Drug discovery

Question 1

How are drug targets validated

Answer 1

siRNA, shRNA, CRISPR/Cas9 and catalytically inactivated protein

Question 2

How are assays used in drug discovery

Answer 2

• engineered cells with reporter constructs
• labelled proteins (e.g. nano-BRET)

Question 3

What are the biomarkers involved drug discovery

Answer 3

transcriptional readouts
protein expression
protein activation state

Question 4

What are the biosciences methods of drug discovery

Answer 4

○ Validate drug targets
○ Develop assays
○ Develop biomarkers
○ In vivo models and pharmacokinetics
○ Primary patient material

Question 5

What are the phases of drug discovery

Answer 5

• bioscience
• biophysics
• medicinal chemist

Question 6

What are the phases of drug discovery

Answer 6

Target selection and validation
Hit identification + validation
Lead identification
Lead optimisation

Question 7

How are drug target validated and choosen

Answer 7

• Target biology [Biological hypothesis (phenotype/cell type), Basis for a therapeutic index]
• Technical feasibility [Biological (assay, biomarkers, disease models), Chemical (HTS/ fragment/ SBDD)]
• Patient stratification [Which disease?, Which subset of patients?]
• Biomarker development [Identifying robust methods to demonstrate drug effects, Amgen study]

Question 8

What did the amgen study show

Answer 8

Of 53 papers termed “landmark” studies, they were able to confirm only 6 (11%) as being robust enough for drug discovery

Question 9

What is KRAS

Answer 9

a GTPase member of the RAS/MAPK family that interacts with other messengers (e.g. PI3K)

Question 10

Why is KRAS amplified/mutated cancers hard to treat

Answer 10

very high GTP/GDP affinity

Question 11

What is CPISPR/Cas9

Answer 11

nuclease-dependent gene-editing
(Less off target effects than si/shRNA but still requires a degree of caution)
Complete loss of function, use can lead to a cell cycle block
Particular liabilities in cells with genomic amplification, Knock-in ability to make point mutations, insertions, rearrangements etc.

Question 12

how do we find hit molecules against the drug target

Answer 12

Chemical libraries require extensive quality control and an associated infrastructure to handle them optimally
Can require a lot of work to determine whether the hits are real: Counter-screening, Orthogonal Assays, Confirmation by NMR or X-ray
Amenable to further synthetic development
No obvious undesirable chemical features

Question 13

Explain the fragment case history of vemurafenib

Answer 13

Kinase assay to identify weak and non-specific scaffold
X-ray crystallography to week out false positive
PIM1 & FGFR1 used as surrogates
B-RAF mutated to make it amenable to structural studies

Question 14

Lead optimisation =

Answer 14

• POTENCY + SELECTIVITY -
  Improvement to
  Pharmacokinetic properties
  Pharmaceutical properties
  Safety/ therapeutic index
  Physicochemical properties

Question 15

What are the points of therapeutic intervention

Answer 15

• Sequester ligands e.g. Bevacizumab for VEGF
• Block receptor ligand binding domain e.g. trastuzumab for HER2
• Inhibit receptor signal transduction e.g. gefitinib for EGFR
• Inhibit downstream signal transduction e.g. vemurafinib for mutant BRAF
• Inhibit transcriptional responses e.g. JQ1 for BRD4

Question 16

What is the kinome

Answer 16

518 Kinases in the genome
Phylogenetically divided into 7 subfamilies
- Receptor and non-receptor
- Protein kinases, Lipid kinases and Carbohydrate kinases
- Tyrosine, Serine/Threonine and Tyrosine/Serine/Threonine substrates
Regulate many processes: e.g. cell cycle, proliferation, survival signalling, metabolism, secretion

Question 17

What are the two types of inhibition caused by kinase inhibitors

Answer 17

Type I/II = Orthosteric
Type III/IV = Allosteric