1OWH

Substituted 2-Naphthamidine Inhibitors of Urokinase

DOI: 10.2210/pdb1OWH/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2003-03-28 Released: 2003-09-30
Deposition Author(s): Wendt, M.D., Rockway, T.W., Geyer, A., McClellan, W., Weitzberg, M., Zhao, X., Mantei, R., Nienaber, V.L., Stewart, K., Klinghofer, V., Giranda, V.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free: 0.265
R-Value Work: 0.211
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

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.

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

(2004) J Med Chem 47: 303-324

PubMed: 14711304 Search on PubMed
DOI: 10.1021/jm0300072
Primary Citation of Related Structures:
1OWK, 1OWJ, 1OWI, 1OWH, 1OWE, 1OWD

PubMed 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.

Organizational Affiliation:

Cancer Research and Structural Biology, Global Pharmaceutical R & D, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, Illinois 60064-6101, USA. mike.d.wendt@abbott.com

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urokinase-type plasminogen activator	A	245	Homo sapiens	Mutation(s): 0 Gene Names: PLAU EC: 3.4.21.73
Find proteins for P00749 (Homo sapiens) Explore P00749 Go to UniProtKB: P00749
NIH Common Fund Data Resources
PHAROS: P00749 GTEx: ENSG00000122861
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
239 Query on 239 Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	6-[(Z)-AMINO(IMINO)METHYL]-N-[4-(AMINOMETHYL)PHENYL]-2-NAPHTHAMIDE C₁₉ H₁₈ N₄ O NLBDETRVUYOIHQ-UHFFFAOYSA-N		Ligand Interaction
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction