The NCI/CADD Group's InChI Usage and Analysis of Tautomerism for InChI V2

Transcription

1 The NCI/CADD Group's InChI Usage and Analysis of Tautomerism for InChI V2 Marc C. Nicklaus Computer-Aided Drug Design (CADD) Group Chemical Biology Laboratory Center for Cancer Research National Cancer Institute National Institutes of Health Frederick, Maryland 21702

2 Chemical Identifier Resolver (CIR) Resolves structure identifiers or representations, i.e. converts one structure identifier/representation into another Usable by humans; but optimized for communication between computers (returns MIME/text pages wherever possible) Launched in June 2009 Planned: major update of services and underlying database, the CADD Group s Chemical Structure DataBase (CSDB) 2

3 Chemical Identifier Resolver (CIR) Flowchart identifier representation http request detection of the identifier type identifier is a hashed structure representation (e.g. InChIKey), or chemical name etc. identifier is a full structure representation (e.g. SMILES, InChI) structure calculation of the requested structure representation e.g. InChI, GIF image http response e.g. CAS number, chemical name database lookup

4 Chemical Identifier Resolver (CIR) Examples: Naproxen sodium MIME type: text/plain Buckyball XMWRBQBLMFGWIX-UHFFFAYSA-N/image?height=300&width=300&bgcolor=black&bondcolor=white

5 Chemical Structure Database (CSDB) in CIR Currently available in CIR: 140 chemical structure databases 120 million structure records 84.6 million unique structures by FICuS 110 million unique Standard InChIKeys for lookup (includes ~25 million derived scaffold and ring structures) ChemNavigator/Sigma iresearch Library compilation of commercially available screening compounds from ~300 international chemistry suppliers PubChem database including pen NCI database, EPA DSSTox databases, NIAID HIV database, NIST Webbook, NLM ChemIDplus, ChemSpider, Commercial Sources / others Asinex, Comgenex, emolecules, ChemNav. iresearch Lib. ~56% PubChem ~38% ~6% others

6 NCI/CADD Structure Identifiers NCI/CADD Structure Identifiers Based on CACTVS hashcodes; 16-digit hex numbers (64 bit unsigned) Fragments Isotopes Charges Tautomers Stereochemistry sensitive sensitive sensitive sensitive sensitive - Na + D D D D D D - + NH 3 H = H C H NH 2 H C H H NH 2 F I C T S = u u u u u H NH 2 H C H NH 2 un-sensitive un-sensitive un-sensitive un-sensitive un-sensitive FICuS identifier: comes closest to how a chemist perceives a compound Sitzmann et al. SAR QSAR Environ. Res. 2008, 19, 1 9 Tautomerism in large small-molecule databases

7 tautomer N NH H NH 2 HNDVDQJCIGZPN-UHFFFAYSA-N 9850FD9F9E2B4E25-FICuS HN N NH 2 HNDVDQJCIGZPN-RXMQYKEDSA-N E92E4BA2869F3611-FICuS H stereoisomers HN H N NH 2 HNDVDQJCIGZPN-YFKPBYRVSA-N 8A7AD1EB498CC76A-FICuS salt Na + HN - N NH 2 UHPNKBYGGMJTIM-UHFFFAYSA-M E5F83F10C5DB080A-FICuS HNDVDQJCIGZPN-UHFFFAYSA-N Histidine Std. InChIKey HN H N NH FD9F9E2B4E25-FICuS FICuS HN Na errors N NH2 HN H N NH charged form HN - + N NH 3 HNDVDQJCIGZPN-UHFFFAYSA-N A3DAE DDE4-FICuS isotope NH N 15 NH 2 H UHPNKBYGGMJTIM-UHFFFAYSA-M E5F83F10C5DB080A-FICuS HNDVDQJCIGZPN-UHFFFAYSA-N 9850FD9F9E2B4E25-FICuS HNDVDQJCIGZPN-CDYZYAPPSA-N B2FDA68AEDA06DB9-FICuS Tautomerism in large small-molecule databases

