Nuclear factor erythroid 2– related factor 2 (NRF2) is a transcription factor and master regulator in multiple metabolic as well as physiological process. It plays a significant role in cancer progression and chemoresistance development. It induces the expression of a large number of cytoprotective proteins with antioxidant and detoxifying roles. NRF2 inhibition by ROS generating biomolecule, Alantolactone (ALT) can be potential approach for ROS-mediated cancer cell death. To study this, we performed in silico and in vitro studies. In in silico studies, we used predicted NRF2 structure by AlphaFold, performed its molecular docking, and molecular dynamic (MD) simulations with ALT. Whereas, in in vitro studies, we performed western blotting to check its translocation into nucleus and qPCR to check its transcriptional activity. We performed Frontier molecular orbitals (FMOs) analysis as well to check reactivity and bioactivity of ALT. Molecular docking results revealed that ALT strongly binds to DNA binding domain of NRF2 with stable molecular dynamics. In vitro studies showed a significant reduction in nuclear NRF2 in taxol resistant cell line (HEY-T30) treated with ALT (30 µM) for 24 h. Our qPCR analysis showed that ALT failed to modulate mRNA expression of NRF2 downstream target genes including glutathione peroxidase-4 (GPX-4) and glutathione reductase (GSR) in MCF-7 cells. Moreover, ProTox-II profiling showed that ALT is non-toxic to other organs and can be safe if it is swallowed. FMOs method showed the reactivity and bioactivity of ALT. ALT can significantly inhibit the NRF2 activity. The inhibition of NRF2 translocation into nucleus might help to reduce the antioxidant enzymes synthesis leading to ROS mediated cell death. Further in vitro and in vivo studies are required to investigate the underlying mechanism in-depth.

Probiotics are live microbes that offer potential health benefits to the host, including modulation of the host immune system, improvement of anti-inflammatory response, enhancement of antibacterial and anti-allergic properties, as well as anti-proliferative properties. These beneficial microorganisms can interact with the gut microbiota to restore an impaired gut microbiome. While probiotics can be sourced from various sources, this study focuses on isolating and characterizing novel probiotic strains from dairy sources, specifically Dahi. To evaluate the probiotic potential of these isolates, various biochemical, morphological, and physiological tests were performed, followed by 16S rRNA gene sequencing to genotype the isolates. The tolerance of the isolates to pH, temperature, and bile salt, as well as their antimicrobial and adhesion ability, was evaluated. The results showed that the identified novel probiotic strains belonged to the Lactobacillus fermentum species, exhibited remarkable tolerance against bile salts, acidic environments, and temperature, and had excellent adhesion ability, indicating their potential as probiotic strains. Additionally, all isolates were non-hemolytic and displayed significant antimicrobial activity against antibiotic-resistant pathogens, such as Escherichia coli and Staphylococcus aureus . The anti-cancer activity of all isolates was also evaluated against the Human colorectal adenocarcinoma cell line (Caco-2), and all isolates showed significant anticancer activity. These findings validate the beneficial therapeutic values of novel probiotic strains isolated from dairy sources, specifically Dahi, and suggest that they could be used in food and drugs to treat various diseases.

The vaginal microbiome plays an essential role in the reproductive health of human females. As infertility increases worldwide, understanding the roles that the vaginal microbiome may have in infertility and in vitro fertilization (IVF) treatment outcomes is critical. To determine the vaginal microbiome composition of 1411 individuals (1255 undergoing embryo transplantation) and their associations with reproductive outcomes, clinical and biochemical features are measured, and vaginal samples are 16S rRNA sequenced. Our results suggest that both too high and too low abundance of Lactobacillus is not beneficial for pregnancy; a moderate abundance is more beneficial. A moderate abundance of Lactobacillus crispatus and Lactobacillus iners (~80%) (with a pregnancy rate of I-B: 54.35% and III-B: 57.73%) is found beneficial for pregnancy outcomes compared with a higher abundance (>90%) of Lactobacillus (I-A: 44.81% and III-A: 51.06%, respectively). The community state type (CST) IV-B (contains a high to moderate relative abundance of Gardnerella vaginalis) shows a similar pregnant ratio (48.09%) with I-A and III-A, and the pregnant women in this CST have a higher abundance of Lactobacillus species. Metagenome analysis of 71 samples shows that nonpregnant women are detected with more antibiotic-resistance genes, and Proteobacteria and Firmicutes are the main hosts. The inherent differences within and between women in different infertility groups suggest that vaginal microbes might be used to detect infertility and potentially improve IVF outcomes.

