Indian Journal of Biochemistry & Biophysics
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Item Characterization of dry Graphite MWCNT hybrid ECG electrodes and the role of biocompatible surfactants fabrication additive on the bio-signal responses(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2025-06) MD, Manoj; Nanda, Anima; Nayak, BK; Sofi, Mohmmad AshaqThis study involves fabrication of a ‘dry’ electrocardiography (ECG) surface electrode using multi-walled carbon nanotubes (MWCNT) and graphite as solid base substrate. Unlike traditional disposable ‘wet’ gelled Ag/AgCl ECG surface electrodes, which can be uncomfortable and irritating due to their metal-based composition, the proposed electrodes are reusable, non-discomforting, and suitable for long-term cardiac monitoring. Electrophoretic deposition (EPD) technique was utilised to fabricate the Graphite MWCNT hybrid ECG (GCHE) electrodes. To reduce the possible toxicity of dispersants, biocompatible surfactants were employed to disperse the MWCNT on to graphite base material. Analysis was performed to determine the electrochemical properties by using electrochemical impedance spectroscopy (EIS) method and ECG responses for bio-signalling properties. The hybrid structure of electrode ensured signal conductivity, reduced artifacts, and allowed stable bio-signal acquisition. Being all-carbon based ECG surface electrodes offers low toxicity & skin irritation, presenting a promising solution for long-term ECG monitoring and wear ability in healthcare system.Item BMSC-derived exosomes regulate the miR-133b/NLRP3 axis to protect against injury to the spinal cord(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2025-06) Jia, Yijia; Lu, Tingsheng; Yang, Jianwen; Luo, ChunshanSpinal cord injury (SCI) can lead to permanent disability in affected patients. Previous studies have indicated that mesenchymal stem cells (MSCs) hold potential as therapeutic tools for treating SCI, but the specific mechanisms underlying their effectiveness have yet to be determined. This study aimed to evaluate the functional significance of exosomes produced from bone marrow mesenchymal stem cells (BMSCs) in treating SCI, explicitly focusing on the regulatory mechanism involving miR-133b and NLRP3. SCI rats received intravenous tail-vein injections of BMSC exosomes (control or miR-133b exosomes). The spinal tissue levels of miR-133b in SCI rats were determined by qPCR. Hind-limb motor function was assessed using Basso Beattie Bresnahan (BBB) scores and Western blot was utilized for analysis of NLRP3 protein levels. Damage and regeneration of spinal neurons were assessed using Nissl, immunofluorescent staining, and immunohistochemistry. Exosomes were successfully harvested from BMSCs following miR-133b transfection, and acute improvements in SCI recovery were observed following the exosomal delivery of miR-133b, as evidenced by short-term improvements in the survival of neurons and associated functional recovery. These miR-133b-containing exosomes were also able to mitigate neuroinflammatory activity by suppressing astrocyte and microglia activation. MiR-133b, at the molecular level, can decrease the production of NLRP3 mRNA by binding to its 3’-untranslated region. As a result, it inhibits the activation of the NLRP3 inflammasome, which is a crucial factor in the neuroinflammatory activity and neuronal damage associated with SCI. The results presented here provide compelling evidence that exosomes isolated from bone marrow-derived microglia overexpressing miR-133b can, at least partially, mitigate the severity of spinal cord injury by targeting the miR-133b/NLRP3 axis in the acute phase. However, due to the short survival time of the subjects, the long-term effects remain unclear, necessitating further investigation of this treatment approach.Item Virtual screening and molecular dynamic simulation to identify the potent SOX2-inhibiting drugs(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2025-06) Pathivada, Vagdevi Sai; Bandyopadhyay, Anannya; Chhabra, RavindreshSex-determining region of Y-box2 (SOX2) is a master regulator of embryonic and induced pluripotent stem cells. SOX2 is also implicated in epithelial mesenchymal transition (EMT) and chemoresistance of cancer cells. Moreover, SOX2 has been described as a biomarker for cancer stem cells in cervical cancer, sarcoma, ovarian cancer, colorectal cancer, head and neck cancer and glioblastoma. The high expression of SOX2 is also negatively correlated with the overall survival of cancer patients which makes it an attractive target for cancer therapy. The current