Dreaming Big and Thinking Small: Applying Medicinal Chemistry

6/22/2016

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Find out more about the AAPS www.aaps.org/annualmeeting 11

Program Themes

• Advancing Product Development through Novel Technology: Material Science, Engineering & Analytical Methodology

• Making New Delivery Modalities a Reality:

Peptides, Proteins & Conjugates • Enhancing Patient Lives through Accelerated Drug

Development • Paving the Way for Precision Medicine: Innovation

& Implementation

Featured Speakers

• Daniel A. Fletcher, Ph.D. (U. California at Berkeley) - diagnostic medical devices to investigate the biophysical mechanisms of disease

• Frederick Balagadde, Ph.D. (K-RITH Durban, South Africa) - microfluidic systems to increase affordable healthcare access

• James Olson, M.D., Ph.D. (Fred Hutchinson Cancer Research Center) - new cancer therapies for children with brain tumors

• Susan Hershenson, Ph.D. (The Bill & Melinda Gates Foundation) - technical expertise & strategic guidance for the therapeutics projects

2016 Drug Design and Delivery Symposium

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Thursday, July 7, 2016

The Chemistry of Sight: Material Innovations in Eye Care and Contact Lenses

Heather Sheardown, Professor of the Department of Chemical Engineering and Canada and Research Chair in Ophthalmic Biomaterials, McMaster University

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Thursday, June 30, 2016

Ice Cream Chemistry

Rich Hartel, Professor of Food Engineering, University of Wisconsin-Madison

Bill Courtney, Culinary Chemist

The 2016 DDDS is co-produced with ACS Division of Medicinal Chemistry and the AAPS 14


“Applying Medicinal Chemistry Strategy to Antibody-Drug-Conjugates”

www.acs.org/acswebinars Slides available now! Recordings will be available to ACS members after one week

L. Nathan Tumey Associate Research Fellow,

Pfizer, Inc.

Peter D. Senter Vice President of Chemistry,

Seattle Genetics

6/22/2016

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Dreaming Big and Thinking Small: Applying Medicinal Chemistry Strategy to Antibody-Drug-Conjugates

L. Nathan Tumey

[email protected]

15

Antibody Drug Conjugates: Targeted Cancer Chemotherapy

Nature Biotechnology, 2012, 30, 631–637. 16

6/22/2016

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The Big and the Small: ADC design overview

Payload Design

• Enzyme/target

potency

• Cytotoxicity

• Efflux

• Permeability

Linker Design

• Cleavable/noncleavable

• Hydrophobicity /

aggregation

• Efflux

• Permeability

Antigen Selection /

Antibody Design

• Target expression

• Internalization

• Binding affinity

• PK (FcRn binding)

Bioconjugation

• ADC biophysical properties

• ADC heterogeneity

• ADC PK exposure

• ADC stability

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Payload chemistry: What payload do we attach?

Payload Series

IC5

0 (

nM

)

MTI DNA RNA Other MOAs

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Payload Sources Total Synthesis

Fermentation/Isolation

Calicheamicin IC50’s = 0.003-1.7 nM DNA Double strand breakage High efflux ratio

Spliceostatins IC50’s = 0.05-0.6 nM RNA Splicing Inhibitor Low efflux ratio

Auristatins IC50’s = 0.07-0.21 nM Tubulin binder High efflux ratio

Tubulysins IC50’s = 0.1-0.8 nM Tubulin binder Low efflux ratio CBI Dimer IC50’s = 0.0007 – 1 nM

DNA Double strand alkylator Low efflux ratio

Selection Criteria

•Potency/Cytotoxicity •Mechanism of Action •Required target occupancy

•ADME properties •Synthetic Tractability/Scalability •Handles for Linker Attachment

Payload chemistry: What payload do we attach?

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Noncleavable

Cleavable

Linker Chemistry: How do we release a payload?

Internalization to lysosome

Complete ADC catabolism

Cathepsin cleavage site

Internalization

to lysosome

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Linker Chemistry: How do we release a payload?

