TY - JOUR
T1 - Small-Molecule Inhibition of the uPAR ⋅ uPA Interaction by Conformational Selection
AU - Xu, David
AU - Bum-Erdene, Khuchtumur
AU - Leth, Julie M
AU - Ghozayel, Mona K
AU - Ploug, Michael
AU - Meroueh, Samy O
N1 - © 2020 Wiley-VCH GmbH.
PY - 2021/1/19
Y1 - 2021/1/19
N2 - The urokinase receptor (uPAR) is a cell surface receptor that binds to the serine protease urokinase-type plasminogen activator (uPA) with high affinity. This interaction is beneficial for extravascular fibrin clearance, but it has also been associated with a broad range of pathological conditions including cancer, atherosclerosis, and kidney disease. Here, starting with a small molecule that we previously discovered by virtual screening and cheminformatics analysis, we design and synthesize several derivatives that were tested for binding and inhibition of the uPAR ⋅ uPA interaction. To confirm the binding site and establish a binding mode of the compounds, we carried out biophysical studies using uPAR mutants, among them uPARH47C-N259C , a mutant previously developed to mimic the structure of uPA-bound uPAR. Remarkably, a substantial increase in potency is observed for inhibition of uPARH47C-N259C binding to uPA compared to wild-type uPAR, consistent with our use of the structure of uPAR in its uPA-bound state to design small-molecule uPAR ⋅ uPA antagonists. Combined with the biophysical studies, molecular docking followed by extensive explicit-solvent molecular dynamics simulations and MM-GBSA free energy calculations yielded the most favorable binding pose of the compound. Collectively, these results suggest that potent inhibition of uPAR binding to uPA with small molecules will likely only be achieved by developing small molecules that exhibit high-affinity to solution apo structures of uPAR, rather than uPA-bound structures of the receptor.
AB - The urokinase receptor (uPAR) is a cell surface receptor that binds to the serine protease urokinase-type plasminogen activator (uPA) with high affinity. This interaction is beneficial for extravascular fibrin clearance, but it has also been associated with a broad range of pathological conditions including cancer, atherosclerosis, and kidney disease. Here, starting with a small molecule that we previously discovered by virtual screening and cheminformatics analysis, we design and synthesize several derivatives that were tested for binding and inhibition of the uPAR ⋅ uPA interaction. To confirm the binding site and establish a binding mode of the compounds, we carried out biophysical studies using uPAR mutants, among them uPARH47C-N259C , a mutant previously developed to mimic the structure of uPA-bound uPAR. Remarkably, a substantial increase in potency is observed for inhibition of uPARH47C-N259C binding to uPA compared to wild-type uPAR, consistent with our use of the structure of uPAR in its uPA-bound state to design small-molecule uPAR ⋅ uPA antagonists. Combined with the biophysical studies, molecular docking followed by extensive explicit-solvent molecular dynamics simulations and MM-GBSA free energy calculations yielded the most favorable binding pose of the compound. Collectively, these results suggest that potent inhibition of uPAR binding to uPA with small molecules will likely only be achieved by developing small molecules that exhibit high-affinity to solution apo structures of uPAR, rather than uPA-bound structures of the receptor.
KW - Binding Sites/drug effects
KW - Cheminformatics
KW - Dose-Response Relationship, Drug
KW - Humans
KW - Models, Molecular
KW - Molecular Conformation
KW - Receptors, Urokinase Plasminogen Activator/antagonists & inhibitors
KW - Small Molecule Libraries/chemistry
KW - Urokinase-Type Plasminogen Activator/antagonists & inhibitors
UR - http://www.scopus.com/inward/record.url?scp=85097203151&partnerID=8YFLogxK
U2 - 10.1002/cmdc.202000558
DO - 10.1002/cmdc.202000558
M3 - Journal article
C2 - 33107192
SN - 1860-7179
VL - 16
SP - 377
EP - 387
JO - ChemMedChem
JF - ChemMedChem
IS - 2
ER -