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Many missense mutations/SNPs of the TCN2 gene (which yield Transcobalamin (TC)) were reported in the literature but no study is available about their effect on binding to vitamin B12(B12) at the structural level experimentally nor computationally. Predict the effect of TC missense mutations/SNPs on binding affinity to B12 and characterize their contacts to B12 at the structural level. TC-B12 binding energy difference from the wildtype (ΔΔGmut) was calculated for 378 alanine scanning mutations and 76 ClinVar missense mutations, repeated on two distinct X-ray structures of holoTC namely 2BB5 and 4ZRP. Destabilizing mutations then went through 100 ns molecular dynamics simulation to study their effect on TC-B12 binding at the structural level employing 2BB5 structure. Out of the studied 454 mutations (378 alanine mutations + 76 ClinVar mutations), 19 were destabilizing representing 17 amino acid locations. Mutation energy results show a neutral effect on B12 binding of several missense SNPs reported in the literature including I23V, G94S, R215W, P259R, S348F, L376S, and R399Q. Compared to the wildtype, all the destabilizing mutations have higher average RMSD-Ligand in the last 25% of the MD simulation trajectories and lower average hydrogen bond count while the other parameters vary. Previously reported TCN2 SNPs with an unknown effect on TC-B12 binding were found to have a neutral effect in the current study based on mutation energy calculations. Also, we reported 17 possible amino acids that destabilize TC-B12 binding upon mutation (four listed in ClinVar) and studied their structural effect computationally. Communicated by Ramaswamy H. Sarma.

Ligand-based pharmacophores, ligand–receptor contact fingerprints, physicochemical descriptors and machine learning were combined to probe binding of potent CLK4 antagonists. GFA-SVR gave the best model. Virtual screening identified 3 nanomolar hits.

Niemann-Pick disease type C (NPC) is an autosomal recessive neurovisceral disease characterized by progressive neurodegeneration with variable involvement of multisystemic abnormalities. Crohn's disease (CD) is an inflammatory bowel disease (IBD) with a multifactorial etiology influenced by variants in

CD36 (cluster of differentiation 36) is a membrane protein involved in lipid metabolism and has been linked to pathological conditions associated with metabolic disorders, such as diabetes and dyslipidemia. A case-control study was conducted and included 177 patients with type-2 diabetes mellitus (T2DM) and 173 control subjects to study the involvement of CD36 gene rs1761667 (G>A) and rs1527483 (C>T) polymorphisms in the pathogenesis of T2DM and dyslipidemia among Jordanian population. Lipid profile, blood sugar, gender and age were measured and recorded. Also, genotyping analysis for both polymorphisms was performed. Following statistical analysis, 10 different neural networks and machine learning (ML) tools were used to predict subjects with diabetes or dyslipidemia. Towards further understanding of the role of CD36 protein and gene in T2DM and dyslipidemia, a protein-protein interaction network and meta-analysis were carried out. For both polymorphisms, the genotypic frequencies were not significantly different between the two groups (p > 0.05). On the other hand, some ML tools like multilayer perceptron gave high prediction accuracy (≥ 0.75) and Cohen’s kappa (κ) (≥ 0.5). Interestingly, in K-star tool, the accuracy and Cohen’s κ values were enhanced by including the genotyping results as inputs (0.73 and 0.46, respectively, compared to 0.67 and 0.34 without including them). This study confirmed, for the first time, that there is no association between CD36 polymorphisms and T2DM or dyslipidemia among Jordanian population. Prediction of T2DM and dyslipidemia, using these extensive ML tools and based on such input data, is a promising approach for developing diagnostic and prognostic prediction models for a wide spectrum of diseases, especially based on large medical databases.