Jeffrey Kern, Phil Brandish et. al.

JACS, 2016

Intracellular

phosphatases

Bioconjugate Chem., 2006, 17, 831-840.

lysosomal

glucoronidase

Acidic hydrolysis

Intracellular reduction

Cancer Chemother.

Pharmacol., 2008, 1027-35.

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Conjugation Chemistry: How do we attach a payload?

Hinge cysteine conjugation Lysine conjugation Site-specific conjugation

Activated ester (often NHS)

Electrophile (often maleimide)

+

+

…

+

+

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Engineered Cysteine

Conjugation Chemistry: How do we attach a payload?

Site specific conjugation: 3 common approaches

Unnatural Amino Acids Enzymatic Conjugation

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Stability of maleimide conjugates

Deconjugation

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Audience Trivia Question

So how big of a problem is this? Approximately what % of drug is lost

from a typical maleimide ADC during 1 week in circulation?

• About one tenth

• A little less then one third

• About half

• A little less than two thirds

25

ANSWER THIS QUESTION ON THE BLUE SCREEN IN ONE MOMENT


So how big of a problem is this? Approximately what % of drug is lost

from a typical maleimide ADC during 1 week in circulation?

• About one tenth

• A little less then one third

• About half

• A little less than two thirds

26


Answer: 60% - almost all of it going to

serum albumin

(note that the T1/2 of an ADC in humans is ~1

week!)

6/22/2016

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Stability of maleimide conjugates

Site dependent

Deconjugation

X

Ring-opening

(improved stability)

To impart stability: 1) Intentionally open the maleimide

Tumey L. N. et al., Bioconjugate Chem.

2014, 25(10), 1871-1880

Lyon R. P. et al., Nature Biotech., 2014, 32(10), 1059-1062

2) Use an alternative electrophile Barbas, C.F. et al., Angew. Chem.

2013, 12592.

3) Attach to a stable site

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% D

AR

lo

ss

%

rin

g-o

pen

ing

Site plays a major role in the conjugate stability

In vivo DAR profile

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Site of conjugation has little effect on in vitro potency

The payload-linker drives the in vitro cytotoxicity – not the site of attachment.

29

Site of conjugation impacts ADC hydrophobicity

Hydrophobic interaction

chromatography (HIC)

ADC hydrophobicity is a function both of

the LP and of the site of conjugation

HIC

RR

T

T

G-F

C

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Robert Lyon et. al., Nature Biotechnology, 2015, 733–735

Hydrophobicity has an impact on ADC PK exposure

Hydrophobic linker-

payloads can result in

reduced ADC exposure

31

Co

ncen

trati

on

(u

g/m

L)

Time (hours)

HIC rrt = 1.35 (AUC = 28500 mg*h/mL)

HIC rrt = 1.91 (AUC = 11000 mg*hr/mL)

Kappa-K183C vc0101 (tAb)

Kappa-K183C vc0101 (ADC)

Fc-L443C vc0101 (tAb)

Fc-L443C vc0101 (ADC)

Site of conjugation can impact ADC PK exposure

Rat PK study

k183C

443C 32

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Site impacts payload release kinetics

Higher HIC retention = faster cleavage

HIC RRT

% C

lea

va

ge

@2

0 m

ins

% c

lea

va

ge


Faster cathepsin-mediated linker cleavage in the lysosome should result in:

• Increased cytotoxicity

• Decreased cytotoxicity

• Little or no effect on cytotoxicity

34


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Faster cathepsin-mediated linker cleavage in the lysosome should result in:

• Increased cytotoxicity

• Decreased cytotoxicity

• Little or no effect on cytotoxicity

Answer: Little or no effect on cytotoxicity

35


Site impacts payload metabolism

Lower efficacy than was anticipated – rapid cleavage of acetate observed in vivo and in vitro.

Inactive metabolite!

