L9 - Exploiting the protein structure/function relationship for drug discovery and design Flashcards
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
Process of SBDD
Target Identification and characterisation, Hit identification
Hit characterisation functional assays (Testing what the hit does to protein function)
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
Explain why BCR-Abl is a good target for drug design
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
many crystal structures of Src-family kinases in complex with substrates
Structure-Activity Relationship (SAR)
characterised for homologous kinases
Explain why HIV-1 protease is good target for drug design
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
Well-defined binding site
Aspartic acid proteases in complex with peptide substrates were available
Structure-Activity relationship (SAR)
Describe how imatinib interacts with its target and the effect of this interaction
High specificity despite being an ATP competitive inhibitor: Imatinib binds only the Abl inactive state (which is variable among tyrosine kinases) making it specific to Abl
Describe how saquinavir interacts with its target and the effect of this interaction
SBDD based on the structure of HIV-1 protease in complex with peptide analogues
HIV-1 protease cleaves the peptide bond between Tyr-Pro and Phe-Pro
The first inhibitors were designed as analogues of the natural ligand
Modified the labile peptide bond to a cleavage resistant hydroxyethelene bond
Side chain substitutions were trialled at the P2 and P3 subsites guided the replacement of the proline by DIQ
Explain how mutations can lead to resistance to drugs
Give an example of a mutation leading to drug resistance
Abl mutations + Imatinib
Many patients develop resistance to imatinib due to mutations of Abl
Most common mutations occur in the ATP binding pocket
Second generation inhibitors such as dasatinib were designed to
overcome resistance due to these mutations
Explain how darunavir 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
Explain how ponatinib overcomes resistance to imatinib
The structure of imatinib and dasatinib bound to Abl showed both
require a hydrogen bond to the hydroxyl group of threonine
Inhibitors that did not have this h-bond were designed.
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
