Targeting Cathepsin L in Cancer Management: Leveraging Machine Learning, Structure-Based Virtual Screening, and Molecular Dynamics Studies.

Cathepsin L (CTSL) expression is dysregulated in a variety of cancers. Extensive empirical evidence indicates their direct participation in cancer growth, angiogenic processes, metastatic dissemination, and the development of treatment resistance. Currently, no natural CTSL inhibitors are approved for clinical use. Consequently, the development of novel CTSL inhibition strategies is an urgent necessity. In this study, a combined machine learning (ML) and structure-based virtual screening strategy was employed to identify potential natural CTSL inhibitors. The random forest ML model was trained on IC50 values. The accuracy of the trained model was over 90%. Furthermore, we used this ML model to screen the Biopurify and Targetmol natural compound libraries, yielding 149 hits with prediction scores >0.6. These hits were subsequently selected for virtual screening using a structure-based approach, yielding 13 hits with higher binding affinity compared to the positive control (AZ12878478). Two of these hits, ZINC4097985 and ZINC4098355, have been shown to strongly bind CTSL proteins. In addition to drug-like properties, both compounds demonstrated high affinity, ligand efficiency, and specificity for the CTSL binding pocket. Furthermore, in molecular dynamics simulations spanning 200 ns, these compounds formed stable protein-ligand complexes. ZINC4097985 and ZINC4098355 can be considered promising candidates for CTSL inhibition after experimental validation, with the potential to provide therapeutic benefits in cancer management.

Screening of four signature genes for clinical testing through bioinformatics and in vitro methods in head and neck squamous cell carcinoma.

Head and neck squamous cell carcinoma (HNSC) is the 6th most common cancer around the globe; its underlying molecular mechanisms and accurate molecular markers are still lacking. In this study, we explored hub genes and their potential signaling pathways through which these genes participate in the development of HNSC. The GSE23036 gene microarray dataset was attained from the GEO (Gene Expression Omnibus) database. Hub genes were identified via the Cytohubba plug-in application of the Cytoscape. The Cancer Genome Atlas (TCGA) datasets and cell lines (HOK and FuDu) were used to evaluate expression variations in the hub genes. Moreover, promoter methylation, genetic alteration, gene enrichment, miRNA network, and immunocyte infiltration analysis were also performed to confirm the oncogenic role and biomarker potential of the hub genes in HNSC patients. Based on the hub gene analysis results, four hub genes, including KNTC1 (Kinetochore Associated 1), CEP55 (Centrosomal protein of 55 kDa), AURKA (Aurora A Kinase), and ECT2 (Epithelial Cell Transforming 2), with the highest degree scores were denoted as hub genes. All these four genes were significantly up-regulated in HNSC clinical samples and cell lines relative to their counterparts. Overexpression of KNTC1, CEP55, AURKA, and ECT2 was also associated with poor survival and various clinical parameters of the HNSC patients. Methylation analysis through targeted bisulfite sequencing of HOK and FuDu cell lines revealed that the overexpression of KNTC1, CEP55, AURKA, and ECT2 hub genes was due to their promoter hypomethylation. Moreover, higher expressions of KNTC1, CEP55, AURKA, and ECT2 were positively correlated with the abundance of the CD4+ T cells and macrophage while with the reduction of CD8+ T cells in HNSC samples. Finally, gene enrichment analysis showed that all hub genes are involved in "nucleoplasm, centrosome, mitotic spindle, and cytosol" pathways. In conclusion, the KNTC1, CEP55, AURKA, and ECT2 genes could be potential biomarkers for HNSC patients and provide a novel insight into the diagnosis and treatment of the disease.

Identifying promising GSK3ß inhibitors for cancer management: a computational pipeline combining virtual screening and molecular dynamics simulations.