8 Chemical Structure Database (current version) calculation of Standard InChIKey and NCI/CADD identifiers (from ~350 million original raw records including multiple database versions) Total unique records: 168,015,387 (includes ~40M derived scaffold and ring structures) original structure record structure normalization parent structure hashcode calculation E_HASHISY NCI/CADD Identifier InChIKeys Standard: 167,722,852 Set 1: 167,722,850 Set 2: 167,722,852 Set 3: 167,698,426 any unique: 167,723,824 FICTS FICuS union set: uuuuu Standard InChIKey 1.04 NCI/CADD Identifiers (unique counts) FICTS: 125,009,738 FICuS: 121,429,689 uuuuu: 108,993,792 (before normalization: ~127M) Standard Set 1 Set 2 Set 3

9 Tautomers Tautomers are isomers that can transform into each other through chemical equilibrium reactions - Prototropic tautomerism: intramolecular movement of a hydrogen atom enol form keto form Strongly environmentdependent (ph, solvent, T, time,... ) - Ring-chain tautomerism: movement of the proton accompanied by opening/closing of a ring cyclic form acyclic form 9

10 Importance of Getting Tautomers Right The existence of multiple tautomeric forms of the same molecule can create problems! Property calculation Variations across tautomers by several orders of magnitude. Eg. pka, logp Registration in databases May lead to duplicate registration, missed molecules in searches, or incorrect identification of two structures as the same compound Clustering diversity (Tanimoto) similarity between tautomers can be very low Ligand docking Hydrogen bonding interactions are different for different tautomers X-ray crystallographic Most important for InChI What is the tautomeric form present in ligandprotein complexes? May impact the success of drug discovery 10

11 NCI/CADD Chemical Structure Database Tautomer Analysis Asinex 100 ChemBridge 90 ComGenex ChemNavigator 80 Columbia University 70 Molecular Screening Center 60 number EPA DSSTox database 50 Specs releases Ambinter BIND BindingDB ChemNavigator KEGG NCI pen Database NIST WebBook NLM ChemIDplus NMRShiftDB Thomson Pharma Wombat Average tautomeric overlap per DB ~0.3% Tautomeric overlap across all DBs: ~10% Structures capable of tautomerism: ~68% tautomeric overlap within each individual database release NCI/DTP PASS Training Set SGC-x ChemDB ZINC percentage of actual duplicates FICTS - FICuS parent structure in each database release frequency ChEBI ChemSpider Sitzmann M, Ihlenfeldt WD, Nicklaus MC. J Comput Aided Mol Des Jun;24(6-7): Tautomerism in large small-molecule databases

12 Tautomerism in Chemoinformatics In reality, tautomerism is a quantum-mechanical effect (orbital changes) In principle calculable at the QM level But incorporating the conditions (solvent, ph,...) is not easy...and these calculations can take weeks for one molecule In chemoinformatics: rule-based (you have maybe 100 ms per structure!) These rules will be correct only in a statistical sense Whether QM or rule-based: one has to agree on what set and ranges of conditions to use to define tautomerism in a practical application, e.g. for identifiers used for compound registration in a database or repository 12

13 Tautomerism and Identifiers Different chemical identifiers are sensitive to tautomerism to different degrees: InChI/InChIKey [IUPAC International Chemical Identifier] one identifier with a layer structure in principle designed to be tautomer-invariant but not all types of common tautomerism used by default (e.g. not invariant by default to keto/enol tautomerism in v. 1.04) NCI/CADD identifiers 1 several identifiers with different sensitivities to chemical features; most important one: FICuS tautomer-invariant 1 Sitzmann et al. SAR QSAR Environ. Res. 2008, 19,

14 Example of Known Issues in InChI 1,4-oxime/nitroso tautomerism not currently handled by InChI. Adding it will break current InChI. H N H N - H N + InChI=1S/C5H5N2/c (5)8/h1-4,7H InChI=1S/C5H5N2/c (5)8/h1-4,8H Dmitrii Tchekhovskoi, IUPAC InChI Committee Meeting, March

