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

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Abstract

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.

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Funding

The authors acknowledged the financial assistance from Universiti Teknologi Malaysia for the Research University Grant (07G78). We would also like to express our gratitude to UTM Digital Centre for the high-performance computing facilities.

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Authors and Affiliations

  1. School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81310, Johor Bahru, Johor, Malaysia

    Mohd Amir Asyraf Mohd Hamzah, Rosnani Hasham, Raja Safazliana Raja Sulong & Zainul Akmar Zakaria

  2. Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Johor Bahru, Johor, Malaysia

    Nik Ahmad Nizam Nik Malek

  3. Institute of Bioproduct Development, Universiti Teknologi Malaysia, 81310, Johor Bahru, Johor, Malaysia

    Maizatulakmal Yahayu

  4. Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, 81310, Johor Bahru, Johor, Malaysia

    Fazira Ilyana Abdul Razak

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  1. Mohd Amir Asyraf Mohd Hamzah
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Highlights

• CFAC 2 and CFAC 3 showed higher total phenolic content and antioxidant activity compared to CACE.

• GC–MS analysis showed phenolic compounds were successfully concentrated in the CFAC 1–3.

• CFAC 3 exhibited enhanced good antibacterial activity compared to CACE.

• Molecular docking analysis supported the antibacterial properties of phenolic compounds present in CFAC 3.

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Mohd Hamzah, M.A.A., Hasham, R., Nik Malek, N.A.N. et al. Structural-based analysis of antibacterial activities of acid condensate from palm kernel shell. Biomass Conv. Bioref. 13, 4241–4253 (2023). https://doi.org/10.1007/s13399-021-02219-w

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