Download - Rod Hubbard | FBDD 2014 | Fragmentology - current topics in fragment based lead discovery
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Fragmentology – current topics in fragment based lead discovery
Rod Hubbard
Vernalis Research & University of York
Zing, Punta Cana - July 2014
York
Cambridge
For slides – [email protected]
Old Slide
Updated
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Fragmentology - agenda
• FBLD at Vernalis • Approach, successes, library
• Hit rates and selectivity • Experience across kinase projects
• Properties of kinase vs PPI hits
• Characterising 3D fragment space - sphericality
• WAC for detecting fragment binding
• Fragments as enzyme activators • Library optimised for SAR by catalog
• GlcNAcase story
• Comments on current state of FBLD
Punta Cana, July 2014
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Fragmentology - agenda
• FBLD at Vernalis • Approach, successes, library
• Hit rates and selectivity • Experience across kinase projects
• Properties of kinase vs PPI hits
• Characterising 3D fragment space - sphericality
• WAC for detecting fragment binding
• Fragments as enzyme activators • Library optimised for SAR by catalog
• GlcNAcase story
• Comments on current state of FBLD
Punta Cana, July 2014
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Optimise fragment Fragment to hit : Incorporate information from SAR by catalog and off-rate screening
-5
0
5
10
15
20
25
30
-50 0 50 100 150 200 250 300
RU
Resp
on
se
Tim e s
Cycle: 95 VER-00082099i 50 nM
Fitted Cycle: 95 VER-00082099i
Cycle: 96 VER-00082099i 500 n
Fitted Cycle: 96 VER-00082099i
Cycle: 97 VER-00082099i 5000
Fitted Cycle: 97 VER-00082099i -4
-2
0
2
4
6
8
-100 -50 0 50 100 150 200 250 300
RU
Resp
on
se
Tim e s
Cycle: 103 VER-00055030l 50 n
Fitted Cycle: 103 VER-00055030l
Cycle: 104 VER-00055030l 500
Fitted Cycle: 104 VER-00055030l
Cycle: 105 VER-00055030l 5000
Fitted Cycle: 105 VER-00055030l
Characterisation
X-ray or NMR guided model
The Vernalis process Hubbard et al (2007), CTMedChem, 7, 1568 Hubbard and Murray (2011), Methods Enzym, 493, 509
Target
Optimise fragment
Hits
Competitive NMR screen Fragment Library
~ 1400 compounds Ave MW 194
Design, Build & Test
N
N SNH2
O
NH
Cl
Cl
ON
NO
OH
OH
O
NH
N O
NN
NH2
OOMe
NN
NH2
SNH
O
N
N
N
NH2
Cl
ClN
SNNH2
NH2
N
NH2
O
OEt
Virtual screen; literature; library (HTS) screen
Screen by SPR, DSF, biochem assay, WAC, Xray
Drug?
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SBDD and FBLD output at Vernalis
• Candidates • Hsp90 - phase II candidate and oral backup - Novartis
• Fragment to lead; rapid structure-based optimisation
• Chk1 – pre-clinical candidate and oral backup
• Fragment growth; structure-based design
• Bcl-2 – protein-protein interaction – Phase I – Servier (Novartis)
• NMR to generate binding models; biophysics to characterise properties
• A2a – gpcr pharmacology – Phase II
• Ligand-based modelling
• FAAH – completed Phase I
• Modelling to incorporate fragment ideas to generate candidate
• Undisclosed from collaborations
Punta Cana, July 2014
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SBDD and FBLD output at Vernalis
• Exploring target biology (“validation”) • PDPK1 – merging fragments with literature compounds
• Pak4 and STK33 – fragment exploration to test literature
• Pim1 – fragment exploration to understand selectivity
• PDHK1 – ORS to identify selective leads from fragments
• Tankyrase – fragment screen by X-ray; off-rate screening
• Undisclosed from collaborations • selective, cell-penetrant, in vivo tolerated inhibitors to
