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A chemical workbench for Biopolymers
ChemAxon User Group Meeting
April, 2017
Joshua A. Bishop, Ph.D.CPH IT & Informatics - MRL IT
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Compound Design & Synthesis Information Cycle
Biological
Testing
Purification
& Registration
Chemical
Synthesis
Design
& Selection
Hypothesis
Generation
Analysis &
Decision-making
Perceived gaps
Capture of valuable high-throughput chemistry
data and use of ELN reactions
Tracking of designs & work-in-progress
Cheminformatics tools integration w/
Spotfire
Building block search and
selection
Data Access
Approach
Adopt services-oriented
architecture from the ground up
Reusable web-components where
possible
Leverage a Data Platform for
ingestion and aggregation
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Biopolymer Workbench - Objectives
3
Goal 1 – Fill unmet gaps in workflow for biopolymer chemists
Goal 1a – Fill unmet TECHNOLOGY gaps as to fill unmet gaps in workflow…
Property
CalculationsAutomated
SynthesisRegistration Purification SAR Tools
COTS
Solutionjavascript
Perception
Engine
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Biopolymer Design-Make-Test
Scientific Workflow
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Biopolymer
Calculator 1
Biopolymer
Calculator 2
Biopolymer
Calculator 3
Export .txt file suitable for
synthesis robotics
Enumerate
desired library
Synthesize
desired library
Screen libraries across
biological assaysPush to
requested assays
Register and purify
successful syntheses
Assay result analysis
Biopolymer SAR tools
HELM
Monomer
Library
Biopolymer Design enumerator
= BioEddie use/services/integration
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Biopolymer Design-Make-Test
Technology Stack
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BP enumerator
HELM monomer
library
BP property calculator 1
Registered virtual
and real biopolymers
BP synthesis request
and registration
Assay Data
BP SAR
Tools
SIM Data Platform
Assay Data collection
BP property calculator 2 BP property calculator 3
Registered
small molecules Databases
Aggregation
Services
Applications
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Biopolymer Enumeration and Design
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Enumeration and DesignBP virtual
registration
MS directed
Synthesis verification
Assay Request
SAR Analysis
Purification and
Formal BP Registration
Robotic Synthesizers
MerMades
BP sequence:
CEXISYZLP
Variables:
X = C,L,P,E, [dMc]
Y = [aI],L,E,R
Z = S,[giT],R,I
EnumerateVirtual Library
Virtual Library
Biopolymer
Specific Calculations
and Predicted Properties Synthesis
Selection
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Biopolymer Enumeration Tools
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Launch BioEddie
Choose HELM file
Enter position(s) to be changed
Enter monomer codes to be changed
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Biopolymer Design
Discngine, BioEddie and Spotfire
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Biopolymer Synthesis Execution Tools
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BP Virtual registration
BioReg
HELM
Monomer
Library
Robotic Synthesizers
MerMades
PLP
Design and
Enumeration
MS directed
Synthesis verificationMerMade
Monomer
Library
Assay Request
SAR Analysis
Purification and
Formal BP Registration
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Registration
and perception
How user interacts in sketcher with entity
How data base interprets
and stores input
NO NEW templates
detected
Registration
and perception
How user interacts in sketcher with entity
NEW templates
detected
Your structure appears to have
novel monomers.
Please remediate.
Show monomers to user that are
not present in library, assign 3
letter code per business rules,
verify with user accuracy, push to
central monomer library
Complete registration
Complex Biopolymers & Singleton/Small Scale DMT
How data base interprets
and stores input
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Biopolymer Purification
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Design and
Enumeration
MS directed
Synthesis verification
Assay Request
SAR Analysis
Virtual
RegistrationSynthesis
Purification and
Formal BP Registration
HELM FileEKB purification
workflow
HELM
Monomer
Library
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Assay Request
and SAR Analysis
Biopolymer SAR Tools
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Design and
Enumeration
MS directed
Synthesis verification
Virtual
RegistrationSynthesis
Purification and
Formal BP Registration
Data Platform
IngestionSpotfire visuals and
BP SAR Tools
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Biopolymer SAR Tools – mockups
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Biopolymer SAR Tools – mockups
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Biopolymer SAR Tools – mockups
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Biopolymer SAR Tools – mockups
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Biopolymer Design-Make-Test
Scientific Workflow
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Biopolymer
Calculator 1
Biopolymer
Calculator 2
Biopolymer
Calculator 3
Export .txt file suitable for
synthesis robotics
Enumerate
desired library
Synthesize
desired library
Screen libraries across
biological assaysPush to
requested assays
Register and purify
successful syntheses
Assay result analysis
Biopolymer SAR tools
HELM
Monomer
Library
Biopolymer Design enumerator
= BioEddie use/services/integration
![Page 18: A chemical workbench for Biopolymers · 2017-11-28 · A chemical workbench for Biopolymers ChemAxon User Group Meeting April, 2017 Joshua A. Bishop, Ph.D. CPH IT & Informatics -](https://reader033.vdocuments.us/reader033/viewer/2022042310/5ed792d767b53e06555d28d3/html5/thumbnails/18.jpg)
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Acknowledgments
Farida Kopti
Matt Walker
Jay Mehta
Charlie Chang
Chris McNally
Iain Wallace
Angie Kantola
Chris Waller
Mark Schreiber
MRL
Rich Tillyer
Rob Garbaccio
Brad Sherborne
Sookhee Nicole Ha
David Tellers
Greg Adams
Songnian Li
Dmitri Pissarnitski
Craig Parish
Tony Siu
Claudio Mapelli
Sustaining Partners
ChemAxon
EPAM
Discngine
MRL IT