Screening Indonesian Pine (Pinus merkusii Jungh at de Vriese) Compound as an Antibacterial Agent: In Vitro and In Silico Study


  • Yuka Fadana Chemistry Department, Faculty of Mathematics and Natural Sciences, Brawijaya University, Malang 65145, Indonesia,
  • Ichda A. Dinana Biology Department, Faculty of Mathematics and Natural Sciences, Brawijaya University, Malang 65145, Indonesia
  • Arie Srihardyastutie Chemistry Department, Faculty of Mathematics and Natural Sciences, Brawijaya University, Malang 65145, Indonesia
  • Rollando Rollando Pharmacy Department, Faculty of Science and Technology, Ma Chung University, Malang 65151, Indonesia
  • Masruri Masruri Chemistry Department, Faculty of Mathematics and Natural Sciences, Brawijaya University, Malang 65145, Indonesia,


in-silico, Escherichia coli, Staphylococcus aureus, pine, antibacterial


Pinus merkusii is empirically used as an antibacterial agent and has been found to have secondary
metabolites such as alkaloids, terpenoids, and flavonoids. This study aims to investigate the antibacterial effects of pine flower extract on gram-positive and gram-negative bacteria. In addition, molecular docking and molecular dynamics simulations were used to understand the underlying mechanism of its antibacterial activity. The antibacterial screening was performed using the disc diffusion method, compound analysis in the extract was carried out using Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS), molecular docking was performed using Autodock Vina integrated into PyRx, and molecular dynamics simulation was run using YASARA Dynamics. The antibacterial test results showed that the pine flower extract had the highest inhibitory effect on Escherichia coli (1.038 ± 0.169 mm) and Staphylococcus aureus (7.154 ± 0.381 mm). Compound analysis of the pine flower extract showed the presence of Myricetin, Epicatechin, Nepetin, Hispidulin, Kaempferol, Luteolin-7-O-rutinoside, and Hesperidin. The molecular docking and molecular dynamics simulation results showed that
Epicatechin, Nepetin, and Luteolin-7-O-rutinoside compounds could inhibit bacterial cell wall formation proteins.


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How to Cite

Fadana, Y., Dinana, I. A., Srihardyastutie, A., Rollando, R., & Masruri, M. (2023). Screening Indonesian Pine (Pinus merkusii Jungh at de Vriese) Compound as an Antibacterial Agent: In Vitro and In Silico Study: Tropical Journal of Natural Product Research (TJNPR), 7(3), 2586–2595. Retrieved from

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