Novel frameshift variant in the PCNT gene associated with Microcephalic Osteodysplastic Primordial Dwarfism (MOPD) Type II and small kidneys.

BACKGROUND: Microcephalic Osteodysplastic Primordial Dwarfism (MOPD) Type II is an autosomal recessive condition encompassing a heterogeneous group of disorders characterized by symmetrical growth retardation leading to dwarfism, microcephaly, and a range of multiple medical complications including neurovascular diseases. Biallelic pathogenic variants in the pericentrin gene (PCNT) have been implicated in its pathogenesis. CASE PRESENTATION: We performed whole-exome sequencing to ascertain the diagnosis of a 2 year and 6 months old boy who presented with severe failure to thrive, microcephaly, and facial gestalt suggestive of MOPD Type II which included features such as retrognathia, small ears, prominent nasal root with a large nose, microdontia, sparse scalp hair, bilateral fifth finger clinodactyly. He had a small ostium secundum atrial septal defect and bilaterally small kidneys. Microcephalic Osteodysplastic Primordial Dwarfism (MOPD) Type II was confirmed based on a pathogenic compound heterozygous frameshift variant in the PCNT gene c.5059_5060delAA | p. Asn1687fs (novel variant) and c.9535dup (p. Val3179fs). His parents were found to be heterozygous carriers for the variants. CONCLUSION: We report a novel frameshift variant in the PCNT gene and a previously unreported phenotype for Microcephalic Osteodysplastic Primordial Dwarfism (MOPD) Type II.

Six Novel ATM Gene Variants in Sri Lankan Patients with Ataxia Telangiectasia.

INTRODUCTION: Ataxia telangiectasia is a rare genetic condition with an estimated prevalence of 1 in 40,000-100,000 live births. This condition predominantly affects the nervous and immune systems. It is characterized by progressive ataxia beginning from early childhood. The neurological deficit associated with this condition affects one's balance, coordination, walking, and speech and can be accompanied by chorea, myoclonus, and neuropathy. They may also have ocular telangiectasias and high levels of blood alpha-fetoprotein (AFP). The ataxia telangiectasia mutated gene (ATM) is associated with this condition and codes for the ATM protein which is a phosphatidylinositol 3-kinase. This gene occupies 150 kb on chromosome 11q22-23 and contains 66 exons encoding a 13 kb transcript. ATM is a relatively large protein with a molecular weight of 350 kDa and 3,056 amino acids. METHODS: Four patients of Sri Lankan origin presenting with features suggestive of ataxia telangiectasia were referred to our genetics center for specialized genetic counseling and testing. Whole-exome sequencing followed by Sanger sequencing was used to confirm the candidate variants. Protein modeling and genotype to phenotype correlation was performed in the identified variants. RESULTS: We observed 6 novel ATM gene variants in four patients with ataxia telangiectasia. The identified variants are as follows: homozygous c.7397C > A (p.Ala2466Glu) and c.510_511delGT (p.Tyr171fs) and compound heterozygous c.5347_5350delGAAA (p.Glu1783fs), c.8137A > T (p.Arg2713 ∗ ) and c.1163A > C (p.Lys388Thr), and c.5227A > C (p.Thr1743Pro). Variant analysis was followed by modeling of the native and altered protein structures. CONCLUSION: We report novel ATM gene variants that have implications on the molecular diagnosis of ataxia telangiectasia.

Novel variant in NSDHL gene associated with CHILD syndrome and syndactyly- a case report.

BACKGROUND: Congenital hemidysplasia with ichthyosiform erythroderma and limb defects also known as CHILD syndrome is an X-linked dominant, male lethal genodermatosis with a prevalence of 1 in 100,000 live births. Mutations in NSDHL gene located at Xq28 potentially impair the function of NAD(P) H steroid dehydrogenase-like protein and is responsible for its pathogenesis. CASE PRESENTATION: The proband was a 9-month-old twin (T2) girl with a healthy twin sister (T1) of Sri Lankan origin born to non-consanguineous parents. She presented with right sided continuous icthyosiform erythroderma and ipsilateral limb defects and congenital hemidysplasia since birth. Notably the child had ipsilateral hand hypoplasia and syndactyly. There were other visceral abnormalities. We performed whole exome sequencing and found a novel heterozygous variant (NSDHL, c.713C > A, p.Thr238Asn). CONCLUSION: We report a novel missense variant in the NSDHL gene that resides in a highly-conserved region. This variant affects the NAD(P) H steroid dehydrogenase-like protein function via reduction in the number of active sites resulting in the CHILD syndrome phenotype and syndactyly.

