Indian Journal of Biochemistry and Biophysics (IJBB)

Carbon nanotubes a promising new generation drug: A detailed journey in biochemical and biomedical fields

Somnath Garai, Shrabani Samanta, Kirti Patel, Milon Banik — Tue, 21 Oct 2025 00:00:00 +0530

Carbon nanotubes (CNTs), which are well known for their multipurpose uses and their place in nanotechnology have particularly received much attention. The present review paper aims to present a summary of the current state of knowledge regarding carbon nanotubes, their history, architecture, fabrication techniques and uses. CNTs were first discovered in 1991 and have been investigated for application in a broad range of industries because of their remarkable mechanical, electrical and thermal characteristics. The synthesis techniques including arc discharge, chemical vapor deposition, and laser ablation of CNTs have been further developed to optimise the quality and end use of the nanotubes. Moreover, the paper covers the antibacterial and antifungal activities of CNTs, as well as their mechanism of action based on evaluations of bacterial and fungal strains, the physical and chemical nature, and the extremely large surface area of CNTs, which is said to disrupt the cell membrane of microbes. Novelty on the surface modification in the past years has expanded the availability of biomedical application such as drug carriers and antibacterial layer. The review also considers the issues concerning the CNT dispersion and the environmental aspects related to the application of CNTs. This paper highlights the progress that has been made in the field of CNTs and these help to underpin the future of nanotechnology and materials science.

Comprehensive in silico analysis of upstream sequences of TaNRT2 gene family of bread wheat: Unveiling effects of hormonal cross-talk on differential homeolog expressions of TaNRT2.1-6 under low nitrogen conditions

Tue, 21 Oct 2025 00:00:00 +0530

Nitrate is one of the major nitrogen forms available in soil that are crucial for plant growth and development. This study employed multiple bioinformatics tools for a comprehensive In silico analysis of approximately 3 kb upstream regions of all TaNRT2 family genes, which encode members of high-affinity nitrate transporters (HATS) in wheat, retrieved from the Chinese Spring reference genome sequence. The analysis concentrated on identifying Cis-Regulatory Elements (CREs), Transcription Factor Binding Sites (TFBS), evolutionary relationships, tandem repeats, and CpG/CpNpG islands. Furthermore, transcript expression patterns were studied based on CREs of three homeologs of TaNRT2.1-6 in root and shoot tissues at the seedling stage under low nitrate conditions along with Gibberellic acid (GA₃) and Salicylic acid (SA). The sequence analysis of 3 kb upstream sequence revealed varied types and occurrences of Cis-Regulatory Elements and Transcription Factor Binding Sites, predicting variations in nitrate-dependent gene expression. Key TFBS (LBD, GATA, NIN-like, Dof, MYB, NAC, MIKC_MADS, and bZIP), involved in growth regulation under low nitrogen conditions, were identified in all TaNRT2 promoters. The present study provides a detailed analysis of the TaNRT2 gene promoters in wheat, offering insights for designing future studies to understand regulatory mechanisms underlying wheat’s N-responsive growth responses.

Predictive analysis of structural interaction among HIV-1 proteins and Class I MHC molecule: A computational approach for therapeutic target

Ankita Bhaduri, Balaka Biswas, Souymadeep Roy, Mousumi Saha, Agniswar Sarkar — Tue, 21 Oct 2025 00:00:00 +0530

Human immunodeficiency virus type 1 (HIV-1) remains a significant global health challenge because it can impair the host’s immune system and establish long-lasting infections. HIV-1 evades immune detection by modulating major histocompatibility complex class I (MHC-I) molecules, which are essential for presenting viral antigens to cytotoxic T lymphocytes (CTLs). The specific molecular interactions involved in this process remain unclear, which poses a challenge for the advancement of targeted therapies. In this study, we employed a systematic computational approach to explore the structural relationships between selected HIV-1 accessory proteins (nef, tat, rev,vpu) and human MHC-I molecules. Analyses included protein sequences evaluation to identify conserved domains and structural motifs, as well as prediction of secondary structures, transmembrane topology, and 3D-modelling for prediction of potential interaction sites. Structural alignments and molecular docking simulations demonstrated substantial conformational compatibility between HIV-1 proteins and MHC-I molecules, particularly in regions critical for immune modulation. The outcomes of this research provide novel insights into the structural mechanisms that underpin HIV-1-mediated immune evasion. This study identifies protein interfaces and conserved motifs related to MHC-I interference, providing insight for designing antiviral strategies to improve immune recognition and control viral persistence.

