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Introduction: Viral infections may disrupt the structural and functional integrity of the nervous system, leading to acute conditions such as encephalitis, and neuropsychiatric conditions as mood disorders, schizophrenia, and neurodegenerative diseases. Investigating viral interactions of human proteins may reveal mechanisms underlying these effects and offer insights for therapeutic interventions. This study explores molecular interactions of virus and human proteins that may be related to neuropsychiatric disorders. Methods: Herpes Simplex Virus-1 (HSV-1), Cytomegalovirus (CMV), Epstein-Barr Virus (EBV), Influenza A virus (IAV) (H1N1, H5N1), and Human Immunodeficiency Virus (HIV1&2) were selected as key viruses. Protein structures for each virus were accessed from the Protein Data Bank and analyzed using the HMI-Pred web server to detect interface mimicry between viral and human proteins. The PANTHER classification system was used to categorize viral-human protein interactions based on function and cellular localization. Results: Energetically favorable viral-human protein interactions were identified for HSV-1 (467), CMV (514), EBV (495), H1N1 (3331), H5N1 (3533), and HIV 1&2 (62425). Besides immune and apoptosis-related pathways, key neurodegenerative pathways, including those associated with Parkinson's and Huntington's diseases, were frequently interacted. A total of 38 human proteins, including calmodulin 2, Ras-related botulinum toxin substrate 1 (Rac1), PDGF-β, and vimentin, were found to interact with all six viruses. Conclusion: The study indicates a substantial number of energetically favorable interactions between human proteins and selected viral proteins, underscoring the complexity and breadth of viral strategies to hijack host cellular mechanisms. Further in vivo and in vitro validation is required to understand the implications of these interactions. [ABSTRACT FROM AUTHOR]

The inducible T-cell costimulator (ICOS) deficiency was first described in 2003. Autosomal re-cessive inherited ICOS deficiency is classified as combined immunodeficiency (CID) and has a wide clinical spectrum including hypogammaglobulinemia, recurrent infections, enteropathies, autoimmunity, lymphoproliferation, and malignancy. WAS/WASL Interacting Protein Family Member 1 (WIPF1) mutation causes WIP deficiency, characterized by thrombocytopenia, immu-nodeficiency, and eczema. Here, we aimed to present a patient with coexisting ICOS and WIP de-ficiency. [ABSTRACT FROM AUTHOR]

Complex biological processes in cells are embedded in the interactome, representing the complete set of protein–protein interactions. Mapping and analyzing the protein structures are essential to fully comprehending these processes' molecular details. Therefore, knowing the structural coverage of the interactome is important to show the current limitations. Structural modeling of protein–protein interactions requires accurate protein structures. In this study, we mapped all experimental structures to the reference human proteome. Later, we found the enrichment in structural coverage when complementary methods such as homology modeling and deep learning (AlphaFold) were included. We then collected the interactions from the literature and databases to form the reference human interactome, resulting in 117 897 non-redundant interactions. When we analyzed the structural coverage of the interactome, we found that the number of experimentally determined protein complex structures is scarce, corresponding to 3.95% of all binary interactions. We also analyzed known and modeled structures to potentially construct the structural interactome with a docking method. Our analysis showed that 12.97% of the interactions from HuRI and 73.62% and 32.94% from the filtered versions of STRING and HIPPIE could potentially be modeled with high structural coverage or accuracy, respectively. Overall, this paper provides an overview of the current state of structural coverage of the human proteome and interactome. [ABSTRACT FROM AUTHOR]

OBJECTIVE: Genome-length association studies have shown that Gasdermin B (GSDMB) and Orosomucoid-like 3 (ORMDL3) genes located on the long arm of chromosome 17 are associated with asthma. In this study, it was aimed to determine the possible relationship between asthma control test (ACT), exercise provocation test (ECT), and fractional nitric oxide (FENO) levels and GSDMB and ORMDL3 gene expressions. METHODS: 59 asthmatic and 38 non-asthmatic children were included in the study. We divided the patient group into two subgroups as mild persistent asthma (29 patients) and moderate persistent asthma (30 patients). ORMDL3, GSDMB gene expression levels, ECT, total IgE levels, and eosinophil counts were measured in all cases. In addition, ACT and FeNO levels were measured in children with asthma. Afterward, the relationship of ORMDL3 and GSDMB gene expression coefficient changes with ECT, ACT, and FeNO was examined. RESULTS: When patients with ACT =15 were compared with patients with ACT =20, ORMDL3 and GSDMB gene expressions were increased 6.74 and 11.74 times, respectively. Comparing patients with ACT =20 and ACT =15 in terms of coefficient changes (ΔCq), higher change values were observed for ΔCq ORMDL3 in patients with ACT =15 (p=0.015). Similarly, when patients with FENO =25 ppb were compared with patients with FENO >25 ppb, ORMDL3 and GSDMB gene expressions were increased by 2.93 and 3.56 times, respectively. When the coefficient changes were compared, no significant difference was found between FENO=25 and FENO >25 patients. There was a slight negative correlation between ΔCq values and ACT score (p=0.003, r=-0.418 for ORMDL3, and p=0.016, r=-0.345 for GSDMB). In addition, we observed a statistically significant positive correlation between ORMDL3 and GSDMB gene expressions (r=0.80, p<0.001). CONCLUSION: We showed that increased ORMDL3 and GSDMB gene expression levels may be associated with ACT scores, FeNO and ECT in asthma. These findings may encourage future studies with larger numbers of subjects that can use gene expression levels in various asthma phenotypes for prognostic prediction. [ABSTRACT FROM AUTHOR]

