Indian Journal of Biochemistry & Biophysics
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Item Morphotaxonomy and Genetic diversity of different Oxalis species in Jharkhand, India(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2024-12) Kumari, Sangita; Pathak, Sumit Kumar; Chauhan, Charupriya; Yadav, VKThe present study deals with the genetic diversity and morphological distribution within a population of Oxalis which are commonly grown in Jharkhand. Five species, namely Oxalis corniculata, Oxalis latifolia, Oxalis debilis, Oxalis triangularis (herbaceous plants) , and Averrhoa carambola (a tree species) , have been considered in the present study. The external morphology of Oxalis corniculata includes a trailing stem, rooting at the nodes, and a tap root, while the three herbaceous species are colonial, stoloniferous, and bulbous, lacking upright stems. Genetic diversity was analyzed using AFLP marker (Amplified Fragment Length Polymorphism) , revealing high genetic variation among the species. Results showed that Oxalis latifolia and Oxalis triangularis are closely related, whereas Averrhoa carambola is genetically distinct. This study highlights how genetic diversity and morphological traits are interconnected, providing insights into plant adaptation and evolution. The findings have implications for local biodiversity conservation and management.Item Evaluation of ethanol extract of Morus nigra L. as an inhibitory agent for DNA-Advanced glycation end product (DNA-AGEs)(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2024-02) Akay, Feryal; Toptanc?, Bircan Çeken; ?nceören, Nesrin; K?z?l, Göksel; K?z?l, MuratIn the developing countries there is a direct correlation between the amount of consumed foods containing starch and the increase in metabolic diseases. In contrast to glucose, fructose cannot be detected in the blood by insulin. Thus, it participates in lipogenesis and increases intracellular lipid accumulation.Reducing sugars results in the development of AGEs (Advanced Glycation End-Compounds) in biological macromolecules as well as some reactive products. These products can cause tissue damage by accumulating in the pathogenesis of a number of diseases by various mechanisms.AGEs can damage antioxidant systems by increasing ROS (reactive oxygen species). In this study, pBR322 DNA was incubated with different concentrations of fructose for 5 days. Damage to the structural system of fructosylated DNA was detected by an increase in fluorescence intensity and hyperchromicity. For five days, fructosylated DNA was treated with varying quantities of Morus nigra L. soxhlet extract and quercetin, and its impact on DNA structural damage was noted. The reduction in hyperchromicity and fluorescence intensity revealed the protective impact of quercetin and M. nigra L. extract on DNA. It has been found that the extract of M. nigra L. and quercetin both scavenge free radicals and reduce fructose-induced DNA damage.Item The comprehensive computational study on PE11 gene of Mycobacterium tuberculosis involved in virulence(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2024-02) Nayak, Manas Kumar; Singh, Neha; Dhull, Kanika Singh; Parida, Preetinanda; Mohakud, Nirmal KumarSince its initial discovery more than a decade ago, Mycobacterium tuberculosis has been the subject of significant scientific intrigue. The PE11 gene plays a pivotal role in mediating host-pathogen interactions within Mtb. Despite the fact that a comprehensive understanding of PE11 activities has yet to be achieved, evidence suggests that PE11 proteins play a role at various levels of the infectious process. According to several publications, PE11 (lipX) proteins, unique to pathogenic mycobacteria, are overexpressed during macrophage infection and inactive in TB patients. In this work, bioinformatics analysis was employed to anticipate the involvement of PE11 in mycobacterial virulence. The physicochemical characteristics, conserved domains, and theme of the obtained sequences were utilized to describe them structurally and functionally. Furthermore, homology modeling assisted in determining the 3-D structure and underlying residues in the active site area that interact with mshB and PPE41. Additionally, we reported on further research that may contribute to a more thorough understanding of the PE11 protein and its role in host-pathogen interactions. The findings presented here can be expanded upon and empirically confirmed.Item Rapid genomic DNA extraction for Soybean (Glycine max L. Merr) using modified CTAB protocol to obtain high-quality DNA(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2024-02) Irsyadi, Muhammad Burhanuddin; Sari, Supriyatin Kartika; Oktiastuti, Erlinda; Rineksane, Innaka AgengMolecular and genetic analysis is one of the critical primary stages, starting with DNA extraction. DNA extraction is an essential preliminary step in molecular research. Extracting