Structure-Guided Design of AMP Mimics That Inhibit Fructose-1,6-bisphosphatase with High Affinity and Specificity

• Published in: Journal of the American Chemical Society Vol. 129; no. 50; pp. 15480 - 15490
• Main Authors: Erion, Mark D, Dang, Qun, Reddy, M. Rami, Kasibhatla, Srinivas Rao, Huang, Jingwei, Lipscomb, William N, van Poelje, Paul D
• Format: Journal Article
• Language: English
• Published: WASHINGTON American Chemical Society 19.12.2007; Amer Chemical Soc
• Subjects: Adenosine Monophosphate - chemical synthesis; Adenosine Monophosphate - chemistry; Adenosine Monophosphate - metabolism; Animals; Binding Sites; Cells, Cultured; Chemistry; Chemistry, Multidisciplinary; Crystallography, X-Ray; Drug Design; Enzyme Inhibitors - chemical synthesis; Enzyme Inhibitors - chemistry; Enzyme Inhibitors - pharmacology; Fructose-Bisphosphatase - antagonists & inhibitors; Fructose-Bisphosphatase - metabolism; Glucose - biosynthesis; Humans; Kinetics; Lead - chemistry; Models, Molecular; Molecular Mimicry; Molecular Structure; Physical Sciences; Purines - chemistry; Rats; Science & Technology; Sensitivity and Specificity; Stereoisomerism; Structure-Activity Relationship; Substrate Specificity; Surface Properties; FRUCTOSE 1,6-BISPHOSPHATASE; ACTIVATED PROTEIN-KINASE; MOLECULAR PHYSIOLOGY; GLYCOGEN-PHOSPHORYLASE; BINDING AFFINITIES; CRYSTAL-STRUCTURE; HUMAN LIVER FRUCTOSE-1,6-BISPHOSPHATASE; CYCLE-PERTURBATION APPROACH; ISOLATED RAT HEPATOCYTES; FREE-ENERGY PERTURBATION
• ISSN: 0002-7863; 1520-5126; 1520-5126
• DOI: 10.1021/ja074869u

AMP binding sites are commonly used by nature for allosteric regulation of enzymes controlling the production and metabolism of carbohydrates and lipids. Since many of these enzymes represent potential drug targets for metabolic diseases, efforts were initiated to discover AMP mimics that bind to AMP-binding sites with high affinity and high enzyme specificity. Herein we report the structure-guided design of potent fructose 1,6-bisphosphatase (FBPase) inhibitors that interact with the AMP binding site on FBPase despite their structural dissimilarity to AMP. Molecular modeling, free-energy perturbation calculations, X-ray crystallography, and enzyme kinetic data guided our redesign of AMP, which began by replacing the 5‘-phosphate with a phosphonic acid attached to C8 of the adenine base via a 3-atom spacer. Additional binding affinity was gained by replacing the ribose with an alkyl group that formed van der Waals interactions with a hydrophobic region within the AMP binding site and by replacing the purine nitrogens N1 and N3 with carbons to minimize desolvation energy expenditures. The resulting benzimidazole phosphonic acid, 16, inhibited human FBPase (IC50 = 90 nM) 11-fold more potently than AMP and exhibited high specificity for the AMP binding site on FBPase. 16 also inhibited FBPase in primary rat hepatocytes and correspondingly resulted in concentration-dependent inhibition of the gluconeogenesis pathway. Accordingly, these results suggest that the AMP site of FBPase may represent a potential drug target for reducing the excessive glucose produced by the gluconeogenesis pathway in patients with type 2 diabetes.