Roland Knispel BIOMOLECULES IN R&D INFORMATICS

Transcription

1 Roland Knispel BIOMOLECULES IN R&D INFORMATICS

2 WHAT S IN A STRUCTURE

3 Cyclosporin A Common name Cyclosporin A CAS number IUPAC name (chemical) (3S,6S,9S,12R,15S,18S,21S,24S,30S,33S)-30-ethyl-33-[(E,1R,2R)-1- hydroxy-2-methylhex-4-enyl]-1,4,7,10,12,15,19,25,28-nonamethyl-6,9,18,24- tetrakis(2-methylpropyl)-3,21-di(propan-2-yl)-1,4,7,10,13,16,19,22,25,28,31- undecazacyclotritriacontane-2,5,8,11,14,17,20,23,26,29,32-undecone IUPAC name (biological) cyclo[((2s)-2-aminobutyryl)-sarcosyl-nmethyl-l-leucyl-l-valyl-n-methyl-lleucyl-l-alanyl-d-alanyl-n-methyl-lleucyl-n-methyl-l-leucyl-n-methyl-lvalyl-n-methyl-(4r)-4-[(e)-but-2-enyl]-4- methyl-l-threonyl] Ref: PubChem CID *ChemAxon generated Sequence-based depiction Canonical HELM* PEPTIDE1{A.[dA].[meL].[meL].[meV].[B MT].[Abu].[Sar].[meL].V.[meL]}$PEPTID E1,PEPTIDE1,11:R2-1:R1$$$ Canonical SMILES CC[C@@H]1NC(=O)[C@H]([C@H](O)[C@ H](C)C\C=C\C)N(C)C(=O)[C@H](C(C)C)N( C)C(=O)[C@H](CC(C)C)N(C)C(=O)[C@H]( CC(C)C)N(C)C(=O)[C@@H](C)NC(=O)[C@ N(C)C1=O)C(C)C Closest natural sequence* AALLVTAGLVL InChI key PMATZTZNYRCHOR-CGLBZJNRSA-N InChI InChI=1S/C62H111N11O12/c (15)52(75)51-56(79)65-43(26-2)58(81)67(18)33-48(74)68(19)44(29-34(3)4)55(78)66-49(38(11)12)61(84)69(20)45(30-35(5)6)54(77)63-41(16)53(76)64-42(17)57(80)70(21)46(31-36(7)8)59(82)71(22)47(32-37(9)10)60(83)72(23)50(39(13)14)62(85)73 (51)24/h25,27,34-47,49-52,75H,26,28-33H2,1-24H3,(H,63,77)(H,64,76)(H,65,79)(H,66,78) /b27-25+/t40-,41+,42-,43+,44+,45+,46+,47+,49+,50+,51+,52- /m1/s1

4 Cyclosporin A Common name Cyclosporin A CAS number IUPAC name (chemical) (3S,6S,9S,12R,15S,18S,21S,24S,30S,33S)-30-ethyl-33-[(E,1R,2R)-1- hydroxy-2-methylhex-4-enyl]-1,4,7,10,12,15,19,25,28-nonamethyl-6,9,18,24- tetrakis(2-methylpropyl)-3,21-di(propan-2-yl)-1,4,7,10,13,16,19,22,25,28,31- undecazacyclotritriacontane-2,5,8,11,14,17,20,23,26,29,32-undecone IUPAC name (biological) cyclo[((2s)-2-aminobutyryl)-sarcosyl-nmethyl-l-leucyl-l-valyl-n-methyl-lleucyl-l-alanyl-d-alanyl-n-methyl-lleucyl-n-methyl-l-leucyl-n-methyl-lvalyl-n-methyl-(4r)-4-[(e)-but-2-enyl]-4- methyl-l-threonyl] Ref: PubChem CID *ChemAxon generated Canonical HELM* PEPTIDE1{A.[dA].[meL].[meL].[meV].[B MT].[Abu].[Sar].[meL].V.[meL]}$PEPTID E1,PEPTIDE1,11:R2-1:R1$$$ Canonical SMILES CC[C@@H]1NC(=O)[C@H]([C@H](O)[C@ H](C)C\C=C\C)N(C)C(=O)[C@H](C(C)C)N( C)C(=O)[C@H](CC(C)C)N(C)C(=O)[C@H]( CC(C)C)N(C)C(=O)[C@@H](C)NC(=O)[C@ N(C)C1=O)C(C)C Closest natural sequence* AALLVTAGLVL 2D structure (Marvin JS) InChI key PMATZTZNYRCHOR-CGLBZJNRSA-N InChI InChI=1S/C62H111N11O12/c (15)52(75)51-56(79)65-43(26-2)58(81)67(18)33-48(74)68(19)44(29-34(3)4)55(78)66-49(38(11)12)61(84)69(20)45(30-35(5)6)54(77)63-41(16)53(76)64-42(17)57(80)70(21)46(31-36(7)8)59(82)71(22)47(32-37(9)10)60(83)72(23)50(39(13)14)62(85)73 (51)24/h25,27,34-47,49-52,75H,26,28-33H2,1-24H3,(H,63,77)(H,64,76)(H,65,79)(H,66,78) /b27-25+/t40-,41+,42-,43+,44+,45+,46+,47+,49+,50+,51+,52- /m1/s1

