Structure-based inhibitor design for an enzyme that binds different steroids: a potent inhibitor for human type 5 17beta-hydroxysteroid dehydrogenase.
Human type 5 17beta-hydroxysteroid dehydrogenase plays a crucial role in local androgen formation in prostate tissue. Several chemicals were synthesized and tested for their ability to inhibit this enzyme, and a series of estradiol derivatives bearing a lactone on the D-ring were found to inhibit its activity efficiently. The crystal structure of the type 5 enzyme in complex with NADP and such a novel inhibitor, EM1404, was determined to a resolution of 1.30 A. Significantly more hydrogen bonding and hydrophobic interactions were defined between EM1404 and the enzyme than in the substrate ternary complex. The lactone ring of EM1404 accounts for important interactions with the enzyme, whereas the amide group at the opposite end of the inhibitor contributes to the stability of three protein loops involved in the construction of the substrate binding site. EM1404 has a strong competitive inhibition, with a Ki of 6.9+/-1.4 nM, demonstrating 40 times higher affinity than that of the best inhibitor previously reported. This is observed despite the fact that the inhibitor occupies only part of the binding cavity. Attempts to soak the inhibitor into crystals of the binary complex with NADP were unsuccessful, yielding a structure with a polyethylene glycol fragment occupying the substrate binding site. The relative crystal packing is discussed. Combined studies of small molecule inhibitor synthesis, x-ray crystallography, enzyme inhibition, and molecular modeling make it possible to analyze the plasticity of the substrate binding site of the enzyme, which is essential for developing more potent and specific inhibitors for hormone-dependent cancer therapy.
Qiu
Wei
W
Canadian Institutes of Health Research Group in Molecular Endocrinology, Laval University Medical Center, Centre Hospitalier de Universités de Québec and Laval University, Quebec G1V 4G2, Canada.
Zhou
Ming
M
Mazumdar
Mausumi
M
Azzi
Arezki
A
Ghanmi
Dalila
D
Luu-The
Van
V
Labrie
Fernand
F
Lin
Sheng-Xiang
SX
D015067:17-Hydroxysteroid Dehydrogenases / Q000737:chemistry*; D015096:3-Hydroxysteroid Dehydrogenases; D000074425:Aldo-Keto Reductase Family 1 Member C3; D000595:Amino Acid Sequence; D001665:Binding Sites; D001667:Binding, Competitive; D018360:Crystallography, X-Ray; D015195:Drug Design; D004791:Enzyme Inhibitors / Q000494:pharmacology*; D005439:Flufenamic Acid / Q000737:chemistry; D006801:Humans; D006860:Hydrogen Bonding; D006911:Hydroxyprostaglandin Dehydrogenases; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D009249:NADP / Q000737:chemistry; D011485:Protein Binding
D004791:Enzyme Inhibitors; D009249:NADP; D005439:Flufenamic Acid; D015067:17-Hydroxysteroid Dehydrogenases; D015096:3-Hydroxysteroid Dehydrogenases; D006911:Hydroxyprostaglandin Dehydrogenases; C487341:AKR1C3 protein, human; D000074425:Aldo-Keto Reductase Family 1 Member C3