Synlogic : January 2021 Corporate Presentation

January 22, 2021 at 01:02 pm

Bringing the

Transformative Power of

Synthetic Biology to

Medicine

Corporate Presentation

January 2021

Forward Looking Statements

This presentation contains "forward-looking statements" that involve substantial risks and uncertainties for purposes of the safe harbor provided by the Private Securities Litigation Reform Act of 1995. All statements, other than statements of historical facts, included in this presentation regarding strategy, future operations, future financial position, future revenue, projected expenses, prospects, plans and objectives of management are forward- looking statements. In addition, when or if used in this presentation, the words "may," "could," "should," "anticipate," "believe," "estimate," "expect," "intend," "plan," "predict" and similar expressions and their variants may identify forward-looking statements. Examples of forward-looking statements include, but are not limited to, the approach we are taking to discover and develop novel therapeutics using synthetic biology; statements regarding the potential of our platform to develop therapeutics to address a wide range of diseases, including: metabolic diseases, inflammatory and immune disorders, and cancer; the future clinical development of Synthetic Biotic medicines; the potential of our technology to treat phenylketonuria and cancer; the expected timing of our anticipated clinical trial initiations and availability of clinical data; the benefit of orphan drug and fast track status; the adequacy of our capital to support our future operations and our ability to successfully initiate and complete clinical trials; the results of our collaborations; and the difficulty in predicting the time and cost of development of our product candidates. Actual results could differ materially from those contained in any forward-looking statement as a result of various factors, including, without limitation: the uncertainties inherent in the preclinical development process; our ability to protect our intellectual property rights; and legislative, regulatory, political and economic developments, as well as those risks identified under the heading "Risk Factors" in our filings with the SEC. The foregoing review of important factors that could cause actual events to differ from expectations should not be construed as exhaustive and should be read in conjunction with statements that are included herein and elsewhere, including the risk factors included in our quarterly report on Form 10-Q filed with the SEC on May 8, 2020, and in any subsequent filings we make with the SEC. The forward-looking statements contained in this presentation reflect our current views with respect to future events. We anticipate that subsequent events and developments will cause our views to change. However, while we may elect to update these forward-looking statements in the future, we specifically disclaim any obligation to do so. These forward-looking statements should not be relied upon as representing our view as of any date subsequent to the date hereof.

Recent Progress: Execution Across the Portfolio

Metabolic Programs

Rapidly progressed metabolic programs

SYNB1618 in PKU Phase 2 SynPheny-1 study initiated
IND for SYNB8802 in Enteric Hyperoxaluria opened and Phase 1 study initiated

Advanced preclinical work in additional undisclosed metabolic indications

Immunomodulation

Immunomodulation in immunology and oncology

SYNB1891 monotherapy demonstrated target engagement and meaningful pharmacodynamic effects
Advancing to combination with anti-PD1 Advanced exploratory work in IBD

We are the premier Synthetic Biology platform engineering bacterial Synthetic Biotic medicines

A New Class of Medicines

We Rationally Design Bacteria

Bacteria and Humans Co-Evolved and Co-Exist

To Provide Clinical Benefit

The Result is Synthetic Biotic Medicines with Potent and Programmable Therapeutic Effects

Building a Diverse Portfolio of Synthetic Biotic Medicines

Platform for Clinical Benefit Across Multiple Disease States

Enabling Engine

Validated	Core Differentiating
Biological
Capabilities
Targets

Where a	Synthetic Biology
Internal + Ginkgo

Synthetic Biotic

medicine is

uniquelyManufacturing of live

Internal Focus:

Metabolic Programs

Consumption of toxic metabolites from

the GI tract

External & Collaboration Focus:

Immunomodulation

positioned to

Synthetic Biotics

impact patients

Regulatory, Translational

& Clinical Dev.

Immunology and oncology: Leveraging the ability of bacteria to interact with the immune system

Enabling Engine

Core Differentiating

Capabilities

Synthetic Biology

Internal + Ginkgo

Manufacturing of live

Synthetic Biotics

Regulatory, Translational

& Clinical Dev.

Enabling Engine: Driver for Success

• Clinical Evidence

Internal Pipeline Focus

>200 humans dosed with Synthetic BioticRa200 HVsmedicinesand pati nts dosed with

	Synthetic biotic medicine
• 4 INDs opened with the U.S. FDA	3 INDs opened with the FDA in
	addition to supportive regulatory

Supportive regulatory feedback fromfeedbackglobalonagenciesapproach from global

regulatory agencies

Safe (>100 years of human experience)Internalprobioticprocess developmentbacterial andchassis

	GMP manufacturing capabilities….
• Core Technology	Collaborations and agreements with
	large pharma partners….

Deep synthetic biology expertise withreGinkgometabolicBioworksd seases basedcollaborationon

consumption of toxic metabolites

•from the GI tract

Modular and reusable synthetic biology components enable iterative,

efficient platform learning

Internal process development and GMP manufacturing capabilities

Robust Pipeline

Exploratory	Preclinical	IND-Enabling	Phase 1	Phase 2
Studies

Phenylketonuria

Enteric Hyperoxaluria Other Metabolic Programs

SYNB1618

SYNB8802

Immuno-Oncology Solid Tumors

SYNB1891

Inflammatory Bowel Disease

Vaccines

Other Inflammation Programs

Key

Metabolic Diseases

Immunomodulation

Synlogic Entering Data Rich Period in the Clinic

Expected Milestone	2020		2021

	early	mid	late

SYNB1618	Initiate Ph.2 study in PKU patients	initiated

PKU	Ph.2 Phe-loweringread-out



SYNB8802	Initiate Ph.1 study in HV and patients	initiated

HOX	Ph.1 patient read-out



	Ph.1 Monotherapy interim update	completed
SYNB1891	Initiate Ph.1 combination study arm

I/O
Ph.1 combination therapy read-out

Significant Clinical Readouts within our Current Cash Window

Why Metabolic Diseases For Synthetic Biotic Medicines?

Validated Biology	Platform Proof of Mechanism
Diseases with known	PKU program demonstrated we
pathophysiology	can consume toxic metabolites
	in the GI tract
Dietary intervention provides
support for GI-based	Subsequent programs build on
approach	experience

	Unique Advantage of SYNB
Unmet Medical Need	Bacteria act catalytically
Across both inherited and
acquired metabolic diseases	Contain multiple enzyme pathways
	Are protected from digestion
	within the GI tract
	© 2021 SYNLOGIC. CORPORATE PRESENTATION. ALL RIGHTS RESERVED. \| 9

Phenylketonuria (PKU)

Emerging treatment

options will continue to

leave many patients

behind

SYNB1618 demonstrates potential to lower Phe in PKU patients

Phase 2 Phe-lowering

trial initiated

Synlogic's Approach to Phenylketonuria (PKU)

Synthetic Biotic Mechanism of Action

Consume Phe in the GI Tract

Reduce Phe in the blood

Julia, living with PKU

PKU Program Status

SYNB1618 was able to consume Phe in healthy volunteers

Synlogic has initiated a Phase 2 Study in PKU patients (SynPheny-1)

Living with PKU:

Parents Expect Their Children to Achieve Their Full Potential

Prospect of severe mental disability and		Early diagnosis and strict diet control enables
institutionalization.		better Phe management.
Parents wanted PKU child to avoid		Parents expect PKU child to achieve full potential,
institutionalized care before adulthood.		college attendance, self-support.

Reality: 25% - 65% of Patients Still Stuggle to Maintain Blood Phe within Target Range

SYNB1618 is Uniquely Positioned to Address Needs Across Ages and Genotypes

		Adult Only		Partial Responders (1/3rd)	All Ages, Genotypes
	Chronic Daily	Long-acting Chronic	Gene Therapies	Daily Oral	Daily Oral	Daily Oral
Marketed
Development
Patient Segment1	Marketed	At Ph1/2 or earlier	Marketed	Phase 3	Ph 2	Ph 1
Infant 0-1
N= ~500
Peds 2-11
N= ~2,800
Peds 12-18
N= ~1,700
Adults
N= 11,5001
	Under REMS			Bh4 Responsive Only
	program

1. Includes 7,500 "lost to follow up" adult patients

SYNB1618 In The Clinic: D5 Tracer Data in Healthy Volunteers

D5 Phe Converted to D5 TCA	D5 TCA Converted to D5 HA	Plasma D5 Phe Blunted

	D5 TCA AUC
20
15
μM*h
10
AUC
5
		BLQ
0
			o			2	2
		b		1		1
	e		e		e
c			1			2
la
P
			Treatment

Data are means and 90% CI

Placebo 1e12 2e12

Urinary HA (mg)

Urinary D5 HA

250 200 150 100 50 0

			o		12			2
			eb				1
				e	e
		c		1		2
	a
l
P
				Treatment

Placebo 1e12 2e12

%CFB D5 Phe

D5 Phe % CFB

20 10 0 -10-20-30-40

		o			2		2
	b		1		1
e		e		e
ac			1			2
Pl
		Treatment

Placebo 1e12 2e12

SYNB1618 Mechanism Confirmed: Accessed D5 Phe Tracer in Gut & Lowered Plasma D5 Phe

SynPheny-1 Phase 2 Proof of Concept Study in PKU

Fasting

Phe

Diet run-in

6 days D5-Phe

AUC

				Fasting
Dose 1	Dose 2		Dose 3	Phe Dose 4
1e11	3e11		1e12		2e12
3 days	3 days		7 days		2 days
		D5-Phe

AUC

Demonstrate Phe Lowering in PKU Patients
- Plasma Phe lowering in fasted state at 1 x 1012 live cells over 7 days
- Post meal D5-Phe AUC lowering at 2 x 1012 live cells (not impacted by diet)
Validate PD Model
- Understand relationship of strain specific biomarkers with plasma Phe lowering
Safety and Tolerability

Patient-Centered Clinical Trial Design & Execution

Directly informed by patient feedback on executing trials in the COVID era

Flexible design allowing home-based or office-based visits

Rigorous & personalized diet control to ensure consistent Phe intake, including 6-dayrun-in

Dose ramp to improve tolerability & compliance

Enteric Hyperoxaluria

Enteric Hyperoxaluria results in significant kidney damage with no available treatment options

SYNB8802 has the potential		SYNB8802 Phase 1 clinical
to meaningfully lower		study initiated ahead of
urinary oxalate levels		schedule

Synlogic's Approach to Enteric Hyperoxaluria

Dietary Sources of Oxalate

Synthetic Biotic Mechanism of Action

Consume Oxalate in the GI Tract

Reduce Oxalate in the urine

Hyperoxaluria

Kidney stones

Enteric Hyperoxaluria Program Status

SYNB8802 was able to consume oxalate in multiple animal models

Synlogic has initiated a Phase 1 Study in healthy volunteers

Hyperoxaluria: Primary vs. Enteric

Primary Hyperoxaluria

Enteric Hyperoxaluria

Pathology

Urinary Oxalate Levels

Onset

Clinical Mgmt

U.S. Epidemiology

Key Players

Family of autosomal recessive monogenic	Pathogenic hyperabsorption of dietary oxalate,
disorders in which liver enzyme deficiency	often accompanies bowel disease or bariatric
results in endogenous oxalate overproduction	surgery

90 - 500 mg / 24 hrs (up to 10x normal)	45 - 130 mg / 24 hrs (up to 3x normal)

Pediatric	Adult

Limited nutrition options; nephrocalcinosis;	Limited nutrition options; treatment of kidney
dialysis; transplant; pyridoxine	stones as they occur; nephrocalcinosis; dialysis

~5,000 - 8,000	200,000 - 250,000

	Number of Patients Affected

Enteric Hyperoxaluria Case Studies:

An Important Cause of Renal Failure

33-Year-Old Female with Crohn's		48-Year-Old Male with Crohn's		47-Year-Old Female with Crohn's


• 33 yo woman with Crohn's requiring		• 48 yo man with Crohn's requiring 2		• 47 yo woman with Crohn's requiring
bowel resection resulting in severe		bowel resections with severe		extensive bowel resections with severe
hyperoxaluria (135 mg/day)		hyperoxaluria (110 mg/day)		hyperoxaluria (114 mg/day)
• Clinical course punctuated by:		• Clinical course punctuated by:		• Clinical course punctuated by:
-	Recurrent kidney stones		-	Recurrent kidney stones		-	Recurrent kidney stones
-	Progressive renal failure		-	Nephrocalcinosis		-	Recurrent obstructive nephropathy
-	Hemodialysis		-	Progressive renal failure		-	Progressive renal failure
- Renal transplant x 1		-	Hemodialysis		-	Bilateral nephrectomies due to
-	Recurrent renal failure		-	Renal transplant			stone-related infections

-	Hemodialysis					-	Hemodialysis

- Renal transplant x 2					-	Renal transplant

						-	Recurrent renal failure

Urinary oxalate levels remains markedly elevated in all patients, despite aggressive medical regimen

Nazzal et al. Nephrol Dial Transplant 2016

Enteric Hyperoxaluria Disease Pathogenesis

GI Based Therapies Have Demonstrated Lowering of Systemic Oxalate

Dietary Oxalate

Stomach

Small

	• Pathogenic hyperabsorption of dietary
	oxalate
Oral	• Dietary oxalate absorbed throughout GI
enzyme	tract

SYNB8802	• Result is urinary oxalate (Uox) > 70mg/day

intestine

Colon

	•	Leads to recurrent kidney stones,
		nephrocalcinosis, kidney failure
Oxalo	•	Treatment must absorb oxalate
bacter
		throughout GI tract, esp. in colon

Intestinal Degradation of Oxalate Throughout GI Tract Could Enhance Oxalate Lowering

SYN-HOX Attenuates Urinary Oxalate Increase

ASN Kidney Week 2020

SYN-HOX Consumes 13C-Oxalate in Mice

SYN-HOX Attenuates Urinary Oxalate Increase In NHPs

C-Oxalate	Creatinine)
13	of
Urine	(ug/mg

0.0008
0.0006
0.0004
			*
0.0002
0.0000
Vh	SYNHOX	SYNHOX	SYNHOX
	CFU	Live cell	Live cell
	Frozen Liq.	Lyo

Oxalate	from vehicle)
Urine	change
	(%

150
100
50	*

0
	Vehicle 5e10 1e11 5e11 1e12
	SYNHOX (CFU)

C-Oxalate	from vehicle)
13	change
Urine
	(%

150

100

50 **

0 Vehicle 5e10 1e11 5e11 1e12

SYNHOX (CFU)

SYN-HOX Consumes Oral Load of Oxalate in Mouse and Non-Human Primate Models

* p< 0.05 , ** p< 0.01 versus vehicle

Enteric Hyperoxaluria: Phase 1 Design Provides PoC Opportunity

Phase 1a

Healthy Volunteers

Multiple Ascending Dose

High oxalate & low calcium diet run-in
Primary: Safety & tolerability
Secondary: Microbial kinetics of strain
Exploratory: Change in plasma and urine biomarkers

Phase 1b

Enteric Hyperoxaluria

Patients

Cross-over

TID dosing
N = 20 patients (Roux-en Y gastric bypass)
UOx >70 mg/day

Roux-en-Y Gastric Bypass Population Provides Opportunity to Demonstrate Urinary Oxalate Lowering in Disease State

Why Diseases of Immune System Regulation

For Synthetic Biotic Medicines?

Cross-talk Between Bacteria and Immune System

Immune system has evolved to recognize bacteria

Bacteria have evolved mechanisms to control the immune response

Unmet Medical Need

Growing need for novel treatments for immunological diseases and cancer

Platform

Preclinical POC for both immune stimulation and immunoregulation

Can produce immune mediators (small molecules, peptides, human cytokines)

Unique Advantage of SYNB

Targeted efficacy and improved safety

Multiple effectors from single Tx strain delivered to site of disease

Immunomodulation & Immuno-Oncology

Synthetic Biotics can be	SYNB1891 + checkpoint		SYNB1891 as monotherapy	Phase 1 data in
engineered for immune	inhibitors have potential		demonstrated target
		combination with Tecentriq
activation or regulation,	for improved efficacy		engagement and
		initiated: data will be
with application to	relative to other STING		meaningful
		available in 2021
immuno-oncology	approaches		pharmacodynamic effects

