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. 2024 Mar 26;10(7):e28118.
doi: 10.1016/j.heliyon.2024.e28118. eCollection 2024 Apr 15.

Anti- Staphylococcus aureus potential of compounds from Ganoderma sp.: A comprehensive molecular docking and simulation approaches

Trang Thi Thu Nguyen  1   2 , Trinh Thi Tuyet Nguyen  1   2 , Hoang Duc Nguyen  1   2 , Tan Khanh Nguyen  3 , Phu Tran Vinh Pham  4 , Linh Thuy Thi Tran  5 , Hong Khuyen Thi Pham  6 , Phu Chi Hieu Truong  6 , Linh Thuoc Tran  1   2 , Manh Hung Tran  6
Affiliations

Anti- Staphylococcus aureus potential of compounds from Ganoderma sp.: A comprehensive molecular docking and simulation approaches

Trang Thi Thu Nguyen et al. Heliyon. .

Abstract

In this study, a series of secondary metabolites from Ganoderma sp. were screened against Staphylococcus aureus protein targets, including as phosphotransacetylase, clumping factor A, and dihydrofolate reductase, using molecular docking simulations. The chemicals that showed the strongest binding energy with the targeted proteins were ganodermanontriol, lucidumol B, ganoderic acid J, ergosterol, ergosterol peroxide, 7-oxoganoderic acid Z, ganoderic acid AM1, ganosinoside A, ganoderic acid D, and 24R-ergosta-7,2E-diene-3β,5α,6β-triol. Interestingly, ganosinoside A showed the greatest affinity for the protein clumping factor A, a result validated by molecular dynamic simulation. Additionally, three natural Ganoderma sp. Strains as Ganoderma lingzhi VNKKK1903, Ganoderma lingzhi VNKK1905A2, and Amauroderma subresinosum VNKKK1904 were collected from Kon Ka Kinh National Park in central land of Vietnam and evaluated for their antibacterial activity against Staphylococcus aureus using an agar well diffusion technique. These results suggest that the fungal extracts and secondary metabolites may serve as valuable sources of antibiotics against Staphylococcus aureus. These findings provided an important scientific groundwork for further exploration of the antibacterial mechanisms of compounds derived from Ganoderma sp. in future research.

Keywords: Ganoderma; Molecular docking simulation; Molecular dynamic; Staphylococcus aureus.

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Conflict of interest statement

The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Trang Thi Thu Nguyen reports financial support was provided by PhD Scholarship Programme of the Vingroup Innovation Foundation (VINIF), Vingroup Big Data Institute (VINBIGDATA), code VINIF.2020.TS.68 (TTTN). Trang Thi Thu Nguyen reports financial support was provided by Vietnam National University, Ho Chi Minh City (VNU-HCM) under grant number C2021-18-12.

Figures

Fig. 1
Fig. 1
The 3D structure of (A) dihydrofolate reductase, (B) clumping factor A and (C) Phosphotransacetylase.
Fig. 2
Fig. 2
Ergosterol peroxide and dihydrofolate reductase interaction.
Fig. 3
Fig. 3
Ganosinoside A and clumping factor A interaction.
Fig. 4
Fig. 4
Ganolucidic acid B and phosphotransacetylase interaction.
Fig. 5
Fig. 5
Dynamic simulation between ganosinoside A and clumping factor A for 100 ns. (A) RMSD. (B) RMSF. (C) Number of hydrogen bond.
See this image and copyright information in PMC

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