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1 Current perspectives in fragmentbased drug discovery Roderick E Hubbard Vernalis (R&D) Ltd, Cambridge YSBL & HYMS, Univ of York, UK ELRIG, September 2012 For a copy of slides – [email protected]

Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

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Page 1: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

1

Current perspectives in  fragment‐based drug discovery

Roderick E Hubbard Vernalis (R&D) Ltd, Cambridge

YSBL & HYMS, Univ of York, UK

ELRIG, September 2012

For a copy of slides –

[email protected]

Page 2: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

2

Pre-Clinical Clinical Trials

Drug Discovery

Discovery

I II III

Medicine

Target Hit IDH2Ls

Lead Optimisation

Page 3: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

3

Structural Biology•

Understanding target mechanism and biology

Structure‐Based Discovery •

Hit identification ‐

virtual screening, fragments

Structure‐Based Design•

Hits to Leads ‐

binding mode, chemotypes, properties

Lead optimisation ‐

affinity, specificity, ADME, p‐chem  properties

Pre-Clinical Clinical Trials

Structure in Drug Discovery

Discovery

I II III

Medicine

Target Hit IDH2Ls

Lead Optimisation

Page 4: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

4

Structural Biology•

Understanding target mechanism and biology

Structure‐Based Discovery •

Hit identification ‐

virtual screening,

fragments

Structure‐Based Design•

Hits to Leads ‐

binding mode, chemotypes, properties

Lead optimisation ‐

affinity, specificity, ADME, p‐chem  properties

Pre-Clinical Clinical Trials

Structure in Drug Discovery

Discovery

I II III

Medicine

Target Hit IDH2Ls

Lead Optimisation

Page 5: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

5

Overview

Summary of FBLD•

The methods

Some examples

The issues•

Fragments, chemical space, novelty and libraries

Fragment evolution•

Non‐conventional targets

Concluding remarks

Page 6: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

6

Overview

Summary of FBLD•

The methods

Some examples

The issues•

Fragments, chemical space, novelty and libraries

Fragment evolution•

Non‐conventional targets

Concluding remarks

Page 7: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

7

Why fragments?

Trying to find compounds that bind to target•

Compounds need to have required shape and chemistry

Page 8: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

8

Why fragments?

Trying to find compounds that bind to target•

Compounds need to have required shape and chemistry

High Throughput Screening•

Compounds decorated in the wrong way

Particularly a problem with new target classes

Page 9: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

9

Why fragments? 

Hits from fragments•

Find small parts that bind

Then grow or merge fragments to create hit compound

Page 10: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

10

Why fragments? 

Hits from fragments•

Find small parts that bind

Then grow or merge fragments to create hit compound

Can also provide ideas•

Deconstruct HTS hits to optimise key interaction motifs

Provides ideas during Hit / lead optimisation•

Scaffold hopping

Page 11: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

11

Trends for new technologies

In the beginning – lots of excitement•

Which can lead to hype and over‐selling

Time

Expectation

Technology Trigger

Analysis / terms initially proposed by Gartner group (Murcko)

Page 12: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

12

Trends for new technologies

In the beginning – lots of excitement•

Which can lead to hype and over‐selling

Time

Expectation

Technology Trigger

Inflated expectations

Analysis / terms initially proposed by Gartner group

Page 13: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

13

Trends for new technologies

Too rapid (often inexpert) deployment•

It doesn’t work ‐

disillusionment

Time

Expectation

Technology Trigger

Trough of Disillusionment

Inflated expectations

Analysis / terms initially proposed by Gartner group

Page 14: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

14

Trends for new technologies

Too rapid (often inexpert) deployment•

It doesn’t work ‐

disillusionment

Time

Expectation

Technology Trigger

Trough of Disillusionment

Inflated expectations

Analysis / terms initially proposed by Gartner group

Page 15: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

15

Trends for new technologies

Eventually, expertise grows•

Begin to understand how and where to apply methods

Time

Expectation

Technology Trigger

Inflated expectations

Trough of Disillusionment

Slope of Enlightenment

Analysis / terms initially proposed by Gartner group

Page 16: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

16

Trends for new technologies

Learn how to integrate the methods into the process •

Add to productivity

Time

Expectation

Technology Trigger

Inflated expectations

Trough of Disillusionment

Slope of Enlightenment

Plateau of productivity

Analysis / terms initially proposed by Gartner group

Page 17: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

17

Fragments

The ideas established in the molecular modelling

/ structural biology  community during the 1980s and early 1990s

First reduced to practice by Abbott in SAR by NMR approach in mid 1990s•

Other pharmaceutical companies unable to replicate success

Approaches developed in small pharma

companies in late 1990s / early  2000s

Astex, Vernalis, Plexxikon, SGX ….. and underground in large pharma

Success has led to increased use•

Not sure which part of this curve we are on – in different organisations!!

