The Mycobacterium tuberculosis SysBorg

The Mycobacterium tuberculosis SysBorg

M. tuberculosis entering a macrophage

Latent stage

Infection process?

Latency?Im

mun

e cl

eara

nce?

Questions in Tuberculosis

Pi

Subvert Host signalling;

live within the enemy

Express antivirulence; Hide

Battle lost

Find surface receptors and enter; Friendship

Life from the perspective of the pathogen

N

Pathogen

GENOME

ORFs

PROTEIN SEQUENCES

SIMILARITY SEARCH ALGORITHMSBLAST, PLHoST, BLASTCLUST,…

FUNCTION PREDICTION BIOCHEMICAL ASSAYBIOPHYSICAL ASSAY

CLONING PROTEIN PRODUCED

TARGET SELECTION ALGORITHMSINVARIANT PEPTIDES, HIGH COST,

PATHOGEN(+) AND HUMAN(-), PDB, SURFACE PREDICTION

IN SILICO TARGET ASSESSMENTUSING M. tuberculosis SysBorg

FINALIZATION OF ORFs (CONSIDER EXPRESSION

ISSUES)

STEPS TO DRUG DISCOVERY

TARGET VALIDATION

Pathogen

GENOME

ORFs

PROTEIN SEQUENCES

SURFACE LOCALIZATION ALGORITHMSPSORT, SPAAN, MAAP,…

SURFACE PREDICTION

USE ANIMAL MODELS

CLONING PROTEIN PRODUCED

FILTERING ALGORITHMSEPITOPE PREDICTION, ALLERGENS,

ANTIGENIC REGIONS, TRANSMEMBRANE REGIONS PATHOGEN(+) AND HUMAN(-),

PDB

IN SILICO CANDIDATE ASSESSMENTUSING M. tuberculosis SysBorg

FINALIZATION OF ORFs (CONSIDER EXPRESSION

ISSUES)

STEPS TO VACCINE DISCOVERY

The Events

Chairman, proposes a networked initiative for tuberculosis

Co-ordinator assigned. Partnership with SilicoGene, Industry established

A first version of structure of SysBorg platform prepared. This had fixed number of Fields

A Brainstorming session was held

A Flexible architecture proposed, where the numbers of Fields, Tables and Units were made flexible Windows version

Combination query samples generated applying boolean and arithmetic operators

Scientists & students collect curated data in structured format

Data Plugged in to the platform

LINUX version also developed

Construction of M. tuberculosis SysBorg is a Mega Project

M. tuberculosis SysBorg

SKB DD

SC

SG

BKM

RR

CNM

BS

VB

MB

BP

YS

SR

RS

GPSR

RCHK

SM

BKM

Networking of expert scientists at the national level

M. tuberculosis SysBorg : A systems Biology platform for infectious diseases using Systems Biology of whole organism

( CSIR Task force Network for in silico drug target discovery )

VPCIACBR NII

IMTECH CDRI IICB RRLJOther partners

What does M.tb do during infection

How does Latency arise

How is the pathogen cleared

Y Y

FAD Fumarate

Coenzyme A

NADHATP

How does M.tb infect

Metabolic and Signalling Network

Activity structuring

annotation drugs geneexpress hostpatho strainpoly pathways

Units

Blocks

Tables

Tables

Tables

Tables Tables

Tables

Tables

Tables

Tables

Tables

Tables

Tables

A Seventh Block

administration

Payments Reports consolidation

Chasing Intellectual Property Rights

Business Development issues

Certification from Scientists

Drafting agreements and signing

Data structuring

Decide on Primary Key

GI Number?

Rv Number?

For Drug Block?

In the Brain storming session scientists elected to use Rv Number following TubercuList created by Stewart Cole’s group but also provide mapping to GI numbers

Anticipated Difficulties – Forced Redundancies

Several drugs or small molecules for each protein

Each drug has several attributes (Fields)

Creation of Redundant entries – Records with repetition of Rv nos.

Several immunochemical data for each protein antigen data

Creation of Redundant entries – Records with repetition of Rv nos.

Each study has different facets of immunochemical data

Another difficulty – Many published reports in the pre-genome sequence era did not use ORF nos. or ORF ids

Mapping with calculated molecular weight is risky

Due to (1) Experimental Errors?

(2) Whether they were whole proteins or degraded or processed?

We will have a Redundant Database with replicate entries

Each entry mapped to a singular PubMed ID is possible. In case of drugs, several PubMed IDs will come.