The outbreak of novel Coronavirus, an enduring pandemic declared by WHO, has consequences to an alarming ongoing public health menace which has already claimed several million human lives. In addition to numerous vaccinations and medications for mild to moderate COVID-19 infection, lack of promising medication or therapeutic pharmaceuticals remains a serious concern to counter the ongoing coronavirus infections and to hinder its dreadful spread. Global health emergencies have called for urgency for potential drug discovery and time is the biggest constraint apart from the financial and human resources required for the high throughput drug screening. However, computational screening or in-silico approaches appeared to be an effective and faster approach to discover potential molecules without sacrificing the model animals. Accumulated shreds of evidence on computational studies against viral diseases have revealed significance of in-silico drug discovery approaches especially in the time of urgency. The central role of RdRp in SARS-CoV-2 replication makes it promising drug target to curtain on going infection and its spread. The present study aimed to employ E-pharmacophore-based virtual screening to reveal potent inhibitors of RdRp as potential leads to block the viral replication. An energyoptimised pharmacophore model was generated to screen the Enamine REAL DataBase (RDB). Then, ADME/T profiles were determined to validate the pharmacokinetics and pharmacodynamics properties of the hit compounds. Moreover, High Throughput Virtual Screening (HTVS) and molecular docking (SP & XP) were employed to screen the top hits from pharmacophore-based virtual screening and ADME/T screen. The binding free energies of the top hits were calculated by conducting MM-GBSA analysis followed by MD simulations to determine the stability of molecular interactions between top hits and RdRp protein. These virtual investigations revealed six compounds having binding free energies of -57.498, -45.776, -46.248, -35.67, -25.15 and -24.90 kcal/ mol respectively as calculated by the MM-GBSA method. The MD simulation studies confirmed the stability of

Supplementary Table S1. 782 genes identified by piggyBac transposon mutagensis in HG3 cell line after fludarabine selection Supplementary Table S2. Gene Symbol/Gene Description Supplementary Table S3A. Molecular characteristics of BRAF mutant cases in the Spanish cohort. Supplementary Table S3B. Molecular characteristics of BRAF mutant cases in the UK LRF CLL4 cohort. Supplementary TableS 4. Genes differentially regulated in HG3 cells after fludarabine selection. Supplementary Table S5. Gene Set Name [# Genes (K)] Supplementary Table S6. Distribution of mutations in the BRAF gene in CLL.

Supplementary Material and Methods in Word format

Supplementary Figure S1. schematic illustration of piggyBac transposon and transposase vectors used. PB IR refers to piggyBac inverted repeats. FRT is flippase recognition target. Supplementary Figure S2. Real-time quantitative PCR analysis confirms efficient depletion of BMP2K and DCK. Supplementary Figure S3. TP53 deficient HCT116 cell line exhibits reduced sensitivity to F-ara-A. Supplementary Figure S4. Protein expression following transient transfection of the putative fludarabine resistance genes DCK, NUDCD3, ARID5B and LARS in HCT116 cell line. Supplementary Figure S5. Vemurafinib normalizes the response to F-ara-A in cells expressing V600E mutant BRAF. Supplementary Figure S6. Hierarchical clustering of differentially expressed genes in pools of HG3 cells resistant to fludarabine. Supplementary Figure S7. Increased phosphorylation of ERK in HG3 pool resistant to fludarabine. Supplementary Figure S8. Distribution of mutations in the BRAF gene in CLL.

Zika virus (ZIKV) pandemic and its implication in congenital malformations and severe neurological disorders had created serious threats to global health. ZIKV is a mosquito-borne flavivirus which spread rapidly and infect a large number of people in a shorter time-span. Due to the lack of effective therapeutics, this had become paramount urgency to discover effective drug molecules to encounter the viral infection. Various anti-ZIKV drug discovery efforts during the past several years had been unsuccessful to develop an effective cure. The NS2B-NS3 protein was reported as an attractive therapeutic target for inhibiting viral proliferation, due to its central role in viral replication and maturation of non-structural viral proteins. Therefore, the current in silico drug exploration aimed to identify the novel inhibitors of Zika NS2B-NS3 protease by implementing an e-pharmacophore-based high-throughput virtual screening. A 3D e-pharmacophore model was generated based on the five-featured (ADPRR) pharmacophore hypothesis. Subsequently, the predicted model is further subjected to the high-throughput virtual screening to reveal top hit molecules from the various small molecule databases. Initial hits were examined in terms of binding free energies and ADME properties to identify the candidate hit exhibiting a favourable pharmacokinetic profile. Eventually, molecular dynamic (MD) simulations studies were conducted to evaluate the binding stability of the hit molecule inside the receptor cavity. The findings of the in silico analysis manifested affirmative evidence for three hit molecules with −64.28, −55.15 and −50.16 kcal/mol binding free energies, as potent inhibitors of Zika NS2B-NS3 protease. Hence, these molecules holds the promising potential to serve as a prospective candidates to design effective drugs against ZIKV and related viral infections.

