Investigating the enzymatic breakdown capability: A comparative study of Aeromonas caviae-derived enzymes in countering the toxicity of phenolic compounds via different approaches--颗粒学报PARTICUOLOGY

Investigating the enzymatic breakdown capability: A comparative study of Aeromonas caviae-derived enzymes in countering the toxicity of phenolic compounds via different approaches

Muhammad Naveed^a *, Sana Miraj Khan^a, Tariq Aziz^b, Tayyab Javed^a, Maida Salah Ud Din^a, Ayesha Saleem^a, Ayaz Ali Khan^c *, Rania Ali El Hadi Mohamed^d, Fahad Al-Asmari^e, Fakhria A. Al-Joufi^f

a Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, 54000, Pakistan
b Laboratory of Animal Health, Food Hygiene and Quality, University of Ioannina, Arta, 47132, Greece
c Department of Biotechnology, University of Malakand, Chakdara, 18800, Pakistan
d Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
e Department of Food and Nutrition Sciences, College of Agricultural and Food Sciences, King Faisal University, Al Ahsa, Saudi Arabia
f Department of Pharmacology, College of Pharmacy, Jouf University, 72341, Aljouf, Saudi Arabia

10.1016/j.partic.2025.06.011

Volume 104, September 2025, Pages 115-127

Received 2 September 2024, Revised 11 June 2025, Accepted 24 June 2025, Available online 27 June 2025, Version of Record 3 July 2025.

E-mail: naveed.quaidian@gmail.com; ayazkhan@uom.edu.pk

Highlights

• Aeromonas caviae shows natural potential in biodegradation due to diverse enzymatic pathways.

• Docking shows synergy of beta-ketoadipate enol-lactone hydrolase and muconate cycloisomerase in phenol breakdown.

• Ligand-protein docking revealed effective interactions in the hybrid biodegradation enzyme model.

• Bioengineered hybrid enzyme showed better docking scores and structural similarity to known homologs.

• Enzyme bioengineering enhanced the biodegradation potential of marine-derived phenolic compounds.

Abstract

Toxic aromatic compounds are widespread environmental pollutants posing significant ecological and health risks due to their persistence and toxicity. Aeromonas caviae is a promising microbial candidate for biodegradation owing to its diverse enzymatic arsenal. This study investigates the cooperative roles of two key enzymes from A. caviae, beta-ketoadipate enol-lactone hydrolase, which is involved in ring-opening hydrolysis, and muconate cycloisomerase, which catalyzes the isomerization of muconate intermediates, in degrading 15 selected toxic compounds using computational methods. Enzyme stability analysis via ExPASy ProtParam indicated an instability index below 40, confirming structural stability. Homology models were constructed and validated with high-quality scores. Molecular docking revealed Acenocoumarol as the compound with the highest binding affinity (−7.8 kcal/mol). Protein-ligand interaction analysis identified key residues involved in Pi-Pi and hydrogen bonding interactions critical for catalysis. Furthermore, a bioengineered hybrid enzyme model demonstrated improved binding precision and structural similarity to homologous proteins. These findings highlight the potential application of A. caviae enzymes in the bioremediation of toxic pollutants. Future experimental validation and enzyme engineering could further enhance their catalytic efficiency for sustainable environmental detoxification.

Graphical abstract

Keywords

Aeromonas caviae; Enzymatic breakdown; Toxicity; Molecular docking; Pollution

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