Novel chemical degradation pathways of proteins mediated by tryptophan oxidation: tryptophan side chain fragmentation

Near UV and Visible Light-Induced Degradation of Bovine Serum Albumin and a Monoclonal Antibody Mediated by Citrate Buffer and Fe(III): Reduction vs Oxidation Pathways

Light exposure during manufacturing, storage, and administration can lead to the photodegradation of therapeutic proteins. This photodegradation can be promoted by pharmaceutical buffers or impurities. Our laboratory has previously demonstrated that citrate-Fe(III) complexes generate the •CO2- radical anion when photoirradiated under near UV (λ = 320-400 nm) and visible light (λ = 400-800 nm) [Subelzu, N.; Schöneich, C. Mol. Pharmaceutics 2020, 17 (11), 4163-4179; Zhang, Y. Mol. Pharmaceutics 2022, 19 (11), 4026-4042]. Here, we evaluated the impact of citrate-Fe(III) on the photostability and degradation mechanisms of disulfide-containing proteins (bovine serum albumin (BSA) and NISTmAb) under pharmaceutically relevant conditions. We monitored and localized competitive disulfide reduction and protein oxidation by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) analysis depending on the reaction conditions. These competitive pathways were affected by multiple factors, including light dose, Fe(III) concentration, protein concentration, the presence of oxygen, and light intensity.

Clickable tryptophan modification for late-stage diversification of native peptides

As the least abundant residue in proteins, tryptophan widely exists in peptide drugs and bioactive natural products and contributes to drug-target interactions in multiple ways. We report here a clickable tryptophan modification for late-stage diversification of native peptides, via catalyst-free C2-sulfenylation with 8-quinoline thiosulfonate reagents in trifluoroacetic acid (TFA). A wide range of groups including trifluoromethylthio (SCF3), difluoromethylthio (SCF2H), (ethoxycarbonyl)difluoromethylthio (SCF2CO2Et), alkylthio, and arylthio were readily incorporated. The rapid reaction kinetics of Trp modification and full tolerance with other 19 proteinogenic amino acids, as well as the super dissolving capability of TFA, render this method suitable for all kinds of Trp-containing peptides without limitations from sequences, hydrophobicity, and aggregation propensity. The late-stage modification of 15 therapeutic peptides (1.0 to 7.6 kilodaltons) and the improved bioactivity and serum stability of SCF3- and SCF2H-modified melittin analogs illustrated the effectiveness of this method and its potential in pharmacokinetic property improvement.

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.'

Ahrné L, Cardoso DR. UV-C light promotes the reductive cleavage of disulfide bonds in β-Lactoglobulin and improves in vitro gastric digestion

β-Lactoglobulin (β-Lg) is the main protein in whey and is known for its allergenicity and resistance to the digestion of pepsin and trypsin. The UV-C photoinduced cleavage of disulfide bonds in β-Lactoglobulin, as promoted by excitation of tryptophan residues (Trp), is shown to induce changes in the protein's secondary structure, significantly reducing the protein's resistance to pepsin digestion. The UV-C light-induced changes in the protein secondary structure are marked by an increase in the contribution of β-sheet and α-helix structures with a concomitantly smaller contribution of the β-turn structural motif. The photoinduced cleavage of disulfide bonds in β-Lg has an apparent quantum yield of ф = 0.0015 ± 0.0003 and was shown by transient absorption laser flash photolysis to arise by two different pathways: a) the reduction of the disulfide bond Cys₆₆Cys₁₆₀ occurs by direct electron transfer from the triplet-excited ³Trp to the disulfide bond due to the existence of a CysCys/Trp triad (Cys₆₆Cys₁₆₀/Trp₆₁) and b) the reduction of the buried Cys₁₀₆Cys₁₁₉ disulfide bond involves a reaction with a solvated electron originated by the photoejection of electrons from the triplet-excited ³Trp decay. The in vitro gastric digestion index for UV-C-treated β-Lg is revealed to have increased significantly by 36 ± 4 % and 9 ± 2 % under simulated elderly and young adult digestive conditions, respectively. When compared to the native protein, the peptide mass fingerprint profile of digested UV-C-treated β-Lg shows a higher content and variety of peptides, including the production of some exclusive bioactive peptides such as PMHIRL and EKFDKALKALPMH.

