Genomics in Drug Discovery @ Organon, Oss 2005-08-22 Tim Hulsen.
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Transcript of Genomics in Drug Discovery @ Organon, Oss 2005-08-22 Tim Hulsen.
Genomics in Drug Discovery
@ Organon, Oss
2005-08-22
Tim Hulsen
Introduction
• Proteins are vital to life:
involved in all kinds of life processes
• Understanding protein functions and relationships is very important for drug design
• Currently, the molecular function of about 40% of the proteins is unknown
Introduction
Determine protein function by using different in silico techniques:
• sequence comparison to known protein sequences• sequence clustering with proteins which have the same
or similar function
Availability of fully sequenced genomes gives us a wealth of information:currently more than 15 eukaryotic genomes have nearly been completely sequenced, over 148 microbial genomes and over 1000 viruses.
Genomics @ Organon:The Protein World project
• All-against-all sequence comparison of complete proteomes from 145 species
• Smith-Waterman algorithm + Z-value (Monte-Carlo statistics)
Protein World and its ambitions
Build and maintain a sequence similarity repository of all complete proteomes and aligning it with “omics” research in the Netherlands
Classification of all proteins into groups of related proteins• A phylogenetic repository• Annotation of new sequences• Mining protein families• Identification of genes common / specific to (groups of) species
Applications of Protein World
Structural properties• Protein comparison coupled to structure related databases
(PDB, SCOP, etc.)
Systems biology • Connecting PW to other databases (pathways, protein
interactions, literature etc.)
Orthology• Annotation of new proteins• To predict discrepancies and similarities between species
Orthology• Describes “the evolutionary relationship
between homologous genes whose independent evolution reflects a speciation event” (Fitch, 1970)
Protein World & Drug Discovery
• Orthologies can be used to transfer function of proteins in model organisms (mice, rats, dogs, etc.) to humans
• Drugs tested on model organisms can have different effects in humans. Why?
• Could be explained by looking at proteins in drug pathways and their orthologs
• Example: trypsin inhibition pathway
Trypsin inhibition pathway (1)
• Organon: thrombin inhibitors• Needed to stop thrombosis (blood clotting)• Thrombin inhibitor on the market: (xi)melagatran, sold as
Exanta (AstraZeneca)
• Proven to be better than warfarin, but …
Trypsin inhibition pathway (2)
• Side effect of thrombin inhibitors: inhibition of trypsin
• Trypsin inhibition -> rise in cholecystokinin (CCK) levels -> stimulation of pancreas -> pancreatic tumors
• Difficult to test in model organisms:– Rat: very strong CCK response– Mouse: weak CCK response– Human: almost no CCK response
Trypsin inhibition pathway (3)
Trypsin inhibition pathway (4)
Ortholog identification methods:
1. Using functional annotation (SPTrEMBL):
2. Best Bidirectional Hit (BBH)
one-to-one relationships3. PhyloGenetic Trees (PGT)
many-to-many relationships
Best Bidirectional Hit (BBH)
• Very easy and quick• Human protein (1) SW best
hit in mouse/rat (2)• Mouse/rat protein (2) SW
best hit in human (3)• If 3 equals 1, the human and
mouse/rat protein are considered to be orthologs
PhyloGenetic Tree (PGT) Human
All
eukaryotic
proteomes
Z>20 RH>0.5*QL
~25,000 groups
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREES
PROTEOME
PROTEOMES
TREE SCANNING
LIST Hs-Mm pairsHs-Rn pairs
Trypsin inhibition pathway (5)
Mm – Hs – Rn - by annotation- BBH- PGT
Trypsin inhibition pathway (6)• PGT method: in some cases too many orthologous
relationships, especially for trypsin (73 in mouse and 62 in rat!)
• BBH method seems to be more usable for this study, but still not gives an explanation for the differences in CCK levels
• Our problem (different CCK responses in Human, Mouse and Rat) cannot be solved only by orthology identification
Combine ortholog analysis with other data Focus on the molecules that are most likely to be
responsible for these differences: CCK and trypsin
Trypsin inhibition pathway (7)
• Current activities:
– Take a better look at regulation: promoter detection?
– Use expression data?
– Structural explanation? Modelling of interactions between the involved molecules
Possible student projects
• Orthology case study: explain differences between humans and model organisms
(like example of trypsin inhibition pathway)
• Chicken project (in collaboration with Wageningen University): comparison of immune system in chickens to i.s. in humans and other vertebrates
• Cluster algorithms
People
• Peter Groenen• Wilco Fleuren• Tim Hulsen• Others @ MDI
• Students?