plant genomic DNA with CTAB buffer takes approximately three days to obtain high-quality DNA. There have yet to be reports regarding effective and efficient soybean genomic DNA extraction methods. This study aimed to obtain a rapid extraction method for soybean with high-quality DNA. This study used a modification of the CTAB method by shortening the duration its stages. The treatments tested were washing soybean leaf and callus organs with ethanol one and two times. The results showed that one-time washing using ethanol absolute obtained the highest average DNA concentrations in leaf and callus organs 458.72 ± 155 ng/?L and 363.87 ± 205 ng/?L, respectively. In addition, DNA purity was obtained 1.99 ± 0.16 and 1.86 ± 0.07, respectively, on A260/280 ratio. Good DNA quality was indicated by the absence of smears on the 1.5% electrophoresis gel. This study demonstrated that extracting plant DNA completed in 70 min to obtain the highest quality DNA.Item In vitro toxicological investigation of Fusarium graminearum toxins in Rattus norvegicus myocardial H9c2 cells(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2024-12) Kalagatur, Naveen Kumar; Nagaraj, Anusuya; Poda, S; Reddy, Salla HemadriMycotoxins are toxic secondary metabolites of fungi that grow on food and feed matrices and significantly harm the health of humans and farm animals. Among the reported mycotoxigenic fungi, Fusarium graminearum has received wide attention due to its ability to produce multiple mycotoxins, including deoxynivalenol (DON), nivalenol (NIV), and zearalenone (ZEA) under diverse climatic conditions. The present study focused on proving in vitro cytotoxicity of F. graminearum toxins (DON, NIV, and ZEA) in H9c2 cells (Rattus norvegicus heart/myocardi). The effect of F. graminearum toxins (FGTs) on cell viability was studied by MTT, LDH, and live/dead cell assays. The cell viability decreased with increasing the quantity of FGTs and was noticed as dose-dependent. The cell viability assays indicated that DON was significantly more toxic than NIV, and both were considerably more toxic than ZEA. The toxicity mechanism of FGTs was revealed by estimating reactive oxygen species (ROS), mitochondrial membrane potential (MMP), and caspase-3 levels. The effect of FGTs on the generation of ROS was observed by fluorescent probe dichloro-dihydro-fluorescein diacetate (DCFH-DA), and the ROS levels were enhanced on the treatment of FGTs. The effect of FGTs on MMP was revealed by rhodamine 123 staining, and MMP levels were depleted with exposure to FGTs. Furthermore, the expression level of caspase-3 was determined by a caspase-3 detection kit, and its levels were enhanced by exposure to FGTs. The studies conclude that FGTs have a potent cytotoxic effect on H9c2 cells and induce death by oxidative stress-mediated apoptosis.Item Stabilization of G-quadruplexes in Intronic Hematopoietic-specific Enhancer of WT1 gene with G-quadruplex targeting ligands: in silico and in vitro techniques(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2024-02) Zidanloo, Saeedeh Ghazaey; Bagherian, ZahraWilms’ tumor 1 (WT1) gene was identified as a tumor-suppressor gene in childhood renal neoplasm, Wilms' tumor, and has an important impact on cell growth and differentiation. So, mutations in WT1 and its over-expression related to not only Wilms’ tumor but also other tumors and leukemias. WT1’s intronic hematopoietic-specific enhancer is GC-rich and could form G-quadruplex structures. Herein, we study the effect of three G-quadruplex stabilizing ligands on the formation and stability of G-quadruplex structures in WT1 intronic hematopoietic-specific enhancer. We designed a truncated sequence of WT1 intronic enhancer (named WT1-I33) with the highest likelihood score of G-quadruplex formation and study the effect of different concentrations of TMPyP4, daunorubicin, and mitoxantrone on G-quadruplex formation in WT1-I33 oligonucleotide using in silico and cell-free assays. The results revealed that WT1-I33 has the potential to form G-quadruplex structures and these structures in WT1 hematopoietic-specific enhancer could be stabilized by the ligands. According to the role of enhancers in transcription, stabilizing of G-quadruplex structures could make the enhancer inaccessible for the transcription factors and transcription of the WT1 gene might be downregulated. These data could help emerge novel gene-specific therapeutic strategies and selective targeting of G-quadruplex structures.Item Molecular docking and dynamics analysis to reveal the therapeutic potential of Dostarlimab against novel immune targets in liver cancer(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2024-11) Pulakuntla, Swetha; Singh, Shri Abhiav; Kuruvalli, Gouthami; Shaik, Althaf Hussain; Reddy, Vaddi DamodaraPD-1/PDL1 pathways in cancer, as a potential ICI. The aim of this study was to use bioinformatics analyses to identify immune