The kinase c-Jun N-terminal Kinase 3 (JNK3) plays an important role in neurodegenerative diseases. JNK3 inhibitors have shown promising results in treating Alzheimer's and Parkinson's diseases. This prompted us to model this interesting target via three established structure-based computational workflows; namely, docking-based Comparative Intermolecular Contacts Analysis (db-CICA), pharmacophore modeling via molecular-dynamics based Ligand-Receptor Contact Analysis (md-LRCA), and QSAR-guided selection of crystallographic pharmacophores. Moreover, we compared the performances of resulting pharmacophores against binding models generated via a newly introduced technique, namely, QSAR-guided selection of docking-based pharmacophores. The resulting pharmacophores were validated by receiver operating characteristic (ROC) curve analysis and used as virtual search queries to screen the National Cancer Institute (NCI) database for promising anti-JNK3 hits of novel chemotypes. Eleven nanomolar and low micromolar hits were identified, three of which were captured by QSAR-guided docking-based pharmacophores.

BACKGROUND The regulatory factor X6 (RFX6), a member of regulatory factor X family, is known to play a key role in the development and differentiation of pancreatic beta cells as well as insulin production and secretion. However, the potential role of RFX6 in type 2 diabetes (T2D) is still unclear. AIM Recent studies have indicated that RFX6 binding to DNA could be disrupted in diabetes. Therefore, in this study we investigated whether genetic mutations are present in the DNA binding domain of RFX6 gene that could abrogate its function in T2D. METHODS A cohort of T2D patients was enrolled in this study, and the gene encoding the DNA binding domain of RFX6 was amplified by polymerase chain reaction and then analysed by direct DNA sequencing. RESULTS The DNA sequence analysis revealed the absence of any exonic mutation. However, we have identified a new heterozygous single nucleotide polymorphism (IVS6+31 C>T) in the intronic region of DNA binding domain gene that is present in 9.2% and 8.5% of diabetic and control people, respectively (P = 0.97). CONCLUSION We report the absence of any significant genetic variant that could affect the function of RFX6-DNA binding domain in T2D.

Introduction: Coronavirus disease (COVID-19) is caused by a relatively new coronavirus strain known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has become a significant worldwide health concern. The hesitancy of people to accept vaccination or implement the preventive measures following vaccination can be considered a serious issue that increases the spread of COVID-19. The objectives of the current study were to assess the knowledge and attitudes toward COVID-19 vaccination and the adoption of preventive measures following vaccination among the general population in Jordan and to compare the perceived stresses between the vaccinated and unvaccinated groups. Methods: An online cross-sectional survey was conducted among adults above the age of 18 years in Jordan during the period June-October 2021. The survey has six sections: (1) socio-demographic characteristics, (2) vaccination status, (3) knowledge of participants about COVID-19 vaccination, (4) attitude of participants about COVID-19 vaccination, (5) implementation of preventive practices among participants following COVID-19 vaccination, and (6) perceived stress toward COVID-19 among vaccinated and unvaccinated participants. Results: 605 respondents (69.8% female and 30.2% male) aged between 30-49 years completed the questionnaire. More than half were married and 40.5% received one (29.8%) or two doses (10.7%) of a vaccine. Generally, they showed a positive attitude toward COVID-19 vaccination with a value of 12.7 out of 19. Most of them (>85%) showed proactive practices following vaccination by implementing some preventive measures such as implementing social distancing, avoiding crowded places, and shaking hands. The average perceived stress scale of the general population in Jordan was moderate with a value of 21.5 out of 40. However, fully or partially vaccinated individuals had a significantly (p=0.03) lower PSS (20.97) than unvaccinated people (21.87). Conclusion: The respondents have a good knowledge and positive attitude towards COVID-19 vaccination with good practices following vaccination. However, unvaccinated individuals were more likely to be stressed than vaccinated people. This study may assist policymakers to enhance the extent of COVID-19 vaccination and reduce the spread of this infection.

