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Team India Consortium with Global Partnership. A CSIR-led initiative for affordable healthcare to the developing world. Council of Scientific and Industrial Research INDIA. http://www.osdd.net.

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slide1

Team India Consortium with Global Partnership

A CSIR-led initiative for affordable healthcare to the developing world

Council of Scientific and Industrial Research

INDIA

http://www.osdd.net

slide2

“When it comes to health, we need to have a balanced view between health as a right and health as a business”

Prof Samir Brahmachari

Director General, CSIR and

Chief Mentor, OSDD

(Ref: Cell (2008) v.133, pp. 201-203)

50

slide3

One person

    • every 20 seconds
    • 1.7 Million people
    • every year
  • In India
    • Nearly 1000 people
    • every day
    • Two people
    • every 3 minutes

TB Kills

Image Credits:  Teseum/Flickr

slide4

Deaths due to Tuberculosis in 2008

Source: GlobalHealthFacts.org

  • More than 2 billion people (~1/3 of world population) is affected with the
  • tubercle bacilli
slide6

“Generations of advances in research and technology have bypassed TB research”- Anthony Fauci, NIAID .

“The field has been too isolated and inward-looking” Dr. Margaret Chan, head WHO

why open source drug discovery
Why Open Source Drug discovery ?
  • Many eye balls make the bug shallow!
  • Lack of market incentive for TB
  • Successful Open Source Models
    • Human Genome Sequencing Initiative
    • Open Source Software Initiative (eg: Linux OS)
    • Android
    • The WWW
slide9

OSDD Platform

System Architecture

Collaborative tools to accelerate neglected diseases research” in the book “Collaborative Computational Technologies for Biomedical Research”. Wiley and Sons. 2011 (in press).

osdd attribution and ip
OSDD: Attribution and IP
  • All contributions on the OSDD portal attributed to the authors with date and time stamp
  • Real time data sharing
  • Click wrap license agreement
    • All contributions treated as Protected Collective Information
      • mandates sharing,
      • attribution,
      • contribute back
osdd view on patents
OSDD View on Patents
  • Two patent applied molecules in hit to lead phase
  • Patentonly to ensure that:
    • Quality assurance in downstream processes
    • Subsequent innovations remain in open source
    • Affordability : through non exclusive licenses
slide12

OSDD – Multipronged approaches

DRUG TARGET BASED

(18 Drug Targets)

NATURAL PRODUCT BASED (135 Phytomolecules )

LIGAND BASED

(Pubchem Bioassay Data/New inhibitors/)

Lead Optimization

Potential hit

slide14

OSDD Open Access Resources

Assembly line for drug discovery

  • I Biological Repository
  • i. Open access clinical strains repository
  • ii. Open access clone repository
  • iii. Open access protein repository
  • II Chemical Repository
  • i. Open access small molecule repository
  • III Open Screening Facility
      • i. Submit your compounds for anti-tuberculosis screening
slide15

Computational Resources developed with

Community participation

http://tbrowse.osdd.net

http://sysborg2.osdd.net

Bhardwaj et al. Tuberculosis (Edinb). 2009 Sep;89(5):386-7

Bhardwaj et al. 2011 John Wiley & Sons, Inc.

Chembio Toolkit

TrapTB

Mtb drug targets database

Workflow engine with federated resources

AmPhyDB

AntimycobacterialPhytomolecule Database

Mtb essen\tial genes database

slide16

COG

Easy RNA Profile IdentificatioN

Database of Conditionally Regulated Proteins

Pathway network & Unique pathways

Drug Targets (TDR/Plos/TDI)

Databases Do not “talk” to each other

Mycobacterial Genome Divergence Database

Operon predictions

(DOOR/VIMSS/Rutherford)

* This is representative set of post-genomics data available on TB

slide17

COG

Easy RNA Profile IdentificatioN

Database of Conditionally Regulated Proteins

Pathway network & Unique pathways

Drug Targets (TDR/Plos/TDI)

Databases now do “talk” to each other !!

