CONFIDENTIAL1 © 2020 Alnylam Pharmaceuticals, Inc.

Vasant Jadhav, PhD

Vice President, Research, Alnylam

OTS, September 26-29, 2020

Human Translation of GalNAc-siRNA

Conjugates with Improved Specificity

CONFIDENTIAL2

Multiple Human POCs Demonstrate Reproducible and Modular Nature of ESC

Conjugate Platform M

ean

(S

EM

) %

AT

Kn

ockd

ow

n

Time (Days)

Mean

(S

EM

) %

C5 K

no

ckd

ow

n

Time (Days)

100

80

60

40

20

0

-20

0 30 60 90 120 150 180

50 mg 200 mg400 mg

600 mg900 mg

Placebo

Cmedisiran

Mean

(S

EM

) %

PC

SK

9 K

no

ckd

ow

n

100

80

60

40

20

0

-20

-40

-60

Time (Months)

0 1 2 3 4 5 6

Placebo

25 mg

100 mg

300 mg

500 mg

800 mg

Inclisiran

100

25

50

25

0

-25

0 40 80 120 160 200

Fitusiran225 mcg/kg

450 mcg/kg

900 mcg/kg

1800 mcg/kg

80 mg

Mean

(S

EM

) %

AL

A K

no

ckd

ow

n

Time (Months)

10100

80

60

40

20

0

-20

-40

0 1 2 3 4 5 6 7 8 9

Placebo

0.035 mg/kg

0.1 mg/kg

0.35 mg/kg

1.0 mg/kg

2.5 mg/kg

Givosiran

1. Fitusiran2. Inclisiran3. Givosiran4. Lumasiran5. Vutrisiran6. Cemdisiran7. ALN-AAT8. ALN-AAT029. ALN-AGT10.ALN-HBV02

(VIR-2218)

CONFIDENTIAL3

Study Conducted by The Medicines Company; Acquired by Novartis International AG

Inclisiran: Investigational RNAi Therapeutics Targeting PCSK9

CONFIDENTIAL4

Study Conducted by The Medicines Company; Acquired by Novartis International AG

Inclisiran: Investigational RNAi Therapeutics Targeting PCSK9

• Inclisiran safety profile similar to placebo, with no adverse changes in laboratory markers

• Injection site events 4.2% - predominantly mild and none persistent

• Numerically fewer CV events reported for inclisiran than placebo (exploratory endpoint)

CONFIDENTIAL5

Characteristics of the Human LFT Signal with Subset of ESC Conjugates:

Does Not Occur Across All Programs, Suggesting Sequence SpecificityALN-AAT01 Phase 1/2 Interim Results

Me

an

[+

/-S

EM

] A

AT

Re

lative

to

Ba

se

line

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1.0

1.1

1.2

1.3

1.4

1.5

1.6

Days since dose

0 20 40 60 80 100 120 140 160 180 200 220 240 260 280 300

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1.0

1.1

1.2

1.3

1.4

1.5

1.6

Placebo (N=5) 0.1 mg/kg (N=3) 0.3 mg/kg (N=3)

1.0 mg/kg (N=3) 3.0 mg/kg (N=3) 6.0 mg/kg (N=3)

PD: Serum AAT Protein Levels Placebo

1.0 mg/kg

3.0 mg/kg

6.0 mg/kg

Safety: Serum ALT Levels

-10 0 10 20 30 40 50 60 70

Days Since Dose

1

4

8

1

4

8

1

4

8

1

4

8

• Anecdotal evidence for RISC-mediated mechanism:

◦ Onset of LFT elevations coincides with onset of maximum RNAi activity

◦ High knockdown appears necessary (but not sufficient) for LFT elevations

• Similar profile seen in other programs with sporadic LFT elevations

CONFIDENTIAL6

Subset of ESC Conjugates Show Rat Hepatotoxicity at Exaggerated Doses

In silico prediction &In vitro efficacy

In vitro screen for predicted off-targets

Rodent Knockdown

Rat Tox @ >100x PD dose

NHP Knockdown DC

Show hepatotoxicity (40%)No hepatotoxicity (60%)