study was intended to identify SOX2 inhibitors with a high binding affinity. Structure based virtual screening was carried out on approved medications against SOX2 with the help of AutoDock VINA, which is included in the PyRx 0.8 package. The compound with the highest affinity was then examined, and structurally comparable compounds were docked to SOX2 protein once again in order to discover a new and more effective inhibitor molecule against SOX2. The docking analysis revealed apatinib as the most efficient anti-SOX2 drug among the known drug molecules. A structural derivative of apatinib, N-(4-Phenoxyphenyl)-2-[(Pyridin-4-ylmethyl) amino] nicotinamide, was identified as an even more effective inhibitor of SOX2 than apatinib.Item Exploring benzothiazole derivatives: Promising PLK1 Inhibitors for cancer therapy through Virtual screening, Molecular docking, and ADMET evaluation(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2025-06) Patel, Shivkant; Shah, Ashish; Sen, Ashim KumarThe search for effective cancer therapies has driven significant interest in targeting Polo-like kinase 1 (PLK1), a crucial regulator of cell cycle progression, mitosis, epithelial-mesenchymal transition, autophagy, and DNA replication. Over expression of PLK1 is frequently observed in various cancers, making it a promising therapeutic target. Given the need for novel and potent PLK1 inhibitors, this study investigates the benzothiazole-containing drug 5f-203, known for inducing cell cycle arrest, as a potential PLK1 inhibitor. Using the PubChem database, novel PLK1 inhibitors were identified with 5f-203 (clinical trial, Phase 1) as the reference molecule. A comprehensive computational approach, including virtual screening, ligand and protein preparation, grid building, and molecular docking, was employed to evaluate co-crystallized ligand 5f-203, screened molecules, and newly designed compounds (N1-N6). Protein validation using ProSA (-7.9), ERRAT (95.36%), and the Ramachandran plot (84.1% residues in favored regions) confirmed model reliability. Lipinski’s rule was applied as an additional filter, and molecular docking revealed binding affinity values ranging from -8.82 to -7.73 kcal/mol, with molecule P1 exhibiting the highest affinity (-8.82 kcal/mol). Interaction analysis showed that 5f-203 formed H-bonds with Arg120 and NH2, while Ala66, Arg122, and Ile118 contributed to pi-alkyl interactions. Newly designed compounds (N1-N6) outperformed 5f-203 in docking scores, with synthetic accessibility below 4.5. ADMET studies further supported their drug-like potential. These findings suggest that the top 10 screened hits and newly designed benzothiazole derivatives hold promise as PLK1 inhibitors, offering a potential avenue for cancer therapy.Item Benzo (a)pyrene exposure reduces CD54 expression on alveolar macrophages and alters apoptosis and inflammatory responses in the lungs(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2025-06) Chauhan, Pooja; Bhardwaj, Nitin; Rajaura, Sumit; Rambabu; Singh, Ashutosh; Ahmed, Mohd ZThe study investigates the role of intracellular cell adhesion molecule-1 (ICAM-1, CD54) expression in alveolar macrophages and associated molecular alterations in benzo (a)pyrene (BaP)-induced lung tumor-bearing mice that provide more profound insight into immune mechanisms in lung cancer. Lung tumors were induced by administering BaP (50 mg/kg body weight, twice a week for four weeks) orally. A single-alveolar cell suspension was stained with fluorescently conjugated antibodies for the demarcation of alveolar macrophages (F4/80 and CD11b cells). CD54 expression on different alveolar macrophages was analyzed based on CD11b/F4/80 gating. The mortality and cell cycle were studied by 7-AAD and PI staining, respectively, and flow cytometric analysis. Our results suggest that CD54 expression is significantly decreased on CD11b+ alveolar macrophages and CD11b+/F4/80+ interstitial macrophages. BaP treatment increased cell mortality, and cell cycle progression was inhibited. The expression of proapoptotic (BAX and Caspase 3) and antiapoptotic (Bcl-2 and Cytochrome C) genes was reduced, but the expression of proinflammatory (IL-6, IL-10, and TNF-?) and anti-inflammatory (IFN-?) genes was significantly increased, but that of TGF-? was decreased. Overall, BaP-induced tumors suppress CD54 expression on alveolar macrophages, induce cellular mortality, inhibit the cell cycle, and alter the expression of pro-apoptotic, anti-apoptotic, and anti-inflammatory genes in murine lungs.Item Circulating myokines and apelin-13 levels as predictive biomarkers for newly diagnosed