Comprehensive molecular analysis identifies eight novel variants in XY females with disorders of sex development.

Disorders of sex development (DSD) are a group of clinical conditions with variable presentation and genetic background. Females with or without development of secondary sexual characters and presenting with primary amenorrhea (PA) and a 46,XY karyotype are one of the classified groups in DSD. In this study, we aimed to determine the genetic mutations in 25 females with PA and a 46,XY karyotype to show correlations with their phenotypes. Routine Sanger sequencing with candidate genes like SRY, AR, SRD5A2, and SF1, which are mainly responsible for 46,XY DSD in adolescent females, was performed. In a cohort of 25 patients of PA with 46,XY DSD, where routine Sanger sequencing failed to detect the mutations, next-generation sequencing of a targeted gene panel with 81 genes was used for the molecular diagnosis. The targeted sequencing identified a total of 21 mutations including 8 novel variants in 20 out of 25 patients with DSD. The most frequently identified mutations in our series were in AR (36%), followed by SRD5A2 (20%), SF1 (12%), DHX37 (4%), HSD17B3 (4%), and DMRT2 (4%). We could not find any mutation in the DSD-related genes in five (20%) patients due to complex molecular mechanisms in 46,XY DSD, highlighting the possibility of new DSD genes which are yet to be discovered in these disorders. In conclusion, genetic testing, including cytogenetics and molecular genetics, is important for the diagnosis and management of 46,XY DSD cases.

A comparative genomic approach to decipher the mutations associated with Nipah viral human isolates from southeast Asia.

Background and Objectives: Multiple outbreaks over two decades and a high mortality rate have emphasized the Nipah virus (NiV) as a priority research area. The study focuses on identifying the mutational landscape in sequences from NiV human isolates from different geographical regions. Materials and Methods: Thirty-seven NiV genomes of human samples from Malaysia, Bangladesh, and India were subjected to phylogeny and metagenomic analysis to decipher the genome variability using MEGA11 software and the meta-CATS web server. Using the Single-Likelihood Ancestor Counting method, the synonymous and nonsynonymous mutations among NiV genes were identified. Further, the nonsynonymous variations were used to identify mutations in all the NiV proteins. Results: The NiV isolates were categorized into NiV-M, NiV-B, and NiV-I clades based on phylogenetic analysis. Metagenomic analysis revealed 1636 variations in the noncoding and coding regions of the genomes of the three clades of NiV. Further analysis of nonsynonymous mutations showed the phosphoprotein to be highly mutating, whereas the matrix protein was stable. Conclusion: Deciphering the mutation pattern using a comparative genomics approach for human isolates provided valuable insight into the stability of NiV proteins which can be further used for understanding variations in host-pathogen interaction and developing effective therapeutic measures.

Docking and molecular dynamics studies of human ezrin protein with a modelled SARS-CoV-2 endodomain and their interaction with potential invasion inhibitors.

Human ezrin protein interacts with SARS-CoV S endodomain and restricts virus fusion, entry, and early events of infection. In general, their binding strength and their structural stability determines their successful entry into the host cells. However, the binding affinity of these two endodomains with the ezrin protein has been elusive due to a paucity of knowledge on the 3D structure. This study modelled the endodomains of both SARS-CoV-1 and SARS-CoV-2 and then docked these models with human ezrin protein. This study establishes that the modelled endodomains of both SARS-CoV-1 and SARS-Cov-2 consisted of three disulphide bridges for self-stabilization. Protein-protein docking listed four salt bridges with a higher buried surface area between ezrin-SARS-CoV-1 endodomain compared to that of ezrin-SARS-CoV-2 with six salt bridges with lower buried surface area. Molecular simulation of the ezrin-SARS-CoV-1 endodomain showed better structural stability with lower Root Mean Square Deviation score compared to that of ezrin-SARS-CoV-2 endodomain due to the substitution of alanine with cysteine residue. Protein-ligand docking studies confirmed better ezrin-drug interaction for quercetin, minocycline, calcifediol, calcitriol, selamectin, ivermectin and ergocalciferol. However, protein-ligand simulation confirmed strong drug-protein interaction during simulation for all the above-listed drugs except for ergocalciferol which could not establish its interaction with the protein during simulation. Strong drug binding within the active site pocket therefore restricts the interaction of viral endodomain and simultaneously stabilizes the ezrin protein. Furthermore, the higher stability between the ezrin after their interaction with the drug moiety could restrict the virus fusion and the infection. This study provides a basis for further development of these drug molecules to clinical trials aiming to identify potential drug molecules which can treat COVID-19 infection.

Identification of Potential Lead Molecules for Zika Envelope Protein from In Silico Perspective.

BACKGROUND: Zika virus is the family member of flavivirus with no reported clinically approved drugs or vaccines in the market till date. This virus is spread by Aedes mosquitoes, and can also be transmitted through sexual contact or blood transfusions. There are reported medical conditions like microcephaly among new-borns delivered by infected pregnant women. The envelope protein of Zika virus is associated with virulence, tropism, mediation of receptor binding and membrane fusion. ED1-EDII domain (K1 loop pocket) is an integral part of the envelope protein and a potential drug target. In the present study, the purpose was to identify the potential lead molecules to dock against K1 loop which could be later considered as flavivirus entry inhibitors. METHODS: Multiple sequence alignment method was considered for the analysis of indels in envelope protein. Phylogenetic tree was constructed based on the alignment. Aliphatic index, GRAVY scores and hydropathy plot of the envelope proteins were calculated for the flavivirus family members. Zika envelope protein was homology modeled and considered for protein-ligand docking analysis with chemical compounds of known functions. RESULTS: As per in silico based analysis, the envelope protein of Zika virus is highly hydrophilic with the least number of amino acid deletions compared to rest of the family members. During docking studies, it was observed that compounds like NITD, compound 6, P02, Doxytetracycline and Rolitetracycline show better binding affinity with Zika envelope protein compared to dengue virus. CONCLUSION: These better binding compounds could be the promising lead molecules for Zika envelope protein which could better block the viral entry.