Structural-based analysis of antibacterial activities of acid condensate from palm kernel shell

Acid condensate (AC) is reported to exhibit various biological activities including antimicrobial, antioxidant, and anti-inflammatory that are valuable in assisting wound healing process. In this study, concentrated AC extract (CACE) obtained from microwave-assisted pyrolysis of palm kernel shells (PKS) was fractionated where fractions with similar profiles were pooled into combined fractions of acid condensate (CFACs). CACE and CFACs were evaluated for their total phenolic content, antioxidant activities, and antibacterial activity towards Escherichia coli , Pseudomonas aeruginosa , Staphylococcus aureus , and Enterococcus faecalis . The antibacterial mode of action of CFAC 3 compounds was evaluated by its binding energy and physical bond formation towards bacterial DNA gyrase (PDB ID: 4DUH) and tyrosyl-tRNA synthetase (PDB ID: 1JIJ) using molecular docking software AutoDock Vina. A total of 134 fractions were obtained and pooled into 9 combined fractions (CFAC 1–9). CFAC 3 had the highest total phenolic content (624.98 ± 8.70 µg gallic acid/mg of sample) that accounted for its highest antioxidant activities (1247.13 ± 27.89 μg Trolox/mg sample for ABTS assay and 24.26 ± 0.71 mmol Fe(II)/mg sample for ferric reducing antioxidant power, FRAP). Gas chromatography–mass spectrometry (GC–MS) revealed phenol and its derivatives as the major compounds in CFAC 3. CFAC 3 exhibited highest antibacterial activities against all tested bacteria particularly against S. aureus with minimum inhibitory concentration (MIC) of 0.10 mg/mL and minimum bactericidal concentration (MBC) of 0.33 ± 0.11 mg/mL . Molecular docking analysis suggested favorable binding energy for all chemical compounds present in CFAC 3, notably 1-butanone, 3-methyl-1-(2,4,6-trihydroxy-3-methylphenyl) towards the DNA gyrase (-6.9 kcal/mol), and tyrosyl-tRNA synthetase (− 7.5 kcal/ mol) enzymes. To conclude, CFAC 3 from PKS has the potential to be used as an alternative antibacterial agent which is biodegradable and a more sustainable supply of raw materials.