2P4J

Crystal structure of beta-secretase bond to an inhibitor with Isophthalamide Derivatives at P2-P3

Summary for 2P4J

• Entry DOI: 10.2210/pdb2p4j/pdb
• Descriptor: Beta-secretase 1, N-[(1S,2S,4R)-2-HYDROXY-1-ISOBUTYL-5-({(1S)-1-[(ISOPROPYLAMINO)CARBONYL]-2-METHYLPROPYL}AMINO)-4-METHYL-5-OXOPENTYL]-5-[METHYL(METHYLSULFONYL)AMINO]-N'-[(1R)-1-PHENYLETHYL]ISOPHTHALAMIDE (3 entities in total)
• Functional Keywords: beta-secretase, memapsin, bace, asp, aspartic protease, acid protease, alzheimer's disease, drug design, structure based drug design, hydrolase
• Biological source: Homo sapiens (human)
• Cellular location: Membrane; Single-pass type I membrane protein: P56817
• Total number of polymer chains: 4
• Total formula weight: 176058.88

Authors

Hong, L.,Ghosh, A.K.,Tang, J. (deposition date: 2007-03-12, release date: 2007-07-24, Last modification date: 2024-11-13)

Primary citation

Ghosh, A.K.,Kumaragurubaran, N.,Hong, L.,Kulkarni, S.S.,Xu, X.,Chang, W.,Weerasena, V.,Turner, R.,Koelsch, G.,Bilcer, G.,Tang, J.
Design, synthesis, and X-ray structure of potent memapsin 2 (beta-secretase) inhibitors with isophthalamide derivatives as the P2-P3-ligands.
J.Med.Chem., 50:2399-2407, 2007

PubMed Abstract: Structure-based design and synthesis of a number of potent and selective memapsin 2 inhibitors are described. These inhibitors were designed based upon the X-ray structure of memapsin 2-bound inhibitor 3 that incorporates methylsulfonyl alanine as the P2-ligand and a substituted pyrazole as the P3-ligand. Of particular importance, we examined the ability of the substituted isophthalic acid amide derivative to mimic the key interactions in the S2-S3 regions of the enzyme active sites of 3-bound memapsin 2. We investigated various substituted phenylethyl, alpha-methylbenzyl, and oxazolylmethyl groups as the P3-ligands. A number of inhibitors exhibited very potent inhibitory activity against mempasin 2 and good selectivity against memapsin 1. Inhibitor 5d has shown low nanomolar enzyme inhibitory potency (Ki=1.1 nM) and very good cellular inhibitory activity (IC50=39 nM). Furthermore, in a preliminary study, inhibitor 5d has shown 30% reduction of Abeta40 production in transgenic mice after a single intraperitoneal administration (8 mg/kg). A protein-ligand X-ray crystal structure of 5d-bound memapsin 2 provided vital molecular insight that can serve as an important guide to further design of novel inhibitors.

PubMed: 17432843
DOI: 10.1021/jm061338s

Experimental method

X-RAY DIFFRACTION (2.5 Å)