Lec 4- target discovery

Question 1

Target Identification

Answer 1

• Target discovery =>
  
  • Target Identification; Target validation; Assay development
• Informatics and Functional genomic
  
  • Bioinformatics; Genomics; Proteomics
• Lead discovery =>
  
  • Assay development; High throughput screening; Biochemistry and Enzymology
• Medical chemistry =>
  
  • Library development; structure-based drug design; medicinal chemistry
• Cellular and molecular pharmacology =>
  
  • In vitro drug activity; Cellular disease models; Drug mechanism of action
• Preclinical development
  
  • PK; In vivo pharmacology; Tox/safety pharmacology

Question 2

Target Identification

Answer 2

• Identifying cellular components that could be targeted for developing new drugs
• Identifying the cellular targets (and off-target effects) of current drugs and new chemical entities (NCE)
• Identifying appropriate therapeutic doses
• Identifying likely efficacy of treatments
• Identifying combination therapies that prevent or circumvent resistance
• METHODS
  
  • High-content (or other) screening
  • Clinical screening
  • Molecular biochemical understanding of the phenotype
  • Systems biology and systems medicine

Question 3

Target Identification

Answer 3

• Targets can be DNA, RNA, proteins (or membranes)
• Most targets for current drugs are enzymes or G-protein coupled receptors (GPCR)
• Most pharmaceuticals are small molecules but between 2003 and 2006 biologicals (antibodies, proteins, enzymes) represented 24% per cent of all new approvals in the US, and are due to overtake small molecules by 2020

Question 4

Sales of biologics

Answer 4

Question 5

Biological screening

Answer 5

1. We need a disease model
   
   • In vitro/Animal models
   • Cell models
   • Some times patients
2. Target identification
   
   • Genomics, proteomics and genetic association
   • Forward genetics
   • Clinical sciences
   • Forward genes/reverse genes
3. Target validation
   
   • Disease tissue expression
   • Modulation in cell models
   • Modulation in animal models

Question 6

forward genetics

Answer 6

• Manipulating a system to try and generate a phenotype that is like the disease we are interested in (an animal model that acts like a human disease)
  
  • Phenotype- how a system behaves
• Forward genetic is when we take a random set of mutation (Chemically or add random DNA) then we screen for things that show the behaviour we want- whatever has changed in the animal could potentially be the cause of the disease (change behaviour of protein due to addition of DNA)
• This is very difficult because it is random

Question 7

reverse genetics

Answer 7

• We think a particular gene may be responsible for a certain disease
• The protein can be knocked out/Mutated
• We can then see whether the animal now shows that disease phenotype
• This is far more selective as it doesn’t involve random screening
  *

Question 8

Genome and proteome approaches

Answer 8

• Just because it behaves like the human disease doesn’t mean that it is the same, they must just show the same symptoms the model may be completely different

1. Genomics
2. Proteomics
3. Genetic association

Question 9

Genome => Transcriptome => Proteome

Answer 9

• Genome: the complete set of sequences in the genetic material of an organism- Static genes dont change but diseases do
• =(transcription) =>
• Transcriptome: the set of expressed genes, i.e. genes transcribed into RNA in a cell at a given point in time
• =(Translation)=>
• Proteome: the set of proteins including their modifications expressed in a cell at a given point in time- responsible for cell function- max info and complexity
• Responsible for the functioning of a cell
• Maximum information- maximum complexity
• Metabolome: The set of endogenous small molecules present in a cell at a given point
  
  • information on enzyme activity and cell status possible to collect high-density data

Question 10

The informtion pyramid

Answer 10

Human genome:

1. 22,000 genes- average 4 splice variants
2. 80,000 transcripts (different mRNAs)- average ~ 10(0) post-translational modifications
3. 800,000 functional entities

Question 11

genomics in the last 20 years

Answer 11

• 1990: US Department of energy and the national institute of health received funding from Congress for the 15-year project to sequence the human genome
• 1995: TIGR publishes the first full DNA sequence of a free-living organism (Haemophilus influenza)
• 1999: First human chromosome sequenced (chromosome 22 by HGP- Sanger)
• 2000: the draft sequence of human genome announced
• 2001: the Full sequence of human genome published, nearly 5 years ahead of original schedules
• 2001-2011: Consolidation, SNP, sequencing of rat, mouse
• Other ‘omics’ technologies start to illuminate genetics information