Single cell necrosis

and/or hepatocellular

degeneration with ↑LFT

2x upper limit of normal

These compounds drop out of

DC selection process

CONFIDENTIAL7

Seed-Based Off-Target Effects Are Important Drivers of Rodent

Hepatotoxicity for Subset of ESC Conjugates

Janas, Schlegel et al. Nat Commun. 2018

2. Competition for RISC

loading with miRNAs

RISC

miRNA

1. Non-RNAi effects e.g. siRNA chemistry, metabolites,

protein binding, drug accumulation

GalNAcGalNAc

GalNAc

Off-target bindingPartial sequence match

3. Undesired seed-based

off-target activity

3’-UTR

CONFIDENTIAL8

ESC+ Seed Pairing Destabilization Strategy Improved Specificity and

Therapeutic Index in Rats

Bramsen et. al. Nucleic Acids Res. 2010

Vaish et. al. Nucleic Acids Res. 2011

Lee et. al. Nat. Comm. 2015

Janas, Schlegel et al. Nat. Comm. 2018

Off-target bindingPartial sequence match

Off-target mRNA 3’-UTR

Antisense loaded RISCpos. 2-8

Undesired off-

target activity

Important Considerations

1. On-target potency must be maintained in vivo

2. Off-target activity should be minimized

(S)-GNA

Rat Liver Histopath

for 30 mg/kg dose

Parent ESC ESC+ AS7-GNA

How would ESC+ design translate in

humans?

• Evaluated ESC+ versions of ALN-HBV and

ALN-AAT01

CONFIDENTIAL9

Improved Specificity of RNAi Activity by VIR-2218

RNA-Seq analysis in HepG2.2.15 cells showed fewer differentially expressed genes and a lower magnitude of gene

dysregulation, supporting reduced off-target effects with VIR-2218 compared with ALN-HBV

Differentially expressed gene

Differentially expressed gene which has a predicted binding site to the siRNA seed sequence

Non-differentially expressed gene

Gene with a predicted binding site to siRNA seed sequence

Average Gene Abundance

1 100 10,000 106

-2

-1

0

1

2 ALN-HBV

Log

2C

hange in G

ene E

xpre

ssio

n

Rela

tive t

o C

ontr

ol

Average Gene Abundance

1 100 10,000 106

-2

-1

0

1

2 VIR-2218

HBV TargetHBV Target

GalNAcGalNAc

GalNAc

GalNAcGalNAc

GalNAc

CONFIDENTIAL10

VIR-2218-1001: Phase 1/2 study design

Double-blind, randomized, placebo-controlled, MAD study in patients with chronic HBV infection

At each dose level, 4 or 8 patients randomized 3 active:1 placebo

HBeAg, hepatitis B e antigen; MAD, multiple ascending dose; SAD, single ascending dose.

MAD

Chronic HBV HBeAg+

MAD

Chronic HBV HBeAg−

20 mg SCx 2 doses n=4

50 mg SCx 2 doses n=8

100 mg SCx 2 doses n=8

200 mg SCx 2 doses n=4

50 mg SCx 2 doses n=4

200 mg SCx 2 doses n=4

SAD

Healthy volunteers

50 mg SC1 dose

100 mg SC1 dose

200 mg SC1 dose

400 mg SC1 dose

600 mg SC1 dose

900 mg SC1 dose

CONFIDENTIAL11

VIR-2218-1001: Phase 1 SAD (Part A, healthy volunteers): ALT

D1 4 8 12 D1 4 8 12 D1 4 8 12 D1 4 8 12 D1 4 8 12 D1 4 8 12 D1 4 8 120

50

100

150

200

ALT

(IU

/mL)

ULN

3x ULN

VIR-2218

Placebo 50 mg 100 mg 200 mg 400 mg 600 mg 900 mg

WeekWeek WeekWeek WeekWeek Week

CONFIDENTIAL12

Human: Treatment-emergent post-baseline ALT elevations in healthy

volunteers with normal ALT at baseline

• No post-baseline ALT elevations to >ULN in the VIR-2218 or ALN-HBV cohorts were associated with increases in bilirubin >ULN

• No changes in functional status of the liver (eg, albumin, coagulation parameters) or clinical signs/symptoms of hepatic

dysfunction were observed in any ALN-HBV- or VIR-2218-treated patient

*Approximate mg/kg dose based on an average adult weight of 60 kg; fixed doses ranged from 50–900 mg. ULN, upper limit of normal.

