Introduction To Chemoinformatics

Introduction to Chemoinformatics
Alexandre Varnek
CHEMOINFORMATICS
Definition (wikipedia)
Cheminformatics (also known as chemoinformatics and chemical
informatics) is the use of computer and informational techniques,
applied to a range of problems in the field of chemistry.
These in silico techniques are used in pharmaceutical companies

in the process of drug discovery.
In the U.S., recent NIH emphasis has been placed on developing

public domain Cheminformatics research by creating six
Exploratory Centers for Cheminformatics Research (ECCRs) as
part of the NIH Molecular Libraries Initiative.
computational
Hit
Target Protein
Filtering,
QSAR,
High Throughout Screening
Docking Large libraries
of molecules
Small Library of selected hits
experimental
Virtual Screening
Major applications of Chemoinformatics
Storage and Search Structure-Property

of chemical information Modeling
In silico
design
Chemoinformatics Why?
amount of information
many millions of compounds and reactions
many millions of publications
Storage, organization and search experimental data
Chemical Databases
Problem: FloodofInformation
30 000 000
> 47 million compounds 25 000 000
# o f str u c tu r e s
20 000 000
5-7 million new compounds / year 15 000 000
10 000 000
5 000 000
800,000 publications / year
0
1965 1970 1975 1980 1985 1990 1995 2000
Year
=> can anyone read 4.000 publications / day ?

Problem: NotEnoughInformation
>47,000,000 chemical compounds
~500,000 3Dstructures on
CambridgeCrystallographic File
we have 3D structures for 0.1 % of all compounds

Chemoinformatics Why?
complex relationships
structure - biological activity
chemical reactivity
Prediction of physical, chemical and biological properties
In silico design of new compounds

Themostfundamentalandlasting
objectiveofsynthesisisnotproduction
ofnewcompoundsbutproductionof
properties
George S. Hammond
Norris Award Lecture, 1968
Chemoinformatics How?
Storage, organization and Prediction of physical,

search experimental data chemical and biological
properties
Encodingmolecularstructuresbydescriptors
Example1: Hansch Analysis
Biological Activity = f (Descriptors) + constant
log1/C = a ( log P )2 + b log P + + Es + C
Hanschs Descriptors can

be broadly classified into
three general types:
Electronic ()
Steric (Es)
Hydrophobic (logP)
Example2: Lipinskiruleoffive
Poor absorption or permeation are more likely when:

Therearemorethan5 Hbonddonors.
Themolecularweightisover500.
TheLogPisover5.
Therearemorethan10 Hbondacceptors.
Molecule is represented by 4 parameters:

- the number of H-bond donor groups;
- the number of H-bond acceptor groups;
- molecular weight;
- logP
Chemoinformatics definition
Chemoinformatics isafield
dealingwithmolecularobjects
(graphs,vectors)in
multidimentional chemicalspace
Theoretical chemistry
Quantum Chemistry
Force Field
Molecular Modelling
Chemoinformatics
Theoretical chemistry
Quantum Chemistry
- Molecular model
- Basic concepts
Force Field - Major applications
Molecular Modelling - Learning approaches
Chemoinformatics
Molecular Model
Quantum Chemistry electrons and nuclei
Force Field atoms and bonds

Molecular Modelling
objects in chemical space

Chemoinformatics (graphs, vectors)
Learning approach
deductive >> inductive

Quantum Chemistry
Force Field deductive inductive

Molecular Modelling
Chemoinformatics deductive << inductive

Chemoinformatics:FromDatatoKnowledge
deductive inductive
learning learning
know- generalization
ledge
information context
measurement
data
calculation
Which approach is more useful for a theoretical design of
compounds possessing desired properties ?
Quantum Chemistry
Force Field Modeling
Chemoinformatics
They are complementary

but Chemoinformatics is the most suitable one for
quantitative predictions of properties
Chemoinformatics definition
Chemoinformatics is a generic term that encompasses the design,
creation, organization, management, retrieval, analysis, dissemination,
visualization, and use of chemical information
G.Paris,1998.
Chemoinformatics is the mixing of those information resources to

transform data into information and information into knowledge for the
intended purpose of making better decisions faster in the area of drug lead
identification and optimization
F.K.Brown,1998
Chemoinformatics is theapplicationofinformatics methods tosolve

chemical problems
J.Gasteiger,2004
Chemoinformatics isafielddealingwithmolecularobjects(graphs,
vectors)inmultidimentional chemicalspace
A. Varnek, 2007
Recommended reading
Chemoinformatics - A Textbook, Johann Gasteiger and

Thomas Engel, Wiley-VCH 2003.
Handbook of Chemoinformatics, Johann Gasteiger,

Wiley-VCH 2003.
An Introduction to Chemoinformatics, Andrew R. Leach,

Valerie J. Gillet, Springer 2007.
Short courses in chemoinformatics, 1 5 June 2009
Day 1
Morning Computer representation of chemical structures A. Varnek
Afternoon Creation and management of chemical databases G. Marcou, A.Varnek
Tutorials with the ChemAxon software
Day 2
Morning Molecular Descriptors A. Varnek
Afternoon Force Field approach. Conformational sampling D. Horvath, A. Varnek
Tutorials with MOE, Codessa Pro
Day 3
Morning Pharmacophores T. Langer, D. Horvath
Afternoon Chemical space, similarity/diversity and chemical library design J. Bajorath
Tutorials with MOE
Short courses in chemoinformatics, 1 5 June 2009
Day 4
Morning
Structure-Property modeling G. Marcou, A.Varnek
Afternoon Tutorials with ISIDA, CODESSA Pro and WEKA
Day 5
Morning Docking E. Kellenberger
Afternoon Virtual screening G. Marcou, D. Horvath, A. Varnek
Tutorials with MOE

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These in silico techniques are used in pharmaceutical companies

In the U.S., recent NIH emphasis has been placed on developing

Storage and Search Structure-Property

Storage, organization and search experimental data

=> can anyone read 4.000 publications / day ?

>47,000,000 chemical compounds

we have 3D structures for 0.1 % of all compounds

Prediction of physical, chemical and biological properties

In silico design of new compounds

Storage, organization and Prediction of physical,

Hanschs Descriptors can

Poor absorption or permeation are more likely when:

Molecule is represented by 4 parameters:

Quantum Chemistry electrons and nuclei

Force Field atoms and bonds

objects in chemical space

deductive >> inductive

Force Field deductive inductive

Chemoinformatics deductive << inductive

Force Field Modeling

They are complementary

Chemoinformatics is the mixing of those information resources to

Chemoinformatics is theapplicationofinformatics methods tosolve

Chemoinformatics - A Textbook, Johann Gasteiger and

Handbook of Chemoinformatics, Johann Gasteiger,

An Introduction to Chemoinformatics, Andrew R. Leach,

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