Related Experiment Video
Updated: Jan 17, 2026
Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
Published on: May 9, 2025
Discovery of a potent ROR1 inhibitor using μs-scale MD simulations, wt-metadynamics, and absolute binding free energy
Shradheya R R Gupta1, Rashmi Rameshwari2, Indrakant Kumar Singh3,4,5
1Department of Biotechnology, SET, Manav Rachna International Institute of Research and Studies, Faridabad, Haryana, 121004, India.
Context:
Receptor tyrosine kinase-like orphan receptor 1 (ROR1) is a cancer-associated pseudokinase with low expression in normal adult tissues but elevated levels in various malignancies, making it a promising therapeutic target. Among ~ 4 million compounds, CHEMBL3926946 emerged as the most promising candidate, demonstrating a persistent binding pose and a well-defined free energy basin. Well-tempered metadynamics (wt-MetaD) revealed a deep minimum of 26.00 ± 2.44 kcal/mol, indicating a highly stable interaction. CHEMBL3926946 exhibited a favourable Absolute Binding Free Energy Perturbation (ABFEP) of - 16.52 ± 0.37 kcal/mol, significantly outperforming the inhibitor Ponatinib (- 8.67 ± 0.94 kcal/mol), supported by persistent interactions with GLU523 and LEU479. This study highlights CHEMBL3926946 as a robust lead for ROR1-targeted cancer therapy and emphasizes the utility of combining wt-MetaD and ABFEP for reliable hit prioritization.
Methods:
We employed a multilayered in silico pipeline integrating high-throughput virtual screening, long-timescale molecular dynamics (MD), wt-MetaD, and ABFEP. Ligands and protein were prepared using the OPLS2005 force field, and all stages up to wt-MetaD were conducted in Maestro (v12.8.117) using the same force field. A library of ~ 4 million compounds yielded 137 candidates, Further shortlisted via MD. 7 high-confidence molecules underwent 5 independent MD replicates with randomized seeds to ensure statistical robustness. The top 3 compounds were validated by 1 μs (1000 ns) simulations to assess long-term conformational stability and wt-MetaD to reveal deep minimum. ABFEP calculations were performed using the CGenFF force field in NAMD 3.0. We benchmarked ABFEP protocol against experimentally validated ligands, successfully reproducing experimental binding free energies (ΔG), confirming the protocol's predictive reliability.
Insights
A novel compound, CHEMBL3926946, shows strong potential for targeting cancer-associated Receptor tyrosine kinase-like orphan receptor 1 (ROR1). Computational methods confirmed its highly stable interaction, outperforming existing inhibitors for ROR1-targeted cancer therapy.
Area of Science:
- Computational chemistry
- Drug discovery
- Molecular modeling
Background:
- Receptor tyrosine kinase-like orphan receptor 1 (ROR1) is a pseudokinase overexpressed in various cancers, presenting a viable therapeutic target.
- Identifying potent and selective inhibitors for ROR1 is crucial for developing novel cancer therapies.
Purpose of the Study:
- To identify and validate novel small-molecule inhibitors targeting ROR1 using advanced computational techniques.
- To evaluate the binding stability and affinity of candidate compounds through molecular dynamics and free energy calculations.
Main Methods:
- Utilized a computational pipeline including high-throughput virtual screening, molecular dynamics (MD), well-tempered metadynamics (wt-MetaD), and Absolute Binding Free Energy Perturbation (ABFEP).
- Screened approximately 4 million compounds, followed by MD-based filtering and rigorous validation of top candidates using 1 μs simulations and wt-MetaD.
- Benchmarked the ABFEP protocol against known ligands to ensure predictive accuracy of binding free energies.
Main Results:
- CHEMBL3926946 demonstrated a highly stable binding pose with a deep free energy minimum (-26.00 ± 2.44 kcal/mol) via wt-MetaD.
- Achieved a favorable Absolute Binding Free Energy Perturbation (ABFEP) of -16.52 ± 0.37 kcal/mol, significantly surpassing the performance of Ponatinib (-8.67 ± 0.94 kcal/mol).
- Identified key interactions with ROR1 residues GLU523 and LEU479 contributing to the compound's strong binding affinity.
Conclusions:
- CHEMBL3926946 is a promising lead compound for ROR1-targeted cancer therapy, exhibiting superior binding stability and affinity compared to existing inhibitors.
- The integrated computational approach combining wt-MetaD and ABFEP proved effective for reliable hit prioritization in drug discovery.
- Further preclinical development of CHEMBL3926946 is warranted for ROR1-driven malignancies.
More Related Videos
08:15Author Spotlight: Network Pharmacology and Molecular Docking to Decipher the Action of Jiawei Shengjiang San Against Diabetic Kidney Disease
Published on: May 10, 2024
08:49Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
