The deleterious variants of N-acetylgalactosamine-6-sulfatase (GalN6S) enzyme trigger Morquio a syndrome by disrupting protein foldings.

Lysosomal enzymes degrade cellular macromolecules, while their inactivation causes human hereditary metabolic disorders. Mucopolysaccharidosis IVA (MPS IVA; Moquio A syndrome) is one of the lysosomal storage disorders caused by a defective Galactosamine-6-sulfatase (GalN6S) enzyme. In several populations, disease incidence is elevated due to missense mutations brought on by non-synonymous allelic variation in the GalN6S enzyme. Here, we studied the effect of non-synonymous single nucleotide polymorphism (nsSNPs) on the structural dynamics of the GalN6S enzyme and its binding with N-acetylgalactosamine (GalNAc) using all-atom molecular dynamics simulation and an essential dynamics approach. Consequently, in this study, we have identified three functionally disruptive mutations in domain-I and domain-II, that is, S80L, R90W, and S162F, which presumably contribute to post-translational modifications. The study delineated that both domains work cooperatively, and alteration in domain II (S80L, R90W) leads to conformational changes in the catalytic site in domain-I, while mutation S162F mainly provokes higher residual flexibility of domain II. These results show that these mutations impair the hydrophobic core, implying that Morquio A syndrome is caused by misfolding of the GalN6S enzyme. The results also show the instability of the GalN6S-GalNAc complex upon substitution. Overall, the structural dynamics resulting from point mutations give the molecular rationale for Moquio A syndrome and, more importantly, the Mucopolysaccharidoses (MPS) family of diseases, re-establishing MPS IVA as a protein-folding disease.Communicated by Ramaswamy H. Sarma.

Dynamics of water-mediated interaction effects on the stability and transmission of Omicron.

SARS-Cov-2 Omicron variant and its highly transmissible sublineages amidst news of emerging hybrid variants strengthen the evidence of its ability to rapidly spread and evolve giving rise to unprecedented future waves. Owing to the presence of isolated RBD, monomeric and trimeric Cryo-EM structures of spike protein in complex with ACE2 receptor, comparative analysis of Alpha, Beta, Gamma, Delta, and Omicron assist in a rational assessment of their probability to evolve as new or hybrid variants in future. This study proposes the role of hydration forces in mediating Omicron function and dynamics based on a stronger interplay between protein and solvent with each Covid wave. Mutations of multiple hydrophobic residues into hydrophilic residues underwent concerted interactions with water leading to variations in charge distribution in Delta and Omicron during molecular dynamics simulations. Moreover, comparative analysis of interacting moieties characterized a large number of mutations lying at RBD into constrained, homologous and low-affinity groups referred to as mutational drivers inferring that the probability of future mutations relies on their function. Furthermore, the computational findings reveal a significant difference in angular distances among variants of concern due 3 amino acid insertion (EPE) in Omicron variant that not only facilitates tight domain organization but also seems requisite for characterization of mutational processes. The outcome of this work signifies the possible relation between hydration forces, their impact on conformation and binding affinities, and viral fitness that will significantly aid in understanding dynamics of drug targets for Covid-19 countermeasures. The emerging scenario is that hydration forces and hydrophobic interactions are crucial variables to probe in mutational analysis to explore conformational landscape of macromolecules and reveal the molecular origins of protein behaviors.

Deciphering the relational dynamics of AF-2 domain of PAN PPAR through drug repurposing and comparative simulations.

Peroxisome proliferator-activated receptors (PPARs) are nuclear receptors, and their activation has been proven to treat mild liver fibrosis, reduce steatosis, inflammation, and the extrahepatic effects of chronic liver disease. Considering the significance of the PPARs, it is targeted for the treatment of Non-Alcoholic Steatohepatitis (NASH), for which currently there is no FDA-approved drug. Lanifibranor is a next-generation highly potential indole sulfonamide derivative that is presently in clinical trial phase III as an anti-NASH drug which fully activates PPARα and PPARδ and partially activates PPARγ. In the current study, a comprehensive computational investigation including 3D-QSAR pharmacophore modeling, MD simulations and binding free energy calculations is performed to get insights into the activation mechanism of the Lanifibranor. Furthermore, FDA-approved drugs were explored for repurposing through virtual screening against each PPAR pharmacophore to identify potential drug candidates. Forasartan, Raltitrexed, and Lifitegrast stood out as potential agonists for PPARα (full agonist), PPARγ (partial agonist), and PPARδ (full agonist), respectively. The findings of the study highlighted a lack of hydrogen bond acceptor feature in Raltitrexed and Lanifibranor which is responsible for partial activation of PPARγ that plays a critical role in preventing lipid accumulation. In addition to this, the significant role of AF2 domain in full and partial activation of PPARs through electrostatic interactions was also revealed, that facilitates the anchoring of ligand within the binding cavity. Moreover, common chemical scaffolds (methyl sulfonyl benzene, butyric acid, and chlorobenzene) identified using Fingerprinting technique were presented in this study which hold the potential to aid in the design and development of target specific novel Pan PPAR medications in future.

Fragment-Based Approaches Identified Tecovirimat-Competitive Novel Drug Candidate for Targeting the F13 Protein of the Monkeypox Virus.

