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(12) Patent Application Publication (10) Pub. No.: US 2005/0118624 A1 Ma Et Al US 2005O118624A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2005/0118624 A1 Ma et al. (43) Pub. Date: Jun. 2, 2005 (54) FLUORESCENT PROBES FOR RIBOSOMES Related U.S. Application Data AND METHOD OF USE (60) Provisional application No. 60/508.401, filed on Oct. (75) Inventors: Zhenkun Ma, Dallas, TX (US); Jing 3, 2003. Li, Dallas, TX (US); In Ho Kim, Irving, TX (US); Yafei Jin, Dallas, TX Publication Classification (US); Anthony Simon Lynch, Dallas, TX (US); Eric Roche, Carrollton, TX (51) Int. Cl. ............................ C12O 1/68; CO7H 17/08; (US); Doug Beeman, Dallas, TX (US) CO7H 21/04 (52) U.S. Cl. ......................... 435/6; 536/24.1; 536/25.32; Correspondence Address: 544/229; 544/230; 536/7.1 JACKSON WALKER LLP SSNETH CENTRAL EXPRESSWAY (57) ABSTRACT RICHARDSON, TX 75080 (US) Fluorescent probes that have binding- affinity to ribosomes. (73) Assignee: Cumbre Inc., Dallas, TX The fluorescent probes are useful tools for identifying small molecules that bind to the 50S or 30S subunits of the (21) Appl. No.: 10/954,996 bacterial and other ribosomes and Serve as novel ribosome inhibitors. These probes are also useful for determining the (22) Filed: Sep. 30, 2004 interactions between a specific ligand and the ribosome. Patent Application Publication Jun. 2, 2005 Sheet 1 of 39 US 2005/0118624 A1 1. 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CO er en Od R O A. ef O en CD R O A. US 2005/0118624 A1 Jun. 2, 2005 FLUORESCENT PROBES FOR RIBOSOMES AND fluorescent probes are useful for the identification of novel METHOD OF USE ribosome ligands that competitively or allosterically replace the fluorescent probes bound to the bacterial ribosome. The 0001. This application claims priority to U.S. Provisional fluorescent probes of the current invention cover various Patent Application, Ser. No. 60/508,401, entitled “Fluores Specific antibiotic binding Sites of bacterial ribosomes and cent Probes for Ribosomes and Method of Use' filed on Oct. allow for the rapid identification of Small molecule leads as 3, 2003, the entire content of which is hereby incorporated potential Starting points for the development of novel anti by reference. microbial agents. In addition, this methodology provides important binding and mechanistic information that allows BACKGROUND for rapid advancement of the initial leads through Structure 0002 The present invention is related to fluorescent based design and optimization. Multiple probes have been probes having high binding affinity to ribosomes and their prepared and optimized for their ribosome binding affinity. uses. The fluorescent probes of this invention are useful The ligands identified by this assay interact with or disturb tools for identifying small molecules that bind to the 50S or important drug binding Sites and are likely to be effective 30S subunits of the bacterial ribosome and serve as novel and selective inhibitors of the ribosome. This assay format ribosome inhibitors. These probes are also useful for deter reduces the number of promiscuous hits due to aggregation mining the interactions between a specific ligand and the or low solubility. The binding site information associated ribosome. with the leads is immediately available and is useful for 0.003 Antibiotics are commonly utilized to fight a variety Structure-based drug design and optimization. of microbial infections. However, many clinically important 0006 Fluorescence polarization competition assays are Strains of bacteria have become resistant to one or more utilized for the study of DNA-DNA, DNA-RNA, DNA classes of the available antibiotics. Novel antimicrobial protein, RNA-protein, protein-protein, and Small molecule agents with activity against these resistant organisms are protein interactions. Fluorescence polarization competition needed for the effective management of resistant microbial assays are also used for Screening Small molecules that infections. Although not wanting to be bound by theory, the inhibit ligand-receptor interactions (Huang, X. J. Biomo bacterial ribosome is one of the most important targets for lecular Screening, 2003, 8, 34-38. Also see Panvera Fluo both naturally occurring and Synthetic antibiotics. Conse rescence Polarization Guide, Third Edition, and references quently, the antibiotics that target the bacterial ribosome are therein). used widely in clinical settings for the treatment of bacterial infections (Chopra, I, Expert Opinion of Investigational 0007 A fluorescent probe based on pleuromutilin is Drugs, 1998, 7, 1237-1244). Examples of naturally occur reported for Screening of ribosome ligands of that specific ring antibiotics or their derivatives targeting the bacterial binding site (Turconi, S., et al. J. Biomolecular Screening, ribosome are the macrollide class, chloramphenicol, clinda 2001, 6, 275-290; Hunt, E. Drugs of the Future, 2000, 25, mycin, the tetracycline class, Spectinomycin, Streptomycin, 1163-1168). The screening was done at low compound the aminoglycoside class and amikacin. Currently, the concentration (10 um, detecting only molecules with bind Oxazolidinone class is the only Synthetic ribosome inhibitor ing constants <4 uM) and in 1% DMSO limiting the solu used clinically. The binding Sites of ribosome antibiotics are bility of detectable compounds. broadly distributed between the 30S and 50S subunits of the 0008 Aminoglycoside-based fluorescent probes are pre ribosome and these antibiotics exert their antibacterial pared to study the binding between aminoglycosides and effects by a variety of mechanisms. In addition, ribosome RNA molecules rather than the ribosome itself (Rando, R. antibioticS exhibit low frequency of mutational resistance R., et al, Biochemistry, 1996, 35, 12338-12346; Biochem against various pathogenic bacteria. The proven druggability istry, 1997, 36, 768-779; Bioorganic and Medicinal Chem of the ribosome, the high number of available binding sites istry Letters, 2002, 12, 2241-2244).
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