assess target biology in suitable disease models
• combining fragments with HTS hits to dissect key binding motifs and mine corporate collections
Punta Cana, July 2014
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Vernalis structures
Ribosome projects
30S
50S
A-site
MDM2
GRP94
PDPK1 Chk1
DNA
gyrase
HSP90b HSP90a
CDK2
Aurora
Akt
Jak Catenin
GTPase
site
Pin1
FAS
Hsp70
P11
HSC70/Bag
Xiap
Pak4
Pim1
PPI-1
Bcl-2
>4000 complexes determined
Grp78
Kinase C PDK2
Bcl-xL
Adenosine
Kinase Target E
Jnk3
PDK3 / E2
Kinase H Kinase J
Target J
Target G Target I tankyrase
Kinase A
Target B
Updated
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Fragment libraries
• The initial Vernalis library from 2004
Library design - JCICS, 44, 2157
87,133 from ACD
100 < MW < 250;
unwanted functionality
7545
Library Size
Medicinal chemistry tractability; availability; cost
553
204
3,794
717
kinase pharmacophore
before 2D 3-point
fingerprint
novelty in
fingerprint vs
Library 1-3
Library I
2918
395
2D 3-point
pharmacophore
fingerprint
357 174 61
100 < MW < 250; unwanted functionality; wanted
functionality; solubility > 2mM
1.79M from rCat*
43,458
Library 2 Library 3 Library 4
Solubility; wanted
functionality;
tractability; availability;
cost
1028
Measure solubility; NMR spectrum; mass spec; stability
729
Library I Library 2 Library 3 Library 4
Manual
Cheminformatics
*rCat – Baurin et al (2004), JCICS, 44, 643
Punta Cana, July 2014
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Fragment libraries
• The initial Vernalis library from 2004
• Subsequent evolution of the library driven by: • Regular QC and restocking
• Solubility, stability, availability of commercial compounds
• Adding fragments from in-house chemistry
• Consider all intermediates generated in-house
• Synthesise bespoke fragments from literature / target ideas
• Experience in evolving fragments
• The reality of synthetic tractability
• Added slightly larger and lipophilic compounds
• Current library at about 1350 fragments
Library design - JCICS, 44, 2157 *rCat – Baurin et al (2004), JCICS, 44, 643
Punta Cana, July 2014
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Fragmentology - agenda
• FBLD at Vernalis • Approach, successes, library
• Hit rates and selectivity • Experience across kinase projects
• Properties of kinase vs PPI hits
• Characterising 3D fragment space - sphericality
• WAC for detecting fragment binding
• Fragments as enzyme activators • Library optimised for SAR by catalog
• GlcNAcase story
• Comments on current state of FBLD
Punta Cana, July 2014
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Hit rates
• Since 2002, over 2050 different fragments have been screened against more than 30 targets • This has been an evolving fragment library
• Screened by ligand-observed NMR, biochemical assay, binding assay, Xray, SPR …..
• For consistency – will consider only the ligand-observed NMR screen results • 1291 fragments were not a hit against any of 19 targets
• No significant difference between hits and non-hits • HA, complexity, nRot ,etc, etc; perhaps SlogP
• Of these 19 targets • 9 are kinases
• 5 can be considered PPIs
Punta Cana, July 2014
This is for ligand-observed NMR screens
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b c a
NMR competitive binding experiment
Fragment Library 1350 + fragments
Assayed in mixtures of 12
Target +
fragments
NMR experiment observes
fragment only if binding
Target +
fragments +
competitor ligand
Has competitor displaced the
fragment? => Specific binding
