Trans-Cinnamaldehyde Inhibitory Activity Against <i>mrkA</i>, <i>treC</i>, and <i>luxS</i> Genes in Biofilm-forming <i>Klebsiella pneumoniae</i>: An In Silico Study


  • Inayati Inayati Doctoral Program of Medical Sciences, Universitas Sebelas Maret Surakarta,Indonesia
  • Nuha H. Arifin Department of Pharmacy, Faculty of Medicine and Health Sciences Universitas Muhammadiyah Yogyakarta
  • Rifky Febriansah Department of Pharmacy, Faculty of Medicine and Health Sciences Universitas Muhammadiyah Yogyakarta
  • Dono Indarto Department of Biochemistry, Faculty of Medicine , Universitas Sebelas Maret Surakarta
  • Betty Suryawati Departement of Microbiology, Faculty of Medicine , Universitas Sebelas Maret Surakarta
  • Hartono Hartono Departement of Physiology , Faculty of Medicine , Universitas Sebelas Maret Surakarta


pkCSM, Molecular Docking, Klebsiella pneumoniae, Trans-Cinnamaldehyde, Antimicrobial


Biofilm-forming Klebsiella pneumoniae is a multidrug resistant organism that causes severe infections in humans. The luxS, treC and mrkA genes play a significant role in the formation of K. pneumoniae biofilms. Cinnamaldehyde has been shown to exhibit antimicrobial and antibiofilm activities against pathogenic bacteria. The present study aims to investigate the antibiofilm activity of cinnamaldehyde in silico.

In silico study was done using Autodock Vina software and pharmacokinetics prediction using the pkCSM strategy. The ability of cinnamaldehyde to inhibit the mrkA, treC, and luxS genes of K. pneumonia was accessed by docking the 3D structure of cinnamaldehyde with the luxS, mrkA, and treC gene receptors. Post-docking analysis such as binding affinities, hydrophobic interactions, and pharmacokinetic predictions were carried out. Cinnamaldehyde showed low binding affinities for the three genes; luxS (-5.6 kcal/mol), mrkA (-5.0 kcal/mol), and treC (-6.0 kcal/mol). The root mean square deviation (RMSD) values were found to be 1.461, 1.210, and 1.426 for luxS, mrkA, and treC gene receptors, respectively. Cinnamaldehyde had a number of hydrophobic interactions as seen in the ligand-receptor interactions for luxS (Lys 13; Asn 15; His 11; Pro 43; Leu 159; and Val 9), mrkA (Phe 157; Ala 162; and Lys 129). Cinnamaldehyde had high bond-free energy similar to that of ciprofloxacin docked with the same gene receptor. From the pharmacokinetics predictions, cinnamaldehyde had a good pharmacokinetics profile. In conclusion, cinnamaldehyde has a high docking score comparable to ciprofloxacin and therefore has a potential for use as antibacterial and antibiofilm agent against Klebsiella pneumoniae.

Author Biography

Inayati Inayati, Doctoral Program of Medical Sciences, Universitas Sebelas Maret Surakarta,Indonesia

Department of Microbiology, Faculty of Medicine and Health Sciences, Universitas Muhammadiyah Yogyakarta


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How to Cite

Inayati, I., Arifin, N. H., Febriansah, R., Indarto, D., Suryawati, B., & Hartono, H. (2023). Trans-Cinnamaldehyde Inhibitory Activity Against <i>mrkA</i>, <i>treC</i>, and <i>luxS</i> Genes in Biofilm-forming <i>Klebsiella pneumoniae</i>: An In Silico Study: Tropical Journal of Natural Product Research (TJNPR), 7(10), 4249–4255. Retrieved from