Time

Expectation

Technology Trigger

Inflated expectations

Trough of Disillusionment

Slope of Enlightenment

Plateau of productivity

Page 18: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

18

Why are fragments different?

A fragment is just a small weak hit

Requires assay(s) that can detect binding reliably 

Methods for evolving fragments (libraries and/or design)

Design of library includes constraints of assay / evolution

Requires structure to get hits on scale of assay•

to generate SAR that drives medicinal chemistry

Track the ligand

efficiency –

binding energy per heavy atom

Affinity10mM 1mM 100M 10M 1M

Fragments MW 110-250

Scaffolds MW 250-350

Lead Compounds

Hit Compound MW 250-500

Page 19: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

19

Screening fragment libraries

Affinity10mM 1mM 100M 10M 1M

Fragments MW 110-250

Scaffolds MW 250-350

Lead Compounds

X-Ray crystallography

Ligand-observed NMR

Surface Plasmon Resonance (SPR)

Enzyme / binding assays (HCS)

Different experimental approaches have  different strengths and limitations 

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)

Page 20: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

20

Biophysical Methods

For the equilibrium

PL(aq)                     P(aq)  +   L(aq)       

Equilibrium constant Kd

= koff

/kon

= ‐RTlnKd

= H°‐TS°kon

koff

Page 21: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

21

Biophysical Methods

For the equilibrium

Can measure kinetics – SPR

PL(aq)                     P(aq)  +   L(aq)       

Equilibrium constant Kd

= koff

/kon

= ‐RTlnKd

= H°‐TS°kon

koff

ResonanceSignal (RU)

Dissociation - koff

Asso

ciat

ion

- kon

Kinetics

ConcentrationTime (s)

KineticsKinetics

Time (s)Time (s)Time (s)Time (s)Time (s)Concentration

Time (s)Concentration

Time (s)

Page 22: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

22

Setting up SPR

Challenge is to immobilise protein on the chip

Various strategies•

Biotinylation

of free NH2

groups => streptavidin

chip•

His tagged protein => Ni chip

Green – Single His Tagged Pin1

-500

0

500

1000

1500

2000

2500

3000

3500

4000

4500

-400 -300 -200 -100 0 100 200 300 4

Adjusted sensorgramRU

Res

pons

e (0

= C

aptu

re 2

sta

rt)

Time (0 = Sample 1 start)

Sample injection

Protein injection

Page 23: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

23

Setting up SPR

Challenge is to immobilise protein on the chip

Various strategies•

Biotinylation

of free NH2

groups => strepatavidin

chip•

His tagged protein => Ni chip

-500

0

500

1000

1500

2000

2500

3000

3500

4000

4500

-400 -300 -200 -100 0 100 200 300 4

Adjusted sensorgramRU

Res

pons

e (0

= C

aptu

re 2

sta

rt)

Time (0 = Sample 1 start)

Sample injectionGreen – Single His Tagged Pin1

Red – Double His Tagged Pin1- 12 aa spacer

Protein injection

See also Fischer et al (2011) Anal Chem,  83:1800 for double‐his tag protocols  applied to SiaP

protein 

Page 24: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

24

b ca

NMR competitive binding experiment

Fragment Library1200 + 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

Unlabelled target – no size limit

+

Page 25: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

25

Optimise fragment

Fragment to hit :SAR by catalogoff‐rate screening

-5

0

510

15

20

25

30

-50 0 50 100 150 200 250 300

RU

Res

pons

e

Time s

-4

-2

0

2

4

6

8

-100 -50 0 50 100 150 200 250 300

RU

Res

pons

e

Tim e s

Characterisation 

X‐ray or NMR  guided model

The Vernalis processHubbard et al (2007), Curr

Topics Med Chem, 7, 1568                       Hubbard and Murray (2011), Methods Enzym, 493, 509

Target

Optimise fragment

Hits

Competitive  NMR screenFragment Library 

~ 1200 compoundsAve MW 190

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

NH2N

NH2

O

OEt

Virtual screen; literature;  library screen

Screen by SPR, DSF, 

biochem

assay, Xray

Drug?

