Fragment Based Drug Discovery

Fragment-Based Drug Discovery

From fragment hit to lead compound

Graduate Lecture Series

Lecture 2

Dr Anthony Coyne([email protected])

Outline

Recap of Lecture 1

Lecture 2 – From fragment hit to lead compound

Hit rate Challenging targetsFragment library design

and composition

Fragment Growing

Cyclin Dependant Kinase (CDK)

Astex

Fragment Merging

Cytochrome P450 (CYP121)

Abell Group

Fragment Linking

Replication Protein A (RPA70A)

Fesik Group

Fragment Development

Target Protein

Secondary ScreeningNMR Spectroscopy

Binding AffinityITC / SPR/ FP

Primary ScreeningThermal Shift / SPR / NMR

X-Ray

Recap of Lecture 1

Thermal Shift

SPR

FP

ITC

NMR

Christina Spry

Fragment Based Drug Discovery - the concept

High-throughput Screening (HTS) Fragment-based drug discovery (FBDD)

Libraries typically > 100,000

Molecular Weight > 300Da

Coverage of chemical space can be poor

Broader range of targets including whole-cell screening

approaches

Affinities typically in the mM range

Can be difficult to optimise hits as the structures can be

complex.

Libraries typically < 5000

Molecular Weight < 300Da

Requires well characterised targets

Affinities typically in the mM range

Iterative step-by-step optimisation possible to increase

the size of the molecule and potency

X-ray crystallography or 2D-NMR guided is critical for

optimisation

Biophysical methods tend to be low-medium throughput

Typically HTS screens are ran in parallel with a FBDD screen

Fragment Based Drug Discovery - Why is there the need for new methodology?

While HTS generally works for most enzyme classes in some cases this does not work

The limitations of HTS was highlighted by researchers from GSK who examined success rates in antibiotic drug discovery over a

five year period. Of the 70 campaigns (67 target based, 3 whole screening) only 5 leads were found

The reason for this failure was that the physicochemical properties of compounds that bind to anti-bacterials are different

(higher MW and lower logP) than other drug targets so HTS libraries are not suitable

This trend is also showing up with some protein-protein interaction targets (AZ – 15 targets and no hits)

FBDD the way forward with these targets?

E.coli ZipA (interacts with FtsZ)

Fragment Based Drug Discovery - Academia can make a impact on this area

Stephen W. Fesik (Vanderbildt University)

Cancer research drug discovery

Seth Cohen (UC San Diego)

Metalloproteins

Iwan De Esch (VU Amsterdam)

NMR Screening

Damien Young (Broad Institute/Baylor)

3D Fragments

Rod Hubbard (University of York/Vernalis)

Kinases, proteases

Paul Wyatt (University of Dundee (DDU))

Neglected diseases

Rob van Montford (ICR Sutton)


Chris Abell (University of Cambridge)


TB drug discovery

While HTS screening is done primarily in the realms of the pharmaceutical industry, fragment based drug discovery is within the

budgets of many academic research groups. This is an ever expanding list

Fragment Based Drug Discovery - Screening Cascade

Target Protein Fragment Library


X-RayBinding Affinity

ITC / SPR

Molecular DesignFragment analoging, Docking

Chemical SynthesisFragment Growing, Fragment Linking

Fragment Merging

Primary ScreeningThermal Shift / SPR / NMR

Other AssaysEnzymatic / FP

Lecture 1

Lecture 2

Iterative Development Cycle

A typical screening of a fragment library through

primary and secondary screening can take 1 - 6

months depending on the system.

Typically fragments will be found to bind with

potencies in the region of 10 mM to 5 mM.

Normally these are in the mid-micromolar region

With the stronger binding fragments these can be

quicker to progress although this is very much

target dependent.

The fragment elaboration step is very much

dependent on the information obtained from the

initial screening cascade.

How is fragment screening carried out?

Fragment Libraries

Typically fragment libraries are put together in-house (Pharma) or are purchased from

suppliers such as Maybridge, Enamine (Academia)

In-house libraries offer the possibility to include scaffolds and fragments that are

not present in commercial fragment libraries

In some cases commercial libraries can be biased to a specific scaffold (e.g. indole or

pyridine) or functional group (COOH)

Current focus of fragment library development is to include as

a diverse set of fragments so that the chemical space covered

Another focus has been to develop 3D fragments

(3DFrag.org). The aim of this is again to increase the diversity

and expand the chemical space of the fragment library.