15 Tautomerism Transform Rules CACTVS: rule set of 21 transforms encoded as (CACTVS-extended) SMIRKS Types of tautomerism covered: rule 1: 1.3 (thio)keto/(thio)enol * rule 2: 1.5 (thio)keto/(thio)enol rule 3: simple (aliphatic) imine rule 4: special imine rule 5: 1.3 aromatic heteroatom H shift rule 6: 1.3 heteroatom H shift rule 7: 1.5 (aromatic) heteroatom H shift (1) rule 8: 1.5 (aromatic) heteroatom H shift (2) rule 9: 1.7 (aromatic) heteroatom H shift rule 10: 1.9 (aromatic) heteroatom H shift rule 11: 1.11 (aromatic) heteroatom H shift rule 12: furanones rule 13: keten/ynol exchange rule 14: ionic nitro/aci-nitro rule 15: pentavalent nitro/aci-nitro rule 16: oxim/nitroso rule 17: oxim/nitroso via phenol rule 18: cyanic/iso-cyanic acids rule 19: formamidinesulfinic acids rule 20: isocyanides rule 21: phosphonic acids * rule 1 has been merged with rule 6 CACTVS by: Wolf-Dietrich Ihlenfeldt, Xemistry GmbH 15

16 Tautomer verlap in Commercial Catalogs Aldrich Market Select (AMS) database of commercially available samples: 5,755,574 molecules ( version) Examples (prices per 1 g): 31,156 conflicts 62,872 molecules n-tuples Conflicts 2 30,619 $313 $ Same original supplier! $188 $300 16

17 Quadruple Tautomeric Case 17

18 But wait, there is more: Ring-Chain Tautomerism exocyclic endocyclic XH: Nucleophilic center, YZ: Electrophilic center Prototropic tautomerism handled by most chemoinformatics tools:...but not ring-chain tautomerism: The need for computer programs that predict ringchain tautomerization, a capability absent from the current tautomer generation programs etc. Y.C. Martin, J Comput Aided Mol Des. 2009: 23: Let s not forget tautomers UR GAL 18

19 Example for Ring-Chain Tautomerism: Warfarin Anticoagulant drug used in the prevention of thrombosis Introduced in 1948 as a pesticide against rats and mice Approved in 1954 for use as a medication Most widely prescribed oral anticoagulant drug in the U.S. Inhibits vitamin K epoxide reductase (recycles oxidized vitamin K1 to its reduced form) 19

20 Tautomerism of Warfarin What to Expect Can exist in principle in as many as 40 topologically distinct tautomeric forms! H H H H H H H H H H H H H H Submitted to PubChem Mentioned in literature Confirmed experimentally Valente E.J. et al., J. Med. Chem. 1977, 20, Karlsson, B.C.G. et al., J. Phys. Chem. B 2007, 111, Porter, R.P., J. Comput. Aided Mol. Des. 2010, 24, Nicholls, I.A. et al., J. Mol. Recognit. 2010, 23,

21 Tautomerism of Warfarin FICuS Identifier H H H H H H D76B88C F1-FICuS D76B88C F1-FICuS D76B88C F1-FICuS 09BB2FAADA1508A7-FICuS H H H D76B88C F1-FICuS D76B88C F1-FICuS D76B88C F1-FICuS 8F5519DD1E62B6B2-FICuS H H H H H D76B88C F1-FICuS D76B88C F1-FICuS D76B88C F1-FICuS Not covered by current rule set! prototropic tautomerism ring-chain 21 tautomerism 21