targets and assess the efficacy of Dostarlimab against these targets. Specifically, we focused on six immune targets: PDL1, AURKA, MELK, NCAPG, PBK, and RACGAP1. Large-scale gene expression studies were performed to identify potential immune targets. The interaction of Dostarlimab with the six chosen targets was assessed through molecular docking. Protein?protein interaction (PPI) simulations were performed using the ClusPro webserver, and molecular dynamics (MD) simulations were conducted using Desmond software. Our results demonstrated that among the selected immune targets, PDL1, a well-known target, exhibited a relatively weak interaction with Dostarlimab. In contrast, the other five targets (AURKA, MELK, NCAPG, PBK, and RACGAP1) showed robust affinity for Dostarlimab based on molecular docking and dynamic simulations. This study suggested that Dostarlimab, an FDA-approved drug and an inhibitor of PD1/PDL1 immunotherapy, has promising potential for use against a panel of immune targets associated with liver cancer. Although PDL1 is a recognized immune target, our findings suggest that the selected novel immune targets may improve therapeutic outcomes. Clinical studies are warranted to validate these findings and establish the reliability of predictive immune targets for the development of effective ICIs for liver cancer patients.Item Transforming expired medicines into TiO2 nanoparticles(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2024-12) Bhullar, S; Goyal, N; Gupta, SThe study aims to synthesize Titanium Dioxide (TiO2) nanoparticles using expired disprin and paracetamol, exploring an innovative approach to curb the hazards posed by discarded expired medicines thereby reducing drug pollution and improving ecological footprint. The sol-gel method was employed to synthesize TiO2 nanoparticles using expired disprin and paracetamol. Various characterization techniques, such as X-Ray Diffraction (XRD), Energy Dispersive Spectroscopy (EDS), Field Emission Scanning Electron Microscopy (FESEM), Selected Area Electron Diffraction (SAED), and Vibrating Sample Magnetometer (VSM), were used to analyse the synthesized nanoparticles. The XRD and EDS analyses confirmed the formation of TiO2 nanoparticles. The nanoparticles synthesized from both paracetamol and disprin showed a dominant anatase phase with stray peaks of rutile and brookite phases. SAED of paracetamol-derived nanoparticles showed a highly crystalline structure. FESEM confirmed the synthesis of uniformly distributed spherical nanoparticles with size range between 5-20 nm. The size of nanoparticles estimated from both XRD and FESEM appear to be in good agreement. VSM confirmed the diamagnetic nature of both paracetamol and disprin-derived nanoparticles. The study demonstrates that synthesizing TiO2 nanoparticles using expired pharmaceuticals can be a promising approach to mitigate the environmental hazards posed by discarded expired medicines. This novel method has the potential to revolutionize the synthesis of nanoparticles and contribute to a more sustainable future.Item Adaptive evolutionary research of the guanylate binding proteins family(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2024-12) Yixuan, Gao; Jian, Gao; Yuqi, Gao; Xingru, Guo; Meng, An; Limeng, Gu; Jiuxia, XieGuanylate binding proteins (GBPs), encoded by the GBP gene family, are a multi-gene family belonging to the immune system. However, their evolutionary characteristics in ungulates are largely unknown. In this study, we identified 259 sequences of seven GBP genes from the unannotated genomes of 37 ungulate species and performed phylogenetic and selection pressure analyses on the GBP genes using comparative genomics approaches. Phylogenetic analysis indicated that GBP2 and GBP3 genes may have widespread homology. Evolutionary analysis revealed significant purifying selection acting on GBP genes during the evolution of ungulates, indicating a high degree of conservation. The GBP3 gene may play a more important role in antiviral defense. Comparative developmental analysis between even-toed ungulates and odd-toed ungulates showed that several members of the GBP gene family (GBP3, GBP4, GBP5, GBP6, and GBP7) exhibited stronger positive selection pressure in even-toed ungulates. The importance of this study lies in filling knowledge gaps, analyzing evolutionary mechanisms, exploring functional differences, and providing a foundation and guidance for future research in related fields. This study clarifies the phylogenetic and evolutionary characteristics of the GBP gene in ungulates, providing valuable data for further research on the evolutionary characteristics of ungulates.Item Spectroscopic, computational, docking, and cytotoxicity studies on 5-chlorobenzimidazole as a Potent anti-breast cancer agent(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2024-12) Kunjumol, VS; Karthik, N; Sumathi, S; Jeyavijayan, SBenzimidazole