“Bioinformatics and Its Emerging Industrial Applications” - Workshop at IIT Delhi

One day
Workshop on

on

“Bioinformatics and Its Emerging Industrial Applications”




February 28, 2009

at

IIT Delhi





Under the Aegis of




Foundation for Innovation & Technology Transfer,
(FITT), IIT Delhi



Scope and Objectives

Recent advances in bioinformatics and the significant increase in the computational powers in the form of super computers have made it possible to utilize the genetic data base (data mining) which has been collected so far. In fact, the success of genome sequencing efforts and bioinformatics resulted in a vast amount of data over the last two decades. The number of genetic sequences in the Gen Bank gene sequence repository of the National Center for Biotechnology Information (NCBI) has increased tremendously over the last two decades. Bioinformatics has to use this mountain of data with the help of super computers in the efforts. Gene mining for understanding life and developing absolute cures for life threatening diseases. The task of the bioinformations is to demonstrate how in-silico simulations facilitates experiments in the laboratory, towards personalized medicine (individual specific drugs with no side effects). Health informatics is another tool which may act as a big aid in this direction. Bioinformatics may have applications not only in pharmaceutical industries but in several other industries.

In fact, significant improvements in the studies of genomics and proteomics, and concurrent progress in X-ray crystallography, nuclear magnetic resonance techniques along with bioinformations have given rise to expectations that the three dimensional structure or reliable homology modeling can be achieved in a reasonably short time. Mapping of the human genome seems to be nearing completion. Chemoinformatics and chemogenomics help in the bioinformatics studies. There is a need to take steps to decipher the language of DNA from an energetic perspective. Metabolic pathway analysis of complete genome sequences enables identification of all members of essential pathways that are present as well as genes that are missing from the potential pathogens. Chemoinformatics and structural genomics would provide substantial knowledge about the increasing number of drug targets. This would trigger the demand for the design and new specific inhibitors or ligands tailored to a particular target. Potential drug targets may be identified through metabolic pathway analysis and choke point analysis.

Molecular modeling and modular dynamics simulations help in revealing the primary and secondary structures of different proteins, with their active sites and folds. Homology or comparative modeling uses experimentally determined protein (3D) structural template to predict the conformation of another protein that has similar amino acid sequence. Homology modeling involves generally 4 steps fold assignment, sequence alignment, model building and model refinement. The sequence of database of proteins with known structures (e.g., PDB- sequence database) is searched with target protein and a protein of known 3 D-structure, the two protein sequences are aligned to identify the optimum correlation between the residences in the template and target sequences. The model of the target protein is constructed and checked with regard to conformational aspects and is corrected or energy minimized using force-field approaches. The use of Pro-check helps in ascertaining the protein structure.

Nanodrugs may cross blood-brain barriers to provide or afford drugs for brain tumours, e.g., curcumin, or other nano-sized compounds Drug development is a very laborious, time consuming, costly, energy intensive, difficult and lengthy process. This job is very tedious and involves even trial and error by using a myriad of different chemical compounds. Bioinformatics approach to perform such a gigantic operation of designing and testing so many molecules by docking (AUTODOCK 3.0) to pathogenic proteins makes the job of drug designing easier. Microarrays are gaining importance in bioinformatics and may add to the acceleration of efforts towards drug designing and drug discovery.
The emergence of multiple drug resistance to human pathogens has necessitated the research for newer molecules or compounds from other antimicrobial substances or other sources. Traditionally, the use of medicinal plants for the treatment of human diseases is well known practice in Ayurvedic, Unani, traditional, focal or Homoeopathic, siddha products, naturopathy, food supplements, functional foods, herbs, etc. systems of medicines. The medicinal plants and other natural product sources have provided leads for antiparastic, antiviral, antifungal, antibacterial, anticancer etc. diseases. Such natural products include flavonoids, flavonolignans, lignanoids, terpenoids, coumarins, aurones, naphthoquinones, alkaloids, steroids, quinolines, thiols, phospholipids etc. . Either active principles like curcumin or a group of compounds have made a drug after pharmacodynamico studies. The organic chemical structures of a myriad number of natural products have been identified and their quantitative structure-activity relationship (QSAR) has been studied. Chemoinformatics may help in finding newer drugs including nanodrugs or ligands. Chemists may modify the chemical structure of compounds to design a newer drug molecule for docking. Its toxicity may be tested subsequently. Combinatorial chemistry may help in the synthesis of a series of possible compounds for docking studies. Thus, bioinformatics may help in generating a large array of potential drug molecules on a hierarchy of molecules which may be tested experimentally in the laboratory. However, bioinformatics may help in reducing the gigantic job to a routine and simple job. Nanobiotechnolgy may also open newer avenues in drug discovery.

