Drug Discovery Part I: Screening for Compounds Jim Wells ...

Drug Discovery
Part I: Screening for Compounds
Jim Wells
& Michelle Arkin
UCSF
Pharmaceuticals:
How do we �nd these things?
Lipitor
Gleevec
Brief history of drug discovery
Human to molecular target
“Age of Botanicals”, Human screening
Founding of FDA (1906) (Safety, Efficacy)
Animal-based screening (anesthetics)
Bacterial cell screening (penicillin)
Tissue screening (GPCR)
Target-based screening (HTS)
Mechanism/structure-based (HIV)
Molecular and cell-based (kinase)
Genomics-based patient pro�ling

Modern drug discovery: target to human
Classes of Drug Molecules
•Small organic molecules (10,000 MW, injectable)
•Vaccines
9 steps from target to pill
Cell
Protein
Animal efficacy
Animal Tox
Human Safety
Efficacy
Registration
NDA �ling
Disease target

Target ID: what’s causing disease
Target validation:
What’s causing the disease?
Infectious agent or host imbalance?
Molecular target leading to disease
• Bacteria: �nd target not in humans
• Host imbalance:
Replace underactive protein (insulin)
Inhibit overactive protein (kinase)
The genome (genetic space) is huge
and lots to search
• ~20,000 human genes that
code for proteins
• Which one is causing the disease

Target validation:
Is the target “druggable”?
•Are there known small molecules that
bind the target or a homolog?
Gleevec binding to BCR-ABL
•Does the target have a site that looks like it
will bind a small molecule (cavity, energetic
hot-spot)?
Small molecules like certain targets
Target % of sm drugs Affinity
(-ΔG per
C,N,O)
GPCR 45 0.5-0.7 kcal
Kinases 4 0.35-0.5 kcal
Protease 2 0.25-0.4 kcal
P-P targets 0

Goals for oral drugs (chemical properties,
Lipinski Rules)
• Low Molecular Weight (

Hit Identi�cation: getting on the board
Ways to identify a hit
• Start with a natural substrate and
make drug-like
• Start with someone else’s hit
(“patent bust”)
• Design a denovo hit by Structurebased
Design
• Screening (HTS or Fragment
methods)
You have to test A LOT of compounds
to �nd a drug

Start with libraries of drug-like molecules
Functional
groups
~ 500,000
compounds
How to handle that many compounds?
• Miniaturization (1 – 100 uL)
• Automation
• Parallel pipetting
• Robotics
• Plate readers
Demo here
• freezers
• Demo liquid handler
• Demo plates

Assay formats: Biochemical
• Use a puri�ed protein and an
activity you can visualize
substrate
• Use when
enzyme
enzyme
• You know what protein you
want to inhibit
• You can express and purify the
protein
• Selectivity among similar
proteins is important
Assay formats: Cell-based
• Screen in whole cells when
• Molecular target known,
but not isolable from cell
• Goal is to alter a cellular
phenotype
• Pathway is known, best
target is not known
Assay formats: Cell-based
• Results read out by
• Whole well
�uorescence/
luminescence
• Cell-by-cell properties

Demo
• Biochemical assays
- Light-box fluorophore
High-content cells screens:
Quantitative microscopy
• Demo
High-content screens:
Quantitative microscopy

% inhibition
Assay quality and Hit selection
Next Steps?
• Retest
• Determine mechanism
• Optimize!
compound #
A hit is just the �rst step to discovering a
drug
Demo
• Chemist in a hood

Introduction to Drug Discovery
Thanks to Kate Augustyn, Steven Chen, and
Kenny Ang
References
High-throughput screening assays for the identi�cation of
chemical probes. Inglese J, et al. Nat Chem Biol. 2007 Aug;
3(8):466-79
Small-molecule inhibitors of protein-protein interactions:
progressing towards the dream. Arkin MR, Wells JA. Nat
Rev Drug Discov. 2004 Apr;3(4):301-17.
The development of imatinib as a therapeutic agent for
chronic myeloid leukemia. Deininger M, Buchdunger E,
Druker BJ. Blood. 2005 Apr 1;105(7):2640-53
Making better drugs: Decision gates in non-clinical drug
development. Pritchard JF, Jurima-Romet M, Reimer ML,
Mortimer E, Rolfe B, Cayen MN. Nat Rev Drug Discov. 2003
Jul;2(7):542-53
Drug Discovery
Part I: Screening for Compounds
Thanks to
Kate Augustyn
Steven Chen
Kenny Ang