Multi-epitope vaccine design using in silico analysis of glycoprotein and nucleocapsid of NIPAH virus.

According to the 2018 WHO R&D Blueprint, Nipah virus (NiV) is a priority disease, and the development of a vaccine against NiV is strongly encouraged. According to criteria used to categorize zoonotic diseases, NiV is a stage III disease that can spread to people and cause unpredictable outbreaks. Since 2001, the NiV virus has caused annual outbreaks in Bangladesh, while in India it has caused occasional outbreaks. According to estimates, the mortality rate for infected individuals ranges from 70 to 91%. Using immunoinformatic approaches to anticipate the epitopes of the MHC-I, MHC-II, and B-cells, they were predicted using the NiV glycoprotein and nucleocapsid protein. The selected epitopes were used to develop a multi-epitope vaccine construct connected with linkers and adjuvants in order to improve immune responses to the vaccine construct. The 3D structure of the engineered vaccine was anticipated, optimized, and confirmed using a variety of computer simulation techniques so that its stability could be assessed. According to the immunological simulation tests, it was found that the vaccination elicits a targeted immune response against the NiV. Docking with TLR-3, 7, and 8 revealed that vaccine candidates had high binding affinities and low binding energies. Finally, molecular dynamic analysis confirms the stability of the new vaccine. Codon optimization and in silico cloning showed that the proposed vaccine was expressed to a high degree in Escherichia coli. The study will help in identifying a potential epitope for a vaccine candidate against NiV. The developed multi-epitope vaccine construct has a lot of potential, but they still need to be verified by in vitro & in vivo studies.

Monkeypox virus: insights into pathogenesis and laboratory testing methods.

The monkeypox virus (MPXV) is a zoonotic pathogen that transmits between monkeys and humans, exhibiting clinical similarities with the smallpox virus. Studies on the immunopathogenesis of MPXV revealed that an initial strong innate immune response is elicited on viral infection that subsequently helps in circumventing the host defense. Once the World Health Organization (WHO) declared it a global public health emergency in July 2022, it became essential to clearly demarcate the MPXV-induced symptoms from other viral infections. We have exhaustively searched the various databases involving Google Scholar, PubMed, and Medline to extract the information comprehensively compiled in this review. The primary focus of this review is to describe the diagnostic methods for MPXV such as polymerase chain reaction (PCR), and serological assays, along with developments in viral isolation, imaging techniques, and next-generation sequencing. These innovative technologies have the potential to greatly enhance the accuracy of diagnostic procedures. Significant discoveries involving MPXV immunopathogenesis have also been highlighted. Overall, this will be a knowledge repertoire that will be crucial for the development of efficient monitoring and control strategies in response to the MPXV infection helping clinicians and researchers in formulating healthcare strategies.

Recent advances in breast cancer cell line research.

Breast cancer, a formidable global health challenge, needs continuous translational research to understand the complexity of mechanisms and improve therapeutic and diagnostic strategies. Breast cancer cell lines are of paramount importance as they significantly contribute to the initial stage of research to understand cancer biology. This review provides insights into targeted therapies and immunotherapies that have emerged using in vitro models and microbiome analysis. It focuses on therapeutic development using cell lines and the limitations of tumor heterogeneity and microenvironment. We explore the evolving landscape of breast cancer cell lines from two-dimensional (2-D) cultures to patient-derived xenograft (PDX) models advancing both fundamental and translational research. Patient-derived xenografts, cell line-derived xenografts (CDX), three-dimensional (3-D) cultures, organoids, and circulating tumor cells (CTC) models provide promising alternatives that capture the intricacies of the tumor microenvironment. This review bridges the gap between traditional cell lines and newer developments exploring the therapeutic and diagnostic advancements and needs for cell lines to expedite the progress in breast cancer research and treatment.

Targeted inhibition of MASTL kinase activity induces apoptosis in breast cancer.