Monkeypox is a serious public health issue in tropical and subtropical areas. Antivirals that target monkeypox proteins might lead to more effective and efficient therapy. The F13 protein is essential for the growth and maturation of the monkeypox virus. F13 inhibition might be a viable therapeutic target for monkeypox. The in silico fragment-based drug discovery method for developing antivirals may provide novel therapeutic options. In this study, we generated 800 compounds based on tecovirimat, an FDA-approved drug that is efficacious at nanomolar quantities against monkeypox. These compounds were evaluated to identify the most promising fragments based on binding affinity and pharmacological characteristics. The top hits from the chemical screening were docked into the active site of the F13 protein. Molecular dynamics simulations were performed on the top two probable new candidates from molecular docking. The ligand-enzyme interaction analysis revealed that the C2 ligand had lower binding free energy than the standard ligand tecovirimat. Water bridges, among other interactions, were shown to stabilize the C2 molecule. Conformational transitions and secondary structure changes in F13 protein upon C2 binding show more native three-dimensional folding of the protein. Prediction of pharmacological properties revealed that compound C2 may be promising as a drug candidate for monkeypox fever. However, additional in vitro and in vivo testing is required for validation.

Medical colleges' challenges and coping strategies in implementing accreditation standards in Pakistan.

Objectives: To explore the challenges faced by medical colleges and coping strategies used in implementing accreditation standards by Pakistan Medical Commission during accreditation inspection 2019. Methods: In this qualitative case study, four medical colleges and their affiliated hospitals from three cities in Khyber Pakhtunkhwa province of Pakistan were selected through purposive sampling. Data was collected through focus group discussions (FGD) through Open-ended questions, based on CIPP (context, input, process, and product) model. Each focus group comprised of Dean, the Director Department of Medical Education (DME) and the Medical Director of the hospital. Data were thematically analyzed and results were based on the CIPP model. Results: Three themes identified were administrative challenges, accreditation challenges and resource challenges. The administrative challenges theme was further explained under subthemes of rules and regulation challenges, documentation and record challenges, and DME-related challenges. The accreditation-related challenges theme was explored in-depth with subthemes of accreditation process-related challenges, accreditation standards-related challenges and curriculum-related challenges. The resource challenges theme was described under sub-themes of infrastructure-related challenges, human resources and financial challenges. The commonest coping strategies adopted by medical colleges were establishing DME, emergency preparatory meetings of staff, and hiring staff on an emergency basis, to overcome administrative, accreditation and resource challenges respectively. Future suggestions for improving the accreditation process in the local context were highlighted. Conclusion: Main challenges identified were administrative challenges, accreditation challenges and resource challenges. Coping strategies by the medical colleges for these challenges are highlighted. The accreditation body should harmonize the process of accreditation with medical colleges and other stakeholders.

Molecular Insights into the Role of Pathogenic nsSNPs in GRIN2B Gene Provoking Neurodevelopmental Disorders.

The GluN2B subunit of N-methyl-D-aspartate receptors plays an important role in the physiology of different neurodevelopmental diseases. Genetic variations in the GluN2B coding gene (GRIN2B) have consistently been linked to West syndrome, intellectual impairment with focal epilepsy, developmental delay, macrocephaly, corticogenesis, brain plasticity, as well as infantile spasms and Lennox-Gastaut syndrome. It is unknown, however, how GRIN2B genetic variation impacts protein function. We determined the cumulative pathogenic impact of GRIN2B variations on healthy participants using a computational approach. We looked at all of the known mutations and calculated the impact of single nucleotide polymorphisms on GRIN2B, which encodes the GluN2B protein. The pathogenic effect, functional impact, conservation analysis, post-translation alterations, their driving residues, and dynamic behaviors of deleterious nsSNPs on protein models were then examined. Four polymorphisms were identified as phylogenetically conserved PTM drivers and were related to structural and functional impact: rs869312669 (p.Thr685Pro), rs387906636 (p.Arg682Cys), rs672601377 (p.Asn615Ile), and rs1131691702 (p.Ser526Pro). The combined impact of protein function is accounted for by the calculated stability, compactness, and total globularity score. GluN2B hydrogen occupancy was positively associated with protein stability, and solvent-accessible surface area was positively related to globularity. Furthermore, there was a link between GluN2B protein folding, movement, and function, indicating that both putative high and low local movements were linked to protein function. Multiple GRIN2B genetic variations are linked to gene expression, phylogenetic conservation, PTMs, and protein instability behavior in neurodevelopmental diseases. These findings suggest the relevance of GRIN2B genetic variations in neurodevelopmental problems.

Association of stress with anxiety and depression during pregnancy.

OBJECTIVE: To find out the association of stress with anxiety and depression during pregnancy and to identify common stressors in women. METHODS: This cross-sectional study was conducted at Divisional Headquarters Teaching Hospital, Kohat, Pakistan, from February 2011 to October 2012, and comprised pregnant women. Convenient sampling technique was used. The participants were administered Urdu-translated version of A-Z perceived stress scale and Aga Khan University anxiety and depression scale. Women with a score of >19 on the Aga Khan University scale were labelled as anxious and depressed. Data was collected on a pre-designed proforma. SPSS 17 was used for data analysis. RESULTS: There were 500 participants with an overall mean age of 28.3±6.3 years. The overall mean stress score on A-Z perceived stress scale was 12.93±5.19 and mean Aga Khan University anxiety and depression scale score was 28.58±13.82. Mean A-Z score was 14.18±4.881 in women with anxiety-depression and 9.75±4.58 in non-depressed women (p<0.001). Mean Aga Khan score in women with >10 stressors was significantly higher (32.18±13.79) compared to women with <10 stressors (19.87±9.30) (p<0.01). A-Z stressors score had significant positive correlation with the Aga Khan scale (p<0.001]. The most common stressors were concern about husband's worries and concern about feeling unwell during pregnancy, present in 433(86.6%) patients each, followed by concern about increase in the prices of everyday goods which was present in 364(72.8%) patients. CONCLUSIONS: The magnitude of stress was significantly associated with high anxiety and depression during pregnancy.