Comprehensive analysis predicting effects of deleterious SNPs of human progesterone receptor gene on its structure and functions: a computational approach.

Progesterone receptor plays a crucial role in the development of the mammary gland and breast cancer. Single nucleotide polymorphisms (SNPs) within its gene, PGR, are associated with the risk of miscarriages and preterm birth as well as many cancers across different populations. The main aim of this work is to investigate the most deleterious SNPs in the PGR gene to identify potential biomarkers for various disease susceptibility and treatments. Both sequence and structure-based computational approaches were adopted and in total 11 nsSNPs have been filtered out of 674 nsSNPs along with seven non-coding SNPs. R740Q, I744T and D746E belonged to a mutation cluster. R740Q, D746E along with S865L altered H-bond interactions within the receptor. The same mutations have been found to be associated with several cancers including uterine and breast cancer among others. It is, therefore, possible that the high-risk SNPs associated with cancers may exert their effect by causing changes in the protein structure, particularly in its bonding patterns, and thus affecting its function. In addition, seven non-coding SNPs that were located in the UTR region created a new miRNA site while three SNPs disrupted a conserved miRNA site. These high-risk SNPs can play an instrumental role in generating a dataset of the PGR gene's SNPs. Thus, the present study may pave the way to design and develop novel therapeutics for overcoming the challenges associated with certain cancers and pregnancy that result from a change in the protein structure and function due to the SNP mutations in the PGR gene.Communicated by Ramaswamy H. Sarma.

In Silico Design of siRNAs for Silencing CLEC5A Receptor as a Potential Therapeutic Approach Against Dengue and Japanese Encephalitis Virus Infection in Human.

Dengue and Japanese encephalitis virus (JEV) are mosquito-borne RNA viruses that can cause severe illness leading to death in the tropics and subtropics. Both of these viruses interact directly with the C-type lectin domain family 5, member A receptor (CLEC5A) on human macrophages which stimulates the release of proinflammatory cytokines. Since blockade of this interaction has been shown to suppress the secretion of cytokines, CLEC5A is considered a potential target for the development of new treatments to reduce virus-induced brain damage. Developing a vaccine against dengue is challenging because this virus can cause disease through 4 different serotypes. Therefore, the vaccine must immunize against all 4 serotypes to be effective, while unvaccinated people still contract JEV and suffer from its complications. Small interfering RNAs (siRNAs) play an important role in regulating gene expression by causing the degradation of target mRNAs. In this study, we attempted to rationally design potential siRNA molecules using various software, targeting the CLEC5A gene. In total, 3 siRNAs were found to be potential candidates for CLEC5A silencing. They showed good target accessibility, optimum guanine-cytosine (GC) content, the least chance of off-target effects, positive energy of folding, and strong interaction with Argonaute2 protein as denoted by a negative docking energy score. In addition, molecular dynamics simulation of the siRNA-Ago2-docked complexes showed the stability of the complexes over 1.5 nanoseconds. These predicted siRNAs might effectively downregulate the expression of the CLEC5A receptor and thus prove vital in the treatment of dengue and JEV infections.

Most frequently harboured missense variants of hACE2 across different populations exhibit varying patterns of binding interaction with spike glycoproteins of emerging SARS-CoV-2 of different lineages.

Since the emergence of SARS-CoV-2 at Wuhan in the Hubei province of China in 2019, the virus has accumulated various mutations, giving rise to many variants. According to the combinations of mutations acquired, these variants are classified into lineages and greatly differ in infectivity and transmissibility. In 2021 alone, a variant of interest (VoI) Mu (B.1.621), as well as, variants of concern (VoC) Delta (B.1.617.2) and Omicron (BA.1, BA.2) and later in 2022, BA.4, BA.5, and BA.2.12.1 have emerged. Since then, the world has seen prominent surges in the rate of infection during short periods of time. However, not all populations have suffered equally, which suggests a possible role of host genetic factors. Here, we investigated the strength of binding of the spike glycoprotein receptor-binding domain (RBD) of the SARS-CoV-2 variants: Mu, Delta, Delta Plus (AY.1), Omicron sub-variants BA.1, BA.2, BA.4, BA.5, and BA.2.12.1 with the human angiotensin-converting enzyme 2 (hACE2) missense variants prevalent in major populations. In this purpose, molecular docking analysis, as well as, molecular dynamics simulation was performed of the above-mentioned SARS-CoV-2 RBD variants with the hACE2 containing the single amino acid substitutions prevalent in African (E37K), Latin American (F40L), non-Finnish European (D355 N), and South Asian (P84T) populations, in order to predict the effects of the lineage-defining mutations of the viral variants on receptor binding. The effects of these mutations on protein stability were also explored. The protein-protein docking and molecular dynamics simulation analyses have revealed variable strength of attachment and exhibited altered interactions in the case of different hACE2-RBD complexes. In vitro studies are warranted to confirm these findings which may enable early prediction regarding the risk of transmissibility of newly emerging variants across different populations in the future.

