidation results in oligomer formation, with this occurring most readily with HOCl and ¹O₂, and a loss of native protein conformation. LC-MS analysis provided evidence for nitrated (from ONOOH), chlorinated (from HOCl) and oxidized residues (all oxidants) with damage detected at Tyr, Trp, and Met residues, together with cleavage of the disulfide (cystine) bond. An intermolecular di-tyrosine crosslink is also formed between Tyr10 and Tyr63. The pattern of these modifications is oxidant specific, with ONOOH inducing a greater range of modifications than HOCl. Comparison of the sites of modification with regions identified as amyloidogenic indicate significant co-localization, consistent with the hypothesis that oxidation may contribute, and predispose B2M, to amyloid formation.

Reactive oxygen species in photosystem II: relevance for oxidative signaling

Reactive oxygen species (ROS) are formed in photosystem II (PSII) under various types of abiotic and biotic stresses. It is considered that ROS play a role in chloroplast-to-nucleus retrograde signaling, which changes the nuclear gene expression. However, as ROS lifetime and diffusion are restricted due to the high reactivity towards biomolecules (lipids, pigments, and proteins) and the spatial specificity of signal transduction is low, it is not entirely clear how ROS might transduce signal from the chloroplasts to the nucleus. Biomolecule oxidation was formerly connected solely with damage; nevertheless, the evidence appears that oxidatively modified lipids and pigments are be involved in chloroplast-to-nucleus retrograde signaling due to their long diffusion distance. Moreover, oxidatively modified proteins show high spatial specificity; however, their role in signal transduction from chloroplasts to the nucleus has not been proven yet. The review attempts to summarize and evaluate the evidence for the involvement of ROS in oxidative signaling in PSII.

Efficient disinfection of SARS-CoV-2-like coronavirus, pseudotyped SARS-CoV-2 and other coronaviruses using cold plasma induces spike protein damage

Coronavirus disease 2019 (COVID-19) has become a worldwide public health emergency, and the high transmission of SARS-CoV-2 variants has raised serious concerns. Efficient disinfection methods are crucial for the prevention of viral transmission. Herein, pulse power-driven cold atmospheric plasma (CAP), a novel sterilization strategy, was found to potently inactivate SARS-CoV-2-like coronavirus GX_P2V, six strains of major epidemic SARS-CoV-2 variants and even swine coronavirus PEDV and SADS-CoV within 300 s (with inhibition rate more than 99%). We identified four dominant short-lived reactive species, ONOO^-, ¹O₂, O₂^- and·OH, generated in response to CAP and distinguished their roles in the inactivation of GX_P2V and SARS-CoV-2 spike protein receptor binding domain (RBD), which is responsible for recognition and binding to human angiotensin-converting enzyme 2 (hACE2). Our study provides detailed evidence of a novel surface disinfection strategy for SARS-CoV-2 and other coronaviruses.

Enhanced antimicrobial activity through the combination of antimicrobial photodynamic therapy and low-frequency ultrasonic irradiation

The rapid increase of antibiotic resistance in pathogenic microorganisms has become one of the most severe threats to human health. Antimicrobial photodynamic therapy (aPDT), a light-based regimen, has offered a compelling nonpharmacological alternative to conventional antibiotics. The activity of aPDT is based on cytotoxic effect of reactive oxygen species (ROS), which are generated through the photosensitized reaction between photon, oxygen and photosensitizer. However, limited by the penetration of light and photosensitizers in human tissues and/or the infiltration of oxygen and photosensitizers in biofilms, the eradication of deeply located or biofilm-associated infections by aPDT remains challenging. Ultrasound irradiation bears a deeper penetration in human tissues than light and, sequentially, can promote drug delivery through cavitation effect. As such, the combination of ultrasound and aPDT represents a potent antimicrobial strategy. In this review, we summarized the recent progresses in the area of the combination therapy using ultrasound and aPDT, and discussed the potential mechanisms underlying enhanced antimicrobial effect by this combination therapy. The future research directions are also highlighted.

