ICIC2014 12 – 15 October Heidelberg, Germany
ICIC 2014 Bio-Brilliance 2014: Building on the Ideas of Others
Nov 28, 2014
There is no such thing as a truly original idea! New science is built on the work of the past. Knowing the history is essential to develop a better insight for future breakthroughs. The mastery of knowledge developed by previous researchers aides in choosing the right path and quickening the process to success. Scientific knowledge continues to grow and overflow. Peer reviewed scientific literature continues to be the prime resource for accessing worldwide scientific knowledge. This presentation will cover how today’s biological research is benefitting from connecting and combining these borrowed ideas.
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ICIC2014
12 – 15 October Heidelberg, Germany
+ =
Brian Burton aka Danger Mouse
ReMiX
Copy, Transform,
Combine
Fragment Based Drug Design
“The guy who invented
the first wheel was an idiot.
The guy who invented
the other three,
HE was a genius.”
Woody Guthrie – American Folk
Musician (1912–1967)
“The words are the
important thing. Don’t worry about tunes.
Take a tune, sing high when
they sing low, sing fast when
they sing slow, and you’ve
got a new tune.”
This Land is Your Land adapted from an old gospel song Oh My
Loving Brother
Henry Ford – American Industrialist
(1863–1947)
“I invented nothing new.
I simply assembled the discoveries of other men behind whom were centuries of work … progress happens when all the factors that make for it are ready and then it is inevitable.”
Mark Twain, American Author
(1835 – 1910)
“All ideas are second-hand,
consciously and unconsciously drawn from a million outside sources. We are constantly littering our literature with disconnected sentences borrowed from books at some unremembered time and now imagined to be our own.”
Fundamental Equation of
Information Science
K[S] + DI Knowledge
Structure
Increment of
Information
Change in
Structure
New Knowledge
Structure
= K[S + DS]
The Origin of a Creative Idea
Step One: Defining
Define the problem you are trying to solve
Step Two: Borrowing
Borrow ideas from places with a similar problem
Step Three: Combining
Connect and combine these borrowed ideas
The Road to Success
13
Literature is filled with Billions of Pages of Useful
Information
Curation: Origin
“Curation, broadly interpreted, is about maintaining and adding value
to, a trusted body of digital information for current and future use.”
Library Museum Biological Research
Today
A typical primary care doctor
must stay abreast of
approximately
10,000 diseases and syndromes,
3,000 medications, and
1,100 laboratory tests.
100 years ago
Physician knows everything in the field of medicine
Leonardo da Vinci - painter,
engineer, musician, and
scientist.
Few Hundred
Years Ago
Evolution of Pharmaceutical Research
In vivo In vitro In silico
Time
In litero
Kinase Patents have Increased
Dramatically
Nu
mb
er
of
Ap
plicati
on
s
Annual Trend
Has anyone in
another company
developed chemical
compounds for a
protein similar to
my target?
Knowledge Networking
Curation involves excerption of pharmacological, Chemical, biological,
and toxicity information from scientific literatures/articles
for each component and its relating facts
Physicochemical properties
Chemical Synthesis Structure
Pharmacology In litero
Database
The Idea of Standards
Roman Chariot
Railroad-track
There are four ways in which a
standard can be produced
1. Ad hoc method
2. De facto method
3. Government-mandate method
4. Consensus method
Kinase Thematic DB
Needles in the Haystack
BioActive
Compound
Neighborhood
Region
other
compounds
i.e. neighbors of a bioactive compound have a higher
probability of behaving in a ‘similar’ bioactive way
QSAR and Drug Design
Statistical tool Molecular
Parameters
MEP
MLP
Volume
log P
…
Biological activity
IC50
Ki
MIC
Permeation
…
Goals: Find a quantitative relationship between the variation of
a biological activity and the variation of molecular parameters
Second Set of Descriptors
Nationality India USA
Number of boy
children
1 0
President of Company Country
Education Science & Engg Legal
Result: Similarity = 0%
Property
(Descriptor)
Person 1
Person 2
First Set of Descriptors
Gender Male Male
Marital Status Married Married
Is he a President Yes Yes
Age Group < 50 < 50
Result: Similarity = 100%
“If I have seen further it is by standing
on the shoulders of Giants.” Sir Isaac Newton, 1676
Pharmacophore:
Looking for common features
Pharmacophore: “ a set of structural features in a molecule that is
recognized at a receptor site and is responsible for that molecule’s
biological activity.”
Pharmacophore Features
Certain features are vectors with a directional component
- Eg., hydrogen bond donors and acceptors
- These are composed of two points.
Most features are represented by a single point
- For example, hydrophobic center
There are limits on the number of points and features.
3D Database Mining using
Pharmacophore Model
In-house
Compounds or
Virtual library
Novel Potential Leads
Generation of pharmacophore models
chemical features based hypotheses
set of active ligands from
literature (curated data)
“The secret to creativity
is knowing how to hide your Sources.” Albert Einstein
Can NASA put a man on the
moon?
NO Source: ‘The cost of lost knowledge’, Geoffrey Petch,
Knowledge Management, Freedom Technology Media Group, October 1998
Apollo 11: man on the moon 1969
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