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QSAR (Quantitative Structure-Activity Relationship)

Definition
Definition
Definition

Quantitative Structure-Activity Relationship (QSAR) is a computational technique that models the relationship between the chemical structure of compounds and their biological activity. By analyzing the structural properties of molecules and their corresponding biological activities, QSAR models can predict the activity of new compounds. It involves statistical and mathematical methods to derive correlations and build predictive models.

Importance in Computational Drug Discovery

  1. Predictive Modeling: QSAR models enable the prediction of biological activity for new compounds, reducing the need for extensive experimental testing.
  2. Lead Optimization: By identifying key structural features that influence activity, QSAR helps in optimizing lead compounds to enhance their efficacy and reduce side effects.
  3. Virtual Screening: QSAR models can be used to screen large libraries of compounds virtually, identifying potential drug candidates efficiently.
  4. Mechanistic Insights: QSAR analysis provides insights into the molecular mechanisms underlying biological activity, aiding in the rational design of new drugs.
  5. Cost and Time Efficiency: Reduces the cost and time associated with experimental drug discovery by focusing resources on the most promising compounds.

Key Tools

1. QSAR Toolbox: Developed by the OECD for building and applying QSAR models.

2. KNIME: An open-source platform integrating various QSAR modeling tools and workflows.

3. DRAGON: Software for calculating molecular descriptors used in QSAR modeling.

4. Molecular Operating Environment (MOE): A comprehensive suite for molecular modeling, including QSAR analysis.

5. DeepOrigin's QSAR Tool: A tool for building and applying QSAR models integrated with other drug discovery tools.

Literature

  1. "Challenges with Multi-Objective QSAR in Drug Discovery"
    1. Publication Date: 2018-07-12
    2. DOI: 10.1080/17460441.2018.1496079
    3. Summary: Reviews the challenges and advancements in multi-objective QSAR, emphasizing its application in multi-target drug design and model prioritization.
  2. "Integrating QSAR Modelling and Deep Learning in Drug Discovery: The Emergence of Deep QSAR"
    1. Publication Date: 2023-12-08
    2. DOI: 10.1038/s41573-023-00832-0
    3. Summary: Discusses key advances in integrating deep learning approaches with QSAR modeling, including deep generative and reinforcement learning in molecular design.
  3. "Application of Ensemble Machine Learning Methods for QSAR Classification of Leukotriene A4 Hydrolase Inhibitors in Drug Discovery"
    1. Publication Date: 2024-09-20
    2. DOI: 10.60084/mp.v2i2.217
    3. Summary: Demonstrates how ensemble machine learning methods enhance QSAR model accuracy, aiding in the identification of promising LTA4H inhibitors.
  4. "Multi-Dimensional QSAR in Drug Discovery"
    1. Publication Date: 2007-12-01
    2. DOI: 10.1016/J.DRUDIS.2007.08.004
    3. Summary: Discusses recent QSAR concepts exploring higher dimensions, such as induced fit, alternative binding modes, and solvation scenarios.
  5. "QSAR-Based Virtual Screening: Advances and Applications in Drug Discovery"
    1. Publication Date: 2018-11-13
    2. DOI: 10.3389/fphar.2018.01275
    3. Summary: Summarizes recent trends and applications of QSAR-based virtual screening in identifying compounds with desired properties.
  6. "Cloud 3D-QSAR: A Web Tool for the Development of Quantitative Structure-Activity Relationship Models in Drug Discovery"
    1. Publication Date: 2020-11-03
    2. DOI: 10.1093/bib/bbaa276
    3. Summary: Introduces Cloud 3D-QSAR, a web tool integrating molecular structure generation, alignment, and interaction field computing for QSAR model development.
  7. "Large Scale Comparison of QSAR and Conformal Prediction Methods and Their Applications in Drug Discovery"
    1. Publication Date: 2019-01-10
    2. DOI: 10.1186/s13321-018-0325-4
    3. Summary: Compares conformal prediction with traditional QSAR methods for large-scale predictions of target-ligand binding, highlighting similarities and differences.
  8. "Virtual Screening, Molecular Docking and QSAR Studies in Drug Discovery and Development Programme"
    1. Publication Date: 2020-07-15
    2. DOI: 10.22270/jddt.v10i4.4218
    3. Summary: Reviews computational tools in structure-based and ligand-based drug design, including virtual screening, molecular docking, and QSAR methods.
  9. "Integrating Genetic Algorithm and LightGBM for QSAR Modeling of Acetylcholinesterase Inhibitors in Alzheimer's Disease Drug Discovery"
    1. Publication Date: 2023-07-20
    2. DOI: 10.60084/mp.v1i2.60
    3. Summary: Explores the use of QSAR studies with genetic algorithm and LightGBM to identify acetylcholinesterase inhibitors for Alzheimer's disease.
  10. "Chemical-Informatics Approach to COVID-19 Drug Discovery: Monte Carlo Based QSAR, Virtual Screening and Molecular Docking Study of Some In-House Molecules as Papain-Like Protease (PLpro) Inhibitors"
    1. Publication Date: 2020-06-22
    2. DOI: 10.1080/07391102.2020.1780946
    3. Summary: Integrates ligand-based drug design strategies to identify potential inhibitors for SARS-CoV-2 PLpro using QSAR, virtual screening, and molecular docking.