Early Stage Drug Discovery and Target Identification

Question 1

Which activities are considered early stage drug discover?

Answer 1

choosing a disease, identifying and validating a target

Question 2

what is involved in lead compound identification?

Answer 2

in vitro bioassays and compound screening

Question 3

what happens after lead compound identification?

Answer 3

lead optimization

Question 4

what happens after lead optimization?

Answer 4

preclinical in vivo studies

Question 5

how long does the discovery/ preclinical phase of the drug discovery pipeline take?

Answer 5

3-6 years

Question 6

how long is the clinical phase of drug discovery?

Answer 6

6-7 years

Question 7

how long does it take and how much does it cost to discover a drug?

Answer 7

10-15 years, ~1 billion dollars

Question 8

an orphan drug treats a disease/disorder that affects _____ people in the US

Answer 8

less than 200,000

Question 9

orphan drug designation means:

Answer 9

government grants for development, tax breaks on clinical study costs, extended market exclusivity

Question 10

antifungals take advantage of _____ in ___ between fungi and humans

Answer 10

significant structural differences/ dihydrofolate reductase

Question 11

genomics

Answer 11

comparison of genomic DNA levels and markers

Question 12

transcriptomics

Answer 12

comparison of mRNA levels and markers

Question 13

proteomics

Answer 13

comparison of total protein levels and markers

Question 14

metabonomics

Answer 14

comparison of levels of cellular metabolites

Question 15

post-genomic target identification: ___, ___, ___, ___, ___

Answer 15

target ID/ target validation/ assay development/ screen for active compounds/ drug development

Question 16

if you have a compound with interesting biological activity and you want to know how it works use

Answer 16

affinity purification (Biotin/Avidin) and bioinformatics

Question 17

if you only have a disease state of interest and you want to know what the potential drug targets are in your model

Answer 17

use genomics (microarrays), proteomics (activity-based protein profiling), and bioinformatics

Question 18

biotin: vitamin _ or vitamin _

Answer 18

H/ B7

Question 19

biotin is _________ for __________ in ______

Answer 19

an enzyme cofactor/ carbon dioxide transfer/ numerous carboxylase enzymes

Question 20

biotin plays an integral role in _______

Answer 20

fatty acid synthesis and catabolism

Question 21

avidin is a ___________ found in egg whites

Answer 21

homotetrameric protein

Question 22

the Kd for avidin/biotin affinity is ___. Normal non-covalet binding interactions in water are in the ________ range

Answer 22

~10^-15 M/ 10^-1-10^-6 M

Question 23

what is the first step of affinity purification?

Answer 23

biotinylate the lead compound. This conjugates structure binds to immobilized avidin

Question 24

after the ligand of interest is attached to immobilized avidin…

Answer 24

cell lysate is added to the column

Question 25

after cell lysate is added to the column in affinity purification…

Answer 25

non-binding proteins are eluted

Question 26

after non-binding proteins are eluted…

Answer 26

free ligand is washed through, eluting the bound protein

Question 27

affinity purification protocol gives you

Answer 27

the protein that binds to your ligand of interest

Question 28

bioinformatics:

Answer 28

the generation of databases and application of computer algorithms to better understand molecular biology

Question 29

________ is a database of 3D protein structures. You can input _______- an it will generate _____-

Answer 29

Target Fishing Dock/ small molecule structures/ potential binding partners based on energy conformations

Question 30

___ is created from ___ using ___ and it contains ______

Answer 30

cDNA/ mRNA/ reverse transcriptase/ no introns

Question 31

how many copies of cDNA can PCR produce in 2 hours

Answer 31

millions

Question 32

genomics approach to target ID:

Answer 32

identify novel disease targets at the level of gene expression by comparing normal and diseased tissues

Question 33

when using a proteomic approach to Target ID you use ________ on your protein sample. The you excise and ____ protein from ______. Then you use ___________ analysis.

Answer 33

two dimensional separation by isoelectricfocusing and SDS-PAGE/ digest protein/ gel/ mass spectroscopy

Question 34

there can be ____ issues with proteomics due to _________ or _______ proteins

Answer 34

purification/ membrane-associated/ highly charged

Question 35

how do you amplify protein for proteomics

Answer 35

you don’t

Question 36

__________ can cause issues with proteomics

Answer 36

post-translational modifications

Question 37

activity-based protein profiling (ABPP) uses

Answer 37

active site-directed probes labeled with a fluorophore or biotin to profile the functional state of enzymes in whole proteomes

Question 38

gene ontology:

Answer 38

bioinformatics initiative to unify representation of genes and gene products across all species

Question 39

cellular component of gene product classification:

Answer 39

where is the protein located?

Question 40

molecular function of gene product classification:

Answer 40

what does it do, individually?

Question 41

biological process of gene product classification:

Answer 41

what does it do, globally?

Question 42

gene ontology in Target ID is a companion to _______ and gives data on ________

Answer 42

microarray analysis/ up or down regulated genes

Question 43

______ predicts 3D structure from gene sequence

Answer 43

Potential Drug Target Database