Mycobacterial Genome Divergence Database

Operon predictions

(DOOR/VIMSS/Rutherford)

More than 100 datasetsencompassing a million data points

slide18

Publication in Tuberculosis 2009

AnshuBhardwaj

DeekshaBhartiya

VinodScaria

NitinKumar

OpenLabNoteBook on SysBorgTB

http://sysborgtb.osdd.net/bin/view/OpenLabNotebook/TBMapDataset

Deeksha Bhartiya

Nitin Kumar

slide19

The “Connect to Decode” Programme

Collaborative Curation

Curated

Annotations

OSDD C2D

Community

800+ Student Researchers

Literature

Annotation Tools

Raw

Annotations

Pathway/Interactome | Gene Ontology | Protein Structure/Fold | Glycomics| Immunome

Genomic

Databases

slide20

“Given enough eyeballs, all bugs are shallow”

-Linus Torvalds

Errors are Discussed by the Community

Errors are corrected by the Community

Errors are marked by the Community for Correction

slide21

Innovative Crowd Sourcing Model for Mtb Systems Biology

Collaborative Curation

Curated

Annotations

Literature

Annotation Tools

Raw

Annotations

Community of >800 student researchers

87% of Mtb genome annotated

Genomic

Databases

Generated the largest Interactome & Metabolic Map of Mtb

slide22

Within weeks, 830 volunteered to re-annotate the entire M. tuberculosis genome. The work started in December 2009 and was completed by April 2010, packing nearly 300 man-years into 4 months!

Source: Munos B. Can Open-Source Drug R&D

Repower Pharmaceutical Innovation?

Clin Pharmacol Ther 2010;87:534–536

The Open-Source Drug Discovery (OSDD), which is dedicated to discovering treatments for diseases that plague the developing world, surprised many when more than 400 of its volunteer researchers reannotated the tuberculosis bacterium genome, wiki style, in just 4 months—record time for such an endeavor

Source: Margie Patlak. Open-Source Science Makes Headway

J Natl Cancer Inst. 2010 Aug 18;102(16):1221-3

slide24

OSDD SInCRe

An Open Source Integrated Computational Resource for the Analysis of the Structural Interactome to predict Off-Site Interactions of Drug Candidates

Nagasuma Chandra, R. Sowdhamini, N. Srinivasan & Sir Tom Blundell

ongoing cheminformatics
Ongoing: Cheminformatics

Community of About 400

PubChem

ChEMBL

DrugBank

HT Virtual screening

Cheminformatics Models

Experimental Assays

Curated molecule datasets

Data Mining and Analysis

  • Other Active Communities:
      • OSDD Women Scientists Forum
      • OSDD Junior Scientists Forum
slide26

Cheminformatics – Large Scale Data Analysis

Data

Processing

Size increases

Heap Size issues

Software

Power MV and WEKA

Output

cheminformatics large scale data analysis
Cheminformatics – Large Scale Data Analysis
  • Accessing large data files from online repository such as Pub Chem.
  • Basic computational resources – 4Gb RAM

Pub Chem

Database

1.04Pb

Max bandwidth - 1-4 Mbps

Local Systems

4Gb RAM

c dac s garuda grid indian grid computing initiative
C-DAC’s Garuda Grid – Indian Grid Computing Initiative
  • C-DAC is R&D organization under Ministry of Communication & Information Technology, India
  • C-DAC’s Garuda Grid is targeted at providing a facility for the scientific community, which would enable them to seamlessly access the distributed resources.
  • Compute Power of GARUDA: ~ 70TFs (6000 CPUs)
  • Currently there are 55 Garuda Partners
  • Has NKN (National Knowledge Network) connectivity at 10Gbps
slide30

OSDD - Linking Institutions and Competencies

45 Hits Selected for Screening

Hits identified through virtual screening are synthesized and tested for enzyme assay

slide31

Creation of Library of Drug Like Compounds

Filtering Criteria for Pruning 50,000 compounds

from Chembridge Database

  • Molecular Weight < 400
  • Remove molecules other than H,C,N,O,F,S,P,Cl,Br, or I
  • ADME properties (Principle descriptors & Prediction of properties) based on 1712 drugs.
  • Shrinking the CLogP window between 1.5 & 5

A physical compound library of drug like compounds. (20,000 compounds)