3D fragments are available from some companies however at

a cost

1 mg ~£40

Some synthetic organic chemistry research groups are

developing methodology that can be applied to the synthesis

of these fragments (e.g. Damien Young (Baylor/Broad) and

James Bull (Imperial))

Expanding area of research

Target Type

What is meant by the term ‘challenging target’?

Initial fragment screening campaigns focused on kinases

These have clearly defined ATP pockets and are

considered more druggable

Typical hit rate: 5-10%

Protein-protein interactions are more difficult to target as

these do not have clearly defined pockets. These tend to

have ‘hot-spots’ on the protein surface where binding

occurs

Typical hit rate: 0.1-4%

CYP121

(Metalloprotein)

Hit rate 3.9%

CDK

(Kinase)

Hit rate 8.7%

RAD51-BRCA2

(Protein-Protein Interaction)

Hit rate 0.2 %

Hit Rate and Ligand Efficiency

Typical fragment screen – the numbers

Target Protein Fragment Library


ITC / SPR

PrimaryThermal Shift / SPR / NMR

Development cycle

800 Fragments

90 Fragments

(11% Hit rate)

28 Fragments

(3.5% Hit rate)

~ 5 Fragments

The hit rate is dependent on the library size and composition. It also depends upon the type of target where the more

‘’challenging’ the target the fewer hits that arise from a fragment screening

Ligand Efficiency is one of a number of metrics used to look at fragment development (Lecture 1)

(Binding energy per atom in a ligand)

LE = DG/NHA

NHA = number of heavy atoms

DG = Gibbs free energy of binding (from KD)

Typically no more than 5 fragments are taken forward for development

LE 0.25-0.50

Murray, C.A.. et al, ACS Med. Chem. Lett., 2014, asap article

The elaboration of fragment hits into chemical probes or drugs aims to improve the affinity from mM to mM and eventually to

nM

Different strategies are employed

What happen when you get a confirmed fragment hit?

Fragment Growing

Fragment Merging

Fragment Linking

How is the potency of a fragment increased?

Fragment Elaboration

This is the most frequent method of increasing potency for a fragment and a number of successful fragment campaigns

have been carried out using this strategy

Typically a single fragment in a binding pocket is ‘grown’ using chemical synthesis to pick up further interactions with the

protein.

This is the case that is the most likely to arise where a single fragment binds to protein or multiple fragments bind to a

specific area of the binding pocket

Structural information on how the ligand binds to the protein is key to guiding fragment development

EnzymeEnzyme

Fragment A

Fragment Growing

Fragment Growing –Kinases (CDK2)

Human Kinome

ATP

ADP

General phosphorylation reaction catalysed by kinases

The first targets that were screened using a fragment

based approach were kinases.

In many cases a key chemotype mimicking the

aminopurine ring typically comes out these fragment

screens

Typically the hit-rate for kinases are high due to the nature

of the ATP binding pocket

A major problem in targeting kinases is selectivity

(over 500 in human genome)

CDK2Fragment Library

500 Fragments

Primary Screening

X-Ray crystallography

(Cocktails of 4 fragments)

X-Ray Crystallography

Isothermal titration calorimetry (ITC)

500 Fragments

>30 Fragments

4 Fragments

With companies such as Astex the screening

is carried out using X-ray crystallography

where the fragment are screened in cocktails

With this type of screening it is important to

ensure when cocktailing there is sufficient

fragment difference to ensure that when the

hits are deconvoluted that the fragment can

be identified

In some cases fragment libraries containing

Br modified fragments is used

Fragment Growing – CDK2 (Astex)

The fragment library was composed of a focused

kinase set, a drug fragment set and compounds

identified by virtual screening against a structure of

CDK 2

Small fragment library size

Fragment Screening Cascade - CDK2

Fragment Screening – X-ray crystallography

How are these fragments binding to

CDK2?