Page 26: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

26

Vernalis experience  

For “good”

active sites (many enzymes):•

If assays configured correctly•

Pay attention to quality of the library –

solubility / aggregation etc

Same hits identified by ligand

observed NMR and SPR

High percentage of validated hits give crystal structures 

Hubbard & Murray (2011), Meth Enzymology, 493, 509

Page 27: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

27

Vernalis experience  

For “good”

active sites (many enzymes):•

If assays configured correctly•

Same hits identified by ligand

observed NMR and SPR

Lots of false negatives from screening by X‐ray

Hubbard & Murray (2011), Meth Enzymology, 493, 509

Page 28: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

28

Vernalis experience  

For “good”

active sites (many enzymes):•

If assays configured correctly•

Same hits identified by ligand

observed NMR and SPR

Lots of false negatives from screening by X‐ray•

Sometimes, multiple soaks  to obtain crystal structure of fragment bound

Suggests not a robust way to screen for fragments•

However, if you have crystals, can be the only way (see later)

0

10

20

30

40

50

60

70

80

90

100

1 2 3 4 5 6

SoaksStructures

Hubbard & Murray (2011), Meth Enzymology, 493, 509

Page 29: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

29

Vernalis experience  

For “good”

active sites (many enzymes):•

If assays configured correctly•

Same hits identified by ligand

observed NMR and SPR

Lots of false negatives from screening by X‐ray•

Requires suitable crystal system – and is a lot of hard work

“Wet”

assays can work sometimes•

But high concentrations (HCS) can confound the assay

Hubbard & Murray (2011), Meth Enzymology, 493, 509

Page 30: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

30

Vernalis experience  

For “good”

active sites (many enzymes):•

If assays configured correctly•

Same hits identified by ligand

observed NMR and SPR

Lots of false negatives from screening by X‐ray•

Requires suitable crystal system – and is a lot of hard work

“Wet”

assays can work sometimes•

But high concentrations (HCS) can confound the assay

Hubbard & Murray (2011), Meth Enzymology, 493, 509

0

10

20

30

40

50

60

70

80

90

HSP

70

PIN

1

PPI-2

PPI-1

HSP

90

KIN

ASE-

1

KIN

ASE-

2

KIN

ASE-

3

FAAH

Assayed up to 35 NMR hits in  biochemical assay for some targets

Concentration limited by DMSO  tolerance

400µM for kinase; 2mM for others

Wide variability

Many hits would be missed by HCS

Page 31: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

31

Vernalis experience  

For “good”

active sites (many enzymes):•

If assays configured correctly•

Same hits identified by ligand

observed NMR and SPR

Lots of false negatives from screening by X‐ray•

Requires suitable crystal system – and is a lot of hard work

“Wet”

assays can work sometimes•

But high concentrations can confound the assay

Calorimetry

(ITC) not yet for screening•

But a robust way of validating / confirming / quantifying binding 

Hubbard & Murray (2011), Meth Enzymology, 493, 509

Page 32: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

32

Vernalis experience  

For “good”

active sites (many enzymes):•

If assays configured correctly•

Same hits identified by ligand

observed NMR and SPR

Lots of false negatives from screening by X‐ray•

Requires suitable crystal system and it is a lot of hard work

“Wet”

assays can work sometimes•

But high concentrations can confound the assay

Calorimetry

(ITC) not yet for screening •

Thermal melt methods •

Differential scanning fluorimetry

(DSF) or Thermal Shift Analysis (TSA)

