Bacterial and viral pathogens

Strategies to defeat the enemyWiesław Swietnicki, Ph.D.

BackgroundSolutions Problems

Therapeutics-antibioticsBacteria

VaccinesBacteria and

viruses

Antibiotic resistanceSpecificity/side effectsPossibility of genetically-

engineered resistance

Recombinant- time to design, limited antigen repertoire

Live- faster, side effects

Therapeutic strategiesSolutions Pros/Cons

Metabolic networkBacteria mostly

Virulence systemsBacteria

Conserved – universal target, longer to develop resistance

Takes time to starve bacteria

Independent of antibiotics/vaccines – can defeat genetically-engineered species

Host kills the pathogenCannot reverse effects of

secreted toxic proteins

VaccinesSolutions Pros/ConsRecombinant

Natural/live

Defined antigen target Intra- and extracellular

pathogensLow costLimited antigen variabilityTime to develop immunity

Broad antigen repertoireLow costVERY effectiveSide effectsTime to develop immunity

Metabolic networkEasy to build a model and analyzeTargets easily identified and structures

known/models builtSelective for bacteriaStrategy- block active siteRational design – tools developedResistance- after along timeRequires low capital to design drugs –

Poland?

Potential targetsClass A, B and C Select AgentsRegular pathogensExamples: amino acid biosynthesis, fatty acid

biosynthesis, nutrient procurementDrugs- small molecules

Examples Bacteria

Small molecules

Metabolic networksGenome sequenced- 1-2 days nowTargets identified- genome analysis

(MetaCyc)- 1 dayModel constructed -1 dayComputational screen – 1 dayIn vitro testing-1 monthAnalogs search and screen– 1 monthOptimization- cell culture - 3-6 monthsFinal test in a cell culture – 1 monthnM and below- X-ray data for co-crystals – 1

year

Virulence systems-rationalGenome sequenced- 1-2 daysTargets identified- systems biology analysis - 1

dayModel constructed -1 dayComputational screen – 1 dayIn vitro testing-1 monthAnalogs search and screen– 1 monthOptimization- cell culture - 3-6 monthsFinal test in a cell culture – 1 monthnM and below- X-ray data for co-crystals – 1 year

Phenotypic screensHTS assay design 1-3 months2000K screen -1-2 weeks50 selectedAnalogs search and screen– 1 monthOptimization- cell culture - 3-6 monthsFinal test in cell culture – 1 monthnM and below- extensive chemistry/QSAR– 1-

2 yearsOff-targets search – 1 year or more

CustomersNATOPharma companies – small to medium size

ExamplesViruses

Live vaccinesGenome sequencing 2-3 daysTarget identification 1 -3 days Cell entry

Protein processingMetabolismViral assemblyStructural proteins

Genetic engineering 3 monthsReconstruction - synthetic biologyEpitope grafting – safe viruses, bacteria

Animal validation 8 months(6 months protocol + 2 months experiments)

Recombinant vaccinesTargets validated 8 monthsSingle/multiple proteins tested 8 monthsVLPs

Capsid assembly system testing 3 months

Animal testing 8 months

Small moleculesCell entry – membrane fusionProtein processing- viral proteasesMetabolism – viral enzymesViral assembly – structural proteins

Each strategy requires - 3+ years to optimize

- an HTS screening system (computational or

experimental)

CustomersNATOPharma companies – small to medium size