2R9X

AmpC beta-lactamase with bound Phthalamide inhibitor

Summary for 2R9X

• Entry DOI: 10.2210/pdb2r9x/pdb
• Related: 2PU2 2R9W
• Descriptor: Beta-lactamase, PHOSPHATE ION, 2-[(1R)-2-carboxy-1-(naphthalen-1-ylmethyl)ethyl]-1,3-dioxo-2,3-dihydro-1H-isoindole-5-carboxylic acid, ... (5 entities in total)
• Functional Keywords: ampc beta-lactamase, pthalamide, antibiotic resistance, hydrolase
• Biological source: Escherichia coli
• Cellular location: Periplasm: P00811
• Total number of polymer chains: 2
• Total formula weight: 80915.48

Authors

Babaoglu, K.,Shoichet, B.K. (deposition date: 2007-09-13, release date: 2008-04-15, Last modification date: 2024-02-21)

Primary citation

Babaoglu, K.,Simeonov, A.,Irwin, J.J.,Nelson, M.E.,Feng, B.,Thomas, C.J.,Cancian, L.,Costi, M.P.,Maltby, D.A.,Jadhav, A.,Inglese, J.,Austin, C.P.,Shoichet, B.K.
Comprehensive mechanistic analysis of hits from high-throughput and docking screens against beta-lactamase.
J.Med.Chem., 51:2502-2511, 2008

PubMed Abstract: High-throughput screening (HTS) is widely used in drug discovery. Especially for screens of unbiased libraries, false positives can dominate "hit lists"; their origins are much debated. Here we determine the mechanism of every active hit from a screen of 70,563 unbiased molecules against beta-lactamase using quantitative HTS (qHTS). Of the 1,274 initial inhibitors, 95% were detergent-sensitive and were classified as aggregators. Among the 70 remaining were 25 potent, covalent-acting beta-lactams. Mass spectra, counter-screens, and crystallography identified 12 as promiscuous covalent inhibitors. The remaining 33 were either aggregators or irreproducible. No specific reversible inhibitors were found. We turned to molecular docking to prioritize molecules from the same library for testing at higher concentrations. Of 16 tested, 2 were modest inhibitors. Subsequent X-ray structures corresponded to the docking prediction. Analog synthesis improved affinity to 8 microM. These results suggest that it may be the physical behavior of organic molecules, not their reactivity, that accounts for most screening artifacts. Structure-based methods may prioritize weak-but-novel chemotypes in unbiased library screens.

PubMed: 18333608
DOI: 10.1021/jm701500e

Experimental method

X-RAY DIFFRACTION (1.9 Å)