Integrating network pharmacology and molecular docking to assess Catharanthus roseus as a natural alternative for leukemia therapy

Tue, 21 Oct 2025 00:00:00 +0530

Leukemia is a cancer caused by abnormal proliferation of leukocyte cells. Conventional treatments, although effective, often cause serious side effects. This study aims to explore the potential of Catharanthus roseus as an alternative therapy for leukemia using network pharmacology and molecular docking approaches. The active compounds of this plant were analyzed and mapped against leukemia biological targets using the PubChem, GeneCards, and KEGG databases. The interaction of compounds with targets was further analyzed through network visualization using Cytoscape and interaction validation was carried out using the molecular docking method using AutoDock4 software. Based on the target search results, 132 targets were found that were relevant to leukemia. PPI analysis showed a relationship between mTOR, HSP90AB1, and MAPK1 proteins with leukemia. Validation of the docking method showed good interaction between active compounds and targets, with an RMSD value of <2 Å. Docking simulations revealed that vindoline has good target binding energies. These results indicate the potential of Catharanthus roseus compounds as leukemia therapies, especially vindoline, which shows optimal interaction with key targets.

Virtual screening of rice phytochemical scaffolds targeting peptide deformylase of Xanthomonas Oryzae pv. Oryzae for the control of bacterial leaf blight

Tue, 21 Oct 2025 00:00:00 +0530

Bacterial leaf blight (BLB) disease of rice, incited by bacterium Xanthomonas Oryzae pv. Oryzae (Xoo) causes huge loss of rice production. For reviving rice production, various bio-hazardous and eco-unfriendly chemical fertilizers, synthetic pesticides and antibiotics have been employed. Thus, the discovery of safe natural pesticides is an effective approach for managing rice BLB disease. In this study, 235 rice phytochemicals were screened to identify most effective bio-pesticide like molecules against Peptide Deformylase of Xoo (XoPDF), which actively participates in the translation process. Through molecular docking and simulation studies, nine potential lead compounds were screened with reference to Actinonin (a known inhibitor). Structural analysis via molecular dynamics suggests better structural stability and binding affinity of XoPDF with the screened leads in relative to Actinonin. Notably, nine leads exhibit structural backbone similarity with the subclass of anthocyanins (natural antibacterial polyphenols) and flavones viz., pelargonin, isorhamnetin, tricin, peonidin, syringetin, cyanidin, chrysoeriol and isoscoparin. In essence, these lead compounds can serve as potential hits for drug design against BLB disease by targeting XoPDF, thereby limiting Xoosurvival and alleviating rice BLB. Since, peptide deformylase (PDF) is found in many other plant pathogens, it can be used as a broad - spectrum disease resistance drug.

Heterocyclic organic compounds extracted from Artemisia judaica (L.) induced caspase-dependent mitochondrial pathway in different breast and liver cancer cell lines: In silico and in vitro studies

Fouzi S Aboud, Majed A Al-Shaeri, Ali T Zari, Ehab MM Ali, Naif Almalki — Tue, 21 Oct 2025 00:00:00 +0530

Oestrogen-dependent cancers, such as breast and liver cancer, depend on oestrogen to develop and grow rapidly. This study evaluated the anticancer activity of extracted heterocyclic compounds from Artemisia judaica (L.) as alternative drug candidates against different oestrogen-sensitive cancer cells. Fresh A. judaica leaves were macerated in 80% ethanol and evaporated using an yellow browncrude extract. Tri-spectroscopy and molecular analytical techniques were used to identify the extracted compounds' bioactive constituents and binding stability. Different normal HSF, and cancer cell lines MCF-7, T47D, MDA-MB-231, and HePG2 were treated with various concentrations of doxorubicin and A. judaica extract for twenty-four h and forty-eight h. The cytotoxic activity of the extracted compounds was evaluated using bio-viability assays. The extracted heterocyclic compounds (benzamide, N-[4-(1H-1,3-benzimidazol-2-yl)-1,2,5-oxadiazol-3-yl] -4-fluoro-, 3-phenyl-6-(4-nitro-phenyl) -4H-(1,2,3) triazole (1,5-d) (1,3,4) oxadiazin-4-one, 2-benzofurancarboxylic acid, 7-methoxy-, (3,4,4-trimethyl-1,2-dioxetan-3-yl) methyl ester, and 2-amino-4,6-diphenyl-pyrimidine) exhibited moderate to well-qualified water solubility, well-binding affinity, and stability with caspase-3, and showed no cytotoxic effects on normal HSF cells with a value of 923.9 ± 5.33 µg/mL and a selectivity index (SI > 2). In contrast, significant inhibition in cell proliferation was observed, particularly in MDA-MB-231 cells with values of 152.7 ± 3.18 µg/mL and 55.18±2.03 µg/mL after 24 and 48 h, respectively, with increased levels of ROS, disruption of MMP that led to increased caspase-3 enzyme, and subsequent induction of cell cycle arrest and apoptosis. We found that atoms such as nitrogen in the extracted heterocyclic compounds made them excellent anticancer medications by targeting DNA and inhibiting oestrogen-sensitive cancer cell progression.

