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  1. Ramadhan DSF, Mahardika RDP, Sukmawaty M, Soe KK, Sim TY, Tang HC, et al.
    Curr Top Med Chem, 2026 Oct 26.
    PMID: 42983184 DOI: 10.2174/0115680266474465260825060836
    INTRODUCTION: An important regulatory aspect of cancer progression is the interaction between p53 and MDM2, particularly in breast cancer, where the excessive presence of MDM2 hampers p53's tumour- suppressing function. Although many natural flavonoids are recognized for their influence on this pathway, they often exhibit suboptimal potency and pharmacokinetic properties. To discover flavonoid derivatives with stronger inhibitory effects on the p53-MDM2 interaction, this research integrates Density Functional Theory (DFT), molecular docking, and AI-enhanced de novo optimization.

    MATERIALS AND METHODS: Validated molecular docking protocols were employed to evaluate 52 flavonoids from the Indonesian Natural Products Database against the p53-MDM2 complex, yielding a validation RMSD value of 0.4935 Å. AI-assisted molecular design was subsequently applied to the top-performing compounds to generate optimized derivatives with improved binding affinity and pharmacokinetic properties. Binding interactions were analyzed using conventional molecular visualization approaches. Drug-likeness, ADME, and toxicity profiles were predicted using SwissADME, ProTox-II, and ADMETlab 2.0. Density Functional Theory (DFT) calculations at the B3LYP/6-31G(d,p) level were performed to evaluate electronic properties and molecular stability. Furthermore, Molecular Dynamics (MD) simulations and MM-GBSA calculations were conducted to investigate the dynamic stability and binding free energy of the selected complexes.

    RESULTS: Among the AI-optimized derivatives, Amentoflavone-1 demonstrated the strongest binding affinity (-5.60 kcal/mol), outperforming Resveratrol (-4.24 kcal/mol). Interaction profiling revealed that hydrophobic interactions and π-π stacking with key residues within the p53-MDM2 binding pocket were the primary stabilizing forces. ADME predictions indicated improved drug-likeness and absorption properties, while toxicity analyses suggested reduced mutagenicity and mitochondrial toxicity, though a moderate hepatotoxicity risk remained. DFT calculations demonstrated favourable HOMO- LUMO energy gaps and frontier molecular orbital characteristics associated with molecular stability and chemical reactivity. Molecular dynamics simulations over 100 ns showed that the p53-MDM2- Amentoflavone-1 complex maintained a stable conformation comparable to the native ligand, as evidenced by RMSD, RMSF, SASA, and radius-of-gyration analyses. In addition, MM-GBSA calculations revealed a binding free energy of -18.37 kcal/mol for Amentoflavone-1, confirming spontaneous and thermodynamically favourable binding to the p53-MDM2 complex.

    DISCUSSION: The integration of AI-driven de novo design with conventional computational modelling successfully enhanced and clarified the pharmacological potential of flavonoid scaffolds. Amentoflavone- 1 exhibited favourable binding interactions consistent with known p53-MDM2 inhibition mechanisms, supported by stable molecular dynamics behaviour and thermodynamically favourable binding profiles. Improvements in ADME and toxicity parameters further suggest that AI-guided structural modification can effectively optimize flavonoid-based inhibitor candidates.

    CONCLUSION: Overall, AI-guided structural optimization improved the binding characteristics, molecular stability, and drug-likeness profile of Amentoflavone-1 relative to its parent compound. Although its binding affinity and MM-GBSA energy remained lower than those of the native ligand, Amentoflavone- 1 demonstrated stable interactions with the p53-MDM2 complex and should be considered a promising preliminary lead compound for further structural refinement and experimental validation.

