Structure-guided design of AMP mimics that inhibit fructose-1,6-bisphosphatase with high affinity and specificity.
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.
Erion
Mark D
MD
Department of Medicinal Chemistry, Metabasis Therapeutics, Inc., 11119 North Torrey Pines Road, La Jolla, California 92037, USA. erion@mbasis.com
Dang
Qun
Q
Reddy
M Rami
MR
Kasibhatla
Srinivas Rao
SR
Huang
Jingwei
J
Lipscomb
William N
WN
van Poelje
Paul D
PD
D000249:Adenosine Monophosphate / Q000138:chemical synthesis / Q000737:chemistry* / Q000378:metabolism*; D000818:Animals; D001665:Binding Sites; D002478:Cells, Cultured; D018360:Crystallography, X-Ray; D015195:Drug Design; D004791:Enzyme Inhibitors / Q000138:chemical synthesis* / Q000737:chemistry / Q000494:pharmacology*; D006597:Fructose-Bisphosphatase / Q000037:antagonists & inhibitors* / Q000378:metabolism; D005947:Glucose / Q000096:biosynthesis; D006801:Humans; D007700:Kinetics; D007854:Lead / Q000737:chemistry; D008958:Models, Molecular; D018716:Molecular Mimicry; D015394:Molecular Structure; D011687:Purines / Q000737:chemistry; D051381:Rats; D012680:Sensitivity and Specificity; D013237:Stereoisomerism; D013329:Structure-Activity Relationship; D013379:Substrate Specificity; D013499:Surface Properties
D004791:Enzyme Inhibitors; D011687:Purines; D007854:Lead; D000249:Adenosine Monophosphate; D006597:Fructose-Bisphosphatase; D005947:Glucose; C030985:purine