NABATIVI –

Novel Approaches to Bacterial Target Identification, Validation and Inhibition

Alessandra Bragonzi, PhD

Infections and Cystic Fibrosis Unit,Division of Immunology, Transplantation and Infectious Disease San Raffaele Scientific Institute

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OUTLINE

• The problem

• Anti-microbial drug resistance

• Pharmaceutics' response

• EU’s response

• How we built the NABATIVI project

• International collaboration

• Multidisciplinary approach

• Scientific excellence

• Major achievement

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OUTLINE

• The problem

• Anti-microbial drug resistance

• Pharmaceutics' response

• EU’s response

• How we built the NABATIVI project

• International collaboration

• Multidisciplinary approach

• Scientific excellence

• Major achievement

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The world-wide threat of resistant pathogens

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What is boosting antimicrobial resistance?

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superbugssuperbugsInsufficient surveillance, prevention and control

Insufficient research and development activities

Absence of new drugs

Insufficient funding

Insufficient coordination of EU efforts

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Why is antimicrobial resistance a global concern?

• kills

• hampers the control of infectious diseases

• threatens a return to the pre-antibiotic era

• increases the costs of health care

• jeopardizes health-care gains to society

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Facts on antimicrobial resistance

• 4 million patients every year

• 25 000 deaths

• economic losses € 1.5 billion

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Who is responsible?

Enterococcus faecium

Staphylococcus aereus

Klebsiella pneumoniae

Acinetobacter baumanni

Pseudomonas aeruginosa

Enterobacter species

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OUTLINE

• The problem

• Anti-microbial drug resistance

• Pharmaceutics' response

• EU’s response

• How we built the NABATIVI project

• International collaboration

• Multidisciplinary approach

• Scientific excellence

• Major achievement

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Pharmaceutics’ response to antimicrobial-resistance

Payne et al. Nature Reviews Drug Discovery 6, 2007

• The industry is cutting research in antimicrobial discovery and development

• Only few big pharmaceutical companies are still involved in antibiotic discovery

• Antibiotic R&D is a lengthy, costly, and risky process due to:

- length of time (10-15 years) from the discovery phase to market

- huge cost of bringing a new drug to market ($800 million to 1.7 billion)

- low reimbursement due to the small market

- low success rate

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Antibacterial pipeline, Big Pharma

Boucher H W et al. Clin Infect Dis. 2013;56:1685-1694

New systemic antibacterial agents approved by the US Food and Drug Administration per 5-year period, through 2012.

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How do we fill the gap ?

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OUTLINE

• The problem

• Anti-microbial drug resistance

• Pharmaceutics' response

• EU’s response

• How we built the NABATIVI project

• International collaboration

• Multidisciplinary approach

• Scientific excellence

• Major achievement

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EU’s response –6th and 7th Framework Programme

• Basic Science

• Prudent use of antibiotics

• New antimicrobials

• Point of care diagnostic tests

• Vaccines

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EU’s response –Translational research for health (unit F3)

• 2.3.1 – Anti-microbial drug resistance

• Management of Gram negative multi-drug resistant infections.

2.3. TRANSLATIONAL RESEARCH IN MAJOR INFECTIOUS DISEASES: TO CONFRONT MAJOR THREATS TO PUBLIC HEALTH2.3.1. Anti-microbial drug resistance including fungal pathogens

2.3.1-1: Novel targets for drugs against Gram negative bacteria.The objective is to identify and validate novel drug targets in order to select lead compounds, which may be derived from natural sources or from synthetic compounds, for future development of a new class of anti-infective drugs against Gram-negative bacteria. Significant industrial involvement, particularly by SMEs, is foreseen in this topic. Funding scheme: Collaborative projects (Small or medium-scale focused research projects with maximum EC contribution of € 6,000,000/project).

SME ≥30%

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OUTLINE

• The problem

• Anti-microbial drug resistance

• Pharmaceutics' response

• EU’s response

• How we built the NABATIVI project

• International collaboration

• Multidisciplinary approach

• Scientific excellence

• Major achievement

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How we built the NABATIVI project

• International Collaboration

Academic SMEs

Alessandra Bragonzi, San Raffaele Scientific Institute, Milano

Miguel Cámara, University of Nottingham

Gerd Döring, Eberhard Karls Univerität Tübingen

John A. Robinson and Leo Eberl, University of Zürich

Giovanni Bertoni, Università degli Studi di Milano

Peter E. Nielsen, University of Copenhagen

Natalia Nekohotieva, KDevExploratory, Stockholm

Do Quoc-Tuan, Greenpharma S.A., Orléans,

Daniel Obrecht, Polyphor, Allschwil

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How we built the NABATIVI project

• Multidisciplinary approach

Drugs

Molecular microbiology

Genomics

Biochemistry

Structural biology

Cell biologyBioinformatics

Clinical research

Pre-clinical research

High-throughput technology

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NABATIVI approaches in response to Call FP7-HEALTH-2007-B

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Discovery Phase Approach A: “from target to lead compounds”•Target identification/validation is done at the beginning

Discovery Phase Approach B: “from drugs to targets”• Target identification runs in parallel to the discovery phase

Targetidentification

Libraryselection/design

Screeningcascade

Hitidentification Hit-to-lead

Leadoptimization

Pre-clinicaldevelopment Phase I Phase II Phase III NDA Launch

Pre-clinical and clinical phases

Discovery phaseA

B

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Pseudomonas aeruginosa selected from ESKAPE pathogens

• 5 million cases in Europe, USA and Japan every year

• Responsible of ≈ 30% of world-wide hospital-acquired infections

• High risk of disease in people with cystic fibrosis, in immunocompromised, burn patients, patients with cancer, and with HIV

• Multi-drug resistant strains

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Scientific approach –Genome - based approach for target identification

PAO1 6.3 Mb

5,570 ORFs

6,7% function experimentally demonstrated(Class 1)

Stover et al. Nature. 2000 Aug 31;406(6799):959-64.