type 2 diabetes mellitus(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2025-07) Al-Rubaye, Abdullah Abbas Hamzah; Mohsin, Ahmed A; Jasim, Walaa EsmailType 2 diabetes mellitus (T2DM) is mostly caused by insulin resistance, while insulin sensitivity can be affected by myokines such as myonectin and irisin. In order to manage metabolic disorders, including T2DM, lipid and glucose metabolism must be regulated by apelin-13. The present study was designed to identify the levels of myonectin, irisin, and apelin-13 in prediabetes and recently developed T2DM that may help in the early diagnosis of the disease. The 180 individuals participated in this cross-sectional study. Four millilitres of venous blood were drawn in the morning after fasting for the whole night. Tests were carried out for each participant involving glucose using the glucose oxidase methods, HbA1c using the ion exchange high-performance liquid chromatography (HPLC) technique, insulin using the sandwich-based electrochemiluminescence immunoassay (ECLIA) technique, myonectin, irisin, and apelin-13 using sandwich-based enzyme-linked immunosorbent (ELISA) technique. Notably, the levels of myonectin and apelin-13 were increased gradually in T2DM more than in prediabetes and healthy controls. Conversely, the irisin level was lowered progressively in T2DM than in prediabetes and healthy subjects with statistical variations (P? 0.001) among study groups. This study concluded that the increased levels of myonectin and apelin-13 as well as decreased irisin levels may be considered predictive biomarkers for the early diagnosis of T2DM.Item Pharmacoinformatic based screening of phytochemicals from Ashwagandha (Withania somnifera) against serine/arginine splicing factor 1 protein in treatment of pancreatic cancer(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2025-06) Kabilan, Shanmugampillai Jeyarajaguru; Kavish, SatheeshPancreatic cancer sometimes referred to as pancreatic ductal adenocarcinoma, a disease in which the tissues of the pancreas develop malignant (cancerous) cells. The main objective of this work was to use in silico molecular modeling tools to predict highly efficacious therapeutic molecules from Withania somnifera, a medicinal plant also known as winter cherry or Ashwagandha, to bind promising targets against pancreatic cancer. Thirty four phytocompounds produced from Withania somnifera were identified using the IMPPAT database, and their structures were found in the PubChem database. A putative target protein called Serine/arginine-rich splicing factor 1 (SRSF1) was matched to every phytocompound. Somniferine (–10.4 kcal × mol–1), Physagulin-D (–10.2 kcal × mol–1), and 27-Deoxywithaferin -A (–10.1 kcal × mol–1), the phytocompounds from Withania somnifera with the highest scores, were selected for further examination and compared with the reference drug CID60750 (–6.7 kcal × mol–1). To verify their druggability, a few top-scoring phytocompounds drug-likeness, pharmacokinetic, and toxicological properties were evaluated. These expected results suggest that in the treatment of pancreatic cancer, phytocompounds inhibit the SRSF1 protein. Additional in vitro and in vivo investigations are required to validate the anticipated characteristics of these substances.Item Exploring MHD convective based SWCNT-MWCNT-GO ternary hybrid nanofluids with variable viscosity and exothermic reactions(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2025-07) Chandrakala, P; Rao, V SrinivasaThe increasing demand for efficient thermal management in industrial applications, renewable energy systems, and advanced cooling technologies necessitates the development of high-performance heat transfer fluids. Ternary hybrid nanofluids, which combine multiple nanoparticles, offer a promising solution by enhancing heat and mass transfer properties beyond conventional fluids. This study investigates the convective heat and mass transfer characteristics of ethylene glycol-based ternary hybrid nanofluids composed of graphene oxide (GO), single-walled carbon nanotubes (SWCNTs), and multi-walled carbon nanotubes (MWCNTs) in a cylindrical annulus under non-uniform heat sources. The governing ordinary differential equations (ODEs) are formulated and numerically solved using MATLAB’s Boundary Value Problem solver (BVP4c). Results indicate that increasing the nanoparticle volume fraction (?) enhances the Nusselt number (Nu) by 15% and the Sherwood number (Sh) by 12%, significantly improving heat and mass transport. Additionally, a 20% increase in thermal efficiency is achieved with higher Grashof number (G) and magnetic