Glycogen synthase kinase-3 (GSK3ß), a serine/threonine protein kinase, has been discovered as a novel target for anticancer drugs. Although GSK3ß is involved in multiple pathways linked to the etiology of various cancers, no specific GSK3ß inhibitor has been authorized for cancer therapy. Most of its inhibitors have toxicity effects therefore, there is a need to develop safe and more potent inhibitors. In this study, a library of 4,222 anti-cancer compounds underwent rigorous computational screening to identify potential candidates for targeting the binding pocket of GSK3ß. The screening process involved various stages, including docking-based virtual screening, physicochemical and ADMET analysis, and molecular dynamics simulations. Ultimately, two hit compounds, BMS-754807 and GSK429286A, were identified as having high binding affinities to GSK3ß. BMS-754807 and GSK429286A exhibited binding affinities of -11.9, and -9.8 kcal/mol, respectively, which were greater than that of the positive control (-7.6 kcal/mol). Further, molecular dynamics simulations for 100 ns were employed to optimize the interaction between the compounds and GSK3ß, and the simulations demonstrated that the interaction was stable and consistent throughout the study. These hits were also anticipated to have good drug-like properties. Finally, this study suggests that BMS-754807 and GSK429286A may undergo experimental validation to evaluate their potential as cancer treatments in clinical settings.

Potential Biomarkers for Parkinson Disease from Functional Enrichment and Bioinformatic Analysis of Global Gene Expression Patterns of Blood and Substantia Nigra Tissues.

The Parkinson disease (PD) is the second most common neurodegenerative disorder affecting the central nervous system and motor functions. The biological complexity of PD is yet to reveal potential targets for intervention or to slow the disease severity. Therefore, this study aimed to compare the fidelity of blood to substantia nigra (SN) tissue gene expression from PD patients to provide a systematic approach to predict role of the key genes of PD pathobiology. Differentially expressed genes (DEGs) from multiple microarray data sets of PD blood and SN tissue from GEO database are identified. Using the theoretical network approach and variety of bioinformatic tools, we prioritized the key genes from DEGs. A total of 540 and 1024 DEGs were identified in blood and SN tissue samples, respectively. Functional pathways closely related to PD such as ERK1 and ERK2 cascades, mitogen-activated protein kinase (MAPK) signaling, Wnt, nuclear factor-κB (NF-κB), and PI3K-Akt signaling were observed by enrichment analysis. Expression patterns of 13 DEGs were similar in both blood and SN tissues. Comprehensive network topological analysis and gene regulatory networks identified additional 10 DEGs functionally connected with molecular mechanisms of PD through the mammalian target of rapamycin (mTOR), autophagy, and AMP-activated protein kinase (AMPK) signaling pathways. Potential drug molecules were identified by chemical-protein network and drug prediction analysis. These potential candidates can be further validated in vitro/in vivo to be used as biomarkers and/or novel drug targets for the PD pathology and/or to arrest or delay the neurodegeneration over the years, respectively.

Characterisation of APS-1 Experimental Models Is Crucial for Development of Novel Therapies.

Autoimmune polyglandular syndrome type 1 (APS-1) is an inherited autosomal disorder. The most common clinical features of the disease include adrenocortical failure, hypoparathyroidism (HP), and chronic mucocutaneous candidiasis (CMC). APS-1 is caused by mutations in the autoimmune regulator (AIRE) gene. AIRE is a transcriptional factor involved in the regulation of thousands of genes in the thymus. It facilitates central tolerance by promoting the ectopic expression of tissue-specific antigens (TSAs) in medullary thymic epithelial cells (mTECs), leading to the deletion of self-reactive thymocytes. Several Aire-deficient mice were developed separately, on different backgrounds; seven published Aire knockout mice show a variety of phenotypes depending on the strain used to generate the experimental model. The first Aire-deficient mice were generated on a "black 6" background almost 20 years ago. The model showed mild phenotype with relatively modest penetrance compared to models generated on BALBc or NOD backgrounds. The generation of all these experimental models is crucial for development and testing new therapeutics as well as reading the response to treatments.

Appraisal of the Antioxidant Activity, Polyphenolic Content, and Characterization of Selected Himalayan Herbs: Anti-Proliferative Potential in HepG2 Cells.

