leslie holsinger, phd

Use of Novel Biomarkers of P. gingivalis Infection and

Neuroinflammation in the GAIN Trial:

An Ongoing Phase 2/3 Clinical Trial Assessing the Activity of Atuzaginstat in

Patients with Mild to Moderate Alzheimer’s Disease

Leslie Holsinger, PhDExecutive Vice President, Research & Development

Cortexyme, Inc.

Annual Biomarkers for Alzheimer’s Disease Summit

August 25, 2021

Disclaimer

Certain information contained in this presentation and statements made orally during this presentation relate to or are based on studies, publications, surveys and

other data obtained from third-party sources and Cortexyme's own internal estimates and research. While Cortexyme believes these third-party sources to be

reliable as of the date of this presentation, it has not independently verified, and makes no representation as to the adequacy, fairness, accuracy or completeness

of, any information obtained from third-party sources. While Cortexyme believes its internal research is reliable, such research has not been verified by any

independent source. This presentation contains information that is highly confidential and/or privileged. The information is intended only for the use of individuals or

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Cortexyme corporate overview

Topline data in

Periodontitis:

by mid-Nov

Phase 2 in

Parkinson’s

Expanding

evidence base

$153.3 MProprietary small

molecules

Topline data in

Alzheimer’s: by

mid-Nov

Coronavirus

program

4

Growing evidence of the important role of the immune

system in Alzheimer’s pathology and risk factors

Many emerging genetic risk factors for sporadic disease relate to immune system function

• Trem2, TLR4, CR1, CD33, Etc.

AD pathology is consistent with host response to a pathogen

• Chronic low grade inflammation

• Complement activation and dysregulation

• Microglial activation

• Inflammasome activation

What is

triggering

abeta42

over-

production?

Deepak Kumar, *Se Hoon Choi, *Kevin J. Washicosky, *William A.

Eimer, Stephanie Tucker, Jessica Ghofrani, Aaron Lefkowitz,

Gawain McColl, Lee E. Goldstein, Rudolph E. Tanzi, Robert D. Moir

Amyloid-β peptide protects against

microbial infection in mouse and worm

models of Alzheimer’s disease

Stephanie J. Soscia, James E. Kirby, Kevin J. Washicosky,

Stephanie M. Tucker, Martin Ingelsson, Bradley Hyman, Mark A.

Burton, Lee E. Goldstein, Scott Duong, Rudolph E. Tanzi, Robert

D. Moir

The Alzheimer’s Disease-Associated Amyloid

β-Protein Is an Antimicrobial Peptide

“Could

Alzheimer’s Stem

From Infections?

It makes sense,

experts say”

Gosztyla, M.G., Brothers, H.M., Robinson, S.R. (2018). Journal

of Alzheimer’s Disease, 64(4), 1495- 1506.

Alzheimer’s Amyloid-b is an antimicrobial

peptide: a review of the evidence

Bruce L. Kagan, Hyunbum Jang, Ricardo Capone,

Fernando Teran Arce, Srinivasan Ramachandran,

Ratnesh Lal, and Ruth Nussinov

Antimicrobial Properties of Amyloid

Peptides

Epidemiological

& twin studies

show that

periodontal

bacteria increase

the risk for

Alzheimer’s

disease

Angela R. Kamer, Elizabeth Pirraglia, Wai Tsui, Henry Rusinek, Shankar

Vallabhajosula, Lisa Mosconi, Li Yi, Pauline McHugh, Ronald G. Craig, Spencer

Periodontal disease associates with

higher brain amyloid load in normal

elderly

Pamela Sparks Stein, DMD; Mark Desrosiers, PhD; Sara Jean Donegan,

SSND, DDS; Juan F. Yepes, DDS, MD, MPH; Richard J. Kryscio, PhD

Tooth loss, dementia and

neuropathology in the Nun Study

Pamela Sparks Stein, Michelle J. Steffen, Charles Smith, Gregory Jicha,

Jeffrey L. Ebersole, Erin Abner, and Dolph Dawson III

Serum antibodies to periodontal

pathogens are a risk factor for

Alzheimer’s disease

6

Elizabeth Krall Kaye, PhD, Aileen Valencia, BS, Nivine Baba, MA, Avron Spiro,

III, PhD, Thomas Dietrich, DMD, and Raul I. Garcia, DMD

Tooth loss and Periodontal Disease

Predict Poor Cognitive Function in

Older Men

Ryan T. Demmer, Faye L. Norby, Kamakshi

Lakshminarayan, Keenan A. Walker, James S. Pankow, Aaron R.

Folsom, Thomas Mosley, Jim Beck, Pamela L. Lutsey

Periodontal Disease and Incident

Dementia: The Atherosclerosis Risk

in Communities Study (ARIC)

http://orcid.org/0000-0002-1975-0405

http://orcid.org/0000-0002-1572-1340

7

Active periodontal disease is associated with rapid decline in Alzheimer’s patientsIde M, et al (2016)

Periodontitis and Cognitive

Decline in Alzheimer’s Disease.

PLoS ONE 11(3)

Mean

ch

an

ge f

rom

base

lin

e A

DA

S-C

og

rati

ng

-2

-1

0

1

2

3

4

5

6

7

8

0 1 2 3 4 5 6 7

Months

ADAS-Cog

No or mild periodontitis(low bacterial load)

Moderate to severe Periodontitis (high bacterial load)

p< 0.005

NeurodegenerationTau fragmentation

ApoE fragmentation

Lysosomal dysfunction

Host response

P. gingivalis

infection

Brain

infiltration

Gingipain

secretionAging

Genetic risk (ApoE4,

TLR4, CR1, TREM2)

Trauma

Bacterial load

Microglia activation

Neuroinflammation

Complement induction

Inflammasome

Amyloid beta production

8

Growing body of evidence shows that bacterial brain infiltration

triggers Alzheimer’s pathology in physiological models

P. gingivalis discovered in the brain of 90-100% of

Alzheimer’s patients

P. gingivalis DNA also

confirmed through

sequencing of multiple

genes in Alzheimer’s

brain tissue and CSF

Gingipain

Immuno-

histochemistry

Source: Dominy et al 2019, Science Advances

P. gingivalis brain infiltration precedes and is

correlated with Alzheimer’s disease symptoms and pathology

Controls Alzheimer’s

Immunohistochemistry

of middle temporal gyrus

microarray

Confirmed with multiple

antibodies/antigens and

PCRArg

inin

e g

ingip

ain

load

(norm

aliz

ed t

o c

ontr

ol)

Source: Collaboration with University of Auckland/ Neurovalida study ****p<0.0001; Dominy et al 2019 Sciences Advances

**** ****

Arg

inin

e g

ingip

ain

load

(norm

aliz

ed t

o c

ontr

ol)

Tau load

(normalized to control)

Source: Adapted from Ilievski, et al.

Chronic oral application of a

periodontal pathogen results in brain

inflammation, neurodegeneration and

amyloid beta production in wild type

mice. PLOS: One 2018

Rela

tiv

e T

NF

alp

ha

gen

e e

xp

ress

ion

Neuroinflammation

2.5

2

1.5

1

0.5

0

P.

gin

giv

ali

s16S

RN

A c

op

ies

/ 5 F

FP

E

x1010

8

6

4

2

0

P. Gingivalis Infiltrates the Brain

Am

ylo

id b

eta

Pla

qu

es

/ fi

eld

0

1

2

3

4

5

6

Amyloid Beta Plaques

# p

Ta

u/

field

0

14

8642

10

12

Tau Tangle-Like Neurons

Mic

rogli

a /

fie

ld

0

14

8642

10

12

Activated Microglia

% I

nta

ct

neu

ron

s /

field

0

80

60

40

20

100

CA1

DG

Neurodegeneration

Evidence of

causation:

