Ramjan Sheikh

To identify novel bioactive compounds, the methanolic leaf extract of Stevia rebaudiana was investigated for its antibacterial and selective cytotoxic activities using integrated in vitro and in silico approaches. Antibacterial and cytotoxic activities were evaluated using agar well diffusion and MTT assays, respectively. S. rebaudiana phytochemicals were evaluated by docking, ADMET/toxicity prediction, 100 ns MD simulations, and MM/PBSA analysis. The methanolic extract exhibited concentration‐dependent antibacterial activity, with the highest inhibition zone observed against S. rubidaea (22.1 ± 0.13 mm at 150 µg/mL). The extract also showed selective cytotoxicity toward HeLa cells (IC ₅₀ ≈ 7.1 mg/mL), whereas Vero cells retained more than 85% viability at the highest tested concentration. Molecular docking identified glutinol acetate and octamethyl picen‐3‐ol as the most favorable phytochemicals. MD simulations revealed complex stability, and MM/PBSA revealed favorable binding with glutinol acetate exhibiting the strongest binding energy (ΔG_bind ‐24.11 kcal/mol) for its binding to Bcl‐2. ADMET and toxicity analyses revealed some drug‐likeness and toxicity concerns, justifying experimental validation. Overall, methanolic S. rebaudiana leaf extract showed antibacterial activity and preferential cytotoxicity against HeLa cells. The predicted interactions with selected protein targets were favorable for glutinol acetate and octamethyl picen‐3‐ol, and they should be further investigated.

Dihydroorotate dehydrogenase (DHODH) is a mitochondrial enzyme involved in de novo pyrimidine biosynthesis and has emerged as a potential target in cancer metabolism and therapy. This study integrated transcriptomic analysis with structure-based drug discovery to investigate the biological significance and therapeutic potential of DHODH in colorectal cancer (COAD and READ). TCGA-COAD and TCGA-READ RNA-seq data were analyzed for differential expression, clinical association, survival, pathway enrichment, immune infiltration, and therapeutic relevance, with GSE44076 used for external validation. DHODH was significantly elevated in colorectal cancer, while its expression showed limited association with overall survival. Enrichment and immune analyses suggested that DHODH may be associated with immune-related processes and the tumor immune microenvironment. CCLE/DepMap analysis further indicated DHODH dependency in a subset of colorectal cancer cell lines. Structure-based virtual screening identified several promising compounds, including (+)-Luguine, Benzyl 2-[(2-cinnamylidene-3-oxo-1-benzofuran-6-yl)oxy]acetate, 2,3,5-trimethyl-6-(3-(4-methylpiperazin-1-yl)-3-oxopropyl)-7H-furo[3,2-g]chromen-7-one, and N-[2-(4-methylphenyl)ethyl]-2-(2-oxo-1,2-dihydroquinolin-3-yl)acetamide. Molecular docking and 100 ns molecular dynamics simulations supported stable ligand-DHODH interactions. MM/PBSA analysis showed favorable binding free energies ranging from -4.98 to -7.69 kcal/mol, with the DHODH-(+)-Luguine complex exhibiting the most favorable predicted binding energy. ADMET analysis further indicated generally acceptable drug-like and pharmacokinetic properties, although compound-specific toxicity concerns were identified. Overall, DHODH may represent a promising therapeutic target in colorectal cancer, while the identified compounds provide potential candidates for further experimental validation as DHODH inhibitors.

Background: Mesothelin (MSLN) is a cell surface glycoprotein that is often over-expressed in various malignancies of humans and has been suggested as a potential therapeutic and diagnostic target. However, its expression profile, clinical implications and drug-targeting potential are not fully understood and needs to be investigated across various cancer types. Objectives: The goal of this study was to systematically characterize the MSLN expression pattern, its prognostic value and functionality in different types of cancers, particularly in pancreatic adenocarcinoma (PAAD), as well as to identify viable therapeutic target opportunities. Methods: Transcriptomic and clinical datasets from TCGA and GEO were used to evaluate the expression of the MSLN gene, diagnostic value, and its prognostic significance. To study the genomic alterations and functional pathways of MSLN, mutation, GO, and KEGG analyses were used. Drug sensitivity correlations were performed with GDSC and CTRP datasets. Structure-based drug discovery involved molecular docking (AutoDock Vina and Maestro Glide), 100 ns molecular dynamics simulations, and MMPBSA binding free energy analysis, followed by drug-likeness and toxicity assessment using SwissADME and ProTox-III. Results: MSLN was found to be over expressed in several cancers, including PAAD, ovarian and mesothelioma, and this was confirmed in the independent GEO datasets. The analysis of ROC curves showed high accuracy for PAAD and stomach adenocarcinoma and moderate to low accuracy for the other cancers. Both survival and Cox regression analyses showed that MSLN was a cancer-type-specific prognostic factor. Analysis of mutations showed low frequencies of genetic changes, suggesting that the mechanism of dysregulation may be transcriptional or epigenetic. Enrichment analysis highlighted immune-related and tumor-microenvironment signaling pathways associated with MSLN. Drug sensitivity analysis suggested association of MSLN expression with response to targeted and selected chemotherapeutic drugs. Molecular docking revealed Withaferin A as the most potent protein binding compound with MSLN with stable protein-ligand interaction as evidenced by molecular dynamics simulations and binding energy analysis. Conclusion: MSLN is a diagnosis and prognosis biomarker that is context dependent and has application in selected cancers, especially pancreatic adenocarcinoma. While Withaferin A shows promising in silico binding and stability against MSLN, predicted toxicity and pharmacokinetic limitations suggest the need for further optimization and experimental validation before therapeutic application.