In silico comprehensive analysis of coding and non-coding SNPs in human mTOR protein.

The mammalian/mechanistic target of rapamycin (mTOR) protein is an important growth regulator and has been linked with multiple diseases including cancer and diabetes. Non-synonymous mutations of this gene have already been found in patients with renal clear cell carcinoma, melanoma, and acute lymphoid leukemia among many others. Such mutations can potentially affect a protein's structure and hence its functions. In this study, therefore, the most deleterious SNPs of mTOR protein have been determined to identify potential biomarkers for various disease treatments. The aim is to generate a structured dataset of the mTOR gene's SNPs that may prove to be an asset for the identification and treatment of multiple diseases associated with the target gene. Both sequence and structure-based approaches were adopted and a wide variety of bioinformatics tools were applied to analyze the SNPs of mTOR protein. In total 11 nsSNPs have been filtered out of 2178 nsSNPs along with two non-coding variations. All of the nsSNPs were found to destabilize the protein structure and disrupt its function. While R619C, A1513D, and T1977R mutations were shown to alter C alpha distances and bond angles of the mTOR protein, L509Q, R619C and N2043S were predicted to disrupt the mTOR protein's interaction with NBS1 protein and FKBP1A/rapamycin complex. In addition, one of the non-coding SNPs was shown to alter miRNA binding sites. Characterizing nsSNPs and non-coding SNPs and their harmful effects on a protein's structure and functions will enable researchers to understand the critical impact of mutations on the molecular mechanisms of various diseases. This will ultimately lead to the identification of potential targets for disease diagnosis and therapeutic interventions.

MNS16A VNTR polymorphism of human telomerase gene: Elucidation of a gender specific potential allele associated with type 2 diabetes in Bangladeshi population.

BACKGROUND: Type 2 diabetes (T2D) is a multifactorial disorder that affects multi-organ and can alter telomerase (encoded by hTERT gene) activity and thus, may affect telomere length. The variable number of tandem repeats MNS16A in hTERT gene facilitates extension of telomeres by regulating telomerase. In the present study, genetic analysis of MNS16A tandem repeats in hTERT gene was performed with the aim of finding out any association of allelic and genotypic variations with the risk of T2D in Bangladeshi population. METHODS: A total of unrelated 395 individuals with T2D and 247 healthy individuals were included in the study. The genotypic and allelic frequencies were determined using allele specific polymerase chain reaction. The association of allelic and genotypic frequencies with risk of T2D was analyzed using logistic regression analysis on the basis of odds ratio at 95% confidence interval. Hardy-Weinberg equilibrium (HWE) test was performed to evaluate the uniformity of the genotypic frequencies and deviation from the HWE was tested using Chi-square test. RESULTS: Logistic regression analyses revealed significant association of short allele containing 243 bp (OR: 1.37 and p = 0.03) with T2D, when the long alleles (commonly found) were considered as reference. The heterozygous genotype 272/302 was significantly associated with the decreased risk of T2D (OR: 0.33, p = 0.001). The combined results of genotypes indicated that the MNS16A polymorphism was significantly associated with the increased risk of T2D under the dominant model (LL vs SL + SS; OR: 2.62, p < 0.0001). Interestingly, short allele 243 was associated with the risk of disease only in male population (OR: 1.62, p = 0.02). The genotype 272/302 was also found to be associated with the decreased risk of T2D when respective data for male was analyzed individually. CONCLUSIONS: We have identified four variable number of tandem repeats with varying patterns of association with T2D in Bangladeshi population and to extend our knowledge of understanding regarding these VNTRs, further large-scale studies are warranted.

Distribution of Holliday junctions and repair forks during Escherichia coli DNA double-strand break repair.

