Indian Journal of Biochemistry and Biophysics (IJBB)

DFT-Based Analysis of 2, 3-dimethyl-2-(3-oxobutyl)-cyclohexanone: Structural, Electronic, Vibrational, and Molecular docking studies for potential anti-cancer applications

Tue, 17 Feb 2026 00:00:00 +0530

The antimicrobial, antibacterial, antioxidant, anti-inflammatory, and anticancer activities of C2D3O (2, 3-dimethyl-2-(3-oxobutyl)-cyclohexanone) are demonstrated. Through the use of FT-IR, UV-Vis, and DFT methodologies, this study investigates its medical applications. The B3LYP/6-311++G(d, p) approach was used to examine the molecular electrostatic potential (MEP), HOMO-LUMO, and geometrical characteristics. High stabilization interactions, including hydrogen bonding and charge delocalization, were computed in 3TMH molecules using the NBO 3.1 tool. Both single and double-bond stability was demonstrated by the optimized structure, which was in good agreement with XRD results.A strong correlation was found between theoretical and experimental vibrational frequencies, with electronic transitions (n→π, n→σ transitions**) identified via TD-DFT. The Veda 04 software confirmed an excellent match between observed and predicted FT-IR spectra. Chemical interactions were examined through ELF-LOL projection mapping, while RDG analysis (using Multiwfn 3.4.1) highlighted strong attraction, repulsion, and weak interactions. Finally, molecular docking of C2D3O with 8D59 demonstrated a binding energy of -4.94 kcal/mol, suggesting potential biomedical applications.

Exploring therapeutic potential of repurposed drugs in chagas disease: An integrated network pharmacology and molecular docking approach

Sai Harini S, Shyamala S, Sabishruthi S — Tue, 17 Feb 2026 00:00:00 +0530

Chagas disease, a neglected tropical illness caused by Trypanosoma cruzi characterized by severe inflammatory response and lethal cardiac complications, making traditional chemo-therapeutics inefficient. Through advanced molecular docking techniques and Network pharmacological approach, we screened 20 FDA approved orphan drugs against Chagas disease to identify their possible mechanism of action. Further these targets were validated by reviewing series of case studies conducted in patients with Chagas disease. Initially the 20 FDA approved drugs were subjected to molecular docking against Trypanosoma cruzi glucokinase. Thirteen Promising drugs with strong binding affinity were chosen for pharmacogenomic profiling through network pharmacology analysis to elucidate complex drug-target-disease relationships, potential therapeutic mechanisms and drug re-purposing opportunities. Our integrated methodology revealed that drugs like Belumosudil, Quizartinib, Vomorolone, Voydeya and Zanubritinib are directly involved in pathways related to Chagas disease. Further docking analysis was conducted between these drugs and their respective highly interacting gene. A detailed case report analysis confirmed their role in pathogenesis of T. cruzi infection. Other 8 drugs are found to be indirectly effective by targeting inflammatory pathways of disease progression. This research presents a multifaceted investigation integrating molecular docking, network pharmacology, and clinical case analysis to explore novel therapeutic strategies for managing the disease.

Gut-brain axis modulation of Prosopis juliflora pods: Integrated in silico and in vivo approach for neuroprotective and gut restorative therapeutics

Preyenga R, A Anita Margret, R Gayathri, Sujidha S, Lokeshwaran S — Tue, 17 Feb 2026 00:00:00 +0530

The invasive spread and ecological burden of Prosopis juliflora, especially its adverse effects on groundwater resources, underscore the urgent need for sustainable ways to utilize this species. This study aimed to valorize P. juliflora by exploring the gut health - promoting, metabolic, and therapeutic potential of its pod extracts. The phytochemical constituents of the aqueous pod extract were characterized using Gas Chromatography-Mass Spectrometry (GC-MS) and Fourier Transform Infrared (FTIR) spectroscopy. Network pharmacology software tools were used to identify the therapeutic significance and gene-level interactions of key bioactive compounds. The zebrafish (Danio rerio) model served as an in vivo system to evaluate toxicity and gut restoration effects. Analytical characterization using GC-MS and FTIR confirmed the presence of important phenolic compounds, alkaloids, flavonoids, and glycosides in the extract. Histopathological evaluation revealed a dose-dependent toxic response, mainly associated with phenolic and flavonoid constituents, with a calculated probit LC₅₀ of 15.20 ppm. Network pharmacology analysis revealed strong interactions between the extract’s bioactive compounds and several neuroprotective and gut-related targets, including GPR30, ESR1, and PPARG. These interactions suggest significant therapeutic potential for supporting neurological health and modulating inflammatory bowel conditions. The in vivo findings further underscore the importance of dose optimization to achieve the best therapeutic outcomes with minimal toxicity, indicating the biomedical potential of P. juliflora in treating gut-brain axis related disorders.

