2CI0

High throughput screening and x-ray crystallography assisted evaluation of small molecule scaffolds for CYP51 inhibitors

Summary for 2CI0

• Entry DOI: 10.2210/pdb2ci0/pdb
• Related: 1E9X 1EA1 1H5Z 1U13 1X8V 2BZ9 2CIB
• Descriptor: CYTOCHROME P450 51, PROTOPORPHYRIN IX CONTAINING FE, (2R)-2-PHENYL-N-PYRIDIN-4-YLBUTANAMIDE, ... (4 entities in total)
• Functional Keywords: heme, heme lipid synthesis, metal-binding, monooxygenase, nadp, oxidoreductase, protein-inhibitor complex, steroid biosynthesis, sterol biosynthesis
• Biological source: MYCOBACTERIUM TUBERCULOSIS
• Total number of polymer chains: 1
• Total formula weight: 52334.07

Authors

Podust, L.M.,Kim, Y.,Yermalitskaya, L.V.,Von Kries, J.P.,Waterman, M.R. (deposition date: 2006-03-16, release date: 2007-07-03, Last modification date: 2023-12-13)

Primary citation

Podust, L.M.,Von Kries, J.P.,Eddine, A.N.,Kim, Y.,Yermalitskaya, L.V.,Kuehne, R.,Ouellet, H.,Warrier, T.,Altekoster, M.,Lee, J.-S.,Rademann, J.,Oschkinat, H.,Kaufmann, S.H.E.,Waterman, M.R.
Small Molecule Scaffolds for Cyp51 Inhibitors Identified by High Throughput Screening and Defined by X-Ray Crystallography
Antimicrob.Agents Chemother., 51:3915-, 2007

PubMed Abstract: Sterol 14alpha-demethylase (CYP51), a major checkpoint in membrane sterol biosynthesis, is a key target for fungal antibiotic therapy. We sought small organic molecules for lead candidate CYP51 inhibitors. The changes in CYP51 spectral properties following ligand binding make CYP51 a convenient target for high-throughput screening technologies. These changes are characteristic of either substrate binding (type I) or inhibitor binding (type II) in the active site. We screened a library of 20,000 organic molecules against Mycobacterium tuberculosis CYP51 (CYP51(Mt)), examined the top type I and type II binding hits for their inhibitory effects on M. tuberculosis in broth culture, and analyzed them spectrally for their ability to discriminate between CYP51(Mt) and two reference M. tuberculosis CYP proteins, CYP130 and CYP125. We determined the binding mode for one of the top type II hits, alpha-ethyl-N-4-pyridinyl-benzeneacetamide (EPBA), by solving the X-ray structure of the CYP51(Mt)-EPBA complex to a resolution of 1.53 A. EPBA binds coordinately to the heme iron in the CYP51(Mt) active site through a lone pair of nitrogen electrons and also through hydrogen bonds with residues H259 and Y76, which are invariable in the CYP51 family, and hydrophobic interactions in a phylum- and/or substrate-specific cavity of CYP51. We also identified a second compound with structural and binding properties similar to those of EPBA, 2-(benzo[d]-2,1,3-thiadiazole-4-sulfonyl)-2-amino-2-phenyl-N-(pyridinyl-4)-acetamide (BSPPA). The congruence between the geometries of EPBA and BSPPA and the CYP51 binding site singles out EPBA and BSPPA as lead candidate CYP51 inhibitors with optimization potential for efficient discrimination between host and pathogen enzymes.

PubMed: 17846131
DOI: 10.1128/AAC.00311-07

Experimental method

X-RAY DIFFRACTION (1.53 Å)