Oral Pg infection

of WT mice

induces AD

pathology after

22 weeks

*p< 0.05,**p<0.01, ***p<0.001, ****p<0.001

Virulence factor inhibition will block gingipain activity, reduce

bacterial load, and normalizes immune function

Microglial

Activation

Aβ-42

Production and Plaques

Tau Tangles

P. Gingivalis

Gingipain

Pyroptosis &

Necrosis

Tau and Other Protein

Fragmentation Neuronal Degradation

and Synaptic Dysfunction

NLRP1 Infla

m

ma some

Assembly & Activation

Complement

Dysregulation

Normally

Functioning Neuron

COR388

Plaque

Alzheimer’s disease Alzheimer’s disease

Tangle

COR388

P. Gingivalis

Gingipain

TNFα

Extracellular

Intracellular

1. Tau is fragmented and aggregated in the AD brain

and by Pg.

2. ApoE is fragmented in the AD brain and by

gingipains.

3. Abeta is overproduced in the AD brain and triggered

by Pg infection in WT mice.

4. Microglia are activated in the AD brain and by Pg.

5. Inflammasomes are activated in the AD brain and by

Pg.

6. Complement is dysregulated in the AD brain and by

gingipains.

7. Neurodegeneration is evident in the AD brain and

caused by Pg gingipains in physiological models

Atuzaginstat (COR388)

Kgp lysine gingipain

inhibitor

Small molecule optimized from proprietary

inhibitor library

• Novel & proprietary small molecule

• Potent: Target IC50 < 50pM

• Selective over 800 human anti-targets

including other cellular proteases

• Orally available, brain penetrant

• Large therapeutic window

Atuzaginstat (COR388) acts upstream of infection

induced Alzheimer’s pathology in wild type mouse

Source: Dominy et al, 2019, Science Advances

0

2,000

4,000

6,000

Co

py #

/ 1

00 n

g D

NA

***

0.00

0.05

0.10

0.15

0.20

pg

/ m

g P

rote

in

***

0.0

0.5

1.0

1.5

2.0

2.5

pg

/ m

g P

rote

in **

0

2,000

4,000

6,000

8,000

10,000

Inte

rneu

ron

s /

mm

3

*

3x oral P.g. / weekCOR388 10 or 30 mg/kg po 2x/day

5 weeks 10 weeks

Mean +/- SEM *p< 0.05,**p<0.01, ***p<0.001

Atuzaginstat Reduces P. gingivalis and Is Efficacious in a

Natural Dog Model of Periodontal Disease

Cessation

of dosing

Source: Aratsu-Kapur et al (2020). Pharmacol Res Perspectives

16

Lysine Gingipain Activity Quantified Using Activity-Based Probes

Cy5

Covalent

Gingipain

Active-site

Inhibitor

Lysine Gingipain Activity Assay

Analysis of in

vitro bacterial

samples

Dominy et al, (2019) Science Advances

Lysine Gingipain Activity Assay

Kgp WB

50kDa -

CAB102 Kgp WB

Aratsu-Kapur et al, (2020) Pharmacol Res Perspectives 8.

Activity-probe analysis

of oral biofluid samples

Cy5 probe

Analysis

of in vivo

samples

17

Atuzaginstat Human Pharmacokinetics in Phase 1

17

• Atuzaginstat absorbed rapidly after oral administration:

- Median Tmax = 0.5-1.5 hours

• Target therapeutic exposure range, predicted from animal models, was achieved with doses as low as 25 mg b.i.d. at steady state:

- Mean Cmax = 25 ng/mL, Mean AUC0-24 178 h*ng/mL

• Good tissue distribution:

- Mean Vd/F = 879 – 1734 L

• Slightly more than linear dose proportionality:

- Slope estimate = 1.7 for Cmax , 1.5 for AUC0-12

• Clearance:

- T1/2 = 4.5 – 4.9 hrs at steady state

- Exposures support BID dosing based on animal models and MOA

• Detected in CSF

• Rat and human 14C-AME studies show no protein adducts

Phase 1 MAD Study in Healthy Older Subjects

Trends To Benefit On Exploratory Cognitive

Measures In Phase 1b Study

Source: Cortexyme Phase 1b study: *p< 0.05, ***p<0.001

Days of treatment Days of treatment Days of treatment

MM

SE

Sco

re

CA

NTA

B c

om

po

site

(Z

sco

re)

Pro

po

rtio

n P

rep

ositio

n: to

tal co

nte

nt

Placebo (n=3)COR388 (n=6)

Winterlight:

Examples of

speech in

75 year old

female with

mild-moderate

AD before and

after

Atuzaginstat

treatment

ApoE fragments are found in AD patient CSF and can be reduced by Atuzaginstat (COR388) treatment

ApoE fragments are found in AD CSF CSF ApoE fragments are reduced in Phase

1b COR388-dosed subjects

Low MW ApoEfragments

Source: Cortexyme Phase 1b study: *p< 0.05Source: Raha et al, 2021 Cell Reports Medicine, submitted

Hum

an C

SF

21

Pivotal P2/3 GAIN Trial Design: Atuzaginstat in Alzheimer’s Disease

• Mild to Moderate: MMSE

12-24

• Ages 55-80

• Stable symptomatic

therapies allowed

• Target N=573

RandomizationScreening

Co-Primary:

ADAS-Cog11 and ADCS-ADL

Secondary:

CDR-SB, MMSE and NPI

Exploratory:

Winterlight, MRI (hippocampal

volume and cortical thickness)

Biomarkers of Pg and

gingipain activity: blood, saliva,

oral biocollections

Biomarkers of Alzheimer’s:

CSF Aβ, tau, p-tau

Markers of disease

modification: MRI volumetric

measures

Endpoints

Key Eligibility Criteria

• Enrollment initiated Apr. 2019; completed Sept. 2020

• Interim analysis in December 2020 successfully

completed with no sample size adjustment

• Top-line data expected Q4 2021

• 233 subjects

• Assessment of pocket depth

and clinical attachment level at

6 and 12 months

Timelines Periodontal REPAIR sub-study

Placebo

Low dose (40 mg BID)

48-week Treatment Period

(Total N=643)

More information: www.gaintrial.com

High dose (80 mg BID)

6-week Safety Follow-up

http://www.gaintrial.com/

22

GAIN Baseline Demographics: Population and Stratification as

Expected

Parameter Overall (N=643)

Age at Informed Consent (years) 69.1 (55 – 80)

Sex

Male 278 (43%)

Female 365 (57%)

Race and Ethnicity

Black or African American 42 (7%)

White, Hispanic or Latino 68 (11%)

White, Not Hispanic/Latino 505 (79%)

Other 10 (2%)

Missing 18 (3%)

Parameter Overall (N=643)

Region

North America 447 (70%)

Europe 196 (30%)

MMSE

Moderate >=12 to <=18 324 (50%)

Mild >=19 to <=24 319 (50%)

ApoE4

ApoE4 Carriers 414 (64%)

Non Carriers 229 (36%)

Cholinesterase Inhibitor/Memantine Use

Yes 476 (74%)

No 167 (26%)

Randomization stratified by Mild/Moderate and ApoE4 +/-

Final data to be confirmed post data lock

2323

Central Nervous System (CSF)

Biomarkers

Peripheral Serum/Plasma

Biomarkers

• Biomarkers of P. gingivalis infection, inflammation and neuroinflammation are being assessed

• A subset of these biomarkers at baseline are currently available and will be discussed today

CNS, Peripheral, and Oral Biomarkers in GAIN Trail

Oral Biofluid Collection

Biomarkers

24

Baseline CSF Biomarkers: Ab 42/40, Tau and P-Tau

EUROIMMUN assays; range of control/AD established by EUROIMMUN

Approximately 84% of GAIN subjects have traditional CSF biomarkers of Alzheimer’s Disease