Activity cliffs (ACs) are defined as closely analogous compounds of significant affinity discrepancies against certain biotarget. In this paper we propose to use AC pair(s) for extracting valid binding pharmacophores through exposing corresponding protein complexes to stochastic deformation/relaxation followed by applying genetic algorithm/machine learning (GA-ML) for selecting optimal pharmacophore(s) that best classify a long list of inhibitors. We compared the performances of ligand-based and structure-based pharmacophores with counterparts generated by this newly introduced technique. Sphingosine kinase 1 (SPHK-1) was used as case study. SPHK-1 is a lipid kinase that plays pivotal role in the regulation of a variety of biological processes including, cell growth, apoptosis, and inflammation. The new approach proved to yield pharmacophore and ML models of comparable accuracies to established ligand-based and structure-based pharmacophores. The resulting pharmacophores and ML models were used to capture hits from the national cancer institute list of compounds and predict their bioactivity categories. Two hits of novel chemotypes showed selective and low micromolar inhibitory IC

Echinomycin (quinomycin A) is a peptide antibiotic from the quinoxaline family, which has a DNA bifunctional intercalating activity and an inhibitor of hypoxia-inducible factor (HIF1α). Echinomycin was discovered in 1957 as a potent antitumor agent; however, it was not successful in clinical use due to its low water solubility and short half-life. To revitalize this potent drug, it is important to increase its aqueous solubility and bioavailability. In this study, echinomycin was loaded into PEGylated pH-sensitive liposomes (PEGLippH) and functionalized with anti-nucleolin aptamer (AptNCL) for selective targeting and pH-responsive release of echinomycin into cancer cells. Echinomycin was complexed with γ-cyclodextrin (ECγCD) to enhance its water solubility and then encapsulated into pH-sensitive liposomes (PEGLippH-ECγCD). Then, liposomes were functionalized with AptNCL (AptNCL-PEGLippH-ECγCD) and the successful functionalization was confirmed by dynamic light scattering (DLS) measurements and gel electrophoresis. Cellular uptake for AptNCL-PEGLippH was evaluated by flow cytometry analysis using MDA-MB-231, MCF7, A549 cancer cell lines with respect to the normal fibroblast cells. The results showed a higher uptake and selectivity for AptNCL-PEGLippH compared to PEGLippH. The anti-proliferative effects of AptNCL-PEGLippH-ECγCD were more potent than PEGLippH-ECγCD by 3.5, 4, and 5 folds for A549, MDA-MB-231, and MCF7, respectively. Selectivity indices (SI) for AptNCL-PEGLippH-ECγCD for the tumor cell lines compared to the normal cell line after 72 h were MDA-MB-231 (43.3), MCF7 (16.9), and A549 (8.5). Furthermore, SI after 3 h for the three cancer cell lines were 4.7, 2.5, 2.8, respectively.

Quinones are a class of cyclic organic compounds that are widely distributed in nature and have been shown to exhibit anti-inflammatory, antioxidant, and anticancerous activities. However, the molecular mechanisms/signaling by which these molecules exert their effect are still not fully understood. In this study, a group of quinone-derived compounds were examined for their potential inhibitory effect against human IRAK1 and IRAK4 kinases in vitro. We have identified five compounds: 1,4-naphthoquinone, emodin, shikonin, plumbagin, and menadione (vitamin K3) as active and selective inhibitors of human IRAK1 enzyme in vitro. The biochemical binding and molecular interactions between the active compounds and IRAK1's catalytic site were demonstrated in silico using structural-based docking and dynamic simulation analysis. Also, 1,4-naphthoquinone was found to effectively inhibit the growth of cancer cell lines overexpressing IRAK1. Furthermore, 1,4-naphthoquinone potently suppressed the production and secretion of key proinflammatory cytokine proteins IL-8, IL-1β, IL-10, TNF-α, and IL-6 in LPS-stimulated PMA-induced human THP-1 macrophages. In conclusion, 1,4-naphthoquinone is an effective inhibitor of IRAK1 kinases and their mediated inflammatory cytokines production in LPS-stimulated PMA-induced human THP-1 macrophages.

