Structural Bioinformatics

in Drug Discovery

Melissa Passino
 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
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 $$$)

Traditional Methods of Drug Discovery

natural
(plant-derived)
treatment for
illness/ailments
↓
isolation of active

compound
(small, organic)
 synthesis
of compound

manipulation of
structure to get
better drug
(greater efficacy,
Aspirin fewer side effects)
Modern Methods of Drug Discovery

What’s 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)
 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
target’s function

↓
high throughput screen (HTS)
- to identify “hits” (compounds with
binding in low nM to low μM range)
 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
 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
 Impact of Structural Bioinformatics
on Drug Discovery

Fig 1 & 2

Fauman et al.

• Speeds up key steps in

DD process by combining Structure-based
Drug Design

aspects of bioinformatics,
structural biology, and
structure-based drug Structural
Biology Bio-
informatics
design
 Identifying Targets:
The “Druggable Genome”
 human genome
polysaccharides lipids nucleic acids proteins

Problems with toxicity, specificity, and

difficulty in creating potent inhibitors
eliminate the first 3 categories...
 human genome
polysaccharides lipids nucleic acids proteins

proteins with
binding site

“druggable genome” = subset of genes which

express proteins capable of binding small drug-like
molecules
 Relating druggable targets
to disease...
Analysis of pharm
industry reveals:
GPCR

• Over 400 proteins

Other 110
used as drug targets
families

• Sequence analysis of
these proteins shows
STY kinases that most targets fall
Cys proteases
within a few major
gene families
Zinc peptidases

Gated ion-
channel Nuclear PDE Serine (GPCRs, kinases,
Ion channels proteases
proteases and
receptor
P450 enzymes
peptidases)
Fig. 3, Fauman et al.
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?
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
SBI in cancer therapy:
MMPIs
• 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
 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
Brown PD. Breast Cancer Res Treat 1998, 52, 125-136.
Whittaker et al. Chem. Rev. 1999, 99, 2735-2776
 MMP-1,3,8

MMP-2

MMP-7

MMP-9

MMP-10 to
13,19,20
MMP-14
to 17

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

 MMP catalysis
“metallo” in MMP = zinc
→ catalytic domain contains 2 zinc atoms

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

 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.

 Peptidic hydroxamate inhibitors

• Specificity for
MMPs over
other MPs

• Better binding
(low nM Ki)

• But poor oral

bioavailability
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…
...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/
 …and used the magic of structural
bioinformatics to design many, many
nonpeptidic hydroxylates.

oral anti- anti-

Ki
bioavailabity growth metastasis

repeat…
Results…
AG3340
“Prinomastat”

• Good oral
bioavailability

• Selective for
specific MMPs
– may implicate their
roles in certain
cancers
 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
 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