10 – 100 Hit
Fragments
Has the advantage can
monitor ligand and
protein in each
experiment
Ligand observed NMR –
no limit on MW of protein
Three ligand-observed
competitive NMR experiments –
a hit in all 3 is Class 1; in 2
experiments is Class2; 1 – Class 3
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Hit rates for kinases at Vernalis
• Nine kinases have been screened in a competitive ligand-observed NMR experiment • (other kinases by biochemical or binding screen)
• Caveat – screened against evolving fragment library with changing instrumentation (cryoprobe / console) and operator (some subjectivity in defining hits)
• (only 565 fragments screened against all 9 targets)
Punta Cana, July 2014
This is for ligand-observed NMR screens
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Hit rates for kinases at Vernalis
• Nine kinases have been screened in a competitive ligand-observed NMR experiment • (other kinases by biochemical or binding screen)
• Caveat – screened against evolving fragment library with changing instrumentation (cryoprobe / console) and operator (some subjectivity in defining hits)
• (only 565 fragments screened against all 9 targets)
Punta Cana, July 2014
This is for ligand-observed NMR screens
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Hit rates for kinases at Vernalis
• Nine kinases have been screened in a competitive ligand-observed NMR experiment • (other kinases by biochemical or binding screen)
• Caveat – screened against evolving fragment library with changing instrumentation (cryoprobe / console) and operator (some subjectivity in defining hits)
• (only 565 fragments screened against all 9 targets)
• Kinase hit rate for all fragments – 12% • Kinase hit rate for the 174 fragments designed as a
kinase focussed sub-library – 8%
Punta Cana, July 2014
This is for ligand-observed NMR screens
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Selectivity
• For the hits from the 565 fragments that were screened against all 9 kinases • Number of fragments that were a hit for a certain
number of kinases (297 were not a hit for any)
Punta Cana, July 2014
96
66
41
26
14 14 8
2 0 0
20
40
60
80
100
120
1 2 3 4 5 6 7 8 9
This is for ligand-observed NMR screens
e.g. – 14 fragments are hits against 6 different kinases
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Selectivity
• For the hits from the 565 fragments that were screened against all 9 kinases • Total number of hits for each kinase
Punta Cana, July 2014
5 28 102 55 37 51 42 32 42
AK CDK2 Kin1 Kin2 Jnk3 Kin3 Pak4 PDPK1 Stk33
AK
CDK2
Kin1
Kin2
Jnk3
Kin3
Pak4
PDPK1
Stk33
This is for ligand-observed NMR screens
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Selectivity Punta Cana, July 2014
5 28 102 55 37 51 42 32 42
AK CDK2 Kin1 Kin2 Jnk3 Kin3 Pak4 PDPK1 Stk33
AK 2
CDK2 6
Kin1 30
Kin2 9
Jnk3 7
Kin3 20
Pak4 13
PDPK1 4
Stk33 8
• For the hits from the 565 fragments that were screened against all 9 kinases • Number of unique hits for each kinase
This is for ligand-observed NMR screens
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• For the hits from the 565 fragments that were screened against all 9 kinases • The number of fragments that hit two targets
• e.g. 12 fragments are hits for both JNK3 and PDPK1
Selectivity Punta Cana, July 2014
5 28 102 55 37 51 42 32 42
AK CDK2 Kin1 Kin2 Jnk3 Kin3 Pak4 PDPK1 Stk33
AK 2 0 2 0 0 1 1 0 0
CDK2 6 14 11 9 8 5 8 13
Kin1 30 35 19 18 21 20 29
Kin2 9 18 20 12 14 12
Jnk3 7 13 9 12 10
Kin3 20 12 7 7
Pak4 13 8 7
PDPK1 4 12
Stk33 8