Whole cell screening

osdd open chemistry
OSDD Open Chemistry

Led by CSIR- CDRI, India’s National Drug Research Laboratory

osdd open chemistry1
OSDD Open Chemistry
  • Challenge

Need novel molecules for screening against TB/Malaria

  • OSDD Approach
  • Open source small molecule synthesis involving 40 chemistry departments from colleges across India
  • Web based collaboration and discussion
slide34

OSDD Team at work in SASTRA

Project implementation through students selected via pan India online primer designing exercise

More than 30 genes cloned in less than 3 months

slide35

POC for downstream experiments

  • Fifteen undergraduate students were given hands on training in various Molecular biology techniques
  • So far, 11 genes have been cloned in pGEM-T easy vector
  • 20 have been cloned in pET28 a/b/c and expressed (Verified by SDS –PAGE)
slide37

Status: OSDD Projects

18

Other projects aim to develop tools, databases and repositories for the OSDD community

19

9

6

2

slide38

OSDD Publications

  • Bhardwaj A, et al. Open Source Drug Discovery- a new paradigm of collaborative research in Tuberculosis drug development. Tuberculosis, 2011 (in press)
  • Bhardwaj A, et al. Collaborative Tools to Accelerate Neglected Disease Research: the Open Source Drug Discovery Model [Book Chapter]in Collaborative Computational Technologies for Biomedical Research, Wiley and Sons, May 2011.
  • Bhat AG, et al. Modeling metabolic adjustment in Mycobacterium tuberculosis upon treatment with Isoniazid. Systems and Synthetic Biology. 2011 Volume 4, Number 4, 299-309.
  • Sharma S, et al. Piperine as an inhibitor of Rv1258c, a putative multidrug efflux pump of Mycobacterium tuberculosis. J AntimicrobChemother. 2010 Aug;65(8):1694-701.
  • Mishra NK, et al. Prediction of cytochrome P450 isoform responsible for metabolizing a drug molecule. BMC Pharmacol. 2010 Jul 16; 10:8.
  • Mathew R, et al. Inhibition of mycobacterial growth by plumbagin derivatives. ChemBiol Drug Des. 2010 Jul 76(1); 34-42.
  • Garg A, et al. KiDoQ: using docking based energy scores to developligand based model for predicting antibacterials. BMC Bioinformatics. 2010 Mar 11;11:125.
  • Bhardwaj A, et al. Open Source Drug Discovery Consortium, TBrowse: an Integrative Genomics Map of Mycobacterium tuberculosis. Tuberculosis (Edinb). 2009 Sep; 89(5):386-7.
  • Bhardwaj A, et al . Open source drug discovery: a global collaborative drug discovery model for tuberculosis. Science and culture, January-February, 2011, vol. 77, nos. 1–2, 22-26.
slide39

Geek Nation: How Indian Science Is Taking Over The World

“..a journey to meet the inventors, engineers and young scientists behind this nation built not on conquest, oil or minerals, but on the scientific ingenuity of its people..”

“.. explores the reason why the government of the most religious country on earth has put its faith in science and technology..”

“..The West may think India is still in the gutter, but it is looking at the stars..”

Author, Angela Saini

slide40

Responses from the OSDD Community

  • I have had a thrilling experience with OSDD for the past 2 years and now I am ready to pursue my PHD at Indiana University
  • Abhik Seal, SBI Employee, Calcutta
  • I can access the CDAC supercomputing facility The Garuda Grid sitting at any place from anywhere in the world.
  • Rajdeep Poddar, Bio IT Application Specialist
  • OSDD is a boon to me, giving me a platform to research when I was at cross roads regarding career ,family and research
  • Swati Gandhi ,Baroda, Gujrat
  • It has been a dream come true and a great learning experience after becoming a part of OSDD
  • Dr Preetha Anil, SIAS, Kerala
  • I still remember what I said to myself on second day of OSDD conference looking into the mirror... “Is this the Shamsudheen from that remote village?????....!!!!!”
  • Shamsudheen K.V ,IGIB
slide41
Together we can …
  • .. and weshould !

http://www.osdd.net

http://c2d.osdd.net

http://sysborg2.osdd.net

Matt Smadley | Flickr.com

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