Real-world evidence from over one million COVID-19 vaccinations is consistent with reactivation of the varicella-zoster virus.

BACKGROUND: Reactivation of the varicella-zoster virus (VZV), which causes herpes zoster (HZ, synonym: shingles) in humans, can be a rare adverse reaction to vaccines. Recently, reports of cases after COVID-19 vaccination have arisen. OBJECTIVES: The aim of this study was to assess whether the frequency of HZ is found to increase after COVID-19 vaccination in a large cohort, based on real-world data. As a hypothesis, the incidence of HZ was assumed to be significantly higher in subjects who received a COVID-19 vaccine (Cohort I) vs. unvaccinated individuals (Cohort II). METHODS: The initial cohorts of 1 095 086 vaccinated and 16 966 018 unvaccinated patients were retrieved from the TriNetX database and were matched on age and gender in order to mitigate confounder bias. RESULTS: After matching, each cohort accounted for 1 095 086 patients. For the vaccinated group (Cohort I), 2204 subjects developed HZ within 60 days of COVID-19 vaccination, while among Cohort II, 1223 patients were diagnosed with HZ within 60 days after having visited the clinic for any other reason (i.e. not vaccination). The risk of developing shingles was calculated as 0.20% and 0.11% for cohort I and cohort II, respectively. The difference was statistically highly significant (P < 0.0001; log-rank test). The risk ratio and odds ratio were 1.802 (95% confidence interval [CI] = 1.680; 1.932) and 1.804 (95% CI = 1.682; 1.934). CONCLUSIONS: Consistent with the hypothesis, a higher incidence of HZ was statistically detectable post-COVID-19 vaccine. Accordingly, the eruption of HZ may be a rare adverse drug reaction to COVID-19 vaccines. Even though the molecular basis of VZV reactivation remains murky, temporary compromising of VZV-specific T-cell-mediated immunity may play a mechanistic role in post-vaccination pathogenesis of HZ. Note that VZV reactivation is a well-established phenomenon both with infections and with other vaccines (i.e. this adverse event is not COVID-19-specific).

Detection of signature volatiles for cariogenic microorganisms.

The development of a breath test by the identification of volatile organic compounds (VOCs) emitted by cariogenic bacteria is a promising approach for caries risk assessment and early caries detection. The aim of the present study was to investigate the volatile profiles of three major cariogenic bacteria and to assess whether the obtained signatures were species-specific. Therefore, the headspaces above cultures of Streptococcus mutans, Lactobacillus salivarius and Propionibacterium acidifaciens were analysed after 24 and 48 h of cultivation using gas chromatography and mass spectrometry. A volatile database was queried for the obtained VOC profiles. Sixty-four compounds were detected within the analysed culture headspaces and were absent (36) or at least only present in minor amounts (28) in the control headspace. For S. mutans 18, for L. salivarius three and for P. acidifaciens five compounds were found to be unique signature VOCs. Database matching revealed that the identified signatures of all bacteria were unique. Furthermore, 13 of the 64 detected substances have not been previously reported to be emitted by bacteria or fungi. Specific VOC signatures were found in all the investigated bacteria cultures. The obtained results encourage further research to investigate the transferability to in vivo conditions towards the development of a breath test.

Targeted therapy of the XIAP/proteasome pathway overcomes TRAIL-resistance in carcinoma by switching apoptosis signaling to a Bax/Bak-independent 'type I' mode.

TRAIL is a promising anticancer agent, capable of inducing apoptosis in a wide range of treatment-resistant tumor cells. In 'type II' cells, the death signal triggered by TRAIL requires amplification via the mitochondrial apoptosis pathway. Consequently, deregulation of the intrinsic apoptosis-signaling pathway, for example, by loss of Bax and Bak, confers TRAIL-resistance and limits its application. Here, we show that despite resistance of Bax/Bak double-deficient cells, TRAIL-treatment resulted in caspase-8 activation and complete processing of the caspase-3 proenzymes. However, active caspase-3 was degraded by the proteasome and not detectable unless the XIAP/proteasome pathway was inhibited. Direct or indirect inhibition of XIAP by RNAi, Mithramycin A or by the SMAC mimetic LBW-242 as well as inhibition of the proteasome by Bortezomib overcomes TRAIL-resistance of Bax/Bak double-deficient tumor cells. Moreover, activation and stabilization of caspase-3 becomes independent of mitochondrial death signaling, demonstrating that inhibition of the XIAP/proteasome pathway overcomes resistance by converting 'type II' to 'type I' cells. Our results further demonstrate that the E3 ubiquitin ligase XIAP is a gatekeeper critical for the 'type II' phenotype. Pharmacological manipulation of XIAP therefore is a promising strategy to sensitize cells for TRAIL and to overcome TRAIL-resistance in case of central defects in the intrinsic apoptosis-signaling pathway.