Accurate repair of DNA double-strand breaks (DSBs) is crucial for cell survival and genome integrity. In Escherichia coli, DSBs are repaired by homologous recombination (HR), using an undamaged sister chromosome as template. The DNA intermediates of this pathway are expected to be branched molecules that may include 4-way structures termed Holliday junctions (HJs), and 3-way structures such as D-loops and repair forks. Using a tool creating a site-specific, repairable DSB on only one of a pair of replicating sister chromosomes, we have determined how these branched DNA intermediates are distributed across a DNA region that is undergoing DSB repair. In cells, where branch migration and cleavage of HJs are limited by inactivation of the RuvABC complex, HJs and repair forks are principally accumulated within a distance of 12 kb from sites of recombination initiation, known as Chi, on each side of the engineered DSB. These branched DNA structures can even be detected in the region of DNA between the Chi sites flanking the DSB, a DNA segment not expected to be engaged in recombination initiation, and potentially degraded by RecBCD nuclease action. This is observed even in the absence of the branch migration and helicase activities of RuvAB, RadA, RecG, RecQ and PriA. The detection of full-length DNA fragments containing HJs in this central region implies that DSB repair can restore the two intact chromosomes, into which HJs can relocate prior to their resolution. The distribution of recombination intermediates across the 12kb region beyond Chi is altered in xonA, recJ and recQ mutants suggesting that, in the RecBCD pathway of DSB repair, exonuclease I stimulates the formation of repair forks and that RecJQ promotes strand-invasion at a distance from the recombination initiation sites.

Correction: Plasma and memory B cell responses targeting O-specific polysaccharide (OSP) are associated with protection against Vibrio cholerae O1 infection among household contacts of cholera patients in Bangladesh.

[This corrects the article DOI: 10.1371/journal.pntd.0006399.].

Association study of leukocyte telomere length and genetic polymorphism within hTERT promoter with type 2 diabetes in Bangladeshi population.

Telomeres are protective cap on the ends of DNA of non-coding tandem repeats of TTAGGG. Human telomerase reverse transcriptase (hTERT) is a catalytic subunit of telomerase that maintains the structure of telomeres. Type 2 diabetes (T2D) affects multi-organ and telomere length by altering telomerase activity. We aimed to evaluate the relative telomere length (RTL) and risk association of rs2853669 with T2D in Bangladeshi population. RTL was measured in 408 unrelated Bangladeshi (224 T2D and 184 healthy) using primers for target gene and reference gene albumin. Genotypic frequencies for rs2853669 were determined using TaqMan® probes. The mean level of age adjusted RTL (AARTL) varied significantly between the healthy and individuals with T2D for all the genotypes with respect to rs2853669. Moreover, healthy individuals had significantly higher AARTL than T2D. Similar findings were observed when study participants were stratified based on their gender. Association studies revealed that under codominant model of inheritance, TC genotype showed protective role against development of type 2 diabetes. This study suggests a possible role of telomere biology in T2DM, but their association needs to be evaluated further with a larger series and matched healthy controls.

Genetic variation of the transcription factor GATA3, not STAT4, is associated with the risk of type 2 diabetes in the Bangladeshi population.

Type 2 diabetes mellitus is a multifactorial metabolic disorder caused by environmental factors and has a strong association with hereditary issues. These hereditary issues result in an imbalance in CD4+T cells and a decreased level of naïve CD4+T cells, which may be critical in the pathogenesis of type 2 diabetes. Transcription factors GATA3 and STAT4 mediate the cytokine-induced development of naïve T cells into Th1 or Th2 types. In the present study, genetic analyses of GATA3 SNP rs3824662 and STAT4 SNP rs10181656 were performed to investigate the association of allelic and genotypic variations with the risk of T2D in the Bangladeshi population. A total of 297 unrelated Bangladeshi patients with type 2 diabetes and 247 healthy individuals were included in the study. The allelic and genotypic frequencies of rs10181656 located in the STAT4 gene were not found to be associated with risk of type 2 diabetes. The GATA3 rs3824662 T allele and mutant TT genotype had a significant association with the risk of T2D [OR: 1.52 (1.15-2.02), X2 = 8.66, p = 0.003 and OR: 2.98 (1.36-6.55), X2 = 7.98, p = 0.04, respectively]. Thus, the present study postulates that the genetic variation of the transcription factor GATA3, not STAT4, is associated with the risk of type 2 diabetes in the Bangladeshi population.

