http://dspace.daffodilvarsity.edu.bd:8080/handle/123456789/6 2026-04-27T00:30:32Z http://dspace.daffodilvarsity.edu.bd:8080/handle/123456789/16182 AMP-RNNpro: a two-stage approach for identification of antimicrobials using probabilistic features Shaon, Md. Shazzad Hossain; Karim, Tasmin; Sultan, Md. Fahim; Ali, Md. Mamun; Ahmed, Kawsar; Hasan, Md. Zahid; Moustafa, Ahmed; Bui, Francis M.; Al-Zahrani, Fahad Ahmed Antimicrobials are molecules that prevent the formation of microorganisms such as bacteria, viruses, fungi, and parasites. The necessity to detect antimicrobial peptides (AMPs) using machine learning and deep learning arises from the need for efficiency to accelerate the discovery of AMPs, and contribute to developing effective antimicrobial therapies, especially in the face of increasing antibiotic resistance. This study introduced AMP-RNNpro based on Recurrent Neural Network (RNN), an innovative model for detecting AMPs, which was designed with eight feature encoding methods that are selected according to four criteria: amino acid compositional, grouped amino acid compositional, autocorrelation, and pseudo-amino acid compositional to represent the protein sequences for efficient identification of AMPs. In our framework, two-stage predictions have been conducted. Initially, this study analyzed 33 models on these feature extractions. Then, we selected the best six models from these models using rigorous performance metrics. In the second stage, probabilistic features have been generated from the selected six models in each feature encoding and they are aggregated to be fed into our final meta-model called AMP-RNNpro. This study also introduced 20 features with SHAP, which are crucial in the drug development fields, where we discover AAC, ASDC, and CKSAAGP features are highly impactful for detection and drug discovery. Our proposed framework, AMP-RNNpro excels in the identification of novel Amps with 97.15% accuracy, 96.48% sensitivity, and 97.87% specificity. We built a user-friendly website for demonstrating the accurate prediction of AMPs based on the proposed approach Review 2024-06-05T00:00:00Z http://dspace.daffodilvarsity.edu.bd:8080/handle/123456789/16181 Ammodaucus Leucotrichus Seed Extract as a Potential Therapy in Animal Models of Rheumatoid Arthritis Induced by Complete Freund Adjuvant and Chicken Cartilage Collagen Djehiche, Cheima; Benzidane, Nadia; Djeghim, Hanene; Tebboub, Mehdi; Mebrek, Saad; Abdelouhab, Katia; Baghiani, Abderrahmane; Charef, Noureddine; Messaoudi, Mohammed; Bensouici, Chawki; Lebsir, Rabah; Emran, Talha Bin; Alsalme, Ali; Cornu, David; Bechelany, Mikhael; Arrar, Lekhmici; Barhoum, Ahmed This study assessed the efficacy of an Ammodaucus leucotrichus seed extract to treat rheumatoid arthritis in rat models of this disease. Rheumatoid arthritis was induced in rats using two methods: immunization with 100 µL of Complete Freund Adjuvant (CFA) and immunization with 100 µL of a 3 mg/ml solution of type II collagen (CII) from chicken cartilage. The therapeutic potential of the extract was assessed at different doses (150, 300, and 600 mg/kg/day for 21 days in the CII-induced arthritis model and for 14 days in the CFA-induced arthritis model) and compared with methotrexate (MTX; 0.2 mg/kg for the same periods), a commonly used drug for rheumatoid arthritis treatment in humans. In both models (CII-induced arthritis and CFA-induced arthritis), walking distance, step length, intra-step distance and footprint area were improved following treatment with the A. leucotrichus seed extract (all concentrations) and MTX compared with untreated animals. Both treatments increased the serum concentration of glutathione and reduced that of complement C3, malondialdehyde and myeloperoxidase. Radiographic data and histological analysis indicated that cartilage destruction was reduced already with the lowest dose of the extract (100 mg/kg/dose) in both models. These results show the substantial antiarthritic potential of the A. leucotrichus seed extract, even at the lowest dose, suggesting that it may be a promising alternative therapy for rheumatoid arthritis and joint inflammation. They also emphasize its efficacy at various doses, providing impetus for more research on this extract as a potential therapeutic agent for arthritis. Review 2024-05-28T00:00:00Z http://dspace.daffodilvarsity.edu.bd:8080/handle/123456789/16180 Mechanistic Review on Therapeutic Potential of Medicinal