www.ccdc.cam.ac.uk

Insight into Molecular Geometry and

Interactions using Small Molecule

Crystallographic Data

John LiebeschuetzCambridge Crystallographic Data Centre,

12 Union Road, Cambridge, UK

john@ccdc.cam.ac.uk

www.ccdc.cam.ac.uk

How much Data is Available?

CSD Growth 1970-2006

419,768 entries June 2007

0

100000

200000

300000

400000

500000

600000

2001 2003 2005 2007 2009

Growth of the Cambridge Structural Database over 40 years

Predicted Growthto 2010

>500,000 entries during 2009

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CSD Data Content

Literature Reference:

G. Bringmann, M. Ochse,

K. Wolf, J. Kraus, K. Peters,

E-M. Peters, M. Herderich,

L. Ake, F. Tayman

Phytochemistry 51,1999, 271

Other text:R-factor: .0506

Colour: pale yellow

Habit: acicular

Polymorph: Form IV

Source: Rothmannia longiflora

4-Oxonicotinamide-1-(1’-beta-D-2’,3’,5’-tri-O-acetyl-

ribofuranoside)

C17 H20 N2 O9

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Molecular Interactions as well as Geometry

HEPPEX

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Cambridge Structural Database System

CambridgeStructuralDatabase

PreQuestDatabase Production

VISTAStatisticalanalysis

MercuryGraphical display,packing analysis

ConQuestDatabase

Search

MogulLibrary of

Molecular Geometry

IsoStarLibrary of

Intermolecular Interactions

Knowledge Bases

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Using Structural Data in molecular modelling for pharmaceutical design

• Intramolecular – 3D geometry– Designing in the desired Conformer

– Validation that models have correct geometry

• Intermolecular – Interactions between molecules– Design of pharmacophores

– Validation of interactions found during modelling

– Identification of new ways to satisfy binding motifs

– Knowledge-based scoring functions for docking

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Designing in the right Conformation (1)

Brameld. K.A., Kuhn, B., Reuter, D.C. and Stahl, M. J. Chem. Inf. Mod, 48(1), 1-24 2008)

It is possible using Conquest to generate incidence histograms for any geometric feature , for any substructure, if sufficient high quality structures including that substructure, are present in the CSD

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Designing in the right Conformation (2)

Sulphonamide is common in drug molecules. Its conformational behaviour well captured by CSD

Ortho Substitution (Blue histogram) shifts the maximum

Pyramidalisation of the N of the sulphonamide can also be explored. This is a common effect in sulphonamides (and piperidines) but is poorly reproduced by modelling software

Brameld. K.A., Kuhn, B., Reuter, D.C. and Stahl, M. J. Chem. Inf. Mod, 48(1), 1-24 2008)

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Designing in the right Conformation (3) : Example 1:

CSD analysis indicates the bioactive conformation is stable only for most active structureBrameld. K.A., Kuhn, B., Reuter, D.C. and Stahl, M. J. Chem. Inf. Mod, 48(1), 1-24 2008)

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Rapid access of geometric information from the CSD

Incorporates pre-computed libraries of bond lengths, valence angles and torsion angles

>20 million individual geometrical parameters derived entirely from the CSD and updated annually

Sketch or import molecule, then click on feature of interest to view distribution, mean values and statistics

Validation of Model Geometry: Mogul

Bruno et al., J. Chem. Inf. Comput. Sci., 44, 2133-2144, 2004

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Select fragment

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Validation of PDB Ligand Geometry

PDB structures suffer from less well defined electron density

Protein X-Ray refinement force fields often are poorly parameterised to reproduce ligand geometries

Sometimes protein crystallographers start with a poor ligand model

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Validation of Ligand structures in the PDB via Protein/Ligand analysis tool Relibase+*

*www.ccdc.cam.ac.uk

Validation of ligand structures found in the PDB

Ligand from 1HAK, Two abnormal torsions indicated

Further examination reveals the piperidine to be Boat form

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• 15% of 100 recent PDB entries have ligand geometry that are almost certainly in significant error (in house analysis using Relibase+/Mogul)

