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Updated: May 31, 2026

Pharmacophore Modeling for Targets with Extensive Ligand Libraries: A Case Study on SARS-CoV-2 Mpro
Published on: September 26, 2025
Combination of pharmacophore model development and binding mode analyses: identification of ligand features essential
Hao-Peng Sun1, Jia Zhu, Fei-Hong Chen
1Key Laboratory of Carcinogenesis and Intervention of Jiangsu Province, China Pharmaceutical University, Nanjing 210009, China.
Abstract:
IκB kinase β (IKKβ) is an important anti-cancer target that plays crucial role in activating the transcription factor NF-κB in response to various inflammatory stimuli. In order to discover novel IKKβ inhibitors, a 3D chemical-feature-based QSAR pharmacophore model was established. A homology model of IKKβ enzyme was also developed to study the binding mode of IKKβ and its inhibitors. The two models were consistent in predicting the binding conformation of IKKβ inhibitor. Based on the virtual screening using the pharmacophore model, 16 compounds from SPECS database were selected after multiple filtrations for biological test. Two compounds with IC(50) values lower than 10 μM were discovered.
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