Cheminformatics

Basic of cheminformatics
What is cheminformatics?
The most accepted definitions of
Cheminformatics are…
1. “Cheminformatics is the combinationation of
chemical synthesis , biological screening and
data mining approaches used to guide drug
discovery and development.”

“C I is the use of computer software to assist in

the acquisition , analysis and management of
data and information relating to chemical
compounds and their properties.”
CI applies IT to chemical data and includes
topics such as chemical databases,
combinatorial library design, structure-activity
relationships and structure based drug design .

The CI offer programs and databases(mainly

for organic and sometimes for inorganic
applications) related to small molecules,
complementing the activities of the
bioinformatics group who concentrate on
biological macromolecules
Like bioinformatics, CI is still being defined. In BI
computers are used to store, retrieve and assist in
understanding biological information, CI is the
organization of chemical data in a logical form to
facilitate the process of understanding and making
inferences. Instead of a text-based retrieval system,
CI uses chemical structure that researchers provide
as input to identify similar compounds that might be
screened for biological activity.

BI deals with large molecules such as proteins

and CI deals with small molecules that are
sythesized in chemical processes says Phil Mchale
vice president for product marketing at MDL
Information System.
The various companies engaged in making
use of CI are
 MDL is a CI company that enables its
customers to store, retrieve, analyze and
make decision based on chemical structures.
Also it links BI and CI world.

Tripos also a CI company focusing mainly on

chemical information and chemical properties
for compounds involved in the early drug
discovery stages.
The various companies engaged in making
use of CI are …
Pharmacopeia is a software company which
includes a BI arm, Genetics computer group as
well as molecular simulations, Synopsys scientific
systems and oxford molecular group . The last
two business form the CI part of pharmacopeia.

Chem Navigator has developed an application

that allows researchers to submit a precise
structure for comparison with more than one
million compounds in its library.
At chem navigator website, commercially
available compounds can be identified ,
purchased and delivered to the researcher
promptly and efficiently.
 The various companies engaged in making
use of CI are…
Anadys pharmaceuticals is a drug discovery
company using CI for linking chemistry and
biology.
Why Cheminformatics?
 The effective management of information is
increasingly recognized by both public and private
sector organizations of all sorts.
 In chemistry, information systems have long played a
vital role in pharmaceuticals , agro chemical and
biotechnological research and where there is a need
to handle not only information in traditional, textual
and numeric databases, but also databases containing
information about 2D and 3D structure of molecules.
Recent developments such as
Computational chemistry
Modern combinatorial chemistry
Drug design and discovery
Data sequence, mining and visualisation
Chemical database design and their management
Chemical information sources
Medicinal chemistry etc.,has resulted in the
emergence of the discipline of CI, which involves
the creation, retrieval, organization,
dissemination and processing of chemical
information .
Scpoe in Cheminformatics
CI is the latest area is now becoming a reality in India
too
Till data advance countries like US, UK, Japan and few
European countries were working on this .
In India CI is making inroad in Indian software,
Department of Bio-Tech Govt of India , R& D
organizations pharmaceuticals and other industries
too.
With thousands of jobs and crores of grants by Govt of
India, CI professionals are growing day by day not only
in India but also in abroad .
CI companies are in great need of people with
knowledge of chemistry and computer skills to handle
the data generated by chemical researchers.
Evolution of Cheminformatics

Chemical Information ( 18th century-1960)

Chemoinformatics (1961-2000)

Cheminformatics (2000-prsent)
Contn…
All these terms basically mean the same thing and
the use of information technology and management
for the process of drug discovery.

Chemical information employs chemical

structures, data storage and computational
methods .

e.g compound registration databases , on-line

chemical literature, SAR analysis (structure activity
relationship) and molecule- property calculation.
Chemical Information System(CIS)

The main purpose of this is to identify a

chemical substance, find compounds similar to
the target compounds and demine the location
of the compound, and it is an inventory system.
Chemical similarity searching databases by
chemical similarities is among the oldest and
most useful techniques in molecular modeling
as practiced by the pharmaceutical industry. It
works because it is generally true that
molecules with similar structure have similar
biological activities
Chemical Information System(CIS)…

The chemical information systems and services

have been established for many years

(i)Justus
Liebig in 1832 founded Annalender
pharmacie

(ii) Chemical abstarct was started in 1907

(iii) First compuetr-based system was established

over
40 years ago
Milestones in Cheminformatics

(i) Identification of a user-defined structural

pattern in a database structure.

