Congenital heart defects (CHD) presented as structural defects in the heart and blood vessels during birth contribute an important cause of childhood morbidity and mortality worldwide. Many Single nucletotide polymorphisms (SNPs) in different genes have been associated with various types of congenital heart defects. NKX 2–5 gene is one among them, which encodes a homeobox-containing transcription factor that plays a crucial role during the initial phases of heart formation and development. Mutations in this gene could cause different types of congenital heart defects, including Atrial septal defect (ASD), Atrial ventricular block (AVB), Tetralogy of fallot and ventricular septal defect. This highlights the importance of studying the impact of different SNPs found within this gene that might cause structural and functional modification of its encoded protein. In this study, we retrieved SNPs from the database (dbSNP), followed by identification of potentially deleterious Non-synonymous single nucleotide polymorphisms (nsSNPs) and prediction of their effect on proteins by computational screening using SIFT and Polyphen. Furthermore, we have carried out molecular dynamic simulation (MDS) in order to uncover the SNPs that would cause the most structural damage to the protein altering its biological function. The most important SNP that was found using our approach was rs137852685 R161P, which was predicted to cause the most damage to the structural features of the protein. Mapping nsSNPs in genes such as NKX 2–5 would provide valuable information about individuals carrying these polymorphisms, where such variations could be used as diagnostic markers.

Introduction: Type 1 Diabetes Mellitus (T1D) is a common autoimmune disorder. Investigating genetic factors that could turn the immune cells to auto-reactive are critical to our understanding of T1D. In this study genetic factors and the affected autoimmunity related molecular mechanisms in familial T1D with parental consanguinity were studied. Materials and Method: Whole Exome Sequencing (WES) was performed in a family with familial T1D. Sanger Sequencing was done to analyze segregation in affected and non-affected. Clinical and molecular aspects were also evaluated. Protein modeling and other in silico tools were used to identify probable impact of genetic abnormalities on the structure and function of protein. Result: We identified a novel homozygous substitution mutation at “c.379A>T:p.Iso127Val” in CD40 Ligand (CD40LG) gene in diabetic siblings by WES. This change was found to be segregating in the affected and non-affected individuals by Sanger sequencing. Parents and non-diabetic siblings were found to be heterozygous carriers of the nucleotide change. The c.379A>T is located within evolutionarily conserved locus of human genome. Functional prediction by Gene Ontology term analysis suggested that immune functions of CD40LG are compromised by this genetic change. Further, by protein-modeling analysis we identified that structure of ligand-binding domain of CD40LG protein, with which it interacts with other immune cells, may also be affected. In silico analysis revealed significantly reduced spatial inter amino acid distance between the site of genetic change and the ligand binding domain in mutant CD40LG. Discussion: Apoptotic elimination of developing auto-reactive T-cells, having the potential to generate an autoimmune response against pancreatic cells, is critical to prevent T1D. This apoptotic removal mechanisms, occurs in thymus and is dependent on highly specific interaction of cell surface molecules as CD40LG on developing T-cells, and the corresponding cell surface molecules on Antigen Presenting Cells (APC). In the diabetic individuals investigated in our study, the mutation in CD40LG gene, caused significant structural damage to its protein, due to which these interactions between mutant CD40LG (present on T-cells) and the corresponding CD40 (present on APC) were probably affected. This loss of interaction between CD40LG bearing T-cells and APC, probably led to escape of auto-reactive T-cells in to immune system, which further generated autoimmune response against the pancreatic tissue, precipitating to T1D among these individuals. Conclusion Genetic investigation of cell surface proteins in autoimmune cells and understanding their mechanism for development of autoimmunity offers prospects for the development of new therapeutic strategies in the approach to probable early diagnosis of T1D.

Indoleamine-2,3-dioxygenase (IDO) an immunoregulatory enzyme and emerging as a new therapeutic drug target for the treatment of cancer. Carboranes, an icosahedral arrangement of eleven boron atoms plus one carbon atom with unique pharmacological properties such low toxicity, isosterism with phenyl ring and stability to hydrolysis. On the other hand, carboranes are known to increase the interaction of ligand with non-polar region of the protein provides an excellent platform to explore these carboranes towards designing and development of novel, potent and target specific drug candidates with further enhanced binding affinities. Despite of their many potential applications, molecular modeling studies of carborane-substituted ligands with macromolecules have been rarely reported. Previously, we have demonstrated the promising high binding affinity of Withaferin-A (WA) for IDO. In this present study, we investigated the effect of carborane substitutions on WA compound towards developing novel analogs for target specific IDO inhibition with better potency. Interesting docked poses and molecular interactions for the carborane substituted WA ligands were elucidated. Based on our In-silico studies, carborane substituted at various position of WA has shown enhanced binding affinity towards IDO, worth of considering for further studies.

Introduction: Hypospadias [MIM: 300633] is one of the most frequent congenital malformations of male external genitalia. The spectrum of genetic variants causing hypospadias is varied, with studies commonly implicating genes critical in the fetal steroidogenic pathway. This is the first genetic study on hypospadias from the Yemen ethnicity and the second to report HSD3B2 mutations in more than one affected individual from the same family.Material and methods: Surgical hypospadias repair was performed on two hypospadias-affected siblings from a consanguineous family. Whole-exome sequencing (WES) was performed to identify the potential pathogenic variant for hypospadias, which was later confirmed by Sanger sequencing. The identified variant was further analyzed for its pathogenicity by using in silico tools such as SIFT, PolyPhen-2, MutationAssessor, MutationTaster, FATHMM, and ConSurf.Results: We identified a novel missense mutation (Chr1:119964631T>A, c.507T>A, p. N169K) in 3β-hydroxysteroid 2-dehydrogenase (HSD3B2) gene by WES. Sanger sequencing confirmed that the variant segregated the disease in the family between the affected and non-affected individuals. Both patients are homozygous, while parents and two unaffected siblings are heterozygous carriers, indicating an autosomal recessive pattern of inheritance. The in silico analysis by all six in silico tools (SIFT, PolyPhen-2, MutationAssessor, MutationTaster, FATHMM, and ConSurf) predicted the variant to be pathogenic/deleterious.Discussion: An abnormal fetal steroidogenic pathway due to genetic influences may affect the development of the male genital tract, including the urethral tract closure and morphogenesis of male genitalia. Furthermore, the pathogenicity of the observed variant in this study, confirmed by multiple in silico tools, characterizes the influence HSD3B2 gene variants may have in the etiology of hypospadias.Conclusion: Understanding of pathogenic manifestation and inheritance of confounding genetic variants in hypospadias is a matter of great concern, especially in familial cases.