supplemental figure and table legend

New variants of SARS-CoV-2 are being reported worldwide. The World Health Organization has reported Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2) and Omicron (B.1.1.529) as the variants of concern. There are speculations that the variants might evade the host immune responses induced by currently available vaccines and develop resistance to drugs under consideration. The first step of viral infection in COVID-19 occurs through the interaction of the spike protein's receptor-binding domain (RBD) with the peptidase domain of the human ACE-2 (hACE-2) receptor. This study aims to get a molecular-level understanding of the mechanism behind the increased infection rate in the alpha variant. We have computationally studied the spike protein interaction in both the wild-type and B.1.1.7 variant with the hACE-2 receptor using molecular dynamics and MM-GBSA based binding free energy calculations. The binding free energy difference shows that the mutant variant of the spike protein has increased binding affinity for the hACE-2 receptor (i.e. ΔG(N501Y,A570D) is in the range -7.2 to -7.6 kcal mol-1) and the results were validated using Density functional theory. We demonstrate that with the use of state-of-the-art computational approaches, we can, in advance, predict the virulent nature of variants of SARS-CoV-2 and alert the world healthcare system.

Centipeda minima (C. minima), is a medicinally important herb commonly called "Sneeze Weed" and widely distributed in humid areas. In China, Malaysia, and Nepal, it is used in folk medicines for the treatment of rhinitis, nasopharyngeal carcinoma, and respiratory disorders, it also exhibits antibacterial, antioxidant and antiprotozoal activity. Recently it is discovered that various bioactive molecule of C. minima has strong potential to be used in the treatment of various neoplasms. Thus, in this review, we aim to summarize and discuss various cellular targets and anticancer mechanisms of different bioactive components of C. minima. The pool of multiple studies suggested that various components of C. minima reduce cell growth, arrest cell cycle at various checkpoints and thereby induce apoptosis in different cancer cells via intrinsic and extrinsic apoptotic pathways. Moreover, these bioactive molecules also modulate different signaling pathways implicated in tumorigenesis including STAT3, NF-?B, ERK1/2, MMPs and AKT. In parallel to antiproliferative effect of C. minima, it also has antimetastatic and antineoplastic activities. A pile of literature clearly supported the anticancer activity of various components of C. minima against multiple human cancer cell lines. Thus, this review will be a milestone in the design and conduct of future research for the development of novel plant-based chemotherapeutics from C. minima.

Correction for 'Computational investigation of the increased virulence and pathogenesis of SARS-CoV-2 lineage B.1.1.7' by N. Arul Murugan et al., Phys. Chem. Chem. Phys., 2022, 24, 20371-20380, https://doi.org/10.1039/D2CP00469K.

The potential to therapeutically alter the genome is one of the remarkable scientific developments in recent years. Genome editing technologies have provided an opportunity to precisely alter genomic sequence(s) in eukaryotic cells as a treatment option for various genetic disorders. These technologies allow the correction of harmful mutations in patients by precise nucleotide editing. Genome editing technologies such as CRISPR (clustered regularly interspaced short palindromic repeat) and base editors have greatly contributed to the practical applications of gene editing. However, these technologies have certain limitations, including imperfect editing, undesirable mutations, off-target effects, and lack of potential to simultaneously edit multiple loci. Recently, prime editing (PE) has emerged as a new gene editing technology with the potential to overcome the above-mentioned limitations. Interestingly, PE not only has higher specificity but also does not require double-strand breaks. In addition, a minimum possibility of potential off-target mutant sites makes PE a preferred choice for therapeutic gene editing. Furthermore, PE has the potential to introduce insertion and deletions of all 12 single-base mutations at target sequences. Considering its potential, PE has been applied as a treatment option for genetic diseases including hemoglobinopathies. β-Thalassemia, for example, one of the most significant blood disorders characterized by reduced levels of functional hemoglobin, could potentially be treated using PE. Therapeutic reactivation of the γ-globin gene in adult β-thalassemia patients through PE technology is considered a promising therapeutic strategy. The current review aims to briefly discuss the genome editing strategies and potential applications of PE for the treatment of β-thalassemia. In addition, the review will also focus on challenges associated with the use of PE.