EXECUTER2 modulates the EXECUTER1 signalosome through its singlet oxygen-dependent oxidation

Oxidative post-translational modifications of specific chloroplast proteins contribute to the initiation of retrograde signaling. The Arabidopsis thaliana EXECUTER1 (EX1) protein, a chloroplast-localized singlet oxygen (¹O₂) sensor, undergoes tryptophan (Trp) 643 oxidation by ¹O₂, a chloroplast-derived and light-dependent reactive oxygen species. The indole side chain of Trp is vulnerable to ¹O₂, leading to the generation of oxidized Trp variants and priming EX1 for degradation by a membrane-bound FtsH protease. The perception of ¹O₂ via Trp643 oxidation and subsequent EX1 proteolysis facilitate chloroplast-to-nucleus retrograde signaling. In this study, we discovered that the EX1-like protein EX2 also undergoes ¹O₂-dependent Trp530 oxidation and FtsH-dependent turnover, which attenuates ¹O₂ signaling by decelerating EX1-Trp643 oxidation and subsequent EX1 degradation. Consistent with this finding, the loss of EX2 function reinforces EX1-dependent retrograde signaling by accelerating EX1-Trp643 oxidation and subsequent EX1 proteolysis, whereas overexpression of EX2 produces molecular phenotypes opposite to those observed in the loss-of- function mutants of EX2. Intriguingly, phylogenetic analysis suggests that EX2 may have emerged evolutionarily to attenuate the sensitivity of EX1 toward ¹O₂. Collectively, these results suggest that EX2 functions as a negative regulator of the EX1 signalosome through its own ¹O₂-dependent oxidation, providing a new mechanistic insight into the regulation of EX1-mediated ¹O₂ signaling.

Riboflavin as a promising antimicrobial agent? A multi-perspective review

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Riboflavin demonstrates antioxidant and photosensitizing properties.

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Riboflavin is able to induce ROS and modulate immune response.

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Riboflavin possesses potent antimicrobial activity when used alone or combined with other anti-infectives.

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The riboflavin biosynthesis pathway serves as an ideal drug target against microbes.

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UVA combination with riboflavin exhibits remarkable antimicrobial effects.

Riboflavin, or more commonly known as vitamin B2, forms part of the component of vitamin B complex. Riboflavin consisting of two important cofactors, flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), which are involved in multiple oxidative-reduction processes and energy metabolism. Besides maintaining human health, different sources reported that riboflavin can inhibit or inactivate the growth of different pathogens including bacteria, viruses, fungi and parasites, highlighting the possible role of riboflavin as an antimicrobial agent. Moreover, riboflavin and flavins could produce reactive oxygen species (ROS) when exposed to light, inducing oxidative damage in cells and tissues, and thus are excellent natural photosensitizers. Several studies have illustrated the therapeutic efficacy of photoactivated riboflavin against nosocomial infections and multidrug resistant bacterial infections as well as microbial associated biofilm infections, revealing the potential role of riboflavin as a promising antimicrobial candidate, which could serve as one of the alternatives in fighting the global crisis of the emergence of antimicrobial resistance seen in different pathogenic microbes. Riboflavin could also be involved in modulating host immune responses, which might increase the pathogen clearance from host cells and increase host defense against microbial infections. Thus, the dual effects of riboflavin on both pathogens and host immunity, reflected by its potent bactericidal effect and alleviation of inflammation in host cells further imply that riboflavin could be a potential candidate for therapeutic intervention in resolving microbial infections. Hence, this review aimed to provide some insights on the promising role of riboflavin as an antimicrobial candidate and also a host immune-modulator from a multi-perspective view as well as to discuss the application and challenges on using riboflavin in photodynamic therapy against various pathogens and microbial biofilm-associated infections.

Effect of macromolecular crowding on protein oxidation: Consequences on the rate, extent and oxidation pathways

Biological systems are heterogeneous and crowded environments. Such packed milieus are expected to modulate reactions both inside and outside the cell, including protein oxidation. In this work, we explored the effect of macromolecular crowding on the rate and extent of oxidation of Trp and Tyr, in free amino acids, peptides and proteins. These species were chosen as they are readily oxidized and contribute to damage propagation. Dextran was employed as an inert crowding agent, as this polymer decreases the fraction of volume available to other (macro)molecules. Kinetic analysis demonstrated that dextran enhanced the rate of oxidation of free Trp, and peptide Trp, elicited by AAPH-derived peroxyl radicals. For free Trp, the rates of oxidation were 15.0 ± 2.1 and 30.5 ± 3.4 μM min-1 without and with dextran (60 mg mL-1) respectively. Significant increases were also detected for peptide-incorporated Trp. Dextran increased the extent of Trp consumption (up to 2-fold) and induced short chain reactions. In contrast, Tyr oxidation was not affected by the presence of dextran. Studies on proteins, using SDS-PAGE and LC-MS, indicated that oxidation was also affected by crowding, with enhanced amino acid loss (45% for casein), chain reactions and altered extents of oligomer formation. The overall effects of dextran-mediated crowding were however dependent on the protein structure. Overall, these data indicate that molecular crowding, as commonly encountered in biological systems affect the rates, and extents of oxidation, and particularly of Trp residues, illustrating the importance of appropriate choice of in vitro systems to study biological oxidations.