22 Tautomerism of Warfarin InChIKey Identifier H H H H H QTXVAVXCBMYBJW-UHFFFAYSA-N VWSXIGYSLWNCBN-VAWYXSNFSA-N GRAAPKVUSREWIL-UHFFFAYSA-N H LSCYDZJASSKSMJ-UHFFFAYSA-N H H H FQEPJULUDFINX-UHFFFAYSA-N UCKRWKACBKRIKB-VAWYXSNFSA-N NNLYDNMZCAHUV-UHFFFAYSA-N PIBBXWKSPNJFI-UHFFFAYSA-N H H H H H PJVWKTKQMNHTI-UHFFFAYSA-N FVSFCRPKSVCTBA-VAWYXSNFSA-N BBSKMPTDUUMKL-UHFFFAYSA-N prototropic tautomerism All InChIKey identifiers are different!! Revamp handling of tautomerism in InChI V.2 ring-chain 22 tautomerism 22

23 Definition of Ring-Chain Tautomerism Rules Baldwin's Rules as starting point J.E. Baldwin, J Chem Soc Chem Comun. 1976: Ring sizes being formed: 3 7 Breaking bonds: exocyclic (exo) or endocyclic (endo) Geometry of carbon atoms: sp 3 (tet), sp 2 (trig) or sp (dig) Disfavoured / favoured ring closures Baldwin s Rules ur Rules 11 ring-chain rules each rule is encoded as a SMIRKS string Guasch, L. et al.. JCIM (under revision) 23

24 6-exo-Trig exo-Dig endo-Trig Examples: Ring-chain tautomerism rules 24

25 Tautomers per Structure in the AMS Database Prototropic Tautomerism 21 Rules Ring-chain Tautomerism 11 Rules Count % Count % no tautomers (single molecule) 1,393, ,297, one tautomer 1,235, , tautomers 833, , tautomers 483, , tautomers 223, , tautomers 889, , tautomers 584, , tautomers 72, , Ring-chain tautomersim is in the minority relative to prototropic tautomerism but it is not an exotic occurrence either tautomers 35, , tautomers 3, , tautomers

26 Procedure: Tautomerism Analysis by Experimental Chemoinformatics Select tautomer tuples from AMS by coverage of types of tautomer transforms chemical diversity solubility availability from same original supplier likelihood to be distinguishable by NMR price Purchase samples Analyze by NMR spectroscopy Goal: measure as function of temperature, solvent, ph, shelf time... Investigate prevalence of tautomeric overlap in a real commercial catalog Test which of the tautomer transform rules may be too aggressive 26

27 NMR Experiments 127 prototropic tautomeric pairs 5 prototropic tautomeric triples 34 ring-chain tautomeric pairs 338 molecules from AMS Solvent: DMS-d6 Room temperature 1 H and 13 C NMR Spectra Bruker AVANCE TM 500 Autosampler (24) 27

28 Keto/enol Tautomerism (conflict 26) 1 H NMR Spectrum 26_1 Same 1 H and 13 C NMR spectrum between samples. Assignment of chemical shifts indicates enol form is present in both samples InChI=1S/C14H12N4S/c1-9-10( )13(19)18(17-9) (11)20-14/h2-3,6-7,19H,4-5H2,1H3 InChIKey=KTGFJMXHLHDQA-UHFFFAYSA-N 13 C NMR Spectrum 26_2 InChI=1S/C14H12N4S/c1-9-10( )13(19)18(17-9) (11)20-14/h2-3,6-7,17H,4-5H2,1H3 InChIKey=HGTVTJWWZHYAQS-UHFFFAYSA-N 28

29 Heteroaromatic Tautomerism (conflict 36) 1 H NMR Spectrum Same 1 H and 13 C NMR spectrum between samples. Double number of peaks, both samples have the same mixture of tautomers. InChI=1S/C9H13ClN4/c1-9(2,3)14-7-6( ) (10)13-7/h5H,4H2,1-3H3,(H,1,13) InChIKey=XRAYTMYJALHNQU-UHFFFAYSA-N 13 C NMR Spectrum InChI=1S/C9H13ClN4/c1-9(2,3)14-7-6( )4-11-8(10)13-7/h5,12H,4H2,1-3H3 InChIKey=PCZNHIHWFBLCGG-UHFFFAYSA-N 29

