Cheminformatics-1.ppt
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This document discusses cheminformatics, which involves the use of computer software and data analysis to study chemical compounds and their properties. It defines cheminformatics as combining chemical synthesis, biological screening, and data mining for drug discovery. The document outlines the history and evolution of the field from chemical information to cheminformatics. It also discusses various companies involved in cheminformatics and how it applies quantitative structure-activity relationships and other methods to guide drug development.
Cheminformatics-1.ppt
- 1. Cheminformatics Dr.Gurumeet C.Wadhawa Karmaveer Bhaurao Patil College,Vashi
- 2. 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.”
- 3. 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
- 4. 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.
- 5. 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.
- 6. 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.
- 7. 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.
- 8. 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 .
- 9. 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.
- 10. Evolution of Cheminformatics Chemical Information ( 18th century-1960) Chemoinformatics (1961-2000) Cheminformatics (2000-prsent)
- 11. 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.
- 12. 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
- 13. 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
- 14. 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)
- 15. 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.
- 16. 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….)
- 17. 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.
- 18. 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
- 19. 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.
- 20. 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
- 21. 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.
- 22. 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.
- 23. 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
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