Genomic surveillance of omicron B.1.1.529 SARS-CoV-2 and its variants between December 2021 and March 2023 in Tamil Nadu, India-A state-wide prospective longitudinal study

A state-wide prospective longitudinal investigation of the genomic surveillance of the omicron B.1.1.529 SARS-CoV-2 variant and its sublineages in Tamil Nadu, India, was conducted between December 2021 and March 2023. The study aimed to elucidate their mutational patterns and their genetic interrelationship in the Indian population. The study identified several unique mutations at different time-points, which likely could attribute to the changing disease characteristics, transmission, and pathogenicity attributes of omicron variants. The study found that the omicron variant is highly competent in its mutating potentials, and that it continues to evolve in the general population, likely escaping from natural as well as vaccine-induced immune responses. Our findings suggest that continuous surveillance of viral variants at the global scenario is warranted to undertake intervention measures against potentially precarious SARS-CoV-2 variants and their evolution.

Next-Generation Sequencing to Study the DNA Interaction

Next-generation sequencing (NGS) has transformed genomics by allowing researchers to sequence DNA and RNA at highest speed, accuracy, and cost-effectiveness. Researchers investigate DNA interactions with the help next-generation sequencing with a great deal of information. Over the last decade, NGS technologies have advanced significantly, with the development of several platforms, including Illumina, PacBio, and Oxford Nanopore, each offering distinct advantages and uses. The use of next-generation sequencing (NGS) has aided in the discovery of genetic variations, gene expression patterns, and epigenetic modifications connected with a variety of diseases, including cancer, neurological disorders, and infectious diseases. By identifying these regions, we can control the expression of genes, cellular signaling pathways, and other key biological processes. NGS is an effective method for researching DNA interactions that has completely transformed the area of genomics. NGS has also played an important part in personalized medicine, enabling the discovery of disease-causing mutations and the creation of targeted medicines. Finally, NGS has transformed the field of genomics, resulting in new discoveries and applications in medicine, environmental sciences, and other fields.

A Computational Investigation on Chitosan Derivatives using Pharmacophore- based Screening, Molecular Docking, and Molecular Dynamics Simulations against Kaposi Sarcoma

BACKGROUND

Cancer is one of the most dangerous illnesses to the human body due to its severity and progressive nature. Kaposi's Sarcoma (KS) tumor can appear as painless purple spots on the legs, foot, or face. This cancer develops in the lining of lymph arteries and blood vessels. Along with the enlargement of lymph nodes, the vaginal region and the mouth portion are the additional target areas of KS. DNA-binding proteins known as Sox proteins are found in all mammals and belong to the HMG box superfamily. They controlled a wide range of developmental procedures, such as the formation of the germ layer, the growth of organs, and the selection of the cell type. Human developmental abnormalities and congenital illnesses are frequently caused by the deletion or mutation of the Sox protein.

AIM

The purpose of this study is to determine the promising Kaposi's sarcoma inhibitors through computational studies.

OBJECTIVE

In this present study computational approaches were used to evaluate the anti- carcinogenic efficacy against Kaposi's sarcoma.

METHODS

Ligand-based pharmacophore screening was performed utilising four different chemical libraries (Asinex, Chembridge, Specs, and NCI Natural products (NSC)) depending on the top hypothesis. The top hits were examined using molecular docking, absorption, distribution, metabolism and excretion. Highest occupied molecular orbital and lowest unoccupied molecular orbital were analysed to determine the lead compounds' biological and pharmacological efficacy. The results of the study indicated that the leading candidates were possible SOX protein inhibitors.

RESULTS

A pharmacophore model to inhibit the production of SOX protein in Kaposi Sarcoma was generated in this computational experiment using a set of 19 Chitosan compounds.

CONCLUSION

The results revealed that the top hits responded to all of the pharmacological druglikening criteria and had the best interaction residues, fitness scores, and docking scores. The resulting leads might be potential Kaposi's Sarcoma alternative treatments.

Systemic assessment of solute carrier family 11-member A1 (rs17235409) gene polymorphism and Mycobacterium Tuberculosis Risk in Asian and caucasian population: A comprehensive updated meta-analysis

Background

The present meta-analysis was assessed to confirm the association between solute carrier family 11-member A1 (SLC11A1) gene (rs17235409) polymorphism with the Mycobacterium tuberculosis infection in the Asian and Caucasian populations.

Methods

A search was conducted using the databases including Google Scholar, Science Direct, Embase, and PubMed to find the case-control studies related to SLC11A1 gene polymorphism and tuberculosis (TB) infection. The MetaGenyo programme was used to perform statistical analyses of the data. The odds ratio and 95% confidence interval were calculated based on genetic models such as allelic model, dominant model, recessive model, and overdominant. The heterogeneity and publication bias for the present study were examined to assess its quality. The study was registered in PROSPERO (ID Number: 461434).