parameter (M), while viscosity (B) and Eckert number (Ec) negatively impact transfer rates. These findings provide valuable insights for optimizing thermal systems, improving energy efficiency, and reducing operational costs in engineering applications.Item The effects of lipoic acid on rat submandibular salivary gland in valproic acid induced oxidative stress(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2025-06) Alev-Tuzuner, Burcin; Turkyilmaz-Mutlu, Ismet Burcu; Ipekci, Hazal; Ustundag, Unsal Veli; Tunali-Akbay, Tugba; Emekli-Alturfan, Ebru; Akyuz, Serap; Yanardag, Refiye; Yarat, Aysen; Ahmad, SarfrazValproic acid (VA), an anticonvulsant drug, has been associated with various toxic effects, primarily through the induction of oxidative stress. This study aimed to investigate the potential protective role of alpha lipoic acid (LA), a potent antioxidant, against VA-induced oxidative damage in rat submandibular salivary glands. Control, LA, VA, and VA+LA are groups. LA was given 1 h prior to VA administration. After 16 days VA injection, the rats were decapitated, and submandibular salivary glands were taken, homogenized, and examined by biochemical analyses. Biochemical analyses showed that submandibular salivary gland glutathione (GSH) level, superoxide dismutase (SOD) and glutathione-S-transferase (GST) activities decreased; malondialdehyde (MDA), sialic acid (SA) and nitric oxide (NO) levels, tissue factor activity increased significantly in the VA group compared to the control group. No significant changes were found in catalase and myeloperoxidase activities. In the VA group, LA administration caused significant increases in GSH and NO levels; decreases in MDA, SA levels and SOD, GST activities. These findings suggest that LA may offer a protective effect against VA-induced oxidative damage in the salivary glands, potentially through its antioxidant properties. This study highlights the therapeutic potential of LA in mitigating oxidative stress and tissue damage induced by VA.Item Exploring the therapeutic potential of Zonisamide derivatives through molecular docking and dynamic studies with GABARAP(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2025-07) Nambiar, Megha P; Anoop, Anakuthil; AR, BijuComputer based drug designing is an effective tool to shortlist promising drug molecules within short span of time. Designing drugs for neurological disorders is a necessity as it has affected millions of lives. Zonisamide is an effective sulfonamide drug administered to control seizures in epilepsy. This work aims to identify promising Zonisamide derivatives that form more stable complexes with inhibitory neurotransmitter GABARAP. We have designed 32 Zonisamide derivatives. These derivatives were optimised using Gaussian 09 and they were docked to the target GABARAP using PyRx software. The hydrophobic groups substituted at the benzene have lowered the binding energy of Zonisamide in most of the cases. Such derivatives were examined for their drug properties, oral activity and safety using ProTox-II, OSIRIS Property Explorer, and LogBB_Pred servers. The GABARAP residues engaged in the interaction with the derivatives were noted from LigPlot+. The top three derivatives namely Z11 ((6-phenylbenzo[d]isoxazol-3-yl)methanesulfonamide), Z19 (5-(tert-butyl)benzo[d]isoxazol-3-yl) methanesulfonamide, and Z20 (5-phenylbenzo[d]isoxazol-3-yl)methanesulfonamide were finalised and the molecular dynamic simulation of their complexes were carried out using GROMACS 2020. Each of the finalised complexes was analysed for its stability, residue flexibility, compactness, solvent accessible surface area and energy. Among the three derivatives, we propose Z11 as the potential GABARAP modulator.Item GC-MS, DFT, LOL, ELF, NCI-RDG, kinetic energy, reactivity, stability, topological molecular descriptors evaluation on 2-propanone, 1-hydroxy-, Isopropyl alcohol and Glycerin: For NLO application(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2025-06) Dhanalakshmi, E; Rajesh, P; Anbarasu, M; Kandan, P; Raaza, A; Prabhaharan, MThe present article provides spectroscopic technique gas chromatography-mass spectrometry (GC-MS) and density functional theory (DFT) analysis to the examined molecular structure of these three compounds namely 2-Propanone, 1-hydroxy-, Isopropyl alcohol and glycerin synthesis from Hybanthus enneaspermus plant by using green method. The optimized structure of title compounds is obtained by using a hybrid DFT/B3LYP/6-311++G(d, p) approach for stability prediction. Molecular descriptors of natural bond orbital (NBO), highest orbital molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), global reactivity, and Mulliken charge to determine its structural characterization, chemical stability and biological aspects interpreted by the same set. Localized orbital locator (LOL), electron localized function (ELF) has been investigated to understand the localization and delocalization of three molecules. The strong, weak and van dar Waals interactions can identify based on electron densityand were estimated by reduced density gradient (RDG) analysis. The thermodynamic properties of entropy (S), capacity (V) and specific heat have been estimated. The dipole moment (µ) and polarizability (?) have been calculated to predict the nature of 2-propanone, 1-hydroxy- (2PH), isopropyl alcohol (IA) and glycerin (GL) molecules and showed excellent nonlinear optical (NLO) candidates. Moreover, the qualitative structure-activity relationship/qualitative structure-property relationship QSAR/QSPR analysis topological descriptors have a strong correlation with physical properties, which is ideally suitable for drug discovery used to prevent enormous biological activity.Item Unveiling the mitigating effect of matcha-silver nanoparticles on radiation-induced ovarian injury in rats(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2025-07) Khateeb, Sahar; Faridi, Uzma; Obidan, Amnah; Albalawi, Mody; Alwabsi, Hayam A; Almutairi, Fahad M; Alalawy, Adel I; Mohamed, MervatRadiotherapy, an essential cancer treatment, poses significant risks to ovarian tissue, especially during whole-body irradiation treatments. This study aims to evaluate the efficacy of silver nanoparticles derived from matcha green tea (M-AgNPs) inmitigating oxidative stress and apoptosis caused by gamma radiation in rat ovaries. The thirty-six rats were partitioned into six groups. Group 1: control; Group 2: 3; normal rats received matcha and M-AgNPs (10 mL/kg) orally for 14 days respectively; Group 4: rats subjected to 6 Gy whole-body gamma radiation. Groups 5 and 6 of irradiated rats received daily oral administrations of matcha and M-AgNPs (10 mL/kg) for a duration of 14 days, respectively. Biochemical and histological investigations were conducted to evaluate oxidative stress, apoptosis, and ovarian tissue architecture. Radiation significantly (P< 0.05) decreased total antioxidant capacity (TAC) and elevated 8-OHdG levels, indicating oxidative damage. The treatment with M-AgNPs mitigated these effects by reducing the concentration of 8-OHdG and enhancing TAC, thereby restoring antioxidant balance. Furthermore, radiation markedly (P< 0.05) elevated p53 and ERK1 expression levels, whereas M-AgNPs treatment significantly (P< 0.05) diminished p53 and ERK1 expression levels in ovarian tissue. Radiation causes several forms of DNA damage, while the treatment with M-AgNPs mitigated this damage. Histopathological evaluations exhibited considerable improvements in the histological characteristics of ovarian tissue following the administration of M-AgNPs in comparison to irradiated rats. According to these findings, M-AgNPs represent one of the most promising methods for mitigating radiation-induced ovarian damage. Additional work is necessary to clarify particular molecular pathways and their long-term effects.Item Tracing the evolutionary history of novel hormone asprosin: An in silico study across vertebrates(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2025-07) Sathoria, Priyanka; Chuphal, Bhawna; Rajagopalan, Vaishnavi; Kajal; Singh, Arya; Tyagi, Khushi; Singh, Jyoti; Rai, Umesh; Roy, BrototiAlthough, asprosin is implicated in regulation of various physiological functions and metabolic disorders, there are no reports in non-mammalian vertebrates except in fish Channa punctata. Hence, in this study we explore the asprosin across the vertebrate group through in silico analysis. This novel hormone is by product of enzymatic cleavage of profibrillin protein (encoded by FBN1 gene) by furin protease. We have focused on the comparative analysis of physicochemical properties, structure and evolutionary relationship of putative asprosin. The physicochemical properties of putative asprosin across the vertebrate groups revealed thermostability, ex vivo stability and its hydrophilic nature. The secondary and tertiary structures of putative asprosin revealed beta strands that provide the stability and help in folding of protein. The sequence homology of putative asprosin primary sequence reveals more than 50% conservation across the vertebrates. The crucial post-translational modifications such as phosphorylation and glycosylation are present in putative