1 - Foundations Flashcards
(20 cards)
What is the main goal of drug discovery?
To find molecules that bind to malfunctioning biological targets and restore their function.
What is computer-aided drug design (CADD)?
Use of computational tools to optimize and speed up drug discovery.
Difference between structure-based and ligand-based drug design?
Structure-based uses target 3D structure (e.g., docking); ligand-based uses known active molecules (e.g., QSAR).
What are small organic molecules made of?
Mostly carbon-carbon and carbon-hydrogen bonds, plus oxygen, nitrogen, sulfur, etc.
What are molecular graphs?
Mathematical representations where atoms = nodes and bonds = edges.
What are molecular fingerprints?
Encoded sets of molecular features used for similarity and modeling.
What are molecular descriptors?
Numerical values describing properties like weight, polarity, or shape.
What does SMILES stand for?
Simplified Molecular Input Line Entry System; a string representation of molecules.
What is the advantage of SELFIES over SMILES?
SELFIES reduce syntax/semantic errors in molecular string representations.
What is biological activity?
A compound’s ability to affect a biological system and produce a measurable response.
What is a biological assay?
A test measuring how a substance affects a biological system.
Examples of biological assay types?
In vitro, ex vivo, in vivo; binding vs functional assays.
What is IC50?
The concentration at which a substance inhibits a process by 50%.
What is pIC50?
The negative logarithm (base 10) of the IC50 value; higher = more potent.
What does ADME stand for?
Absorption, Distribution, Metabolism, and Excretion.
What is Lipinski’s Rule of Five?
A set of criteria to assess drug-likeness based on H-bond donors, acceptors, MW, and logP.
What is QSAR?
Quantitative Structure–Activity Relationship; links molecular structure to biological activity.
What is QSPR?
Quantitative Structure–Property Relationship; models physical or chemical properties.
Why is assay data challenging?
It’s expensive, limited, imbalanced, and often noisy.
What are major bioactivity databases?
PubChem, ChEMBL, BindingDB, DrugBank, Papyrus.