derivatives are an important family of drugs because of their biological characteristics and potential for cytotoxicity. In this study, 5-chlorobenzimidazole (5CBZ) computations were performed utilizing the 6-311++G(d,p) basis set and the B3LYP approach. The fundamental frequencies as well as geometric optimization have been determined. The molecule's computed and observed FT-Raman, FTIR, and UV-vis spectra have been compared. Using the charge density distributions that might be correlated to the biological response, the energy gap among HOMO-LUMO and molecule electrostatic potentials has been shown. The overlap population (OPDOS), partial (PDOS), and total (TDOS) densities of states are used to study molecular orbital contributions. Natural Bond Orbital Analysis (NBO) has been utilized to explore numerous inter and intramolecular interactions. Molecular atomic charges have been explored using the Fukui function and Mulliken analysis. The 1H and 13C NMR chemical shifts were calculated with the gauge-independent atomic orbital (GIAO) technique. The likeness of the molecule as drugs has been revealed using molecular docking and ADMET prediction. Further research has been done on the molecule's cytotoxicity and antibacterial properties. Finally, we have identified that the molecule is a favorable pharmacological candidate for anti-breast cancer effects.Item Investigation of cholinergic inhibition by donepezil-rimegepant hybrids in alzheimer’s disease: An in silico study(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2024-12) Asokan, Karthikeyan; Paranthaman, SelvarenganAlzheimer's disease (AD) is a neurodegenerative disorder that causes damage to brain cells, resulting in memory loss, thinking, and executive skills. AD is widely recognized as a most prevalent type of dementia that occurs in elder people. Although few medications like donepezil are available to treat AD, a new and effective drug is the need of the hour. Hence, in the present study, an in silico approach is used to investigate the cholinergic inhibition by donepezil-rimegepant hybrids. Inspired by the structure of donepezil and rimegepant, Donepezil-Rimegepant (DR) hybrids are generated using a hybridization-based design strategy. Their biological activity towards acetylcholinesterase, (AChE) butyrylcholinesterase (BuChE) and amyloid ? (A?) peptides is investigated using computational techniques such as DFT and molecular docking. Our DFT calculations indicate that the DR13 is highly stable than the other hybrids considered in this study. Similarly, our molecular docking study revealed that DR13 has strong interactions with AChE, BuChE, and A? peptide. While considering donepezil and the rimegepant region in DR hybrid, later has strong binding with the protein targets considered in this study. This is due to the presence of two F atoms in the benzyl region of rimegepant. These halogens form strong noncovalent interactions with the amino acid residues in the protein targets. Therefore, based on our in silico studies DR13 is proposed as a good candidate molecule for designing a new drug against AD.Item ADAM8 influences the activity of synovial macrophages and fibroblast-like synoviocytes in osteoarthritis(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2024-12) Wang, Li; Ji, Kewei; Chen, Junfeng; Ou, Guoyi; Yao, Qinglan; Tan, YouguangOsteoarthritis (OA) is the most widely diagnosed form of disabling joint disease, and the polarization of macrophages has been demonstrated to influence OA pathogenesis. The knockdown of ADAM8 (a disintegrin and metalloprotease 8) can suppress OA phenotypes, prompting the present study exploring the potential ability of ADAM8 to regulate fibroblast-like synoviocyte (FLS) phenotypes through its effects on the polarization macrophages, ultimately impacting OA progression. Analyses of protein and mRNA expression were conducted through Western immunoblotting and qPCR, the levels of inflammatory factors were assessed by ELISA. While CCK-8 and lactage dehydrogenase release assays were used to quantify cell proliferation and viability. The migratory and invasive activity of FLS cells was also assessed through wound healing and Transwell approaches. The results revealed that M1 macrophages were found to express high levels of ADAM8, thereby promoting inflammatory cytokine production. Knocking down ADAM8 was sufficient to suppress M1 macrophage polarization, thereby indirectly suppressing FLS proliferative, migratory, and invasive activity.These findings suggest thatADAM8 is a key mediator of OA-related inflammation through its ability to promote pro-inflammatory factor expression within M1 macrophages. ADAM8 was also determined to shape FLS phenotypes through the modulation of the polarization of these macrophages, ultimately influencing the progression of OA.Item Apoptotic effect of antioxidants with silver and titanium dioxide nanoparticles on glioblastoma