Microtubule-associated serine/threonine kinase-like (MASTL) (or Greatwall kinase (GWL)) is an important cell cycle regulating kinase that regulates the G2-M transition. Uncontrolled MASTL activity is implicated in breast cancer progression. To date, very few inhibitors have been reported against this protein. Here, structure-based computational modeling indicates that the natural product flavopiridol (FLV) binds strongly to MASTL and these results are validated using molecular dynamics simulation studies. An in vitro kinase assay reveals an EC50 (effective concentration) value of FLV to be 82.1 nM and a better IC50 compared to the positive reference compound, staurosporine. FLV is found to inhibit MASTL kinase activity, arresting the cell growth in the G1 phase and inducing apoptosis in breast cancer cells. Consistent with these results differential gene expression obtained using RNA sequencing studies, and validated by RT PCR and immunoblot analysis, indicate that MASTL inhibition induces cell cycle arrest and apoptotic-related genes. Furthermore, metastasis- and inflammation-related genes are downregulated. Thus, the deregulation of MASTL signaling pathways on targeted inhibition of its kinase activity is revealed. This study lays a strong foundation for investigating FLV as a lead compound in breast cancer therapeutics.

Genomic epidemiology of SARS-CoV-2 from Uttar Pradesh, India.

The various strains and mutations of SARS-CoV-2 have been tracked using several forms of genomic classification systems. The present study reports high-throughput sequencing and analysis of 99 SARS-CoV-2 specimens from Western Uttar Pradesh using sequences obtained from the GISAID database, followed by phylogeny and clade classification. Phylogenetic analysis revealed that Omicron lineages BA-2-like (55.55%) followed by Delta lineage-B.1.617.2 (45.5%) were predominantly circulating in this area Signature substitution at positions S: N501Y, S: D614G, S: T478K, S: K417N, S: E484A, S: P681H, and S: S477N were commonly detected in the Omicron variant-BA-2-like, however S: D614G, S: L452R, S: P681R and S: D950N were confined to Delta variant-B.1.617.2. We have also identified three escape variants in the S gene at codon position 19 (T19I/R), 484 (E484A/Q), and 681 (P681R/H) during the fourth and fifth waves in India. Based on the phylogenetic diversification studies and similar changes in other lineages, our analysis revealed indications of convergent evolution as the virus adjusts to the shifting immunological profile of its human host. To the best of our knowledge, this study is an approach to comprehensively map the circulating SARS-CoV-2 strains from Western Uttar Pradesh using an integrated approach of whole genome sequencing and phylogenetic analysis. These findings will be extremely valuable in developing a structured approach toward pandemic preparedness and evidence-based intervention plans in the future.

Therapeutic natural compounds Enzastaurin and Palbociclib inhibit MASTL kinase activity preventing breast cancer cell proliferation.

Microtubule-associated serine/threonine kinase-like (MASTL) regulates mitotic progression and is an attractive target for the development of new anticancer drugs. In this study, novel inhibitory molecules were screened against MASTL kinase, a protein involved in cell proliferation in breast cancer. Natural source-derived drugs Enzastaurin and Palbociclib were selected to identify their role as MASTL kinase inhibitors. Cytotoxic activity, kinase activity, and other cell-based assays of Enzastaurin and Palbociclib were evaluated on human breast cancer (MCF-7) cells. The potential natural compounds caused cytotoxicity in MCF-7 cells in a dose- and time-dependent manner. Further analysis by Annexin V and PI staining indicated that both drugs are potent inducers of apoptosis. Enzastaurin induced G2/M phase arrest, while Palbociclib caused G1 arrest. MASTL kinase activity was significantly abrogated with both the compounds showing EC50 values of 17.13 µM and 10.51 µM, respectively. Taken together, these data strongly suggest that Enzastaurin and Palbociclib possess the ability to inhibit MASTL kinase activity and induce cell death in breast cancer cells, thus exhibiting significant therapeutic potential.