25

Elevated vWF, A2M in Majority of GAIN Serum Samples at Baseline

• Cortexyme is analyzing a set of

exploratory serum biomarkers

• Highlighted here:- vWF, a marker of vascular

injury; ULN 106 ug/mL

- A2M, an endogenous protease

inhibitor, ULN 2.3 mg/mL

- Benchmarked against a

normal population for 100

healthy subjects aged 20-50

years (MyriadRBM)


26

P. gingivalis specific IgG elevated in serum at baseline indicating

systemic infection

100% of GAIN subjects have

evidence of systemic P. gingivalis

exposure with detectable antibodies;

78% have IgG antibody titers that

correlate with oral periodontal

disease symptoms

Collaboration with H. Hasturk, Forsyth Institute; range and assay from Nobel et al, 2019


27

Over 90% of GAIN Subjects in the Periodontal REPAIR

Sub-Study Have Moderate to Severe Periodontal Disease at Baseline

0

1 0

2 0

3 0

4 0

5 0

6 0

7 0

8 0

9 0

1 0 0

% o

f s

ub

jec

ts

N o n e -

M i l d

M o d e r a t e -

S e v e r e

0

4

8

1 2

1 6

2 0

2 4

2 8

3 2

Nu

mb

er

of t

ee

th

N o n e -

M i l d

M o d e r a t e -

S e v e r e

Periodontal Diagnosis Number of teeth%

of

subje

cts

Num

ber

of

teeth

Diagnosis based on Pocket Depth and Clinical Attachment Loss Measures (N=233)


28

CSF Analytes: Use Of The CSF/Serum Albumin Index

• This is an index of blood-brain barrier (BBB) integrity,

adjusted for the serum albumin concentration

• This index is increased in BBB dysfunction

• Defined as CSF albumin (mg/L) / serum albumin (g/L)

• CSF/serum albumin index >9 = evidence of BBB loss

of integrity

CSF/Serum Albumin Index

• Utilizing a standard CSF and serum albumin assay,

the majority (98%) of GAIN Trail subjects (mild to

moderate AD) have an index <9, indicating

integrity of the BBB at the time of sample

collection

• This may vary over time, with gender and age

1

1 0

N = 4 7 6

Alb

um

in i

nd

ex

(C

SF

/Se

ru

m)

log

sc

ale

A v e r a g e A l b u m i n I n d e x = 3 . 5

95% CI 3.26-3.77


29

Baseline CSF Biomarkers: Serum and CNS Contribution To Levels

1 1 0 1 0 0

0 . 0 1

0 . 1

1

a l b u m i n i n d e x ( C S F / S e r u m )

l o g s c a l e

Ab

eta

ra

tio

(A

b4

2/A

b4

0)

log

sc

ale

r = - 0 . 0 3

N e g l i g i b l e c o r r e l a t i o n

N = 4 6 3

1 1 0 1 0 0

1 0

1 0 0

1 0 0 0

1 0 0 0 0


l o g s c a l e

p1

81

-ta

u(p

g/m

L)

log

sc

ale

r = 0 . 0 4


N = 4 7 5

1 1 0 1 0 0

1 0 0 0 0

1 0 0 0 0 0

1 0 0 0 0 0 0


l o g s c a l e

Co

mp

lem

en

t C

9 (

pg

/mL

)

log

sc

ale

r = 0 . 6 4

M o d e r a t e C o r r e la t i o n

N = 4 5 8

1 1 0 1 0 0

1

1 0

1 0 0

1 0 0 0


l o g s c a l e

CS

F a

nti-

Pg

an

tib

od

y (

EU

)

log

sc

ale

r = 0 . 2 2

v e r y w e a k c o r r e l a t i o n

N = 4 7 2

1 1 0 1 0 0

0 . 0 1

0 . 1

1


l o g s c a l e

Ab

eta

ra

tio

(A

b4

2/A

b4

0)