Lead (Pb) pollution is a severe environmental condition that inhibits the growth of plants by causing oxidative stress and interference with cellular and molecular functions. Genotypic variation in stress tolerance has been identified in wheat varieties (Triticum aestivum L.), but there has been limited evidence of integrated physiological, biochemical, and transcriptomic responses to Pb. Pb exposure (0-3 mM lead acetate) had significant effect on shoot height and root length in all wheat varieties with root being more sensitive than shoot. The BARI Gom 30 genotype variety showed a relatively higher tolerance with BARI Gom 25 being the most sensitive. The markers of oxidative stress (H₂O₂ and MDA) were increased in a dose-dependent manner, which indicates enhanced cellular damage under Pb stress. The initial increase in antioxidant enzymes (CAT, POD, and APX) occurred at moderate intensity and declined at high concentrations, indicating that defense capacity is broken down at high levels of stress. Transcriptomic analysis of wheat root tissues (GEO accession: GSE235844) identified differentially expressed genes that were related to regulation of oxidative stress, ion transport, protein degradation, and transcriptional control. These molecular responses were correlated with observed physiological and biochemical alterations, which indicate well-coordinated mechanisms of stress-responses. Dataset integration revealed the important pathways that are involved in redox balance and stress adaptation. The physiological, biochemical, and molecular responses involved in Pb toxicity in wheat are interconnected with each other. Genotypic differences in tolerance highlight the importance of genetic factors in stress adaptation. This integrative analysis provides mechanistic insights into Pb stress responses and supports future breeding of heavy metal-tolerant wheat varieties.

Background: Probiotics have attracted much attention recently because of their potential health benefits and aim at correcting the imbalance of gut microbiota. Dairy fermented foods play an important role as a probiotic carrier, and fermented dairy products like dahi are well known for their ability to maintain the viability of bacteria and their acceptance by consumers. Nevertheless, the production of low‐cost, locally manufactured probiotic products that possess antimicrobial activity against food pathogens is relatively scarce. The principal goal of this current study was to isolate a new potential probiotic strain to prepare contamination‐free probiotic dahi in a dosage form with a desired shelf life. Method: To achieve our target, firstly, probiotic dahi was prepared by a probiotic strain, Lactobacillus acidophilus JB2CON (OM909067) (identified by 16S sequencing) isolated from natural dahi in Dhaka, Bangladesh. Probiotic potential was assessed by transmission electron microscopy, acid and bile tolerance, hemolytic activity, antibiotic sensitivity, and antagonistic activity against pathogens, while sensory acceptance of the probiotic dahi was evaluated by 16 participants using a 9‐point hedonic scale. Results: The isolate exhibited five probiotic features by in vitro test and had an antagonistic effect against four different bacterial pathogens and Candida albicans . More interestingly, it inhibited Escherichia coli ( d i a m e t e r of z o n e of i n h i b i t i o n = 15.75 ± 0.35) the most. In the time‐kill analysis method, E. coli was killed within 5.50 h of fermentation. In the antibiotic sensitivity test, the isolated bacterial species exhibited clear inhibition, with ampicillin producing the largest zone (69.33 ± 11.06 mm), followed by tylosin (67.33 ± 6.43 mm). In the acid tolerance test, the probiotic count decreased by ~3.3 log units after 24 h, while bile salt exposure (0.025% and 0.5% oxgall) reduced viable counts in a concentration‐dependent manner. The probiotic dahi prepared in this study was rated as “moderately liked” by 16 participants using a 9‐point hedonic scale. Stability testing identified 14 days as the optimal shelf life, with increased probiotic counts and no adverse effect of minor pH changes on dahi taste. Conclusion: The most significant impact of this research is that the probiotic dahi of our experiment might be used as a cheap option for preventing pathogenic E. coli ‐related foodborne diseases worldwide, especially in underdeveloped countries like Bangladesh.