Early Stage Drug Discovery and Target Identification Flashcards
Which activities are considered early stage drug discover?
choosing a disease, identifying and validating a target
what is involved in lead compound identification?
in vitro bioassays and compound screening
what happens after lead compound identification?
lead optimization
what happens after lead optimization?
preclinical in vivo studies
how long does the discovery/ preclinical phase of the drug discovery pipeline take?
3-6 years
how long is the clinical phase of drug discovery?
6-7 years
how long does it take and how much does it cost to discover a drug?
10-15 years, ~1 billion dollars
an orphan drug treats a disease/disorder that affects _____ people in the US
less than 200,000
orphan drug designation means:
government grants for development, tax breaks on clinical study costs, extended market exclusivity
antifungals take advantage of _____ in ___ between fungi and humans
significant structural differences/ dihydrofolate reductase
genomics
comparison of genomic DNA levels and markers
transcriptomics
comparison of mRNA levels and markers
proteomics
comparison of total protein levels and markers
metabonomics
comparison of levels of cellular metabolites
post-genomic target identification: ___, ___, ___, ___, ___
target ID/ target validation/ assay development/ screen for active compounds/ drug development
if you have a compound with interesting biological activity and you want to know how it works use
affinity purification (Biotin/Avidin) and bioinformatics
if you only have a disease state of interest and you want to know what the potential drug targets are in your model
use genomics (microarrays), proteomics (activity-based protein profiling), and bioinformatics
biotin: vitamin _ or vitamin _
H/ B7
biotin is _________ for __________ in ______
an enzyme cofactor/ carbon dioxide transfer/ numerous carboxylase enzymes
biotin plays an integral role in _______
fatty acid synthesis and catabolism
avidin is a ___________ found in egg whites
homotetrameric protein
the Kd for avidin/biotin affinity is ___. Normal non-covalet binding interactions in water are in the ________ range
~10^-15 M/ 10^-1-10^-6 M
what is the first step of affinity purification?
biotinylate the lead compound. This conjugates structure binds to immobilized avidin
after the ligand of interest is attached to immobilized avidin…
cell lysate is added to the column
after cell lysate is added to the column in affinity purification…
non-binding proteins are eluted
after non-binding proteins are eluted…
free ligand is washed through, eluting the bound protein
affinity purification protocol gives you
the protein that binds to your ligand of interest
bioinformatics:
the generation of databases and application of computer algorithms to better understand molecular biology
________ is a database of 3D protein structures. You can input _______- an it will generate _____-
Target Fishing Dock/ small molecule structures/ potential binding partners based on energy conformations
___ is created from ___ using ___ and it contains ______
cDNA/ mRNA/ reverse transcriptase/ no introns
how many copies of cDNA can PCR produce in 2 hours
millions
genomics approach to target ID:
identify novel disease targets at the level of gene expression by comparing normal and diseased tissues
when using a proteomic approach to Target ID you use ________ on your protein sample. The you excise and ____ protein from ______. Then you use ___________ analysis.
two dimensional separation by isoelectricfocusing and SDS-PAGE/ digest protein/ gel/ mass spectroscopy
there can be ____ issues with proteomics due to _________ or _______ proteins
purification/ membrane-associated/ highly charged
how do you amplify protein for proteomics
you don’t
__________ can cause issues with proteomics
post-translational modifications
activity-based protein profiling (ABPP) uses
active site-directed probes labeled with a fluorophore or biotin to profile the functional state of enzymes in whole proteomes
gene ontology:
bioinformatics initiative to unify representation of genes and gene products across all species
cellular component of gene product classification:
where is the protein located?
molecular function of gene product classification:
what does it do, individually?
biological process of gene product classification:
what does it do, globally?
gene ontology in Target ID is a companion to _______ and gives data on ________
microarray analysis/ up or down regulated genes
______ predicts 3D structure from gene sequence
Potential Drug Target Database
