Biomolecule toolkit - ChemAxon · 2016 •Biomolecule support in Plexus Suite •Rule-based bulk...

BIOMOLECULE TOOLKIT

Roland Knispel

www.amgenscience.com

www.amgenscience.com

JChem

• API (Java and REST-ful) for

– Standardization

– Centralized DB storage

– Registration of entities and batches with custom

business logic

– Search by sequence/chemical structure/metadata

– Conversion to/from Mol/FASTA/HELM

– Property calculations

• Integrates with

– Almost there: InstantJChem, planned: Plexus

Connect

– Texelia BioScity, planned: IDBS E-Workbook

Biomolecule Toolkit

Pharma / Biotech / Institutes

• BMS, GSK, Lundbeck, Merck, Novartis, Pfizer,

Roche

Software vendors

• ACD/Labs, Arxspan, Biochemfusion, BioMax,

Biovia, ChemAxon, NextMove, Scilligence

Content / Service Providers

• EBI (ChEMBL), eMolecules, quattro

Regulative authorities

• Acceptable format for substance submissions

under ISO11238 implementation guidelines (FDA

and others)

The HELM ecosystem

6

CASE STUDY: CHEMBL V21

Tools for getting started with HELM, and content curation

• 19773 peptide

biotherapeutics with

associated activity data

• Molecules served as HELM

or chemical structure file

• ChEMBL interface:

searchable by CompoundID,

chemical structure or select

metadata

CHEMBL v21

- KNIME

- Standardizer node

Ungroup S-groups, Strip

salts/solvents, Remove

explicit hydrogens,

Neutralize structure,

Aromatize, Standardize

functional groups

Standardize Convert Canonicalize Store/Search

CHEMBL297610

Tools used

- KNIME

- Biomolecule Toolkit

- BioEddie for image

rendering

- 3 wrong

conversions in

ChEMBL data set

identified


PEPTIDE1{E.C.G.[X1091]}$$$$

wrong

PEPTIDE1{E}|PEPTIDE2{C.G.[X10

91]}$PEPTIDE1,PEPTIDE2,1:R3-

1:R1$$$

correct

Tools used

CHEMBL223118

- KNIME


- 864 HELM

notations in

ChEMBL changed

- Allows direct

comparison of

HELM notations


Tools used

Before:

PEPTIDE1{[ac].[dE].[Phe(4-Cl)].[d3-

Pal]}|PEPTIDE2{D.R.[dNal].L.K}|PEPT

IDE3{P.[dDpr].[am]}$PEPTIDE2,PEPT

IDE3,5:R2-

1:R1|PEPTIDE2,PEPTIDE1,5:R3-



1:R3$$$Before:

PEPTIDE1{G.Y.G.F}$PEPTIDE1,PEPTID

E1,4:R2-1:R1$$$

After:

PEPTIDE1{F.G.Y.G}$PEPTIDE1,PEPTID

E1,4:R2-1:R1$$$

After:

PEPTIDE1{[ac].[dE].[Phe(4-Cl)].[d3-

Pal].D.R.[dNal].L.K.P.[dDpr].[am]}$PEPTI

DE1,PEPTIDE1,11:R3-


2:R3$$$

CHEMBL412009

CHEMBL42623


Search by:

- Sequence (incl.

wildcards)

- Chemical structure

- Modifications

- Metadata


Tools used

USE CASE: ANTIBODY REGISTRATION

Using Instant JChem/MiniReg + Biomolecule Toolkit

Customer specification of an antibody:

• VL sequence / sequence (EIVLWQSPGT…)

• VH sequence / sequence (QVQIVQSGAE…)

• Fv backbone (scaffold) / text field (“CBr6”)

- Antibody definitions registered from file template

- Duplicate check and batch handling

- Assay data uploading

- Form views and reporting

Antibody registration

Delivered to the customer

BIOMOLECULE TOOLKIT AS A

PLATFORM

Registration DB

Architecture

Biomolecule Toolkit

Java API

REST-ful WS

Files (e.g. MOL,

FASTA, HELM)

Registration Client

Web

JChem for Office

Plexus Connect

Instant JChemSince 16.8.1

Q4

2017

Your application

- Create new project

pointing to

Biomolecule Toolkit

DB

- Grid view with

molecule

visualization

Since v16.8.1: Biomolecules in IJC

- Create new project

pointing to

Biomolecule Toolkit

DB

- Grid view with

molecule visualization

- Form views with

additional data

- Querying

Since v16.8.1: Biomolecules in IJC

Proof of concept – to be delivered to customers 2017

IDBS EWB Web – bringing HELM support into an ELN

Mockups only!!! – POC development won‘t be possible til UGM

HELM (auto-generated): untitled_molecule_file3.mol

HELM (auto-generated):

untitled_mole...

BIOEDDIE

A JS-based HELM editor for the web

- Easy structure/

sequence editing

- Supports no-

structure

components

- Native HELM support

- Multi-level

annotations

- Clear visualisation

- Customizable views

- JS application

BioEddie

- Standalone

- Bundled with

Biomolecule Toolkit

Beta tests running now

Contact biotoolkit-

[email protected]

to sign up

Release in September

BioEddie

mailto:[email protected]

ROADMAP

Q4 2016

• Biomolecule support in Plexus Suite

• Rule-based bulk import/editing of biomolecules

• BioEddie product release

Q1/2 2017

• Design/developabilityassessment/SAR analysis

2017

• Biomolecule support in JChem for Office applications

• IDBS E-Workbook integration

Roadmap

SUMMARY

Summary

• Curation and standardization of existing

content

• Structure management á la JChem/Marvin incl.

registration

• Biomolecule and bio-asset data management

platform for desktop and web

• New BioEddie (JS-based HELM editor)

THANK YOU

Roland Knispel

Biomolecule toolkit - ChemAxon · 2016 •Biomolecule support in Plexus Suite •Rule-based bulk...

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