OBJECTIVE: Patients with Inborn Errors of Immunity, also known as Primary Immunodeficiency (PID), are prone to recurrent bacterial infections and these patients often require lifelong IgG replacement therapy. The aim of this presentation is to evaluate the efficacy, safety, and patient satisfaction in PID patients receiving subcutaneous immunoglobulin (SCIG) treatment and to share our expe-riences. METHODS: Twenty-one patients who were followed up with the diagnosis of PID by our Pediatric Allergy and Immunology Clinic and received regular intravenous immunoglobulin therapy (IVIG) befo-re starting SCIG treatment were included in the study. RESULTS: A total of 21 patients were included in the study. 10 of the patients (47.6%) were female, 11 (52.4%) were male, and the mean age was 8.8±4.42 years. Five of the patients were Syrian patients living in the refugee camp. Threshold IgG levels of the patients were evaluated every 3 months. IgG levels were significantly higher than baseline IVIG levels at weeks 3, 6, and 12 of SCIG treatment, respectively. There was no significant difference between 3rd, 6th and 12th months of SCIG treatment. A statistically significant decrease was observed in the frequency of infections in patients who received SCIG treatment (p=0.003). During SCIG treatment, the total infection rate was 4.1/person/year. According to the TSQM-9 satisfaction questionnaire, the annual hospitalization rate was 0.9/patient/year for IVIG and 0.4/patient/year for SCIG (p>0.005), and 61.9% of patients were moderately satisfied, 14.2%. 19% were very satisfied and 4.7% were not satisfied with the treatment. When the satisfaction criteria were evaluated, it was observed that the patients mostly (71%) were satisfied with the absence of vascular access prob-lems and the comfort of self-application at home. CONCLUSION: SCIG therapy causes high serum IgG levels and a reduced frequency of infections and can be a safe, effective, and well-tolerated treatment alternative in patients with PID with high patient satisfaction. [ABSTRACT FROM AUTHOR]

Summary We present a web-based server for navigating and visualizing possible interactions between SARS-CoV-2 and human host proteins. The interactions are obtained from HMI_Pred which relies on the rationale that virus proteins mimic host proteins. The structural alignment of the viral protein with one side of the human protein–protein interface determines the mimicry. The mimicked human proteins and predicted interactions, and the binding sites are presented. The user can choose one of the 18 SARS-CoV-2 protein structures and visualize the potential 3D complexes it forms with human proteins. The mimicked interface is also provided. The user can superimpose two interacting human proteins in order to see whether they bind to the same site or different sites on the viral protein. The server also tabulates all available mimicked interactions together with their match scores and number of aligned residues. This is the first server listing and cataloging all interactions between SARS-CoV-2 and human protein structures, enabled by our innovative interface mimicry strategy. Availability and implementation The server is available at https://interactome.ku.edu.tr/sars/. [ABSTRACT FROM AUTHOR]

The virulence factor Type IV pili (T4P) are surface appendages used by the opportunistic pathogen Pseudomonas aeruginosa for twitching motility and adhesion in the environment and during infection. Additionally, the use of these appendages by P. aeruginosa for biofilm formation increases its virulence and drug resistance. Therefore, attenuation of the activity of T4P would be desirable to control P. aeruginosa infections. Here, a computational approach has been pursued to screen natural products that can be used for this purpose. PilB, the elongation ATPase of the T4P machinery in P. aeruginosa , has been selected as the target subunit and virtual screening of FDA-approved drugs has been conducted. Screening identified two natural compounds, ergoloid and irinotecan, as potential candidates for inhibiting this T4P-associated ATPase in P. aeruginosa . These candidate compounds underwent further rigorous evaluation through molecular dynamics (MD) simulations and then through in vitro twitching motility and biofilm inhibition assays. Notably, ergoloid emerged as a particularly promising candidate for weakening the T4P activity by inhibiting the elongation ATPases associated with T4P. This repurposing study paves the way for the timely discovery of antivirulence drugs as an alternative to classical antibiotic treatments to help combat infections caused by P. aeruginosa and related pathogens.Communicated by Ramaswamy H. Sarma.