Electrochemical biosensor based on singlet oxygen generated by molecular photosensitizers

Here a sensing strategy with the integration of photosensitizer and electrochemical analysis was present. The photosensitizer, Zinc(II) tetraphenylporphyrin (ZnTCPP), was functionalized graphene oxide (GO) to form complex (ZnTCPP/GO) as the electrode material and generated singlet-oxygen (¹O₂) in the presence of air under light illumination. Due to the special electronic structure of ¹O₂, hydroquinone (HQ) could react with ¹O₂ to produce electrochemically-detectable products, benzoquinone (BQ). Meanwhile, the formed BQ could be reduced on the electrode, completing the redox cycling. The ZnTCPP/GO modified ITO electrode produces a stable and enhanced photocurrent signal under 420 nm irradiation in air-saturated buffer, compared with in N₂-saturated buffer. On the other hand, l-glutathione (GSH) as a signalling molecule plays important role in physiological process, which was employed as model to investigated the sensing performance. Coupling with HQ oxidized by ¹O₂, a GSH sensor was constructed on the basis the redox cycling of HQ. A sensitive reduction of photocurrent is observed with the addition of GSH, due to the GSH could be oxidized by the generated ¹O₂ to form GSSG. The biosensor displayed good performance in a broad concentration range of 0-150 μM, with a lower detection limit of 1.3 μM at an S/N ratio of 3, and could be used in practical application. This work affords a platform for constructing the biosensor with ¹O₂ instead of enzyme via on/off light switching.

Singlet-Oxygen-Induced Phospholipase A2 Inhibition: A Major Role for Interfacial Tryptophan Dioxidation

Several studies have revealed that various diseases such as cancer have been associated with elevated phospholipase A2 (PLA2 ) activity. Therefore, the regulation of PLA2 catalytic activity is undoubtedly vital. In this study, effective inactivation of PLA2 due to reactive species produced from cold physical plasma as a source to model oxidative stress is reported. We found singlet oxygen to be the most relevant active agent in PLA2 inhibition. A more detailed analysis of the plasma-treated PLA2 identified tryptophan 128 as a hot spot, rich in double oxidation. The significant dioxidation of this interfacial tryptophan resulted in an N-formylkynurenine product via the oxidative opening of the tryptophan indole ring. Molecular dynamics simulation indicated that the efficient interactions between the tryptophan residue and phospholipids are eliminated following tryptophan dioxidation. As interfacial tryptophan residues are predominantly involved in the attaching of membrane enzymes to the bilayers, tryptophan dioxidation and indole ring opening leads to the loss of essential interactions for enzyme binding and, consequently, enzyme inactivation.

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.

Photosensitized Protein Damage by DiethyleneglycoxyP(V)tetrakis(p-n-butoxyphenyl)porphyrin Through Electron Transfer: Activity Control Through Self-aggregation and Dissociation

DiethyleneglycoxyP(V)tetrakis(p-n-butoxyphenyl)porphyrin (EGP(V)TBPP) forms a self-aggregation in an aqueous solution, and the photoexcited state of this molecule was effectively deactivated. Association with human serum albumin (HSA), a water-soluble protein, causes dissociation of the self-aggregation, resulting in recovery of the photosensitizer activity of EGP(V)TBPP. Under visible light irradiation, EGP(V)TBPP photosensitized HSA oxidation. The photosensitized singlet oxygen-generating activity of EGP(V)TBPP was confirmed by near-infrared emission measurement. A singlet oxygen quencher, sodium azide, partially inhibited the HSA photodamage; however, the quenching effect was estimated to be 57%. Another 43% of the HSA photodamage could be explained by the electron transfer mechanism. The redox potential of EGP(V)TBPP and the calculated Gibbs energy of electron transfer from tryptophan to photoexcited EGP(V)TBPP demonstrated the possibility of HSA oxidation through electron extraction. Fluorescence lifetime measurements of EGP(V)TBPP verified the electron transfer from HSA. The photosensitizer activity of EGP(V)TBPP can be controlled through an association with biomolecules, such as protein, and the electron transfer-mediated biomolecule photooxidation plays an important role in photodynamic therapy under hypoxia.

