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J Herbmed Pharmacol. 2025;14(4): 514-523.
doi: 10.34172/jhp.2025.52928
  Abstract View: 18
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Short Communication

Exploring marine natural compounds: In silico investigation of Halimeda tuna natural compounds for PPAR-γ targeting in type 2 diabetes

Aiyi Asnawi 1* ORCID logo, Ellin Febrina 2 ORCID logo, Widhya Aligita 3 ORCID logo, Nina Nurafiani Putri 1 ORCID logo, Anne Yuliantini 1 ORCID logo, Deden Indra Dinata 1 ORCID logo, Hamidah Rahman 4 ORCID logo, Purnawan Pontana Putra 5 ORCID logo

1 Department of Pharmacochemistry, Faculty of Pharmacy, Universitas Bhakti Kencana, Jl. Soekarno-Hatta No. 754, Bandung 40617, Indonesia
2 Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Jl. Raya Bandung-Sumedang km. 21, Jatinangor 45363, Indonesia
3 Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Bhakti Kencana, Jl. Soekarno-Hatta No. 754, Bandung 40617, Indonesia
4 Department of Public Health, Faculty of Health Sciences, Universitas Muhammadiyah Maluku Utara, Jl. KH. Ahmad Dahlan No. 100 Ternate 97719, North Maluku, Indonesia
5 Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Andalas, Padang, 25163, Indonesia
*Corresponding Author: Aiyi Asnawi, Email: aiyi.asnawi@bku.ac.id

Abstract

Introduction: The peroxisome proliferator-activated receptor gamma (PPAR-γ) is a crucial regulator of glucose metabolism and insulin sensitivity, making it a primary target for diabetes therapy. Halimeda tuna, a marine alga, has shown potential as a source of bioactive chemicals with possible anti-diabetic effects. However, there is little information on the particular interactions of H. tuna-derived natural compounds with PPAR-γ. This research aimed to find prospective lead compounds by molecular docking and to evaluate their stability and interaction dynamics with the PPAR-γ using molecular dynamics simulations.

Methods: The natural compounds were downloaded from http://knapsack3d.sakura.ne.jp/, then refined based on Lipinski’s criteria, and optimized for molecular docking. The PPAR-γ macromolecule (PDB ID 1I7I) was also refined to retain only the receptor and its native natural compound (AZ2). Molecular docking was carried out using AutoDock 4.2 to analyze the binding energy and binding mode. To evaluate the stability of the natural compound-receptor complexes, molecular dynamics simulations were conducted for 100 ns using Gromacs 2023.

Results: The molecular docking studies showed that the binding energies for M12 and M7 were -10.77 kcal/mol and -9.91 kcal/mol, respectively. However, when molecular dynamics (MD) simulations were conducted, the total energy values became more negative, with M12 showing -48.25 kcal/mol and M7 -40.13 kcal/mol.

Conclusion: M12 (2-desoxypleniradin-L-|A-arabinopyranoside, 2-acetate) appears to be a promising candidate as a potential PPAR-γ inhibitor for treating type 2 diabetes.


Implication for health policy/practice/research/medical education:

This study demonstrated the potential of discovering anti-diabetic lead compounds from Halimeda tuna, including M12, using molecular docking and their stability and interaction dynamics through molecular dynamics (MD) simulations. The results suggested that these techniques might be useful in identifying promising natural compounds for PPAR-γ, which could serve as lead compounds for T2DM treatment. This highlighted the importance of incorporating computational tools into research practices to accelerate drug discovery, reduce costs, and improve the precision of identifying bioactive molecules. Furthermore, the findings encouraged further exploration of marine bioactive compounds, potentially expanding the scope of natural products in the search for novel therapeutic agents.

Please cite this paper as: Asnawi A, Febrina E, Aligita W, Putri NN, Yuliantini A, Dinata DI, et al. Exploring marine natural compounds: In silico investigation of Halimeda tuna natural compounds for PPAR-γ targeting in type 2 diabetes. J Herbmed Pharmacol. 2025;14(4):514-523. doi: 10.34172/jhp.2025.52928.

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Submitted: 27 Jan 2025
Revision: 26 Jun 2025
Accepted: 16 Jul 2025
ePublished: 01 Oct 2025
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