Background: Since the coronavirus disease 2019 (COVID-19) was declared a pandemic, there was no doubt that vaccination is the ideal protocol to tackle it. Within a year, a few COVID-19 vaccines have been developed and authorized. This unparalleled initiative in developing vaccines created many uncertainties looming around the efficacy and safety of these vaccines. This study aimed to assess the side effects and perceptions following COVID-19 vaccination in Jordan. Methods: A cross-sectional study was conducted by distributing an online survey targeted toward Jordan inhabitants who received any COVID-19 vaccines. Data were statistically analyzed and certain machine learning (ML) tools, including multilayer perceptron (MLP), eXtreme gradient boosting (XGBoost), random forest (RF), and K-star were used to predict the severity of side effects. Results: A total of 2213 participants were involved in the study after receiving Sinopharm, AstraZeneca, Pfizer-BioNTech, and other vaccines (38.2%, 31%, 27.3%, and 3.5%, respectively). Generally, most of the post-vaccination side effects were common and non-life-threatening (e.g., fatigue, chills, dizziness, fever, headache, joint pain, and myalgia). Only 10% of participants suffered from severe side effects; while 39% and 21% of participants had moderate and mild side effects, respectively. Despite the substantial variations between these vaccines in the presence and severity of side effects, the statistical analysis indicated that these vaccines might provide the same protection against COVID-19 infection. Finally, around 52.9% of participants suffered before vaccination from vaccine hesitancy and anxiety; while after vaccination, 95.5% of participants have advised others to get vaccinated, 80% felt more reassured, and 67% believed that COVID-19 vaccines are safe in the long term. Furthermore, based on the type of vaccine, demographic data, and side effects, the RF, XGBoost, and MLP gave both high accuracies (0.80, 0.79, and 0.70, respectively) and Cohen’s kappa values (0.71, 0.70, and 0.56, respectively). Conclusions: The present study confirmed that the authorized COVID-19 vaccines are safe and getting vaccinated makes people more reassured. Most of the post-vaccination side effects are mild to moderate, which are signs that body’s immune system is building protection. ML can also be used to predict the severity of side effects based on the input data; predicted severe cases may require more medical attention or even hospitalization.

Background Human soluble epoxide hydrolase plays a major role in cardiovascular homeostasis. Genetic variants in the EPHX2 gene among different ethnic groups are associated with cardiovascular complications, such as hypertension. However, no reports regarding the association of EPHX2 genotype with hypertension among type II diabetic (T2D) patients of Middle Eastern Jordanian origin exist. Objective The current study aimed to elucidate the association of the EPHX2 allele, genotype, and haplotype with T2D, hypertension, and parameters of lipid profile parameters among Jordanian T2D patients. Methods Ninety-three genomic DNA samples of non-diabetic controls and 97 samples from T2D patients were genotyped for EPHX2 rs4149243, rs2234914, and rs751142 genetic variants. The DNA samples were amplified using polymerase chain reaction (PCR) and then sequenced using Applied Biosystems Model (ABI3730x1). The functionality of intronic EPHX2 variants was predicted using the in silico Berkely Drosophila Genome Project software. Results We found no significant (P > 0.05) association between the EPHX2 rs4149243, rs2234914, and rs751142 allele, genotype, and haplotype and the incidence of T2D and hypertension. Additionally, no association (P > 0.05) between these EPHX2 genetic variants with the baseline total cholesterol, low- and high-density lipoproteins, and triglycerides among both non-diabetic and diabetic volunteers was found. However, we found an inter-ethnic variation (χ2 -test, p value ˂ 0.05) in the allele frequency of the EPHX2 rs4149243 and rs2234914 variants between Jordanians and other ethnic populations. Also, the in silico Berkely Drosophila Genome Project software predicted that the intronic EPHX2 rs4149243 could alter the splicing of intron 7. Conclusions It can be concluded from this study that EPHX2 rs4149243, rs2234914, and rs751142 genetic variants do not play a role in the development of T2D and hypertension among Jordanian T2D patients. Further genetic studies with larger sample sizes are needed to find out the association of other functional EPHX2 variants with cardiovascular diseases among T2D patients in Jordan.

The new coronavirus disease (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has recently put the world under stress, resulting in a global pandemic. Currently, there are no approved treatments or vaccines, and this severe respiratory illness has cost many lives. Despite the established antimicrobial and immune-boosting potency described for honey, to date there is still a lack of evidence about its potential role amid COVID-19 outbreak. Based on the previously explored antiviral effects and phytochemical components of honey, we review here evidence for its role as a potentially effective natural product against COVID-19. Although some bioactive compounds in honey have shown potential antiviral effects (i.e., methylglyoxal, chrysin, caffeic acid, galangin and hesperidinin) or enhancing antiviral immune responses (i.e., levan and ascorbic acid), the mechanisms of action for these compounds are still ambiguous. To the best of our knowledge, this is the first work exclusively summarizing all these bioactive compounds with their probable mechanisms of action as antiviral agents, specifically against SARS-CoV-2.

