Structural Bioinformatics in Drug Discovery

1
Structural Bioinformatics in Drug Discovery

• Melissa Passino

2
Structural Bioinformatics

• What is SBI?
• Structural bioinformatics is a subset of
  bioinformatics concerned with the use of
  biological structures proteins, DNA, RNA,
  ligands etc. and complexes thereof to further our
  understanding of biological systems.
• http//biology.sdsc.edu/strucb.html

3
SBI in Drug Design and Discovery

• SBI can be used to examine
• drug targets (usually proteins)
• binding of ligands
• ?
• rational drug design
• (benefits saved time and )

4
Traditional Methods of Drug Discovery

• natural
• (plant-derived) treatment for illness/ailments
• ?
• isolation of active
  compound
• (small, organic)

5

• synthesis
• of compound
• ?
• manipulation of structure to get better drug
• (greater efficacy,
• fewer side effects)

Aspirin
6
Modern Methods of Drug Discovery
NEW and IMPROVED!

• Whats different?
• Drug discovery process begins
• with a disease (rather than a treatment)
• Use disease model to pinpoint relevant
  genetic/biological components (i.e. possible drug
  targets)

7
Modern Drug Discovery

• disease ? genetic/biological target
• ?
• discovery of a lead molecule
• - design assay to measure function of
  target
• - use assay to look for modulators of
  targets function
• ?
• high throughput screen (HTS)
• - to identify hits (compounds with
  binding in low nM to low µM range)

8
Modern Drug Discovery

• small molecule hits
• ?
• manipulate structure to increase potency
• i.e. decrease Ki to low nM affinity
• ?
• optimization of lead molecule into candidate
  drug
• fulfillment of required pharmacological
  properties
• potency, absorption, bioavailability, metabolism,
  safety
• ?
• clinical trials

9
Interesting facts...

• Over 90 of drugs entering clinical trials fail
  to make it to market
• The average cost to bring a new drug to market is
  estimated at 770 million

10
Impact of Structural Bioinformatics on Drug
Discovery
Fig 1 2 Fauman et al.

• Speeds up key steps in DD process by combining
  aspects of bioinformatics, structural biology,
  and structure-based drug design

11
Identifying Targets The Druggable Genome
12
Problems with toxicity, specificity, and
difficulty in creating potent inhibitors
eliminate the first 3 categories...
human genome
polysaccharides
nucleic acids
proteins
lipids
13
druggable genome subset of genes which
express proteins capable of binding small
drug-like molecules
human genome
polysaccharides
nucleic acids
proteins
lipids
proteins with binding site
14
Relating druggable targets to disease...

• Analysis of pharm industry reveals
• Over 400 proteins used as drug targets
• Sequence analysis of these proteins shows that
  most targets fall within a few major gene
  families (GPCRs, kinases, proteases and
  peptidases)

Fig. 3, Fauman et al.
15
Assessing Target Druggability

• Once a target is defined for your disease of
  interest, SBI can help answer the question
• Is this a druggable target?
• Does it have sequence/domains similar to known
  targets?
• Does the target have a site where a drug can
  bind, and with appropriate affinity?

16
Other roles for SBI in drug discovery

• Binding pocket modeling
• Lead identification
• Similarity with known proteins or ligands
• Chemical library design / combinatorial chemistry
• Virtual screening
• Lead optimization
• Binding
• ADMET

17
SBI in cancer therapyMMPIs
18

• Inability to control metastasis is the leading
  cause of death in patients with cancer (Zucker et
  al. Oncogene. 2000, 19, 6642-6650.)
• Matrix metalloproteinase inhibitors (MMPIs) are a
  newer class of cancer therapeutics
• can prevent metastasis (but not cytotoxic) may
  also play role in blocking tumor angiogenesis
  (growth inhibition)
• Used to treat major cancers lung, GI, prostate

19
What is an MMP?

• Family of over 20 structurally related
  proteinases
• Principal substrates
• protein components of extracellular matrix
  (collagen, fibronectin, laminin, proteoglycan
  core protein)
• Functions
• Breakdown of connective tissue tissue remodeling
  
• Role in cancer
• Increased levels/activity of MMPs in area
  surrounding tumor

20
Brown PD. Breast Cancer Res Treat 1998, 52,
125-136.
21
Whittaker et al. Chem. Rev. 1999, 99, 2735-2776
22
MMP-1,3,8
MMP-2
MMP-7
MMP-10 to 13,19,20
MMP-9
Whittaker et al. Chem. Rev. 1999, 99, 2735-2776
MMP-14 to 17
23
MMP catalysis

• metallo in MMP zinc
• ? catalytic domain contains 2 zinc atoms

Whittaker et al. Chem. Rev. 1999, 99, 2735-2776
24
Peptidic inhibitors

• Structure based design
• based on natural substrate collagen
• zinc binding group
• Poor Ki values, not very selective (inhibit other
  MPs)

Brown PD. Breast Cancer Res Treat 1998, 52,
125-136.
25
Peptidic hydroxamate inhibitors

• Specificity for MMPs over other MPs
• Better binding (low nM Ki)
• But poor oral bioavailability

26
A (not very) long time ago, in a town (not too)
far away

• lived a company named Agouron
• and this company had a dream, a dream to design
  a nonpeptidic hydroxamate inhibitor of MMPs

27
...so they made some special crystals

• used x-ray crystallography/3D structure of
  recombinant human MMPs bound to various
  inhibitors
• ?
• to determine key a.a. residues, ligand
  substituents needed for binding

Gelatinase A
http//www.rcsb.org/pdb/
28
and used the magic of structural bioinformatics
to design many, many nonpeptidic hydroxylates.
anti-metastasis
oral bioavailabity
anti-growth
Ki
repeat
29
Results

• AG3340
• Prinomastat
• Good oral bioavailability
• Selective for specific MMPs
• may implicate their roles in certain cancers

30
Prinomastat

• Evidence showing prevention of lung cancer
  metastasis in rat and mice models
• Clinical trials
• ? non small cell lung cancer
• ? hormone refractory prostate cancer
• stopped at Phase 3 (Aug 2000) because did not
  show effects against late stage metastasis

31
Morals of the story

• SBI can be used as basis for lead discovery and
  optimization
• MMPs are good targets for chemotherapy to help
  control metastasis
• but MMPIs must be combined with other cytotoxic
  drugs to get maximum benefits, and used at
  earliest stage possible