Small Molecules Engage Hot Spots through Cooperative
Binding To Inhibit a Tight Protein–Protein Interaction
Degang Liu
David Xu
Min Liu
William Eric Knabe
Cai Yuan
Donghui Zhou
Mingdong Huang
Samy O. Meroueh
10.1021/acs.biochem.6b01039.s001
https://acs.figshare.com/articles/journal_contribution/Small_Molecules_Engage_Hot_Spots_through_Cooperative_Binding_To_Inhibit_a_Tight_Protein_Protein_Interaction/4762213
Protein–protein
interactions drive every aspect of cell
signaling, yet only a few small-molecule inhibitors of these interactions
exist. Despite our ability to identify critical residues known as
hot spots, little is known about how to effectively engage them to
disrupt protein–protein interactions. Here, we take advantage
of the ease of preparation and stability of pyrrolinone <b>1</b>, a small-molecule inhibitor of the tight interaction between the
urokinase receptor (uPAR) and its binding partner, the urokinase-type
plasminogen activator uPA, to synthesize more than 40 derivatives
and explore their effect on the protein–protein interaction.
We report the crystal structure of uPAR bound to previously discovered
pyrazole <b>3</b> and to pyrrolinone <b>12</b>. While
both <b>3</b> and <b>12</b> bind to uPAR and compete with
a fluorescently labeled peptide probe, only <b>12</b> and its
derivatives inhibit the full uPAR·uPA interaction. Compounds <b>3</b> and <b>12</b> mimic and engage different hot-spot
residues on uPA and uPAR, respectively. Interestingly, <b>12</b> is involved in a π–cation interaction with Arg-53,
which is not considered a hot spot. Explicit-solvent molecular dynamics
simulations reveal that <b>3</b> and <b>12</b> exhibit
dramatically different correlations of motion with residues on uPAR.
Free energy calculations for the wild-type and mutant uPAR bound to
uPA or <b>12</b> show that Arg-53 interacts with uPA or with <b>12</b> in a highly cooperative manner, thereby altering the contributions
of hot spots to uPAR binding. The direct engagement of peripheral
residues not considered hot spots through π–cation or
salt-bridge interactions could provide new opportunities for enhanced
small-molecule engagement of hot spots to disrupt challenging protein–protein
interactions.
2017-02-10 00:00:00
pyrazole 3
uPAR binding
40 derivatives
12 bind
small-molecule inhibitors
12 exhibit
pyrrolinone 12
small-molecule engagement
urokinase receptor
Compounds 3
small-molecule inhibitor
binding partner
Free energy calculations
urokinase-type plasminogen activator uPA
12 show
crystal structure
Small Molecules Engage Hot Spots
hot-spot residues
pyrrolinone 1
peptide probe
Arg -53
salt-bridge interactions
dynamics simulations
Cooperative Binding