Bioinformatic analysis of cervical cancer-associated hub genes and repurposing of 5-fluorouracil and gemcitabine as potential therapeutic agents

Tue, 21 Oct 2025 00:00:00 +0530

Cervical cancer represents a major health issue worldwide. This study aimed to identify hub genes and signaling pathways associated with cervical cancer, and evaluate the efficacy of FDA-approved drugs against these hub proteins. From the Gene Expression Omnibus (GEO), we identified 239 genes (GSE26511) and 248 genes (GSE41827) that are differentially expressed in cervical cancer, which include 145 genes that are up-regulated and 94 that are down-regulated, along with 174 up-regulated genes and 74 down-regulated genes. By protein-protein interaction network (PPI) indicated 6 key genes for GSE26511 (ID2, FGF2, CLIC4, MED14, NGEF, TCF4) and 6 key genes for GSE41827 (ATF3, BCL2, MAF, MYC, TP53, HMOX). Molecular docking analysis of FDA-approved drugs (5-fluorouracil and gemcitabine) against 12 key proteins revealed potent binding affinities, with ID2 shown binding affinity of -5.2 kcal/mol when interacting with 5-fluorouracil, while CLIC4 shown a binding affinity of -7.2 kcal/mol with gemcitabine, along with 5 hydrogen bonds. Furthermore, MYC exhibit strong binding affinity with both drugs, and TP53 displayed a binding affinity of -5.6 kcal/mol with 5-fluorouracil and gemcitabine with hydrogen bonds. These results indicate that key proteins identified from the study show enhanced binding affinities with FDA-approved drugs, offering insights for targeted therapies in cervical cancer.

Extraction, purification, and bioevaluation of phycoerythrin from Halymenia refugium against pathogenic bacteria and A549 lung cancer cell line

Tue, 21 Oct 2025 00:00:00 +0530

Lung cancer is still among the most frequent cancer-induced deaths, and the traditional and modern treatment options usually lead to severe side effects and lack effectiveness. In this case, the bioactive properties of phycoerythrin (PE), which was extracted in the red alga Halymenia refugium, were evaluated. It was extracted using freeze-thaw method, and subsequently purified via ion-exchange chromatography. Extraction technique yielded 5.36 mg of the pigment / g of the alga. The qualitative analyses revealed the presence of flavonoids (6.91 mg/g) and phenolics (2.29 mg GAE/g). The antioxidant properties of PE exhibited good scavenging of DPPH (91.2%), ABTS (81.5%), and phosphomolybdate (86.15%). PE was able to inhibit α-amylase by 88.30% (IC₅₀ = 30.81 µg/mL) and β-glucosidase by 91.06% (IC₅₀ = 36.34 µg/mL) and defined its anti-diabetic property. anti-inflammatory activity was successfully investigated and confirmed through total protein denaturation (94.09% inhibition, IC₅₀ = 44.62 µg/mL) and egg albumin denaturation (85.57% inhibition, IC₅₀ = 47.31 µg/mL) assays. Phycoerythrin checked the growth of A549cells to 63.95 % at a specified concentration of 75mM.A good inhibition was observed in bacterial antagonism against S. aureus and B. subtilis. These findings suggested that phycoerythrin from H. refugium exhibited strong antioxidant, antidiabetic, anti-inflammatory, antimicrobial, and cytotoxic potential, supporting its development as a natural multifunctional therapeutic agent.

