Development of Serine Protease Inhibitors Displaying a Multicentered Short (<2.3 Å) Hydrogen Bond Binding Mode:  Inhibitors of Urokinase-Type Plasminogen Activator and Factor Xa

• Published in: Journal of medicinal chemistry Vol. 44; no. 17; pp. 2753 - 2771
• Main Authors: Verner, Erik, Katz, Bradley A, Spencer, Jeffrey R, Allen, Darin, Hataye, Jason, Hruzewicz, Witold, Hui, Hon C, Kolesnikov, Aleksandr, Li, Yong, Luong, Christine, Martelli, Arnold, Radika, Kesavan, Rai, Roopa, She, Miles, Shrader, William, Sprengeler, Paul A, Trapp, Sean, Wang, Jing, Young, Wendy B, Mackman, Richard L
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 16-08-2001
• Subjects: Amidines - chemical synthesis; Amidines - chemistry; Binding Sites; Biological and medical sciences; Crystallography, X-Ray; Factor Xa Inhibitors; Humans; Hydrogen Bonding; Indoles - chemical synthesis; Indoles - chemistry; Medical sciences; Miscellaneous; Models, Molecular; Pharmacology. Drug treatments; Serine Proteinase Inhibitors - chemical synthesis; Serine Proteinase Inhibitors - chemistry; Spectrometry, Fluorescence; Spectrophotometry, Ultraviolet; Structure-Activity Relationship; Urokinase-Type Plasminogen Activator - antagonists & inhibitors; Human; u-Plasminogen activator; Serine endopeptidases; Enzyme; Nitrogen heterocycle; Active site; Benzene derivatives; Coagulation Factor Xa; Inhibitor enzyme complex; Binding site; In vitro; Modeling; Peptidases; Amidine; Structure activity relation; Molecular model; Bicyclic compound; Phenols; Hydrolases; Aromatic compound; Chemical synthesis
• ISSN: 0022-2623; 1520-4804
• DOI: 10.1021/jm0100638

Novel scaffolds that bind to serine proteases through a unique network of short hydrogen bonds to the catalytic Ser195 have been developed. The resulting potent serine protease inhibitors were designed from lead molecule 2-(2-hydroxyphenyl)1H-benzoimidazole-5-carboxamidine, 6b, which is known to display several modes of binding. For instance, 6b can recruit zinc and bind in a manner similar to that reported by bis(5-amidino-2-benzimidazolyl)methane (BABIM) (Nature 1998, 391, 608−612). Alternatively, 6b can bind in the absence of zinc through a multicentered network of short (<2.3 Å) hydrogen bonds. The lead structure was optimized in the zinc-independent binding mode toward a panel of six human serine proteases to yield optimized inhibitors such as 2-(3-bromo-2-hydroxy-5-methylphenyl)-1H-indole-5-carboxamidine, 22a, and 2-(2-hydroxybiphenyl-3-yl)-1H-indole-5-carboxamidine, 22f. Structure−activity relationships determined that, apart from the amidine function, an indole or benzimidazole and an ortho substituted phenol group were also essential components for optimal potency. The affinities (K i) of 22a and 22f, for example, bearing these groups ranged from 8 to 600 nM toward a panel of six human serine proteases. High-resolution crystal structures revealed that the binding mode of these molecules in several of the enzymes was identical to that of 6b and involved short (<2.3 Å) hydrogen bonds among the inhibitor hydroxyl oxygen, Ser195, and a water molecule trapped in the oxyanion hole. In summation, novel and potent trypsin-like serine protease inhibitors possessing a unique mode of binding have been discovered.