Fragment Growing - Kinases

%I 64% (1 mM)%I 54% (1 mM)

IC50 0.185 mM IC50 0.120 mM

Fragment Growing – CDK Series 1 and 2

Series 1

%I 64% (1 mM)

IC50 7 mM

IC50 1.9 mM

Series discontinued as optimisation below low micromolar is not

straightforward (LE not maintained through optimisation)

Series 2

%I 54% (1 mM)

IC50 1.6 mM

IC50 30nM

Series discontinued as while it showed good cellular activity did

not show good in-vivo activity

Fragment Growing – CDK Series 3

IC50 185 mM

LE 0.57IC50 3 mM

LE 0.42IC50 97 mM

LE 0.39

IC50 3 nM

LE 0.45

IC50 47 nM

LE 0.40

AT7519

Fragment growing of the initial indazole hit led to a compound with a 50 fold increase in potency. Removal of the phenyl

ring of the indazole offered a new startpoint and this was subsequently elaborated to a compound with a IC50 of 47 nM

with only a small drop in LE (AT7519)

Interestingly the piperidine is protruding out of the pocket toward solvent and the two chlorine atoms in the 2 and 6

position of the phenyl ring fill small hydrophobic pockets on the protein

AT7519 is currently in Phase II clinical trials and has shown good indications against a range of human tumor cell lines

The structure of AT7519 makes amenable to scale-up which is important in the later stage clinical trials

Series 3

Fragment Growing – Pros and Cons

Pros Cons

Fragment growing is one of the most used methods

for increasing potency of a fragment.

Choosing the right fragment is important and this is

driven by synthetic tractability and other medicinal

chemistry considerations. With well developed

chemistry the fragments can be elaborated with

ease.

Multiple series can be taken forward using a

fragment growing strategy. The fragment

development is carried out in a stepwise manner

Other successful fragment merging strategies

DNA Ligase – Astex

NAMPT – Genentech

b-Secretase – numerous companies

CDK4/CDK6 - Astex

X ray-crystallography is key to determine the

position of the fragments in the binding pocket

Without X-ray information fragment growing can be

difficult.

This is where a number of fragments bind to a protein and bind in a similar region

Using structural information the overlap of the fragments can be combined using chemical synthesis to increase the

potency.

This is the case that is the most likely to arise where there is a common scaffold with variation on the substitution pattern

is observed

Structural information on how the ligand binds to the protein is key to guiding fragment development


Enzyme Enzyme

Fragment A

Fragment B

Fragment Merging

Merged

fragment

Fragment Merging – CYP’s (M. tuberculosis)

Cytochrome P450’s in M. tuberculosis

M. Tuberculosis contains 20 CYP’s of which the function of only five has been fully characterized.

This is an unusually high number of CYPs for the size of the genome

Human: 57 CYP’s (3234 Mb)

M. Tuberculosis: 20 CYP’s (4.4 Mb H37Rv)

E. Coli: 0 CYP’s ( 4.6 Mb)

Other organisms such as E. Coli do not contain any CYP’s and the M.tb genome contains a 200-fold gene density compared to

the Human genome

High density of CYP’s suggests importance in M. tuberculosis survival

.Hudson S.A. et al, Biochem J., 2014, 57, 2455-2461

CYPome (M.tb)

CYP121

CYP125

CYP51

Fragment Merging – CYP121 (M. tuberculosis)

Sterol 14 a-demethylase

(40% sequence similarity with HsCYP51B1)

Cholesterol oxidase

(Other associated M. tb CYP’s CYP124 and CYP142)

Cyclodipeptide synthetases

(unique reaction to M. tb – no Hs comparison)

cYY Mycocyclosin


CYP121Fragment Library

665 Fragments

Secondary Screening

NMR Spectroscopy

(WaterLOGSY, CPMG and STD)

Primary Screening

Thermal Shift (Hit > 0.8oC)

X-Ray Crystallography

Isothermal titration calorimetry (ITC)

665 Fragments

66 Fragments

(55 Fragments NMR)

9.9 % Hit rate

26 Fragments

(cYY Displaced)

(3.9% Hit rate)

5 Fragments

KD = 0.40 mM

LE = 0.39

KD = 1.60 mM

LE = 0.29

KD = 0.27 mM

LE = 0.35

KD = 3.0 mM

LE = 0.26

KD = 1.70 mM

LE = 0.32

Fragment screening against CYP121 yielded 5 fragments that were chosen to be

carried forward for elaboration

The KD of these fragments were in the range of between 0.27-3.0 mM which is

typically expected for fragment binding

The ligand efficiency (LE) of these fragments was good

How are these fragments binding to CYP121?