e.g. 12 fragments are hits for
both JNK3 and PDPK1
This is for ligand-observed NMR screens
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Fragmentology - agenda
• FBLD at Vernalis • Approach, successes, library
• Hit rates and selectivity • Experience across kinase projects
• Properties of kinase vs PPI hits
• Characterising 3D fragment space - sphericality
• WAC for detecting fragment binding
• Fragments as enzyme activators • Library optimised for SAR by catalog
• GlcNAcase story
• Comments on current state of FBLD
Punta Cana, July 2014
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Properties of all fragments Punta Cana, July 2014
0
200
400
600
800
0 1 2 3 4 5 6 7 8 More
Fre
qu
en
cy
Hydrogen Bond Donors
0
200
400
600
800
1000
0 1 2 3 4 5 6 7 8 More
Fre
qu
en
cy
Hydrogen Bond Acceptors
1 51
202
466 494 422
315
59 27 11 0 0
200
400
600
6 8 10 12 14 16 18 20 22 24 More
Fre
qu
en
cy
Number of Heavy Atoms
14
958 957
116 3 0 0
500
1000
1500
0 1 2 3 4 More
Fre
qu
en
cy
Nring
0 3 11 77 272
591 785
280 29 0
0
500
1000
-4 -3 -2 -1 0 1 2 3 4 More
Fre
qu
en
cy
SlogP
180
457 534
478
235 118
33 9 3 1 0 0
200
400
600
0 1 2 3 4 5 6 7 8 9 More
Fre
qu
en
cy
Nrot
3.1 ± 1.3 1.3 ± 0.9
13.9 ± 3.0 1.0 ± 1.0
2.3 ± 1.5 1.6 ± 0.6
This is for ligand-observed NMR screens
6 8 10 12 14 16 18 20 22 -4 -3 -2 -1 0 1 2 3
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0 4
56
150 173
140
97
26 11 4 0 0 #N/A 0
50
100
150
200
6 8 10 12 14 16 18 20 22 24 26 More
Fre
qu
en
cy
Number of Heavy Atoms kinase hits
0 0 2 10 60
163
296
118 11 0
0
100
200
300
400
-4 -3 -2 -1 0 1 2 3 4 MoreFr
eq
ue
ncy
SLogP kinase hits
Properties of kinase hits Punta Cana, July 2014
1 51
202
466 494 422
315
59 27 11 0 0
200
400
600
6 8 10 12 14 16 18 20 22 24 More
Fre
qu
en
cy
Number of Heavy Atoms
0 3 11 77 272
591 785
280 29 0
0
500
1000
-4 -3 -2 -1 0 1 2 3 4 More
Fre
qu
en
cy
SlogP 13.9 ± 3.0 1.0 ± 1.0
This is for ligand-observed NMR screens
14.1 ± 2.8
Heavy atom count reflects the library (we don’t have high HA count compounds)
SlogP slightly higher for hits
1.2 ± 0.9
6 8 10 12 14 16 18 20 22
6 8 10 12 14 16 18 20 22
-4 -3 -2 -1 0 1 2 3
-4 -3 -2 -1 0 1 2 3
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1 51
202
466 494 422
315
59 27 11 0 0
200
400
600
6 8 10 12 14 16 18 20 22 24 More
Fre
qu
en
cy
Number of Heavy Atoms
0 4
56
150 173
140
97
26 11 4 0 0 #N/A 0
50
100
150
200
6 8 10 12 14 16 18 20 22 24 26 More
Fre
qu
en
cy
Number of Heavy Atoms kinase hits
0 0 2 10 60
163
296
118 11 0
0
100
200
300
400
-4 -3 -2 -1 0 1 2 3 4 MoreFr
eq
ue
ncy
SLogP kinase hits
Properties of kinase and PPI hits Punta Cana, July 2014
0 3 11 77 272
591 785
280 29 0
0
500
1000
-4 -3 -2 -1 0 1 2 3 4 More
Fre
qu
en
cy
SlogP 13.9 ± 3.0 1.0 ± 1.0
This is for ligand-observed NMR screens
14.1 ± 2.8 1.2 ± 0.9
0 4
23
68 76
68
50
10 9 4 0 0 0
20
40
60
80
6 8 10 12 14 16 18 20 22 24 26 More
Fre
qu
en
cy
Number of Heavy Atoms PPI hits
0 0 2 2 17
64
138
79
10 0
50
100
150
-4 -3 -2 -1 0 1 2 3 More
Fre
qu
en
cy
SlogP PPI hits 14.3 ± 3.1 1.4 ± 0.9
SlogP even higher for PPI hits
6 8 10 12 14 16 18 20 22
6 8 10 12 14 16 18 20 22
-4 -3 -2 -1 0 1 2 3
-4 -3 -2 -1 0 1 2 3
6 8 10 12 14 16 18 20 22 -4 -3 -2 -1 0 1 2 3
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Kinase fragments that are hits for a PPI
• There are 661 fragments that are hits against any kinase
• There are 312 fragments that are hits against any PPI
• Interestingly the number of fragments that are hits against both kinase and PPIs is 214; this seems like a higher percentage than you would think, by chance.
