Work

Bioactive fraction of Piper crocatum as a potential antibacterial agent: LC-MS identification, docking study, molecular dynamics, and ADMET prediction

Year: 2025

Type: article

Abstract: • Antibacterial activity of Piper crocatum fraction against Enterococcus faecalis was evaluated using combined in vitro and in silico approaches. • Four major compounds: 3-Hydroxy-4-methoxy-cinnamic acid, Androsterone, Aschantin, and E-p-Coumaric acid, were identified by LC-MS and assessed through docking, MD simulation, and ADMET prediction. • Aschantin showed the strongest binding affinity and stable MD interactions, but poor ADMET properties. • 3-Hydroxy-4-methoxy-cinnamic acid exhibited favorable MM/GBSA energy, stable RMSF, and a superior pharmacokinetic profile. • Study highlights the importance of integrating MD stability and ADMET profiling to identify natural compounds with potential as oral MurA inhibitors. Endodontic treatment failure is frequently associated with Enterococcus faecalis infection. Piper crocatum (red betel) contains bioactive compounds with potential antibacterial properties. This study evaluated the antibacterial effect of the n-hexane:ethyl acetate (9:1) fraction of P. crocatum against E. faecalis and assessed the pharmacological potential of its compounds through molecular docking, molecular dynamics (MD) simulation, and ADMET prediction. Antibacterial activity was tested using the agar diffusion method, and the active fraction was analyzed by LC-MS. Four major compounds were identified: 3-hydroxy-4-methoxy-cinnamic acid (1) , androsterone (2) , aschantin (3) , and E-p-coumaric acid (4) . The 10% fraction exhibited moderate inhibition. Docking results showed that aschantin had the strongest binding affinity against MurA, PBP, DNA Gyrase B, and DNA Ligase. MD simulations confirmed complex stability with low RMSD values and consistent hydrogen bonding. Meanwhile, 3-hydroxy-4-methoxy-cinnamic acid (1) demonstrated favorable binding free energy (MM/GBSA), stable RMSF profiles, and superior pharmacokinetic properties, including high bioavailability and no CYP inhibition. Despite its strong affinity and MD stability, aschantin (3) displayed poor solubility and unfavorable ADMET characteristics, which may limit its oral drug potential. In conclusion, aschantin is a promising antibacterial lead due to its strong target affinity and MD stability, whereas 3-hydroxy-4-methoxy-cinnamic acid (1) presents safer pharmacokinetic properties and potential for future drug development.

Source: Current Research in Biotechnology

DOI: 10.1016/j.crbiot.2025.100364

Authors: Devi Meliani, Trisna Yuliana, Dikdik Kurnia

Institutions: Padjadjaran University, Universitas Jenderal Achmad Yani

Language: English

Topic: Piperaceae Chemical and Biological Studies

Subfield: Pharmacology

Field: Pharmacology, Toxicology and Pharmaceutics

Domain: Life Sciences

SDG: Good health and well-being

Open Access status: gold

Estimated APC paid: $2,890