Hudson S.A. et al, Angew. Chem. Int. Ed, 2012, 51, 9311-9316

Fragment Merging – CYP121 (X-Ray Crystallography)

Heme binder through

NH2

Difficult to merge with

other fragments

Heme binder through NH2

Fragment Merging of

the two compounds

together

Non-heme binder

however shows two

distinct binding poses in

the X-Ray crystal

structure

Fragment Merging

Non-heme binder.

Merge with the

triazole fragment

Two distinct binding regions in CYP121 where fragments bind to the heme iron or further up the

pocket. There are a number of possible fragment merging strategies possible to increase potency



Strategy 1 (Heme binders)

Strategy 2 (Non-heme binders)

KD = 0.40 mM

LE = 0.39

KD = 1.60 mM

LE = 0.29 KD = 28 mM

LE = 0.39

Increase in potency when the two fragments are merged together.

Overlap in X-ray crystal structure on merged compound shows almost identical overlay with original fragments.

Ligand efficiency is maintained

KD = 3.0 mM

LE = 0.26

KD = 1.7 mM

LE = 0.32

No binding observed

Merging of these two compounds gave no increase in potency and had the opposite effect where no binding was

observed for the merged compounds.

Unsuccessful merging strategy



Strategy 3 (Non-heme binder)

KD = 1.7 mM

LE = 0.32KD = 2.8mM

LE < 0.20KD = 0.50 mM

LE = 0.24

KD = 40 mM

LE = 0.30

Merging of the two poses of the 1,2,4-triazole into a 1,5 disubstituted 1,2,3-triazole gave a compound which bound in a

similar pose as the initial fragment hit however the potency was much poorer

Further elaboration of the triazole ring to a pyrazole and subsequently an aminopyrazole had a significant effect on the

potency where this increased to 40 mM with a slight drop in ligand efficiency.

Successful merging strategy however further elaboration needed in order to increase the potency

With the three strategies in CYP121 only one gave an increase in potency where the fragments were directly

merged


Hudson, S.A., et al, ChemMedChem, 2013, 8, 1451-1455

Fragment Merging – Pros and Cons

Pros Cons



Without X-ray information fragment merging is

difficult.

In some cases there is a potential overlap between

the fragments however the strategy might fail due to

the number/difficulty of synthetic steps.

Where a merged compound is synthesised in some

cases no in binding affinity is observed possibly due

to subtle electronic/steric changes in the merged

molecule

In many cases there is more than one fragment

that binds into the pocket and overlap is easy to

see using X-ray crystallography.

The synthetic chemistry to synthesise the

fragments can be facile especially where the

fragment scaffolds are well studied (e.g. indoles,

pyridines)

Other successful fragment merging strategies

- Nicotonamide phosphoribosyltransferase

(NAMPT) (Genentech)

- Chymase (Boehringer Ingelheim)

- Mcl-1 (Fesik – Vanderbildt)

- AmpC (Shoichet – UCSF)

- PI3 Kinase (Pfizer)

- AChBP (De Esch – VU Amsterdam)


This is where a number of fragments bind to a protein and in different regions of the binding pockets or on the surface of

a protein

Using structural information the fragments can be linked using chemical synthesis to increase the potency.

This is the most difficult approach to increasing potency as there has to be an optimal linker as well as ensuring the

binding interactions of the fragments are maintained

Only a handful of sucessful examples in the literature especially against protein-protein interaction targets

Enzyme Enzyme

Fragment B

Fragment A Fragment A

Fragment B

Fragment Linking

Fragment Linking – Protein-Protein Interactions

p53-HDM2

Bcl-BAD RAD51-BRC4

Protein-Protein interactions (PPI’s) are found throughout biological

systems. Typically these are defined as difficult targets as success

rates in targeting these has been low especially using HTS approaches.

Unlike conventional targets they do not have distinct binding pockets

however they have what is known as ‘hot-spots’ typically on the surface

of the protein

FBDD has been used successfully against a number of these

targets however none to date have been approved as drugs

although in a number of cases there are compounds in Phase I/II

development.