asprosin. Asprosin was observed to be subjected to purifying selection, suggesting limited changes in structure and function of asprosin over extensive evolutionary period. Further, phylogenetic analysis of asprosin showed that bony fishes form a separate clade distinct from mammals, birds, reptiles and amphibians. This study for the first time provides an insight into the conservation of fbn1 encoded profibrillin protein, furin cleavage site in profibrillin protein and its C-terminal cleavage product, asprosin, across the vertebrate groups. The conserved physicochemical properties and strong purifying selection showed that asprosin was under strong evolutionary pressure.Item Investigating the role of phytochemicals from Euphorbia pulcherrima and Ricinus communis in modulating estradiol 17-beta -dehydrogenase 1 activity for breast cancer treatment(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2025-07) Shinde, Prashali; Singh, Gurdeep; Salunke, Mohini; Wakure, Balaji; Kardile, Deepak; Kashid, SnehalCancer, characterized by uncontrollable cell proliferation, poses a significant global health challenge, with breast cancer being one of the most prevalent and lethal forms. Despite advancements in treatment, the rising prevalence and mortality rates underscore the need for innovative therapeutic approaches. This study focuses on the first enzyme of the HSD17B family, specifically the HSD17B1 enzyme, known for its role in estrogen production and its impact on the spread of breast cancer cells. Targeting this enzyme, particularly 17-beta-Hydroxysteroid dehydrogenase type 1 (17-beta-HSD1), presents a promising avenue for treatment. Utilizing molecular docking and molecular dynamics simulations, we investigated the binding potential of phytoconstituents from Euphorbia pulcherrima and Ricinus communis on the Estradiol 17-beta-Dehydrogenase 1 enzyme. The study focuses on compounds such as Rutin, Kaempferol-3-O-Glcoside, Stigmasterol, Beta-sitosterol, and Germanicol.Kaempferol-3-O-Glucoside and Stigmasterol also show potential, emphasizing the importance of specific interactions alongside docking scores. Molecular dynamics simulations reveal varying degrees of stability among the complexes, with Kaempferol-3-O-Glucoside demonstratingstable binding configuration, Stigmasterol showing higher flexibility, and Rutin displaying moderate structural fluctuations. This integrated approach provides a comprehensive understanding ligand-protein interactions, offering valuable insights for the design and optimization of potential therapeutic compounds targeting Estradiol 17-beta-Dehydrogenase in treatment of breast cancer.Item Identification of hub genes in monocyte macrophages of high and low peak bone mass populations and early diagnostic biomarkers for osteoporosis(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2025-07) Xiao, Jing; Ding, Rui; Xu, Zhiyuan; Deng, Zhiwei; Xie, Juntong; Qiu, YiyanOsteoporosis (OP) , a degenerative condition defined by osteopenia, is strongly influenced by peak bone mass (PBM) . However, the early diagnosis of osteoporosis remains incompletely understood. This study aims to identify early diagnostic biomarkers in populations with low PBM and to validate their clinical significance in the diagnosis, treatment, and prevention of osteoporosis. We obtained three microarray datasets (GSE2208, GSE97498, and GSE64433) from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were screened using the limma package. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed. Protein-protein interaction network (PPI) analysis and visualization were conducted with String and Cytoscape. CytoHubba was used to identify hub genes, and relevant miRNAs were predicted using CyTargetLinker in Cytoscape. Finally, the hub genes and predicted miRNA expression were confirmed via RT-qPCR experiments in peripheral blood monocytes of ovariectomy (OVX) mice. We identified 747 DEGs from GSE2208 and 1238 DEGs from GSE97498 and identified 58 overlapping DGEs between these two datasets. The enriched GO terms and pathways were determined, including “TNF signaling pathway, plasma membrane, protease binding, and positive regulation of I-kB kinase/NF-kB signaling.” Ten hub genes (TNF, FN-1, CCR2, HB-EGF, MMP14, NOD2, SOCS3, IFNAR1, IRAK3, PRKACB) were selected from the overlapping DEGs. Additionally, 42 target miRNAs were identified for the ten hub genes using CyTargetLinker. Eight miRNAs were selected after cross-validation with the osteoporosis miRNA expression profiling dataset (GSE64433) . In RT-qPCR experiments, the ten hub genes and eight predicted miRNAs in the blood