https://repository.auw.edu.bd/handle/123456789/674 2026-05-09T11:32:39Z 2026-05-09T11:32:39Z Ishaque Ira, Nabila Jaishee, Nishika Saha, Ayan Naidoo, Devashan Islam, Shazneen Tasnim Tani, Tazneen Hossain Roy, Ayan https://repository.auw.edu.bd/handle/123456789/3055 2026-02-18T06:15:32Z 0001-01-01T00:00:00Z

Development of a multi-epitope vaccine candidate against Sindbis virus through integrated immunoinformatics approaches and molecular dynamics simulations Ishaque Ira, Nabila; Jaishee, Nishika; Saha, Ayan; Naidoo, Devashan; Islam, Shazneen Tasnim; Tani, Tazneen Hossain; Roy, Ayan Sindbis virus (SINV), belonging to the genus Alphavirus, is the causative agent of Pogosta disease in humans. The clinical infection is characterized by fever, malaise, rash, myalgia, and arthralgia, which is generally self limiting. Chronic infection with SINV triggers autoimmune conditions that lead to persistent arthritis. Despite its clinical relevance, no licensed vaccine is currently available for the prevention of SINV infection. To the best of our knowledge, this study presents the first in silico design and evaluation of a multi-epitope vaccine candidate against SINV. Using an integrated immunoinformatics framework, the SINV structural polyprotein was sys tematically screened, leading to the identification of twelve highly antigenic immunological hotspots, derived from both experimentally validated and computationally predicted B-cell and T-cell epitopes. These epitopes were rationally assembled into a 317–amino acid multi-epitope vaccine construct using suitable linkers and the human β-defensin 2 as an immunostimulatory adjuvant. The designed construct exhibited favorable antigenicity, non-toxicity, stability, and physicochemical properties. Molecular docking and molecular dynamics simulations demonstrated encouraging interactions between the vaccine construct and innate immune receptors TLR-2 and TLR-4, highlighting its potential to trigger immune responses. Immune simulation predicted robust humoral and cell-mediated immune responses, while codon optimization and in silico cloning into the pETite vector indicated expression feasibility in Escherichia coli K12. This work proposes a novel immunoinformatics and molecular dynamics–based vaccine design pipeline for Sindbis virus and presents a computationally validated multi-epitope vaccine candidate, providing a foundation for future experimental validation toward effective vaccine development.

0001-01-01T00:00:00Z Sharmin Hossain, Nanziba Tasnim, Nishat Ferdoush, Jannatul Roy, Ayan Saha, Suvash C. Saha, Ayan https://repository.auw.edu.bd/handle/123456789/3052 2026-02-18T06:15:14Z 0001-01-01T00:00:00Z

Next-generation lung-cancer-on a-chip: toward personalized therapy, AI, and CRISPR-driven models Sharmin Hossain, Nanziba; Tasnim, Nishat; Ferdoush, Jannatul; Roy, Ayan; Saha, Suvash C.; Saha, Ayan

0001-01-01T00:00:00Z Roy, Ayan https://repository.auw.edu.bd/handle/123456789/833 2026-02-18T06:15:22Z 2024-01-01T00:00:00Z

South African Journal of Botany Roy, Ayan Type 2 Diabetes Mellitus (T2DM) is a chronic metabolic dysfunction characterized by hyperglycemia. T2DM is a growing global epidemic with diffuse complications, including a high mortality rate. High blood sugar can be lowered by impeding the activities of pancreatic a-amylase and intestinal a-glucosidase enzymes. Although there are a number of orthodox medications used in the management of hyperglycemia, medicinal plants remain a veritable option in many cultures of the world owing to their overall efficacy and affordabil- ity. This study was designed to investigate the hypoglycemic potential of Syzygium cordatum leaf extract frac- tions in the retardation of pancreatic a-amylase and intestinal a-glucosidase enzymes in vitro. The bioactive components of the active fractions were identified using the Gas Chromatography-Mass Spectrometry (GC- MS) and their potential hypoglycemic properties were assessed using the molecular in silico modelling approach. The in vitro a-amylase and a-glucosidase inhibitory activities of S. cordatum revealed that the organic solvent fractions retarded the digestive enzymes considerably although the standard drug (acarbose) had the least half-maximal inhibitory concentration (IC50) value. Analytical and computational analysis iden- tified the potential of cubenol, to interact with important residues of a-glucosidase and a-amylase emphasiz- ing its hypoglycemic potential. The result of this study revealed that S. cordatum is a rich source of pharmacologically important bioactive compounds with a remarkable capacity to retard a-amylase and a-glucosidase enzymes. Cubenol was identified as an efficient and safe hypoglycemic agent of S. cordatum.

2024-01-01T00:00:00Z Roy, Ayan https://repository.auw.edu.bd/handle/123456789/826 2026-02-18T06:15:29Z 2024-01-01T00:00:00Z

Computational Insights into Captopril’s Inhibitory Potential Against MMP9 and LCN2 in Bladder Cancer: Implications for Therapeutic Application Roy, Ayan Objectives: Captopril is a commonly used therapeutic agent in the management of renovascular hypertension (high blood pressure), congestive heart failure, left ventricular dysfunction following myocardial infarction, and nephropathy. Captopril has been found to interact with proteins that are significantly associated with bladder cancer (BLCA), suggesting that it could be a potential medication for BLCA patients with concurrent hypertension. Methods: DrugBank 5.0 was utilized to identify the direct protein targets (DPTs) of captopril. STRING was used to analyze the multiple protein interactions. TNMPlot was used for comparing gene expression in normal, tumor, and metastatic tissue. Then, docking with target proteins was done using Autodock. Molecular dynamics simulations were applied for estimate the diffusion coefficients and mean-square displacements in materials. Results: Among all these proteins, MMP9 is observed to be an overexpressed gene in BLCA and its increased expression is linked to reduced survival in patients. Our findings indicate that captopril effectively inhibits both the wild type and common mutated forms of MMP9 in BLCA. Furthermore, the LCN2 gene, which is also overexpressed in BLCA, interacts with captopril-associated proteins. The overexpres- sion of LCN2 is similarly associated with reduced survival in BLCA. Through molecular docking analysis, we have identified specific amino acid residues (Tyr179, Pro421, Tyr423, and Lys603) at the active pocket of MMP9, as well as Tyr78, Tyr106, Phe145, Lys147, and Lys156 at the active pocket of LCN2, with which captopril interacts. Thus, our data provide compelling evidence for the inhibitory potential of captopril against human proteins MMP9 and LCN2, both of which play crucial roles in BLCA. Conclusion: These discoveries present promising prospects for conducting subsequent validation studies both in vitro and in vivo, with the aim of assessing the suitability of captopril for treating BLCA patients, irrespective of their hypertension status, who exhibit elevated lev- els of MMP9 and LCN2 expression.

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