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has recently emerged in China and caused a disease called coronavirus disease 2019 (COVID-19). The virus quickly spread around the world, causing a sustained global outbreak. Although SARS-CoV-2, and other coronaviruses, SARS-CoV and Middle East respiratory syndrome CoV (MERS-CoV) are highly similar genetically and at the protein production level, there are significant differences between them. Research has shown that the structural spike (S) protein plays an important role in the evolution and transmission of SARS-CoV-2. So far, studies have shown that various genes encoding primarily for elements of S protein undergo frequent mutation. We have performed an in-depth review of the literature covering the structural and mutational aspects of S protein in the context of SARS-CoV-2, and compared them with those of SARS-CoV and MERS-CoV. Our analytical approach consisted in an initial genome and transcriptome analysis, followed by primary, secondary and tertiary protein structure analysis. Additionally, we investigated the potential effects of these differences on the S protein binding and interactions to angiotensin-converting enzyme 2 (ACE2), and we established, after extensive analysis of previous research articles, that SARS-CoV-2 and SARS-CoV use different ends/regions in S protein receptor-binding motif (RBM) and different types of interactions for their chief binding with ACE2. These differences may have significant implications on pathogenesis, entry and ability to infect intermediate hosts for these coronaviruses. This review comprehensively addresses in detail the variations in S protein, its receptor-binding characteristics and detailed structural interactions, the process of cleavage involved in priming, as well as other differences between coronaviruses.

Type 2 diabetes mellitus (T2DM) is a multifactorial disease associated with many genetic polymorphisms, among them is the FokI polymorphism in the vitamin D receptor (VDR) gene. In this case-control study, samples from 82 T2DM patients and 82 healthy controls were examined to investigate the association of the FokI polymorphism and lipid profile with T2DM in the Jordanian population. DNA was extracted from blood and genotyped for the FokI polymorphism by polymerase chain reaction (PCR) and DNA sequencing. Lipid profile and fasting blood sugar were also measured. There were significant differences in high-density lipoprotein (HDL) cholesterol and triglyceride levels between T2DM and control samples. Frequencies of the FokI polymorphism (CC, CT and TT) were determined in T2DM and control samples and were not significantly different. Furthermore, there was no significant association between the FokI polymorphism and T2DM or lipid profile. A feed-forward neural network (FNN) was used as a computational platform to predict the persons with diabetes based on the FokI polymorphism, lipid profile, gender and age. The accuracy of prediction reached 88% when all parameters were included, 81% when the FokI polymorphism was excluded, and 72% when lipids were only included. This is the first study investigating the association of the VDR gene FokI polymorphism with T2DM in the Jordanian population, and it showed negative association. Diabetes was predicted with high accuracy based on medical data using an FNN. This highlights the great value of incorporating neural network tools into large medical databases and the ability to predict patient susceptibility to diabetes.

Type 2 diabetes mellitus (T2DM) is a multifactorial disease associated with many genetic polymorphisms; among them is the FokI polymorphism in the vitamin D receptor (VDR) gene. In this case-control study, samples from 82 T2DM patients and 82 healthy controls were examined to investigate the association of the FokI polymorphism and lipid profile with T2DM in the Jordanian population. DNA was extracted from blood and genotyped for the FokI polymorphism by polymerase chain reaction (PCR) and DNA sequencing. Lipid profile and fasting blood sugar were also measured. There were significant differences in high-density lipoprotein (HDL) cholesterol and triglyceride levels between T2DM and control samples. Frequencies of the FokI polymorphism (CC, CT and TT) were determined in T2DM and control samples and were not significantly different. Furthermore, there was no significant association between the FokI polymorphism and T2DM or lipid profile. A feed-forward neural network (FNN) was used as a computational platform to predict the persons with diabetes based on the FokI polymorphism, lipid profile, gender and age. The accuracy of prediction reached 88% when all parameters were included, 81% when the FokI polymorphism was excluded, and 72% when lipids were only included. This is the first study investigating the association of the VDR gene FokI polymorphism with T2DM in the Jordanian population, and it showed negative association. Diabetes was predicted with high accuracy based on medical data using an FNN. This highlights the great value of incorporating neural network tools into large medical databases and the ability to predict patient susceptibility to diabetes.

