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How Difficult Is It to Discover New Novel Antibacterials? How Difficult Is It to Discover New Antibacterials? Lynn L. Silver, Ph.D. LL Silver Consulting, LLC

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Page 1: How Difficult Is It to Discover New Novel Antibacterials? How Difficult Is It to Discover New Antibacterials? Lynn L. Silver, Ph.D. LL Silver Consulting,

How Difficult Is It to Discover New Novel

Antibacterials?

How Difficult Is It to Discover New Antibacterials?

Lynn L. Silver, Ph.D.LL Silver Consulting, LLC

Page 2: How Difficult Is It to Discover New Novel Antibacterials? How Difficult Is It to Discover New Antibacterials? Lynn L. Silver, Ph.D. LL Silver Consulting,

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Antibacterials at FDA 2000-2011Compound Usage Class Active versus

resistanceDiscovery of class

Fail at FDA Pass at FDA

Linezolid Systemic IV/oral Oxazolidinones MRSA 1978 2000

Ertapenem Systemic IV/IM Carbapenem 1976 2001

Cefditoren Systemic oral Cephalosporin 1948 2001

Gemifloxacin Systemic oral Fluoroquinolone 1961 2003

Daptomycin Systemic oral Lipopeptide MRSA 1987 2003

Telithromycin Systemic oral Macrolide+ EryR S. pneumo 1952 2004

Tigecycline Systemic IV Tetracycline+ TetR 1948 2005

Faropenem Systemic oral Penem 1978 2006

Retapamulin Topical Pleuromutilin MRSA 1952 2007

Dalbavancin Systemic IV Glycopeptide 1953 2007

Doripenem Systemic IV Carbapenem 1976 2007

Oritavancin Systemic IV Glycopeptide+ VRE 1953 2008

Cethromycin Systemic oral Macrolide+ EryR S. pneumo 1952 2009

Iclaprim Systemic IV Trimethoprim+ TrmR 1961 2009

Besifloxacin Ophthalmic Fluoroquinolone 1961 2009

Telavancin Systemic IV Glycopeptide+ VRE 1953 2009

Ceftobiprole Systemic IV Cephalosporin+ MRSA 1948 2009

Ceftaroline Systemic IV Cephalosporin+ MRSA 1948 2010

Fidaxomicin Oral CDAD Lipiarmycin 1975 Due soon

Page 3: How Difficult Is It to Discover New Novel Antibacterials? How Difficult Is It to Discover New Antibacterials? Lynn L. Silver, Ph.D. LL Silver Consulting,

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Discovery Timeline

1935

1940

1945

1955

1950

1965

1960

1970

1975

1980

1985

1990

1995

2000

2005

1930

fusidic acid

polymyxin

oxazolidinones

daptomycin

carbapenem

monobactams

mupirocin

fosfomycin

streptogramins

nalidixic acid

rifamycintrimethoprim

vancomycin

novobiocincycloserine

lincomycin

cephalosporin

chlortetracyclinechloramphenicol

streptomycin

bacitracin

penicillinsulfonamide

metronidazole

erythromycinisoniazid

Last novel agent to reach the clinic was discovered in 1987

pleuromutilin

2010

DaptomycinLinezolid

Bactroban Synercid

Retapamulin

NorfloxacinImipenem

cephamycinlipiarmycin

Fidaxomicin

Although development andmodification of old classeshas proceeded – no newly discovered novel classes havemade it to the clinic in 24 years

Page 4: How Difficult Is It to Discover New Novel Antibacterials? How Difficult Is It to Discover New Antibacterials? Lynn L. Silver, Ph.D. LL Silver Consulting,

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Discovery Strategies

1935

1940

1945

1955

1950

1965

1960

1970

1975

1980

1985

1990

1995

2000

2005

Whole cell p

henotypic scre

ens

Empirical “k

ill the bug” s

creens

The Golden Age

Enzyme and binding assays

Genomics ID

s novel

conserved targets

Microbial p

hysiology, b

iochemistry

and genetics used to

ID antibiotic

targets and esse

ntial genes

2010

Screening for and design of novelantibacterials was vigorously pursued by Big Pharma until recently

Page 5: How Difficult Is It to Discover New Novel Antibacterials? How Difficult Is It to Discover New Antibacterials? Lynn L. Silver, Ph.D. LL Silver Consulting,

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Consider… If Big Pharma (and biotechs) have been largely

unsuccessful in finding novel antibacterials to develop…

Will that be reversed by Increasing financial incentives? Revising regulatory policy?

