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Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

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Molecular Docking and MD Modeling Techniques for the Development of Novel ROS1 Kinase Inhibitors.

Mohammad Jahoor Alam¹, Arshad Jamal¹, Shaik Daria Hussain²

¹Department of Biology, College of Science, University of Ha'il, Ha'il 2440, Saudi Arabia.

Pharmaceuticals (Basel, Switzerland)

|February 27, 2026

Summary

This study identifies four novel drug candidates effective against mutated ROS1, a key factor in chemotherapy resistance. These compounds show promise for overcoming resistance to kinase inhibitors like crizotinib in cancer treatment.

Keywords:

MD simulation MM-GBSA ROS1 crizotinib molecular docking

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Published on: July 8, 2025

Area of Science:

Oncology
Computational Chemistry
Drug Discovery

Background:

Chemotherapy resistance is a major obstacle in cancer treatment.
The Gly2032Arg mutation in ROS1 (a receptor tyrosine kinase) confers resistance to crizotinib.
Targeting mutated ROS1 is crucial for developing new anti-cancer therapies.

Purpose of the Study:

To identify novel drug candidates targeting the Gly2032Arg-mutated ROS1 protein.
To computationally screen for molecules effective against crizotinib-resistant ROS1.
To provide new therapeutic strategies for cancers with ROS1 mutations.

Main Methods:

In silico modeling of the Gly2032Arg-mutated ROS1 protein.
Structure-based virtual screening of the PubChem database.
Molecular docking, MM-GBSA, molecular dynamics (MD) simulations, and DFT calculations.

Main Results:

Identified four promising drug candidates (PubChem CID: 67463531, 72544946, 139431449, 139431487) with high docking scores and drug-likeness.
Validated binding affinity and stability of protein-ligand complexes through MM-GBSA and MD simulations.
Elucidated molecular features of identified compounds using DFT.

Conclusions:

The identified compounds demonstrate potential efficacy against mutated ROS1 targets.
This research offers a new avenue for developing drugs to overcome chemotherapy resistance.
The findings contribute to the development of targeted cancer therapies.