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NABATIVI scientific approach –Step 1: genome-wide screening for targets identification

ScreeningsAntisense librariesTransposon libraries

Results

University of Nottingham Università degli Studi di Milano

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University of Nottingham San Raffaele Scientific InstituteUniversità degli Studi di Milano

Eberhard Karls Univerität TübingenSan Raffaele Scientific Institute

University of Zürich

Eberhard Karls Univerität TübingenSan Raffaele Scientific Institute

Genome-wide screening 57.360

404

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NABATIVI scientific approach –Step 2: pathogenicity in different model system

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Genomic Target database

(GTD)

NABATIVI scientific approach –Step 3: target inhibition by high-throughput technology

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NH

NB

OO

NB

OO

NH

PNA

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Genomic Target database

(GTD)Purified target-based HTS:

• Plant extracts (800)• Pure natural compounds (480)• Synthetic compounds (45000)• Database AMBINTER 18 M

compounds

KDevExploratory, Stockholm

Greenpharma S.A., Orléans,

Determination of the druggability of selected targets

Greenpharma S.A., Orléans,

NABATIVI scientific approach –Step 3: target inhibition by high-throughput technology

Antisense targeting of selected targets by peptide nucleic acids

University of Copenhagen

NABATIVI approaches in response to Call FP7-HEALTH-2007-B

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Targetidentification

Libraryselection/design

Screeningcascade

Hitidentification Hit-to-lead

Leadoptimization

Pre-clinicaldevelopment

Phase I Phase II Phase III NDA Launch

Synthesis of a library of Protegrin I analogues by PEM technology

MIC determination

Initial hits with broad spectrum antimicrobial activity and lack of hemolytic activity

Selective anti-Pseudomonas compounds with novel SAR

POL7001

LptD, a β-barrel outer membrane transporter is the target of POL7001 and POL7080

Efficacy studies in animal models of sepsis and respiratory infections

POL7080: preparations for a first Phase IIa clinical trial

under NABATIVI

Discovery Phase Approach B: “from drugs to targets”• Target identification runs in parallel to the discovery phase• Most antibiotics have been identified by this approach

POL7080

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NABATIVI scientific approach –Step 4: target identification running in parallel to the discovery phase

O

NH

NN

O

HO

HO

N

ON

N

H

H

O

H

NN

O

H O

H O

N

O

NH

N

O

H

N

Me

O

H O

N

H

N

O

NH

H3NH3N

HNH2N

H2N

NHH2N

H2N

H3N H3NH3N

NH

HO

LptD

Srinivas N, et al. Science. 2010Bragonzi A. Sci. Transl. Med. 2010

• LptD is an essential gene in P. aeruginosa and the target for novel drug POL7001 and POL7080

Polyphor Ltd.

University of Zurich

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NABATIVI scientific approach –Step 4: translational research up to clinical trial

POL7080

POL7001

Discovery phase Pre-IND Clinical phase

Polyphor Ltd.

San Raffaele Scientific Institute

• Novel drug POL7001 is active against MDR P. aeruginosa strains

• In pre-clinical studies including models of airway infections and septicemia, POL7001 showed higher efficacy when compared to clinically approved antibiotics

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POL7080 indications for P. aeruginosa infections

Indications for Pseudomonas infections

Urinary tract infectionsVentilator-associatedpneumonia (VAP)

Pseudomonas infectionin cystic fibrosis

(Mukoviscidosis)

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NABATIVI - Major achievements

Targetidentification

Libraryselection/design

Screeningcascade

Hitidentification Hit-to-lead

Leadoptimization

Discovery phaseA

Pre-clinicaldevelopment Phase I Phase II Phase III NDA Launch

Pre-clinical and clinical phasesB

A genomic target database of P. aeruginosa is assembled

Novel hits and PNAs are identified and are currently under validation

LptD as novel target for drug with novel mechanism of action is identified

POL7080 successfully completed Phase I and will start Phase II at the end of 2013

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NABATIVI – novel drug

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NABATIVI – hit the target !

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Critical success factors for NABATIVI project

• Integrated multidisciplinary research at European level was successful in novel drug discovery;

• Academia and a small innovative company worked together productively to fill the gap left by the migration of big pharmaceuticals away from antibacterial development;

• Combined scientific approaches, including exploitation of post-genomic information, were successful in identifying novel drugs;

• Optimal translation of the results into the clinic through appropriate pre-clinical models

Molecular microbiology

Genomics

Biochemistry

Structural biology

Cell biologyBioinformatics

Clinical research

High-throughput technology

Pre-clinical research Drugs