Why protein-protein interactions as targets?

Fragment Linking – Protein-Protein Interaction Inhibitors (FBDD)

Bcl-XL – Fragment Linking Approaches (Fesik (Abbott))

1st site

2nd site

1st site 2nd site

KD = 0.3 mM

1st site binder

KD = 4.3 mM

2nd site binder

Ki = 1.4 mM Ki = 36 nM

ABT263

Phase II

Ki < 0.5 nM

MW 973

One of the first successful examples of fragment linking against Bcl-XL where the initial fragment linking with an alkene gave a

significant drop in potency. Second site binder discovered through ‘SAR by NMR’

Subsequent elaboration led to the development of ABT273 which has a Ki <0.5 nM although the molecular weight of this

compound is large (MW 973). Looking at this structure there are still some components of the initial fragment hits present.

Do PPI inhibitors need to be higher in molecular weight due to the nature of the PPI interface?

Fragment Linking – Replication Protein A (RPA70N)

Replication Protein A: Stephen W. Fesik (Vanderbildt) PhD Connectut

PostDoc – Yale

Abbott (20 years)

Currently at Vanderbildt

University

Replication Protein A (RPA) is essential for eukaryotic DNA replication,

damage response and repair

The N-terminal domain of the RPA70 subunit (RPA70N) interacts with a wide

range of DNA processing proteins.

Small molecule inhibitors of these protein-protein interactions are of interest

as they have the potential as anticancer drugs in conjunction with

radiotherapy or chemotherapeutic agents

A number of X-ray crystal structures have been solved of RPA70N and show

distinct binding regions for both small molecules and peptides

Apo structure

(RPA70N)

Overlay of structure showing interaction

with the P53N fragment (Green)

Small molecule (VU079104) binding in a

site adjacent to P53 binding site

(Orange) (RPA70N)

RPA70NFragment Library

14976 Fragments

149 Fragments

(Hit Rate 1%)


Site 1 Binders

52

KD 0.63-5 mM

LE up to 0.35

Site 1 and Site 2 Binders

81

Site 2 Binders

16

KD 0.49-5 mM

LE up to 0.28

Primary Screening

1H-15N HSQC 2D Protein Based NMR

Site 1 Binders (1H-15N HSQC 2D NMR)

Site 2 Binders (1H-15N HSQC 2DNMR)

The fragment library was screened in cocktails of 12

fragments and at a concentration of 20 mM.

Once a hit was obtained the mixture was deconvoluted.


KD = 0.64 mM

LE = 0.24

Site 1 Binders Site 1 and Site 2 BindersSite 2 Binders

KD = 1.85 mM

LE = 0.31

KD = 0.71 mM (S1)

LE = 0.29

KD = 1.4 mM (S2)

LE = 0.26

KD = 0.58 mM (S1)

LE = 0.22

KD >2.0 mM (S2)

KD = 1.12 mM

LE = 0.28

KD = 1.62 mM

LE = 0.23

Rotation of the

phenyl ring off

the furan

A number of fragment-linking strategies are possible


KD = 1.4 mM (Site 2)

LE = 0.26

KD = 0.58 mM (Site 1)

LE = 0.22

NMR KD = 26 mM

FP KD = 20 mM

(good agreement)

NMR KD = 1.9 mM

Fragment Linking

Fragment Linking – Replication Protein A (RPA70N) – Further applications

NMR KD = 1.9 mMFITC-DFTADDLEEWFALAS-NH2

FITC-DFTADDLEEWZALLL---NH2

FP KD = 4.8 mM

FP KD = 220 nM

Fragment Linked Compound

Modified Stapled Peptide

While the fragment linked compound gave a KD (1.9 mM) with a ligand efficiency of 0.23 a further study by Fesik and co-

workers used the information from the fragment screening to develop a modified peptide which incorporated the

dichlorophenyl unnatural amino acid and this gave a peptide which bound with a KD of 220 nM

Fesik, S.W. et al, J. Med. Chem., 2014, 57, 2455-2461

Fesik, S.W. et al, J. Med. Chem., 2013, 56, 9242-9250

Fesik, S.W. et al, Biochemistry., 2013, 52, 6515-6524

Fesik, S.W. et al, ACS Med.Chem. Lett., 2013, 4, 601-605

With the study of RPA70N the proximity of the fragments makes introducing a linker seem facile however this is not always

the case.