5 Cyclosporin A Common name Cyclosporin A CAS number IUPAC name (chemical) (3S,6S,9S,12R,15S,18S,21S,24S,30S,33S)-30-ethyl-33-[(E,1R,2R)-1- hydroxy-2-methylhex-4-enyl]-1,4,7,10,12,15,19,25,28-nonamethyl-6,9,18,24- tetrakis(2-methylpropyl)-3,21-di(propan-2-yl)-1,4,7,10,13,16,19,22,25,28,31- undecazacyclotritriacontane-2,5,8,11,14,17,20,23,26,29,32-undecone IUPAC name (biological) cyclo[((2s)-2-aminobutyryl)-sarcosyl-nmethyl-l-leucyl-l-valyl-n-methyl-lleucyl-l-alanyl-d-alanyl-n-methyl-lleucyl-n-methyl-l-leucyl-n-methyl-lvalyl-n-methyl-(4r)-4-[(e)-but-2-enyl]-4- methyl-l-threonyl] Ref: PubChem CID *ChemAxon generated Canonical HELM* PEPTIDE1{A.[dA].[meL].[meL].[meV].[B MT].[Abu].[Sar].[meL].V.[meL]}$PEPTID E1,PEPTIDE1,11:R2-1:R1$$$ Canonical SMILES CC[C@@H]1NC(=O)[C@H]([C@H](O)[C@ H](C)C\C=C\C)N(C)C(=O)[C@H](C(C)C)N( C)C(=O)[C@H](CC(C)C)N(C)C(=O)[C@H]( CC(C)C)N(C)C(=O)[C@@H](C)NC(=O)[C@ N(C)C1=O)C(C)C Closest natural sequence* AALLVTAGLVL Sequence BioEddie InChI key PMATZTZNYRCHOR-CGLBZJNRSA-N InChI InChI=1S/C62H111N11O12/c (15)52(75)51-56(79)65-43(26-2)58(81)67(18)33-48(74)68(19)44(29-34(3)4)55(78)66-49(38(11)12)61(84)69(20)45(30-35(5)6)54(77)63-41(16)53(76)64-42(17)57(80)70(21)46(31-36(7)8)59(82)71(22)47(32-37(9)10)60(83)72(23)50(39(13)14)62(85)73 (51)24/h25,27,34-47,49-52,75H,26,28-33H2,1-24H3,(H,63,77)(H,64,76)(H,65,79)(H,66,78) /b27-25+/t40-,41+,42-,43+,44+,45+,46+,47+,49+,50+,51+,52- /m1/s1

6 In a workflow* How to make transition seamless How chemist refines structure Original Modified How SAR is performed *See Joshua Bishop, UGM presentation, 2017, San Francisco

7 THE TOOLS Equivalents of Marvin JS and Jchem Base for large molecules

8 BioEddie - JS application for all major browsers - Easy editing - No-structure components - Native support for MOL/HELM/sequence

9 BioEddie - JS application for all major browsers - Easy editing - No-structure components - Native support for MOL/HELM/sequence - Customizable views - Multi-level annotations

10 BioEddie Recently added capabilities Domain support in sequences for e.g. antibodies Improved support for HELM2 specification

11 BioEddie Next up Library manager (shared with Biomolecule Toolkit) HELM2 group support for e.g. ADCs Canvas layout improvements

12 Biomolecule Toolkit API (Java and REST-ful) for Native HELM support (HELM, HELM2, xhelm) 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

13 Biomolecule Toolkit MTGCRLCYWEC Enumerate (Pos. 3) / Find (distance=1) MT A CRLCYWEC MT L CRLCYWEC MT I CRLCYWEC MT V CRLCYWEC MT T CRLCYWEC MT[Dha]CRLCYWEC MT[Hse]CRLCYWEC MT[Nle]CRLCYWEC MT[Nva]CRLCYWEC MT[Sar]CRLCYWEC MT[Aha]CRLCYWEC Recently added capabilities support Improved support for HELM2 specification Entity type filter for querying Next up KNIME/PP nodes Search for similar sequence Position-based sequence enumeration Genealogy tracking

14 USE CASE: LIBRARY MANAGEMENT Using Marvin JS, BioEddie + Biomolecule Toolkit

15 Marvin JS + BioEddie

16 Marvin JS + BioEddie

17 Marvin JS + BioEddie Synchronizing...

18 Marvin JS + BioEddie Synchronizing...

19 Marvin JS + BioEddie

20 Marvin JS + BioEddie Synchronizing...

21 Marvin JS + BioEddie Synchronizing...

22 New monomer User draws structure Monomer library check Registration Verify and curate structure Not found? Push to library Add missing data

23 New monomer Synchronizing... New

24 BIOMOLECULE TOOLKIT AS A PLATFORM

25 Biomolecules in Instant JChem - Create new project pointing to Biomolecule Toolkit DB - Grid view with molecule visualization

26 Biomolecules in Instant JChem - Create new project pointing to Biomolecule Toolkit DB - Grid view with molecule visualization - Form views with additional data - Querying

27 Texelia BioScity - Data management/tracking and inventory for the Bio/Chem lab

28 Mockups only!!! POC development won t be possible til UGM HELM (auto-generated): untitled_mole... HELM (auto-generated): untitled_molecule_file3.mol IDBS EWB Web bringing HELM support into an ELN More on this by Paul Denny-Gouldson, IDBS

29 Summary Platform or add-on to provide large molecule informatics support Seamless transition between chemical space and sequence space HELM-compliant

30 THANK YOU