WITHDRAWN: Therapeutic Targeted Approaches for Covid-19 Treatment

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Exploring TEAD2 as a drug target for therapeutic intervention of cancer: A multi-computational case study.

Transcriptional enhanced associate domain (TEAD) is a family of transcription factors that plays a significant role during embryonic developmental processes, and its dysregulation is responsible for tumour progression. TEAD is considered as druggable targets in various diseases, namely cancer, cardiovascular diseases and neurodegenerative disorders. Previous structural studies revealed the importance of the central hydrophobic pocket of TEAD as a potential target for small-molecule inhibitors and demonstrated flufenamic acid (FLU) (a COX-2 enzyme inhibitor) to bind and inhibit TEAD2 functions. However, to date, no drug candidates that bind specifically to TEAD2 with high selectivity and efficacy have been developed or proposed. Within this framework, we present here a case study where we have identified potential TEAD2 inhibitor candidates by integrating multiple computational approaches. Among the candidates, the top two ranked compounds ZINC95969481 (LG1) which is a fused pyrazole derivative and ZINC05203789 (LG2), a fluorene derivative resulted in much favourable binding energy scores than the reference ligand, FLU. The drug likeliness of the best compounds was also evaluated in silico to ensure the bioavailability of these compounds particularly LG1 as compared to FLU thus providing a strong rationale for their development as leads against TEAD. Molecular dynamics simulations results highlighted the role of key residues contributing to favourable interactions in TEAD2-LG1 complex with much favourable interaction and binding free energy values with respect to the reference compound. Altogether, this study provides a starting platform to be more exploited by future experimental research towards the development of inhibitors against TEAD, a persuasive strategy for therapeutic intervention in cancer treatment.

Exposure of androgen mimicking environmental chemicals enhances proliferation of prostate cancer (LNCaP) cells by inducing AR expression and epigenetic modifications.

Exposure to environmental endocrine disrupting chemicals (EDCs) is highly suspected in prostate carcinogenesis. Though, estrogenicity is the most studied behavior of EDCs, the androgenic potential of most of the EDCs remains elusive. This study investigates the androgen mimicking potential of some common EDCs and their effect in androgen-dependent prostate cancer (LNCaP) cells. Based on the In silico interaction study, all the 8 EDCs tested were found to interact with androgen receptor with different binding energies. Further, the luciferase reporter activity confirmed the androgen mimicking potential of 4 EDCs namely benzo[a]pyrene, dichlorvos, genistein and ß-endosulfan. Whereas, aldrin, malathion, tebuconazole and DDT were reported as antiandrogenic in luciferase reporter activity assay. Next, the nanomolar concentration of androgen mimicking EDCs (benzo[a]pyrene, dichlorvos, genistein and ß-endosulfan) significantly enhanced the expression of AR protein and subsequent nuclear translocation in LNCaP cells. Our In silico studies further demonstrated that androgenic EDCs also bind with epigenetic regulatory enzymes namely DNMT1 and HDAC1. Moreover, exposure to these EDCs enhanced the protein expression of DNMT1 and HDAC1 in LNCaP cells. These observations suggest that EDCs may regulate proliferation in androgen sensitive LNCaP cells by acting as androgen mimicking ligands for AR signaling as well as by regulating epigenetic machinery. Both androgenic potential and epigenetic modulatory effects of EDCs may underlie the development and growth of prostate cancer.

A database of wild rice germplasm of Oryza rufipogon species complex from different agro-climatic zones of India.