Antimicrobial photodynamic therapy (aPDT) for biofilm treatments. Possible synergy between aPDT and pulsed electric fields

Currently, microbial biofilms have been the cause of a wide variety of infections in the human body, reaching 80% of all bacterial and fungal infections. The biofilms present specific properties that increase the resistance to antimicrobial treatments. Thus, the development of new approaches is urgent, and antimicrobial photodynamic therapy (aPDT) has been shown as a promising candidate. aPDT involves a synergic association of a photosensitizer (PS), molecular oxygen and visible light, producing highly reactive oxygen species (ROS) that cause the oxidation of several cellular components. This therapy attacks many components of the biofilm, including proteins, lipids, and nucleic acids present within the biofilm matrix; causing inhibition even in the cells that are inside the extracellular polymeric substance (EPS). Recent advances in designing new PSs to increase the production of ROS and the combination of aPDT with other therapies, especially pulsed electric fields (PEF), have contributed to enhanced biofilm inhibition. The PEF has proven to have antimicrobial effect once it is known that extensive chemical reactions occur when electric fields are applied. This type of treatment kills microorganisms not only due to membrane rupture but also due to the formation of reactive compounds including free oxygen, hydrogen, hydroxyl and hydroperoxyl radicals. So, this review aims to show the progress of aPDT and PEF against the biofilms, suggesting that the association of both methods can potentiate their effects and overcome biofilm infections.

Detection of Oxidative Stress Induced by Nanomaterials in Cells-The Roles of Reactive Oxygen Species and Glutathione

The potential of nanomaterials use is huge, especially in fields such as medicine or industry. Due to widespread use of nanomaterials, their cytotoxicity and involvement in cellular pathways ought to be evaluated in detail. Nanomaterials can induce the production of a number of substances in cells, including reactive oxygen species (ROS), participating in physiological and pathological cellular processes. These highly reactive substances include: superoxide, singlet oxygen, hydroxyl radical, and hydrogen peroxide. For overall assessment, there are a number of fluorescent probes in particular that are very specific and selective for given ROS. In addition, due to the involvement of ROS in a number of cellular signaling pathways, understanding the principle of ROS production induced by nanomaterials is very important. For defense, the cells have a number of reparative and especially antioxidant mechanisms. One of the most potent antioxidants is a tripeptide glutathione. Thus, the glutathione depletion can be a characteristic manifestation of harmful effects caused by the prooxidative-acting of nanomaterials in cells. For these reasons, here we would like to provide a review on the current knowledge of ROS-mediated cellular nanotoxicity manifesting as glutathione depletion, including an overview of approaches for the detection of ROS levels in cells.

Role of Kynurenine Pathway in Oxidative Stress during Neurodegenerative Disorders

Neurodegenerative disorders are chronic and life-threatening conditions negatively affecting the quality of patients’ lives. They often have a genetic background, but oxidative stress and mitochondrial damage seem to be at least partly responsible for their development. Recent reports indicate that the activation of the kynurenine pathway (KP), caused by an activation of proinflammatory factors accompanying neurodegenerative processes, leads to the accumulation of its neuroactive and pro-oxidative metabolites. This leads to an increase in the oxidative stress level, which increases mitochondrial damage, and disrupts the cellular energy metabolism. This significantly reduces viability and impairs the proper functioning of central nervous system cells and may aggravate symptoms of many psychiatric and neurodegenerative disorders. This suggests that the modulation of KP activity could be effective in alleviating these symptoms. Numerous reports indicate that tryptophan supplementation, inhibition of KP enzymes, and administration or analogs of KP metabolites show promising results in the management of neurodegenerative disorders in animal models. This review gathers and systematizes the knowledge concerning the role of metabolites and enzymes of the KP in the development of oxidative damage within brain cells during neurodegenerative disorders and potential strategies that could reduce the severity of this process.