30 Ring-Chain Tautomerism (conflict 652) 1 H NMR Spectrum Same 1 H and 13 C NMR spectrum between samples. Assignment of chemical shifts indicates open form is present in both samples InChI=1S/C14H14N22S/c (8)19-14(11)16-12 (15-13) /h3,5,7,12,16H,1-2,4,6H2,(H,15,17)/t12-/m0/s1 InChIKey=XMZKSUZSNNZEDZ-LBPRGKRZSA-N 13 C NMR Spectrum InChI=1S/C14H14N22S/c15-13(17) (10)19-14 (12) /h3-4,7-8H,1-2,5-6H2,(H2,15,17) InChIKey=VKEHQTAMAUSRIS-UHFFFAYSA-N 30

31 Preliminary Results More than 200 spectra have been analyzed so far. VERY PRELIMINARY conclusions: Around 80% of prototropic tautomeric cases and 50% of ring-chain tautomeric cases show the same 1 H and 13 C NMR spectra Usually the same visual appearance of the samples of a pair (texture, color etc.) corresponds to identical NMR results. We have assigned the chemical shifts of some spectra to determine which tautomer is present in the samples. Some tautomeric conflicts, e.g. involving triazole, imidazole or pyrazole moieties, are practically indistinguishable by standard NMR experiments: 12_1 12_2 InChI=1S/C6H4BrN3/c (3-4) /h1-3H,(H,8,9,10) InChIKey=BQCIJWPKDPZNHD-UHFFFAYSA-N InChI=1S/C6H4BrN3/c (3-4) /h1-3H,(H,8,9,10) InChIKey=BQCIJWPKDPZNHD-UHFFFAYSA-N We are starting to review the tautomeric rules based on the NMR results. 31

32 Tautomerism ngoing and Planned Activities Database of tautomerism data (structures; ratios, interconversion rates, relative energies...) from literature, both experimental and computational IUPAC Working Group: Redesign of Handling of Tautomerism for InChI V2 Agree on conditions for tautomerism in InChI Addition of ring-chain tautomerism rule set Recommendation for a tautomerism rule set for InChI V2 Definition of a canonical tautomer 32

33 Acknowledgements NCI/CADD Team Alexey Zakharov Laura Guasch Megan Peach Marc Nicklaus Markus Sitzmann ChemNavigator Scott Hutton PubChem Xemistry GmbH Wolf-Dietrich Ihlenfeldt All other database providers InChI Team

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35 Unique Representation of Chemical Structures NCI/CADD Structure Identifiers based on hashcodes calculated by the chemoinformatics toolkit CACTVS HN N NH 2 H CACTVS hashcodes: 9850FD9F9E2B4E25 represent a chemical structure uniquely as 16-digit hexadecimal number (64-bit unsigned) high sensitivity to structural features of a compound change if connectivity changes

36 tautomer N NH H NH 2 HNDVDQJCIGZPN-UHFFFAYSA-N 9850FD9F9E2B4E25-FICuS HN N NH 2 HNDVDQJCIGZPN-RXMQYKEDSA-N E92E4BA2869F3611-FICuS H stereoisomers HN H N NH 2 HNDVDQJCIGZPN-YFKPBYRVSA-N 8A7AD1EB498CC76A-FICuS salt Na + HN - N NH 2 UHPNKBYGGMJTIM-UHFFFAYSA-M E5F83F10C5DB080A-FICuS HNDVDQJCIGZPN-UHFFFAYSA-N Std. InChIKey HN H N NH FD9F9E2B4E25-FICuS FICuS HN Na errors N NH2 HN H N NH charged form HN - + N NH 3 HNDVDQJCIGZPN-UHFFFAYSA-N A3DAE DDE4-FICuS isotope NH N 15 NH 2 H UHPNKBYGGMJTIM-UHFFFAYSA-M E5F83F10C5DB080A-FICuS HNDVDQJCIGZPN-UHFFFAYSA-N 9850FD9F9E2B4E25-FICuS HNDVDQJCIGZPN-CDYZYAPPSA-N B2FDA68AEDA06DB9-FICuS

