Advanced application in Proteomics...!!

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Target Identification using Unique
Polymer Technology (UPT)
Overview of Company, Technology & New Case Studies of UPT
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Company Overview – Conception & Growth
Slide Number 2
Founded
2010
SCLC Tech for
Target ID
2013
UPT Technology for
Target ID
2014
2 Internal Drug Discovery Programs (virtual pharma model)
Target ID Technologies
Serving > 20 external, global drug
discovery efforts
Biopharmaceutical
Characterization Services
2016
Serving > 5 external biological
development program of large
biopharma companies
Protein Analysis Services
2016
Serving > 20 external academic and
biopharma start-up research

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Premises, Problem Statement and Value
Slide Number 3
Discovery Program Identified a bioactive (small-molecule, peptide,
protein, antibody) however the target(s), the cellular binding partners, of
bioactive is not known
• Information of Target of bioactive will allow
• Rational optimization of bioactive
• Drug-Efficacy biomarker discovery, patient stratification and
commercial differentiation by clarifying the action mechanism of
bioactive
• Early ‘de-risking’ of program by characterizing ‘off-target(s)’ of the
bioactive

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Our Focus = Target Identification
Slide Number 4
Our >10 years expertise allows us to evaluate the ‘fit-for-purpose’
technology for every program
and
then we deploy appropriate Technology for right target from a
portfolio of Technology
Different Technologies
1) UPT = Unique Polymer Technology, 2) SCLS = Subcellular Location Specific Target Capture Technology, 3) COMP = ‘in-silico’ target
ID workflows, 4) TBB = Traditional Bead/Biotinylated Molecule Based Method, 5) TPP = Thermal Proteome Profiling
Target Identification / Deconvolution is not Trivial
=
A single Tool / Technology May Not necessarily solve the problem for all

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Shantani’s Proprietary Target-ID Technologies
Slide Number 5
Technology Uniqueness Final Value
Unique Polymer
Technology (UPT)
Bait-Molecule ‘as-such’ without
derivatization are used for target ID
(Label-free Technology)
• Quick Target Profiling allowing a ‘Go/No Go’
development decision for phenotypically screened
compounds
• Rapid target profiling of multiple compounds to save
time and cost
SubCellularLocation
Specific Target
Capture Technology
(SCLS)
Subcellular Probes establishes
Target Location and Identity
• Precise Target Information driving rational lead
development
• Low False Positives saving time during target
validation
Computational
Supreme (Comp-S)
• Significantly Narrowed down list of targets to be
validated, saving time
• Assist in bringing selectivity while lead development
/ optimization

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Generic Target-ID Technologies
Slide Number 6
Technology Uniqueness Final Value
Traditional Bead /
Biotin / Photoaffinity
Based Approaches
(TBB)
Bait-Molecule showing cellular
EC50 > 5 µM and < 40 µM can go
through the process
• Target Profiling allowing a ‘Go/No Go’ development
decision for phenotypically screened compounds
having lower activity.
Thermal Proteome
Profiling
Bait-Molecule ‘as-such’ without
derivatization are used for target ID
(Label-free Technology)
• Orthogonal technique to verify the target

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We stand-by our work and can ‘follow-on’ on
identified Targets
• We are well-equipped to validate the identified targets in step-
wise manner
• Step-1: Computational Docking of Bait-Molecule with Identified Targets (if target
crystal structure is available)
• Step-2: Biophysical interaction study of Bait-Molecule with Identified Targets (if
protein is commercially available. If not, we can overexpress and purify the
protein for validation)
• Step-3: Functional Relevance Studies (siRNA knock down / overexpression of
target and assay of bait-molecule activity)
Slide Number 7

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Unique Polymer Technology (UPT)
Overview of Technology & Case Studies
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Technology Background (…1)
• Weak molecular interaction forces of a organic molecule are utilized
in immobilizing them on a surface (polymer matrix) that provides
complementary weak interactions.
• Molecules are immobilized in random orientation on the polymer
matrix and thus a molecule specific affinity matrix is prepared.
• Molecule Specific Affinity Matrix is then utilized in enriching its
target proteins from relevant biological lysates.
• Enriched proteins are identified using Mass-Spectrometry.
Slide Number 9

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Technology Background and Workflow (…2)
Slide Number 10
References:
1. Hati S. et al. Nature-Scientific Report (2016) 6:32213.
2. Bathula C. et al. Org Biomol Chem (2016) 14:8053-63.
3. Saxena C. Expert Opinion on Drug Discovery (2016) 11:1017-1025.
4. Patent Application :PCT/IN2017/000002, Priority Date January 2016

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Target ID of a novel cancer-preventive drug candidate
(client – South USA based Cancer Center)
Slide Number 11
• Scenario:
• Drug discovery program identified a compound that shows cancer prevention properties
• Shantani was contacted and client provided ~20 mg of compound
• Time-lines at Shantani: 7-9 Weeks (Shantani additionally cultured the relevant cell-lines)
• Final Deliverable: Target was identified and validated

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UPT Workflow at Shantani
Slide Number 12
Selection of Appropriate Matrix Surface
for Preparing Molecule Specific Affinity
Matrix
Affinity Pull-Down of Protein Interacting Partners, Identification of
Protein using Mass-Spec and Target Deconvolution
Average # of Protein
Identified in triplicate
control (compound not
loaded) experiment =
116
Average # of Protein
Identified in triplicate
compound loaded
matrix experiment =
136
Analysis of Identified Proteins suggested enrichment of
eight proteins in compounded loaded matrix
3 proteins were removed as PPI suspects
1 out of rest of the 5 proteins was prioritized based on its possible
role in the observed phenotype