log

sc

ale

r = - 0 . 0 3


N = 4 6 3

1 1 0 1 0 0

1 0

1 0 0

1 0 0 0

1 0 0 0 0


l o g s c a l e

p1

81

-ta

u(p

g/m

L)

log

sc

ale

r = 0 . 0 4


N = 4 7 5

1 1 0 1 0 0

1 0 0 0 0

1 0 0 0 0 0

1 0 0 0 0 0 0


l o g s c a l e

Co

mp

lem

en

t C

9 (

pg

/mL

)

log

sc

ale

r = 0 . 6 4


N = 4 5 8

1 1 0 1 0 0

1

1 0

1 0 0

1 0 0 0


l o g s c a l e

CS

F a

nti-

Pg

an

tib

od

y (

EU

)

log

sc

ale

r = 0 . 2 2


N = 4 7 2

• Concentration increases in CSF with

increasing albumin index suggesting

minimal central nervous system production

• Concentrations in CSF are independent of the albumin

index suggesting some central nervous system production

as expected

Complement C9 Ab42/Ab40 ratio and p181-tau


30

New Data: Baseline CSF Anti-Pg IgG Levels Provide Evidence of

CNS Infection in AD

1 1 0 1 0 0

0 . 0 1

0 . 1

1


l o g s c a l e

Ab

eta

ra

tio

(A

b4

2/A

b4

0)

log

sc

ale

r = - 0 . 0 3


N = 4 6 3

1 1 0 1 0 0

1 0

1 0 0

1 0 0 0

1 0 0 0 0


l o g s c a l e

p1

81

-ta

u(p

g/m

L)

log

sc

ale

r = 0 . 0 4


N = 4 7 5

1 1 0 1 0 0

1 0 0 0 0

1 0 0 0 0 0

1 0 0 0 0 0 0


l o g s c a l e

Co

mp

lem

en

t C

9 (

pg

/mL

)

log

sc

ale

r = 0 . 6 4


N = 4 5 8

1 1 0 1 0 0

1

1 0

1 0 0

1 0 0 0


l o g s c a l eC

SF

an

ti-

Pg

an

tib

od

y (

EU

)

log

sc

ale

r = 0 . 2 2


N = 4 7 2

CSF anti-Pg IgG

Collaboration with Hatice Hasturk, DDS PhD, Forsyth Institute

• All subjects with baseline CSF available for

analysis (N=472) were positive for anti-P.

gingivalis IgG in CSF

• Only 2% of subjects have loss of BBB

integrity, as measured by albumin index >9

• Anti-Pg IgG concentration in CSF is largely

independent of the albumin index indicating

central nervous system production in

addition to levels found in serum

• The presence of these antibodies further

supports a direct P. gingivalis infection in

the central nervous system


31

Summary

• Data continue to accumulate supporting the gingipain hypothesis of Alzheimer’s, periodontal disease

and other degenerative disorders

• The GAIN trial, has been rigorously designed and implemented to be a key clinical proof of concept

and potentially pivotal trial

• Biomarker data are being used to understand the therapeutic effect of atuzaginstat on key biological

markers of AD and neurodegeneration

• Biomarkers of P. gingivalis infection level, immune response, and gingipain activity are being

assessed to characterize Pg baseline levels and response to treatment

• Baseline data support that this is an appropriate population for testing atuzaginstat for AD- Biomarkers for Aβ, Total tau and p-Tau 181 in CSF

- Pg antibodies in serum and CSF

- Periodontal disease data in the dental REPAIR sub-study

• New data on baseline anti-Pg IgG levels in CSF supports a contribution from a CNS infection

• Topline data will be reported by mid-Nov

32

Acknowledgements

• Advisory Board & other academiccollaborators

• Development Partners

• Clinical trial site personnel

• Study participants and caregivers

• Cortexyme Biomarker team• Shirin Aratsu Kapur• Debasish Raha• Mai Nguyen• Sean Broce• T. Harshani Peiris• Diana Eilerts

• Cortexyme Research and ClinicalDevelopment teams

33

THANK YOU

leslie holsinger, phd

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