Results

This current study revealed the association between the SLC11A1 gene polymorphism with TB. The statistical value obtained at P < 0.05 was deemed to be statistically significant. The meta-analysis results revealed that allele contrast and recessive models are significant association between SLC11A1 gene polymorphism with risk of TB infections, and dominant and overdominant models have no significant association with TB risk. In addition, the subgroup analysis based on the ethnicity dominant revealed a significant association with the risk of TB. Therefore, this results that the gene SLC11A1 has a significant association for allelic and recessive and has no significant association for dominant and overdominant with the risk of TB.

Conclusion

According to the data retrieved from the database with respect to the present study revealed that SLC11A1 gene polymorphism rs17235409 for allelic, recessive models have been associated with TB infections, but dominant and overdominant models have not been associated with TB infections.

Antiangiogenic Potential of Troxerutin and Chitosan Loaded Troxerutin on Chorioallantoic Membrane Model

Angiogenesis is crucial to the development of cancer because it allows the transport of oxygen, nutrients, and growth factors as well as the spread of tumors to distant organs. Inhibitors of angiogenesis prevent the formation of blood vessels that allow tumor cells to shrink, rather than promote tumor growth. Chitosan acts as a carrier for many drugs, since the compound has various properties such as biodegradable, less toxicity, more stable, simple, easy to prepare, and biocompatible. The aim of the current study was to evaluate the efficacy of chitosan nanoparticles encapsulated with troxerutin (Chi-Trox NPs) against angiogenesis and cancer in ova chick chorioallantoic membrane (CAM) model. Chi-Trox NPs were synthesized using a nanoprecipitation method and were characterized by various analyses. 24 hours' fertilized eggs (6 eggs/group) were treated with native Trox and Chi-Trox NPs for 5 days. The antiangiogenic activity was evaluated by morphometric, histopathological, immunohistochemical (CD104 and vimentin), and mRNA expression of MMP and FGF2 using RT-PCR. The anticancer activity was evaluated by histopathological, immunohistochmical (CD44), and mRNA expression of FGF2 and MMP. The synthesized chitosan NPs were successfully encapsulated with troxerutin, and the loading efficiency of chitosan NPs was found to be 86.4 ± 0.12% and 13.2 ± 0.16% respectively. Morphometric analysis of Chi-Trox NPs showed a considerable decrease in the number of blood vessels compared with control and native Trox. The histopathological observation of CAM confirmed that Chi-Trox NPs induce a significant reduction in inflammatory cells and the thickness of blood capillaries compared to control and native Trox. The immunohistochemical evaluation of CAM revealed Chi-Trox decreased CD104, vimentin and CD44 protein levels were compared with control and native Trox. Furthermore, the mRNA expression levels of FGF2 and MMP were significantly downregulated compared to their native forms. From the obtained results, Chi-Trox NPs possess significant inhibition of angiogenesis and can be used as therapeutic agents for cancer in the future.

Anti-angiogenic effect of nano-formulated water soluble kaempferol and combretastatin in an in vivo chick chorioallantoic membrane model and HUVEC cells

The present study evaluated the efficacy of nano-formulated water-soluble kaempferol and combretastatin alone and combined against the native kaempferol and combretastatin on angiogenesis. The solvent evaporation method was used to synthesize the nano-formulated water-soluble kaempferol and combretastatin and characterized using various analyses such as dynamic light scattering (DLS) and Fourier-transform infrared (FT-IR) spectroscopy.The anti-angiogenic activity of native, nano-formulated water-soluble kaempferol and combretastatin was investigated by cell viability on HUVEC and A498 cell lines, while chick chorioallantoic membrane (CAM) assay was utilized to assess morphometric and histopathological changes, and mRNA expressions of VEGF-A and FGF2 using qRT-PCR. MTT assay results revealed that the combination of nano-formulated water-soluble kaempferol and combretastatin significantly reduced the cell viability compared to control, individual treatments of native, nano-formulated water-soluble kaempferol, and combretastatin. Morphometric analysis of CAM showed that treatment with nano-formulated water-soluble kaempferol and combretastatin caused a substantial decrease in density, vessel network, branch points, and nets of CAM blood vessels. The histopathological results of CAM showed the irregular shape of blood vessels at the thin stratum of chronic endoderm, and blood capillaries were diminished compared to the control. In addition, the mRNA expression levels of VEGF-A and FGF2 were significantly decreased compared with native forms. Therefore, the findings of this study indicate that nano-formulated water-soluble combretastatin and kaempferol suppress angiogenesis by preventing the activation of endothelial cells and suppressing factors of angiogenesis. Moreover, a combination of nano-formulated water-soluble kaempferol and combretastatin worked much better than individual treatments.

