Integrating Network Pharmacology and In Silico Analysis to Explore the Bioactive Compounds Against Gastric Cancer Treatment.

Gastric cancer (GC) has become a major challenge in oncology research, primarily due to its detection at advanced stages. In this study, we identified and validated the pharmacological mechanisms involved in treating gastric cancer using an integrated approach combining network pharmacology, molecular docking, and a dynamic approach. Gastric cancer-related genes were obtained from DisGeNET, Genecard, and Malacard databases, while potential targets of bioactive compounds were predicted using SwissTargetPrediction.

AScirRNA: A novel computational approach to discover abiotic stress-responsive circular RNAs in plant genome.

In the realm of plant biology, understanding the intricate regulatory mechanisms governing stress responses stands as a pivotal pursuit. Circular RNAs (circRNAs), emerging as critical players in gene regulation, have garnered attention in recent days for their potential roles in abiotic stress adaptation. A comprehensive grasp of circRNAs' functions in stress response offers avenues for breeders to manipulating plants to develop abiotic stress resistant crop cultivars to thrive in challenging climates.

A novel heterozygote allele in caprine melanocortin 1 receptor (MC1R) gene: an association with heat stress traits.

Climate change negatively influences the productive and reproductive abilities of goats. There is a need to understand the relationship between heat stress and genes that may aid in the development of climate-resilient goats. Melanism variation in goats plays a role in thermoregulation, in which the melanogenic genes have a pleiotropic effect on the regulation of physiological responses and behavior that are altered due to heat stress in the animals.

Structural Elucidation of Inter-CARD Interfaces involved in NOD2 Tandem CARD Association and RIP2 Recognition.

Nucleotide-binding and oligomerization domain-containing protein 2 (NOD2) recognizes the muramyl dipeptide and activates the NF-κB signaling cascade following its interaction with receptor-interacting protein 2 (RIP2) via caspase recruitment domains (CARDs). The NOD2-RIP2 interaction is not understood well due to inadequate structural information. Using comparative modeling and multimicrosecond timescale molecular dynamics simulations, we have demonstrated the association of NOD2-CARDs (CARDa-CARDb) and their interaction with RIP2.

PredCRG: A computational method for recognition of plant circadian genes by employing support vector machine with Laplace kernel.

Background: Circadian rhythms regulate several physiological and developmental processes of plants. Hence, the identification of genes with the underlying circadian rhythmic features is pivotal. Though computational methods have been developed for the identification of circadian genes, all these methods are based on gene expression datasets.

Identification and futuristic role of novel polymorphism of caprine PrP gene.

The Caprine Prion Protein (PrP) gene polymorphism in three different native Indian goat populations of Southern Odisha, namely Ganjam (a registered breed of India), Ghumusari and Raighar was studied. The 876 bp amplified segment of PrP gene contains full length coding sequence of 771 bp. In Ganjam and Ghumusari goats, any difference of nucleotide sequence was not identified.

An in vivo and in silico analysis of novel variation in TMBIM6 gene affecting cardiopulmonary traits of Indian goats.

Transmembrane Bax Inhibitor Motif-containing 6 (TMBIM6) gene acts as calcium leak channel and negatively regulates autophagy and autophagosome formation. The TMBIM6 gene was amplified and searched for variation in three different goat populations (i.e.

Arabinosyltransferase C enzyme of , a potential drug target: An insight from molecular docking study.

Multi-drug resistant in (M.tb) is considered as major bottleneck in the treatment and cure of tuberculosis (TB). Several anti-tubercular drugs fail in its efficacy due to drug-resistant M.

Interactions between Ibuprofen and Silicified-MCC: Characterization, Drug Release and Modeling Approaches.

Analysis of the binding interactions of ibuprofen and silicified-microcrystalline cellulose (SMCC) has been undertaken. Co-processing of ibuprofen with SMCC was carried out by solid state ball milling, and aqueous state equilibration followed by freeze drying to investigate the effect of silicified-microcrystalline cellulose on ligand. Molecular docking study revealed that ibuprofen formed complex through hydrogen bond with microcrystalline cellulose (MCC) and silicon dioxide (SiO2); the binding energy between MCC and SiO2, and ibuprofen and SMCC were found as -1.