Genetics of PCOS: A systematic bioinformatics approach to unveil the proteins responsible for PCOS.

Polycystic ovary syndrome (PCOS) is a hormonal imbalance in women, which causes problems during menstrual cycle and in pregnancy that sometimes results in fatality. Though the genetics of PCOS is not fully understood, early diagnosis and treatment can prevent long-term effects. In this study, we have studied the proteins involved in PCOS and the structural aspects of the proteins that are taken into consideration using computational tools. The proteins involved are modeled using Modeller 9v14 and Ab-initio programs. All the 43 proteins responsible for PCOS were subjected to phylogenetic analysis to identify the relatedness of the proteins. Further, microarray data analysis of PCOS datasets was analyzed that was downloaded from GEO datasets to find the significant protein-coding genes responsible for PCOS, which is an addition to the reported protein-coding genes. Various statistical analyses were done using R programming to get an insight into the structural aspects of PCOS that can be used as drug targets to treat PCOS and other related reproductive diseases.

Mutation-based structural modification and dynamics study of amyloid beta peptide (1-42): An in-silico-based analysis to cognize the mechanism of aggregation.

Alzheimer's disease is the prevalent cause of premature senility, a progressive mental disorder due to degeneration in brain and deposition of amyloid ß peptide (1-42, a misfolded protein) in the form of aggregation that prevails for a prolonged time and obstructs every aspect of life. One of the primary hallmarks of the neuropathological disease is the accretion of amyloid ß peptide in the brain that leads to Alzheimer's disease, but the mechanism is still a mystery. Several investigations have shown that mutations at specific positions have a significant impact in stability of the peptide as predicted from aggregation profiles. Here in our study, we have analyzed the mutations by substituting residues at position A22G, E22G, E22K, E22Q, D23N, L34V and molecular dynamics have been performed to check the deviation in stability and conformation of the peptide. The results validated that the mutations at specific positions lead to instability and the proline substitution at E22P and L34P stalled the aggregation of the peptide.

To study percentage distribution of target genes encoding proteins of different classes in Helicobacter pylori strain J99 and identification of potential therapeutic targets to reduce its proliferation.

Helicobacter pylori are one of the most common bacterial pathogens in humans whose seropositivity increases with age and low socio-economic status. Due to presence of its pathogenic-island causes chronic persistent and atrophic gastritis in adults and children that often culminate in development of gastric and duodenal ulcers. Studies indicate that infected individuals have two to sixfold increased risk of developing gastric cancer and mucosal associated lymphoid tissue lymphoma compared to their uninfected counterparts. The complete genome sequences have provided a plethora of potential drug targets. Subtractive study holds the promise of providing a conceptual framework for identification of potential drug targets and providing insights to understand the biological regulatory mechanisms in diseases, which are playing an increasingly important role in searching for novel drug targets from the information contained in genomics. In this paper, we discuss subtractive study approaches for identifying drug targets, with the emphasis on the modelling of target protein and docking of the modelled protein with probable ligand by using computational tools.

ENZPRED-enzymatic protein class predicting by machine learning.

Recent times have seen flooding of biological data into the scientific community. Due to increase in large amounts of data from genome and other sequencing projects become available, being diverted on to Insilco approach for data collection and prediction has become a priority also progresses in sequencing technologies have found an exponential function rise in the number of newly found enzymes. Commonly, function of such enzymes is determined by experiments that can be time consuming and costly. As new approaches are needed to determine the functions of the proteins these genes encode. The protein parameters that can be used for an enzyme/ non-enzyme classification includes features of sequences like amino acid composition, dipeptide composition, grand Average of hydropathicity (GRAVY), probability of being in alpha helix, probability of being in beta sheet Probability of being in a turn. We show how large-scale computational analysis can help to address this challenge by help of java and support vector machine library. In this paper, a recently developed machine learning algorithm referred to as the svm library Learning Machine is used to classify protein sequences with six main classes of enzyme data downloaded from a public domain database. Comparative studies on different type of kernel methods like 1.radial basis function, 2.polynomial available in SVM library. Results show that RBF method take less time in training and give more accurate result then other kernel methods to also less training time compared to other kernel methods. The classification accuracy of RBF is also higher than various methods in respect of available sequences data.