Is there an easier methodology available for fragment linking?

New Fragment Linking Approaches – In-situ Click Chemistry

Huisgen (1968)

Sharpless and Fokin (2002)

Sharpless (2004)

1,4 and 1,5 isomer formed in a 1:1

ratio. Need to be heated over 80oC

Cu - 1,4-isomer

Ru - 1,5-isomer

Azide chemistry has undergone a renaissance with the advent of the CuAAC, RuAAC and SPAAC by Sharpess, Fokin, Meldal

and Bertozzi

In-situ click chemistry approach has

no metals present and the formation

of the product is templated by the

protein. The 1,4 or the 1,5 isomer can

be formed. Only select number of

examples have been reported

Acetylcholine esterase (AChE) (Sharpless et al (2004))

Enzymes as reaction vessels

Catalytic

binding site

Peripheral

binding site

Narrow ‘gorge’

between the two sites

Acetylcholine esterase (AChE) is a key component of neurological function and is a known drug target

This has two distinct binding sites, catalytic binding site and a peripheral binding site with a narrow ‘gorge’ between them.

There has been a number of inhibitors developed against the catalytic binding site and these have extended into the

narrow ‘gorge’

This was used as a test case to look at the ‘in-situ’ approach to linking the two active sites.


PhD. Stanford University

(E.E. Van Tamelen)

PostDoc – Stanford

University and Harvard

Acetylcholine esterase (Sharpless et al (2004))

Tacrine (catalytic side binder, KD = 18 nM) and propidium (peripherial site binder, KD = 1.1 mM) were used as a test

cases where each has been appended with an azide or alkyne

A library of 8 tacrine and 8 propidium (8 x 8 array) derivatives were synthesised with variation in the alkyl chain length

which were then incubated with the AChE in pairs (azide/alkyne)

The 1,5-isomer (syn) was selectively synthesised in-situ where the potency was measured to be 14 pM and the 1,5-

isomer was not observed.

Why is there a difference in the potency of these isomers?

syn (1,5-isomer)

99 fM

anti (1,4-isomer)

14 pM

140 fold drop in potency


Only isomer observed with

‘in-situ’ approachSynthesised using CuAAC


In-situ Fragment Linking Concept

Acetylcholine esterase (Sharpless et al (2004))

Has been applied to targeting other proteins – Abl tyrosine kinase, Carbonic anhydrase, Histone deacetylase 8, Nictonic

acetylcholine receptors, EthR.

Conventional fragment screeningAppend fragments with ‘reactive’ functional groups – guided by X-ray

crystallography. Incubate an array of these modified fragments with the

protein and allow the protein to choose the optimal fragment linker length.

This strategy could be applied to find an linker by allowing the enzyme to choose the optimal length

Fragment Linking – Pros and Cons

Pros Cons

One of the most difficult strategies to carry out as

there are not many cases where different fragments

bind into different regions of the enzyme

The ideal linker can be difficult to find



Without X-ray information fragment linking is

difficult.

This is seen as one of the best ways to increase

potency of two or more fragments binding to an

enzyme.

In theory a compound derived from linking

fragments with an ideal linker is expected to

have a Gibbs free energy of bonding better than

the sun of the individual binding fragments

(superadditivity)

Other successful fragment linking strategies

- Pantothenate synthetase (Abell -

Cambridge)

- EthR – (Abell – Cambridge)

- Bcl-Xl (Fesik – Abbott)

- Chitinase (Omura – Tokyo)

- LDHA (Astra Zeneca)

- HSP90 (Abbott)

Fragment Elaboration Strategies – A Comparison

Fragment

Growing

Fragment

Merging

Fragment

Linking

Enzyme

Fragment

Fragment elaboration strategies

Fragment growing: easiest option however

structural information is required in order to

grow the fragments

Fragment merging: Where fragments overlap

this is a good option however structural

information is key. In some cases the merged

compounds can be difficult to synthesise

Fragment linking: Observing two or more

fragments binding in separate parts of the

binding pocket is rare. Linking fragments

together optimally is very difficult. Structural

information is key

Fragment Based Drug Discovery - Where are we with? (2013)