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Target Validation at Shantani
Slide Number 13
To gain confidence that identified protein
is a putative target Test-Compound
structure was docked with it
Target Activity Assay was designed, optimized and then test-
compound’s activity was evaluated
Compound
Structure
Confidential
Experiments were
carried out in
triplicate and were
repeated on three
different days
Identified Target active site was predicted to
be substantially blocked by test-compound
Substantial decrease in ‘in-vitro’ activity of identified target in
presence of test-compound validated the interaction

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Toxicity Profiling using UPT (Client – one of the
biggest global pharma)
Slide Number 14
• Scenario:
• BACE-I inhibitor, one of the promising therapies for Alzheimer’s
• Preclinical compounds shows ocular toxicity in animal models
• Client provided: ~20 mg (Multiple molecules)| Cell-Lines – RPE (relevant to Ocular Toxicity)
• Time-lines at Shantani: 5-7 Weeks
• Final Deliverable: Information of Off-Target driving toxicity

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UPT Workflow at Shantani
Slide Number 15
Selection of Appropriate Matrix Surface for
Preparing Molecule Specific Affinity Matrix
Affinity Pull-Down of Protein Interacting Partners, Identification of
Protein using Mass-Spec and Target Deconvolution
Average # of Protein Identified
in triplicate control
(compound not loaded)
experiment = 220
Average # of Protein
Identified in triplicate
compound loaded matrix
experiment = 260
Analysis of Identified Proteins suggested enrichment of
twelve proteins in compounded loaded matrix
These proteins belonged to only two class of proteins
Relevance of both the protein class with respect to Ocular
Toxicity was evaluated and list was narrowed down to 3 proteins
One of the Cathepsin family member was identified and later validated as culprit for toxicity

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Target ID of a novel drug candidate for male
contraception (client – mid-west USA based Medical
Center)
Slide Number 16
• Scenario:
• Drug discovery program identified a compound that shows antispermatogenic effect in
animal studies
• Bead based affinity pull-down identified potential target candidates that could not be
validated
• Shantani was contacted and client provided ~20 mg of compound
• Time-lines at Shantani: 7-9 Weeks (Shantani procured Rat Testis and used it as Biological System
for Target ID)
• Final Deliverable: Very small list of highly putative targets directly linked with spermatogenesis

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UPT Workflow at Shantani
Slide Number 17
Selection of Appropriate Matrix Surface
for Preparing Molecule Specific Affinity
Matrix
Affinity Pull-Down of Protein Interacting Partners, Identification of
Protein using Mass-Spec and Target Deconvolution
Average # of Protein
Identified in triplicate
control (compound not
loaded) experiment =
168
Average # of Protein
Identified in triplicate
compound loaded
matrix experiment =
169
Analysis of Identified Proteins suggested enrichment of
six proteins in compounded loaded matrix
One of the enriched target protein was Aldh1a1
Aldh1a1 shares > 68% sequence similarity with Aldh1a2, a target
protein known for antispermatogenesis for a different molecule

18. www.shantani.com
Target ID of a novel antiviral drug candidate
(client – an Indian Institute)
Slide Number 18
• Scenario:
• Drug discovery program identified a compound that shows antiviral (influenza) activity
• Shantani was contacted and client provided ~20 mg of compound and the host cell lysate
• Time-lines at Shantani: 3-4 Weeks
• Final Deliverable: Very small list of highly putative targets that are highly associated with the
phenotype

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UPT Workflow at Shantani
Slide Number 19
Selection of Appropriate Matrix Surface
for Preparing Molecule Specific Affinity
Matrix
Affinity Pull-Down of Protein Interacting Partners, Identification of
Protein using Mass-Spec and Target Deconvolution
Average # of Protein
Identified in triplicate
control (compound not
loaded) experiment =
285
Average # of Protein
Identified in triplicate
compound loaded
matrix experiment =
253
Analysis of Identified Proteins suggested enrichment of
nine proteins in compounded loaded matrix
Two of the top enriched target protein was eIF3g and eIF-4H
Both the proteins are known to play significant role in viral
replication

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Conclusions from UPT based Chemical-
Proteomics Methodologies
• UPT method is capable of identifying ‘on/off’ targets of Small Molecules.
• ‘Bait-molecule’ derivation and SAR information not needed for Target ID.
• Target Deconvolution can be carried out as fast as in 5 weeks.
• False-positive identification rates can be controlled by running multiple
experimental replicates.
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Several Successful Examples
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Value across the discovery and development cycle
Slide Number 22

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Target ID and Client Engagement Workflow
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Go/No Go Decision Point
If molecule can not be immobilized –
Project Abandoned
(Current Success Rate > 90%)
Project
Information
from Client
Decision
on use of
UPT
Shantani Deliver
Identity of
Deconvoluted
Target(s)
+
Techno-commercial
Target Knowledge
Package
(additionally
charged)
If mutually
decided
Shantani
Takes up
Target
Validation
Work as
separate
project
0-2 weeks 0-5 weeks

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Our Key Strengths
• Globally Competitive Science
• High Ethical and Professional Standards
• Networked Operational Model for Cost-Effectiveness
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Our Customer’s Profile
World’s Largest
Chemical Producer
HQ - Germany
East Coast-USA based
one of the Largest
Pharmaceutical
Company

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Shantani R&D Center @ Innovation Park

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Thank You.
Connect for further discussions
Saba Naaz Siddique
saba@shantani.com
http://www.shantani.com
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