cancer cells in BALB/C mice(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2024-12) Khojastehkiakola, Sara; Heshmati, Masomeh; Hashemi, Mehrdad; Entezari, MalihehGlioblastoma is one of the most aggressive cancers affecting people globally. Numerous studies have demonstrated that nanoparticles possess potential anti-cancer properties. Nanoparticles have shown promising results in delivering drugs to the brain, although they can have side effects. One possible solution to these issues is the development of nanoparticles combined with antioxidants to improve their efficacy. This study aimed to investigate the impact of curcumin, vitamin C, and vitamin E, in combination with silver and titanium dioxide nanoparticles, on cytotoxicity and their effects on TFAM and miR-455 expression. In this study, the glioma model was induced in female BALB/C mice by implanted Gl261 cells. After two weeks, the animals were sacrificed, and tumor tissue samples were collected to evaluate apoptosis levels using MTT and flow cytometry. In addition, RNA was extracted to examine the expression of Bax, Bcl-2, miR-455, and TFAM genes in the tumor cells. Our study reveals the positive impact of combining vitamin C, vitamin E, and curcumin with Ag and TiO2 NPs on altering Bax and Bcl-2 gene expression, thereby enhancing apoptosis. The data indicated that using nanoparticles in conjunction with antioxidants decreased the levels of TFAM and miR-455, which could potentially reduce the growth of glioma tumor cells. These results suggest that combining antioxidants with Ag and TiO2 nanoparticles can significantly enhance their apoptosis-inducing effects. This combination therapy can prevent metastasis by reducing the expression of miR-455 and TFAM. Overall, this strategy improves glioma cancer therapy by targeting genes involved in tumorigenesis.Item Trace elements as potential biomarkers for oral squamous cell carcinoma(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2024-11) Gadde, Samata; Upadhyayula, Maruthi Kumar; Krishna, Boggula Vamsi; Poda, SOral cancer encompasses a range of tumors affecting the oral cavity, throat, and salivary glands. Oral Squamous Cell Carcinoma (OSCC) is the most common type, particularly in Southeast Asia, where it constitutes one-third of all body cancers. Patients with advanced OSCC generally experience much poorer outcomes compared to those with early-stage disease. This highlights the need for reliable biomarkers to better understand cancer development. Trace elements, crucial for various physiological processes, have been proposed as potential biomarkers for cancer due to their roles in formation and progression. This study investigates changes in serum levels of trace elements—copper, iron, zinc, and magnesium—in patients with OSCC compared to healthy age-matched controls. Conducted in Telangana, the study involved 100 OSCC patients and 100 controls. Methods used for trace element estimation include Ferrozine, DBDC, colorimeter, and calmagite. The study aims to evaluate how individual and combined risk factors, such as smoking, alcohol use, and tobacco chewing, affect trace element concentrations. Results revealed that OSCC patients had significantly higher serum copper levels, while their serum iron, zinc, and magnesium levels were lower. The study also found that combined risk factors had a greater impact on trace element levels than individual risk factors.Item In silico analysis and expression profiling for Resistance Gene Analogues (RGAs) and defence-related genes in early germinating conditions of rice against bakanae disease caused by Fusarium fujikuroi(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2024-11) Thakur, Swagata; Syed, Sharmeen Ekbal; Pandey, Shashi; Sharma, Sapna; S, Gopala Krishnan; Saharan, Mahendra Singh; Bashyal, Bishnu MayaRice is a popular staple food in the world. Rice production is generally affected by many biotic and abiotic stresses. Among the biotic stresses affecting rice, bakanae has emerged as a serious challenge to Indian rice growers. Plant resistance gene analogues (RGAs) are genes with conserved domains and motifs that contribute to host resistance to disease. RGAs are frequently utilized in breeding programs and play a significant role in plant defence. The present study aimed to find out resistance gene analogues (RGAs) and other defence-related genes which might provide resistance to bakanae during the early germination stage of rice. A total of 32 gene IDs were selected from the previously reported transcriptome study of the bakanae-infected resistant and susceptible plants. The protein structures, active domains and biological functions were predicted via bioinformatical analysis. The predicted proteins were identified to possess one or more of the following features - hydrolase activity and carbohydrate metabolism, kinase activity, Rx_N domain, Rx_CC domain, NB-ARC domain, LRR domain, ADP/ATP binding