• Thinking about this further ……
Punta Cana, July 2014
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Fragmentology - agenda
• FBLD at Vernalis • Approach, successes, library
• Hit rates and selectivity • Experience across kinase projects
• Properties of kinase vs PPI hits
• Characterising 3D fragment space – sphericality
• WAC for detecting fragment binding
• Fragments as enzyme activators • Library optimised for SAR by catalog
• GlcNAcase story
• Comments on current state of FBLD
Punta Cana, July 2014
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All fragments in library Punta Cana, July 2014
Rod
Disc
Sphere
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Kinase fragments Punta Cana, July 2014
Rod
Disc
Sphere
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PPI fragments Punta Cana, July 2014
Rod
Disc
Sphere
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All fragments in library Punta Cana, July 2014
Increasing
sphericality (S) –
from 0 to 1
Roughley and Hubbard submitted
Rod
Disc
Sphere
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PPI
Sphericality of fragments and hits
• Consider just those with S > 0.02
• Plot is the percentage of hits with a particular sphericality (removed 0-0.02) • Kinase hits marginally less spherical
• PPI hits more reflective of overall library
Punta Cana, July 2014
0
1
2
3
4
5
6
7
8
0 0.1 0.2 0.3 0.4 0.5 0.6
All
kinase
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More details on Sphericality
• Consider accessible conformations
• All non-H atoms converted to C • Heavy atoms such as Br distort the PMI
• Br is 7 times the mass of C; vdw only 1.7 x
• Use original bond lengths so most of volume retained
• Consider what coverage a library provides
• Count occupancy of S bins – an S index which can be used to characterise / compare libraries
Punta Cana, July 2014
Roughley and Hubbard submitted
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Correlation of S with other measures Punta Cana, July 2014
Nrot HAC NAr NSat Fsp3
VolsurfG VolsurfR VolsurfS Volsurf V PBF
Sph
eric
alit
y Roughley and Hubbard submitted
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3D fragments
• Most of the compounds in fragment libraries are commercially available small molecules • Medicinal chemist emphasis on chemical tractability
• Some use privileged fragments from existing drugs
• Most of the fragments are flat heterocycles • This is fine for some targets (kinases, ATPases)
• Perhaps limiting for other (new) target classes
• Probably don’t have the compounds in our libraries yet to answer the question about relevance • Progressed PPI hits (cf Astex as well) have more sp3
character in the binding scaffold
• The challenge will be synthetic tractability
Punta Cana, July 2014
Updated
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Fragmentology - agenda
• FBLD at Vernalis • Approach, successes, library
• Hit rates and selectivity • Experience across kinase projects
• Properties of kinase vs PPI hits
• Characterising 3D fragment space – sphericality
• WAC for detecting fragment binding
• Fragments as enzyme activators • Library optimised for SAR by catalog
• GlcNAcase story
• Comments on current state of FBLD
Punta Cana, July 2014
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Screening fragment libraries
• Different experimental approaches have different strengths and limitations
Punta Cana, July 2014
Affinity 10mM 1mM 100mM 10mM 1mM
Fragments MW 110-250
Scaffolds MW 250-350
Lead Compounds
X-Ray crystallography
Ligand-observed NMR
Surface Plasmon Resonance (SPR)
Enzyme / binding assays (HCS)
Isothermal Titration Calorimetry (ITC)
Hit Compound MW 250-500
Protein-observed NMR
Differential scanning fluorimetry (DSF / TSA)
Hubbard & Murray (2011), Meth Enzymology, 493, 509
Mass spectrometry (MS)
Weak Affinity Chromatography (WAC)
Updated
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New ideas in fragment screening
• Need for rapid, cheap, robust, generic method for detecting weak binding
• Currently investigating weak affinity chromatography • collaboration with Ohlson, Linneaus Univ (Elinor Melby)
• Immobilise target to silica beads in capillary column
• Flow over (mixture of) ligands
• Detect with UV; identify with mass spec
• Retention time related to affinity
Duong-Thi M et al (2011), Anal Biochem
Old Slide
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WAC for HSP90
• 111 fragments screened by WAC, NMR, SPR, FP and Tm shift • Selected fragments also by ITC
• Green is hit; pink is non-hit • Blank cells means not determined
• Good consistency across methods • FP and Tm give many false negatives
• WAC advantage is amount of protein and speed
• Currently investigating for other proteins • Key is preparation of the column
ITC X-ray Tm FP SPR NMR WAC
Old Slide Meiby et al (2013) Anal Chem 85(14):6756-6
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38
Fragmentology - agenda
• FBLD at Vernalis • Approach, successes, library
• Hit rates and selectivity • Experience across kinase projects
• Properties of kinase vs PPI hits