Novel compounds with antiangiogenic and antiproliferative potency for growth control of testicular germ cell tumours.

BACKGROUND: Testicular germ cell tumour (TGCT) is the most common cause of death from solid tumours in young men and especially for platinum-refractory patients novel treatment approaches are urgently needed. Using an in silico screening approach for the detection of novel cancer drugs with inhibitory effects on the tyrosine kinase activity of growth factors (e.g., VEGFR, PDGFR), we identified two compounds (HP-2 and HP-14) with antiangiogenic and antiproliferative potency, which were evaluated in endothelial cell models and TGCT cells. RESULTS: HP-2 and HP-14 effectively inhibited the growth of VEGFR-2-expressing TGCT cell lines (Tera-1, Tera-2 and 2102EP) and endothelial cell models, while they failed to supress the growth of VEGFR-2-lacking tumour cells. cDNA-microarrays revealed an inhibition of the expression of several growth factor receptors and related signal transduction molecules. Vascular endothelial growth factor (VEGF)-induced cell migration was also potently inhibited. Cell cycle-regulating proteins such as p21 and p27 were upregulated, leading to an S-phase arrest. Additional in vivo evaluations confirmed the antiangiogenic potency and good tolerability of the novel substances. CONCLUSION: Our data show that the identified novel compounds inhibit the growth of TGCT cells and decrease angiogenic microvessel formation. The mode of action involves cell cycle arresting effects and changes in the expression pattern of several angiogenic genes. The novel compounds may qualify as new candidates for targeted treatment of TGCT and merit further evaluation.

Loops In Proteins (LIP)--a comprehensive loop database for homology modelling.

One of the most important and challenging tasks in protein modelling is the prediction of loops, as can be seen in the large variety of existing approaches. Loops In Proteins (LIP) is a database that includes all protein segments of a length up to 15 residues contained in the Protein Data Bank (PDB). In this study, the applicability of LIP to loop prediction in the framework of homology modelling is investigated. Searching the database for loop candidates takes less than 1 s on a desktop PC, and ranking them takes a few minutes. This is an order of magnitude faster than most existing procedures. The measure of accuracy is the root mean square deviation (RMSD) with respect to the main-chain atoms after local superposition of target loop and predicted loop. Loops of up to nine residues length were modelled with a local RMSD <1 A and those of length up to 14 residues with an accuracy better than 2 A. The results were compared in detail with a thoroughly evaluated and tested ab initio method published recently and additionally with two further methods for a small loop test set. The LIP method produced very good predictions. In particular for longer loops it outperformed other methods.

Matching organic libraries with protein-substructures.

We present a general approach which allows automatic identification of sub-structures in proteins that resemble given three-dimensional templates. This paper documents its success with non-peptide templates such as beta-turn mimetics. We considered well-tested turn-mimetics such as the bicyclic turned dipeptide (BTD), spiro lactam (Spiro) and the 2,5-disubstituded tetrahydrofuran (THF), a new furan-derivative which was recently developed and characterized. The detected geometric similarity between the templates and the protein patches corresponds to r.m.s.-values of 0.3 A for more than 80% of the constituting atoms, which is typical for active site comparisons of homologous proteins. This fast automatic procedure might be of biomedical value for finding special mimicking leads for particular protein sub-structures as well as for template-assembled synthetic protein (TASP) design.

Conservation of substructures in proteins: interfaces of secondary structural elements in proteasomal subunits.

It is observed that during divergent evolution of two proteins with a common phylogenetic origin, the structural similarity of their backbones is often preserved even when the sequence similarity between them decreases to a virtually undetectable level. Here we analyzed, whether the conservation of structure along evolution involves also the local atomic structures in the interfaces between secondary structural elements. We have used as study case one protein family, the proteasomal subunits, for which 17 crystal structures are known. These include 14 different subunits of Saccharomyces cerevisiae, 2 subunits of Thermoplasma acidophilum and one subunit of Escherichia coli. The structural core of the 17 proteasomal subunits has 23 secondary structural elements. Any two adjacent secondary structural elements form a molecular interface consisting of two molecular patches. We found 61 interfaces that occurred in all 17 subunits. The 3D shape of equivalent molecular patches from different proteasomal subunits were compared by superposition. Our results demonstrate that pairs of equivalent molecular patches show an RMSD which is lower than that of randomly chosen patches from unrelated proteins. This is true even when patch comparisons with identical residues were excluded from the analysis. Furthermore it is known that the sequential dissimilarity is correlated to the RMSD between the backbones of the members of protein families. The question arises whether this is also true for local atomic structures. The results show that the correlation of individual patch RMSD values and local sequence dissimilarities is low and has a wide range from 0 to 0.41, however, it is surprising that there is a good correlation between the average RMSD of all corresponding patches and the global sequence dissimilarity. This average patch RMSD correlates slightly stronger than the C(alpha)-trace RMSD to the global sequence dissimilarity.