Preparation, validation and use of a vasoactive tryptophan-derived hydroperoxide and relevant control compounds

The L-tryptophan-derived tricyclic hydroperoxide cis-WOOH was recently identified as a novel and biologically important factor for regulating vascular tone and blood pressure under inflammatory conditions and potentially other cellular redox signaling events. cis-WOOH is highly labile and currently not available commercially. In this protocol, we provide procedures for the synthesis, purification, quantification and characterization of cis-WOOH, its epimer trans-WOOH and their respective alcohols (cis-WOH and trans-WOH). Photo-oxidation of L-tryptophan (L-Trp) results in a mixture containing cis-WOOH and trans-WOOH, which are separated and purified by semi-preparative HPLC. cis-WOH and trans-WOH are then produced by sodium borohydride reduction and purified by semi-preparative HPLC. Characterization of cis-WOOH and trans-WOOH and the reduced alcohol variants is achieved using HPLC, fluorescence, NMR and liquid chromatography-tandem mass spectrometry. The protocol provides instructions for storage and quantification, as well as ways to test the stability of these hydroperoxides in commonly used buffers and media. Finally, we describe examples of how to monitor the formation of cis-WOOH in biological samples. The protocol ensures reasonable yield (11%) and purity (>99%) of cis-WOOH and control compounds in 5-6 d and outlines conditions under which cis-WOOH is stable for several months.

Degradation Products of Tryptophan in Cell Culture Media: Contribution to Color and Toxicity

Biomanufacturing processes may be optimized by storing cell culture media at room temperature, but this is currently limited by their instability and change in color upon long-term storage. This study demonstrates that one of the critical contributing factors toward media browning is tryptophan. LC-MS technology was utilized to identify tryptophan degradation products, which are likely formed primarily from oxidation reactions. Several of the identified compounds were shown to contribute significantly to color in solutions but also to exhibit toxicity against CHO cells. A cell-culture-compatible antioxidant, a-ketoglutaric acid, was found to be an efficient cell culture media additive for stabilizing components against degradation, inhibiting the browning of media formulations, and decreasing ammonia production, thus providing a viable method for developing room-temperature stable cell culture media.

Metabolic profiling of epidermal and mesophyll tissues under water-deficit stress in Opuntia ficus-indica reveals stress-adaptive metabolic responses

Cactus pear (Opuntia ficus-indica) is a high productivity species within the Cactaceae grown in many semiarid parts of the world for food, fodder, forage, and biofuels. O. ficus-indica utilises obligate crassulacean acid metabolism (CAM), an adaptation that greatly improves water-use efficiency (WUE) and reduces crop water usage. To better understand CAM-related metabolites and water-deficit stress responses of O. ficus-indica, comparative metabolic profiling was performed on mesophyll and epidermal tissues collected from well-watered and water-deficit stressed cladodes at 50% relative water content (RWC). Tissues were collected over a 24-h period to identify metabolite levels throughout the diel cycle and analysed using a combination of acidic/basic ultra-high-performance liquid chromatography/tandem mass spectrometry (UHPLC/MS/MS) and gas chromatography/mass spectrometry (GC/MS) platforms. A total of 382 metabolites, including 210 (55%) named and 172 (45%) unnamed compounds, were characterised across both tissues. Most tricarboxylic acid (TCA) cycle and glycolysis intermediates were depleted in plants undergoing water-deficit stress indicative of CAM idling or post-idling, while the raffinose family oligosaccharides (RFO) accumulated in both mesophyll and epidermal tissues as osmoprotectants. Levels of reduced glutathione and other metabolites of the ascorbate cycle as well as oxylipins, stress hormones such as traumatic acid, and nucleotide degradation products were increased under water-deficit stress conditions. Notably, tryptophan accumulation, an atypical response, was significantly (24-fold) higher during all time points in water-deficit stressed mesophyll tissue compared with well-watered controls. Many of the metabolite increases were indicative of a highly oxidising environment under water-deficit stress. A total of 34 unnamed metabolites also accumulated in response to water-deficit stress indicating that such compounds might play important roles in water-deficit stress tolerance.