Plants and their Pharmacologically Active Molecules for Targeting Metabolic Syndrome Gauttam, Vinod Kumar; Munjal, Kavita; Chopra, Hitesh; Ahmad, Aftab; Rana, Mahesh Kumar; Kamal, Mohammad Amjad Metabolic syndrome (MetS) therapy with phytochemicals is an emerging field of study with therapeutic potential. Obesity, insulin resistance, high blood pressure, and abnormal lipid profiles are all components of metabolic syndrome, which is a major public health concern across the world. New research highlights the promise of phytochemicals found in foods, including fruits, vegetables, herbs, and spices, as a sustainable and innovative method of treating this illness. Anti-inflammatory, antioxidant, and insulin-sensitizing qualities are just a few of the many positive impacts shown by bioactive substances. Collectively, they alleviate the hallmark symptoms of metabolic syndrome by modulating critical metabolic pathways, boosting insulin sensitivity, decreasing oxidative stress, and calming chronic low-grade inflammation. In addition, phytochemicals provide a multimodal strategy by targeting not only adipose tissue but also the liver, skeletal muscle, and vascular endothelium, all of which have a role in the pathogenesis of MetS. Increasing evidence suggests that these natural chemicals may be useful in controlling metabolic syndrome as a complementary treatment to standard medication or lifestyle changes. This review article emphasizes the therapeutic potential of phytochemicals, illuminating their varied modes of action and their ability to alleviate the interconnected causes of metabolic syndrome. Phytochemical-based interventions show promise as a novel and sustainable approach to combating the rising global burden of metabolic syndrome, with the ultimate goal of bettering public health and quality of life. Review 2023-12-28T00:00:00Z http://dspace.daffodilvarsity.edu.bd:8080/handle/123456789/16176 Alkaloid-based modulators of the PI3K/Akt/mTOR pathway for cancer therapy: Understandings from pharmacological point of view Mokhfi, Fatima Zohra; Amin, Md Al; Zehravi, Mehrukh; Sweilam, Sherouk Hussein; Arjun, Uppuluri Varuna Naga Venkata; Gupta, Jeetendra Kumar; Vallamkonda, Bhaskar; Balakrishnan, Anitha; Challa, Manjula; Singh, Jyoti; Prasad, P. Dharani; Ali, Syed Salman; Ahmad, Irfan; Doukani, Koula; Emran, Talha Bin This review aims to summarize the role of alkaloids as potential modulators of the PI3K/Akt/mTOR (PAMT) pathway in cancer therapy. The PAMT pathway plays a critical role in cell growth, survival, and metabolism, and its dysregulation contributes to cancer hallmarks. In healthy cells, this pathway is tightly controlled. However, this pathway is frequently dysregulated in cancers and becomes abnormally active. This can happen due to mutations in genes within the pathway itself or due to other factors. This chronic overactivity promotes cancer hallmarks such as uncontrolled cell division, resistance to cell death, and increased blood vessel formation to nourish the tumor. As a result, the PAMT pathway is a crucial therapeutic target for cancer. Researchers are developing drugs that specifically target different components of this pathway, aiming to turn it off and slow cancer progression. Alkaloids, a class of naturally occurring nitrogen-containing molecules found in plants, have emerged as potential therapeutic agents. These alkaloids can target different points within the PAMT pathway, inhibiting its activity and potentially resulting in cancer cell death or suppression of tumor growth. Research is ongoing to explore the role of various alkaloids in cancer treatment. Berberine reduces mTOR activity and increases apoptosis by targeting the PAMT pathway, inhibiting cancer cell proliferation. Lycorine inhibits Akt phosphorylation and mTOR activation, increasing pro-apoptotic protein production and decreasing cell viability. In glioblastoma models, harmine suppresses mTORC1. This review focuses on alkaloids such as evodiamine, hirsuteine, chaetocochin J, indole-3-carbinol, noscapine, berberine, piperlongumine, and so on, which have shown promise in targeting the PAMT pathway. Clinical studies evaluating alkaloids as part of cancer treatment are underway, and their potential impact on patient outcomes is being investigated. In summary, alkaloids represent a promising avenue for targeting the dysregulated PAMT pathway in cancer, and further research is warranted. Review 2024-01-01T00:00:00Z