Structural Modeling of Drosophila melanogaster Gut Cytochrome P450s and Docking Comparison of Fruit Fly Gut and Human Cytochrome P450s

Drosophila melanogaster is a prominent model organism in developmental biology research and in studies related to pathophysiological conditions like cancer and Alzheimer's disease. The fruit fly gut contains several cytochrome P450s (CYP450s) which have central roles in Drosophila development and in the normal physiology of the gut. Since the crystal structures of these proteins have not been deciphered yet, we modeled the structure of 29 different D. melanogaster gut CYP450s using Prime (Schrödinger). The sequences of chosen D. melanogaster gut CYP450s were compared with that of their human counterparts. The common gut (and liver) microsomal CYP450s in humans were chosen for structural comparison to find the homology and identity % of D. melanogaster CYPs with that of their human counterparts. The modeled structures were validated using PROCHECK and the best fit models were used for docking several known human pharmacological agents/drugs to the modeled D. melanogaster gut CYP450s. Based on the binding affinities (ΔG values) of the selected drug molecules with the modeled fly gut CYPs, the plausible differences in metabolism of the prominent drugs in humans and fly were projected. The gut is involved in absorption of oral drugs/pharmacological agents and hence, upregulation of intestinal CYP450 and their reactions with endobiotics and xenobiotics is envisaged. The insights gleaned from this work can validate D. melanogaster as a model organism for studying intestinal drug metabolism, particularly in the context of a) toxicology of pharmacological agents to the gut cells and b) how gut P450 metabolites/products can influence gut homeostasis. This work can help establish a platform for further in vitro investigations on how intestinal CYP450 metabolism can influence gut health. The data from this work can be used for further in silico studies and this work can serve as a platform for future in vitro investigations on intestinal CYP450-mediated metabolism of endo- and xeno-biotics in D. melanogaster.

Antiangiogenic role of natural flavonoids and their molecular mechanism: an update

Background

Angiogenesis is the development of new blood vessels from the existing vasculature, which is important in normal developmental processes. Angiogenesis is a key step in tumor growth, invasion, and metastasis. Angiogenesis is necessary for the proper nourishment and removal of metabolic wastes from tumor sites. Therefore, modulation of angiogenesis is considered a therapeutic strategy of great importance for human health.

Main body

Numerous bioactive plant compounds are recently tested for their antiangiogenic potential. Among the most frequently studied are flavonoids which are abundantly present in fruits and vegetables. Flavonoids inhibit angiogenesis and metastasis through the regulation of multiple signaling pathways. Flavonoids regulate the expression of VEGF, matrix metalloproteinases (MMPs), EGFR, and inhibit NFB, PI3-K/Akt, and ERK1/2 signaling pathways, thereby causing strong antiangiogenic effects. This present review aimed to provide up-to-date information on the molecular mechanisms of antiangiogenic properties of natural flavonoids.

Conclusion

Presently developed antiangiogenic drugs in malignant growth treatment do not meet assumptions about adequacy and safety. So further investigations are needed in this field in the future. More recently, flavonoids are the most effective antiangiogenic agent, by inhibition of signaling pathways.

Inhibition studies of HBV DNA polymerase using seed extracts of Pongamia pinnata

Several antiviral compounds for HBV have been identified from traditionally used medicinal plants. We have earlier described the immune modulation properties of P. pinnata, a traditionally used Indian medicinal plant. Therefore, it is of interest to explore the anti-Hepatitis B virus activity of P. pinnata extracts by in-vitro screening assays. This study clearly demonstrated that the 5mg/ml concentration of the aqueous extract significantly inhibited the virus binding. Further, the spectral study was carried out for finding active compounds. The active chalcone derivatives namely, glabaarachalcone, and isopongachromene were isolated from P. pinnata aqueous seed extracts by standard spectral procedures. Virtual screening data shows that glabaarachalcone, and isopongachromene bound with HBV DNA polymerase protein target.

Identification of potential inhibitors for Penicillinbinding protein (PBP) from Staphylococcus aureus

Staphylococcus aureus is an infectious agent that causes severe skin and soft tissue infection in hospitalized patients. Therefore, it is of interest to develop potent inhibitors for S. aureus. Penicillin Binding protein (PBP) is a known drug target for inhibition of cell wall biosynthesis in S. aureus. Hence, PBP was screened with compounds from six databases using virtual screening approaches. Results shows that the screened lead compound produced higher docking score (-9.87 kcal/mol) compared to resistant drugs. Antimicrobial activity using screened lead compounds and resistant drugs showed maximum activity in potential screened compounds compared to resistant compounds.