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Updated: Jan 31, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
Discovery of potent, orally bioavailable ERK1/2 inhibitors with isoindolin-1-one structure by structure-based drug
Dezhong Ji1, Lingzhi Zhang2, Qihua Zhu3
1Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 21009, China.
Abstract:
Constitutive activation of MAPK (RAS/RAF/MEK/ERK) pathway is frequently observed in many tumors and thus has become an interesting therapeutic target for cancer therapy. Despite the successful development of BRAF and MEK inhibitors in clinic treatment, resistance often appears to re-enhance ERK1/2 signaling. Inspired by the central role of the ERK1/2 signaling cascade in cancer, we describe the scaffold-hopping generation of a series of isoindolin-1-one ERK1/2 inhibitors. Our new compounds could inhibit proliferation of KRAS and BRAF mutant cells lines at low nanomolar concentrations. Compound 22a possesses acceptable pharmacokinetic profiles and showed considerable in vivo antitumor efficacy in a HCT-116 xenograft model, providing a promising basis for further optimization towards clinical ERK1/2 inhibitors.
Insights
New isoindolin-1-one compounds effectively inhibit cancer cell proliferation by targeting the ERK1/2 pathway. Compound 22a demonstrated significant in vivo antitumor efficacy, offering a promising foundation for developing novel cancer therapeutics.
Area of Science:
- Oncology
- Medicinal Chemistry
- Molecular Biology
Background:
- The Mitogen-Activated Protein Kinase (MAPK) pathway, specifically the RAS/RAF/MEK/ERK cascade, is constitutively activated in numerous cancers, making it a key therapeutic target.
- Acquired resistance to existing BRAF and MEK inhibitors often involves the reactivation of ERK1/2 signaling, necessitating the development of new therapeutic strategies.
Purpose of the Study:
- To design and synthesize novel isoindolin-1-one derivatives as inhibitors of the ERK1/2 signaling pathway.
- To evaluate the in vitro antiproliferative activity of these compounds against cancer cell lines with specific mutations (KRAS, BRAF).
- To assess the in vivo antitumor efficacy and pharmacokinetic properties of lead compounds.
Main Methods:
- Scaffold-hopping approach was employed to generate a series of isoindolin-1-one compounds targeting ERK1/2.
- In vitro proliferation assays were conducted on KRAS and BRAF mutant cancer cell lines.
- Pharmacokinetic profiling and in vivo antitumor efficacy studies using a HCT-116 xenograft mouse model were performed for optimized compounds.
Main Results:
- The newly synthesized isoindolin-1-one compounds demonstrated potent inhibition of cancer cell proliferation at low nanomolar concentrations.
- Compound 22a exhibited favorable pharmacokinetic properties.
- Compound 22a showed significant in vivo antitumor efficacy in the HECT-116 xenograft model.
Conclusions:
- The developed isoindolin-1-one derivatives represent a promising new class of ERK1/2 inhibitors.
- Compound 22a serves as a strong preclinical candidate for further optimization towards clinical development as an anti-cancer drug.
- Targeting the ERK1/2 pathway remains a viable strategy for overcoming resistance in cancer therapy.
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