Plasma and memory B cell responses targeting O-specific polysaccharide (OSP) are associated with protection against Vibrio cholerae O1 infection among household contacts of cholera patients in Bangladesh.

BACKGROUND: The mediators of protection against cholera, a severe dehydrating illness of humans caused by Vibrio cholerae, are unknown. We have previously shown that plasma IgA as well as memory B IgG cells targeting lipopolysaccharide (LPS) of Vibrio cholerae O1 correlate with protection against V. cholerae O1 infection among household contacts of cholera patients. Protection against cholera is serogroup specific, and serogroup specificity is defined by the O-specific polysaccharide (OSP) component of LPS. Therefore, we prospectively followed household contacts of cholera patients to determine whether OSP-specific immune responses present at the time of enrollment are associated with protection against V. cholerae infection. METHODOLOGY: In this study, we enrolled two hundred forty two household contacts of one hundred fifty index patients who were infected with Vibrio cholerae. We determined OSP-specific memory B cells and plasma IgA, IgG and IgM antibody responses on study entry (day 2). PRINCIPLE FINDINGS: The presence of OSP-specific plasma IgA, IgM, and IgG antibody responses on study entry were associated with a decrease in the risk of infection in household contacts (IgA, p = 0.015; IgM, p = 0.01, and IgG, p = 0.024). In addition, the presence of OSP-specific IgG memory B cell responses in peripheral blood on study entry was also associated with a decreased risk of infection (44% reduction; 95% CI: 31.1 to 99.8) in contacts. No protection was associated with cholera toxin B subunit (CtxB)-specific memory B cell responses. CONCLUSION: These results suggest that immune responses that target OSP, both in plasma and memory responses, may be important in mediating protection against infection with V. cholerae O1.

In silico identification of potential epitopes present in human adenovirus proteins for vaccine design and of putative drugs for treatment against viral infection.

In silico approach using computational biology to design best probable epitopes and/or drug target(s) has given an edge to foresee active components for the treatment of many infectious diseases. This study aims to investigate the best probable epitopes from fiber, hexon and penton base proteins as well as probable drug targets to prevent and to cure adenovirus infection, respectively. After retrieving protein sequences, analysis of selection pressure; prediction of continuous/discontinuous B cell epitopes along with their antigenicity, immunogenicity, allergenicity; T cell epitopes along with their population coverage and echelon of conservancy were performed. Out of three proteins, fiber protein underwent the highest degree of selection pressure. Five peptides from fiber C-5, hexon C-5 and D-8, penton base B-3 and C-5 proteins were considered as the best potential B cell epitopes. Further analyses revealed that peptides present in fiber C-5, hexon C-5, penton base B-3 and C-5 proteins fulfilled the criteria of having surface accessibility, hydrophilicity, flexibility, antigenicity and beta turn. Several regions of proteins were identified as discontinuous B cell epitopes. Interestingly, a peptide present in 692-699 region of hexon C-5 and six amino acids at positions 100, 102, 105, 108, 112 and 114 of penton base B-3 proteins were recognized both as continuous and discontinuous B cell epitopes. Of all the predicted T cell epitopes, three nonamers from hexon C-5, D-8 and penton base C-5 proteins may elicit strong immune response by activating both humoral and cellular immunity as these were found to overlap with those of B cell epitopic peptides. Considering non-allergen, conservancy and population coverage properties, "SGYDPYYTY" of hexon protein C-5 was further validated using in silico docking study for its interaction with the HLA allele. This study also demonstrated the possibility of compounds like 3-(azepan-1-ium-1-yl) propane-1-sulfonate and E-5842 as the potential inhibitors of penton base and hexon proteins that could act as more effective drugs against the virus compared to the current ones. Therefore, further in vitro and animal model experiments using these predicted epitopes and compounds may pave the way for newer and more effective treatment approaches against adenovirus infection.

Interaction of Quercetin of Onion with Axon Guidance Protein Receptor, NRP-1 Plays Important Role in Cancer Treatment: An In Silico Approach.