Diatom-like silica-protein nanocomposites for sustained drug delivery of ruthenium polypyridyl complexes

Inspired by the unique glass cell wall of diatom, we design a new nanostructure of human serum albumin nanoparticle (HSANP) coated with silica (HSA/SiO₂), which consists of a core-satellite assembly of small silica nanoparticles on a single HSANP. The HSA/SiO₂ nanoparticles are used for delivering ruthenium polypyridyl complexes into cells. The silica coating increases the Ru loading efficiency, and prevents the burst release of Ru from HSA/SiO₂. The Ru release rate can be controlled by adjusting the amount of coated silica on HSANP, affording a drug delivery system with controlled drug release rate. The Ru-HSA/SiO₂ nanoparticles show high stability in physiological condition, and significantly increase the Ru uptake into cells, which proceeds via clathrin-mediated endocytosis into the lysosomes. The silica coating takes no effect on the fluorescence intensity and ROS generation of loaded Ru in HSA/SiO₂. Furthermore, Ru4-HSA/SiO₂ exhibit weak cytotoxicity in dark, however, the nanodrug can be activated by light irradiation and generate ROS to damage cells, thus achieving an excellent photodynamic therapy efficiency. Therefore, the diatom-like nanostructure can function as sustained drug delivery nanocarrier of ruthenium polypyridyl complex and can be used for bioimaging and photodynamic therapy.

Photostability of l-tryptophan in aqueous solution: Effect of atmosphere and antioxidants addition

l-Tryptophan (l-Trp) is an amino acid important in nutrition, and mainly provided by food supplements. However, it is known to be unstable under light irradiation, which is an issue for the nutrition and feed industry. In the present study, the photostability of l-Trp was studied in acidic aqueous solutions under air and under an inert atmosphere, N₂. The photodegradation was followed using UV-visible and fluorescence spectroscopy after photolysis. Moreover, molecular orbitals and bond dissociation energies calculations, and electron spin resonance spectroscopy were performed. From all these results, a photodegradation occurring through a free radical pathway was suggested. Interestingly, several antioxidants were tested to improve the photostability of l-Trp, especially during irradiation under air, since the l-Trp was evidenced to be much less stable under air than under N₂. The results showed that sodium benzoate or EDTA were not efficient, but antioxidants such as chlorogenic acid, ascorbic acid or potassium sorbate improved significantly the photostability of l-Trp in acidic solutions.

Oxidative Properties of Polystyrene Nanoparticles with Different Diameters in Human Peripheral Blood Mononuclear Cells (In Vitro Study)

With the ongoing commercialization, human exposure to plastic nanoparticles will dramatically increase, and evaluation of their potential toxicity is essential. There is an ongoing discussion on the human health effects induced by plastic particles. For this reason, in our work, we assessed the effect of polystyrene nanoparticles (PS-NPs) of various diameters (29, 44 and 72 nm) on selected parameters of oxidative stress and the viability of human peripheral blood mononuclear cells (PBMCs) in the in vitro system. Cells were incubated with PS-NPs for 24 h in the concentration range of 0.001 to 100 µg/mL and then labeled: formation of reactive oxygen species (ROS) (including hydroxyl radical), protein and lipid oxidation and cell viability. We showed that PS-NPs disturbed the redox balance in PBMCs. They increased ROS levels and induced lipid and protein oxidation, and, finally, the tested nanoparticles induced a decrease in PBMCs viability. The earliest changes in the PBMCs were observed in cells incubated with the smallest PS-NPs, at a concentration of 0.01 μg/mL. A comparison of the action of the studied nanoparticles showed that PS-NPs (29 nm) exhibited a stronger oxidative potential in PBMCs. We concluded that the toxicity and oxidative properties of the PS-NPs examined depended to significant degree on their diameter.

Photo-oxygenation by a biocompatible catalyst reduces amyloid-β levels in Alzheimer's disease mice

Amyloid formation and the deposition of the amyloid-β peptide are hallmarks of Alzheimer's disease pathogenesis. Immunotherapies using anti-amyloid-β antibodies have been highlighted as a promising approach for the prevention and treatment of Alzheimer's disease by enhancing microglial clearance of amyloid-β peptide. However, the efficiency of antibody delivery into the brain is limited, and therefore an alternative strategy to facilitate the clearance of brain amyloid is needed. We previously developed an artificial photo-oxygenation system using a low molecular weight catalytic compound. The photocatalyst specifically attached oxygen atoms to amyloids upon irradiation with light, and successfully reduced the neurotoxicity of aggregated amyloid-β via inhibition of amyloid formation. However, the therapeutic effect and mode of actions of the photo-oxygenation system in vivo remained unclear. In this study, we demonstrate that photo-oxygenation facilitates the clearance of aggregated amyloid-β from the brains of living Alzheimer's disease model mice, and enhances the microglial degradation of amyloid-β peptide. These results suggest that photo-oxygenation may represent a novel anti-amyloid-β strategy in Alzheimer's disease, which is compatible with immunotherapy.