Rice is a staple food for the people of Asia that supplies more than 50% of the food energy globally. It is widely accepted that the crop domestication process has left behind substantial useful genetic diversity in their wild progenitor species that has huge potential for developing crop varieties with enhanced resistance to an array of biotic and abiotic stresses. In this context, Oryza rufipogon, Oryza nivara and their intermediate types wild rice germplasm/s collected from diverse agro-climatic regions would provide a rich repository of genes and alleles that could be utilized for rice improvement using genomics-assisted breeding. Here we present a database of detailed information on 614 such diverse wild rice accessions collected from different agro-climatic zones of India, including 46 different morphological descriptors, complete passport data and DNA fingerprints. The information has been stored in a web-based database entitled 'Indian Wild Rice (IWR) Database'. The information provided in the IWR Database will be useful for the rice geneticists and breeders for improvement of rice cultivars for yield, quality and resilience to climate change.Database URL: http://nksingh.nationalprof.in: 8080/iwrdb/index.jsp.

Identification of new inhibitors against human Great wall kinase using in silico approaches.

Microtubule associated serine/threonine kinase (MASTL) is an important Ser/Thr kinase belonging to the family of AGC kinases. It is the human orthologue of Greatwall kinase (Gwl) that plays a significant role in mitotic progression and cell cycle regulation. Upregulation of MASTL in various cancers and its association with poor patient survival establishes it as an important drug target in cancer therapy. Nevertheless, the target remains unexplored with the paucity of studies focused on identification of inhibitors against MASTL, which emphasizes the relevance of our present study. We explored various drug databases and performed virtual screening of compounds from both natural and synthetic sources. A list of promising compounds displaying high binding characteristics towards MASTL protein is reported. Among the natural compounds, we found a 6-hydroxynaphthalene derivative ZINC85597499 to display best binding energy value of -9.32 kcal/mol. While among synthetic compounds, a thieno-pyrimidinone based tricyclic derivative ZINC53845290 compound exhibited best binding affinity of value -7.85 kcal/mol. MASTL interactions with these two compounds were further explored using molecular dynamics simulations. Altogether, this study identifies potential inhibitors of human Gwl kinase from both natural and synthetic origin and calls for studying these compounds as potential drugs for cancer therapy.

Understanding the Interactions of High-Mobility Group of Protein Domain B1 with DNA Adducts Generated by Platinum Anticancer Molecules Using In Silico Approaches.

Platinum coordination compounds having cis geometry are frequently prescribed for various types of cancers. Protein dysregulation is one of the major factors contributing towards cancer metastasis. Head and neck squamous cell carcinoma (HNSCC) is one of the cancers where platinum-based compounds are used either alone or in combination with radiation as therapy. The underlying interactions of these compounds with both DNA and proteins are crucial for the drug response. The compounds forms DNA adducts which are recognized by conserved, non-chromosomal high-mobility group box 1 (HMGB1) proteins. In the present study, we report the molecular dynamics simulations with the aim of understanding the behavior of platinum molecules that bind DNA. The binding pocket is identified using molecular docking approach. The sixteen mer stretch of the DNA-(d(CC(5IU)CTCTGGACCTTCC) * d(GGAAGGTCCAGAGAGG)) duplex containing G*G* is the major adduct of the anti-tumor molecule. We have performed comparison of inhibitory potential of the already known inhibitors of HNSCC against HMGB1-binding pocket using simulations and docking. Variations in the binding site are observed for these inhibitors-DNA-protein ternary complexes involving defined groups. We have validated our results using geometry-based docking transformations against the specific binding site as well as blind docking that involves complete protein for the identification of specific binding site. Effective dose of the compound reflects its activity. The interactions between DNA and HMGB1 are defined by hydrogen bonds and van der Waals contacts. However, the ternary complex stabilization is mediated by hydrogen bonding and hydrophobic interactions. Significant deviations are observed in the RMSD values. We have classified the inhibitors in two categories where group A compounds shows interactions against the HMGB1 domain box B and group B toward both boxes A and B. Experimental IC50 values corroborates with the binding energies of the compounds. We propose the predicted pattern of binding as specific for platinum inhibitors. These studies are a new addition to the existing structural-activity relationship-based pharmacophore generation with a potential for use in the treatment of head and neck squamous cell carcinoma. The compounds can be validated as lead molecules using in vitro and in vivo experiments.