Heat the protein in presence of fluorescence dye and measure Tm – look 

for a shift on ligand

binding

For a number of targets we have assessed validated NMR hits (for

which a 

crystal structure) in DSF•

8 to 23% confirmation rate

Not a robust way to screen for fragments (in our hands)•

Can be useful to screen for cryptic (allosteric) sites

Temp

Fluo

rese

nce

NH

O

O

OH

CH3 CH3

ON

O

NH CH3

NClOH

OH

OH

Hubbard & Murray (2011), Meth Enzymology, 493, 509

Page 33: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

33

Vernalis experience  

For “good”

active sites (many enzymes):•

If assays configured correctly•

Same hits identified by ligand

observed NMR and SPR

Lots of false negatives from screening by X‐ray•

Requires suitable crystal system and it is a lot of hard work

“Wet”

assays can work sometimes•

But high concentrations can confound the assay

Calorimetry

(ITC) not yet for screening •

Thermal melt methods unreliable•

Weak fragments can bind without stabilizing protein

Can find cryptic / allosteric

sites (sometimes)

Hubbard & Murray (2011), Meth Enzymology, 493, 509

Page 34: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

34

Vernalis experience  

For “good”

active sites (many enzymes):•

If assays configured correctly•

Same hits identified by ligand

observed NMR and SPR

Lots of false negatives from screening by X‐ray•

Requires suitable crystal system and it is a lot of hard work

“Wet”

assays can work sometimes•

But high concentrations can confound the assay

Calorimetry

(ITC) not yet for screening •

Thermal melt methods unreliable•

Weak fragments can bind without stabilizing protein

Can find cryptic / allosteric

sites (sometimes)

For non‐conventional sites (such as protein‐protein):•

Many issues•

Overbinding, problems due to compound properties

Cross‐validate binding by different techniques

Need for faster, more sensitive, less resource intensive methods

Hubbard & Murray (2011), Meth Enzymology, 493, 509

Page 35: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

35

Overview

Summary of FBLD•

The methods

Some examples

The issues•

Fragments, chemical space, novelty and libraries

Fragment evolution•

Non‐conventional targets

Concluding remarks

Page 36: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

36

Using fragments

Finding fragments that bind is not difficult•

A good way of assessing target “ligandability”

0%

1%

2%

3%

4%

5%

6%

7%

8%

0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4

D score

Cla

ss 1

hits

rate

s

Low hit rates (< 2%)High hit rates (> 2%)

Kinases(3-5% hit rate)

protein-protein interaction(0.4-3% hit rate)

Poor targets

1Calculate druggability

Chen & Hubbard (2009), JCAMD, 23, 603

Page 37: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

37

Using fragments

Finding fragments that bind is not difficult•

A good way of assessing target “ligandability”

Low hit rate can indicate difficult to progress•

See also Hajduk (2005) J Med Chem, 48, 2518

0%

1%

2%

3%

4%

5%

6%

7%

8%

0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4

D score

Cla

ss 1

hits

rate

s

Low hit rates (< 2%)High hit rates (> 2%)

Kinases(3-5% hit rate)

protein-protein interaction(0.4-3% hit rate)

Poor targets

1Calculate druggability

Chen & Hubbard (2009), JCAMD, 23, 603

Page 38: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

38

Using fragments

Finding fragments that bind is not difficult

The challenge is knowing what to do with the hits•

Link, grow or merge

Known LigandsVirtual Screening hits

Screen

Detailed Design

Screen

Screen 1 Optimise 1 Screen 2 Optimise 2 LinkLINK

GROW

MERGE

Page 39: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

39

Using fragments

Finding fragments that bind is not difficult

The challenge is knowing what to do with the hits•

Link,

grow

or merge

ScreenGROW

Page 40: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

40

Using fragments

Finding fragments that bind is not difficult•

A good way of assessing target “ligandability”

The challenge is knowing what to do with the hits•

Growing – CHK1 example

Chk-1 IC50 >100µM

LE ~ 0.39

Page 41: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

41

Using fragments

Finding fragments that bind is not difficult•

A good way of assessing target “ligandability”

The challenge is knowing what to do with the hits•

Growing – CHK1 example

Chk-1 IC50 = 5µM

LE = 0.39

GI50 HCT116 >80µM

pH2AX (MEC) – inactive

Page 42: Current perspectives in fragment based drug discovery · Understanding target mechanism and biology • Structure‐Based Discovery • Hit identification ‐ virtual screening, fragments

42

Using fragments

Finding fragments that bind is not difficult•

A good way of assessing target “ligandability”