• Characterising 3D fragment space - sphericality
• WAC for detecting fragment binding
• Fragments as enzyme activators • Library optimised for SAR by catalog
• GlcNAcase story
• Comments on current state of FBLD
Punta Cana, July 2014
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York fragment library - 2011
unwanted functionality Input Supplier
Library
HA filter
Schulz et al (2011), JCAMD, 25, 611-620
Fragments List Non-Fragments
Identify diverse fragment
with largest number of
similar Non-Fragments
Remove fragment from
Fragments List
Remove Nearest Neighbours
from Non-Fragments
Fragment Set
A fragment library that maximally represents available chemicals
Useful for SAR by Catalog
Old Slide
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Fragmentology - agenda
• FBLD at Vernalis • Approach, successes, library
• Hit rates and selectivity • Experience across kinase projects
• Properties of kinase vs PPI hits
• Characterising 3D fragment space - sphericality
• WAC for detecting fragment binding
• Fragments as enzyme activators • Library optimised for SAR by catalog
• GlcNAcase story
• Comments on current state of FBLD
Punta Cana, July 2014
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O-GlcNAc is an essential PTM
• O-linked β-D-N-acetylglucosamine – post-translational modification at serine and threonine hydroxyls – a nucleocytoplasmic modification
• Abundant and essential for life in metazoans – complex biology
• Implicated in numerous disease processes - diabetes, cancer, neurodegeneration
• Large and growing list of O-GlcNAcylated proteins
• Only two modifying enzymes OGT and OGA
• Mechanisms of substrate and site-specific regulation not yet understood
Punta Cana, July 2014
Darby, Landstrom, Davies et al submitted
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Bacterial orthologue – BtGH84
• Family 84 glycoside hydrolase
• 40% identity with human OGA domain
• Crystal structure available
• Low micromolar (class-wide unselective) inhibitors developed previously • tool compounds
• Fragment screen of 91 fragments • Ligand observed NMR
• PUGNac as competitor
• Investigated both competitive and non-competitive inhibitors
Punta Cana, July 2014
PUGNAc Thiamet G
Darby, Landstrom, Davies et al submitted
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Fragment hits
• High hit rate – 24%; two classes of hits • 18 competitive wit hPUGNAc
• 4 non-competitive with PUGNAc
• Hits “validated” in activity assay
Punta Cana, July 2014
Darby, Landstrom, Davies et al submitted
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BtGH84 is activated by a fragment
• Non-competitive fragment M1E05 enhances BtGH84 activity
• Confirmed with alternative substrate, many controls
• Activation is concentration dependent
• Increases the Vmaxapp and reduces the Km
app - 2.5 mM to 1.3 mM
Punta Cana, July 2014
Darby, Landstrom, Davies et al submitted
M1E05
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BtGH84 is activated by a fragment
• Non-competitive fragment M1E05 enhances BtGH84 activity
• Confirmed with alternative substrate, many controls
• Activation is concentration dependent
• Increases the Vmaxapp and reduces the Km
app - 2.5 mM to 1.3 mM
• Assay, NMR and ITC confirm that M1E05 affects PUGNAc binding
Punta Cana, July 2014
M1E05
Darby, Landstrom, Davies et al submitted
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Thienopyrimidine analogues
Punta Cana, July 2014
M1E05
Darby, Landstrom, Davies et al submitted
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Thienopyrimidine analogues
• So far – no crystal structures of these bound
• (solubility issues)
• STD competition assay showed S054 competes for same site
• Non-essential activator kinetics suggests mechanism
• Compounds stabilise folding of loop required for catalysis
• Have a negative effect on Tm in thermal shift assay
• Better compounds required for chemical biology
• But interesting possibilities in industrial biotechnology / bioprocessing
Punta Cana, July 2014
Darby, Landstrom, Davies et al submitted
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48
Fragmentology - agenda
• FBLD at Vernalis • Approach, successes, library
• Hit rates and selectivity • Experience across kinase projects
• Properties of kinase vs PPI hits
• Characterising 3D fragment space - sphericality
• WAC for detecting fragment binding
• Fragments as enzyme activators • Library optimised for SAR by catalog
• GlcNAcase story
• Comments on current state of FBLD
Punta Cana, July 2014
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Technology cycle
• Rather “management consultant” but a useful reminder
• Drug discovery has “suffered” such cycles for many methods
• Structure-based design
• Combinatorial chemistry
• Genomics and post-genomic technologies
• etc
• etc
• Key is gaining sufficient expertise and learning how and when to apply the techniques
Punta Cana, July 2014
Time
Expectation
Technology
Trigger
Inflated
expectations
Trough of
Disillusionment
Slope of
Enlightenment
Plateau of
productivity
Bezdek initially, then Gartner group (Murcko for pharma)
