PDBsum entry 1owe

Hydrolase

PDB id: 1owe

Contents

Protein chain

245 a.a. *

Ligands

SO4 ×3

675

Waters ×223

* Residue conservation analysis

PDB id:

1owe

Name:

Hydrolase

Title:

Substituted 2-naphthamidine inhibitors of urokinase

Structure:

Urokinase-type plasminogen activator. Chain: a. Fragment: residues 179-423. Synonym: upa, u-plasminogen activator. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: plau. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108.

Resolution:

1.60Å R-factor: 0.210 R-free: 0.236

Authors:

M.D.Wendt,T.W.Rockway,A.Geyer,W.Mcclellan,M.Weitzberg,X.Zhao, R.Mantei,V.L.Nienaber,K.Stewart,V.Klinghofer,V.L.Giranda

Key ref:

M.D.Wendt et al. (2004). Identification of novel binding interactions in the development of potent, selective 2-naphthamidine inhibitors of urokinase. Synthesis, structural analysis, and SAR of N-phenyl amide 6-substitution. J Med Chem, 47, 303-324. PubMed id: 14711304 DOI: 10.1021/jm0300072

Date:

28-Mar-03 Release date: 30-Sep-03

Protein chain

P00749  (UROK_HUMAN) -  Urokinase-type plasminogen activator from Homo sapiens

Seq: 431 a.a.

Struc: 245 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.4.21.73 - u-plasminogen activator.
• Reaction: Specific cleavage of Arg-|-Val bond in plasminogen to form plasmin.

DOI no: 10.1021/jm0300072

J Med Chem 47:303-324 (2004)

PubMed id: 14711304

Identification of novel binding interactions in the development of potent, selective 2-naphthamidine inhibitors of urokinase. Synthesis, structural analysis, and SAR of N-phenyl amide 6-substitution.

M.D.Wendt, T.W.Rockway, A.Geyer, W.McClellan, M.Weitzberg, X.Zhao, R.Mantei, V.L.Nienaber, K.Stewart, V.Klinghofer, V.L.Giranda.

ABSTRACT

The preparation and assessment of biological activity of 6-substituted 2-naphthamidine inhibitors of the serine protease urokinase plasminogen activator (uPA, or urokinase) is described. 2-Naphthamidine was chosen as a starting point based on synthetic considerations and on modeling of substituent vectors. Phenyl amides at the 6-position were found to improve binding; replacement of the amide with other two-atom linkers proved ineffective. The phenyl group itself is situated near the S1' subsite; substitutions off of the phenyl group accessed S1' and other distant binding regions. Three new points of interaction were defined and explored through ring substitution. A solvent-exposed salt bridge with the Asp60A carboxylate was formed using a 4-alkylamino group, improving affinity to K(i) = 40 nM. Inhibitors also accessed two hydrophobic regions. One interaction is characterized by a tight hydrophobic fit made with a small dimple largely defined by His57 and His99; a weaker, less specific interaction involves alkyl groups reaching into the broad prime-side protein binding region near Val41 and the Cys42-Cys58 disulfide, displacing water molecules and leading to small gains in activity. Many inhibitors accessed two of these three regions. Affinities range as low as K(i) = 6 nM, and many compounds had K(i) < 100 nM, while moderate to excellent selectivity was gained versus four of five members of a panel of relevant serine proteases. Also, some selectivity against trypsin was generated via the interaction with Asp60A. X-ray structures of many of these compounds were used to inform our inhibitor design and to increase our understanding of key interactions. In combination with our exploration of 8-substitution patterns, we have identified a number of novel binding interactions for uPA inhibitors.