L9 - Exploiting the protein structure/function relationship for drug discovery and design Flashcards
(14 cards)
Describe the rationale of structure-based drug design
Target-ligand interactions give insight into how the ligand regulates the protein activity
This guides the development of small molecules (drug) that have greater affinity or specificity for the target
Features of the drug design process
- Target Identification and characterisation (disease modifying target, find its active/reg site, characterise ligand interac at the site)
- Hit identification (finding a ligand that has an interaction with the binding site) - natural ligand, novel ligands, docking, de novo
- Hit characterisation functional assays (Testing what the hit does to protein function and if it does what you want)
- Target-Hit characterisation (How does the hit interact with the protein)
- Hit modification (Modify hit structure based on the Structure Activity Relationship determined in the previous steps)
List the features of a good drug target for SBDD
Disease-modifying, well-characterised structure, well-defined binding site, structure activity relationship
examples of structure based drug design
imatinib- CML
- found through high throughput screening -> hit mod -> func + struc analysis
darunavir- HIV
- found through known natural ligand -> struct characterization, mod of hit + functional characrisation
7-cephalosporonic acid - B-lactim antibiotic synthesis
- known intermed and product, high throughput screening, docking, de novo
Explain why BCR-Abl is a good target for drug design (target identification)
Fusion is disease-causing
- The BCR-Abl fusion is a singular cause of CML
Well characterised structure
- Abl contains the well-conserved Protein Kinase (PK) domain
Well-defined binding site
- crystal structures of Src-family kinases in complex with substrates is known
Structure-Activity Relationship (SAR)
- characterised for homologous kinases
explain the Hit identification process of making imatinib
through high throughput screening (rapid identification of active sites teh modulate function)
found a tyrosine kinase inhibitor and modified it to improve specificity for abl, and increase bioavailability
Explain why HIV-1 protease is good target for drug design (target identification)
Disease-modifying
- Essential for virus survival: required for maturation of virus particles into infectious form
Well characterised structure
- X-ray structure of HIV-1 protease known
- dyad of aspartic acid res
Well-defined binding site
- Aspartic acid proteases in complex with peptide substrates are available
Structure-Activity relationship (SAR)
hit identification and modification to be HIV-1 protease resistant
- a modified labile peptide bond to a cleavage resistant hydroxyethylene bond
- sidechain substitutes the proline for DIQ
- dramatically improved inhibition
= saquinavir
How does imatinib interact with abl to produce its inhibition (target-hit characterisation)
HIgh affinity at abl protein forming many stabilising connection across the N-C lobes
High specificity despite being an ATP competitive inhibitor: Imatinib binds only to the Abl in its inactive state (which is highly variable among tyrosine kinases) making it specific to Abl
Target hit characterisation and modification of saquinavir
saquinavir had poor bioavailability
created a series of of rationally based solutions to improve bioavailability by mimicking peptide bonds
Explain how mutations of abl led to imatinib resistance and how are they overcome
Most common mutations occur in the ATP binding pocket -> reducing the binding capacity of the drug
Second generation inhibitors such as dasatinib - > contained modifications that altered that required less stabilising contacts while still
Explain how saquinavir was optimised to prevent resistance occurring due to mutations of amino acids
HIV-protease has documented mutations to almost half the residues but not the backbone
optimise drug interactions with protein backbone and minimise interactions with side-chains using X-ray structures and biochemical assays
= darunavir
Explain how imatinib/dasatinib were modified to overcome resistance
T315I located on the ATP binding pockets and renders ineffective
The structure of imatinib and dasatinib bound to Abl showed both require a hydrogen bond to the hydroxyl group of threonine (T315I)
Inhibitors were modified to not have this h-bond.
= ponatinib
Describe how knowledge of protein structure can facilitate biosynthesis of cephalosporin antibiotics.
To enzymatically convert CPC to 7-ACA required a long two-step process. The goal was to create a one-step conversion.
Using a WT of the original enzyme as a starting point they modelled
