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Updated: Mar 11, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
New potential inhibitors of mTOR: a computational investigation integrating molecular docking, virtual screening and
Roger Kist1, Rafael Andrade Caceres1,2
1a Health Sciences Postgraduate Program of Federal University of Health Sciences of Porto Alegre - UFCSPA , Porto Alegre City , Brazil.
Abstract:
The mTOR (mammalian or mechanistic Target Of Rapamycin), a complex metabolic pathway that involves multiple steps and regulators, is a major human metabolic pathway responsible for cell growth control in response to multiple factors and that is dysregulated in various types of cancer. The classical inhibition of the mTOR pathway is performed by rapamycin and its analogs (rapalogs). Considering that rapamycin binds to an allosteric site and performs a crucial role in the inhibition of the mTOR complex without causing the deleterious side effects common to ATP-competitive inhibitors, we employ ligand-based drug design strategies, such as virtual screening methodology, computational determination of ADME/Tox properties of selected molecules, and molecular dynamics in order to select molecules with the potential to become non-ATP-competitive inhibitors of the mTOR enzymatic complex. Our findings suggest five novel potential mTOR inhibitors, with similar or better properties than the classic inhibitor complex, rapamycin.
Insights
Researchers identified five novel compounds that may inhibit the mammalian or mechanistic Target Of Rapamycin (mTOR) pathway. These potential inhibitors show promise for cancer therapy, offering an alternative to rapamycin with potentially fewer side effects.
Area of Science:
- Biochemistry and Molecular Biology
- Pharmacology and Drug Discovery
- Oncology
Background:
- The mammalian or mechanistic Target Of Rapamycin (mTOR) pathway is a critical regulator of cell growth and metabolism.
- Dysregulation of the mTOR pathway is implicated in the development of various cancers.
- Rapamycin and its analogs (rapalogs) are classical inhibitors targeting an allosteric site on the mTOR complex.
Purpose of the Study:
- To discover novel, non-ATP-competitive inhibitors of the mTOR enzymatic complex.
- To identify potential therapeutic agents for cancer treatment with improved safety profiles compared to ATP-competitive inhibitors.
Main Methods:
- Utilized ligand-based drug design strategies, including virtual screening.
- Employed computational determination of ADME/Tox properties for selected molecules.
- Applied molecular dynamics simulations to assess molecular interactions and stability.
Main Results:
- Identified five novel molecular entities with potential mTOR inhibitory activity.
- These compounds demonstrated favorable properties, comparable or superior to rapamycin.
- The identified inhibitors function via a non-ATP-competitive mechanism.
Conclusions:
- The study successfully identified promising novel mTOR inhibitors through computational drug design.
- These findings offer a foundation for developing new targeted cancer therapies.
- Further preclinical and clinical investigations are warranted to validate these potential drug candidates.
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