Subconjunctivally Implanted Hydrogels for Sustained Insulin Release to Reduce Retinal Cell Apoptosis in Diabetic Rats.

PURPOSE: Diabetic retinopathy (DR) is a leading cause of blindness in diabetic patients that involves early-onset retinal cell loss. Here, we report our recent work using subconjunctivally implantable hydrogels for sustained insulin release to the retina to prevent retinal degeneration. METHODS: The hydrogels are synthesized by UV photopolymerization of N-isopropylacrylamide and a dextran macromer containing oligolactate-(2-hydroxyetheyl methacrylate) units. Insulin was loaded into the hydrogels during the synthesis. The ex vivo bioactivity of insulin released from the hydrogels was tested on fresh rat retinas using immunoprecipitation and immunoblotting to measure insulin receptor tyrosine and Akt phosphorylation. The biosafety and the effect on the blood glucose of the hydrogels were evaluated in rats 2 months after subconjunctival implantation. The release of insulin from the hydrogels was studied both in vitro in PBS (pH 7.4), and in vivo using confocal microscopy and RIA kit. The in vivo bioactivity of the released insulin was investigated in diabetic rats using DNA fragmentation method. RESULTS: The hydrogels could load insulin with approximately 98% encapsulation efficiency and continuously release FITC-insulin in PBS (pH = 7.4) at 37°C for at least 5 months depending on their composition. Insulin lispro released from the hydrogels was biologically active by increasing insulin receptor tyrosine and Akt serine phosphorylation of ex vivo retinas. In vivo studies showed normal retinal histology 2 months post subconjunctival implantation. Insulin released from subconjunctivally implanted hydrogels could be detected in the retina by using confocal microscopy and RIA kit for 1 week. The implanted hydrogels with insulin lispro did not change the blood glucose level of normal and diabetic rats, but significantly reduced the DNA fragmentation of diabetic retinas for 1 week. CONCLUSIONS: The developed hydrogels have great potential to sustain release of insulin to the retina via subconjunctival implantation to minimize DR without the risk of hypoglycemia.

Bioinformatics: promises and progress.

Bioinformatics is a multidisciplinary science that solves and analyzes biological problems. With the quantum explosion in biomedical data, the demand of bioinformatics has increased gradually. Present paper provides an overview of various ways through which the biologists or biological researchers in the domain of neurology, structural and functional biology, evolutionary biology, clinical science, etc., use bioinformatics applications for data analysis to summarise their research. A new perspective is used to classify the knowledge available in the field thus will help general audience to understand the application of bioinformatics.

Identification of calcium binding sites on calsequestrin 1 and their implications for polymerization.

Biophysical studies have shown that each molecule of calsequestrin 1 (CASQ1) can bind about 70-80 Ca(2+) ions. However, the nature of Ca(2+)-binding sites has not yet been fully characterized. In this study, we employed in silico approaches to identify the Ca(2+) binding sites and to understand the molecular basis of CASQ1-Ca(2+) recognition. We built the protein model by extracting the atomic coordinates for the back-to-back dimeric unit from the recently solved hexameric CASQ1 structure (PDB id: ) and adding the missing C-terminal residues (aa350-364). Using this model we performed extensive 30 ns molecular dynamics simulations over a wide range of Ca(2+) concentrations ([Ca(2+)]). Our results show that the Ca(2+)-binding sites on CASQ1 differ both in affinity and geometry. The high affinity Ca(2+)-binding sites share a similar geometry and interestingly, the majority of them were found to be induced by increased [Ca(2+)]. We also found that the system shows maximal Ca(2+)-binding to the CAS (consecutive aspartate stretch at the C-terminus) before the rest of the CASQ1 surface becomes saturated. Simulated data show that the CASQ1 back-to-back stacking is progressively stabilized by the emergence of an increasing number of hydrophobic interactions with increasing [Ca(2+)]. Further, this study shows that the CAS domain assumes a compact structure with an increase in Ca(2+) binding, which suggests that the CAS domain might function as a Ca(2+)-sensor that may be a novel structural motif to sense metal. We propose the term "Dn-motif" for the CAS domain.