Neuropilin-1 (NRP-1) is a transmembrane glycoprotein receptor whose distinct sites bind semaphorins and vascular endothelial growth factor family members to mediate the role of these ligands in neuronal axon guidance and angiogenesis, respectively. Similarly, Eph receptors and ephrin ligands play critical roles in various biological functions, and deregulated activation of Eph/ephrin signaling in humans is thought to lead to tumorigenesis. Therefore, in this paper, an attempt was made to elucidate the inhibition potential of nine bioactive compounds from four different native spices of Bangladesh against this couple of receptors via molecular docking study. The molecular docking study was carried out using Vina docking protocol. Finally, the receptor-ligand interaction analysis was carried out using the Discovery Studio Client package. Quercetin and diosgenin of onion showed favorable binding with NRP-1 with low binding energy of -7.8 and -7.2 kcal/mol, respectively, in comparison with the control inhibitor (-6.1 kcal/mol). The study suggests that ligand interaction with the residues Asp 48, Thr 44, Thr 77, Tyr 81, Trp29, Ile 143 of NRP-1 and Lys 653, Phe 765, Ser 763, Thr 699, Ile 683 of Eph might be critical for the inhibitory activity of these receptors. The study provides evidence for consideration of quercetin and diosgenin of onion as valuable small ligand molecules for targeting NRP-1 receptor in treatment and prevention of neurological disorders as well as cancer.

In silico proposition to predict cluster of B- and T-cell epitopes for the usefulness of vaccine design from invasive, virulent and membrane associated proteins of C. jejuni.

PURPOSE: Campylobacter jejuni is the one of the leading causes of bacterial diarrheal illness worldwide. This study aims to design specific epitopes for the utility of designing peptide vaccine(s) against C. jejuni by targeting invasive, virulent and membrane associated proteins like FlaA, Cia, CadF, PEB1, PEB3 and MOMP. METHODS: In the present study, various immunoinformatics approaches have been applied to design a potential epitope based vaccine against C. jejuni. The tools include Bepipred, ABCpred, Immune Epitope databse (IEDB) resource portal, Autodock vina etc. RESULTS: Peptides "EINKN", "TGSRLN", "KSNPDI", "LDENGCE" respectively from FlaA, MOMP, PEB3, CadF proteins were found to be the most potential B cell epitopes while peptides "FRINTNVAA", "NYFEGNLDM", "YKYSPKLNF", "YQDAIGLLV", "FRNNIVAFV" and "LIMPVFHEL" respectively from Fla, CadF, MOMP, PEB1A, PEB3 and Cia might elicit cell mediated immunity and "IFYTTGSRL" from MOMP protein might elicit both humoral and cell-mediated immunity. All these potential peptidic epitopes showed almost 80-100 % conservancy in different strains of C jejuni with varying proportions of population coverage ranging from 22-60 %. Further authentication of these peptide epitopes as probable vaccine candidate was mediated by their binding to specific HLA alleles using in silico docking technique. CONCLUSION: Based on the present study, it could be concluded that these predicted epitopes might be used to design a vaccine against C. jejuni bacteria and thus, could be validated in model hosts to verify their efficacy as vaccine.

O-Specific Polysaccharide-Specific Memory B Cell Responses in Young Children, Older Children, and Adults Infected with Vibrio cholerae O1 Ogawa in Bangladesh.

Cholera caused by Vibrio cholerae O1 confers at least 3 to 10 years of protection against subsequent disease regardless of age, despite a relatively rapid fall in antibody levels in peripheral blood, suggesting that memory B cell responses may play an important role in protection. The V. cholerae O1-specific polysaccharide (OSP) component of lipopolysaccharide (LPS) is responsible for serogroup specificity, and it is unclear if young children are capable of developing memory B cell responses against OSP, a T cell-independent antigen, following cholera. To address this, we assessed OSP-specific memory B cell responses in young children (2 to 5 years, n = 11), older children (6 to 17 years, n = 21), and adults (18 to 55 years, n = 28) with cholera caused by V. cholerae O1 in Dhaka, Bangladesh. We also assessed memory B cell responses against LPS and vibriocidal responses, and plasma antibody responses against OSP, LPS, and cholera toxin B subunit (CtxB; a T cell-dependent antigen) on days 2 and 7, as well as days 30, 90, and 180 after convalescence. In all age cohorts, vibriocidal responses and plasma OSP, LPS, and CtxB-specific responses peaked on day 7 and fell toward baseline over the follow-up period. In comparison, we were able to detect OSP memory B cell responses in all age cohorts of patients with detectable responses over baseline for 90 to 180 days. Our results suggest that OSP-specific memory B cell responses can occur following cholera, even in the youngest children, and may explain in part the age-independent induction of long-term immunity following naturally acquired disease.