SYNB1891 Induces Potent Anti-tumoral Effects

Effects Superior to 'Naked' STING Agonist in Animal Model of Cold Tumor

109 CFU, i.t. (SYNB or SYNB1891)

	B16-F10 tumors	d1			d4			d7		d21
	~100 mm3,
randomize groups
)	2500

3												EcN
(mm	2000

Volume
1500											= Dose


Tumor	1000
500

	0
	0	2	4	6	8	10	12	14	16	18	20	22
					Study Day

SYNB1891 109 CFU, i.t. or 50 ug ADU-S100, i.t.

B16-F10 tumors
d1	d4	d7	d32
~100 mm3,
randomize groups

	2000		Saline



3			SM STING agonist
)
(mm
1500		SYNB1891

= Dose

Volume	1000

Tumor	500

	0
	0	4	8	12	16	20	24	28	32

Days on Study

SYNB1891-CP-001 Study Design: Multidose Tolerability, IT Mono and Combo

Proof of mechanism: exploratory biomarkers in advanced solid tumors or lymphomas

Arm 1: Monotherapy Cohorts		Arm 2: Combination Cohorts - Atezolizumab

Sentinel Patient	Starting dose Arm 1	Sentinel Patient
Day 7 safety Eval	is Cohort 3 dose	Day 7 safety Eval
(1e7)

Patient 2 & 3

Safety	Repeat for	Arm 1	Safety
Cohort 4
Evaluation	each cohort	Evaluation

POM/Exploratory Biomarkers

PD response (tumor biopsy):

TILs, IFN b, IFN dependent gene expression (Nanostring)
Immunohistochemistry
Kinetics of SYNB1891 (qPCR)

Systemic PD effects (blood):

Serum cytokines levels
Kinetics of SYNB1891 (qPCR)

Repeat for	Recommended	Enroll <20
Ph2 Dose	patients at
each cohort
(RP2D)	RP2D

SYNB1891 Advanced Into Combo. Therapy Arm of Ph. 1 With Tecentriq

SYNB1891 is safe and well-tolerated as an intratumoral injection with no dose limiting toxicities or infections to date

SYNB1891 demonstrates target engagement as assessed by upregulation of IFN-stimulated genes and T-cells

SYNB1891 demonstrates meaningful pharmacodynamic effects including systemic cytokine responses observed in two subjects

Evidence of durable stable disease was observed in two patients

Monotherapy dose escalation will continue in parallel to combination dose escalation of SYNB1891 with fixed dose of Atezolizumab (Tecentriq)

Combination therapy data will be available in H2 2021

3rd Quarter 2020 Summary Results

Balance Sheet (unaudited)		30 Sept 2020	30 June 2020

Cash, Cash Equivalents, and Short & Long Term Marketable Securities		$102.0 M	$109.1M

		Three Months Ended
Statement of Operations (unaudited)		30 Sept 2020	30 Sept 2019
R&D Expenses		$10.5 M	$10.6 M
G&A Expenses		$3.0 M	$3.9 M
Net Loss		$(13.2 M)	$(13.3M)
Net loss per share - basic and diluted*	$(0.36)	$(0.39)
Weighted Average Shares Outstanding*		36.3 M	34.2 M

Strong Cash Position with Runway into 2022

* weighted average shares used in computing net loss per shares - basic and diluted

Aoife Brennan, MB ChB President & CEO

Gregg Beloff, JD

Interim CFO

Dave Hava, PhD

CSO

Caroline Kurtz, PhD

Head of Product

Development

Synlogic Leadership

Richard Riese, MD PhD

CMO

Antoine Awad

COO

Daniel Rosan

Head of Corp. Finance &

Investor Relations

Board

Peter Barrett, Chair	Ed Mathers
Atlas Venture
NEA

Mike Burgess	Richard Shea
Turnstone Biologics
Syndax

Chau Khuong	Michael Heffernan
Orbimed Advisors
Collegium

Nick Leschly	Patricia Hurter
Bluebird Bio
Lyndra Therapeutics

Collaborators

Appendix:

Engineering

Synthetic Biotic

Medicines

Synthetic Biotic Medicines: A New Class of Cellular Medicines

Cellular	Programmable	Synthetic Biotic

	Medicine

Bacterial Chassis		Synthetic Biology
Non-pathogenic		Reusable Parts

Bacterial Chassis

Inducer-Promoter Switch

Inducer

Toxin

Biomarker

Promoter

Effector

Metabolic

Biomarker

Effector Design

Conversions

Safety Features

Reusable Parts Enable Rapid Iteration of Rationally Designed Prototypes

Photo credit: NIH Image Gallery

Library of Parts to Generate Prototypes

Synthetic Biology Library Rapidly Generates Drug Candidates

Component

Bacterial Chassis

Effector 1

Effector 2

….

Switch

Safety Features

Benefit

Probiotic: Decades of human

use & safety data

Proteins for activity: Can

generate biomarkers

Inducer-promoter pair: Controls gene expression

Auxotrophies: Prevents growth within or external to the body

Toxin		Inducer	Biomarker 1


		Effector 1	P
PheP:		Biomarker 1
High-
Affinit	Metabolic
y

Uptak		Effector 2		P

Biomarker 2

SYNB1618 Design

Built from Synthetic Library Specifically to Consume Phe

Component Approach

Bacterial Chassis		E. coli Nissle

Switches		FNR & AraC
		promoter

PumpPheP

Effector 1

PAL3 Enzyme

Effector 2

LAAD Enzyme

Safety Features		dap

Benefit

Probiotic - decades of human

use & safety data

Promoters control expression during manufacturing and at site of action

Pumps Phe into cell

Degrades Phe to TCA

(measurable biomarker of

activity)

Alt. Phe-consuming pathway

Auxotrophy - requires

diaminopimelic acid (DAP) to

grow

Hippuric Acid (HA)

Phenylalanine (Phe)

(TCA)

	PAL3	Pfnr
PheP:	Phe	Trans-cinnamic	dap
High-		acid (TCA)
Affinity
Uptake

Metabolic Conversions

LAAD ParaC

Phe	Phenylpyruvate (PP)

Phenyl-lactic acid

(PLA)

SYNB8802 Design

Engineered to Convert Oxalate to Formate for the Treatment of Enteric Hyperoxaluria

Component Approach

Bacterial Chassis		E. coli Nissle

Switch		FNR promoter

Pump		OxLT
		OxdC and
Effector 1		associated
		components

Benefit

Decades of human use

Inducer-promoter pair

Pumps oxalate in & formate

out

Catalyzes conversion of

oxalate to formate

	Oxalate	D
				D DDFormate
Ox/formate	D		D DD		02
Pump (OxLT)		D D
D
D	Oxalate			Formate
				thyA
DATPCoA+	:			FRC

Affinity
Ppi +
Uptake			Formyl CoA
	Oxalyl CoA
AMP			Metabolic

OxdC

Safety Features		thyA		Controls growth

SYNB1891 Design

Leveraging the Ability of Bacteria to Interact with the Immune System to Turn a Cold Tumor Hot

Component

Bacterial Chassis

Switch

Effector:

STING Agonist

Safety Features

Benefit

Targeting to antigen presenting cells in

the tumor microenvironment.

Innate immune activation

STING-agonist production restricted to hypoxic TME for sustained payload delivery

Innate immune activator compounds

with chassis effect

Dual auxotrophies inhibit bacterial

proliferation outside of tumor

	dacA	Pfnr		thyA
			dapA

ATP +		Cyclic-di-AMP
ATP		(STING Agonist)

301 BINNEY ST., #402, CAMBRIDGE, MA 02142

TEL: 617-401-9975

WEB:WWW.SYNLOGICTX.COMEMAIL:INFO@SYNLOGICTX.COM

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Synlogic Inc. published this content on 22 January 2021 and is solely responsible for the information contained therein. Distributed by Public, unedited and unaltered, on 22 January 2021 18:01:08 UTC

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Synlogic : January 2021 Corporate Presentation

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