Machine learning prediction of methionine and tryptophan photooxidation susceptibility

Photooxidation of methionine (Met) and tryptophan (Trp) residues is common and includes major degradation pathways that often pose a serious threat to the success of therapeutic proteins. Oxidation impacts all steps of protein production, manufacturing, and shelf life. Prediction of oxidation liability as early as possible in development is important because many more candidate drugs are discovered than can be tested experimentally. Undetected oxidation liabilities necessitate expensive and time-consuming remediation strategies in development and may lead to good drugs reaching patients slowly. Conversely, sites mischaracterized as oxidation liabilities could result in overengineering and lead to good drugs never reaching patients. To our knowledge, no predictive model for photooxidation of Met or Trp is currently available. We applied the random forest machine learning algorithm to in-house liquid chromatography-tandem mass spectrometry (LC-MS/MS) datasets (Met, n = 421; Trp, n = 342) of tryptic therapeutic protein peptides to create computational models for Met and Trp photooxidation. We show that our machine learning models predict Met and Trp photooxidation likelihood with 0.926 and 0.860 area under the curve (AUC), respectively, and Met photooxidation rate with a correlation coefficient (Q²) of 0.511 and root-mean-square error (RMSE) of 10.9%. We further identify important physical, chemical, and formulation parameters that influence photooxidation. Improvement of biopharmaceutical liability predictions will result in better, more stable drugs, increasing development throughput, product quality, and likelihood of clinical success.

M. jannaschii FtsZ, a key protein in bacterial cell division, is inactivated by peroxyl radical-mediated methionine oxidation

Oxidation and inactivation of FtsZ is of interest due to the key role of this protein in bacterial cell division. In the present work, we studied peroxyl radical (from AAPH, 2,2'-azobis(2-methylpropionamidine)dihydrochloride) mediated oxidation of the highly stable FtsZ protein (MjFtsZ) from M. jannaschii, a thermophilic microorganism. MjFtsZ contains eleven Met, and single Tyr and Trp residues which would be expected to be susceptible to oxidation. We hypothesized that exposure of MjFtsZ to AAPH-derived radicals would induce Met oxidation, and cross-linking (via di-Tyr and di-Trp formation), with concomitant loss of its functional polymerization and depolymerization (GTPase) activities. Solutions containing MjFtsZ and AAPH (10 or 100 mM) were incubated at 37 °C for 3 h. Polymerization/depolymerization were assessed by light scattering, while changes in mass were analyzed by SDS-PAGE. Amino acid consumption was quantified by HPLC with fluorescence detection, or direct fluorescence (Trp). Oxidation products and modifications at individual Met residues were quantified by UPLC with mass detection. Oxidation inhibited polymerization-depolymerization activity, and yielded low levels of irreversible protein dimers. With 10 mM AAPH only Trp and Met were consumed giving di-alcohols, kynurenine and di-Trp (from Trp) and the sulfoxide (from Met). With 100 mM AAPH low levels of Tyr oxidation (but not di-Tyr formation) were also observed. Correlation with the functional analyses indicates that Met oxidation, and particularly Met164 is the key driver of MjFtsZ inactivation, probably as a result of the position of this residue at the protein-protein interface of longitudinal interactions and in close proximity to the GTP binding site.

Molecular features toward high photo-CIDNP hyperpolariztion explored through the oxidocyclization of tryptophan

Photo-chemically induced dynamic nuclear polarization (photo-CIDNP) is a promising solution to the inherent lack of sensitivity in NMR spectroscopy. It is particularly interesting in biological systems since it operates in water, at room temperature, and it can be repeated if the bleaching of the system can be controlled. However, the photo-CIDNP signal enhancement is well below those of other hyperpolarization techniques. While DNP, PHIP, and SABRE reach polarization enhancements of 10³ to 10⁴-fold, photo-CIDNP enhancement is typically only one order of magnitude for ¹H and two orders of magnitude for ¹³C in the amino-acids tryptophan and tyrosine. Here we report on a photo-oxidation product of tryptophan that is strongly photo-CIDNP active under continuous wave light irradiation. In conjunction with the dye Atto Thio 12, a ¹H signal enhancement of 120-fold was observed on a 600 MHz spectrometer, while at 200 MHz the enhancement was 380-fold. These enhancements in signal to noise correspond to a reduction in measurement time of 14 400-fold and 144 400-fold, respectively. The enhancement for ¹³C is estimated to be over 1200-fold at 600 MHz which corresponds to an impressive measurement time reduction of 1 440 000-fold. This photo-CIDNP active oxidation product of tryptophan has been identified to be 3α-hydroxypyrroloindole. The reasons for its improved signal enhancement compared to tryptophan have been further investigated.