0.1–0.3 1 3 1–3 7 10 150

Hig

hest T

reatm

ent-

em

erg

ent

Post-

baselin

e A

LT

Ele

vation

1×ULN

3×ULN

5×ULN

10×ULN

ALN-HBV, mg/kg VIR-2218, mg/kg*

GalNAcGalNAc

GalNAc

GalNAcGalNAc

GalNAc

CONFIDENTIAL13

ALN-AAT01 Phase 1/2 Study

Design

Part A:

N= 8 per cohort, double blind, randomized 3:1 active:placebo

5th (10mg/kg) cohort optional

SAD-only Phase 1 in males and females

ALN-AAT02 Phase 1/2

Study Design

CONFIDENTIAL14

ALN- AAT01 ALN-AAT02

Structure*

Efficacy Up to 89% KD Up to 89% KD

Liver Safety

(ALT >3x ULN)1/15 (up to 6 mg/kg dose) 0/18 (up to 6 mg/kg dose)

Positive ESC+ Human POCALN-AAT02 Clinical Activity and Safety

* Images are representative

GalNAcGalNAc

GalNAc

GalNAcGalNAc

GalNAc

0 2 4 6 8 1 0 1 2

0 . 0

0 . 5

1 . 0

1 . 5

2 . 0

S t u d y W e e k

Se

ru

m A

AT

(g

/L)

0 . 3 m g / k g

1 . 0 m g / k g

3 . 0 m g / k g

P L A C E B O

L L O Q

S i n g l e D o s e A L N - A A T 0 2

0 2 4 6 8 1 0 1 2

0 . 0

0 . 5

1 . 0

1 . 5

2 . 0

S t u d y W e e k

Se

ru

m A

AT

(g

/L)

0 . 3 m g / k g

1 . 0 m g / k g

3 . 0 m g / k g

P L A C E B O

L L O Q

S i n g l e D o s e A L N - A A T 0 2

0 2 4 6 8 1 0 1 2

0 . 0

0 . 5

1 . 0

1 . 5

2 . 0

S t u d y W e e k

Se

ru

m A

AT

(g

/L)

0 . 3 m g / k g

1 . 0 m g / k g

3 . 0 m g / k g

L L O Q

P L A C E B O

S i n g l e D o s e A L N - A A T 0 1

CONFIDENTIAL15

ESC+ Technology: Basis of Alnylam Product Engine Source of Sustainable InnovationSource of Sustainable Innovation

2006 2011 2018 2020 2020-30

Delivery

Targets

Products

• Expect 2-4 INDs per year

• Large number of opportunities

• Organic capability & growth

CONFIDENTIAL16

Summary

• ESC+ strategy mitigates seed-mediated off-target effects, improves specificity and further expands therapeutic window of siRNA conjugates in preclinical species

• Achieved encouraging translation of ESC+ design in humans◦ Directly assessed the impact of the new ESC+ design with follow-on compounds in two separate programs

(same sequence but new ESC+ design)

• Multiple additional ESC+ conjugates have advanced into clinical development

CONFIDENTIAL17 © 2020 Alnylam Pharmaceuticals, Inc.

To those who say “impossible, impractical, unrealistic,” we say:

CHALLENGE ACCEPTED

Mark Schlegel

Rubina Parmar

Svetlana Shulga-Morskaya

Huilei Xu

Ivan Zlatev

Terence Cawley

Klaus Charisse

Anna Bisbe

Rajeev Kallanthottathil

Ryan Malone

Jonathan O'Shea

Yongfeng Jiang

Onur Yilmaz

Saket Agarwal

Carole Harbison

Natalie Keirstead

Brenda Carito

Samantha Chigas

Sean Dennin

Kristin Fong

Paul Gedman

Wendell Davis

Mano Manoharan

Nate Taneja

Christopher Theile

Jeff Rollins

Stacy Seide

Alfica Sehgal

Jingxuan Liu

Dan Berman

Patrick Haslett

Martin Maier

Kevin Fitzgerald

Toni Hayes

Emma Henchy

Lauren Moran

Elena Ooms

Rachel Peters

Kristina Perry

Kellie D’Angelo

Catrina Wong

Michael Placke

Jing-Tao Wu

Peter Smith

Phil Pang

Xiao Ding

Cara Pilowa

Richie Phan

Richie Phan

Ling Shen

Sneha Gupta

Christy Hebner

Ed Gane

Professor of Medicine

New Zealand Liver Transplant Unit

Yesse Anglero-Rodriguez

Abigail Liebow

Tuyen Nguyen

Sarah LeBlanc

Charalambos Kaittanis,

Joseph Barry,

Adam Castoreno

Bob McGarr

Joseph Vogel

Hank Lin

Chris Maclauchlin

Diana Najarian

Stephen Huang

Jae Kim

David Hymes

Tad Wyrzykiewicz

Sunyoung Cho

Colleen McKiernan

Gabriel Robbie

Varun Goel

Jaime Harrop

Sean McGrath

Acknowledgements