What has prevented novel discovery? The need to address scientific obstacles

Page 6: How Difficult Is It to Discover New Novel Antibacterials? How Difficult Is It to Discover New Antibacterials? Lynn L. Silver, Ph.D. LL Silver Consulting,

6

Gene-to-Drug ApproachNovel antibacterial targets

High Throughput Screening

Candidates

Genomics

Small molecule ‘Hits’

Preclinical testing

Clinical Trials

Small molecule ‘Leads’

Drug

Inhibit the enzyme

Inhibit bacterial growthSmall molecule ‘Hits’

Small molecule ‘Leads’Inhibit bacterial growth by inhibiting the enzyme

Druglike propertiesLow resistance potential

Compounds kill by other means

Compounds can’t enter

Same as for other drugs

Almost all have high resistance potential

ezabez ab Candidates

Page 7: How Difficult Is It to Discover New Novel Antibacterials? How Difficult Is It to Discover New Antibacterials? Lynn L. Silver, Ph.D. LL Silver Consulting,

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Improve chemical sources Remove toxic, detergent, reactive compounds from

libraries Define physicochemical characteristics specifying bacterial

entry & efflux Revive natural product screening

Pursue targets with low resistance potential

The Obstacles to Antibacterial Discovery

Page 8: How Difficult Is It to Discover New Novel Antibacterials? How Difficult Is It to Discover New Antibacterials? Lynn L. Silver, Ph.D. LL Silver Consulting,

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-lactamsGlycopeptides

CycloserineFosfomycin

Rifampin

AminoglycosidesTetracyclines

ChloramphenicolMacrolides

LincosamidesOxazolidinones

Fusidic AcidMupirocin

NovobiocinFluoroquinolones

SulfasTrimethoprimMetronidazole

DaptomycinPolymyxin

gram positive

CM

Cytoplasm

OM

Gram negative

CMPe

ripla

sm

Cytoplasm

P. aeruginosa

Almost all “gram positive”drugs are active (biochemically)on the analogous gram negative targets – but the drugs are not antibacterial vs gram negatives

Impermeability and efflux of G- render many agents inactive

P. Aeruginosa is more problematic due to strong efflux and reduced permeability

The bacterial entry problem

Page 9: How Difficult Is It to Discover New Novel Antibacterials? How Difficult Is It to Discover New Antibacterials? Lynn L. Silver, Ph.D. LL Silver Consulting,

9

Antibacterials Useful in Systemic Monotherapy

ANTIBACTERIAL TARGET-lactams multiple penicillin binding proteins [PBPs]

synthesis of cell wall peptidoglycanGlycopeptides D-ala-D-ala of peptidoglycan substrateTetracycline rRNA of 30s ribosome subunitAminoglycosides rRNA of 30s ribosome subunitMacrolides rRNA of 50s ribosome subunitLincosamides rRNA of 50s ribosome subunitChloramphenicol rRNA of 50s ribosome subunitOxazolidinones rRNA of 50s ribosome subunit Fluoroquinolones bacterial topoisomerases (gyrase and topo IV)Metronidazole DNADaptomycinmembranes

No high-level resistance by single-step mutation

All have multiple targets or targets encoded by multiple genes

enzymes

Targets with low resistance potential

Examine successful antibacterials

Page 10: How Difficult Is It to Discover New Novel Antibacterials? How Difficult Is It to Discover New Antibacterials? Lynn L. Silver, Ph.D. LL Silver Consulting,

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Single Enzyme Targets of Antibiotics in Clinical Use

ANTIBIOTIC TARGETrifampicin RNA polymeraseisoniazid InhA streptomycin 30s ribosome/rpsL trimethoprim DHFR (FolA) sulfamethoxazole PABA synthase (FolP) novobiocin DNA gyrase B subunit mupirocin Ile tRNA-synthetasefosfomycin MurA

