Structure-activity studies of oxazolidinone analogs as RNA-binding agents.

Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA.
Bioorganic & Medicinal Chemistry Letters (Impact Factor: 2.33). 08/2006; 16(13):3600-4. DOI: 10.1016/j.bmcl.2006.03.068
Source: PubMed

ABSTRACT We have synthesized and tested a series of novel 3,4,5-tri- and 4,5-disubstituted oxazolidinones for their ability to bind two structurally related T box antiterminator model RNAs. We have found that optimal binding selectivity is found in a small group of 4,5-disubstituted oxazolidinones.

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    ABSTRACT: Deprotonation thermochemistry of Oxazolidin-2-one (OXA), Oxazolidine-2-thione (OXA-S), and Oxazolidine-2-selone (OXA-Se) has been studied in order to find the most acidic site and relative acidities of these heterocyclics at various sites. The deprotonation enthalpies at MP2/6-311++G**//MP2/6-31+G* and B3LYP/6-31+G* levels, while the free energies for deprotonation process and pKa values at B3LYP/6-31+G* level both in gas and aqueous phase (using PCM continuum model) of the anions of the three heterocyclics have been computed at 298 K. Calculated aqueous phase pKa values of OXA vary by ~6–7 units from the experimental aqueous phase pKa values of OXA and its derivatives. The deprotonation at the nitrogen is favored in OXA over the carbon atoms in contrast to the OXA-S and OXA-Se where in the deprotonation at the carbon attached to the nitrogen is most preferred. Deprotonation at this carbon induces an important C–O bond rupture in OXA-S and OXA-Se promoting an energetically favored ring-opening process. The finding offers a rare case when C–H acidity is able to dominate over the N–H acidity. In order to explain the relative stabilities, relative acidities and deprotonation enthalpies various characteristics of these molecules as well as their anions such as molecular electrostatic potential surface (MEP), frontier molecular orbital (FMO) features, chemical hardness, softness have been governed. The three dimensional MEP maps and HOMO–LUMO orbitals encompassing these molecules yield a reliable relative stability and reactivity (in terms of acidity) map displaying the most probable regions for deprotonation. The differential distribution of the electrostatic potential over the neutral and anionic species of OXA, OXA-S, and OXA-Se molecules is authentically reflected by HOMO–LUMO orbitals and NBO charge distribution analysis. The lone pair occupancies, second order delocalization energies for orbital interactions and the distribution of atomic charges over the entire molecular framework as obtained from natural bond orbital (NBO) analysis are found to faithfully replicate the predictions from the MEP maps and HOMO–LUMO band gaps in respect of explaining the relative stabilities and acidities in most of the cases. Good linear correlations have been obtained between HOMO–LUMO gap and pKa values in the aqueous phase for OXA and OXA-S molecules.
    Structural Chemistry 08/2013; 25(4):1111-1132. DOI:10.1007/s11224-013-0382-2 · 1.90 Impact Factor
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    ABSTRACT: Riboswitches and other noncoding regulatory RNA are intriguing targets for the development of therapeutic agents. A significant challenge in the drug discovery process, however, is the identification of potent compounds that bind the target RNA specifically and disrupt its function. Essential to this process is an effectively designed cascade of screening assays. A screening cascade for identifying compounds that target the T box riboswitch antiterminator element is described. In the primary assays, moderate to higher throughput screening of compound libraries is achieved by combining the sensitivity of fluorescence techniques with functionally relevant assays. Active compounds are then validated and the binding to target RNA further characterized in secondary assays. The cascade of assays monitor ligand-induced changes in the steady-state fluorescence of an attached dye or internally incorporated 2-aminopurine; the fluorescence anisotropy of an RNA complex; and, the thermal denaturation fluorescence profile of a fluorophore-quencher labeled RNA. While the assays described have been developed for T box riboswitch-targeted drug discovery, the fluorescence methods and screening cascade design principles can be applied to drug discovery efforts targeted toward other medicinally relevant noncoding RNA. © 2015 Elsevier Inc. All rights reserved.