17 Questions
What is the bitstring for Cyclobutan?
1010
How are the answers represented in the result of this process?
As a list of binary values - either true (1) or false (0).
What is the purpose of non-hashed fingerprints?
To encode precisely defined structural patterns.
What does each pattern in the fingerprints activate?
A certain number of positions (bits) in the fingerprint.
What is omitted in the fingerprints?
H-atoms.
What does the acronym ADME(T) stand for?
Absorption, Distribution, Metabolism, Elimination/excretion, Toxicity
What is Lipinski's Rule of 5 (RO5) used for?
To predict the likelihood of a compound becoming an orally active drug.
What does SAcore in the context of drug discovery stand for?
Synthetic Accessibility score
What are Structural Alerts in drug discovery?
Molecular patterns associated with specific types of toxicity.
What is the Tanimoto coefficient (Tc) used for?
To assess similarity between chemical structures encoded by bitstrings.
What do Pharmacophore Models aim to do in drug discovery?
To identify compounds that match specific features for biological activity.
What is the main difference between Structure-Based Drug Design (SBDD) and Ligand-Based Drug Design (LBDD)?
SBDD involves molecular docking calculations between each molecule and the biological target, while LBDD uses a set of geometric rules and/or physical-chemical properties obtained by QSAR studies.
What is Virtual Screening in drug design?
Virtual Screening is a computational approach to assess the interaction of an insilico library of small molecules with the structure of a target macromolecule to identify new molecules with desired activity.
What is the purpose of applying a scoring function in Structure-Based Drug Design?
The scoring function is applied to evaluate the affinity between a molecule and the biological target.
Name two databases commonly used in Virtual Screening for drug discovery.
SciFinder, ZINC, PubChem, ChemSpider
What are the two types of filters used to reduce the number of compounds in Virtual Screening?
Filters for applicability domain and filters to estimate 'drug-likeness'.
List three properties of a drug according to the text.
High affinity to a protein target, soluble, permeable
Study Notes
Bitstring and Fingerprints
- The bitstring is a binary representation of a molecule, used to encode molecular structures.
- In fingerprints, answers are represented as a binary vector, where 1 indicates the presence of a feature and 0 indicates its absence.
Non-Hashed Fingerprints
- Non-hashed fingerprints are used to store the original pattern of features in a molecule, allowing for more detailed analysis.
Fingerprints Activation
- Each pattern in the fingerprints activates a specific feature or chemical group in a molecule.
Omissions in Fingerprints
- Fingerprints often omit certain features or chemical groups that are not relevant for the specific application.
ADME(T)
- ADME(T) stands for Absorption, Distribution, Metabolism, Excretion, and Toxicity, which are key pharmacokinetic and pharmacodynamic properties of a drug.
Lipinski's Rule of 5 (RO5)
- Lipinski's Rule of 5 is used to evaluate the drug-likeness of a molecule, predicting its ability to be orally absorbed and permeable.
SAcore
- SAcore stands for Synthetic Accessibility score, which measures the ease of synthesizing a compound.
Structural Alerts
- Structural Alerts are substructures or patterns in a molecule that may cause unwanted biological or toxic effects.
Tanimoto Coefficient (Tc)
- The Tanimoto Coefficient is used to measure the similarity between two molecules, based on their fingerprints.
Pharmacophore Models
- Pharmacophore Models aim to identify the essential features of a molecule required for biological activity, to guide drug design.
Structure-Based vs Ligand-Based Drug Design
- The main difference between Structure-Based Drug Design (SBDD) and Ligand-Based Drug Design (LBDD) is that SBDD uses the 3D structure of the target protein, while LBDD uses the properties of known active ligands.
Virtual Screening
- Virtual Screening is a computational method used to identify potential drug candidates by searching large databases of compounds against a target protein or pharmacophore model.
Scoring Function
- The purpose of applying a scoring function in Structure-Based Drug Design is to predict the binding affinity of a ligand to a target protein.
Databases for Virtual Screening
- Two commonly used databases for Virtual Screening are Zinc and ChemBlaster.
Filters in Virtual Screening
- There are two types of filters used to reduce the number of compounds in Virtual Screening: physicochemical filters (e.g., logP, molecular weight) and pharmacophore filters (e.g., presence of specific functional groups).
Properties of a Drug
- According to the text, three properties of a drug are:
- Absorption
- Distribution
- Metabolism
Test your knowledge on the absorption, distribution, metabolism, elimination/excretion (ADME) process of drugs, as well as Lipinski's Rule of 5 and beyond. Explore topics like drug travel, pharmacological responses, toxicity, drug targets, and more.
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