4QIR

Crystal structure of Aminopeptidase N in complex with the phosphinic dipeptide analogue LL-(R,S)-2-(pyridin-3-yl)ethylGlyP[CH2]Phe

Summary for 4QIR

• Entry DOI: 10.2210/pdb4qir/pdb
• Related: 4PU2 4PVB 4PW4 4QHP 4QME 4QPE
• Descriptor: Aminopeptidase N, 3-{[(R)-1-amino-3-(pyridin-3-yl)propyl](hydroxy)phosphoryl}-(S)-2-benzylpropanoic acid, GLYCEROL, ... (7 entities in total)
• Functional Keywords: alanine aminopeptidase, aminopeptidase n, m1 family peptidases, 3-{[(r)-1-amino-3-(pyridin-3-yl)propyl](hydroxy)phosphoryl}-(s)-2-benzylpropanoic acid, hydrolase
• Biological source: Neisseria meningitidis MC58
• Total number of polymer chains: 1
• Total formula weight: 100108.11

Authors

Nocek, B.,Joachimiak, A.,Berlicki, L.,Vassiliou, S.,Mucha, A. (deposition date: 2014-06-01, release date: 2014-09-24, Last modification date: 2024-11-06)

Primary citation

Vassiliou, S.,Weglarz-Tomczak, E.,Berlicki, L.,Paweczak, M.,Nocek, B.,Mulligan, R.,Joachimiak, A.,Mucha, A.
Structure-guided, single-point modifications in the phosphinic dipeptide structure yield highly potent and selective inhibitors of neutral aminopeptidases.
J.Med.Chem., 57:8140-8151, 2014

PubMed Abstract: Seven crystal structures of alanyl aminopeptidase from Neisseria meningitides (the etiological agent of meningitis, NmAPN) complexed with organophosphorus compounds were resolved to determine the optimal inhibitor-enzyme interactions. The enantiomeric phosphonic acid analogs of Leu and hPhe, which correspond to the P1 amino acid residues of well-processed substrates, were used to assess the impact of the absolute configuration and the stereospecific hydrogen bond network formed between the aminophosphonate polar head and the active site residues on the binding affinity. For the hPhe analog, an imperfect stereochemical complementarity could be overcome by incorporating an appropriate P1 side chain. The constitution of P1'-extended structures was rationally designed and the lead, phosphinic dipeptide hPhePψ[CH2]Phe, was modified in a single position. Introducing a heteroatom/heteroatom-based fragment to either the P1 or P1' residue required new synthetic pathways. The compounds in the refined structure were low nanomolar and subnanomolar inhibitors of N. meningitides, porcine and human APNs, and the reference leucine aminopeptidase (LAP). The unnatural phosphinic dipeptide analogs exhibited a high affinity for monozinc APNs associated with a reasonable selectivity versus dizinc LAP. Another set of crystal structures containing the NmAPN dipeptide ligand were used to verify and to confirm the predicted binding modes; furthermore, novel contacts, which were promising for inhibitor development, were identified, including a π-π stacking interaction between a pyridine ring and Tyr372.

PubMed: 25192493
DOI: 10.1021/jm501071f

Experimental method

X-RAY DIFFRACTION (1.701 Å)