Bioengineering a Light-Responsive Encapsulin Nanoreactor: A Potential Tool for In Vitro Photodynamic Therapy

Encapsulins, a prokaryotic class of self-assembling protein nanocompartments, are being re-engineered to serve as "nanoreactors" for the augmentation or creation of key biochemical reactions. However, approaches that allow encapsulin nanoreactors to be functionally activated with spatial and temporal precision are lacking. We report the construction of a light-responsive encapsulin nanoreactor for "on demand" production of reactive oxygen species (ROS). Herein, encapsulins were loaded with the fluorescent flavoprotein mini-singlet oxygen generator (miniSOG), a biological photosensitizer that is activated by blue light to generate ROS, primarily singlet oxygen (¹O₂). We established that the nanocompartments stably encased miniSOG and in response to blue light were able to mediate the photoconversion of molecular oxygen into ROS. Using an in vitro model of lung cancer, we showed that ROS generated by the nanoreactor triggered photosensitized oxidation reactions which exerted a toxic effect on tumor cells, suggesting utility in photodynamic therapy. This encapsulin nanoreactor thus represents a platform for the light-controlled initiation and/or modulation of ROS-driven processes in biomedicine and biotechnology.

Reactivity and degradation products of tryptophan in solution and proteins

Tryptophan is one of the essential mammalian amino acids and is thus a required component in human nutrition, animal feeds, and cell culture media. However, this aromatic amino acid is highly susceptible to oxidation and is known to degrade into multiple products during manufacturing, storage, and processing. Many physical and chemical processes contribute to the degradation of this compound, primarily via oxidation or cleavage of the highly reactive indole ring. The central contributing factors are reactive oxygen species, such as singlet oxygen, hydrogen peroxide, and hydroxyl radicals; light and photosensitizers; metals; and heat. In a multi-component mixture, tryptophan also commonly reacts with carbonyl-containing compounds, leading to a wide variety of products. The purpose of this review is to summarize the current state of knowledge regarding the degradation and interaction products of tryptophan in complex liquid solutions and in proteins. For the purposes of context, a brief summary of the key pathways in tryptophan metabolism will be included, along with common methods and issues in tryptophan manufacturing. The review will focus on the conditions that lead to tryptophan degradation, the products generated in these processes, their known biological effects, and methods which may be applied to stabilize the amino acid.

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.

Rapid Airborne Influenza Virus Quantification Using an Antibody-Based Electrochemical Paper Sensor and Electrostatic Particle Concentrator

Airborne influenza viruses are responsible for serious respiratory diseases, and most detection methods for airborne viruses are based on extraction of nucleic acids. Herein, vertical-flow-assay-based electrochemical paper immunosensors were fabricated to rapidly quantify the influenza H1N1 viruses in air after sampling with a portable electrostatic particle concentrator (EPC). The effects of antibodies, anti-influenza nucleoprotein antibodies (NP-Abs) and anti-influenza hemagglutinin antibodies (HA-Abs), on the paper sensors as well as nonpulsed high electrostatic fields with and without corona charging on the virus measurement were investigated. The antigenicity losses of the surface (HA) proteins were caused by H₂O₂ via lipid oxidation-derived radicals and ¹O₂ via direct protein peroxidation upon exposure of a high electrostatic field. However, minimal losses in antigenicity of NP of the influenza viruses were observed, and the concentration of the H1N1 viruses was more than 160 times higher in the EPC than the BioSampler upon using NP-Ab based paper sensors after 60 min collection. This NP-Ab-based paper sensors with the EPC provided measurements comparable to quantitative polymerase chain reaction (qPCR) but much quicker, specific to the influenza H1N1 viruses in the presence of other airborne microorganisms and beads, and more cost-effective than enzyme-linked immunosorbent assay and qPCR.