Photochemical Fingerprinting Is a Sensitive Probe for the Detection of Synthetic Cannabinoid Receptor Agonists; toward Robust Point-of-Care Detection

With synthetic cannabinoid receptor agonist (SCRA) use still prevalent across Europe and structurally advanced generations emerging, it is imperative that drug detection methods advance in parallel. SCRAs are a chemically diverse and evolving group, which makes rapid detection challenging. We have previously shown that fluorescence spectral fingerprinting (FSF) has the potential to provide rapid assessment of SCRA presence directly from street material with minimal processing and in saliva. Enhancing the sensitivity and discriminatory ability of this approach has high potential to accelerate the delivery of a point-of-care technology that can be used confidently by a range of stakeholders, from medical to prison staff. We demonstrate that a range of structurally distinct SCRAs are photochemically active and give rise to distinct FSFs after irradiation. To explore this in detail, we have synthesized a model series of compounds which mimic specific structural features of AM-694. Our data show that FSFs are sensitive to chemically conservative changes, with evidence that this relates to shifts in the electronic structure and cross-conjugation. Crucially, we find that the photochemical degradation rate is sensitive to individual structures and gives rise to a specific major product, the mechanism and identification of which we elucidate through density-functional theory (DFT) and time-dependent DFT. We test the potential of our hybrid "photochemical fingerprinting" approach to discriminate SCRAs by demonstrating SCRA detection from a simulated smoking apparatus in saliva. Our study shows the potential of tracking photochemical reactivity via FSFs for enhanced discrimination of SCRAs, with successful integration into a portable device.

Interaction effects between macromolecules and photosensitizer on the ability of AlPc and InPc-loaded PHB magnetic nanoparticles in photooxidatizing simple biomolecules

The parameters used in the preparation of polymeric nanoparticles can influence its ability to photooxidate biomolecules. This work evaluated the effects of four parameter to prepare Poly(3-hydroxybutyrate) (PHB) nanoparticle loaded with aluminum and indium phthalocyanine (AlPc and InPc), together with iron oxide nanoparticles, assessing their influence on the size, the entrapment efficiency, and the nanoparticles recovery efficacy. The capability of free, and encapsulated, AlPc and InPc in photooxidating the bovine serum albumin (BSA) and tryptophan (Trp) was monitored by fluorescence. The AlPc-loaded nanoparticles had a larger size and a greater entrapment efficiency than that obtained by InPc-loaded nanoparticles. The free InPc was more efficient than the free AlPc to photooxidize the BSA and Trp; whereas the encapsulated AlPc was more efficient than encapsulated InPc to photooxidize the biomolecules. The higher hydrophobicity of the AlPc, combined with the greater aggregation state and the major interaction with the BSA, quenching the capacity of the free AlPc to photooxidate the biomolecules; whereas the greater interaction of the AlPc with PHB reduce the aggregation effect on the free molecules in the aqueous phase and increase the entrapment efficiency, resulting in an improving of the photodynamic efficiency and an increase of the photooxidation rate constant.

Pediatric Brain Tumors: Signatures from the Intact Proteome

The present investigation aimed to explore the intact proteome of tissues of pediatric brain tumors of different WHO grades and localizations, including medulloblastoma, pilocytic astrocytoma, and glioblastoma, in comparison with the available data on ependymoma, to contribute to the understanding of the molecular mechanisms underlying the onset and progression of these pathologies. Tissues have been homogenized in acidic water−acetonitrile solutions containing proteases inhibitors and analyzed by LC−high resolution MS for proteomic characterization and label-free relative quantitation. Tandem MS spectra have been analyzed by either manual inspection or software elaboration, followed by experimental/theoretical MS fragmentation data comparison by bioinformatic tools. Statistically significant differences in protein/peptide levels between the different tumor histotypes have been evaluated by ANOVA test and Tukey’s post-hoc test, considering a p-value > 0.05 as significant. Together with intact protein and peptide chains, in the range of molecular mass of 1.3−22.8 kDa, several naturally occurring fragments from major proteins, peptides, and proteoforms have been also identified, some exhibiting proper biological activities. Protein and peptide sequencing allowed for the identification of different post-translational modifications, with acetylations, oxidations, citrullinations, deamidations, and C-terminal truncations being the most frequently characterized. C-terminal truncations, lacking from two to four amino acid residues, particularly characterizing the β-thymosin peptides and ubiquitin, showed a different modulation in the diverse tumors studied. With respect to the other tumors, medulloblastoma, the most frequent malignant brain tumor of the pediatric age, was characterized by higher levels of thymosin β4 and β10 peptides, the latter and its des-IS form particularly marking this histotype. The distribution pattern of the C-terminal truncated forms was also different in glioblastoma, particularly underlying gender differences, according to the definition of male and female glioblastoma as biologically distinct diseases. Glioblastoma was also distinguished for the peculiar identification of the truncated form of the α-hemoglobin chain, lacking the C-terminal arginine, and exhibiting oxygen-binding and vasoconstrictive properties different from the intact form. The proteomic characterization of the undigested proteome, following the top-down approach, was challenging to originally investigate the post-translational events that differently characterize pediatric brain tumors. This study provides a contribution to elucidate the molecular profiles of the solid tumors most frequently affecting the pediatric age, and which are characterized by different grades of aggressiveness and localization.