Spare parts for helix-helix interaction.

About 6000 contact regions (patches) of helix-to-helix packing from 300 well-resolved non-homologous protein structures were considered. The patches were defined by the spatial helical neighbors and were estimated in atomic detail using a variable distance criterion. The following questions are addressed. (1) Are the amino acid preferences and atomic composition of distinct types of helical patches indicative for the type of their neighbor? Distributions of size, atomic composition and packing density are compared for different types of helical interfaces. Thereby contact preferences are derived for parts of secondary structures adjoining each other or pointing towards the solvent. (2) Is it possible to cluster helical patches according to their structural similarity? For these purposes the patches were classified with an automatic sequence-independent superposition procedure which yields a distinctively reduced set of representative interfaces. On this basis, the methodology for finding exchangeable patches in different proteins is demonstrated.

Sequence information within proteasomal prosequences mediates efficient integration of beta-subunits into the 20 S proteasome complex.

The maturation of proteases is governed by prosequences. During the biogenesis of the highly oligomeric eukaryotic 20 S proteasome five different prosequence-containing subunits have to be integrated and processed either by autocatalysis or by neighbouring subunits. To analyse the functional impact of proteasomal prosequences during complex formation, the propeptide of the facultative subunit beta1i/LMP2 was truncated to nine amino acid residues or completely deleted. Additionally, the charged residues within the truncated beta1i/LMP2 version were replaced by neutral residues. While deletion did not affect subunit incorporation, the presence of charged residues within the truncated version of the LMP2 propeptide diminished incorporation efficiency, an effect that was restored upon replacement of the charged amino acids against neutral components. During immunoproteasome formation, incorporation and processing of inducible proteasome beta-subunits are cooperative processes. We demonstrate a linear correlation of the levels of beta2i/MECL1 and beta1i/LMP2 within 20 S proteasomes, suggesting a physical interaction to be the molecular basis for the biased incorporation of both subunits. In the absence of beta5i/LMP7, precursor complexes containing unprocessed beta1i/LMP2 accumulated. The contribution of beta5i/LMP7 on the cooperative formation of a homogeneous population of immunoproteasome is therefore most likely based on an acceleration of the beta1i/LMP2 and potentially of beta2i/MECL1 processing kinetics.

Homonyms and synonyms in the Dictionary of Interfaces in Proteins (DIP).

MOTIVATION: Should reports on molecular mimicry in particular cases, e.g. responsible for cross-reactivity, be considered as accidental or as a general principle in protein evolution? To answer this question, two types of similarity have to be considered: those in homologues (synonyms) and resemblance between patches from unrelated proteins (homonyms). RESULTS: All interfaces from known protein structures were collected in a comprehensive data bank [Dictionary of Interfaces in Proteins (DIP)]. A fast, sequence-independent, three-dimensional superposition procedure was developed to search automatically for geometrically similar surface areas. Surprisingly, we found a large number of structurally similar interfaces on the surface of unrelated proteins. Even patches from different types of secondary structure were found resembling each other. The putative functional meaning of homonyms is demonstrated with striking examples.

Dictionary of interfaces in proteins (DIP). Data bank of complementary molecular surface patches.

