Targeting CDK7 in Breast CancerSimak Ali

Department of Surgery & Cancer

27th-28th JANUARY 2020: ICC, BIRMINGHAM

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Declaration of Interests:• Patents on CDK7 inhibitors• Licensing CDK7i with Carrick Therapeutics• BCN Catalyst grant with Pfizer

Transcriptional Dysregulation is a Common Feature in Cancer

o Tight control of gene expression is necessary for normal cell function

o Cancers feature dysregulated gene expression programs and frequent ‘addiction’ to specific regulators of

gene expression

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Transcriptional Dysregulation is a Common Feature in Cancer

o Tight control of gene expression is necessary for normal cell function

o Cancers feature dysregulated gene expression programs and frequent ‘addiction’ to specific regulators of

gene expression

− Over-expression/amplification/mutation of transcription factors: MYC, RUNX, TAL1, WT1, …

− transcription factor gene rearrangements: TMPRSS2-ERG et al (prostate), ESR1-YAP1 etc (breast), PML-

RARA etc (APL), MLL-AF4 (ALL), . . .

− Mutations in chromatin re-modelling factors: Mediator, p300/CBP, MLLs, EZH2, . . .

− Enhancer rearrangements/mutations: IgH-MYC (Burkitt’s Lymphoma), CTCF/Cohesin binding regions, . . .

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Transcriptional Dysregulation is a Common Feature in Cancer

o Tight control of gene expression is necessary for normal cell function

o Cancers feature dysregulated gene expression programs and frequent ‘addiction’ to specific regulators of

gene expression

− Over-expression/amplification/mutation of transcription factors: MYC, RUNX, TAL1, WT1, …

− transcription factor gene rearrangements: TMPRSS2-ERG et al (prostate), ESR1-YAP1 etc (breast), PML-

RARA etc (APL), MLL-AF4 (ALL), . . .

− Mutations in chromatin re-modelling factors: Mediator, p300/CBP, MLLs, EZH2, . . .

− Enhancer rearrangements/mutations: IgH-MYC (Burkitt’s Lymphoma), CTCF/Cohesin binding regions, . . .

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− Signaling transcription factors:

− Prostate cancer is androgen receptor dependent, activating AR mutations are common

− 70% of breast cancers are dependent on the estrogen receptor

Targeting Transcription in Cancero Can we directly target the transcriptional machinery in cancer?

⏤ ER in Breast cancer

⏤ AR in Prostate cancer

⏤ Retinoic acid receptors in acute promyelocytic leukaemia

o Targeting enzymes involved in transcriptional control

⏤ Histone acetylases, histone deacetylases, histone methylases, ATPase-dependent chromatin

remodellers

⏤ Histone deacetylase inhibitors (panobinostat, belinostat, hydroxamic acid…) have been

approved for leukaemias/lymphomas/myeloma

⏤ Protein kinases

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Cyclin-Dependent Kinases (CDK) are Required for Transcription

CDK7 (TFIIH) CDK9 CDK12/13 CDK9 CDK12Cyclin H Cyclin T1 Cyclin K Cyc T1 Cyc K

from Galbraith 2019

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CDK7 Regulates Estrogen Receptor Activity

Transcription (AF-1) DNA Hormone Binding (AF-2)Binding

PSer118

ER

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o Phosphorylation @ Ser118 promotes ER activityo Ser118 phosphorylation is associated with

response to endocrine therapies in clinical samples

TFIIH

CDK7

MAT1

CyclinH

-6 -4 -2 0 2 40

100

200

300

400

Estrogen Concentration (nM)

Rel

ativ

e E

R A

ctiv

ity

+CDK7

Hypersensitivity to Estrogen

Vehicle EstrogenTamoxifen0

100

200

300

400

Rea

ltive

ER

Act

ivity

Control

CDK7

Increased tamoxifen agonism

First-Generation Selective CDK7 Inhibitor – BS-181

Ali et al Cancer Res 2009Heathcote et al J Med Chem 2010

Modelling Roscovitine in the CDK7 ATP binding pocket N

N NNH

HN

Ph

OH

HO OH N

N NNH

HN

Ph

NH2

Kinase Roscovitine BS-194 BS-181IC50 (µM) IC50 (µM) IC50 (µM)

