Chemoinformatics.ppt

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.

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.

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)

 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.
Contn…

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…

Chemoinformatics.ppt

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Chemoinformatics.ppt