  2. Wongsa C, Wongyikul P, Chokevittaya P, Nititammaluk A, Soe KK, Phinyo P, et al.
    J Allergy Clin Immunol Glob, 2025 Feb;4(1):100366.
    PMID: 39649686 DOI: 10.1016/j.jacig.2024.100366
    BACKGROUND: Inhaled corticosteroid (ICS)-containing regimens are the mainstay for treating asthma despite usually being ineffective in noneosinophilic asthma (NEA). Data on the prevalence of NEA versus eosinophilic asthma (EA) in mild-to-moderate asthma are limited.

    OBJECTIVE: We performed a systematic review of the prevalence of mild-to-moderate asthma in adolescents and adults using sputum inflammatory cell analysis and their responses to ICS.

    METHODS: We searched electronic databases (PubMed, Scopus, EMBASE, Cochrane) for studies in adolescents and adults with mild-to-moderate asthma. The primary outcome was the prevalence of asthma subtypes based on sputum inflammatory cell analysis, categorized into EA and NEA. The secondary outcome involved comparing asthma outcomes between different subtypes after ICS therapy. Certainty of evidence was reported for each pooled analysis.

    RESULTS: Eighteen studies involving 3,533 adolescents and adults with mild-to-moderate asthma were reviewed. The pooled prevalence (95% confidence interval) of NEA was estimated at 40.39% (27.54, 53.93) in patients with ICS naive with very low certainty of evidence. On reevaluating sputum cytology, the disease of approximately 20% to 30% of patients initially diagnosed as NEA transitioned to the EA subtype. EA patients showed significant improvements in asthma symptoms after ICS therapy: forced expiratory volume in 1 second (standardized mean difference, 0.79; 95% confidence interval, 0.30, 1.27), and airway hyperresponsiveness (standardized mean difference, 1.34; 95% confidence interval, 0.29, 2.40). NEA patients exhibited limited response.

    CONCLUSION: A high proportion of adolescents and adults with mild-to-moderate asthma were identified with NEA subtype disease, which exhibited a poor response to ICS. A thorough diagnostic evaluation before initiating treatment should be integrated into clinical practice.Registered in PROSPERO (CRD42023484334).

  3. Wee AK, Takayama K, Chua JL, Asakawa T, Meenakshisundaram SH, Onrizal, et al.
    BMC Evol. Biol., 2015 Mar 29;15:57.
    PMID: 25888261 DOI: 10.1186/s12862-015-0331-3
    BACKGROUND: Mangrove forests are ecologically important but globally threatened intertidal plant communities. Effective mangrove conservation requires the determination of species identity, management units, and genetic structure. Here, we investigate the genetic distinctiveness and genetic structure of an iconic but yet taxonomically confusing species complex Rhizophora mucronata and R. stylosa across their distributional range, by employing a suite of 20 informative nuclear SSR markers.

    RESULTS: Our results demonstrated the general genetic distinctiveness of R. mucronata and R. stylosa, and potential hybridization or introgression between them. We investigated the population genetics of each species without the putative hybrids, and found strong genetic structure between oceanic regions in both R. mucronata and R. stylosa. In R. mucronata, a strong divergence was detected between populations from the Indian Ocean region (Indian Ocean and Andaman Sea) and the Pacific Ocean region (Malacca Strait, South China Sea and Northwest Pacific Ocean). In R. stylosa, the genetic break was located more eastward, between populations from South and East China Sea and populations from the Southwest Pacific Ocean. The location of these genetic breaks coincided with the boundaries of oceanic currents, thus suggesting that oceanic circulation patterns might have acted as a cryptic barrier to gene flow.

    CONCLUSIONS: Our findings have important implications on the conservation of mangroves, especially relating to replanting efforts and the definition of evolutionary significant units in Rhizophora species. We outlined the genetic structure and identified geographical areas that require further investigations for both R. mucronata and R. stylosa. These results serve as the foundation for the conservation genetics of R. mucronata and R. stylosa and highlighted the need to recognize the genetic distinctiveness of closely-related species, determine their respective genetic structure, and avoid artificially promoting hybridization in mangrove restoration programmes.

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