monocytes of OVX mice were further validated. The study found that the hub genes and predicted miRNAs are potentially linked to OP development and may serve as biomarkers for the early screening of individuals at high risk of OP, thus playing a pivotal role in OP prevention and treatment. This provides a valuable foundation for further experimental studies and clinical applications.Item Identification of potential therapeutic targets of fatty acids for inflammatory bowel diseases: An in silico approach(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2025-07) PV, Thillany; Ediriweera, Meran Keshawa; Madasu, Pavan Kumar; Chandran, ThyageshwarInflammatory bowel diseases (IBD) are chronic disorders of the gastrointestinal tract, often associated with long-term adverse effects from conventional therapies. Here we investigated the potential of a collection of odd- and even-chain fatty acids (FAs) as alternative therapeutic agents for IBD. IBD-associated genes were retrieved from DisGeNET and the Therapeutic Target Database, while the molecular structures of 14 odd-chain and 58 even-chain FAs were obtained from PubChem. ADME profiling was conducted using SwissADME, and target prediction was performed via SwissTargetPrediction and STITCH, followed by interaction network construction using Cytoscape. Gene ontology and KEGG pathway enrichment analyses were carried out using the DAVID bioinformatics tool. The analysis identified pristanic acid, stearic acid, oleic acid and its isomers, and eicosapentaenoic acid as potential candidates for IBD therapy. GO analysis revealed involvement in inflammatory responses and extracellular matrix disassembly, while KEGG pathway analysis indicated significant associations with the TNF, IL-17, HIF-1, and PI3K-Akt signaling pathways, all of which play crucial roles in IBD. These findings were further supported by molecular docking studies that showed strong interactions between the identified FAs and key proteins in these pathways. Overall, the results suggest that fatty acids may modulate signaling pathways relevant to IBD, though further in vitro and in vivo validation is required.Item Understanding the conformational dynamics of an intrinsically disordered protein bound to a small molecule(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2025-07) Sharma, Babli; Mattaparthi, Venkata Satish KumarIntrinsically disordered proteins (IDPs) have been implicated in a wide range of human diseases. Due to their intrinsic conformational variability, IDPs are generally not effective for conventional structure-based drug design. Recently, ZZW-115 has been identified as a promising inhibitor of NUPR1 (an IDP whose overexpression is involved in various cancers), offering a potential lead for the development of novel cancer therapies. Understanding the conformational dynamics is crucial for comprehending the inhibitory action of ZZW-115, revealing the binding modes and dynamic interactions between ZZW-115 and NUPR1. Here, we present a computational study employing atomic-level Molecular dynamics (MD) simulations coupled with Umbrella sampling (US) to investigate the binding of ZZW-115 to NUPR1, elucidating the conformational changes and dynamics involved in the interaction. The Potential of Mean Force (PMF) plot showed a minimum value of 9Å at NUPR1-ZZW-115 separation with a dissociation energy of 2 kcal/mol. From Root Mean Square Deviation (RMSD) and secondary structure analysis, the conformational dynamics of NUPR1 was found to be varied as a function of its centre of mass (CoM) distance from ZZW-115. The NUPR1-ZZW-115 complex with the lowest potential energy extracted from the PMF plot was used to study the conformational dynamics of NUPR1 in unbound and complex form. The study reveals specific residues and binding pockets in NUPR1's disordered region that bind to ZZW-115, providing valuable insights into its inhibitory mechanism, enabling the development of effective drug design for therapeutic purposes.Item Exploring the role of plant associating bacteria as bioinoculants and their beneficial effects in phytostimulation: A Review(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2025-06) Aribindi, Akshay; Upadhyayula, Maruthi Kumar; Boggula, Vamsi Krishna; Vundela, Shwetha ReddyWith an increase in global demand for food without unwanted environmental issues stresses a need for sustainable agriculture. Up till now, conventional agricultural methods focused on obtaining great crop yields from the use of chemical fertilizers but overlooked the hazardous concerns that are leading to soil depletion. These chemical fertilizers adversely