Neurochondrin (NCDN) is a cytoplasmatic neural protein of importance for neural growth, glutamate receptor (mGluR) signaling, and synaptic plasticity. Conditional loss of Ncdn in mice neural tissue causes depressive-like behaviors, impaired spatial learning, and epileptic seizures. We report on NCDN missense variants in six affected individuals with variable degrees of developmental delay, intellectual disability (ID), and seizures. Three siblings were found homozygous for a NCDN missense variant, whereas another three unrelated individuals carried different de novo missense variants in NCDN. We assayed the missense variants for their capability to rescue impaired neurite formation in human neuroblastoma (SH-SY5Y) cells depleted of NCDN. Overexpression of wild-type NCDN rescued the neurite-phenotype in contrast to expression of NCDN containing the variants of affected individuals. Two missense variants, associated with severe neurodevelopmental features and epilepsy, were unable to restore mGluR5-induced ERK phosphorylation. Electrophysiological analysis of SH-SY5Y cells depleted of NCDN exhibited altered membrane potential and impaired action potentials at repolarization, suggesting NCDN to be required for normal biophysical properties. Using available transcriptome data from human fetal cortex, we show that NCDN is highly expressed in maturing excitatory neurons. In combination, our data provide evidence that bi-allelic and de novo variants in NCDN cause a clinically variable form of neurodevelopmental delay and epilepsy, highlighting a critical role for NCDN in human brain development.

New variants of SARS-CoV-2 are being reported worldwide. More specifically, the variants reported in South Africa (501Y.V2) and United Kingdom (B.1.1.7) were found to be more contagious than the wild type. There are also speculations that the variants might evade the host immune responses induced by currently available vaccines and develop resistance to drugs under consideration. The first step of viral infection in COVID-19, occurs through the interaction of receptor binding domain (RBD) of the spike protein with peptidase domain of the human ACE-2 (hACE-2) receptor. So, possibly the mutations in the RBD domain of spike protein in the new variants could modulate the protein-protein interaction with hACE-2 receptor leading to the increased virulence. In this study, we aim to get molecular level understanding into the mechanism behind the increased infection rate due to such mutations in these variants. We have computationally studied the interaction of the spike protein in both wild-type and B.1.1.7 variant with hACE-2 receptor using combined molecular dynamics and binding free energy calculations using molecular mechanics-Generalized Born surface area (MM-GBSA) approach. The binding free energies computed using configurations from minimization run and low temperature simulation show that mutant variant of spike protein has increased binding affinity for hACE-2 receptor (i.e. ΔΔG(N501Y,A570D) is in the range −20.4 to −21.4 kcal/mol)The residue-wise decomposition analysis and intermolecular hydrogen bond analysis evidenced that the N501Y mutation has increased interaction between RBD of spike protein with ACE-2 receptor. We have also carried out calculations using density functional theory and the results evidenced the increased interaction between three pairs of residues (TYR449 (spike)-ASP38 (ACE-2), TYR453-HIE34 and TYR501-LYS353) in the variant that could be attributed to its increased virulence. The free energies of wild-type and mutant variants of the spike protein computed from MM-GBSA approach suggests that latter variant is stable by about −10.4 kcal/mol when compared to wild type suggesting that it will be retained in the evolution due to increased stability. We demonstrate that with the use of the state-of-the art of computational approaches, we can in advance predict the more virulent nature of variants of SARS-CoV-2 and alert the world health-care system.

The antibiotic residues in the food chain are a growing public health concern due to their involvement in the development of antimicrobial resistance, mutagenicity, carcinogenicity, hypersensitivity, bone marrow suppression, and disruption of gut microbiota. The indiscriminate use of antibiotics for the treatment of diseases and improved animal production results in the deposition of these residues in milk, eggs, and meat although their use is not highlighted for the foods consumed by human beings. Moreover, the antibiotics consumed in the clinical settings and animal production are excreted into the environment at a large scale which may adversely disturb the terrestrial and aquatic ecosystems. The matter can become more momentous soon because the production of food animals at an industrial scale will significantly increase the use of antimicrobials. The problem caused by these antibiotic residues in the food chain is two-fold; the direct toxicity to humans and the possibility of the emergence of resistant bacterial strains ultimately leading to the failure of antibiotic therapy. Present article critically analyses the factors contributing to the presence of antibiotic residues in the food chain and their implications and perilous impact on consumers and proposes the possible ways to reduce the antimicrobial residues in the food.