Cancer is a major health problem in many parts of the world. Conventional anticancer treatments are painful, expensive, and unsafe. Therefore, demand is increasing for cancer treatments preferentially in the form of functional foods or nutritional supplements. Kefir, a traditional fermented milk dairy product, has significant antimutagenic and antitumor properties. This research addresses the hypothesis that kefir's anticancer properties are affected by fermentation conditions. Initially, kefir extracts prepared under standard conditions were screened against 7 cancer cell lines using the tetrazolium dye 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide colorimetric assay. Colon cancer and chronic myelogenous leukemia cells were found to be most susceptible to kefir extracts. Subsequently, a factorial design was implemented to assess the effects of 3 fermentation times (24, 48, and 72 h), 3 kefir-to-milk ratios (2, 5, and 10% wt/vol), and 3 fermentation temperatures (4, 25, and 40°C) on kefir's anticancer properties. Remarkably, exploration of the fermentation conditions allowed the anticancer properties of kefir to be enhanced by 5- to 8-fold against susceptible cell lines. Overall, these results demonstrate the possibility of optimizing the anticancer properties of kefir as a functional food in cancer therapy.

We previously combined molecular dynamics (classical or simulated annealing) with ligand-receptor contacts analysis as a means to extract valid pharmacophore model(s) from single ligand-receptor complexes. However, molecular dynamics methods are computationally expensive and time-consuming. Here we describe a novel method for extracting valid pharmacophore model(s) from a single crystallographic structure within a reasonable time scale. The new method is based on ligand-receptor contacts analysis following energy relaxation of a predetermined set of randomly deformed complexes generated from the targeted crystallographic structure. Ligand-receptor contacts maintained across many deformed/relaxed structures are assumed to be critical and used to guide pharmacophore development. This methodology was implemented to develop valid pharmacophore models for PI3K-γ, RENIN, and JAK1. The resulting pharmacophore models were validated by receiver operating characteristic (ROC) analysis against inhibitors extracted from the CHEMBL database. Additionally, we implemented pharmacophores extracted from PI3K-γ to search for new inhibitors from the National Cancer Institute list of compounds. The process culminated in new PI3K-γ/mTOR inhibitory leads of low micromolar IC

Little is known about the prevalence of Giardia duodenalis in human patients in Jordan and all previous studies have used direct microscopy, which lacks sensitivity. The present study developed a novel quantitative PCR (qPCR) assay at the β-giardin (bg) locus and evaluated its use as a frontline test for the diagnosis of giardiasis in comparison with a commercially available ELISA using nested PCR and sequencing of the glutamate dehydrogenase (gdh) locus (gdh nPCR) as the gold standard. A total of 96 human faecal samples were collected from 96 patients suffering from diarrhoea from 5 regions of Jordan and were screened using the ELISA and qPCR. The analytical specificity of the bg qPCR assay revealed no cross-reactions with other genera and detected all the Giardia isolates tested. Analytical sensitivity was 1 Giardia cyst per μl of DNA extract. The overall prevalence of Giardia was 64.6%. The clinical sensitivity and specificity of the bg qPCR was 89.9% and 82.9% respectively compared to 76.5 and 68.0% for the ELISA. This study is the first to compare three different methods (ELISA, bg qPCR, nested PCR and sequencing at the gdh locus) to diagnose Jordanian patients suffering from giardiasis and to analyze their demographic data.