36

6/22/2016

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Lesson Learned: Sites that result in minimal HIC

retention are resistant to in vitro enzymatic metabolism.

ACS Med.Chem.Letters, 2016, in press

0%

20%

40%

60%

80%

100%

0 20 40 60 80

Time (h)

Mo

us

e P

las

ma

% P

are

nt

rem

ain

ing

334C

392C

347C 388C

k183C

443C

R² = 0.9353

0%

10%

20%

30%

40%

50%

1 1.1 1.2 1.3 1.4

% A

ce

tate

cle

ava

ge

a

t 2

h

HIC RRT


0

400

800

1200

1600

0 20 40 60 80Tu

mo

r vo

lum

e (

mm

3)

Days

Improved stability = improved efficacy

ADC biophysical properties in vitro metabolism in vivo efficacy / metabolism

Hinge conjugate (DAR4)

(rapid in vivo metabolism)

334C conjugate (DAR2)

(no in vivo metabolism)


38

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Site impacts conjugatability: Uncialamycin

SEC after attempted conjugation to Tras-A114C:

39

Mutant LCMS DAR %Agg % Right shifted K246C 0.8 1% 0% K334C 1.5 2.6% 0% Q347C 1.4 21% 63% Y373C 1.2 0% 36% S375C 1.8 0.6% 0%

E380C 1.8 0% 100% (only slight) E388C 1.3 0% 68% K392C 2 2.5% 2.5% N421C 1.4 77% 0% L443C 1.8 87% 0%

kap-A111C 0.7 0% 50% kap-K149C 0.9 3% 50%

kap-K183C 1.9 0% 87% (only slight) kap-K188C 1.4 11% 39%

Screening of site-

mutants enabled the

conjugation of LPs that

were otherwise

intractable. All 4

uncialamicin LPs were

successfully attached

to the 392 and 375

sites.

A114C:

Site impacts conjugatability: Uncialamycin

HIC RRT

1.24

1.28

1.87

1.34

1.59

40

6/22/2016

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Summary

• ADC discovery efforts require a seamless integration of large-molecule

design and small molecule design.

• A “toolbox” of conjugation sites allows for rapid optimization to solve

conjugation, stability, and metabolism problems.

• ADC biophysical properties are becoming an important component of

predicting in vitro and in vivo ADC stability.

Key Take-Home Message: We are gradually moving away from empiricism and towards

a “prospective” set of rules for ADC design.

41

Merck

Jeffrey Kern, Phil Brandish et. al.

JACS, 2016

Roche/Genentech

Thomas Pillow et. al.

Nature, 2015

LCK inhibitor

Peter Schultz

JACS, 2015

The next horizon: Growing interest in non-oncology ADCs

42

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Acknowledgements

Carolyn Leverett

Jesse Teske

S. Chetan Sukuru

Jack Bikker

Melissa Wagenaar

Pharmacokinetics, Dynamics, and Metabolism

Frank Barletta

Jo-Ann Wentland

Tracey Clark

Mauricio Leal

Xiaogang (Sean) Han

Brian Rago

Fengping Li

Cong Wei

Steve Hansel

Worldwide Medchem

Chris O’Donnell

Edmund Graziani

Chakrapani Subramanyam

Russell Dushin

Frank Koehn

Beth Vetelino

Sujiet Puthenveetil

Jeff Casavant

Andreas Maderna

Anokha Ratnayake

Zecheng Chen

Matt Doroski

Hud Risley

Alex Porte

Gary Filzen

Ludivine Moine

Dahui Zhou

Ken Dirico

Global Biologic Technologies

Will Somers

Lioudmila Tchistiakova

Kim Marquette

Sadhana Jain

Mark Krebs

Madan Katragadda

Rita Agostinelli

Nicole Piche-Nicholas

Ryan Jackobek

Eric Bennett

Amy Tam

Laura Lin

Eric Sousa

Tao He

Oncology Research

Hans Peter Gerber

Puja Sapra

Pavel Strop

Kathy Delaria

Frank Loganzo

Kiran Khandke

Manoj Charati

William Hu

Sylvia Musto

Judy Lucas

Nadira Prashad

Ellie Muszynska

Jacob Vineberg

43

Backup slides

44

6/22/2016

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The ideal scenario

Biological Stability

Small set of highly

preferred sites

“The Universe of Sites”

