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  • CADD Techniques: Specific Drug Design

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    Yana Qis
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    The document discusses techniques for computer-aided drug design (CADD). It describes structure-based drug design which involves designing drugs based on the 3D structure of a protein target. It also describes ligand-based drug design which involves designing drugs based on the activity and chemical structure of known ligands that bind the target, without knowledge of the protein structure. The document outlines key CADD techniques like molecular docking, pharmacophore modeling, quantitative structure-activity relationship analysis, and predictive toxicology, which are used to identify potential drug candidates.

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    Notes 5

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    The document discusses techniques for computer-aided drug design (CADD). It describes structure-based drug design which involves designing drugs based on the 3D structure of a protein target. It also describes ligand-based drug design which involves designing drugs based on the activity and chemical structure of known ligands that bind the target, without knowledge of the protein structure. The document outlines key CADD techniques like molecular docking, pharmacophore modeling, quantitative structure-activity relationship analysis, and predictive toxicology, which are used to identify potential drug candidates.

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    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
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    6 views7 pages

    CADD Techniques: Specific Drug Design

    Uploaded by

    Yana Qis
    The document discusses techniques for computer-aided drug design (CADD). It describes structure-based drug design which involves designing drugs based on the 3D structure of a protein target. It also describes ligand-based drug design which involves designing drugs based on the activity and chemical structure of known ligands that bind the target, without knowledge of the protein structure. The document outlines key CADD techniques like molecular docking, pharmacophore modeling, quantitative structure-activity relationship analysis, and predictive toxicology, which are used to identify potential drug candidates.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
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    of 7

    Specific

    CADD Techniques Drug Design

    Structure- &
    Ligand-based
    Drug Design

    Molecular
    ADMET
    docking

    1
    &
    &
    Pharmacokinetic and Predictive Protein-ligand
    Molecular
    Toxicology
    Toxicity Predictions Dynamics Interaction
    CADD
    Techniques

    Quantitative
    Structure-
    Pharmacophore activity
    Relationship
    (QSAR)

    Identify Contribution of Each


    Bioactivity-favored Functional Group on
    Functional Groups Bioactivity
    Structure-based Drug Design Ligand-based Drug Design
    • Drug design based on 3D structure of a protein • Drug design based on ligand’s activity and its
    • Protein = known; ligand = unknown chemical structure
    • Protein-ligand interaction is unknown

    Identify active sites Fragment fitting Bridging

    • Protein = known; ligand = known


    Data collection Structure superimposition

    Fragment Growing

    Pharmacophore

    QSAR

    Fragment Linking Optimum drug candidate


    Specific
    CADD Techniques Drug Design

    Structure- &
    Ligand-based
    Drug Design

    Molecular
    ADMET
    docking

    1
    &
    &
    Pharmacokinetic and Predictive Protein-ligand
    Molecular
    Toxicology
    Toxicity Predictions Dynamics Interaction
    CADD
    Techniques

    Quantitative
    Structure-
    Pharmacophore activity
    Relationship
    (QSAR)

    Identify Contribution of Each


    Bioactivity-favored Functional Group on
    Functional Groups Bioactivity
    Structure-activity relationship (SAR)
    • An manual analysis to study the effects of compounds’
    structure on their bioactivity
    • Solely rely on personal knowledge and capability in analyzing
    the data
    • Three important elements to be compared
    • Type of functional groups

    1. Hydroxyl group is the most potent


    functional group
    2. Hydroxyl group improved the activity
    3. Methyl group improved the activity
    • Example: but such improvement is lower than
    that of hydroxyl group

    20 µM 12 µM 2 µM
    Structure-activity relationship (SAR)
    • Three important elements to be considered
    • Character (effects) of functional groups
    • EDG or EWG > Affects electron density>may affect Pi-Pi interaction

    1. Hydroxyl and methyl groups


    are EDGs
    2. Hydroxylated compound is the
    most active compound while
    • Example chlorinated (EWG) compound
    is the weakest compound.
    3. High Electron density promotes
    activity
    20 µM 12 µM 2 µM
    Structure-activity relationship (SAR)
    • Three important elements to be considered
    • Character (effects) of functional groups
    • Polarity > Affects hydrophilicity>may affect hydrogen bonding

    • Example
    1. Hydroxyl is the most polar
    functional group followed by
    chloro and non-polar alkyl
    groups
    20 µM 12 µM 2 µM 2. Hydroxylated compound is the
    most active compound while
    • Size, shape, and length of functional groups/fragments chlorinated (EWG) compound is
    the weakest compound.
    3. High polarity promotes activity
    Blue contours = Electron deficient groups (more positive) increase activity
    Red contours = Electron rich groups (less positive) increase activity.

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