on the origins of three-dimensionality in drug-like molecules
TRANSCRIPT
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in partnership with
Making the discoveries that defeat cancer
On the Origins of Three-Dimensionality in Drug-Like Molecules Dr Nathan Brown Group Leader, In Silico Medicinal Chemistry Cancer Research UK Cancer Therapeutics Unit Division of Cancer Therapeutics The Institute of Cancer Research, London
Chemical Computing Group Conference, Vienna, Austria, 2016 Thursday 19th May, 2016 @nathanbroon
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Overview 2
• Motivations for enhanced three-dimensionality
• Descriptors of three-dimensionality
• PMI: Principal Moments of Inertia
• PBF: Plane of Best Fit
• Three-dimensionality analyses of drug-like space
• Extant drug-like molecules
• ‘Retrosynthetic’ analyses
• Fragmentation analyses
• Virtual libraries
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Structural Moieties Promoting 3D 3
Quaternary Centres
Bridged Bicycles
Conformational Restriction
Spiro Ring Systems
Effexor XR (Venlafaxine)
$1,431 Million (19th) ANTIDEPRESS. & MOOD STAB.
Avapro (Irbesartan)
$370 Million (91st) ANGIOTEN-II ANTAG, PLAIN
Spiriva (Tiotropium)
$1,594 Million (14th) ANTICHOLINERGIC+B2-STIM
Zetia (Ezetimibe)
$986 Million (31st) CHOLEST.&TRIGLY. REGULATOR
28/12/1993
30/01/2004
30/09/1997
25/10/2002
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Motivation: Three-Dimensional Molecules
• Mimicking natural products
• Natural products frequently incorporate 3D scaffolds
• Improvement in properties
• 3D shape often conveys improved aqueous solubility
• Addressing new and challenging drug targets
• e.g. protein-protein interactions
4
PDB: 3MXF
(+)-JQ1
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Escape from Flatland… 5
1. Lovering, F.; Bikker, J.; Humblet, C. Escape from Flatland: Increasing Saturation as an Approach to Improving Clinical Success. J. Med. Chem. 2009, 52, 6752-6756.
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PMI: Principal Moments of Inertia 6
NPR1
NP
R2
0.
5
1
0 0.5 1
disc
rod sphere
ChEMBL Drug-Like Small Molecules
Intuitive in Presentation Size Independent
1. Meyers, J.; Carter, M.; Mok, N. Y.; Brown, N. On The Origins of Three-Dimensionality in Drug-Like Molecules. Future Med. Chem. submitted.
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PBF: Plane of Best Fit 7
ChEMBL Drug-Like Molecules
0.00
0.25
0.50
0.75
1.00
1.25
1.50
1.75
2.00
Pla
ne
of B
est F
itSimple in Concept Size Dependency
Unbound Descriptor
1. Meyers, J.; Carter, M.; Mok, N. Y.; Brown, N. On The Origins of Three-Dimensionality in Drug-Like Molecules. Future Med. Chem. submitted. 2. Firth, N. C.; Brown, N.; Blagg, J. Plane of Best Fit: A Novel Method to Characterize the Three-Dimensionality of Molecules. J. Chem. Inf. Model. 2012, 52, 2516-
2525.
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Plane of Best Fit 8
0Å
1Å
0.16Å 0.27Å
0.64Å
0.80Å 1.06Å
0.40Å
1. Firth, N. C.; Brown, N.; Blagg, J. Plane of Best Fit: A Novel Method to Characterize the Three-Dimensionality of Molecules. J. Chem. Inf. Model. 2012, 52, 2516-2525.
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9 PMI & PBF – Perfect Partners
1. Firth, N. C.; Brown, N.; Blagg, J. Plane of Best Fit: A Novel Method to Characterize the Three-Dimensionality of Molecules. J. Chem. Inf. Model. 2012, 52, 2516-2525.
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Scaffold Tree Fragmentation 10
Parent Level 3 Level 2 Level 1 2 Level 0
Simple & Intuitive Rules Mimics Chemist Thinking
Systematic Evaluation
1. Schuffenhauer, A.; Ertl, P.; Roggo, S.; Wetzel, S.; Koch, M. A.; Waldmann, H. The Scaffold Tree – Visualization of the Scaffold Universe by Hierarchical Classification. J. Chem. Inf. Model. 2007, 47, 47-58.
2. Langdon, S. R.; Brown, N.; Blagg, J. Scaffold Diversity of Exemplified Medicinal Chemistry Space. J. Chem. Inf. Model. 2012, 51, 2174-2185.
