Explainable artificial intelligence-assisted virtual screening and bioinformatics approaches for effective bioactivity prediction of phenolic cyclooxygenase-2 (COX-2) inhibitors using PubChem molecular fingerprints.
COX-2 inhibitors
Cyclooxygenase-2
Explainable artificial intelligence
Molecular dynamics
Shapley explanations
Journal
Molecular diversity
ISSN: 1573-501X
Titre abrégé: Mol Divers
Pays: Netherlands
ID NLM: 9516534
Informations de publication
Date de publication:
10 Jan 2024
10 Jan 2024
Historique:
received:
11
07
2023
accepted:
22
11
2023
medline:
11
1
2024
pubmed:
11
1
2024
entrez:
10
1
2024
Statut:
aheadofprint
Résumé
Cyclooxygenase-2 (COX-2) inhibitors are nonsteroidal anti-inflammatory drugs that treat inflammation, pain and fever. This study determined the interaction mechanisms of COX-2 inhibitors and the molecular properties needed to design new drug candidates. Using machine learning and explainable AI methods, the inhibition activity of 1488 molecules was modelled, and essential properties were identified. These properties included aromatic rings, nitrogen-containing functional groups and aliphatic hydrocarbons. They affected the water solubility, hydrophobicity and binding affinity of COX-2 inhibitors. The binding mode, stability and ADME properties of 16 ligands bound to the Cyclooxygenase active site of COX-2 were investigated by molecular docking, molecular dynamics simulation and MM-GBSA analysis. The results showed that ligand 339,222 was the most stable and effective COX-2 inhibitor. It inhibited prostaglandin synthesis by disrupting the protein conformation of COX-2. It had good ADME properties and high clinical potential. This study demonstrated the potential of machine learning and bioinformatics methods in discovering COX-2 inhibitors.
Identifiants
pubmed: 38200203
doi: 10.1007/s11030-023-10782-9
pii: 10.1007/s11030-023-10782-9
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© 2024. The Author(s), under exclusive licence to Springer Nature Switzerland AG.
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