https://repository.auw.edu.bd/handle/123456789/697 2026-05-15T08:44:24Z 2026-05-15T08:44:24Z Ira, Nabila Ishaque Jaishee, Nishika Saha, Ayan Naidoo, Devashan Islam, Shazneen Tasnim Tani, Tazneen Hossain Roy, Ayan https://repository.auw.edu.bd/handle/123456789/3056 2026-02-18T06:15:16Z 0001-01-01T00:00:00Z

Development of a multi-epitope vaccine candidate against Sindbis virus through integrated immunoinformatics approaches and molecular dynamics simulations Ira, Nabila Ishaque; 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/123456789/3054 2026-02-18T06:15:21Z 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 Saha, Ayan https://repository.auw.edu.bd/handle/123456789/860 2026-02-18T06:15:32Z 2013-01-01T00:00:00Z

A COMPREHENSIVE STUDY ON ANTIOXIDANT, ANTIBACTERIAL, CYTOTOXIC AND PHYTOCHEMICAL PROPERTIES OF AVERRHOA CARAMBOLA Saha, Ayan Experiment was conducted on petroleum ether extract of a bark part of Averrhoa carambola in order to find out various phytochemicals in this plant and to evaluate this plant’s cytotoxicity, ability to impede bacterial growth and ability to work against harmful molecules like free radicals with the help of antioxidants that are present in it. To make sure that the findings are accurate, a number of samples of this plant were collected from different places of Bangladesh. Existence of flavonoid, carbohydrate, glycoside and steroid in the petroleum extract of Averrhoa carambola was confirmed by conducting a phytochemical screening. The disc diffusion method, where ten pathogenic bacteria were used, confirmed that the extract is capable of showing good action against pathogenic organisms. But among these ten bacteria, the extract’s zone of inhibitions were comparatively larger in cases of Salmonella typhi, Pseudomonas aeruginosa, Escherichia coli and Bacillus megaterium, which clearly indicates that the extract is able to exhibit remarkable antibacterial action against these bacteria. The cytotoxic action of the extract was measured by using the Brine Shrimp Lethality Bio-assay method. Using this method, the value of LC50 was calculated as 19.95. The extract’s phenolic content was estimated as 62.504 mg/g GAE, and the amount of flavonoid in it was 24.107 mg/g of quercetin equivalent. A slight increase in the DPPH radical scavenging activity of Averrhoa carambola was observed when the concentration of the extract was enhanced. In comparison to the IC50 value of 11.20μg/mL of ascorbic acid, which was considered as a reference in the test, the IC50 value of the plant extract was estimated as 125.429μg/mL.

2013-01-01T00:00:00Z Saha, Ayan https://repository.auw.edu.bd/handle/123456789/859 2026-02-18T06:15:17Z 2013-01-01T00:00:00Z

Computational analysis of bovine alpha-1 collagen sequences Saha, Ayan Bovine collagen alpha-1 is a naturally occurring extracellular matrix protein found in tendons and other connective tissues. It plays a vital role in cell growth, differentiation, attachment, and migration. Recent findings have established that collagen alpha-1 is involved in osteogenesis imperfecta phenotype in cattle but deep information about other members of this large family is not available so far. So with a view to finding a new edge and attempt to figure out a correlation among the well attributed Bovine alpha-1 collagen sequences are executed and analyzed. To do so, comparative analysis among the 28 members of collagen family has been carried out using Computational tools. Consequently, based on the physico-chemical, secondary structural, functional and phylogenetic classifications, we have selected collagen 12, 14 and 20 as targets for pathological conditions. These proteins belong to the FACIT family and significantly showed low glycine and proline content, high instability and aliphatic index. Moreover, FACIT family collagens contain multiple triple helical domains and being members of the FACIT family, bovine collagen 12, 14, 20 do not form fibrils by themselves but they are associated to collagen 1 associated fibrils. These collagen molecules might be crucial candidates to detect and understand the process of matrix remodeling in diseases especially in the arena of cellular compartments. Collagen is the most abundant family of fibrous proteins in mammals which is secreted by the connective tissue cells [1]. To note about its localization, it is found mostly in flesh and connective tissues in vertebrates [2]. Collagen structure is a triple helix with three different chains and these three alpha chains are wound around one another to form the superhelix structure which gives the long, stiff structure of collagen protein [3]. The amino acids in collagen are arranged in such a manner that glycine is present in every third residue [4]. Glycine is the smallest amino acid and thus fits perfectly in the helix and allows the alpha chains to wrap around together to form the superhelix. Collagen is rich in glycine and proline residues. So, other than glycine in every third residue, the remaining two amino acids are mostly occupied by proline. Pro-collagens are inactive precursors of collagens. During the synthesis of collagen, pro-collagens are synthesized at first. The mature active collagen molecules are formed by the action of peptidases cleaving the pro-peptides at the N and C terminals. Vitamin C acts as a cofactor in conversion of pro-collagens to collagens. Pro-collagens are cleaved only after secretion from the cells by proteolytic enzymes. Pro-collagens are fibrillar molecules which are lot more (about a thousand fold) stable than the collagen fibrils. Cleaving of pro-collagens to collagens inside the cell can lead to catastrophic consequences. Collagen is the most abundant protein of the extracellular matrix (ECM). ECM is an intricate network of macromolecules filling the extracellular space inside the tissues. Other than collagens, ECM is rich in proteoglycans, glycoproteins and proteases [5]. In vertebrates, the main function of ECM is to serve as a scaffold to stabilize the physical structure of tissues.

2013-01-01T00:00:00Z