Production, characterization and application of thermostable, alkaline α-amylase (AA11) from Bacillus cereus strain SP-CH11 isolated from Chilika Lake.

An alkaliphile bacterial strain designated as CH11 was isolated from the sediments of Chilika Lake, Odisha. The isolate showed stupendous growth and production of α-amylase at pH 10.0.

Elucidating the molecular interaction of Zebrafish () peptidoglycan recognition protein 2 with diaminopimelic acid and lysine type peptidoglycans using approaches.

Peptidoglycan recognition proteins (PGRPs) belong to the family of pattern recognition receptor, represent the major constituent of innate immunity. Although PGRPs are structurally conserved through evolution, their involvement in innate immunity is different in vertebrates and invertebrates. They are highly specific towards recognition of ligands and can hydrolyze bacterial peptidoglycans (PGNs).

Insights into the mode of flavin mononucleotide binding and catalytic mechanism of bacterial chromate reductases: A molecular dynamics simulation study.

Enzymes from natural sources protect the environment via complex biological mechanisms, which aid in reductive immobilization of toxic metals including chromium. Nevertheless, progress was being made in elucidating high-resolution crystal structures of reductases and their binding with flavin mononucleotide (FMN) to understand the underlying mechanism of chromate reduction. Therefore, herein, we employed molecular dynamics (MD) simulations, principal component analysis (PCA), and binding free energy calculations to understand the dynamics behavior of these enzymes with FMN.

Bioactivity guided isolation of antidiabetic and antioxidant compound from J. Koenig bark.

The present study was designed to identify antidiabetic and antioxidant constituents from ethanol bark extract of a medicinally important mangrove plant J. Koenig, using in vitro bioactivity-guided fractionation. The repeated fractionation of ethanol bark extract (XGEB) by silica gel column chromatography yielded a compound with strong antidiabetic and antioxidant potential.

Functional diversity and metabolic profile of microbial community of mine soils with different levels of chromium contamination.

Microbial communities provide useful information about any chemical and physical changes in the environment and play an essential role in maintaining soil fertility. Biolog® eco-plates method was used to study the functional diversity of microbial communities, and their correlation with soil organic carbon (OC), microbial biomass and activities, under three different soil conditions of Sukinda chromite mining area of Odisha, India during August 2016. The OC, available nitrogen, available phosphorus and available potash were significantly (< 0.

Drug-in-mucoadhesive type film for ocular anti-inflammatory potential of amlodipine: Effect of sulphobutyl-ether-beta-cyclodextrin on permeation and molecular docking characterization.

Mucoadhesive type ocular film has been prepared for studying the anti-inflammatory potential of amlodipine (AML) on carrageenan-induced rabbit model and the effect of sulphobutyl-ether-beta-cyclodextrin on corneal permeation was tested. Hydroxypropyl methylcellulose (HPMC) ocular film was prepared after complexation of amlodipine with β-cyclodextrin, (BCD), hydroxypropyl β-cyclodextrin (HPCD), and sulfobutylether β-cyclodextrin (SBCD). The film without cyclodextrin showed a maximum swelling, and erosion to the highest extent.

Drug Target Identification and Elucidation of Natural Inhibitors for : An Study.

Environmental microbes like has been established as a causative agent for various infectious diseases in human. Again, development of drug resistance in challenged to combat against the infection. Identification of potential drug target and proposing a novel lead compound against the pathogen has a great aid and value.

NOD1CARD Might Be Using Multiple Interfaces for RIP2-Mediated CARD-CARD Interaction: Insights from Molecular Dynamics Simulation.

The nucleotide-binding and oligomerization domain (NOD)-containing protein 1 (NOD1) plays the pivotal role in host-pathogen interface of innate immunity and triggers immune signalling pathways for the maturation and release of pro-inflammatory cytokines. Upon the recognition of iE-DAP, NOD1 self-oligomerizes in an ATP-dependent fashion and interacts with adaptor molecule receptor-interacting protein 2 (RIP2) for the propagation of innate immune signalling and initiation of pro-inflammatory immune responses. This interaction (mediated by NOD1 and RIP2) helps in transmitting the downstream signals for the activation of NF-κB signalling pathway, and has been arbitrated by respective caspase-recruitment domains (CARDs).

