1. Strategies to defeat the enemy
Wiesław Swietnicki, Ph.D.

2. Background
Solutions Problems
 Therapeutics-antibiotics
Bacteria
 Vaccines
Bacteria and viruses
 Antibiotic resistance
 Specificity/side effects
 Possibility of genetically-
engineered resistance
 Recombinant- time to design,
limited antigen repertoire
 Live- faster, side effects

3. Therapeutic strategies
Solutions Pros/Cons
 Metabolic network
Bacteria mostly
 Virulence systems
Bacteria
 Conserved – universal target,
longer to develop resistance
 Takes time to starve bacteria
 Independent of
antibiotics/vaccines – can defeat
genetically-engineered species
 Host kills the pathogen
 Cannot reverse effects of
secreted toxic proteins

4. Vaccines
Solutions Pros/Cons
 Recombinant
 Natural/live
 Defined antigen target
 Intra- and extracellular
pathogens
 Low cost
 Limited antigen variability
 Time to develop immunity
 Broad antigen repertoire
 Low cost
 VERY effective
 Side effects
 Time to develop immunity

5. Metabolic network
 Easy to build a model and analyze
 Targets easily identified and structures known/models
built
 Selective for bacteria
 Strategy- block active site
 Rational design – tools developed
 Resistance- after along time
 Requires low capital to design drugs – Poland?

6. Potential targets
 Class A, B and C Select Agents
 Regular pathogens
 Examples: amino acid biosynthesis, fatty acid
biosynthesis, nutrient procurement
 Drugs- small molecules

7. Bacteria
Small molecules

8. Metabolic networks
 Genome sequenced- 1-2 days now
 Targets identified- genome analysis (MetaCyc)- 1 day
 Model constructed -1 day
 Computational screen – 1 day
 In vitro testing-1 month
 Analogs search and screen– 1 month
 Optimization- cell culture - 3-6 months
 Final test in a cell culture – 1 month
 nM and below- X-ray data for co-crystals – 1 year

9. Virulence systems-rational
 Genome sequenced- 1-2 days
 Targets identified- systems biology analysis - 1 day
 Model constructed -1 day
 Computational screen – 1 day
 In vitro testing-1 month
 Analogs search and screen– 1 month
 Optimization- cell culture - 3-6 months
 Final test in a cell culture – 1 month
 nM and below- X-ray data for co-crystals – 1 year

10. Phenotypic screens
 HTS assay design 1-3 months
 2000K screen -1-2 weeks
 50 selected
 Analogs search and screen– 1 month
 Optimization- cell culture - 3-6 months
 Final test in cell culture – 1 month
 nM and below- extensive chemistry/QSAR– 1-2 years
 Off-targets search – 1 year or more

11. Customers
 NATO
 Pharma companies – small to medium size

12. Viruses

13. Live vaccines
 Genome sequencing 2-3 days
 Target identification 1 -3 days
Cell entry
Protein processing
Metabolism
Viral assembly
Structural proteins
 Genetic engineering 3 months
Reconstruction - synthetic biology
Epitope grafting – safe viruses, bacteria
 Animal validation 8 months
(6 months protocol + 2 months experiments)

14. Recombinant vaccines
 Targets validated 8 months
 Single/multiple proteins tested 8 months
 VLPs
Capsid assembly system testing 3 months
Animal testing 8 months

15. Small molecules
 Cell entry – membrane fusion
 Protein processing- viral proteases
 Metabolism – viral enzymes
 Viral assembly – structural proteins
Each strategy requires
- 3+ years to optimize
- an HTS screening system (computational or
experimental)

16. Customers
 NATO
 Pharma companies – small to medium size