Natural antioxidants derived from plants have played a vital role in preventing a wide range of human chronic conditions and provide novel bioactive leads for investigators in pharmacotherapy discovery. This work was designed to examine the ethnopharmacological role of Urtica dioica (UD), Capsella bursa-pastoris (CBP), and Inula racemosa (IR). The total phenolic and flavonoid contents (TPC and TFC) were illustrated through colorimetric assays, while the antioxidant activity was investigated through DPPH and ABTS assays. The evaluation of phytochemicals by FT-IR of UD and CBP revealed high contents of aliphatic amines, while IR showed a major peak for ketones. The antioxidant activity, TPC and TFC were highest in the ethanol extract of UD, followed by CBP, and IR showed the lowest activity. All of the extracts revealed significant antioxidant capacities along a dosage gradient. Through a HPLC analysis at a wavelength of 280 nm, UD leaves demonstrated an intense peak of quercetin, and the peak for rutin was less intense. CBP (whole plant), instead, demonstrated a major yield of rutin, and a peak for quercetin was not observed in CBP. IR (rhizomes) showed both quercetin and rutin. All of the extracts were significantly cytotoxic to HepG2 cells after 48 h with the trend IR > UD > CBP. The outcomes of this study may be effective in the selection of specific plants as realistic sources of the bioactive components that might be useful in the nutraceutical progression and other biomedical efficacies.

Structural Homology-Based Drug Repurposing Approach for Targeting NSP12 SARS-CoV-2.

The severe acute respiratory syndrome coronavirus 2, also known as SARS-CoV-2, is the causative agent of the COVID-19 global pandemic. SARS-CoV-2 has a highly conserved non-structural protein 12 (NSP-12) involved in RNA-dependent RNA polymerase (RdRp) activity. For the identification of potential inhibitors for NSP-12, computational approaches such as the identification of homologous proteins that have been previously targeted by FDA-approved antivirals can be employed. Herein, homologous proteins of NSP-12 were retrieved from Protein DataBank (PDB) and the evolutionary conserved sequence and structure similarity of the active site of the RdRp domain of NSP-12 was characterized. The identified homologous structures of NSP-12 belonged to four viral families: Coronaviridae, Flaviviridae, Picornaviridae, and Caliciviridae, and shared evolutionary conserved relationships. The multiple sequences and structural alignment of homologous structures showed highly conserved amino acid residues that were located at the active site of the RdRp domain of NSP-12. The conserved active site of the RdRp domain of NSP-12 was evaluated for binding affinity with the FDA-approved antivirals, i.e., Sofosbuvir and Dasabuvir in a molecular docking study. The molecular docking of Sofosbuvir and Dasabuvir with the active site that contains conserved motifs (motif A-G) of the RdRp domain of NSP-12 revealed significant binding affinity. Furthermore, MD simulation also inferred the potency of Sofosbuvir and Dasabuvir. In conclusion, targeting the active site of the RdRp domain of NSP-12 with Dasabuvir and Sofosbuvir might reduce viral replication and pathogenicity and could be further studied for the treatment of SARS-CoV-2.

Nanoemulsions: Formulation, characterization, biological fate, and potential role against COVID-19 and other viral outbreaks.

Viral diseases are emerging as global threats. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), that causes coronavirus disease (COVID-19), has severe global impacts. Safety, dosage, and potency of vaccines recently approved for emergency use against SARS-CoV-2 need further evaluation. There is still no effective treatment against COVID-19; therefore, safe, and effective vaccines or therapeutics against SARS-CoV-2 are urgently needed. Oil-in-water nanoemulsions (O/W NEs) are emerging as sophisticated, protective, and therapeutic platforms. Encapsulation capacity, which offers better drug pharmacokinetics, coupled with the tunable surfaces present NEs as promising tools for pharmaceutical applications. The challenges facing drug discovery, and the advancements of NEs in drug delivery demonstrate the potential of NEs against evolving diseases, like COVID-19. Here we summarize current COVID-19 knowledge and discuss the composition, stability, preparation, characterization, and biological fate of O/W NEs. We also provide insights into NE structural-functional properties that may contribute to therapeutic or preventative solutions against COVID-19.