Bioinformatics does not help only in drug discovery but this also has several other applications in energy, food, chemical fermentation or other industries. In fact, enzyme production and identification of potential microbes for the different biochemical actions is also a very labour and energy intensive, lengthy, costly and tedious job. Bioinformatics can help in revealing the potential microorganisms which may be selected for studies for the production of active enzymes in good yields by using BLAST, gene and protein data banks. The examples include e.g., in energy industries i.e, the discovery of potential microbes for use in hydrogen, biodiesel , ethanol, lipase enzyme production, chiral separations, or for biorefining of fossil fuels. Similar uses of bioinformatics in food and fermentation or chemical industries may be found through gene data mining or nanotechnology.

It is certain that success of future bioinformatics would hinge upon high-performing super computers in developing further computational biology. The role of chemoinformatics, chemistry of natural products, synthetic organic chemistry, artificial intelligence or robotics in this field may not be under emphasized, e.g. the use of artificial neural network in the studies of the function of brain and its networking. Bioinformatics may have great applications not only in pharmaceutical industries but in other industries such as fuel or energy, food, chemical, fermentation and bioengineering or nanobiotechnology based industries. Future would see a huge broadening of horizon of application of bioinformatics in several industries and not just limited to drug industries only e.g., searching suitable microbes for DNA, specialized enzymes, DNA motors etc.

The key driving force for the present day in silicon drug design endeavors are the availability of structural information of targets, emergence of reliable energy functions, discovery and designing of newer molecules and their multiple derivatisation for docking and availability of high end super computers. Bioinformatics may open a new era of therapeutics research which will reduce the time, cost and labour in drug discovery. This way also help the scientists to design better and more efficient chemical trials. Automated drug design in silico seems a reliable dream in the near future where nanobiotechnology may also open newer avanues never seen before.

The following topics would be covered:
1. Computational Biology and Drug Discovery
2. Drug Designing
3. Protein Modeling
4. Genetic Mining and Molecular Bioinformatics
5. Chemical Molecular Modeling and Designing
6. Medicinal Chemistry and Combinatorial Chemistry
7. Chemistry of Natural Products and Drug Designing – QSAR
8. Leads from Alternate Systems of Medicines
9. Microarrays
10. Other Applications of Bioinformatics in Biological H¬¬2 production, Biodiesel, Bioethanol, Biomethane production, Enzyme Engineering, Fermentation, Chemical, Food etc. Industries
11. Chemoinformatics
12. Nanobiotechnology and Nano drugs
13. Health informaics
14. Bioenergatics and Bioinformatics
15. Future Scope


Speakers

Prof. D. K. Sharma, Centre for Energy Studies, IIT Delhi
Prof. B. Jayaram, Head, Chemistry Department, IIT Delhi and
Prof. Saroj Mishra, Former Head, Biochemical Engineering and Biotechnology Departments, IIT Delhi and other Speakers from Outside.

METHODOLOGY:

Lectures and Discussions

WHO SHOULD ATTEND:

Engineers, Scientists, Managers and Other Executives working in the areas of medicines, biotechnology energy, oil refineries, fuel technology, chemical technology, fermentation, food, enzyme engineering etc.

Registration Fee* After Dec. 15, 2008 Before or on Dec. 15, 2008

- Students Rs. 2500/- Rs. 2000/-
- Scientists from academic institutes
and R&D organizations Rs. 4500/- Rs. 3600/-
- Industries Rs. 5000/- Rs. 3600/-

• There will be 20% (early bird) concession in the registration fee for the participants who register before December 15, 2008

Registration fee payable by DD/Cheque (Delhi A/c) in favour of “FITT, IIT Delhi”

Last date for registration: February 16, 2009

DATES AND VENUE:

Date: February 28, 2009
Venue: Centre for Energy Studies, IIT Delhi

ACCOMMODATION

This is a non-residential programme. The participants are expected to make their own arrangements for stay. Subject to availability, the organizers will try to book accommodation on payment basis within the guest houses of IIT Delhi, if requested sufficiently in advance through the Registration Form.



For any further information, contact:
Coordinator
Prof. D.K. Sharma
Centre for Energy Studies
Indian Institute of Technology, Delhi
Hauz Khas, New Delhi – 110 016
Tel : 2659 1256, Mob: 9818227168
e-mail: sharmadk@ces.iitd.ernet.in


REGISTRATION FORM

One day Workshop on
Bioinformatics and Its Emerging Industrial Applications
(February 28, 2009)

Name Dr/Mr/Ms .:_____________________________________________

Designation :______________________________________________

Organization :______________________________________________

Address :_____________________________________________

_______________________________________________

Email: ________________________________

Phone: _______________________________

Fax: _________________________________

Fees Payable to “FITT, IIT Delhi” Draft/Cheque No.: __________________________

Dated: ________________________________ Drawn on : (Bank)__________________________

Rs. __________________________________


Signature of applicant





Please send your registrations to:
Mr. K.K.Roy
Manager (Tech./Admn.)
Foundation for Innovation and Technology Transfer (FITT)
Indian Institute of Technology Delhi (IITD)
Hauz Khas, New Delhi-110016
Phone : 011-2659 7285, 2659 7164
Fax: 011-2685 1169
Email: krityroy@yahoo.com
uttamaswal@hotmail.com