The challenge is knowing what to do with the hits•

Growing – CHK1 example

Chk-1 IC50 = 0.2µM

LE = 0.33

GI50 HCT116 = 4µM

pH2AX (MEC) = 7µM

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Using fragments

Finding fragments that bind is not difficult•

A good way of assessing target “ligandability”

The challenge is knowing what to do with the hits•

Growing – CHK1 example

Chk-1 IC50 = 0.013µM

LE = 0.39

GI50 HCT116 = 1.8µM

pH2AX (MEC) =0.2µM

Series members further optimised to identify Candidate V158411

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Using fragments: Hsp90

NNH

OH

OH

O

O

NO

OH

OH

O

NH

N O

OO

OH

OH

RBT-8667 (VER-63579)FP IC50 = 0.28MGI50 = 6M

VER-52296FP IC50 = 0.009MGI50 = 0.014M

RBT-26617 (VER-26617)FP IC50 = ~ 1mM

Starting fragment Hit from SAR by Catalogue (also MTS and VS)

• GI50 in HCT116 colon cell line

FP IC50 = 0.28MGI50 = 6M

FP IC50 = 0.009MGI50 = 0.014M

FP IC50 = ~1mM

D93 G97K58

F138

L107

rCatN

O

O

O

O

Phase II Candidate(Novartis)

D93G97

K58

F138

L107

Brough et al (2008) J Med Chem 51,196‐218Roughley et al (2012) Top Curr

Chem

, 317, 61

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Overview

Summary of FBLD•

The methods

Some examples

The issues•

Fragments, chemical space, novelty and libraries

Fragment evolution•

Non‐conventional targets

Concluding remarks

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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

Pin1 example

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Pin1 Story

Proline

isomerase

persuasive biological  rationale that key oncology target

Structure available + D‐peptide tool compound

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48

Pin1 Story

Proline

isomerase

persuasive biological  rationale that key oncology target

Fragments identified: fragment to hit evolution•

No correlation between biophysical and enzyme assays

NH

OH

O

H3C

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49

Pin1 Story

Proline

isomerase

persuasive biological  rationale that key oncology target

Fragments identified: fragment to hit evolution

Issue with over‐binding –

multiple copies of  fragment binding to the protein – SPR and Xray

NH

OH

O

H3C

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50

Pin1 Story

Proline

isomerase

persuasive biological  rationale that key oncology target

Fragments identified: fragment to hit evolution

Issue with over‐binding –

multiple copies of  fragment binding to the protein – SPR and Xray

Designed 3D fragment – progressed multiple  series < 100nM on target showing cellular activity

Potter AJ et al,  Bioorg

Med Chem 

Lett. 2010; 20:586‐590

N

NH

HN

O

O

HO

O

CH3NH

OH

O

H3C

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51

3D fragments

Proline

isomerase

persuasive biological  rationale that key oncology target

Fragments identified: fragment to hit evolution

Issue with over‐binding –

multiple copies of  fragment binding to the protein – SPR and Xray

Designed 3D fragment – progressed multiple  series < 100nM on target showing cellular activity

Some initiatives underway to introduce more 3D  fragments

The challenge will be synthetic tractability•

Watch this space

Potter AJ et al,  Bioorg

Med Chem 

Lett. 2010; 20:586‐590

N

NH

HN

O

O

HO

O

CH3NH

OH

O

H3C

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52

Overview

Summary of FBLD•

The methods

Some examples

The issues•

Fragments, chemical space, novelty and libraries

Fragment evolution•

Non‐conventional targets

Concluding remarks

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53

Exploiting the dissociation rate constant

Cannot improve association rate constant above ~10‐8

M‐1s‐1

No point in drug discovery, too many membranes in the way!

Dissociation rate constant can be infinite (ie

covalent!)