CDK1 1.8 0.030 8.1CDK2 0.1 0.003 0.9CDK4 15.3 20.0 33.0CDK5 0.2 0.030 3.0CDK6 28.0 35.5 47.0CDK7 0.5 0.25 0.02CDK9 1.2 0.1 4.2

50x

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ICEC0942 – an Oral, Selective CDK7 Inhibitor

CDK7CDK2CDK9CDK1CDK5CDK6CDK4

0.01

0.1

1

10

100

IC50

(µM

)

In vitro CDK inhibition assay

Patel et al 2018 MCT

+ 140 other kinases

CDK7

CDK9

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ICEC0942 Inhibits Growth of ER+ BC cells in vivo

0 2 4 6 8 10 12 140

2

4

6

Days

Rel

ativ

e Tu

mou

r Vol

umes

MCF7 Xenograft

VehicleICEC0942

p=0.

0001

ICEC0942 100 mg/kg/day

10Patel et al 2018 MCT

n=12

ICEC0942 is Effective in Combination with Endocrine Therapies

0

25

50

75

100

Rel

ativ

e G

row

th (%

)

ICEC0942 (µM) 0 0.1 0

Tamoxifen Faslodex

1.0 0 0.11.0

0.1 1.01.0 0.1

*# *

#

(µM)

*#

*#

0 1.0 0 0.11.0

0.1 1.00.1

MCF7 Cells In vitro

11Patel et al 2018 MCT

0 3 6 9 121518012345

DaysRel

ativ

e Tu

mou

r Vo

lum

e VehicleICEC0942TamoxifenICEC0942/Tamoxifen

p=0.0006

p<0.0001

p<0.0001

MCF7 Tumour Xenograft

ICEC0942 50 mg/kg/day

n=8

Resistance to Targeted Therapies in ER+ Breast Cancer

o Resistance to Hormone Therapies

o Development of estrogen-independence through augmentation of growth factor signalling

o Estrogen receptor mutations – Identifiable in 25-40% of advanced breast cancer

o Resistance to CDK4/6 inhibitors

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CDK7 is a Key Regulator of the Cell Cycle CDKs

M G1

G2

S

CDK4/6Cyclin D

P

CDK2P

Cyclin E

CDK2Cyclin A

P

CDK1Cyclin B

P

CDK1Cyclin A

P

G0G0

RB

E2F

P

P P P

P

CyclinHMAT1

CDK7

o CDK7 phosphorylates Cell Cycle CDKs in the Activating T-Loop – promotes CDK activity and/or

interaction with its cognate cyclin

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NN O

N

NH

O

N

N

NH2

+

SO

O OOH

PalbociclibPD-0332991

Ibrance

RibociclibLEE011Kisqali

AbemaciclibLY2835219Verzenios

CDK7 is a Key Regulator of the Cell Cycle CDKso ICEC0942 inhibits CDK1/CDK2 phosphorylation

o ICEC0942 inhibits CDK2 and CDK4/6-mediated RB phosphorylation

M G1

G2

S

CDK4/6Cyclin D

P

CDK2P

Cyclin E

CDK2Cyclin A

P

CDK1Cyclin B

P

CDK1Cyclin A

P

G0G0

RB

E2F

P

P P P

P

CyclinHMAT1

CDK7

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Resistance to Targeted Therapies in ER+ Breast Cancer

o Resistance to Hormone Therapies

o Development of estrogen-independence through augmentation of growth factor signalling

o Estrogen receptor mutations – Identifiable in 25-40% of advanced breast cancer

o Resistance to CDK4/6 inhibitors

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CDK7 inhibitors

CDK7 Inhibitor Portfolio – ATP Competitive Inhibitors

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ICEC0942

HNNH

NHN

N

N

OH

LDC4297

HN

N N

N

NH

N

N

N

O

LY-3405105NN

NNH

N

OO

NO

N

NH2

NH

HN

N NN

BS-181

CDK1-CycB = 8100CDK2-CycE = 880CDK4-CycD1 = 33000CDK6-CycD1 = 47000CDK7-CycH-Mat1 = 21CDK9-CycT = 4200

CDK1-CycA1 = 1800CDK2-CycA1 = 620CDK4-CycD1 = 49,000CDK6-CycD1 =34,000CDK7-CycH-MAT1 = 40CDK9-CycT1 = 1200