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PMI: Scaffold Tree Analysis of ChEMBL Return to Flatland…
11
Level 5 Level 4 Level 3
Level 2 Level 1 Level 0
Medicinal Chemistry Relevant Scaffolds Tend Towards Planarity
1. Meyers, J.; Carter, M.; Mok, N. Y.; Brown, N. On The Origins of Three-Dimensionality in Drug-Like Molecules. Future Med. Chem. submitted.
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PBF: Scaffold Tree Analysis of ChEMBL Return to Flatland…
12
1. Meyers, J.; Carter, M.; Mok, N. Y.; Brown, N. On The Origins of Three-Dimensionality in Drug-Like Molecules. Future Med. Chem. submitted.
Parents 8 7 6 5 4 3 2 1 0
Scaffold Tree Levels
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Medicinal Chemistry Relevant Scaffolds Tend Towards Planarity
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Scaffolds versus ChEMBL Parents 13
A B C D E F G H
Increasing PBF
★ Core scaffold Parent molecules
1. Meyers, J.; Carter, M.; Mok, N. Y.; Brown, N. On The Origins of Three-Dimensionality in Drug-Like Molecules. Future Med. Chem. submitted.
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Scaffolds versus ChEMBL Parents 14
A H
★ Core scaffold Parent molecules
1. Meyers, J.; Carter, M.; Mok, N. Y.; Brown, N. On The Origins of Three-Dimensionality in Drug-Like Molecules. Future Med. Chem. submitted.
Modulation of Three-Dimensionality Easier with Planar Scaffolds
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Scaffold versus ChEMBL Parent Molecules 15
A B C D E F G H
Increasing PBF Fig 4 PBF distribution from all eight cores in one plot
A B C D E F G H
0.00
0.25
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1.00
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Fig 6 PBF distribution from all eight cores in one plot
A B C D E F G H
0.00
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More Three-Dimensional Scaffolds Do Not
Necessarily Translate into More Three-Dimensional
Structures
1. Meyers, J.; Carter, M.; Mok, N. Y.; Brown, N. On The Origins of Three-Dimensionality in Drug-Like Molecules. Future Med. Chem. submitted.
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SynDiR – Synthetic Disconnection Rules 16
• New retrosynthetic fragmentation scheme published in 2015
1. Firth, N. C.; Atrash, B.; Brown, N.; Blagg, J. MOARF, an Integrated Workflow for Multiobjective Optimization: Implementation, Synthesis, and Biological Evaluation. J. Chem. Inf. Model. 2015, 55, 1169-1180.
Most Substructures Tend Towards Planarity Three-Dimensionality may Originate from Planar Moieties
Actual Occurrence
Unique Occurrence
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SynDiR – Synthetic Disconnection Rules 17
Most Substructures Tend Towards Planarity Three-Dimensionality may Originate from Planar Moieties
1. Meyers, J.; Carter, M.; Mok, N. Y.; Brown, N. On The Origins of Three-Dimensionality in Drug-Like Molecules. Future Med. Chem. submitted.
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Scaffold versus Enumerated Libraries 18
A B C D E F G H
Increasing PBF
★ Core scaffold Enumerated library
1. Meyers, J.; Carter, M.; Mok, N. Y.; Brown, N. On The Origins of Three-Dimensionality in Drug-Like Molecules. Future Med. Chem. submitted.
Medicinal Chemistry Relevant Scaffolds Tend Towards Planarity
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Scaffold versus Enumerated Libraries 19
A B C D E F G H
Increasing PBF
Fig 4 PBF distribution from all eight cores in one plot
A B C D E F G H
0.00
0.25
0.50
0.75
1.00
1.25
1.50
Pla
ne
of
Be
st
Fit
Fig 6 PBF distribution from all eight cores in one plot
A B C D E F G H
0.00
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1.25
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of
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Greater Increase in Three-Dimensionality when Starting from Flatter
Scaffolds…
…but final structures are more 3D!
1. Meyers, J.; Carter, M.; Mok, N. Y.; Brown, N. On The Origins of Three-Dimensionality in Drug-Like Molecules. Future Med. Chem. submitted.
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Summary & Conclusions
Presented approaches to analysing three-dimensionality
• Exemplified medicinal chemistry space
• Paring back structures to scaffolds
• Fragmenting into constituent substructures
• Enumerating virtual libraries
When and where can we enrich three-dimensionality?
• Constituent substructures are relatively planar
• Our medicinal chemistry scaffolds are typically flat
• Three-dimensionality can be modulated in design
• We do not need inherent three-dimensionality in scaffolds & groups
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Acknowledgements 21
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Acknowledgements 22
Cancer Research UK Grant No. C309/A8274
In Silico Medicinal Chemistry
• Fabio Broccatelli
• Michael Carter
• Nick Firth
• Teresa Kaserer
• Sarah Langdon
• Josh Meyers
• Yi Mok
• Lewis Vidler
Medicinal Chemistry
• Julian Blagg