45

2010-2011: Site may have impact on PK

A114C

E380C*

L398C

L443C

V422C

Conventional*

Control Ab

Antibody/Time

(anti-IgG)

ADC/Time

(anti-MMAD)

The 380C-mcMMAD has good tAb PK but poor ADC PK. Why??

46

6/22/2016

24

Lyon R. P. et al., Nature Biotech.,

2014, 32(10), 1059-1062

Tumey L. N. et al., Bioconjugate Chem.,

2014, 25(10), 1871-1880

Christie, R. J. et al, J. Controlled

Release (2015), Ahead of Print.

Using ring-opening to block deconjugation

Blocking deconjugation: Forced ring opening

Blocking deconjugation: Spontaneous ring opening

47

48




The 2016 DDDS is co-produced with ACS Division of Medicinal Chemistry and the AAPS


Pfizer, Inc.


Seattle Genetics

6/22/2016

25


49 http://bit.ly/2016ddds


50







Ice Cream Chemistry



6/22/2016

26

51




The 2016 DDDS is co-produced with ACS Division of Medicinal Chemistry and the AAPS


Pfizer, Inc.


Seattle Genetics

Find out more about the AAPS www.aaps.org/annualmeeting 52

Program Themes

• Advancing Product Development through Novel Technology: Material Science, Engineering & Analytical Methodology

• Making New Delivery Modalities a Reality:

Peptides, Proteins & Conjugates • Enhancing Patient Lives through Accelerated Drug

Development • Paving the Way for Precision Medicine: Innovation

& Implementation

Featured Speakers

• Daniel A. Fletcher, Ph.D. (U. California at Berkeley) - diagnostic medical devices to investigate the biophysical mechanisms of disease

• Frederick Balagadde, Ph.D. (K-RITH Durban, South Africa) - microfluidic systems to increase affordable healthcare access

• James Olson, M.D., Ph.D. (Fred Hutchinson Cancer Research Center) - new cancer therapies for children with brain tumors

• Susan Hershenson, Ph.D. (The Bill & Melinda Gates Foundation) - technical expertise & strategic guidance for the therapeutics projects

6/22/2016

27

Join the ACS Division of Medicinal Chemistry Today!

Find out more about the ACS MEDI Division www.acsmedchem.org 53

For $25 ($10 for students), You Will Receive:

• A free copy of our annual medicinal chemistry review volume (over 600 pages, $160 retail price)

• Abstracts of MEDI programming at national meetings

• Access to student travel grants and fellowships

How has ACS Webinars benefited you?

®

“An informative and inspirational webinar. Medicinal chemists must embrace the challenge of providing efficacious drugs for all diseases as we move towards personalized medicines.”

Tito Akindele, Ph.D. Researcher, Nagase Laboratory of Medicinal Chemistry International Institute for Integrative Sleep Medicine (IIIS) World Premier International Research Center Initiative (WPI) University of Tsukuba, Japan

Quote in reference to: http://www.acs.org/content/acs/en/acs-webinars/drug-discovery/drug-career.html

Be a featured fan on an upcoming webinar! Write to us @ [email protected] 54

6/22/2016

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@acswebinars

youtube.com/acswebinars


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Benefits of ACS Membership


Chemical & Engineering News (C&EN) The preeminent weekly news source.

NEW! Free Access to ACS Presentations on Demand® ACS Member only access to over 1,000 presentation recordings from recent ACS meetings and select events.

NEW! ACS Career Navigator Your source for leadership development, professional education, career services, and much more.

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Dreaming Big and Thinking Small: Applying Medicinal Chemistry