J. Bezdek, IEEE Transactions on Fuzzy Systems. Feb. 1993, pp. 1-6 Old Slide
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Typical timelines - kinase
• Crystal structure and fragment screen in 4 months • More than 120 fragment hits (NMR screen)
Punta Cana, July 2014
0 4 8 12 16 20 24 months
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Typical timelines - kinase
• Extensive fragment to lead campaign • Crystal structures of >80 fragment complexes
• Identified novel binding modes in more than 2 series
• Five lead series identified within 12 months • “conventional” structure-guided fragment evolution
Punta Cana, July 2014
0 4 8 12 16 20 24 months
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Typical timelines - kinase
• Extensive fragment to lead campaign • Crystal structures of >80 fragment complexes
• Identified novel binding modes in more than 2 series
• Five lead series identified within 12 months • “conventional” structure-guided fragment evolution
Punta Cana, July 2014
0 4 8 12 16 20 24 months
log (affinity)
10 nM
10 µM
100µM
1µM
100 nM
Time (months) 2 4 6
HTS
Fragment
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Typical timelines - kinase
• Lead optimisation on two series • In vivo active, highly potent and selective compounds
identified within 24 months
Punta Cana, July 2014
0 4 8 12 16 20 24 months
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Typical timelines – PPI
• Project initiated • No progressable hits from HTS
• Fragment screen at Vernalis
• Often requires adaptation of methods • Crystal structures not possible with fragments bound
• Models generated from limited NMR information
• New assays to track compound properties
• Intensive exploration of fragment SAR
• Iteration to develop assays to identify tool compounds
Punta Cana, July 2014
0 1 2 3 4 5 6 years
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Typical timelines – PPI
• For a particular project • Initial lead series identified within 2 years
• Insufficient ligand efficiency – designed new scaffolds
Punta Cana, July 2014
0 1 2 3 4 5 6 years
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Typical timelines – PPI
• Lead series identified after a further year • Adequate ligand efficiency and potential for optimisation
• Robust model of SAR from NMR guided models
Punta Cana, July 2014
0 1 2 3 4 5 6 years
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Typical timelines – PPI
• Biophysics and structure-guided optimisation led to candidate after further 2.5 years • Once inhibitors less than about 100nM then crystal
structure possible
• This is representative of more than one project at Vernalis • Requires a commitment to the long haul
Punta Cana, July 2014
0 1 2 3 4 5 6 years
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Technology cycle
• For conventional targets
• Highly productive – gives lots of choice; main issues are organisational
• If structure-enabled – then detailed structure-based design possible
• Opportunities to mine HTS hits; you always learn something from fragments
• For non-conventional targets
• (and where structures are hard to obtain)
• It takes time – and not yet clear how often fragments can be successful
• The assays are often a real barrier for new classes of target • Catch 22 – need tool compound to validate to find tool compound
• Often – not clear what the target actually is (partners, PTM state etc)
• Integration with biophysical methods can be key; pragmatic application of the most appropriate methods to recognise and solve problems
Punta Cana, July 2014
Time
Expectation
Technology
Trigger
Inflated
expectations
Trough of
Disillusionment
Slope of
Enlightenment
Plateau of
productivity
Bezdek initially, then Gartner group (Murcko for pharma)
J. Bezdek, IEEE Transactions on Fuzzy Systems. Feb. 1993, pp. 1-6 Old Slide
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End
• References in the slides acknowledge who did the work
• FBLD conference
• 2014 – September 21st -24th - Basle
• http://www.fdld2014.org
• Deadline for poster abstracts - end of August or until full
• Registration limited to 200 attendees – it is filling up
For slides – [email protected] Punta Cana, July 2014
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Vernalis Research Overview
• Approximately 65 staff in research
• Based in Cambridge, UK (Granta Park)
• Structure-based drug discovery since 1997
• Distinctive expertise combines X-ray, NMR, ITC and SPR to enable drug discovery against established and novel targets
• A growing reputation for solving problems in early drug discovery against challenging targets (PPIs, novel classes)
• Portfolio of discovery projects
• Six development candidates generated in the past four years
• Cell active lead compounds generated against 13 targets
• Internal Vernalis projects in oncology and anti-infectives
• Collaborations across all therapeutic areas
• e.g. oncology, neurodegeneration, anti-infectives
• Novartis, GSK, Lundbeck, Genentech, Asahi Kasei, Servier
• Aim to establish additional collaborations through 2014/15