site, and cytochrome site. Representatives of all the highlighted features were selected to prepare a set of 10 genes which were further evaluated for their expression in the inoculated seeds during germination via real-time PCR-based quantification. Four different rice genotypes viz, C101A51, Pusa 1342, PB1, and PB1121 with respective disease reaction types as highly resistant (HR), resistant (R), susceptible (S) and highly susceptible (HS) to bakanae were inoculated with two isolates of F. fujikuroi, F1121 and F1728. Based on the qPCR expression analysis of rice genotypes, RGA 2, RGA 5(b), and RGA 5(c) were found as potential candidate RGAs which might play role in providing resistance against bakanae in the early germination stage. Our study also identified one negative regulator i.e. GDSL esterase in the early stages of interaction due to its constant downregulation in different combinations of host-pathogen interactions. The outcome of this work will support the selection of essential RGAs and defence-related genes in resistance breeding programmes against bakanae disease.Item Computational screening, docking and simulation analysis of phytochemicals from Senna auriculata against multiple targets of Mycobacterium tuberculosis(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2024-11) Karamarathodi, Neeraja; Binukumar, Shreya Manjusha; Das, Subhankar; Sundararajan, Sadhana; Karunakaran, Keerthana; Muniyan, RajinirajaTuberculosis is an infectious disease caused by potential pathogenic bacteria Mycobacterium tuberculosis (Mtb) that causes more than ~1.5 million deaths every year. The reason for its successful infection rate is owed to its resilient, tough mycolic acid-rich cell wall that makes the antibiotics hard to penetrate into the cell and its ability to manipulate the immune system. In addition, drug resistance has become a major concern. For the above-mentioned reasons, incessant attempts are being made to identify novel drug targets and newer natural anti-tubercular drugs to control the spread of TB. In the previous study, ethnobotanically important medicinal plants Trachyspermum copticum and Senna auriculata were evaluated for anti-mycobacterial potential against M. smegmatis. The crude extracts were analyzed in Gas Chromatography-Mass Spectrometry (GC-MS) to identify potential anti-TB compounds. In the current study, a total of 53 phytochemicals identified and mentioned in literature from medicinal plants Trachyspermum copticum and Senna auriculata in addition to the phytochemicals obtained from the GC-MS analysis were subjected to in silico docking evaluation against important drug targets of Mycobacterium tuberculosis. Most targets chosen in the study contribute to cell wall metabolism of Mtb. From the exhaustive docking analysis, lupeol and stigmasterol are identified as potential multitargeted anti-TB compounds and proposed as drug candidates. Molecular dynamic simulation studies revealed stable interaction of stigmasterol with FbiB, MmpL3 and EmbC making it a potential multi-target compound.Item Evaluating the anti-cancer activity of myricetin in the management of oral cancer using in silico analysis(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2024-11) Sinnarkar, Shruti; Kumbhar, Gauri M; S, Ladke Vaibhav; Bhawalkar, Jitendra; Mahajan, JanhaviMyricetin has been examined in various types of human cancer cells. However, there have been very few studies on oral cancer. The aim of this research was to assess Myricetin's anticancer potential in oral cancer using in silico network analysis. The in silico analysis included the determination of drug-likeness prediction, prediction of common targets between oral cancer and myricetin, Protein-Protein Interactions (PPI), hub genes, top 10 associated pathways by Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO), and molecular docking experiments. 22 common genes were obtained and were seen to be involved in the Ras signaling pathway, PI3K-Akt signaling pathway, chemical carcinogenesis-ROS, Pathways in cancer, and microRNAs in cancer. The most common genes involved in the top 10 pathways were AKT1, EGFR, and MET which were seen associated with the PI3K-Akt signaling pathway which may be the key pathway through which myricetin may aid in treating oral cancer. Molecular docking also indicated its drug-like activity against oral cancer having a high affinity for AKT1. According to the findings, myricetin possesses anticancer effects and has the potential to be employed as a chemotherapy medication. The in silico approach applied in this study can serve as a paradigm for future research in the development of effective cancer treatments.Item Repurposing drugs as uS12 ribosomal protein inhibitors to overcome UTI resistance in MDR Pseudomonas strains: In silico and in vitro study(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2024-11) Sharma, Pooja; Tripathi, Abhay