• The good news - For structures deposited before 2000 the figure is 26%

evaluation of pdb ligand dataset from 1990's with Mogul and Relibase

correct34%

wrong26%

not unusual40% correct

wrong

not unusual

evaluation of most recent pdb ligand dataset with Mogul and Relibase

correct29%

wrong16%

not unusual55%

correct

wrong

notunusual

Pre 2000 2006

Validation of ligand structures found in the PDB using Mogul

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Designing in the right Conformation (3) : Large Rings

Brameld. K.A., Kuhn, B., Reuter, D.C. and Stahl, M. J. Chem. Inf. Mod, 48(1), 1-24 2008)

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Validation of ligand structures found in the PDB

Ligand from 1HAK, Two abnormal torsions indicated

Further examination reveals the piperidine to be Boat form

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Mogul 1.3: Ring Conformations

• Mogul currently holds data on bonds, angles and torsions.

• In the 2010 release of the Cambridge Structural Database System Mogul will also contain a comprehensive ring knowledge base

• Ring libraries from α-Mogul 1.3 have been introduced into Gold 4.1 to allow knowledge- based ring-flexing during docking

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A Knowledge Base of Intermolecular Interactions

Experimental data from:

Cambridge Structural Database

Protein Data Bank (protein-ligand complexes only)

Theoretical potential energy minima (DMA, IMPT)

Typical Uses:

Probability of an interaction occurring

Preferred geometries

Design Strategies

IsoStar

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central group: -CONH2

contact group: NH

IsoStar Methodology

Search CSD or PDB for structures containing contact

Superimpose hits and display distribution

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IsoStar Scatterplots vs. Density MapsN-H donors around amide C=O

Scatterplot Contour surface

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IsoStar –indole and isoxazole interactions with faces of phenyl rings

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Using Intermolecular information to build pharmacophores from proteins

Use intermolecular information (IsoStar) to map a protein binding site (e.g. using SuperStar, an extra module to the CSDS )

Create a pharmacophore from this information (possible in SuperStar) c.f. GRID/FLAP

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Motif searching

Certain signature interaction motifs might be key to identifying inhibitor substructures of interest. Can we identify such motifs in the CSD and thereby uncover new ideas?

Materials Mercury: A new tool for the drug development and crystal design community

Most tools are specific to small molecule crystals ....

However ….

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1. Comparison of crystal structures: polymorphs, solvates etc can identify significant ‘packing features’.

2. We can then search the CSD using ‘Packing Feature Search’

Packing Feature Search

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H-bonding Motif Search: Kinase Binding Motifs

CDK2 Complex – 1ke8 Set up a ‘Packing Feature Search’ around Hinge Region

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H-bonding Motif Search: Kinase Binding Motifs

MISTOX WUSQAC

Provides ideas for new motifs – Fragment based design

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• Protein/Ligand Docking relies on a scoring function to rank binding poses

– Scoring functions may be Molecular Mechanics based, Empirical or Knowledge Based

• A Knowledge Based score is calculated by the sum of atom-atom potentials derived from a crystallographic database

The atom-atom potential = - log

• Knowledge based scoring functions (PMF, Bleep, DrugScore, ASP) have been developed using protein-ligand data (PDB)

• The CSD contains better resolved structures and a much greater variety of chemical functionality than the PDB

– DrugScoreCSD has demonstrably improved performance over DrugScore (Velec, Gohlke & Klebe, J. Med. Chem., 48 (2005), 6296 )

observed interactions

Knowledge-based scoring using small molecule structural data

reference state

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Uses of Small Molecule Structural Data in Drug Design: Conclusions

• Use in Model Validation -

– Geometry of designed synthetic candidates

– Geometry of X-ray derived Ligand Structures

– Intermolecular interactions of a candidate structure with a model of binding site

• Design of Pharmacophores

• Search for fragments fitting a binding motif

• Creation of robust and versatile Knowledge-Based scoring functions for docking

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Acknowledgements

Thank you for your attention

Jana HennemanJames Chisholm