In Silico Analysis of Catechol 2,3-Dioxygenase Enzyme from Pseudomonas putida and Degradation of PAHs Through Molecular Docking: Research Article

Ruba Shahbaz; Safia Mengal; M. Tariq Hasni; Faiza Batool; Aysha Nawaz; Urwa Rehman; Muhammad Fahad; Sonia Ashiq; Amna Faiz; Ejaz Rasul; Wisha Asif; Sadia Zakir; Rabail Afzal; Ramsha Nawaz

doi:10.31580/h5swrb19

Authors

Ruba Shahbaz Department of Microbiology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
Safia Mengal Institute of Public Health, Government of Balochistan, Health Department, Quetta, Pakistan
M. Tariq Hasni Department of Orthopedics, Bolan Medical College/Sandeman Provincial, Hospital Quetta, Pakistan
Faiza Batool Department of Biochemistry, University of Agriculture, Faisalabad, Pakistan
Aysha Nawaz Department of Microbiology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
Urwa Rehman Department of Microbiology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
Muhammad Fahad Department of Microbiology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
Sonia Ashiq Department of Microbiology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
Amna Faiz Department of Microbiology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
Ejaz Rasul Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
Wisha Asif Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
Sadia Zakir Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
Rabail Afzal Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
Ramsha Nawaz Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan

DOI:

https://doi.org/10.31580/h5swrb19

Keywords:

AlphaFold, Bioremediation, Catechol 2,3-dioxygenase, Environmental pollution, Molecular docking, Pseudomonas putida, Polycyclic aromatic hydrocarbons (PAHs)

Abstract

Polycyclic Aromatic Hydrocarbons (PAHs) are persistent environmental pollutants known for their carcinogenic and mutagenic effects, presenting serious threats to human health and ecological balance. Despite the established role of catechol 2,3-dioxygenase (C23O) in PAH degradation, its binding interactions with high-molecular-weight PAHs remain inadequately understood. This study aims to computationally analyze the structural and functional interactions between catechol 2,3-dioxygenase from Pseudomonas putida and several toxic PAHs to explore its bioremediation potential. The enzyme structure was predicted using AlphaFold 3 and validated by Ramachandran plot analysis, confirming a stable conformation. Pollutant structures were retrieved from PubChem, and molecular docking was conducted using CB-dock2. Among the tested pollutants, indeno[1,2,3-cd]pyrene exhibited the strongest binding affinity (–7.8 kcal/mol), followed by benzo[b]fluoranthene (–7.7 kcal/mol) and dibenz[a,h]anthracene (–7.6 kcal/mol). Key residues involved in binding interaction of indeno[1,2,3-cd]pyrene and enzyme included Phe218, Ala198, Arg150, Lys197, Asp152, Phe267, His199, Gly270, Asp271, Gly269, and Tyr271. The interactions were primarily stabilized by hydrogen bonding, van der Waals forces, π–π stacking, and π-alkyl interactions. Toxicological analysis confirmed the high environmental and health risks associated with these PAHs. These findings highlight catechol 2,3-dioxygenase as a promising enzymatic candidate for the biodegradation of high-molecular-weight PAHs. However, in vitro and in vivo validations are essential to confirm its functional performance under real environmental conditions.

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In Silico Analysis of Catechol 2,3-Dioxygenase Enzyme from Pseudomonas putida and Degradation of PAHs Through Molecular Docking

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