Molecular surface areas of proteins are responsible for selective binding of ligands and protein-protein recognition, and are considered the basis for specific interactions between different parts of a protein. This basic principle leads us to study the interfaces within proteins as a learning set for intermolecular recognition processes of ligands like substrates, coenzymes, etc., and for prediction of contacts occurring during protein folding and association. For this purpose, we defined interfaces as pairs of matching molecular surface patches between neighboring secondary structural elements. All such interfaces from known protein structures were collected in a comprehensive data bank of interfaces in proteins (DIP). The up-to-date DIP contains interface files for 351 selected Brookhaven Protein Data Bank entries with a total of about 160,000 surface elements formed by 12,475 secondary structures. For special purposes, the inclusion of additional structures or selection of subgroups of proteins can be performed in an easy and straightforward manner. Atomic coordinates of the constituents of molecular surface patches are directly accessible as well as the corresponding contact distances from given atoms to their neighboring secondary structural elements. As a rule, independent of the type of secondary structure, the molecular surface patches of the secondary structural elements can be described as quite flat bodies with a length to width to depth ratio of about 3:2:1 for patches consisting of more than ten atoms. The relative orientation between two docking patches is strongly restricted, due to the narrow distribution of the distances between their centers of mass and of the angles between their normal lines, respectively. The existing retrieval system for the DIP allows selection (out of the set of molecular patches) according to different criteria, such as geometric features, atomic composition, type of secondary structure, contacts, etc. A fast, sequence-independent 3-D superposition procedure was developed for automatic searches for geometrically similar surface areas. Using this procedure, we found a large number of structurally similar interfaces of up to 30 atoms in completely unrelated protein structures.

Inverse sequence similarity in proteins and its relation to the three-dimensional fold.

Nowadays the most successful strategy for the prediction of the tertiary structure of proteins is the homology-based modelling using known structures. A real chance to predict the general fold of a protein arises only in cases with a sufficient sequence homology (e.g. 27% over 100 residues). In this analysis we examine the phenomenon of inverse sequence similarity (ISS) in proteins and its structural meaning. In sequence data bases we found a lot of examples for ISS up to 34% identity over 204 residues and a surprisingly large number of self-inverse protein sequences. By inspection of inverse similar sequence pairs with known tertiary structures we observe that inverse sequence alignments above the threshold indicating structural similarity generally do not imply comparable folds for both. From our analysis we conclude that the straightforward employment of ISS for protein structure prediction fails even above the known threshold for 'safe similarity'.

On alpha-helices terminated by glycine. 1. Identification of common structural features.

About one third of all helices is terminated by residues with a positive torsion angle phi. 74% of them are glycines. This strong propensity can be explained by typical bifurcated three-center hydrogen bonds which are only compatible with a positive torsion angle phi, causing helix termination. An algorithm was developed to identify these structural features in alpha-helices. 158 out of 456 helices in 79 different well-refined protein structures examined in our analysis were found to have a glycine with this special conformation which have been conserved remarkably during evolution.

On alpha-helices terminated by glycine. 2. Recognition by sequence patterns.

Consensus sequence patterns were constructed to describe helix ends with a characteristic conformation caused by specific three-center hydrogen bonds. This special type of hydrogen bond pattern comprises about one third of all helices and mostly contains glycine with a positive torsion angle phi at the helix ends. After a simple clustering procedure 6 resulting consensus sequence patterns were able to identify 501 out of 575 helix ends in the Brookhaven Protein Data Bank, showing the above-mentioned features. The patterns did not detect any false segment, but numerous sequence segments not identified by structural criteria were recognized. It is likely that they are indeed helices terminated by glycine with a positive torsion angle phi.

Occurrence of bifurcated three-center hydrogen bonds in proteins.

Analysis of 13 high-resolution protein X-ray crystal structures shows that 1204 (24%) of all the 4974 hydrogen bonds are of the bifurcated three-center type with the donor X-H opposing two acceptors A1, A2. They occur systematically in alpha-helices where 90% of the hydrogen bonds are of this type; the major component is (n + 4)N-H ... O = C(n) as expected for a 3.6(13) alpha-helix, and the minor component is (n + 4)N-H ... O = C(n + 1), as observed in 3(10) helices; distortions at the C-termini of alpha-helices are stabilized by three-center bonds. In beta-sheets 40% of the hydrogen bonds are three-centered. The frequent occurrence of three-center hydrogen bonds suggests that they should not be neglected in protein structural studies.

Prediction of prolyl residues in cis-conformation in protein structures on the basis of the amino acid sequence.

In proteins most peptide bonds are in trans-conformation: the torsion angle omega = 180 degrees. Only few show cis-conformation in known protein structures (omega = 0 degrees). Most of them are prolyl residues. About 6% of about 4000 prolyl residues are in cis-conformation. Between trans- and cis-prolyl residues significant differences are observed in the surrounding sequences. E.g. there are large amounts of aromatic residues N-terminally in case of cis-prolyl residues, but in the case of trans-prolyl residues more aromatic amino acids occur C-terminally. But in all cases there are only complex patterns which are indicative of cis- and trans-conformation, respectively. Considering the neighbours (+/- 6 residues) of prolyl residues and their physicochemical properties we find 6 different patterns which allow one to assign correctly about 75% of known cis-structured prolyl residues, whereby no false positive one is predicted.