AAV9-mediated AIRE gene delivery clears circulating antibodies and tissue T-cell infiltration in a mouse model of autoimmune polyglandular syndrome type-1.

OBJECTIVES: Autoimmune polyglandular syndrome type-1 (APS-1) is a monogenic recessive disorder characterised by multiple endocrine abnormalities, chronic mucocutaneous candidiasis and high titres of serum autoantibodies. To date, no curative treatment is available; current therapies manage the symptoms rather than treating the cause and have major side effects. APS-1 is caused by mutations in the autoimmune regulator (AIRE) gene. AIRE mediates central tolerance by directing the ectopic expression of tissue-specific antigens (TSAs) in medullary thymic epithelial cells, causing the deletion of self-reactive thymocytes. Therefore, loss-of-function mutations in AIRE result in a multisystem autoimmune disease. Because of the monogenic aetiology of APS-1 and availability of an APS-1 mouse model, we have explored the option of restoring functional AIRE using adeno-associated virus serotype 9 (AAV9). METHODS: The efficacy of AAV9-AIRE (AAV9 carrying AIRE cDNA) gene therapy was assessed in an APS-1 mouse model. We performed intrathymic injection of AAV9-AIRE into APS-1 mouse model using ultrasound imaging technique to accurately locating the thymus. We evaluated the efficiency of this approach alongside measures of autoimmunity and histology of target tissues. RESULTS: Intrathymic injection of AAV9-AIRE demonstrated high transduction efficiency and restored AIRE expression in the thymus. AIRE gene delivery led to a significant increase in TSA expression, and importantly a significant reduction of serum autoantibodies in treated versus control mice, which fell to near-undetectable levels by 4 weeks post-treatment. Furthermore, histological analysis of treated animals showed near-normal tissue morphology with no lymphocytic infiltrations, a hallmark of untreated Aire-deficient mice. CONCLUSION: This study has demonstrated the feasibility of AAV9-AIRE as a vehicle for gene therapy for APS-1.

Whole Exome Sequencing Identifies Three Novel Mutations in the ASPM Gene From Saudi Families Leading to Primary Microcephaly.

Autosomal recessive primary microcephaly (MCPH) is a neurodevelopmental defect that is characterized by reduced head circumference at birth along with non-progressive intellectual disability. Till date, 25 genes related to MCPH have been reported so far in humans. The ASPM (abnormal spindle-like, microcephaly-associated) gene is among the most frequently mutated MCPH gene. We studied three different families having primary microcephaly from different regions of Saudi Arabia. Whole exome sequencing (WES) and Sanger sequencing were done to identify the genetic defect. Collectively, three novel variants were identified in the ASPM gene from three different primary microcephaly families. Family 1, showed a deletion mutation leading to a frameshift mutation c.1003del. (p.Val335*) in exon 3 of the ASPM gene and family 2, also showed deletion mutation leading to frameshift mutation c.1047del (p.Gln349Hisfs*18), while in family 3, we identified a missense mutation c.5623A>G leading to a change in protein (p.Lys1875Glu) in exon 18 of the ASPM gene underlying the disorder. The identified respective mutations were ruled out in 100 healthy control samples. In conclusion, we found three novel mutations in the ASPM gene in Saudi families that will help to establish a disease database for specified mutations in Saudi population and will further help to identify strategies to tackle primary microcephaly in the kingdom.

Quality of Life of asthmatic children and their caregivers.