A novel in silico approach for identifying defense-related biomarkers from Neurospora crassa during plant associations to understand pathogenicity mechanisms

Tue, 17 Feb 2026 00:00:00 +0530

Neurospora crassa, an ideal eukaryotic model organism, offers key advantages for studying various biological processes. While it is predominantly known for its saprotrophic lifestyle, thriving on dead, decaying organic matter and burnt vegetation, investigations on their pathogenicity potential and the nature of its association with living plants remain largely unexplored and limited. A novel gene analysis pipeline has been proposed for the identification of defense-related biomarkers through an in silico biocomputational approach. GSE34098, a gene expression dataset from the GEO database, has been utilized as a source for our study. Deployment of a customized Python script in this pipeline has enabled gene refinement of 10,926 DEGs and in protein enrichment processes. Comprehensive parametric gene and interactome analyses identified five key proteins as potential biomarkers. These findings are substantiated by scientific literature, which contribute to validating the outcomes of the current study. The implementation of the proposed workflow will help in the identification of key biomolecules of elicitor and effector potential involved in pathogenicity mechanisms. Importantly, insights regarding the potential of the host and the corresponding pathogen’s ability to impact each other can be understood. The knowledge of the same can pave way to improve crop resilience.

Generating an efficient BACE1 inhibitor for the treatment of Alzheimer’s disease based on AI-powered ADMET analysis, Molecular docking and Molecular dynamics studies

Latha V, Gomathi V, Hari Ram S, Vidhyavathi RM, Prabhu D — Tue, 17 Feb 2026 00:00:00 +0530

Alzheimer’s disease (AD) is an early stage of dementia due to neurodegenerative disorder that affects the cognitive functions, memory patterns, and learning skills. BACE1 (beta-site amyloid precursor protein cleaving enzyme 1) is a crucial protein involved in the progression of AD. There are many clinical trials being carried out targeting BACE1 for the treatment of AD. However, they critically face limitations to succeed as approved drugs. Hence, this work is aimed to identify novel BACE1 inhibitors using AI-driven drug development processes. Using WADDAICA tool, 300 similar ligands based on the structural features of Atebecestat, AZD3839, LY2811376 are generated and then ADMET analysis was done. The molecular docking studies with BACE1 protein complexes (PDB ID: 7DCZ, 4B05, 4YBI) were helpful to identify 3 ligands as promising BACE1 inhibitors having low-binding energy, and by conducting 100 ns molecular dynamic simulation study, a minimal fluctuations was demonstrated with the considerable duration. Finally, an efficient BACE1 inhibitor M6 {O=C(N(C1CC1)Cc1cccc(c1)c1cccnc1)
c1cccc(c1)n1nncc1} with good binding affinity, potency (-7.83 Kcal/mol, 1.83 μM), and high BBB permeability for the treatment of AD is sub-selected from the huge volume of chemical spaces, which will be helpful to narrow down the time factor and can pave ways for subsequent in-vitro studies.