We will never be able to use many data available in the literature

Caveats

Result of a query

Multiple data on some ORFs and little or no data on many ORFs

Antigens Table

Total Non-redundant

Post Genome era of M. tuberculosis

Should experiments be repeated –

If yes, then who will fund?If no, then how do we benefit?

We just have to live with it!

annot

ABCPredBetaBarrelOuterMembraneProteinsCDC1551HorizontalTransferDNABinderDuplicatedGenesEssentialGeneGeneFunctionPredictionOfIntergenicRegionInterdomInteractionsInvariantSignaturesLiteratureOperonMapTableOperonsORFFunctionsOrthologousGenesPrintsPatternsPrositePatternsPsortSubcellularLocalisationRNABinderRv2GIRvHorizontalTransferUnfoldedandFolded

IN OPEN SOURCE PORTAL (OPEN SOURCE DRUG DISCOVERY)

USE R, BIOCONDUCTOR, WIKI/TWIKI drugs

FirstLineDrugsFirstLineDrugsStructureActivity

SecondLineDrugsDrugResistance

NewDrugEntitiesDrugFailures

DrugResponseRNAProteinTDRTargets

4 Basic questions to be pursued: How does a pathogen infect its host?

How does latency arise?What is the process of infection?

How pathogens are cleared by our immune system?

geneexpress

MtbStrainWiseExpressionZScoresCodonAdaptationIndexCodonAdaptationIndexCDC1551CodonAdaptationIndexH37RaExperimentallyValidatedEssentialGenesGenesRequiredForOptimalGrowthGQuadraplexIntergenic3

GeneticComparisonNonEssentialGenesGQuadraplexIntergenicGQuadraplexIntragenic1GquadraplexintragenicGQuadraplexRegulatory2GQuadraplexRegulatoryHighProbabilityOfEssentialGenesIntergenicRegionsHighExpressionGeneEIntergenicRegionsHighExpressionPmiRNABindingSites

IN OPEN SOURCE PORTAL (OPEN SOURCE DRUG DISCOVERY)

USE R, BIOCONDUCTOR, WIKI/TWIKI

hostpatho

AntigensHostMimicry

MtbPersistanceSurfaceAdhesion

VaccineCandidatesPad

4 Basic questions to be pursued: How does a pathogen infect its host?

How does latency arise?What is the process of infection?

How pathogens are cleared by our immune system?

IN OPEN SOURCE PORTAL (OPEN SOURCE DRUG DISCOVERY)

USE R, BIOCONDUCTOR, WIKI/TWIKI

pathways

NewTransporterPathwayReactionSTKinasesPhosphatasesGenomeScaleMetabolicReactionNetwork

proteininteract

ProteinInteractionProteinProteinInteractionValues

strainpoly

InDelintergenicInDelintragenic

InterspersedRepetitiveSNPintragenicSNPintergenic

RvMIRUGenePositionTransposonMutantsFinal

4 Basic questions to be pursued: How does a pathogen infect its host?

How does latency arise?What is the process of infection?

How pathogens are cleared by our immune system?

Targeting Microbial Surface Proteins for therapeutics

Attachment mediated by adhesins

Colonization and pathogenesis

Drug OR Antibody bind to adhesins and abrogate binding of pathogens to host cell receptors

FOUR CLASSES OF ADHESINS ARE KNOWN IN PATHOGENS

All proteins of M. tuberculosis 3997

Give me proteins with Pad >= 0.7

201

How many proteins are in Antigens table?

15

How many proteins have no match with Human proteins

57

Amit Sinha, Ayush Raman, Archana Pan, B.K.Malik, Balvinder Singh, Beena Pillai, Bhanot Priyamwada Sinha,Chabinath N. Mandal, Charu Kapil Richa, Chitra Dutta, Chitra Dutta, Debasis Dash, Debojyoti Chakraborty, Faraz Alam Ansari, G.P. Singh, Gajendra Pal Singh Raghava, Gargi Guhathakurta, Ipsita Chanda, Manoj Hariharan, Mekapati Bala Subramanyam, Mridula Bose, Mudgal Haymanti, Muthiah Gnanamani, Nanda Ghoshal, Pallavi Sarmah, Rakesh K. Sharma, Ranjan Basu, Ravishankar Ramachandran, Rupanjali Chaudhuri, Srinivasan Ramachandran*, Sabyasachi Das, Samir K. Brahmachari, Sandip Paul, Sanjib Chatterjee, Shantanu Chowdhury, Simone Gupta, Souvik Maiti, Subhagata Ghosh, Suchir Arora, Sudipto Saha, Sumit Deb, Vani Brahmachari, Vikram Kumar, Vinod Scaria, Yasha Bhasin, Yogendra Singh