how difficult is it to discover new novel antibacterials? how difficult is it to discover new...
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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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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
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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
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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
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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
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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
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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
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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
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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
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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
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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 …
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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
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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
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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
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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
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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
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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