Repurposing of statins: An in silico approach aimed at inflammation resolution pathways

Tue, 17 Feb 2026 00:00:00 +0530

The study was performed to evaluate the in silico binding ability of different statins against the enzymes involved in inflammation resolution pathways to enlighten the role of statins in resolution of inflammation and as a goal to repurpose statins as inflammation resolution drugs. The protein structures of four enzymes involved in the synthesis of Specialized Pro Resolving Mediators (SPMs) viz., 12-lipoxygenase (12-LoX), 15-lipoxygenase (15-LoX), 5-lipoxygenase (5-LoX) and Aspirin acetylated cycloxygenase-2 (CoX-2) were retrieved from PDB and were used as receptors. Statins such as Atorvastatin, Simvastatin, Lovastatin, Rosuvastatin, Fluvastatin, Pravastatin and Pitavastatin were used as ligands and their 3D structures were obtained from PubChem database for computational molecular docking. The ligand interaction analysis was performed using AutoDock Vina and Biovia Discovery studio visualizer. The statins showed better binding affinities with 15-LoX and CoX-2 than the other two enzymes, which correlated with the in vivo efficacy of statins as reported earlier. Of all the statins, Pitavastatin and Atorvastatin exhibited better binding interactions with the docked enzymes. Statins are well-known for their cholesterol-lowering effects, but findings from this study suggest they may also be repurposed to promote the resolution of inflammation, which might open-up new possibilities for preventing serious chronic diseases.

Targeting neuroinflammation: Anti-alzheimer’s mechanism of Cassia fistula via in silico approaches

Tue, 17 Feb 2026 00:00:00 +0530

Alzheimer's disease (AD) is a primary factor in neurodegeneration and dementia, with more research linking it to chronic neuroinflammation caused by the excessive activation of intracellular signaling pathways. This study investigates the anti-inflammatory properties of Cassia fistula phytoconstituents on two significant neuroinflammatory targets, SRC kinase and STAT3, using in-silico methodologies. Eleven chemicals identified by LC-MS profiling of methanolic extracts were analyzed using molecular docking utilizing AutoDock Vina v1.2.0. Fucosterol has the highest binding affinity for SRC (-10.3 kcal/mol) and STAT3 (-6.6 kcal/mol). We used Schrödinger's Desmond module to conduct a 100 ns molecular dynamics simulation to assess the stability and interactions of the fucosterol-SRC complex with other molecules. The molecule demonstrated stability in the simulation, exhibiting consistent hydrogen bonding and hydrophobic interactions. Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) free energy simulations indicated favorable binding energetics. A DFT analysis demonstrated the electrical characteristics of fucosterol, highlighting a minimal HOMO-LUMO energy gap and an electrophilic potential. Principal Component Analysis (PCA) of the molecular dynamic’s trajectory demonstrated minimal conformational variations, suggesting structural stability of the bound complex. This comprehensive computational investigation reveals fucosterol derived from Cassia fistula as a prospective natural inhibitor of neuroinflammatory signaling in Alzheimer's disease.

The Impact of genistein on oxidative stress biomarkers in erythrocytes: A study in IPD patients

Nikhila Khola, Kareena Moar, Surekha Dabla, Pawan Kumar Maurya — Tue, 17 Feb 2026 00:00:00 +0530

The pathophysiology of Idiopathic Parkinson’s disease (IPD), a progressive neurodegenerative condition, is extensively affected by oxidative stress. IPD is a multifactorial disease in which oxidative stress damage the systemic cellular system, along with the central nervous system. However, the peripheral biomarkers imbalance and therapeutic responses in IPD remain restricted. In this study, erythrocytes from healthy control and IPD patients were used to evaluate the impact of Genistein on oxidative stress biomarkers. The assessment was conducted on medically appropriate blood samples collected from 95 subjects out of which (n=45) are healthy control and (n=50) are IPD patients. The impact of genistein were assessed against oxidative stress induced by 10mM H₂O₂, evaluated by quantifying the levels of MDA, GSH, SOD and Catalase after co-incubation of erythrocytes with genistein (10^-7M to 10^-5M) and H₂O₂. The outcomes showed elevated MDA levels and SOD activity (P<0.001) and decreased catalase activity and GSH levels (P<0.001) after incubation with H₂O₂. Genistein, when administered in vitro, effectively mitigated oxidative stress-induced damage in red blood cells from all individuals. These findings, validate the present study by providing genistein’s systemic antioxidant effectiveness and reinforcing the significance of erythrocyte-based oxidative indicators in IPD. This study helps to fulfil the gap of growing demand for reliable, non-invasive biomarkers to evaluate the oxidative stress in IPD.

