Chem 195 Drug Discovery

1
Chem 195 - Drug Discovery

• Lecture 4 - Target Selection and Intellectual
  Property

2
Todays Agenda and References

• Tour of HTS at Chiron on 3/8 - who is interested?
• Target Selection and Validation
• Read DD2001.pdf, Metcalf.pdf reviews
• Additional material on Renin-Angiotensin system
  will be posted on the web site
• Intellectual Property
• http//www.uspto.gov/patft/index.html
• http//www.ajobonline.com/wol.php?taskviewarticl
  eID5
• Project Update

3
How to Organize Drug Discovery?

• Therapeutic Areas
• CNS, Oncology, Infectious Disease
• Disciplines
• biology, chemistry, pharmacology, etc.
• Technology Platforms
• Small Molecules, Human Antibodies, Protein
  Therapeutics
• Molecular Scaffolds
• Kinases, proteases, GPCRs, ion channels

4
Concepts in Target Identification

• What kind of data contribute to a target
  rationale?
• What kind of data link a target with a mechanism
  of action with a pathology?
• Correlation and Causality
• Expression levels or isolation of infectious
  agent
• Kochs postulates for infectious diseases
• Molecular phenotypes
• Dominant negatives

5
In Vivo Data is Critical for Linking Molecules
with Disease

• Issues for Diseases and Models
• Acute models vs. chronic diseases
• Transgenic Models
• Gene Knockouts
• Complications with separating embryonic
  development from Disease
• Differences between humans and rodents
• Species Specificity

6
Once a Target is Defined - What next?

• Pathways and Targets
• A given pathway can contain many targets
• How to decide on which one?
• Druggability
• Privileged Target Families
• Privileged Small Molecule Scaffolds
• Discovering a phenotype by blocking one member of
  a pathway doesnt mean thats the best drug target

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Target Evaluation

• Druggability - see PfizerHTS.pdf
• Targets with small molecule ligands are preferred
• Proteinprotein interactions are more difficult
• Key challenges are selectivity, potency, and oral
  bioavailability

8
Target Evaluation

• Privileged target families and structures
• Ability to discovery small molecule, selective,
  orally bioavailable compounds
• Reflect similar phenomena
• GPCRs (7TM receptors) and benzodiazepines
• Kinases - ATP binding site
• Proteases - peptide backbone, mechanism and
  structure based approaches

9
Target Mechanisms

• Given a Molecular Hypothesis
• Agonist (activator)
• Direct activator - biologic?
• Reduce/inhibitor degradation/inhibition
• Block uptake - Prozac
• Increase synthesis of activator - sulfonyl ureas
  in type II diabetes

10
Target Mechanisms

• Given a Molecular Hypothesis
• Antagonist (inhibitor)
• Decrease production of activator - antisense
• Block synthetase/convertase enzyme - ACE
  inhibitors
• Block activatorreceptor binding - anti-receptor
  antibodies, receptor antagonists
• Block receptor signaling - receptor tyrosine
  kinase inhibitors

11
Targets and Pathways

• Pathway Examples
• The Renin-Angiotensin System in Hypertension

Asp-Arg-Val-Tyr-Ile-His-Pro-Phe-His-Leu
Val-Ile-His ...
Angiotensinogen
Renin
Bradykinin
Asp-Pro-Pro-Gly-Phe-Ser-Pro- Phe-Arg
Asp-Arg-Val-Tyr-Ile-His-Pro-Phe His-Leu
Angiotensin Converting Enzyme (ACE)
Angiotensin I
Inactive Fragments
Asp-Arg-Val-Tyr-Ile-His-Pro-Phe
Angiotensin II
Increase in blood pressure
AII Receptor Two Subtypes
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Potential Target

• Renin
• Aspartyl proteinase - 2 genes in rodents 1 in
  humans
• Exopeptidase - two carboxylate sidechains
  involved in GABC for water attack on peptide bond
• Rate determining step in AII production
• Although very potent inhibitors were discovered
  no molecules with sufficient oral bioavailability
  were ever developed
• Renin inhibitors were potent HIV protease
  inhibitor leads and led to the first antivirals
  for HIV

13
Potential Target

• ACE - angiotensin converting enzyme
• Zn metalloproteinase - activated water molecule
  hydrolyzes peptide bonds with electrophilic
  assistance from Zn ion
• Creates AII from A1 and degrades bradykinin
• Endocarboxydipeptidase - cleaves off 2 amino
  acids
• Membrane bound enzyme

14
ACE Inhibitor Discovery

• B. jararaca peptides potentiated bradykinin
  activity and blocked Ang1 to Ang2 conversion
• Pyr-Trp-Pro-Arg-Pro-Gln-Ile-Pro-Pro
• Teprotide - reduced blood pressure in vivo!
• C-terminal Pro seemed to be required based on
  peptide structure-activity relationships
• Ondetti et al., Science 196 441-444 (1977)

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Mercks Approach to ACE
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Mercks SAR leading to Captopril
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Evolution of ACE Inhibitors
Proline Carboxylate Required from Peptide SAR
In Vivo Hydrolysis
Zn coordination
Remove thiol Add phenyl Make ester
BMS work
Remove thiol Use Lys Instead of Phe
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Ace Inhibitor Clinical Use

• ACE inhibitors - Captopril
• Normalize blood pressure in 50 of hypertensives
• With a diuretic (AII increases water retention
  through aldosterone) such as one of the
  sulfonamides blood pressure reduction is seen in
  90 of patients
• Side effects especially cough are common

19
Potential Target

• Angiotensin II Receptors
• G-protein coupled receptors
• Multiple subtypes - tissue specific distributions
• Knock-out mice
• Possible way around side-effects with ACE
  inhibitors

First AII Receptor antagonist
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Blood Pressure Regulation
Most successful drugs work by more than one
mechanism
21
Blood Pressure Regulation
22
Target Selection Summary

• Combine disease rationale and molecular
  understanding with pragmatism
• Assume the biology will be more complicated than
  you think
• Believe in vivo data

23
Intellectual Property

• Patents and Trade Secrets
• Time limited right to exclude others from
  making, using, or selling your invention
• Useful
• Novel
• Not Obvious
• Enablement - To one skilled in the art
• Cant patent something which exists in Nature
• Composition of Matter vs. Use vs. Tool patents
• Genes, genomes, and who owns what?

24
Useful WEB Resources on IP

• http//www.uspto.gov/patft/index.html
• http//www.ajobonline.com/wol.php?taskviewarticl
  eID53

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Intellectual Property

• Patents on Biological Entities
• What is patentable?
• A partial gene sequence?
• A complete gene sequence?
• A gene sequence with a function?
• A gene and protein sequence?
• A human gene if you have a rodent gene sequence?
• A 95 identical sequence to one you have
  described?
• A small molecule ligand that binds to the protein
  encoded by your gene?
• ..

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Intellectual Property

• Chemical Patents - what do you get?
• The molecules you made
• Molecules which are related
• Molecules you can think of
• Processes for making molecules
• Tools for making molecules
• Quantitative descriptions - specific stereoisomers

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Possible Project Indications - Class Suggestions

• Gliomas (brain tumors)
• Allergy
• Polycystic kidney disease
• Heart Attacks - Acute Myocardial Infarctions
• Multiple Sclerosis
• Migraine
• Malaria
• Filariasis