We have seen that it is the key driver of potency•

As have others (review Copeland, Future Med. Chem. 3(12), 2011)

koff (s-1)kon (M-1s-1)KD =

James Murray, Steve Roughley

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54

Exploiting the dissociation rate constant

Cannot improve association rate constant above ~10‐8

M‐1s‐1

No point in drug discovery, too many membranes in the way

Dissociation rate constant can be infinite (ie

covalent)

We have seen that it is the key driver of potency•

As have others (review Copeland, Future Med. Chem. 3(12), 2011)

Independent of concentration•

Exploit this to assess unpurified

reactions, off‐rate screening (ORS)

koff (s-1)kon (M-1s-1)KD =

James Murray, Steve Roughley

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Historical Hsp90: thienopyrimidines•

200 nM – 5 M IC50

by FP assay

Re‐prepared compounds by Suzuki reaction

Minimal work‐up•

Evaporate, partition

Purity 50 – 80 % (LCMS)

Screened by ORS

N

N S

Cl

NH2O

ON

N SNH2O

O

RB(OH)2

R

DMF / H2O

NaHCO3

Pd(Ph3P)2Cl2100 ºC Microwave 10 min

Off rate screening (ORS): ExampleJames Murray, Steve Roughley

A: Pure starting materialB: Faux reactionC: Purified productD: Crude reaction

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56

3UH4Novartis (2012)

Tankyrase

Introduction

Axin

is targeted for turnover through poly‐D‐ribose  labelling

by Tankyrase.  This removes axin, which has a 

role in stabilising

‐catenin

Inhibition of Tankyrase

has been proposed to enhance  the degradation of ‐catenin, an indirect way of affecting 

the WNT‐pathway

Crystal structure of tankyrase

available in 2007

2RF5 Structural Genomics Consortium (2007)

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Tankyrase

Introduction

Axin

is targeted for turnover through poly‐D‐ribose  labelling

by Tankyrase.  This removes axin, which has a 

role in stabilising

‐catenin

Inhibition of Tankyrase

is therefore proposed to enhance  the degradation of ‐catenin, an indirect way of affecting  the WNT‐pathway

Crystal structure of tankyrase

available in 2007

At Vernalis:•

Initially – low levels of protein production – insufficient 

material for fragment screen by NMR•

Able to produce large numbers of apo‐crystals that 

preliminary trials showed were suitable for ligand

soaking

Alba Macias, Chris Graham and team

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Tankyrase

Hit identification

Crystals

Soaked fragments in pools of 8

Data collection (up to1.6Å

resolution)

Streamlined structure solution

Characterised by SPR and TSA

62 hits from 1563fragments

Alba Macias, Chris Graham and team

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Tankyrase

Fragment to hit evolution

The most attractive fragments were not suitable for rapid chemistry

Designed a modified fragment

Off‐rate screening libraries identified vectors and substituents•

Crystals soaked directly with reaction mixtures

Lead Series driven using combinations of tools•

Computational chemistry

X‐ray crystallography•

SPR (ORS), DSF

Medicinal Chemistry

Properties•

5 nM

vs

TNKS2, high ligand

efficiency (0.60)

Affects PD markers in cells (stabilises Axin2, inhibits WNT pathway)

Tools to probe the biology

Alba Macias, Chris Graham and team

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60

Overview

Summary of FBLD•

The methods

Some examples

The issues•

Fragments, chemical space, novelty and libraries

Fragment evolution•

Non‐conventional targets

Concluding remarks

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Concluding remarks

Straight forward to find fragments for most sites on most proteins•

Opportunities for new “3D”

fragments

The challenge is knowing what to do with the fragments•

Off‐rate screening allows exploration of vectors

Evolving fragments in absence of structure?

For conventional targets•

Lots of options and starting points

Provides opportunity for “good”

medicinal chemistry

For non‐conventional targets•

Provides starting points when other techniques fail

Close support from biophysics is crucial

Not necessarily faster•

But hopefully better

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End

References in the slides acknowledge who did the work

FBLD2012:

Fragment Based Lead DiscoverySan Francisco: 23-26 Sep 2012

(http://www.fbldconference.org)

For a copy of slides –

[email protected]

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Vernalis Overview

Approximately 60 staff in research•

Based in Cambridge, UK (Granta

Park)

Recognised for innovation and delivery in structure and fragment‐ based drug discovery

Structure‐based drug discovery since 1997•

Distinctive expertise combining X‐ray, NMR, ITC and SPR to enable 

drug discovery against established and novel, challenging targets 

Portfolio of discovery projects•

Six development candidates generated in the past six years

Protein structure, fragments and modelling integrated with medicinal  chemistry

Internal projects in oncology•

Collaborations with large and small pharma

across all therapeutic areas

Aim to establish additional collaborations during 2012 / 13