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Updated: Nov 11, 2025

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
Multiple machine learning, molecular docking, and ADMET screening approach for identification of selective inhibitors
Baddipadige Raju1, Himanshu Verma1, Gera Narendra1
1Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India.
Abstract:
Cytochrome P4501B1 is a ubiquitous family protein that is majorly overexpressed in tumors and is responsible for biotransformation-based inactivation of anti-cancer drugs. This inactivation marks the cause of resistance to chemotherapeutics. In the present study, integrated in-silico approaches were utilized to identify selective CYP1B1 inhibitors. To achieve this objective, we initially developed different machine learning models corresponding to two isoforms of the CYP1 family i.e. CYP1A1 and CYP1B1. Subsequently, small molecule databases including ChemBridge, Maybridge, and natural compound library were screened from the selected models of CYP1B1 and CYP1A1. The obtained CYP1B1 inhibitors were further subjected to molecular docking and ADMET analysis. The selectivity of the obtained hits for CYP1B1 over the other isoforms was also judged with molecular docking analysis. Finally, two hits were found to be the most stable which retained key interactions within the active site of CYP1B1 after the molecular dynamics simulations. Novel compound with CYP-D9 and CYP-14 IDs were found to be the most selective CYP1B1 inhibitors which may address the issue of resistance. Moreover, these compounds can be considered as safe agents for further cell-based and animal model studies. Communicated by Ramaswamy H. Sarma.
Insights
Researchers identified novel selective inhibitors for Cytochrome P4501B1 (CYP1B1), a protein overexpressed in tumors that causes drug resistance. These identified compounds may overcome chemotherapy resistance and are potentially safe for further studies.
Area of Science:
- Biochemistry
- Pharmacology
- Computational Chemistry
Background:
- Cytochrome P4501B1 (CYP1B1) is overexpressed in tumors and inactivates anti-cancer drugs, leading to chemotherapy resistance.
- Identifying selective CYP1B1 inhibitors is crucial for overcoming this drug resistance.
Purpose of the Study:
- To identify selective inhibitors of Cytochrome P4501B1 (CYP1B1) using integrated in-silico approaches.
- To find novel compounds that can overcome drug resistance in cancer treatment.
Main Methods:
- Development of machine learning models for CYP1A1 and CYP1B1 isoforms.
- Screening of small molecule and natural compound databases.
- Molecular docking, ADMET analysis, and molecular dynamics simulations for selectivity and stability assessment.
Main Results:
- Two novel compounds, CYP-D9 and CYP-14, were identified as highly selective CYP1B1 inhibitors.
- These compounds demonstrated stability and key interactions within the CYP1B1 active site.
- The identified inhibitors show potential for overcoming chemotherapy resistance and are deemed safe for further preclinical studies.
Conclusions:
- Novel selective CYP1B1 inhibitors (CYP-D9 and CYP-14) were identified using in-silico methods.
- These compounds offer a promising strategy to address drug resistance in cancer therapy.
- The identified inhibitors are suitable for subsequent cell-based and animal model investigations.
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