CDK1-CycB1 = 20000CDK2-CycE1 = 20000CDK4-CycD1 = 2830CDK6-CycD1 = 8079CDK7-CycH-Mat1 = 92.8CDK9-CycT1 = 6320CDK12-CycK = 14780

CDK1-CycB = 54CDK2-CycE = 64CDK4-CycD ≥ 1000CDK6-CycD ≥ 1000CDK7-CycH-MAT1 ≤ 5CDK9-CycT = 1711

ICEC0942 in the ATP Binding pocket of CDK7

Model based on structure of ICEC0942 with CDK2Hazel et al 2017

CDK7 Inhibitor Portfolio – Covalent CDK7 Inhibitors

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YKL-5-124

NHN

O

N

NHN

NH

O

NH

O

SY-1365

Cl

N NH

N

NHN N

HN

NOH

O

H

H

H

Cl

NH

N

NH

NH

NH

NN

O

OTHZ1

Cl

NH

N

NH

NH

NH

NN

O

OTHZ2

CDK2-CycE1 = 2117CDK7-CycH-MAT1 = 84CDK9-CycT1 = 914CDK12-CycK = 204

CDK1-CycB = 97CDK2-CycA = 222CDK4-CycD = 68CDK7-CycH = 14CDK9-CycT = 194

CDK7-CycH = 3.8

CDK7-CycH-MAT1 = 9.7CDK2-CycA = 1300CDK9-CycT1 = 3020

Model of YKL-5-124 with CDK7Olson et al 2019

CDK7 Inhibitors in the Clinico SY-1365 – ClinicalTrials.gov Identifier: NCT03134638

⎯ Phase 1 – May 2017

⎯ IV administration - Advanced solid tumours - Discontinued Oct 2019

o LY3405105 – ClinicalTrials.gov Identifier: NCT03770494

⎯ Phase 1 – Dec 2018

⎯ Oral administration - Advanced solid tumours

o ICEC0942 (CT7001) – ClinicalTrials.gov Identifier: NCT03363893

⎯ Phase 1 – Dec 2017

⎯ Oral administration – Advanced Solid tumours

⎯ Dose finding completed

⎯ New cohorts:

⎯ HR+/HER2- BC – Monotherapy @240 mg daily, combination with fulvestrant @360 mg daily

⎯ TNBC monotherapy – recruiting 50 patients @360 mg daily

⎯ Prostate Cancer – CRPC monotherapy – recruiting 25 patients @360 mg daily18

SY-1365 Cl

N NH

N

NHN N

HN

NOH

O

H

H

H

LY-3405105NN

NNH

N

OO

NO

N

ICEC0942

HNNH

NHN

N

N

OH

ConclusionsIn vitro and in vivo findings identify CDK7 inhibitors as important new cancer therapeutics

o In ER+ BC as monotherapy, or in combination with hormone therapies

o In ER-negative BC as monotherapy

o Other cancer types, including prostate cancer, lung cancer, ovarian cancer, glioblastoma

Toxicities?o CDK7 is essential in embryonic development

o CDK7 is dispensable in adult tissues, but cell loss due to CDK7 insufficiency was observed in rapidly proliferating

tissues (CDK7KO mice – Ganuza et al 2012 EMBO J). Long-term effects of CDK7i treatment?

Continuing determination of CDK7 inhibitor action and function of key targets will therefore be essential for:

o identifying the most appropriate cancer types and patients for CDK7 inhibitors,

o defining the optimal therapeutic window balancing dependencies in cancer cells, with those in normal tissues is likely

to be critical for successful implementation of CDK7i.

o Identifying combination settings will help to ameliorate potential toxicities, e.g. with hormonal therapies – as with

CDK4/6i

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Acknowledgements

Hetal PatelHailing FanChun-Fui LaiVan NguyenMani PeriyasamyGeorgina SavaKirsty BalachandranRaed FarzanCarolina GemmaIsabella GoldsbroughAlison HarrodAnup Singh

LakiBuluwela

CharlesCoombes

Matt Fuchter, Tony BarrettDepartment of Chemistry,Imperial College London

Lesley-AnnMartin

MitchDowsett

StephenJohnston

Institute for Cancer Research & the Royal Marsden

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Fui

Alison

Hetal Van Mani

TBA