In silico investigation on the effect of p27 phosphorylation in regulating Cdk2/CyclinA complex

Khyati Goswami, Prerana Kalita, Trishna Deka, Venkata Satish Kumar Mattaparthi — Tue, 17 Feb 2026 00:00:00 +0530

p27 is an intrinsically disordered protein which belongs to the Cip/Kip family. It inhibits the cyclin-dependent kinase (Cdk)/cyclin complexes which results in the regulation of cell cycle, during the G1 to S phase transition. Phosphorylation of p27 at specific sites such as Y74, Y88, T187, and P188 may alter its function. In vitro studies showed that phosphorylation of p27 at residues Y74 and Y88 resulted in enhancement of Cdk2 activity. However, the exact molecular details are unknown. This study uses molecular dynamics (MD) simulation and trajectory analyses to study the effect of phosphorylation of p27 at the Y74 and Y88 residues. We carried out MD simulation for 50 ns using AMBER20, and performed root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent-accessible surface area (SASA), and hydrogen bonding analyses. We studied protein-protein interaction using PDBsum server. It has been found that there is an increase in binding affinity of phosphorylated p27 for Cdk2, but it weakens the Cdk2/cyclin A association. We observed shifts in RMSD, RMSF, and hydrogen bonding patterns which shows that there are conformational changes, thus providing insights into the increase in Cdk2 activity and its regulatory role in cell cycle.

Computational modeling for predicting the drug metabolism: A novel approach for developing new drugs and to predict drug interactions

KRS Sambasiva Rao, T Bhanuteja, TE Gopalakrishna Murthy, B Sudheer Chowdary — Tue, 17 Feb 2026 00:00:00 +0530

Drug metabolism (DM) plays the crucial role in the drug therapy and research as it influences the pharmacokinetics (PK), Pharmacodynamic (PD) of the drug, decides the drug’s efficacy and safety and drug interactions (DDIs). An exogenous compound includes the drugs, toxins and other foreign materials undergoes metabolism. The current review represents the computational approaches to predict the drug metabolism in human. This explains the metabolism related aspects for a drug molecule related to the type of enzyme that metabolise, binding sites on the substrate, metabolites formation process and drug-drug interactions. As the usage of multiple drugs containing regimens is increased, the identification and prediction of drug interactions is gaining importance in the personalized medication. The present review also exemplified using a case study by using the propionic derivatives drugs metabolism prediction by using in silico software’s Bio Transformer 3 and AutoDock vina against enzymes Cytochrome P 450 and transferase enzymes. The binding score obtained for the above molecules and enzymes guiding safer and more effective drug design. Finally, based on the study concluded that every drug had their individual enzyme and metabolism process even though they are structurally similar.

CSIR NIScPR — Tue, 17 Feb 2026 00:00:00 +0530

IJBB

Indian Journal of Biochemistry and Biophysics (IJBB)

DFT-Based Analysis of 2, 3-dimethyl-2-(3-oxobutyl)-cyclohexanone: Structural, Electronic, Vibrational, and Molecular docking studies for potential anti-cancer applications

Exploring therapeutic potential of repurposed drugs in chagas disease: An integrated network pharmacology and molecular docking approach

Gut-brain axis modulation of Prosopis juliflora pods: Integrated in silico and in vivo approach for neuroprotective and gut restorative therapeutics

A novel in silico approach for identifying defense-related biomarkers from Neurospora crassa during plant associations to understand pathogenicity mechanisms

Generating an efficient BACE1 inhibitor for the treatment of Alzheimer’s disease based on AI-powered ADMET analysis, Molecular docking and Molecular dynamics studies

Repurposing of statins: An in silico approach aimed at inflammation resolution pathways

Targeting neuroinflammation: Anti-alzheimer’s mechanism of Cassia fistula via in silico approaches

The Impact of genistein on oxidative stress biomarkers in erythrocytes: A study in IPD patients

In silico investigation on the effect of p27 phosphorylation in regulating Cdk2/CyclinA complex

Computational modeling for predicting the drug metabolism: A novel approach for developing new drugs and to predict drug interactions

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