Targeting the epidermal growth factor receptor: exploring the potential of novel inhibitor N-(3-ethynylphenyl)-6, 7-bis (2-methoxyethoxy) quinolin- 4-amine using docking and molecular dynamics simulation.

Head and neck squamous cell carcinoma (HNSCC) is a major cause of cancer related death. The epidermal growth factor receptor (EGFR) pathway is over expressed in HNSCC. EGFR regulates the HNSCC by inducing signalling events responsible for regulating key tumorigenic processes such as proliferation, inhibition of apoptosis, cell adhesion/ motility, growth and survival. Present study evaluates the potential of N-(3-Ethynylphenyl)-6, 7-bis (2-methoxyethoxy) quinolin-4-amine as a new inhibitor for EGFR. We have explored the binding and inhibitory potential of the compound using molecular docking, structural interactions fingerprinting and molecular dynamics studies. The inhibitor exhibits extensive interactions with the EGFR catalytic site in the form of hydrogen bonds, pi-pi bond and salt bridges. It shows high specificity and binding affinity towards the protein. The compound can further be explored for its potential to serve in the diagnosis and treatment of HNSCC. The quantitative prediction provides a scope for future experimental testing, facilitating the understanding of the crosstalks between signalling pathways.

Prediction of a new surface binding pocket and evaluation of inhibitors against huntingtin interacting protein 14: an insight using docking studies.

Protein-protein interactions play an important role in regulating the expression of huntingtin protein (htt). Expansion of polyglutamine tracts in htt results in neurodegenerative Huntington disease. Huntingtin interacting protein (HIP14) is an important interacting partner of htt and the altered interactions have been proposed to play an important role in disease progression. In the present study, an attempt has been made to explore the potential of several known Huntington inhibitors to inhibit HIP14. The docking studies have resulted in the identification of a novel binding site for these inhibitors distinct from the previously known ankyrin repeat domain. The results have been validated using geometry based docking transformations against the other binding pocket. The specificity of binding has been determined with high values of both accuracy and precision. Nine potential inhibitors obtained after screening belong to three distinct classes of compounds viz, carbohydrates (deoxy-glucose), alcohols (including phenolic scaffold) and tetracycline. The compounds form stable complex with protein exhibiting optimal intermolecular and Gibbs free energy. The hydrogen bonding and hydrophobic interactions predominantly contribute to the stability of these complexes. The present study identifies metoprolol, minocyclines and 18 F fluorodeoxyglucose as the best inhibitors that bind specifically to the new site. Therefore, these compounds can further be exploited for their potential to serve in the diagnosis and treatment of Huntington disease. The quantitative predictions provide a scope for experimental testing in future.

Exploring the positional importance of aromatic residues and lysine in the interactions of peptides with the Plasmodium falciparum Hsp70-1.

Plasmodium falciparum harbors an essential relict plastid called the apicoplast that is involved in several important biosynthetic processes. Over 500 nuclear encoded proteins are imported into the organelle that is now recognized as an important therapeutic target. These proteins contain an N-terminal transit peptide sequence essential for apicoplast targeting during which the P. falciparum Hsp70-1 plays an important role. In the present study, we have focused on the in vitro interactions of PfHsp70-1 with synthetic peptides endowed with transit peptide like features. The peptides exhibit higher affinity for PfHsp70-1 in the presence of ADP compared to ATP. The results highlight the positional importance of selected residues in the designed peptides for affinity. They suggest that better peptide affinity for the protein requires a Lys at second position, retention of aromatic residue at the last position, and absence of acidic residues at any position in the transit peptides. Overall, the present work is the first in vitro fluorescence-based study of PfHsp70-1 with peptides possessing transit peptide-like features.