OBJECTIVES: To assess Quality of Life (QOL), and its associated factors between asthmatic children and their caregivers, and determine the correlation between QOL of patients and caregivers, at King Abdulaziz University Hospital (KAUH), Jeddah. METHODS: A cross-sectional study was conducted among eligible participants who attended Pediatric Pulmonology Outpatient Clinic of KAUH, during 2016/2017. A data collection sheet was used. The standardized Arabic version of Pediatric Asthma Quality of Life Questionnaire (PAQLQ) for children aged 7 - 17 years was completed. The caregiver who accompanied the child fulfilled the Pediatric Asthma Caregiver's Quality of Life Questionnaire (PACQLQ). Descriptive and inferential analyses were performed. RESULTS: QOL scores were reduced among asthmatic children who had other type of allergy, or a family history of allergies. Uncontrolled management of asthma presented by frequent waking-up at night, frequent wheezes, visiting Emergency Rooms (ER), or hospital admission was associated with poor QOL of both asthmatic children and their caregivers. There is a positive correlation between child symptoms domain of PAQLQ and emotional domain of PACQLQ of their caregivers. CONCLUSION: Uncontrolled asthma was associated with poor QOL of asthmatic child and caregivers. Better management of asthma is recommended to improve their QOL.

Epigallocatechin-3 Gallate Inhibits STAT-1/JAK2/IRF-1/HLA-DR/HLA-B and Reduces CD8 MKG2D Lymphocytes of Alopecia Areata Patients.

BACKGROUND: Alopecia areata (AA) is associated with Interferon- γ (IFN-γ) mediated T-lymphocyte dysfunction and increased circulating Interleukine-17 (IL-17) levels. Epigallocatechin-3-gallate (EGCG) specifically inhibits IFN-γ pathways and unlike Janus Kinase 1 and 2 (JAK1/JAK2) inhibitors (tofacitinib, ruxolitinib), EGCG is safer, more cost-effective, and is a topically active agent. Our objective is to test the mode of action of EGCG in vitro and ex vivo using HaCat, Jurkat cell lines, and peripheral blood mononuclear cells (PBMCs) of AA patients and healthy controls (HCs), respectively. METHODS: distribution of T helper cells (Th1, Th17), and cytotoxic cells (CD8) in PBMCs isolated from 30 AA patients and 30 HCs was investigated by flowcytomterty. In vitro treatment of HaCat and Jurkat cells with 40 µm EGCG for 48 h was performed to measure the level of phosphorylation of signal transducer and activator of transcription protein STAT1, and replicated in ex vivo model using PBMCs of AA patients. RESULTS: Interestingly, 40 µm EGCG is capable of completely inhibiting phosphorylation of STAT1 after 48 h in HaCat and Jurkat cells and ex vivo in PBMCs of AA patients. Based on QPCR data, the action of EGCG on p-STAT1 seems to be mediated via downregulation of the expression of JAK2 but not JAK1 leading to the inhibition of human leukocyte antigens (HLA-DR and HLA-B) expression probably via IRF-1. On the other hand, AA patients have significantly increased levels of Th1, Th17, and CD8 cells and the production of IFN-γ and IL-17 by PBMCs in AA patients was significantly higher compared to HC; p = 0.008 and p = 0.006, respectively. Total numbers of CD8+ cells were not significantly different between treated and untreated samples. However, CD8+ cells with positive Natural killer group 2 member D (NKG2D) transmembrane receptor (CD8+ NKG2D+ subset) was significantly reduced when PBMCs were treated with 20 µm EGCG for 48 h. CONCLUSION: These results suggest that EGCG has a synergistic action that inhibits expression of HLA-DR and HLA-B molecules via the IFN-γ pathway to maintain immune privilege in HF; also it reduces CD8+ NKG2D+ subset.

Delayed Guillain-Barré Syndrome after Bariatric Surgery: A Report of Three Cases.

Surgeries carry a risk of complications. Polyneuropathies, including Guillain-Barré syndrome (GBS), are potential complications of bariatric surgery. The incidence of these conditions is expected to increase as these surgeries become increasingly popular. We present a case report of three patients who developed a polyneuropathy after bariatric surgery. GBS was diagnosed in each patient, with nutritional deficiencies being suspected as a contributing factor. All patients began a 5-day intravenous immunoglobulin course in addition to receiving rehabilitative support, multivitamins, intravenous thiamine, vitamin D (therapeutic dose), and selenium. The patients' symptoms improved but did not completely resolve. GBS can be a complication of bariatric surgery. Although a clear cause-effect relationship cannot be established for the present cases, the cumulative literature on the subject suggests that it is important to include it as a potential risk when counseling patients for such surgeries.