Phase I Phase II Phase III

Approved

Vemurafenib

(BRAF Kinase)

AT13387

(HSP90 Astex)

AT7519

CDK2

AT9283

(Aurora, Astex)

AUY922

(HSP90 Vernalis)

Indeglitazar

(Plexxikon)

ABT8693

(VGEF, Abbott)

Navitoclax

(ABT263)

LY2886721

(BACE1, Lilly)

LY517717

(Fxa, Lilly)

PLX3397

(FMS, Plexxikon)

ABT518

ABT737

AZD3839

AZD5363

DG-051

IC776

JNJ-42756493

LEE011

LP-261

LY2811376

PLX5568

SGX-393

SGX-523

SNS-314

MK-8931

(BACE1, Merck)

Many of the drugs in Phase II/III are from smaller pharma companies. There is the distinct lack of compounds derived from a

fragment based approach in development from the big two – GSK and Pfizer

Future Directions

What does the future hold for fragment-based drug discovery?

Fragment-based drug discovery is here to stay and has become common place alongside HTS as a means for finding

compounds that bind to a target.

Fragment library design to expand the coverage of chemical space is an active area of research however these

fragments need to be synthetically accessible (synthetic organic chemistry)

Developments in fragment screening capabilities are key where the screening time needs to shortened and the amount

of protein used needs to be minimised.

Fragment elaboration strategies need to be faster and the application of methodologies such as ‘in-situ’ click chemistry

needs to be developed

Further drugs to be approved for clinical use

Key References

A three stage biophysical screening cascade for

fragment-based drug discovery

Mashalidis, E.H., Sledz, P., Lang, S., Abell, C

Nature Protocols, 2013, 8(11), 2309-2324

Fragment-based approaches in drug discovery and

chemical biology

Scott, D.E, Coyne, A.G., Hudson S.A., Abell, C

Biochemistry, 2012, 51(25), 4990-5003

Recent developments in fragment-based drug

discovery

Congreve, M., Chessari, G., Tisi, D., Woodhead, A.J.,

J. Med Chem., 2008 51 (13), 3661-3680

Structural biology in fragment-based drug design

Murray, C.W., Blundell, T.L.

Curr. Opin, Struct. Biol., 2010 20 (4), 497-507

Drugging challenging targets using fragment-based

approaches

Coyne, A.G., Scott, D.E, Abell, C

Curr. Opin. Chem. Biol, 2010, 14 (3), 299-307

Fragment based drug discovery and X-ray

crystallography (Topics in Current Chemistry)

Davis, T.G, Hyvönen, M,. (Eds)

Springer, 2012

ISBN: 3642275397

Fragment based drug discovery : A practical approach

Zartler, E., Shapiro, M (Eds)

Wiley-Blackwell, 2012

ISBN: 0470058137

Fragment based approaches in drug discovery : 34

(Methods and principles in Medicinal Chemistry)

Jahnke, W., Erlansson, D.A., Mannhold, R., Kubinyi, H. (Eds)

Wiley-VCH 2006

ISBN: 3527312919

http://practicalfragments.blogspot.co.uk

gives an up to date overview of what research is been carried

out in both academia and industry

Reaching the high-hanging fruit in drug discovery at

protein-protein interfaces

Wells, J.A., McClendon, C. L.

Nature, 2007, 450 (13), 1001-1009

Modulators of protein-protein interactions

Milroy, L-G., Grossmann, T.N. Hennig, S., Brunsved, L.,

Ottmannm C.

Chem. Rev, 2014, asap article (doi 10.1021/cr400698c)

Fragment-based approaches to finding novel small molecules that bind to proteins are now firmly established in drug

discovery and chemical biology. Initially developed primarily in a few centers in the biotech and pharma industry, this

methodology has now been adopted widely in both the pharmaceutical industry and academia. After the initial success

with kinase targets, the versatility of this approach has now expanded to a broad range of different protein classes such

as metalloproteins and protein-protein interactions. In the course of these two lectures we will explore the different

strategies for finding a fragment hit and the subsequent elaboration strategies used in order to increase potency to

develop a lead compound.

Science

Fragment Based Drug Discovery