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<p><i>Dendrobium crumenatum</i> grows extensively in Indonesia, with certain specimens preserved in nature conservation areas such as the Bogor Botanical Gardens (BBG) and the Ujung Kulon National Park (UKNP). Nevertheless, its abundance is frequently underutilized. This study investigated the metabolite profiles of <i>D. crumenatum</i> (leaf and stem) preserved in BBG and UKNP based on untargeted metabolomics of UHPLC-HRMS. The samples were classified using Principal Component Analysis (PCA), Variable Importance in Projection (VIP), heatmap, K-means, and correlation network plots. The <i>D. crumenatum</i> samples were further evaluated for their antioxidant and antibacterial activities, and the mechanism was predicted through molecular docking targeting specific enzymatic processes in pathogenic bacteria. The results showed a correlation between the metabolite profile and the geographical location of each conservation site. Soil nitrogen content and rainfall significantly affected the abundance of metabolites in <i>D. crumenatum</i> leaves and stems. UKNP leaves exhibit greater antioxidant activity through the ABTS radical scavenging (IC<sub>50</sub> 99.23&#xa0;µg/mL) and FRAP (200.78&#xa0;mg TE/g) mechanisms. Meanwhile, BBG leaves have the highest antioxidant activity by inhibiting DPPH radicals (IC<sub>50</sub> 242.5&#xa0;µg/mL). It might be attributed to the electron transfer associated with a high concentration of phenolic compounds. BBG leaf and stem extracts provided the highest inhibition against <i>P. aeruginosa</i> with values of 70.15% and 86.44%, respectively. Further study by molecular docking on Penicillin-Binding Protein 2 (PBP2) expressed by <i>P. aeruginosa</i> showed that the abundant phenolic compounds from the metabolomic profile exhibited strong binding affinity.</p>

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UHPLC/HRMS-Based Metabolomic Profiling, Antioxidant, and Antibacterial Activity of Dendrobium crumenatum from the Different Regions of Indonesian Conservation Areas

  • 期刊论文

  • 发表日期：

    2026年5月14日

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  • Salsabila Aqila Putri,
  • Khoirun Nisa,
  • Danang Wahyu Purnomo,
  • Ade Erma Suryani,
  • Ponco Yuliyanto

摘要

Dendrobium crumenatum grows extensively in Indonesia, with certain specimens preserved in nature conservation areas such as the Bogor Botanical Gardens (BBG) and the Ujung Kulon National Park (UKNP). Nevertheless, its abundance is frequently underutilized. This study investigated the metabolite profiles of D. crumenatum (leaf and stem) preserved in BBG and UKNP based on untargeted metabolomics of UHPLC-HRMS. The samples were classified using Principal Component Analysis (PCA), Variable Importance in Projection (VIP), heatmap, K-means, and correlation network plots. The D. crumenatum samples were further evaluated for their antioxidant and antibacterial activities, and the mechanism was predicted through molecular docking targeting specific enzymatic processes in pathogenic bacteria. The results showed a correlation between the metabolite profile and the geographical location of each conservation site. Soil nitrogen content and rainfall significantly affected the abundance of metabolites in D. crumenatum leaves and stems. UKNP leaves exhibit greater antioxidant activity through the ABTS radical scavenging (IC50 99.23 µg/mL) and FRAP (200.78 mg TE/g) mechanisms. Meanwhile, BBG leaves have the highest antioxidant activity by inhibiting DPPH radicals (IC50 242.5 µg/mL). It might be attributed to the electron transfer associated with a high concentration of phenolic compounds. BBG leaf and stem extracts provided the highest inhibition against P. aeruginosa with values of 70.15% and 86.44%, respectively. Further study by molecular docking on Penicillin-Binding Protein 2 (PBP2) expressed by P. aeruginosa showed that the abundant phenolic compounds from the metabolomic profile exhibited strong binding affinity.