(ii) Use of graph -searching Algorithm.

(iii)For the storage and retrieval of 2D

chemical structure .(later, 3D also)
From Chemical Information to
Chemoinformatics
The first journal for the subject , Journal of
chemical documentation started in 1961.
The name changed to Journal of chemical
information and computer science in 1975.

The first book computer handling of chemical

structure information appeared on this subject in 1971

The first international conference on this subject was

held in 1973 at Noordwijkerhout and every three
years since 1987.
Definitions of Chemoinformatics

The use of information technology management

has become a critical part of the drug discovery
process”

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 lead identification and organist ion ”
F.K Brown (1998)
(It deals with the mixing of IT and management to
tranform data….)
Definitions of Chemoinformatics
 In cheminformatics there are only two primary questions
i. What to test next ? and
ii. What to make next?
The main processes within drug discovery are lead
identification where lead is something that has
activity in the low micro molecular range and lead
optimization, which is the process of transforming a
lead into a drug candidate.
 “Chemoinformatics is a generic term that
encompasses the design , creation, organization,
management, retrieval, analysis ,dissemination,
visualization and use of chemical information”

 Development of effective and efficient tools that
can exploit the chemical and biological explosion.
QSAR: Quantitative Structure
Activity Relationship
QSAR – are mathematical relationship linking
chemical structure and pharmacological
activity in a quantitative manner for a series
of compounds , methods, which can be used
in QSAR include various regression and
pattern recognition techniques.

(i) 2D Structure Searching (ii) 3D Structure Searching

(iii) 2D Similarity Searching (iv) Current interest in 3D similarity

measures
From chemoinformatics to cheminformatics
(….already seen)
From cheminformatics to combichem.
 The drive in pharmaceutical currently and most currently in
the decades to come, is the human genome project (HGP).
The information stored in our three billion base pairs is a
“gold mine” for new molecular targets to treat diseases with
huge unmark therapeutic need. eg., AIDS and Cancer

 Millions of gene sequences will translate into thousands of

high throughput screens (HTS). Thousands of HTS will
require millions of new chemicals. Millions of new chemicals
will require millions of input regarding structure, purity,
diversity, etc.

 There is no way the technology currently available in the

industry can cope with these numbers. With the advent of
combinatorial chemistry (combichem) there is a high demand
for synthetic chemists as well as combichem and chemical
information scientists.
History of chemical information
science
 Chemical information has been collected and
indexed for more than 100 years now, for most of
the time in the form of books and journals.
The printed materials (costly and time
consuming) .
Books also go missing and journals spend time at
the binders
Since people are at the mercy of whatever index is
available and searching in time consuming
Photocopy of the printed page – word processors
(or) computer program
Chemistry material started appearing “on-line”
form 1982
In 1995, the world wide web started emerging
Societies, Conferences and
Journals
The oldest means of communication with
talks and demonstration remains important
till the date.
 The royal society and other academies had
formalized many scientists communicate their
results to one another by private letters (or)
through scientific correspondents. The royal
society published ‘Philosophical Transactions’
giving birth to the scientific paper.
Contn…
1778: Chemisches Journal is thought to be the
first chem. Journal. Lornez Von Crell established
and published it from 1778 to 1784. It was renamed
as Chemisches Annalen and published from 1784 to
1803.
1789: Antoine Laurent Lavoisier et al
established Annales de chimie.
1832: Annalen der Pharmacie – changed the
name to Justus Liebigs Annalen der chemie
and then to European Journal of Organic
Chemistry.
1841: The chemical society of London was
established.
Contn…
1847: Quarterly Journal of the chemical
society of Londen (later Journal of the
chemical society) was first published in
1871. It began including abstract of the
chemical literature.
1848: The American Association of
Advancement of Science (AAAS) was
founded (a sec devoted to chem).
1857: The Societe Chemique de Paris…
THANK YOU

DR.A.PASCAL REGIS.
ASSOCIATE PROFESSOR
DEPT OF CHEMISTRY
ST,JOSEPH’S COLLEGE
TRICHY -2