4HA5

Structure of BACE Bound to (S)-3-(5-(2-imino-1,4-dimethyl-6-oxohexahydropyrimidin-4-yl)thiophen-3-yl)benzonitrile

Summary for 4HA5

• Entry DOI: 10.2210/pdb4ha5/pdb
• Descriptor: Beta-secretase 1, L(+)-TARTARIC ACID, 3-{5-[(2E,4S)-2-imino-1,4-dimethyl-6-oxohexahydropyrimidin-4-yl]thiophen-3-yl}benzonitrile, ... (4 entities in total)
• Functional Keywords: bace1, alzheimers, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Homo sapiens (human)
• Cellular location: Membrane; Single-pass type I membrane protein: P56817
• Total number of polymer chains: 2
• Total formula weight: 93598.91

Authors

Strickland, C.,Mandal, M. (deposition date: 2012-09-25, release date: 2012-10-17, Last modification date: 2024-10-16)

Primary citation

Mandal, M.,Zhu, Z.,Cumming, J.N.,Liu, X.,Strickland, C.,Mazzola, R.D.,Caldwell, J.P.,Leach, P.,Grzelak, M.,Hyde, L.,Zhang, Q.,Terracina, G.,Zhang, L.,Chen, X.,Kuvelkar, R.,Kennedy, M.E.,Favreau, L.,Cox, K.,Orth, P.,Buevich, A.,Voigt, J.,Wang, H.,Kazakevich, I.,McKittrick, B.A.,Greenlee, W.,Parker, E.M.,Stamford, A.W.
Design and Validation of Bicyclic Iminopyrimidinones As Beta Amyloid Cleaving Enzyme-1 (BACE1) Inhibitors: Conformational Constraint to Favor a Bioactive Conformation.
J.Med.Chem., 55:9331-9345, 2012

PubMed Abstract: On the basis of our observation that the biaryl substituent of iminopyrimidinone 7 must be in a pseudoaxial conformation to occupy the contiguous S1-S3 subsites of BACE1, we have designed a novel fused bicyclic iminopyrimidinone scaffold intended to favor this bioactive conformation. Strategic incorporation of a nitrogen atom in the new constrained ring allowed us to develop SAR around the S2' binding pocket and ultimately resulted in analogues with low nanomolar potency for BACE1. In particular, optimization of the prime side substituent led to major improvements in potency by displacement of two conserved water molecules from a region near S2'. Further optimization of the pharmacokinetic properties of this fused pyrrolidine series, in conjunction with facile access to a rat pharmacodynamic model, led to identification of compound 43, which is an orally active, brain penetrant inhibitor that reduces Aβ(40) in the plasma, CSF, and cortex of rats in a dose-dependent manner.

PubMed: 22989333
DOI: 10.1021/jm301039c

Experimental method

X-RAY DIFFRACTION (1.83 Å)