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Screening of allosteric inhibitors and
inhibitors of protein-protein
interactions
Joel Eggert
Kinase inhibitors
Orthosteric
Foda & Seeliger, 2014.
Kinase inhibitors
Orthosteric
Allosteric
Foda & Seeliger, 2014.
Allosteric inhibitors
• Advantages
– Highly specific
– Lower chances of side effects
– Overcome clinically acquired resistance
– Barely explored
Allosteric inhibitors
• Disadvantages
– Allosteric sites are often unknown
– Hard to predict the outcome
– Higher divergence between species
High-throughput screen of allosteric
inhibitors
Goal: identify targets that can stabilize the enzyme in a catalytically
inactive conformation
Recombinant cSrc
Site-directed mutagenesis
+ Cys
activation loop
O/N
Acrylodan
Mass
spec
Triplicates:
acrylodan-cSrc (100 nM)
Compounds: 10 and 50 µM
15-30 min, RT
Simard et al., 2009
inhibitor
Type I
Type II
Type III
binding
active site
active + allosteric site
allosteric site
kinase
active state
inactive state
inactive state
Simard et al., 2009
inhibitor
Type I
Type II
Type III
binding
active site
active + allosteric site
allosteric site
kinase
active state
inactive state
inactive state
Simard et al., 2009
inhibitor
Type I
Type II
Type III
binding
active site
active + allosteric site
allosteric site
kinase
active state
inactive state
inactive state
Simard et al., 2009
Simard et al., 2009
Inhibitors of protein-protein
interactions
http://www.singerinstruments.com/application/yeast-2-hybrid
Chemical library:
>156 000 compounds
(300-600 kDa)
Fragment-screening and fragmentbased drug design (FBDD)
Low molecular weight
compounds
NMR
Bind – target protein?
Weak interactions [mM]
Fragment hits
Structure-based optimization
(fragment linking etc)
Lead compound
Sheng et al., 2015
Sheng et al., 2015
References
Foda, Z. H. & Seeliger, M. A. Kinase inhibitors: An allosteric add-on. Nat. Chem.
Biol. 10, 796–797 (2014).
Nussinov, R. & Tsai, C.-J. Allostery in disease and in drug discovery. Cell 153,
293–305 (2013).
Hajduk, P. J. & Greer, J. A decade of fragment-based drug design: strategic
advances and lessons learned. Nat. Rev. Drug Discov. 6, 211–219 (2007).
Simard, J. R. et al. A new screening assay for allosteric inhibitors of cSrc. Nat.
Chem. Biol. 5, 394–396 (2009).
Sheng, C., Dong, G., Miao, Z., Zhang, W. & Wang, W. State-of-the-art strategies
for targeting protein-protein interactions by small-molecule inhibitors. Chem.
Soc. Rev. 44, 8238–8259 (2015).
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