Question 12

Single Nucleotide Polymorphisms (SNP’s)

Answer 12

• When a single base differs between individuals (being A instead of G, for example
• A variation must occur in at least 1% of the population to be considered an SNP
• SNPs occur about once every 100-300 base pairs along the human genome, are the bulk of 3 million variations found in the human genome, and makeup about 90% of all human genetic variation
• The frequency of a particular polymorphism tends to remain stable in the population
• Unlike the other, rarer kinds of variations, many SNPs occur in genes and in the surrounding regions of the genome that control their expression or some other functions
• The effect of a single SNP on a gene may not be large- perhaps influencing the activity of the encoded protein in a subtle way- but even subtle effects can influence susceptibility to common diseases (e.g.E4 of ApoE in Alzheimer’s disease)
• Give information on genetic predisposition, likely response to specific therapy, prognosis, some specific, some less clear
• Not the whole story- environmental factors, protective SNPs, epigenetic info

Question 13

What will genomics need to deliver

Answer 13

• The $1000 genome
  
  • The use of genomics for disease profiling and personalised medicine requires that we are able to perform genome analysis- genome sequencing and SNP analysis- for an individuals at a moderate price
    *

Question 14

What will genomics need to deliver- SNP genotyping

Answer 14

• Discovering and typing SNPs and other forms of genetic variation on a large scale across the genome
• Developing high-resolition maps of genetic variation and haplotypes
• Developing methods for the large-scale experimental and statistical analysis of genetic variation, haplotypes and complex triats
• Developing statistical methods to relate genetic variation to phenotype

Question 15

What will genomics need to deliver- functional genomics

Answer 15

• Identification of function of genes in the cell- known and unknown

Question 16

The new genomics revolution

Answer 16

• High throughput next-generation sequencing has completely changed the landscape
• The first fully sequenced free-living organism has Haemophilus Influenzae in 1995
• By 2007 some 650 non-viral organisms sequenced
• By 2009 over 1700 non-viral organisms sequenced

Question 17

The new genomics revolution

Answer 17

• High throughput next-generation sequencing has completely changed the landscape
• Complete Genomics offers a human genome sequencing service with 40-fold coverage priced at US$ 5,000
• March 2010 China bought 128 new HiSeq 2000 genome sequencers for the BGI
• Pacific Biosciences real-time sequencing will reduce data collection time and cost
• The $1000 human genome is just around the corner

Question 18

Genomics

Answer 18

• Can compare genomes from disease and identify genes that correlate with disease
• Can correlate model systems (mouse, fly) with human
• The understanding of how this dysfunction changes the phenotype can then be used to identify potenital target genes or gene products for drugs

Question 19

Personalised medicine

Answer 19

• Record individual genome information, and use this to predict most effective treatment (drug, dose, etc) or likely susceptibility and predisposition to diseae
• Expect to be able to prescribe the most appropriate treatment for some condition, especially cancer, in the near future by biomarker typing
• In the more distant future want an indication of susceptibility likely drug efficacy and dose response (therapeutic index) and selecting most appropriate treatment, will add huge value to genome data
• For the understanding at the biochemical level still problems- 47% of human genome still unknown function (29% still hypothesised)

Question 20

Transcriptomics

Answer 20

• Transcriptomics: the genome wide study of mRNA expression levels
• The transcriptome is set of all mRNA molecules (or transcripts) in one or a population of biological cells for a given set of environment circumstances
• Unlike the genome, which is ficed for a given organism (apart from genetic polymorphisms), the transcriptome varies depending upon the context of the experiment

Question 21

Transcriptomics

the next stage of genomics research will begin to derive meaningful knowledge from the DNA sequence

Answer 21

• Specific details of gene expression in targeted approaches- e.g. which genes activated by a specific protein
• General discovery experiements- no particular hypothesis but used to identify interesting genes e.g. which genes are highly expressed in brain tumours but not in healthy brain tissue
• Disease classification. Single markers often not sufficient to distinguish 2 similar disease e.g. cancer. The expression profiles of a larger number of genes can provide accurate diagnosis
• Functional annotation. If genes of unknown function show similar expression patterns to a characterized gene- functions are similar
• To identify drug targets. If the gene expression profile caused by a mutation is similar to that caused by a drug, it is likely the drug interacts with and inactivates the protein afftected by the mutation
• Time courses. Analysis is genome wide and data can be collected relatively simply (not cheap)