1ZRB

Thrombin in complex with an azafluorenyl inhibitor 23b

Summary for 1ZRB

• Entry DOI: 10.2210/pdb1zrb/pdb
• Descriptor: thrombin, 11-peptide hirudin fragment, 3-AZA-9-HYDROXY-9-FLUORENYLCARBONYL-L-PROLYL-2-AMINOMETHYL-5-CHLOROBENZYLAMIDE, N-OXIDE, ... (4 entities in total)
• Functional Keywords: thrombin; thrombin inhibitor complex, blood clotting, hydrolase-inhibitor complex, hydrolase/inhibitor
• Biological source: Homo sapiens (human); More
• Cellular location: Secreted, extracellular space: P00734; Secreted: P28504
• Total number of polymer chains: 2
• Total formula weight: 35064.45

Authors

Stauffer, K.J.,Williams, P.D.,Selnick, H.G.,Nantermet, P.G.,Newton, C.L.,Homnick, C.F.,Zrada, M.M.,Lewis, S.D.,Lucas, B.J.,Krueger, J.A.,Pietrak, B.L.,Lyle, E.A.,Singh, R.,Miller-Stein, C.,White, R.B.,Wong, B.,Wallace, A.A.,Sitko, G.R.,Cook, J.J.,Holahan, M.A.,Stranieri-Michener, M.,Leonard, Y.M.,Lynch Jr., J.J.,McMasters, D.R.,Yan, Y. (deposition date: 2005-05-19, release date: 2005-06-07, Last modification date: 2024-10-30)

Primary citation

Stauffer, K.J.,Williams, P.D.,Selnick, H.G.,Nantermet, P.G.,Newton, C.L.,Homnick, C.F.,Zrada, M.M.,Lewis, S.D.,Lucas, B.J.,Krueger, J.A.,Pietrak, B.L.,Lyle, E.A.,Singh, R.,Miller-Stein, C.,White, R.B.,Wong, B.,Wallace, A.A.,Sitko, G.R.,Cook, J.J.,Holahan, M.A.,Stranieri-Michener, M.,Leonard, Y.M.,Lynch Jr., J.J.,McMasters, D.R.,Yan, Y.
9-hydroxyazafluorenes and their use in thrombin inhibitors
J.Med.Chem., 48:2282-2293, 2005

PubMed Abstract: Optimization of a previously reported thrombin inhibitor, 9-hydroxy-9-fluorenylcarbonyl-l-prolyl-trans-4-aminocyclohexylmethylamide (1), by replacing the aminocyclohexyl P1 group provided a new lead structure, 9-hydroxy-9-fluorenylcarbonyl-l-prolyl-2-aminomethyl-5-chlorobenzylamide (2), with improved potency (K(i) = 0.49 nM for human thrombin, 2x APTT = 0.37 microM in human plasma) and pharmacokinetic properties (F = 39%, iv T(1/2) = 13 h in dogs). An effective strategy for reducing plasma protein binding of 2 and improving efficacy in an in vivo thrombosis model in rats was to replace the lipophilic fluorenyl group in P3 with an azafluorenyl group. Systematic investigation of all possible azafluorenyl P3 isomers and azafluorenyl-N-oxide analogues of 2 led to the identification of an optimal compound, 3-aza-9-hydroxyfluoren-9(R)-ylcarbonyl-l-prolyl-2-aminomethyl-5-chlorobenzylamide (19b), with high potency (K(i) = 0.40 nM, 2x APTT = 0.18 microM), excellent pharmacokinetic properties (F = 55%, T(1/2) = 14 h in dogs), and complete efficacy in the in vivo thrombosis model in rats (inhibition of FeCl(3)-induced vessel occlusions in six of six rats receiving an intravenous infusion of 10 microg/kg/min of 19b). The stereochemistry of the azafluorenyl group in 19b was determined by X-ray crystallographic analysis of its N-oxide derivative (23b) bound in the active site of human thrombin.

PubMed: 15801822
DOI: 10.1021/jm049423s

Experimental method

X-RAY DIFFRACTION (1.9 Å)