Transcript Chemoinformatics, cheminformatics, chemical informatics

Chemoinformatics,
cheminformatics, chemical
informatics: What is it?
Gary Wiggins
C371
August 2004
1
Jürgen Bajorath on
Chemoinformatics, etc.
Chem-, chemi-, or chemo-informatics

Focus on the information resources needed to
optimize the properties of a ligand to become
a drug (Frank Brown, 1998)
Decision support by computational means
Drug discovery
Chemical Informatics: the application of
information technology to chemistry (not
with a specific focus on drug discovery)
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Frank Brown’s Definition
…the mixing of information resources to
transform data into information and
information into knowledge, for the
intended purpose of making decisions
faster in the arena of drug lead
identification and optimisation.

Brown, F.K. “Chemoinformatics, what it is and how does it impact
drug discovery.” Annual Reports in Medicinal Chemistry, 1998,
33, 375-384.
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Related Terms per Bajorath
Chemometrics


Application of statistical methods to chemical
data and the derivation of relevant statistical
models and descriptors
Increasingly difficult to distinguish between
chemometrics and chemoinformatics
Discovery informatics—acknowledges that
gaining knowledge from chemical data
alone is insufficient for success in drug
discovery
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Bajorath’s Conclusions
Boundaries between bioinformatics and
chemoinformatics are fluid

Both should be closely combined or merged
to significantly impact biotechnology or
pharmaceutical research
Bajorath, Jürgen, Ed. Chemoinformatics: Concepts, Methods, and Tools for
Drug Discovery. (Methods in Molecular Biology; 275) Humana Press:
Totawa, NJ, 2004.
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Cheminformatics, etc. in the Lit,
March 2000
Prevalance of -informatics terms in the literature
# Retrievals Containing Term
Term
Science Citation Index
SciFinder Scholar
(Web of Science)
Bioinformatics
364
720
Chemical Informatics
20
6
Chemoinformatics
included
7
Chemiinformatics
included
0
Cheminformatics
included
9
6
Cheminformatics, etc. in the Lit,
31 July 2003
Prevalance of -informatics terms in the literature
# Retrievals Containing Term
Term
Science Citation Index
SciFinder Scholar
(Web of Science)
Bioinformatics
1830
5685
Chemical Informatics
13
12
Chemoinformatics
32
42
Chemiinformatics
1
2
Cheminformatics
30
56
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Dmitrii Ivanovich Mendeleev,
1834-1907
Discoverer of the Periodic Table—
An Early “Chemoinformatician”
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Why Mendeleev?
Faced with a large amount of data, with
many gaps, Mendeleev:

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
Sought patterns where none were obvious,
Made predictions about properties of
unknown chemical substances, based on
observed properties of known substances,
Created a great visualization tool!
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The Periodic Table of the
Elements by Mark Winter
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What is Chemical Informatics?
Chemical informatics is the application of
information technology to help chemists
investigate new problems and organize,
analyze, and understand scientific data in
the development of novel compounds,
materials, and processes.
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Indiana University MS in
Chemical Informatics
Major aspects of chemical informatics



Information Acquisition: Methods for
generating and collecting data empirically
(experimentation) or from theory (molecular
simulation)
Information Management: Storage and
retrieval of information
Information Use: Data Analysis, correlation,
and application to problems in the chemical
and biochemical sciences
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Specialized Chemistry Degree Options
at Indiana University
BS in Informatics with a chemistry or biology
cognate (essentially a minor)
MS in Chemical Informatics
MS in Bioinformatics
PhD in Science Informatics (expected Fall 2005)
http://www.informatics.indiana.edu
MLS or MIS with a specialization in chemical
information
http://www.slis.indiana.edu
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IU’s MS in Chemical Informatics
Developed jointly by the School of
Informatics and chemistry departments at
IUB and IUPUI
First students admitted at IUPUI in fall
2001 and at IUB in fall 2002
Graduates: 4
Currently enrolled: 11
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Unique Program at IUPUI
Laboratory Informatics track at IUPUI
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Instrumentation and data interfacing
Laboratory notebooks
Laboratory Information Management Systems
(LIMS)
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Graduate Courses in Chemical
Informatics at Indiana University
C571 Chemical Information Technology
http://www.indiana.edu/~cheminfo/C571/571home.html
C572 Molecular Modeling &
Computational Chemistry
http://www.indiana.edu/~cheminfo/C572/572home.html
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JCICS – Major Research Areas
Chemical Information




Text Searching
Structure and Substructure Searching
Databases
Patents
George W.A. Milne
C571 Lecture
Fall 2002
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JCICS – Major Research Areas
Chemical Computation

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Quantum Mechanics
Statistics (regression, neural nets, etc.)
QSAR, QSPR
Graph Theory
DNA Computing
George W.A. Milne
C571 Lecture
Fall 2002
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JCICS – Major Research Areas
Molecular Modeling

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3D Structure Generation
3D Searching (pharmacophores)
Docking
George W.A. Milne
C571 Lecture
Fall 2002
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JCICS – Major Research Areas
Biopharmaceutical Computation