Aim: Ligand-based pharmacophore modeling requires long list of inhibitors, while pharmacophores based on single ligand–receptor crystallographic structure can be too restricted or promiscuous. Methodology: This prompted us to combine simulated annealing molecular dynamics (SAMD) with ligand–receptor contacts analysis as means to construct pharmacophore model(s) from single ligand–receptor complex. Ligand–receptor contacts that survive numerous heating-cooling SAMD cycles are considered critical and are used to guide pharmacophore development. Results: This methodology was implemented to develop pharmacophores for acetylcholinesterase and protein kinase C-θ. The resulting models were validated by receiver-operating characteristic analysis and in vitro bioassay. Assay identified four new protein kinase C-θ inhibitors among captured hits, two of which exhibited nanomolar potencies. Conclusion: The results illustrate the ability of the new method to extract valid pharmacophores from single ligand–protein complex.

Background Inherited retinal dystrophies (IRDs) are characterized by extreme genetic and clinical heterogeneity. There are many genes that are known to cause IRD which makes the identification of the underlying genetic causes quite challenging. And in view of the emergence of therapeutic options, it is essential to combine molecular and clinical data to correctly diagnose IRD patients. In this study, we aimed to identify the disease‐causing variants (DCVs) in four consanguineous Jordanian families with IRDs and describe genotype–phenotype correlations. Methods Exome sequencing (ES) was employed on the proband patients of each family, followed by segregation analysis of candidate variants in affected and unaffected family members by Sanger sequencing. Simulation analysis was done on one novel CLRN1 variant to characterize its effect on mRNA processing. Clinical evaluation included history, slit‐lamp biomicroscopy, and indirect ophthalmoscopy. Results We identified two novel variants in CLRN1 [(c.433+1G>A) and (c.323T>C, p.Leu108Pro)], and two recurrent variants in ABCA4 [(c.1648G>A, p.Gly550Arg) and (c.5460+1G>A)]. Two families with the same DCV were found to have different phenotypes and another family was shown to have sector RP. Moreover, simulation analysis for the CLRN1 splice donor variant (c.433+1G>A) showed that the variant might affect mRNA processing resulting in the formation of an abnormal receptor. Also, a family that was previously diagnosed with nonsyndromic RP was found to have Usher syndrome based on their genetic assessment and audiometry. Conclusion Our findings extend the spectrum of CLRN1‐ and ABCA4‐associated IRDs and describe new phenotypes for these genes. We also highlighted the importance of combining molecular and clinical data to correctly diagnose IRDs and the utility of simulation analysis to predict the effect of splice donor variants on protein formation and function., We identified novel and recurrent CLRN1 and ABCA4 disease‐causing variants in four Jordanian families with inherited retinal dystrophies. One of the ABCA4 variants was found in two unrelated families but surprisingly caused two different phenotypes.

Background and Objectives: This study aimed to investigate the possible association between exclusive breastfeeding duration during early infancy and susceptibility to allergy and influenza in adulthood. Furthermore, we also investigated the association of breastfeeding duration with DNA methylation at two sites in the promoter of the toll-like receptor-1 (TLR1) gene, as well as the association between DNA methylation of the toll-like receptor-1 (TLR1) gene and susceptibility to different diseases. Materials and Methods: Blood samples were collected from 100 adults and classified into two groups according to breastfeeding duration (

Owing to specific and compelling gene silencing, RNA interference (RNAi) is expected to become an essential approach in treating a variety of infectious, hemato-oncological, cardiovascular, and neurodegenerative conditions. The mechanism of action of small interfering RNA (siRNA) is based on post-transcriptional gene silencing. siRNA molecules are usually specific and efficient in the knockdown of disease-related genes. However, they are characterized by low cellular uptake and are susceptible to nuclease-mediated degradation. Therefore, siRNAs require a carrier for their protection and efficient delivery into target cells. The current review highlights the siRNA-based mechanism of action, challanges, and recent advances in clinical applications.