Human cataractous lenses contain cross-links produced by crystallin-derived tryptophanyl and tyrosyl radicals

Protein insolubilization, cross-linking and aggregation are considered critical to the development of lens opacity in cataract. However, the information about the presence of cross-links other than disulfides in cataractous lenses is limited. A potential role for cross-links produced from tryptophanyl radicals in cataract development is suggested by the abundance of the UV light-sensitive Trp residues in crystallin proteins. Here we developed a LC-MS/MS approach to examine the presence of Trp-Trp, Trp-Tyr and Tyr-Tyr cross-links and of peptides containing Trp-2H (-2.0156 Da) in the lens of three patients diagnosed with advanced nuclear cataract. In the proteins of two of the lenses, we characterized intermolecular cross-links between βB2-Tyr¹⁵³-Tyr¹⁰⁴-βA3 and βB2-Trp¹⁵⁰-Tyr¹³⁹-βS. An additional intermolecular cross-link (βB2-Tyr⁶¹-Trp²⁰⁰-βB3) was present in the lens of the oldest patient. In the proteins of all three lenses, we characterized two intramolecular Trp-Trp cross-links (Trp¹²³-Trp¹²⁶ in βB1 and Trp⁸¹-Trp⁸⁴ in βB2) and six peptides containing Trp -2H residues, which indicate the presence of additional Trp-Trp cross-links. Relevantly, we showed that similar cross-links and peptides with modified Trp-2H residues are produced in a time-dependent manner in bovine β-crystallin irradiated with a solar simulator. Therefore, different crystallin proteins cross-linked by crystalline-derived tryptophanyl and tyrosyl radicals are present in advanced nuclear cataract lenses and similar protein modifications can be promoted by solar irradiation even in the absence of photosensitizers. Overall, the results indicate that a role for Trp-Tyr and Trp-Trp cross-links in the development of human cataract is possible and deserves further investigation.

Interaction between high-density lipoproteins and inflammation: Function matters more than concentration!

High-density lipoprotein (HDL) plays an important role in lipid metabolism and especially contributes to the reverse cholesterol transport pathway. Over recent years it has become clear that the effect of HDL on immune-modulation is not only dependent on HDL concentration but also and perhaps even more so on HDL function. This review will provide a concise general introduction to HDL followed by an overview of post-translational modifications of HDL and a detailed overview of the role of HDL in inflammatory diseases. The clinical potential of HDL and its main apolipoprotein constituent, apoA-I, is also addressed in this context. Finally, some conclusions and remarks that are important for future HDL-based research and further development of HDL-focused therapies are discussed.

A Photoprotective Effect by Cation-π-Interaction? Quenching of Singlet Oxygen by an Indole Cation-π Model System

We investigated the effect of the cation-π interaction on the susceptibility of a tryptophan model system toward interaction with singlet oxygen, that is, type II photooxidation. The model system consists of two indole units linked to a lariat crown ether to measure the total rate of removal of singlet oxygen by the indole units in the presence of sodium cations (i.e. indole units subject to a cation-π interaction) and in the absence of this interaction. We found that the cation-π interaction significantly decreases the total rate of removal of singlet oxygen (k_T ) for the model system, that is, (k_T  = 2.4 ± 0.2) × 10⁸  m^-1  s^-1 without sodium cation vs (k_T  = 6.9 ± 0.9) × 10⁷  m^-1  s^-1 upon complexation of sodium cation to the crown ether. Furthermore, we found that the indole moieties undergo type I photooxidation processes with triplet excited methylene blue; this effect is also inhibited by the cation-π interaction. The chemical rate of reaction of the indole groups with singlet oxygen is also slower upon complexation of sodium cation in our model system, although we were unable to obtain an exact ratio due to differences of the chemical reaction rates of the two indole moieties.

Radical rearrangement and transfer reactions in proteins

Radical rearrangement and transfer reactions play an important role in the chemical modifications of proteins in vivo and in vitro. These reactions depend on protein sequence, as well as structure and dynamics. Frequently, these reactions have well-defined precedents in the organic chemistry literature, but their occurrence in proteins provides a stage for a number of novel and, perhaps, unexpected reaction products. This essay will provide an overview over a few representative examples of radical rearrangement and transfer reactions.

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.

Chemical and physical instabilities in manufacturing and storage of therapeutic proteins

Development of a robust biologic drug product is accomplished by extensive formulation and process development screening studies; however, even in the most optimal formulation, a protein can undergo spontaneous degradation during manufacture, storage, and clinical use. Chemical changes to amino acid residues, such as oxidation of methionine or tryptophan, or changes in charge such as deamidation or carbonylation, can induce conformational changes in the overall protein structure, potentially leading to changes in physical - in addition to chemical - stability. Oxidation is often caused by light exposure or the presence of metal ions or peroxides. Asparagine deamidation is more likely to occur at higher pH and/or elevated temperature. Mechanical and interfacial stresses during manufacturing can lead to physical instabilities (i.e. various forms of aggregation). A well-defined manufacturing process and effective in-process controls are essential in minimizing chemical and physical instabilities, enabling robust production and distribution of a safe and efficacious drug product. In this work, the authors provide a review of developments in these areas over the past two years, with emphasis on manufacturability of therapeutically relevant proteins and protein-based drug products.