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  1. Dash R, Das R, Junaid M, Akash MF, Islam A, Hosen SZ
    Adv Appl Bioinform Chem, 2017;10:11-28.
    PMID: 28356762 DOI: 10.2147/AABC.S115859
    Ebola virus (EBOV) is one of the lethal viruses, causing more than 24 epidemic outbreaks to date. Despite having available molecular knowledge of this virus, no definite vaccine or other remedial agents have been developed yet for the management and avoidance of EBOV infections in humans. Disclosing this, the present study described an epitope-based peptide vaccine against EBOV, using a combination of B-cell and T-cell epitope predictions, followed by molecular docking and molecular dynamics simulation approach. Here, protein sequences of all glycoproteins of EBOV were collected and examined via in silico methods to determine the most immunogenic protein. From the identified antigenic protein, the peptide region ranging from 186 to 220 and the sequence HKEGAFFLY from the positions of 154-162 were considered the most potential B-cell and T-cell epitopes, correspondingly. Moreover, this peptide (HKEGAFFLY) interacted with HLA-A*32:15 with the highest binding energy and stability, and also a good conservancy of 83.85% with maximum population coverage. The results imply that the designed epitopes could manifest vigorous enduring defensive immunity against EBOV.
  2. Seder N, Abu Bakar MH, Abu Rayyan WS
    PMID: 33488102 DOI: 10.2147/AABC.S292143
    Introduction: Malaysian stingless bee honey (Trigona) has been aroused as a potential antimicrobial compound with antibiofilm activity. The capability of the gram-negative bacillus P. aeruginosa to sustain a fatal infection is encoded in the bacterium genome.

    Methods: In the current study, a transcriptome investigation was performed to explore the mechanism underlying the biofilm dispersal of P. aeruginosa after the exposure to Trigona honey.

    Results: Microarray analysis of the Pseudomonas biofilm treated by 20% Trigona honey has revealed a down-regulation of 3478 genes among the 6085 screened genes. Specifically, around 13.5% of the down-regulated genes were biofilm-associated genes. The mapping of the biofilm-associated pathways has shown an ultimate decrease in the expression levels of the D-GMP signaling pathway and diguanylate cyclases (DGCs) genes responsible for c-di-GMP formation.

    Conclusion: We predominantly report the lowering of c-di-GMP through the down-regulation of DGC genes as the main mechanism of biofilm inhibition by Trigona honey.

  3. Permana A, Akili AWR, Hardianto A, Latip JB, Sulaeman AP, Herlina T
    Adv Appl Bioinform Chem, 2024;17:179-201.
    PMID: 39931375 DOI: 10.2147/AABC.S495947
    PURPOSE: Alzheimer's disease (AD) is a progressive neurodegenerative disorder with limited treatment options, necessitating the development of safer and more effective therapies. The potential of alkaloids derived from the genus Erythrina as acetylcholinesterase (AChE) inhibitors is being investigated to enhance acetylcholine levels in the brain, which is crucial for the treatment of AD. The objective of this study is to identify Erythrina alkaloids with strong inhibitory capacity against AChE and favorable pharmacokinetic profiles.

    MATERIALS AND METHODS: A multi-step computational approach was employed, beginning with the virtual screening of 143 Erythrina alkaloid structures using molecular docking against the human AChE crystal structure. The binding affinities were compared with the known AChE inhibitor, galantamine. The top alkaloid, 8-oxoerymelanthine (128), was subjected to further analysis through molecular dynamics simulations, with the objective of evaluating its stability and interactions. In silico ADMET predictions were conducted to assess the pharmacokinetic properties. The applicability of Lipinski's Rule of Five was applied to evaluate oral drug-likeness.

    RESULTS: 8-Oxoerymelanthine (128) exhibited the highest binding affinity and remarkable stability in molecular dynamics simulations. The toxicity predictions indicated a low risk of mutagenicity, hepatotoxicity, and cardiotoxicity. Pharmacokinetic assessments indicated good absorption, moderate blood-brain barrier penetration, and favorable metabolic and excretion profiles, supporting its potential as an orally active drug candidate.

    CONCLUSION: 8-Oxoerythmelanthine (128) exhibits strong potential as an AChE inhibitor with a favorable balance of efficacy, safety, and pharmacokinetic properties. These results warrant further investigation in preclinical and clinical studies to validate its therapeutic potential and safety for Alzheimer's disease treatment.

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