37 Chemical Identifier Resolver (CIR) examples: MIME type: text/plain Buckyball XMWRBQBLMFGWIX-UHFFFAYSA-N/image?height=300&width=300&bgcolor=black&bondcolor=white

38 Partial InChIKey Lookup (in preparation) resolve Standard InChIKey into full structure representation: Ethanol CC CC CC[H2+] C(C()([2H])[2H])[2H] CC()([2H])[2H] C(C)([2H])([2H])[2H] CC[17H] C(C)[2H] [14CH3]C CC

39 Chemical Structure Database (current version) InChI/InChIKey (Version 1.04) calculated with four InChI flag sets: Standard Set, Set 1 & Set 2: addition of hydrogen atoms by CACTVS Set 3: addition of hydrogen atoms by the InChI library CACTVS Standard : Add H Standard InChIKey Set 1 : Add H DNTADDH W0 FIXEDH RECMET NEWPS SPXYZ SAsXYZ Fb Fnud KET 15T Set 2 : Add H DNTADDH W0 FIXEDH RECMET NEWPS SPXYZ SAsXYZ Fb Fnud KET 15T Set 3 : Add H DNTADDH W0 FIXEDH RECMET NEWPS SPXYZ SAsXYZ Fb Fnud KET 15T

40 Unique Representation of Chemical Structures NCI/CADD Structure Identifiers MDL Molfile MDL SDF SMILES ChemDraw cdx PDB original structure record structure normalization parent structure hashcode calculation E_HASHISY NCI/CADD Identifier MDL SDF SMILES database FICTS FICuS uuuuu we calculate a set of parent structures with different sensitivity to chemical features fine grained representation of chemical structures

41 NCI/CADD Chemical Structure Database Tautomer Analysis 30 occurrence of tautomerism-critical molecules within each individual database release (%) number database releases frequency average: ~9.5% of FICuS parent structures Sitzmann M, Ihlenfeldt WD, Nicklaus MC. J Comput Aided Mol Des Jun;24(6-7):

42 Ring-chain tautomerism in a real database Most commonly applicable ring-chain tautomerism rules in the AMS Database SMIRKS rule Count % 3-exo-Trig 65, exo-Trig 10, exo-Trig 7,506, exo-Trig 5,289, exo-Trig 4,185, exo-Dig 179, exo-Dig 472, exo-Dig 3,293, endo-Trig 169, endo-Trig 156, endo-Trig 65, Most common 42

43 Imine/amine tautomerism (conflict 5) 1 H NMR Spectrum 5_1 Same 1 H and 13 C NMR spectrum between samples. Assignation of chemical shifts indicates imine form is present in both samples 5_2 InChI=1S/C14H11FN6/c ( (15)5-3-8) (6-16)13(17)21(14)20-11/h2-5,17,19H,7H2,1H3 InChIKey=ZDHCKDWMHUPE-UHFFFAYSA-N 13 C NMR Spectrum InChI=1S/C14H11FN6/c ( (15)5-3-8) (6-16)13(17)21(14)20-11/h2-5H,7,17H2,1H3 InChIKey=ZUXILZLWKBIETJ-UHFFFAYSA-N 43

44 InChI/InChIKey Resolver

45 InChI/InChIKey Resolver loose coupling of InChI resolvers provided by different organizations central list of resolvers each resolver must provide a specific protocol.

46 InChI/InChIKey Resolver Evan Bolton (NCBI, NLM, NIH) Valery Tkachenko (RSC/ChemSpider) Marc Nicklaus (CADD Group, NCI, NIH) Steven Bachrach (Trinity University) Antony Williams (RSC/ChemSpider) Markus Sitzmann (CADD Group, NCI, NIH)

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