All are subject to single-step high level resistance

USEMulti-drugTB therapyMulti-drug TB therapyMulti-drug TB therapyCombo w/ SulfasCombo w/ TrimethoprimMulti-drug therapyTopical therapyUTI

Page 11: How Difficult Is It to Discover New Novel Antibacterials? How Difficult Is It to Discover New Antibacterials? Lynn L. Silver, Ph.D. LL Silver Consulting,

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Based on existing antibacterial drugs…

Successful monotherapeutic antibacterials Not subject to single-site mutation to high level resistance

because they are multi-targeted Current drugs inhibiting single enzymes

Generally used in combination because they are subject to single mutation to significant resistance

THUS: "Multitargets" are preferable to single enzyme targets for systemic monotherapy

BUT: The search for single enzyme inhibitors has been the mainstay of novel discovery for at least 20 years …

Page 12: How Difficult Is It to Discover New Novel Antibacterials? How Difficult Is It to Discover New Antibacterials? Lynn L. Silver, Ph.D. LL Silver Consulting,

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If single enzyme targets give rise to resistance in the laboratory…

Determine if the in vitro (laboratory) resistance is likely to translate to resistance in the clinic Standardize the use of models for evolution of

resistance under therapeutic conditions To validate targets, test target/lead pairs in these

models

Pursue multitargets

Page 13: How Difficult Is It to Discover New Novel Antibacterials? How Difficult Is It to Discover New Antibacterials? Lynn L. Silver, Ph.D. LL Silver Consulting,

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A way forward Targets

For single-enzyme inhibitors: Robust modeling of resistance Pursue multi-targets

Chemicals Deduce rules for bacterial entry and efflux, especially in G- Clean up libraries and incorporate rules for entry Revive Natural Products

With better chemicals, return to empirical discovery Collaboration between academe and industry

Computation for multitargeting Modeling of resistance Chemistry for cell entry and efflux avoidance

Page 14: How Difficult Is It to Discover New Novel Antibacterials? How Difficult Is It to Discover New Antibacterials? Lynn L. Silver, Ph.D. LL Silver Consulting,

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Page 15: How Difficult Is It to Discover New Novel Antibacterials? How Difficult Is It to Discover New Antibacterials? Lynn L. Silver, Ph.D. LL Silver Consulting,

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Antibacterials Are Chemically Unlike other Drugs

Mammalian targets ≠ antibacterial targets Many antibacterials must enter bacterial cells

gram negative

gram positive only

other drugs +

MW = SIZE

cLog

D7.

4 = G

REAS

INES

S

Page 16: How Difficult Is It to Discover New Novel Antibacterials? How Difficult Is It to Discover New Antibacterials? Lynn L. Silver, Ph.D. LL Silver Consulting,

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-6.0

-4.0

-2.0

0.0

2.0

4.0

6.0

8.0

0 200 400 600 800 1000 1200MW = SIZE

cLog

P =

Gre

asin

ess

Cytoplasm-targeted antibacterials

Gram positive only Cytoplasmic

Gram negative cytoplasmicentry by diffusion

Gram negative cytoplasmiccarrier-mediated transport

Page 17: How Difficult Is It to Discover New Novel Antibacterials? How Difficult Is It to Discover New Antibacterials? Lynn L. Silver, Ph.D. LL Silver Consulting,

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Compound and fragment profiling

binding/docking to bacterial proteins

An approach to new multitargets:Sorting targets by their ligands

Candidate multitargets

Can be done computationally

Page 18: How Difficult Is It to Discover New Novel Antibacterials? How Difficult Is It to Discover New Antibacterials? Lynn L. Silver, Ph.D. LL Silver Consulting,

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What is Antibacterial Multitargeting?

GlcNAc

MurNAc PP-C55

Gyrase Topo IV

Lipid II

ciprofloxacin

daptomycinvancomycin

gentamicintetracyclinechloramphenicollinezoliderythromycin

Targeting the products of multiple genes – or the product of their function – such that single mutations cannot lead to high level resistance Two or more essential gene products with

similar active sites: DNA Gyrase & Topisomerase IV Products of identical genes : rRNA Essential structures produced by a pathway where

structural changes cannot be made by single mutations: Membranes

These and other known multiargets have been pursued More may be uncovered by computation based on structural

studies of bacterial proteins and the small molecule “ligands” that bind to them