Size-driven fluorescent properties in Nanophotonics

Tue, 21 Oct 2025 00:00:00 +0530

Despite the diverse application of nanotechnology, nanophotonics is still behind the curtains. There's limited insight into how intrinsic and extrinsic factors affects the photonic properties of nanoparticles. In this work, an attempt is made to critique the nature of particles exploiting its micro, nano, and quantum size as intrinsic factors. This fluorescence can be regulated with the aid of extrinsic factors too viz- temperature, pH etc. Ex-vivo study in hepatic tissue portray bioaccumulation as well as enzymatic shifts. Fluorescence decreases with increases in temperature but tends to be constant at 262C for all three sizes and it increases with increases in pH with transition between pH=2 and 4 however, this increase is maximum in Quantum size. Concentration has parabolic gradient in all three sizes. Quantum particles show greater accumulation and effect on peroxidase activity as compared to other sizes. It is concluded that the fluorescence intensity of particles increases with decrease in size. However, its value can be regulated by altering extrinsic factors. Size variations also meet with extent of bioaccumulation. As reduced peroxidase activity indicates compromised antioxidant defence and increased susceptibility to oxidative damage. These studies serve as basis for engineering application of fluorophores regulating their fluorescent properties.

Detection of root-knot nematode disease in cucumber under protected cultivation in Kumaon region

Tue, 21 Oct 2025 00:00:00 +0530

The increasing adoption of protected cultivation in India has led to significant challenges, one of the most serious being the infestation of root-knot nematodes (RKNs), particularly Meloidogyne spp., which threaten sustainable vegetable production. Despite its importance, limited attention has been given to the identification and characterization of RKNs under protected cultivation in hilly regions. Addressing this gap, the present study was undertaken to investigate the RKN populations affecting cucumber crops grown under polyhouse conditions in the Kumaon hills of Uttarakhand, a part of the Indian Himalayan region. A field survey was conducted during 2021–2022 in farmers' polyhouses growing cucumbers. Random sampling was employed by dividing each polyhouse into four units to assess spatial variability in nematode distribution. Integrative taxonomic methods were used, combining symptomatology, morphometric analysis, and molecular identification. Morphological characterization was performed on males, second-stage juveniles (J2), and adult females, with detailed morphometric measurements at various stages. Molecular identification involved amplification and sequencing of the rDNA ITS region. Phylogenetic analysis revealed that the ITS sequence obtained formed a distinct clade, closely related to the Meloidogyne incognita isolate OP030611.1. This study provides the first authentic characterization and report of M. incognita infecting cucumber under protected cultivation in the hilly terrain of Uttarakhand. The findings offer valuable insights into the nematode's occurrence and distribution in the mid-Indian Himalayan region. The study highlights the need for regular surveillance and monitoring of RKN populations to inform integrated nematode management strategies and ensure the sustainability of cucumber production under protected conditions.

CSIR-NIScPR — Tue, 21 Oct 2025 00:00:00 +0530

IJBB

Indian Journal of Biochemistry and Biophysics (IJBB)

Carbon nanotubes a promising new generation drug: A detailed journey in biochemical and biomedical fields

Comprehensive in silico analysis of upstream sequences of TaNRT2 gene family of bread wheat: Unveiling effects of hormonal cross-talk on differential homeolog expressions of TaNRT2.1-6 under low nitrogen conditions

Predictive analysis of structural interaction among HIV-1 proteins and Class I MHC molecule: A computational approach for therapeutic target

Integrating network pharmacology and molecular docking to assess Catharanthus roseus as a natural alternative for leukemia therapy

Virtual screening of rice phytochemical scaffolds targeting peptide deformylase of Xanthomonas Oryzae pv. Oryzae for the control of bacterial leaf blight

Heterocyclic organic compounds extracted from Artemisia judaica (L.) induced caspase-dependent mitochondrial pathway in different breast and liver cancer cell lines: In silico and in vitro studies

Bioinformatic analysis of cervical cancer-associated hub genes and repurposing of 5-fluorouracil and gemcitabine as potential therapeutic agents

Extraction, purification, and bioevaluation of phycoerythrin from Halymenia refugium against pathogenic bacteria and A549 lung cancer cell line

Size-driven fluorescent properties in Nanophotonics

Detection of root-knot nematode disease in cucumber under protected cultivation in Kumaon region

Contents