Metabolism evolution based on network degrees of orthologous enzymes.

The evolution of orthologous proteins opens a new era of research where the concepts of orthology and paralogy have become more and more substantial, as the whole-genome comparison allows their identification in complete genomes. Functional specificity of proteins is understood to be conserved among orthologs but it shows much more variability among paralogs. We used this laying claim to identify inter-species interactions based on orthologous protein networks which are crucial for understanding the evolution of orthologous proteins. We analyzed six classes of enzymatic protein sequence data using the node degrees of orthologous proteins. The results demonstrated the evolutionary importance of the fatty acid syntheses and the photosynthetic system in algae. Methods which have successfully exploited network structure at many different levels of detail are a cornerstone of systems biology.

Review on chemogenomics approach: interpreting antagonist activity of secreted frizzled-related protein 1 in glaucoma disease with in-silico docking.

Computer-aided drug discovery is a growing frontier in science. It covers different sub areas like chemoinformatics and chemogenomics. Chemogenomics is one of the emerging inter-disciplinary approaches in drug discovery, which combines conventional ligand based approach with biological information of drug targets. The main goal of this review is to check effective application of chemogenomics in understanding interactions between all possible ligands and their potential drug targets at molecular level. Recent studies revealed that increased expression of sFRP1an inhibitor of Wnt signalling pathway, seems to be responsible for Elevated Intracellular Pressure (IOP) in glaucoma patients. Glaucoma is a worldwide spread disease. Here, secreted frizzled-related protein-1 (sFRP1) has been used as a target protein. An important role of sFRP1, an antagonist of Wnt signalling pathway, has been found in regulating IOP. Wnt3a ligand protein and a natural compound from marine source Mycaperoxide H - have been used as ligands. In-silico docking of these ligands with sFRP family implies answers to many intricate queries in drug development field. Using above mentioned ligand-protein model in this study, application of chemogenomics has tried to explore the interaction of active site of proteins with the novel ligands. Henceforth, the present review will focus on predictive in-silico chemogenomic approaches with computer aided drug design could be used in drug design domain in identifying new targets in various diseases, in time and cost effective manner.

In silico investigation and structural characterization of virulent factor and a metallo peptidase present in Helicobacter pylori strain J99.

VacA is a high-molecular weight multimeric pore-forming protein encoded by the chromosomal gene vacA of Helicobacter pylori J99 strian. It plays a significant role in the development of gastric cancer in human by inducing the formation of vacuoles. Genomics and proteomics features of an organism have provided a plethora of potential drug targets. The crystal structure of VacA is not available in any structural database; hence a 3D structure is very essential for structural studies and discovery of potential inhibitors against proteins. In this study 3D structure of VacA is modelled a by using Bhageerath: an energy based web enabled computer software suite. According to our study VacA steriochemical validation shows 91.7% residues are in allowed region of Ramachandran plot. Further validation was done by WHAT CHECK to provide evidence that the distribution of the main chain bond lengths and omega bond angles were within limits with Z-score 1.0 and error values are negligible. The modelled protein was submitted to Protein Model Database and can be downloaded with PMDID PM0077963. Further we found that metallo peptidase "M3" cleaves VacA and helps in import mechanism in mitochondria. Structure of metallo peptidase is also not available in any structural database so we modelled and validated its structure. With the help of docking studies we blocked the active site of metallo peptidase by ligand LA3 and 294 with binding energy -5.9 and -5.2 KJ/mol respectively, thus prevented import mechanism of VacA in mitochondria. The inhibitors identified from our study were LA3 and 294 ligands. The investigation concluded that these drugs could be used as the potential inhibitors against the damage of stomach and duodenum, which ultimately reduces the likelihood of ulcer as well as gastric cancer.