affect soil structure, decrease fertility, damage soil flora, and lead to soil erosion. In this scenario, understanding the natural mechanisms of plant-microbe interactions in the rhizospheric environment can potentially lead a way towards eco-friendly agriculture, as the plant associating bacteria prompting phytostimulation can be the key players in unlocking sustainable alternative for conventional fertilizers. Plant growth-promoting bacteria (PGPB) are a distinct class of soil microorganisms that promote plant growth and yields by enhancing nutrient delivery and shielding the plants against diseases. Nitrogen-fixing bacteria such as Rhizobium and Azotobacter, for instance, fix atmospheric nitrogen into a usable form for plants, which minimizes synthetic fertilizers' requirement. Some other PGPB genera such as Pseudomonas and Bacillus induce root and shoot elongation by synthesizing phytohormones. These bacteria also provide protection to plants by synthesizing antimicrobial substances and increasing the competitive nature of the rhizosphere. Bacteria like Azospirillum, Enterobacter, and Flavobacterium also stimulate plant growth by producing phytohormones under specific environmental conditions. Utilization of PGPB as bio-stimulants in agriculture is a promising method for sustainable agriculture, minimizing dependence on chemical fertilizers and maintaining soil health. This approach would play an important role in sustaining a balanced ecosystem along with increasing agricultural productivity.Item Antimicrobial and antibiofilm potential of Morus macroura against Streptococcus pneumoniae(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2025-06) Zomuansangi, Ruth; Singh, Amit; Yadav, Mukesh KumarStreptococcus pneumoniae is a respiratory pathogen that causes infectious disease such pneumonia, Otitis media, meningitis. Despite the availability of pneumococcal conjugated vaccine, the prevalence and infection of bacteria is high due the serotypes not covered in vaccine, antibiotic-resistant strains, and biofilm mode of growth. Therefore, it is essential to continue research for novel antibiofilm agents. Here, we investigated the antimicrobial and antibiofilm potential of Morus macroura extracts against S. pneumoniae. The biofilm biomass was detected by microplate-static model, the viable bacteria were detected by cfu counts, the morphology of biofilm were analyzed using live/dead staining and confocal microscopy, and the bioactive compounds were detected by Gas Chromatography-Mass Spectrometry (GC-MS). The Minimum Inhibitory Concentration of methanolic extract against S. pneumoniae was 256 ?g/mL. At this concentration, the extract inhibited biofilm formation and eradicated 76% of pre-established biofilms. Time-kill experiments and confocal microscopy revealed bactericidal activity and disruption of bacterial cell membranes. The GC-MS analysis identified 25 bioactive compounds in the methanolic extract, with the maximum peak area for Neophytadiene, Linolenic acid methyl ester and phytol. The extract was not cytotoxic towards human nasal epithelial cells. These findings suggest that S. pneumoniae extract contain bioactive compounds that possess antibiofilm/antimicrobial potential, and can be explored to develop new antimicrobial agents.Item Computational, Spectroscopic, Hirshfeld surface, Molecular docking and Topological studies on 2-bromo-5-methylpyridine as potent anti-cancer agent(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2025-07) Kumar, J Senthil; Jyothi, N Siva; Sumathi, S; Karthik, N; Jeyavijayan, S2-Bromo-5-methylpyridine (2BMP) has been found to show FTIR and FT-Raman spectra in the 3500-400 cm-1. The density functional theory (DFT/B3LYP) method was applied to determine the structure, frequencies, Raman activities, and infrared intensities of the molecule using 6-311++G(d,p). The study of molecular orbital contributions has been done with the use of the DOS spectrum. Natural bond orbital (NBO) analysis has been used to calculate the stability of a molecule resulting from hyper-conjugative ???* exchanges and charge delocalisation. Furthermore, the 2BMP's Fukui function, Mulliken charges, and NMR chemical shifts have been examined. Thermodynamic, LOL, and ELF characteristics were investigated topologically in relation to temperature. The binding affinities of breast cancer inhibitors like 1ERE, 1AQU, and 4OAR are found as -5.1, -5.4, and -5.4 Kcal/mol from the docking study. Prescription medications and these affinities are similar. Through ADMET analysis, the degree of drug-likeness in a molecule has been investigated and evaluated.