MCB153: Fundamentals of Drug
Discovery/Molecular
Therapeutics
Professor Andrew Dillin, PhD – MCB-IMM/Helen Wills Neuroscience
Professor Sarah Stanley – MCB-IMM/ School of Public Health
dillin@Berkeley.edu
Fundamentally Changed the World As We Know It (FCWAWKI)
So, you want to treat/cure a disease that is
currently unmet?
Do you treat the Cause or the Symptoms?
Sometimes the cause is obvious (lack of Vitamin C for Scurvy),
Have research knowledge of cause
(receptor tyrosine kinase activity for some forms of cancer),
and sometimes cause unknown/not clear
(Chronic fatigue syndrome)
Do you know about the molecular biology
that has gone wrong in the disease state?
Answer = Yes.
Q1: Is it a GAIN of cellular pathway/function?
(Cancers are prime example)
Q2: Is it a LOSS of cellular pathway/function?
(Cystic Fibrosis is a prime examples)
ABL is tyrosine kinase that normally shuttles to the nucleus to phosphorylate to regulate nuclear proteins.
BCR-ABL fusion is stuck in cytoplasm and ABL inappropriately phosphorylates growth control pathway members
Let’s address a GAIN of function: Chronic
Myeloid Leukemia (CML)
Many CML patients have a chromosomal translocation
BCR = breakpoint cluster region (unknown, tyrosine kinase and Rho GTPase)
ABL = gene from Abelson murine leukemia virus (tyrosine Kinase)
ABL is tyrosine kinase that normally shuttles to the nucleus to phosphorylate to regulate nuclear proteins.
BCR-ABL fusion is stuck in cytoplasm and ABL inappropriately phosphorylates growth control pathway members
What would the goal be to treat/cure BCRABL CML patients?
Reduce/eliminate BCR-ABL
How?
1) Small Molecule Inhibitor
2) CRISPR?
3) Antibody therapy?
Gleevec mimics ATP
And binds into the ATP binding
of ABL…..
But, many tyrosine kinases
Do the same thing……
Gleevec refined to bind
Only a small subset of Tyr-kinases
https://www.nature.com/scitable/topicpage/gleevec-thebreakthrough-in-cancer-treatment-565/
Gleevac is great, but how was it found?
Gleevac
BCR-ABL
How was Gleevac discovered?
Hint….it binds to the ATP site of ABL.
Step 1: Researchers at Ciba-Giegy (Novartis) investigating ATP analogs (10,000S) that could block kinases (100s)
Step 2: Cells from BCR-ABL patients screened for accelerated death/lack of growth with compounds from 1.
Step 3. 10s of compounds affect BCR-ABL cells, but normal cells. Pick several to begin lead optimization.
Lead optimization…..fuzzy at best.
Several candidates from the lead discovery phase are
chosen for further experimentation and cover (hopefully) different pharmacophores to determine:
Most potent
Least Toxic
Most specific to target
Patentable
Pharmacophore……. "an ensemble of steric and electronic features that
is necessary to ensure the optimal supramolecular interactions with a
specific biological target and to trigger (or block) its biological response"
Tetracyclines
Linezolid
Tetracyclines and Linezolid are antibiotics that
inhibit mitochondrial ribosome
Penicillin …. Vancomycin are a class of pharmacphore
Antibiotics that block cell wall synthesis of bacteria
The process of lead optimization
Non-sedating antihistamines
(Seldane had safety issues and forced
Better optimization for Allegra)
Sometimes trying to reconfigure the lead
compound leads to increased potency…at a cost!
Fentanyl is 1000x more potent, but still has respiratory depression
(you’ll learn more about novel µ-opiod receptor antagonists that ”dial-out” this deadly side-effect in the Pain lectures)
Now that we have a more potent lead
compound, do we have a clinical candidate?
What else should we know before putting
it into animals and then humans?
Summary from Friday’s Lecture
Questions to be addressed before beginning drug identification campaign
1)
2)
3)
4)
5)
6)
7)
8)
9)
Do we know anything about the mechanism?
Is the defect a gain-of-function? Loss-of-function?
Do we have a validated target?
Do we have a fast, reliable screen to test molecules that hit target?
Do we have a measure of selectivity?
How many different pharmacophores do we have?
Do we have freedom to operate (Are our pharmacophores clear of patent claims?)?
How do our leads look in regards to Pharmacokinetics/Pharmacodynamics?
How does the ADME look?
If 1-9 look promising, do we have a drug?
Defining a clinical candidate is
a parallel process
ADME ---Absorption, Distribution,
Metabolism and Excretion
area (Figure 6.1).2
1991
5% 5%
30%
11%
10%
39%
2000
Lack fo efficacy
PK Properties
Clinical safety
Toxicity
Commercial
Cost of goods
Formulation
Other/Unknown
4%
8%
6%
19%
24%
8%
12%
19%
Lack fo efficacy
PK Properties
Clinical safety
Toxicity
Commercial
Cost of goods
Formulation
Other/Unknown
FIGURE 6.1 In 1991, poor pharmacokinetic properties caused an estimated 39% of clinical failures in the pharmaceutical industry. By 2000, an increased focus on designing compounds with improved physicochemical properties resulted in a significant decrease in the
contribution of poor pharmacokinetics to drug failure. Only 8% of clinical failures could be
attributed to poor pharmacokinetic properties.
In an ideal world, it would be possible to monitor changes in drug con-
Test of ADME:
• Plasma Stability - follow half-life of compound in human plasma at
37C
• Aqueous Stability - follow half-life in H2O
• Solution Stability - more applicable for IV formulations
• Bioassay solubility - specific for each compound, its target and assay
conditions
P-gp Efflux - P-glycoprotein Efflux (multi-drug
resistance pump)
Cyp450 inhibition…
~75% of drugs are processed by Cyp450s
57 Cyp450s, mostly in our liver
Cyp450s are used to detoxify xenobiotics
BBB penetration - Blood Brain Barrier
Permeability….
• Oral - how well does it get taken up by gut endothelial cells?
• IV - how well is it taken up blood vessel endothelial cells?
• Etc….
What does “preclinical” mean?
Test in animal models for?
Toxicity
Efficacy
Side-effects
Mouse Model of Alzheimer’s Disease
Human Disease
Genes put into Mouse
Mouse models of BCR/ABL Cancers
https://www.science.org/doi/10.1126/science.1099480
What if there are no animal models????
For example, there are no animal models for Cystic Fibrosis,
but there are several drugs to treat the disease. How did this happen?
1) Take clinical candidate straight into humans?
2) Ex vivo human tissue studies (primary cell/organ and organoids)
Making organoids
https://www.aiche.org/resources/publications/cep/2018/may/
going-small-big-creating-organoids-regenerative-medicine
Making a drug has low probability, takes a long time and is costly
1 of 24 programs are successful. Costs = 17 Boeing 737 jets!
In the end, there can still be failures…..
Vioxx (Merck) = awesome anti-inflammatory, but small population had ischemia
Baycol (Bayer AG) = great for lowering cholesterol and cardiovascular events, but some people had
Rhabdomyolysis (break down of muscle)
ABSORPTION
(a)
249
(b)
FIGURE 6.3 (a) The oral pharmacokinetic profile of a drug is determined by its absorption, distribution, metabolism, and excretion. (b) Oral delivery of a drug leads to an initial