Ligand-based pharmacophore modeling require relatively long lists of active compounds, while a pharmacophore based on a single ligand-receptor crystallographic structure is often promiscuous. These problems prompted us to combine molecular dynamics (MD) simulation with ligand-receptor contacts analysis as means to develop valid pharmacophore model(s). The particular ligand-receptor complex is allowed to perturb over a few nano-seconds using MD simulation. Subsequently, ligand-receptor contact points (≤2.5 Å) are identified. Ligand-receptor contacts maintained above certain threshold during molecular dynamics simulation are considered critical and used to guide pharmacophore development. We termed this method as Molecular-Dynamics Based Ligand-Receptor Contact Analysis. We implemented this new methodology to develop valid pharmacophore models for check point kinase 1 (Chk1) and beta-secretase 1 (BACE1) inhibitors as case studies. The resulting pharmacophore models were validated by receiver operating characteristic curved analysis against inhibitors obtained from CHEMBL database.

Phlebotomine sand flies are the known vectors of Leishmania parasites. New approaches in vaccination against Leishmania have investigated the possibility of integrating Phlebotomus papatasi salivary proteins to enhance the immune response and protect against the transmission of the infection. The aim of the present study was to screen human immune responses to wild sand fly saliva and evaluate immunogenic salivary proteins. Blood samples were collected from donors in control and sand fly infested areas. Antibodies specific for sand fly antigens in donor plasma were probed using immunoblotting. In addition, recall proliferation capability of peripheral blood mononuclear cells (PBMC) was tested after sand fly salivary homogenates stimulation. The significant immunogenic salivary proteins (SPs) identified by immunoblotting were SP28, SP32, and SP36. A specific proliferative response of PBMC after stimulation with sand fly salivary homogenates was evident in donors that have antibody responses against sand fly salivary proteins. Individuals with antibody recognition to a higher number of salivary proteins (i.e., 3 or more SP bands) showed lower PBMC proliferative responses after in vitro stimulation with salivary gland homogenates (SGH) only in the sand fly infested, leishmaniasis free area. Interestingly, the presence of a humoral immune response to many SP antigens inversely correlates with a strong cell-mediated immune response (CMI). It was also noticed that some other heavily expressed antigens, in sand fly salivary homogenate, lack or have weak humoral immune reactivity in exposed individuals. Therefore, considering these antigens alone as CMI activators, without including the immunodominant humoral immune response proteins, needs future investigation.

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which emerged in December 2019 and caused the coronavirus disease 2019 (COVID-19) pandemic, took the world by surprise with an unprecedented public health emergency. Since this pandemic began, extraordinary efforts have been made by scientists to understand the pathogenesis of COVID-19, and to fight the infection by providing various preventive, diagnostic and treatment opportunities based on either novel hypotheses or past experiences. Despite all the achievements, COVID-19 continues to be an accelerating health threat with no specifically approved vaccine or therapy. This review highlights the recent advances in COVID-19 infection, with a particular emphasis on nanomedicine applications that can help in the development of effective vaccines or therapeutics against COVID-19. A novel future perspective has been proposed in this review based on utilizing polymersome nano-objects for effectively suppressing the cytokine storm, which may reduce the severity of COVID-19 infection.

Congenital diarrhea and enteropathies (CODEs) are a group of monogenic disorders that often present with severe diarrhea in the first weeks of life. Enteric anendocrinosis (EA), an extremely rare cause of CODE, is characterized by a marked reduction of intestinal enteroendocrine cells (EC). EA is associated with recessively inherited variants in Neurogenin-3 (NEUROG3) gene. Here we investigate a case of a male infant who presented with mysterious severe malabsorptive diarrhea since birth. Thorough clinical assessments and laboratory tests were successful to exclude the majority of differential diagnosis categories. However, the patient's diagnosis was not established until the genetic test using whole-exome sequencing (WES) was performed. We identified a novel homozygous missense disease-causing variant (DCV) in NEUROG3 (c.413C>G, p.Thr138Arg). Moreover, molecular dynamic simulation analysis showed that (p.Thr138Arg) led to a global change of the NEUROG3 orientation affecting its DNA binding capacity. To the best of our knowledge, this is the first time to apply WES to reach a differential diagnosis of patients with CODEs. Our study not only expands our knowledge about NEUROG3 variants and their clinical consequences but also proves that WES is a very effective tool for the diagnosis of CODEs. This might be of value in early diagnosis of diseases and prenatal CODEs detection.