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Drug Design
Combinatorial Chemistry
Protein and Enzyme Structure
Membrane Structure
ADME-related Research
George W.A. Milne
C571 Lecture
Fall 2002
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Desirable Skills for Chemistry Grads
George W.A. Milne
C571 Lecture, Fall 2002
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Application of Cheminformatics
in the Drug Industry
The computer is used to analyze the
interactions between the drug and the
receptor site and design molecules with an
optimal fit.
Once targets are developed, libraries of
compounds are screened for activity with
one or more relevant assays using High
Throughput Screening.
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Application of Cheminformatics
in the Drug Industry
Hits are then evaluated for binding,
potency, selectivity, and functional activity.
Seeking to improve:


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

Potency
Absorption
Distribution
Metabolism
Elimination
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Some Methods and Tools
Structure/Activity Relationships
Genetic Algorithms
Statistical Tools (e.g., recursive pairing)
Data Analysis Tools
Visualization
Hardware Developments
Chemically-Aware Web Language (CML)
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CAS Indexing of a Relevant
Article
“The impact of informatics and
computational chemistry on synthesis and
screening.” Manly, Charles J.; LouiseMay, Shirley; Hammer, Jack D. Drug
Discovery Today (2001), 6(21), 1101-1110.
A review with 87 references
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Controlled Vocabulary Indexing
of the Manly Article
Chemistry
High throughput screening
Drug screening
Bioinformatics
Combinatorial chemistry
Drug design
Molecular modeling
Pharmacokinetics
Combinatorial library
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Informatics Components (per
Dow Chemical Visitors)
Architecture
LIMS
Substance
Registry
Components
Electronic
Records Mgmt
of an
Informatics Process Data
Mgmt
System
Integration &
User
Interface
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Chemical R&D vs.
Pharmaceutical R&D
Much smaller number of substances tested in a
week
Much larger number of tests to consider
Answers tend to come in shades of gray rather
than yes or no
Targets change frequently in chemical R&D
Must integrate a large variety of sources that
were not designed for integration
New approach to taxonomy is needed.
--L. David Rothman
The Dow Chemical Co.
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Characteristics of a Chemical
Informatics Faculty Member
Appreciates the value of algorithms
Is interested in data mining, data
modeling, and relational database systems
Pays attention to searching issues and the
literature
Has compatability and commonality with
bioinformatics research
Is able to talk to computer scientists.
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Major Journals
Journal of Chemical Information and Computer
Sciences (ACS): to split in 2005 into:

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Journal of Chemical Information and Modeling
Journal of Chemical Theory and Computation
Journal of Molecular Graphics and Modelling
(Elsevier)
Journal of Combinatorial Chemistry (ACS)
Journal of Proteome Research (ACS)
Proteomics (Wiley-VCH)
Molecular and Cellular Proteomics (ASBMB)
Acta Crystallographica (IUCr)
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Chemical Informatics Textbooks
Leach, Andrew R.; Gillet, Valerie J. An
Introduction to Chemoinformatics. Kluwer, 2003.
ISBN 1-4020-1347-7
Gasteiger,Johann;Engel, Thomas.
Chemoinformatics: A Textbook. Wiley-VCH,
2003. ISBN 3-527-30681-1
Bajorath, Jürgen, Ed. Chemoinformatics:
Concepts, Methods, and Tools for Drug
Discovery. (Methods in Molecular Biology; 275)
Humana, 2004. ISBN 1-58829-261-4
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Reference Works
Encyclopedia of Computational Chemistry, Schleyer, P. von R.;
Allinger, N.L.; Clark, T.; Gasteiger, J.; Kollman, P.A.; Schaefer, H.F.;
Shreiner, P.R. (Eds.). 5 v. Wiley, Chichester, 1998.
Gasteiger, Johann J., ed. Handbook of Chemoinformatics: From
Data to Knowledge. 4 v. Wiley-VCH, 2003. ISBN 3-527-30680-3
Reviews in Computational Chemistry. Wiley-VCH, 1990Paris, Greg. Bibliography: Chemical Information Retrieval and 3D
Searching.
http://panizzi.shef.ac.uk/cisrg/links/grep/chemDB.4.html
SIRCh: Chemical Informatics Home Page at Indiana University
http://www.indiana.edu/~cheminfo/informatics/cinformhome.html
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Conclusion
Chemical Informatics is an evolving field
with many facets.
It will become increasingly important in
areas of chemistry outside the drug
industry.
It will play an increasing role in the
developing area of proteomics.
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Bibliography
Brown, F.K. “Chemoinformatics, what it is and how does it impact drug
discovery.” Annual Reports in Medicinal Chemistry, 1998, 33, 375-384.
Glen, Robert. “Developing tools and standards in molecular informatics.”
Chemical Communications, 2002, (23), 2745-2747.
Hann, Mike; Green, Richard. “Chemoinformatics—a new name for an old
problem?” Current Opinion in Chemical Biology, 1999, 3(4), 379-383.
Lipinski, C.A.; Lombardo, F.; Dominy, B.W.; Feeney, P.J. “Experimental and
computational approaches to estimate the solubility and permeability in drug
discovery and development settings. Advanced Drug Delivery Reviews,
1997, 23, 3-15.
Rosso, Eugene. “Chemistry plans a structural overhaul.” Nature
(Naturejobs) 12 September 2002, 419(6903).
http://www.nature.com/naturejobs/careersandrecruitment/2002.html
Rothman, L. David. “Information management for research in the chemical
industry.” Abstracts of Papers, 223rd ACS National Meeting, Orlando, FL,
United States, April 7-11, 2002 (2002), CINF-044.
Smith, Chris. “Cheminformatics: Redefining the crucible.” The Scientist,
2002, 16(8), 40.
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