Dev; Kalra, Aakanksha; Chouhan, BhartiMultidrug-resistant (MDR) strains of Pseudomonas spp.in UTI (urinary tract infection) present a substantial worldwide health concern, requiring the development of novel approaches to identify alternative therapeutic interventions. This investigation utilizes a computational drug repurposing approach utilizing in silico docking studies to investigate the potential repurposing of 63 currently available non-antibiotic drugs and a control substance, streptomycin, against the uS12 ribosomal protein. The uS12 protein serves as a potential target for inhibiting translation in bacteria, potentially contributing to the mechanism by which streptomycin exerts control. The objective was to identify potential candidates that possess the capability to inhibit essential drug-resistant targets, specifically uS12. Based on our research, the observed binding energy of the control was determined to be -6 kilocalories per mole. Additionally, out of the total 63 samples tested, only 12 were found to exhibit binding energy in the range of -5.8 kilocalories per mole and above. The computational analysis of the pharmacokinetics of the 12 drugs reveals a diverse range of outcomes that support both oral and intravenous administration routes for the gathered drugs. The results of the in vitro minimum inhibitory concentration (MIC) analysis, Rhamnolipid, and Phycocyanin inhibition assays conducted on various strains of Pseudomonas spp. indicated that amlodipine, hydroxychloroquine, 5FU, Indomethacin, ascorbic acid, and calaptin exhibited higher potency compared to other drugs. The MIC values for these drugs ranged from 8.60 to 116.93 µg/mL. The results of this study show potential for expediting drug development using in silico repurposing methods, as well as addressing the urgent issue of antibiotic resistance in Urinary tract infections.Item Evaluation of phenotypic characters and total phenol content in T1 putative transgenic yellow cosmos (Cosmos sulphureus Cav.) with SoSPS1 transgene(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2024-11) Purwantoro, Aziz; Swandari, Tantri; Respatie, Dyah Weny; Sawitri, Widhi Dyah; Murti, Rudi HariIn this study, phenotypic characters and biochemical analysis observed from leaves were carried out to evaluate the T1 population of transgenic cosmos that had inserted SoSPS1 (Sucrose Phosphate Synthase isoform in sugarcane) by floral dip using A. tumefaciens strain GV3101 carrying the recombinant plasmid pRI101AN-SoSPS1 and nptII gene as a selection marker. Sucrose phosphate synthase plays an essential role in sugar accumulation. Furthermore, the gene insertion is prospectively predicted to influence plant growth characteristics and accumulation of biochemical compounds. Information related to the impact of SoSPS1 overexpression on the accumulation of biochemical compounds in yellow cosmos is still relatively rare. The research material is cosmos seeds that have been transformed in previous research. Phenotypic characters according to UPOV descriptors, confirmation of the presence of the SoSPS1 gene, and biochemical analysis (reduction sugar, total sugar, sucrose, total phenol, and chlorophyll a, and b) were observed in the T1 plant population. The results showed the segregation of growth type, stem anthocyanin, branch density, and an increase in the character of internode length (24.64%) and diameter of the stem (12.21%). The chlorophyll content of leaves of transgenic and wild-type plants showed similar levels: increased phenol content (17.52%), reduced sugar (28.77%), and total sugar (14.71%). The higher phenol content in the transgene cosmos can make this plant a suitable resource for possible production of bioherbicide.Item Assessment of quality protein parameters of Zea mays L. through high throughput biochemical analysis(CSIR-National Institute of Science Communication and Policy Research (NIScPR), 2024-10) G, Adinarayana; V, Ratnakar; D, Ramya; S, Vijay; G, Pavan Kumar; P, Sateesh Kumar; Rao, KRS SambasivaMaize is one of the world’s mostly cultivated crops which are consumed by the humans. The quality of maize protein is a vital factor in combating human malnutrition, a problem that is rapidly increasing among children. This study focuses on enhancing maize's protein quality by increasing lysine and tryptophan concentrations while reducing zein content. Seventeen in-house maize lines were analyzed for key biochemical characteristics. Among these, the CML161 line stood out, with a total protein content of 11.831%. The tryptophan and lysine contents in CML161 were 0.68% and 3.3%, respectively. Additionally, the total starch content in CML161 was found to be 37.8%. The endosperm modification test showed 100% opaqueness in the CML161 variety. Based on these findings, it can be concluded that CML161 contains a quality protein content of 5.74%, making it a promising candidate for further studies aimed at addressing malnutrition.