The type of target influence the type of drug

• Main drugs’ categories– Small molecules – Biologicals (e.g. antibodies, hormones, etc)

• The drug discovery process for the two categories of drugs is not exactly the same

• In the rest of the presentation we will mainly focus on that for small molecules

Target selection

General criteria for target choice

• Druggability: likelihood of being able to modulate a target with a drug

Target selection

Druggability of small molecules targetsDruggability of small molecules targets

polysaccharides

lipids

nucleic acids

proteins

Problems with toxicity, specificity, and difficulty in creating adequate ligands narrow mainly to protein the druggable targets

Target selection

XX

X

DruggabilityDruggabilityOnly 10% of the human genome represents druggable targets, and only half of those are relevant to disease.

Target selection

GPCR

STY kinases

Zinc peptidases

Serine proteases

PDE

Other 110 families

Cys proteases

Gated ion-channel Ion channels

Nuclear receptor

P450 enzymes

Analysis of current drug targets shows that most targets fall within a few major protein families (GPCRs, kinases, proteases and peptidases)

GPCR

STY kinases

Zinc peptidases

Serine proteases

PDE

Other 110 families

Cys proteases

Gated ion-channel Ion channels

Nuclear receptor

P450 enzymes

Analysis of current drug targets shows that most targets fall within a few major protein families (GPCRs, kinases, proteases and peptidases)

The genome project and the“omics” era

Target identification

The suffix -ome- as used in biology refers to a totality of some sort

Genetic code

Genetic Genetic codecode

GenomeGenome

TrascriptomeTrascriptomeProteomeProteome

MetabolomeMetabolome

PathwaysPathways

static

dynamic

DNADNA RNARNA ProteinsProteins

Complexity

Target identification

Transcriptome: gene expression profiling

However, it should be kept in mind that does not exist a complete match between the trascriptome and the proteome.

Only a part of the genome is expressed in any given moment in both physiological and pathological conditions.

Identification of difference in expression profile between physiological and pathological states could lead to the identification of new targets.

Target identification

Techiniques to measure simoultaneously expression of multiple genes

Differential display

Subtractive cDNA library

S.A.G.E Serial analysis of gene expression

Microarray

Target identification

Gene microarray

Expression level of 20.000 Expression level of 20.000 genes could be measured genes could be measured simoultaneouslysimoultaneously

1,28cm1,28cm

GeneChip Probe Array

18µm18µm

Target gene is present inTarget gene is present inthousands of copiesthousands of copies

* **

**Hybridized Cell

Target identification

Gene microarray applied to target discovery

(Costingan et al., BMC Neuroscience 2002)

Target identification

Gene microarray applied to target discovery

Target identification

Ingenuity’s NetworkCV L5 CGW L5

GENE Rx/Lx Rx/LxAR -2.05 -1.21CACNA2D1 6.63 6.58DLG4 -1.82 -1.63GABRA1 -12.69 -6.88GABRA5 2.74 1.90GABRG2 -6.01 -5.29GRIA2 -8.52 -5.38HTR1D -35.11 -13.23HTR3A -11.38 -6.00HTR3B -81.76 -41.32KCNA4 -5.62 -3.56KCNAB1 -5.67 -3.89KCND3 -5.17 -3.97KCNIP1 -2.61 -2.76KCNIP2 -5.05 -4.15KCNIP3 -5.28 -3.59NTRK1 -3.30 -2.75RET -3.59 -2.76SYT1 -2.28 -1.72SYT9 -3.32 -2.80TAC1 -4.61 -3.61TRPV1 -8.81 -4.93

Target identification

CV L5 Rx vs. Lx fold changes on topCGW L5 Rx vs. Lx fold changes on bottom

Proteomics

• Allow to identify difference in protein expression under different physiological and pathological conditions

• It is possible the identification of post-translation modifications (e.g. phosphorylation and glycosilation)

• It is more time consuming and require more sophisticated instruments than gene expression profiling.

Target identification

2D-gel analysis

pI

MW

ProteomicsTarget identification

Preoteomics applied to target identification

Target identification