Study of miRNA Based Gene Regulation, Involved in Solid Cancer, by the Assistance of Argonaute Protein.

Solid tumor is generally observed in tissues of epithelial or endothelial cells of lung, breast, prostate, pancreases, colorectal, stomach, and bladder, where several genes transcription is regulated by the microRNAs (miRNAs). Argonaute (AGO) protein is a family of protein which assists in miRNAs to bind with mRNAs of the target genes. Hence, study of the binding mechanism between AGO protein and miRNAs, and also with miRNAs-mRNAs duplex is crucial for understanding the RNA silencing mechanism.

Structural and functional insights into CARDs of zebrafish (Danio rerio) NOD1 and NOD2, and their interaction with adaptor protein RIP2.

Nucleotide-binding and oligomerization domain-containing protein 1 (NOD1) and NOD2 are cytosolic pattern-recognition receptors (PRRs) composed of an N-terminal caspase activation and recruitment domain (CARD), a central NACHT domain and C-terminal leucine-rich repeats (LRRs). They play a vital role in innate immune signaling by activating the NF-κB pathway via recognition of peptidoglycans by LRRs, and ATP-dependent self-oligomerization of NACHT followed by downstream signaling. After oligomerization, CARD/s play a crucial role in activating downstream signaling via the adaptor molecule, RIP2.

Structural models of zebrafish (Danio rerio) NOD1 and NOD2 NACHT domains suggest differential ATP binding orientations: insights from computational modeling, docking and molecular dynamics simulations.

Nucleotide-binding oligomerization domain-containing protein 1 (NOD1) and NOD2 are cytosolic pattern recognition receptors playing pivotal roles in innate immune signaling. NOD1 and NOD2 recognize bacterial peptidoglycan derivatives iE-DAP and MDP, respectively and undergoes conformational alternation and ATP-dependent self-oligomerization of NACHT domain followed by downstream signaling. Lack of structural adequacy of NACHT domain confines our understanding about the NOD-mediated signaling mechanism.

Structural and dynamic investigation of bovine folate receptor alpha (FOLR1), and role of ultra-high temperature processing on conformational and thermodynamic characteristics of FOLR1-folate complex.

The folate receptor alpha (FOLR1) present in milk has widely been studied to investigate the effects of pasteurization, ultra-high temperature (UHT) processing and fermentation on net folate concentration. However, the folate binding mechanism with FOLR1, and effect of temperature on FOLR1-folate complex is poorly explored till now in bovine milk which is a chief resource of folate. Despite of enormous importance of folic acid and the routine intake of bovine milk, folic acid deficiency diseases are common in human race.

Exploration of the binding modes of buffalo PGRP1 receptor complexed with meso-diaminopimelic acid and lysine-type peptidoglycans by molecular dynamics simulation and free energy calculation.

The peptidoglycan recognition proteins (PGRPs) are the key components of innate-immunity, and are highly specific for the recognition of bacterial peptidoglycans (PGN). Among different mammalian PGRPs, the PGRP1 binds to murein PGN of Gram-positive bacteria (lysine-type) and also have bactericidal activity towards Gram-negative bacteria (diaminopimelic acid or Dap-type). Buffaloes are the major sources of milk and meat in Asian sub-continents and are highly exposed to bacterial infections.

Structural insights into the MDP binding and CARD-CARD interaction in zebrafish (Danio rerio) NOD2: a molecular dynamics approach.

Nucleotide binding and oligomerization domain (NOD2) is a key component of innate immunity that is highly specific for muramyl dipeptide (MDP)-a peptidoglycan component of bacterial cell wall. MDP recognition by NOD2-leucine rich repeat (LRR) domain activates NF-κB signaling through a protein-protein interaction between caspase activating and recruitment domains (CARDs) of NOD2 and downstream receptor interacting and activating protein kinase 2 (RIP2). Due to the lack of crystal/NMR structures, MDP recognition and CARD-CARD interaction are poorly understood.