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Recently, we reported a general assay for enzyme catalysis based on the yeast three-hybrid assay, Chemical Complementation, which is intended to expand the range of chemical reactions to which directed evolution can be applied. Here, Chemical Complementation was applied to a glycosynthase derived from a retaining glycosidase, an important class of enzymes for carbohydrate synthesis. Using the yeast three-hybrid assay, the glycosynthase activity of the E197A mutant of the Cel7B from Humicola insolens was linked to transcription of a LEU2 reporter gene, making cell growth dependent on glycosynthase activity in the absence of leucine. Then the LEU2 selection was used to isolate the most active glycosynthase from a Glu197 saturation library, yielding an E197S Cel7B variant with a 5-fold increase in glycosynthase activity. These results not only establish Chemical Complementation as a platform for the directed evolution of glycosynthases, but also show the generality of this approach and the ease with which it can be applied to new chemical reactions.

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A novel series of RORγ inhibitors was identified starting with the HTS hit 1. After SAR investigation based on a prospective consideration of two drug-likeness metrics, ligand efficiency (LE) and fraction of sp 3 carbon atoms (Fsp 3 ), significant improvement of metabolic stability as well as reduction of CYP inhibition was observed, which finally led to discovery of a selective and orally efficacious RORγ inhibitor 3z.KEYWORDS: Th17, immunological diseases, nuclear receptor, RORγ, ligand efficiency (LE), fraction of sp 3 carbon atoms (Fsp 3 )T wo decades after the discovery of Th1 and Th2 cells, a third subset of T helper cells called Th17 cells was identified and has drawn considerable attention since it was suggested to play a central role in the pathogenesis of various autoimmune diseases such as psoriasis and rheumatoid arthritis. 1,2 Among several regulatory pathways in which Th17 development and function are involved, the one regulated by the nuclear receptor RORγ appears to be crucial for controlling the differentiation and function. 3 Given its validity as an emerging drug target for treatment of immunological diseases, many research groups have made significant efforts in the discovery of RORγ modulators in recent years. 4−19 Since starting our RORγ inhibitor program in 2003, we discovered several structurally diverse hits after a HTS campaign. 20 From these hits we selected compound 1 as the first hit-to-lead series for optimization. In addition to being reasonably potent against RORγ (hLUC EC 50 = 1.7 μM, FRET EC 50 = 0.85 μM), compound 1 also demonstrated >20-fold selectivity over five nuclear receptors (hRORα, hFXR, hRXRα, hPR, and hPPARγ) and was structurally unique in comparison to other nuclear receptor modulators. 16−18 However, this compound has several drawbacks. For example, the microsomal stability in liver microsomes is poor with only 18% remaining at 10 min in human liver microsomes. It also has a modest time-dependent human CYP3A4 inhibition (IC 50 = 4 μM) probably due to some reactive metabolites formed by the oxidation of 1. The ligand efficiency is only 0.25, far below the literature consensus value (0.30) for a drug-like molecule. 21 The concept of ligand efficiency (LE) was first introduced by Kuntz 22 and is widely accepted as a reliable index of drug-like qualities. 23 Improvement of LE inevitably results in lower molecular weight and higher potency. We reasoned that a strategy of increasing LE and lowering the lipophilicity should therefore significantly improve the drug-like properties of compound 1. In addition, compound 1 is a rather flat molecule with a fraction of saturated carbons (Fsp 3 ) of 0.24. Fsp 3 is a newer index representing drug-likeness. 24 Lovering et al. pointed out that a decrease of Fsp 3 value would result in an increased incidence of CYP inhibition. 25 The desired Fsp 3 value is over 0.47 according to the literature. 24 Thus, we considered that improvement of the poor Fsp 3 value of compound 1 would be a rational way to overcome the CYP inhibi...

DNA methylation is an important epigenetic modification involved in transcriptional regulation, nuclear organization, development, aging, and disease. Although DNA methyltransferases have been characterized, the mechanisms for DNA demethylation remain poorly understood. Using a cell-based reporter assay, we performed a functional genomics screen to identify genes involved in DNA demethylation. Here we show that RNF4 (RING finger protein 4), a SUMO-dependent ubiquitin E3-ligase previously implicated in maintaining genome stability, plays a key role in active DNA demethylation. RNF4 reactivates methylation-silenced reporters and promotes global DNA demethylation. Rnf4 deficiency is embryonic lethal with higher levels of methylation in genomic DNA. Mechanistic studies show that RNF4 interacts with and requires the base excision repair enzymes TDG and APE1 for active demethylation. This activity appears to occur by enhancing the enzymatic activities that repair DNA G:T mismatches generated from methylcytosine deamination. Collectively, our study reveals a unique function for RNF4, which may serve as a direct link between epigenetic DNA demethylation and DNA repair in mammalian cells.epigenetics | DNA repair | base excision repair D NA methylation plays important roles in transcriptional regulation, genomic imprinting, and mammalian development (1). Deregulation of this important epigenetic modification has been implicated in a number of diseases, including cancer and developmental defects (2). Methylation of DNA occurs at the 5 C position of the CpG dinucleotide and is mediated by DNA methyltransferases (DNMTs) (3). The de novo methyltransferases DNMT3a and DNMT3b are mainly responsible for introducing cytosine methylation at previously unmethylated CpG sites, whereas the maintenance methyltransferase DNMT1 copies preexisting methylation patterns into the newly synthesized DNA strand during DNA replication (4).Dynamic DNA methylation is critical during development (1, 5). Although maintenance and de novo methylation mediated by DNMTs are relatively well understood (4), the mechanisms of DNA demethylation are still elusive (6). Passive demethylation can occur through the inhibition of DNMT1 activity, causing a loss in the methylation pattern during DNA replication. Rapid genome-wide demethylation is observed during gametogenesis and postfertilization, suggesting an active demethylation mechanism independent of DNA replication. Recent studies have identified several factors that are involved in active DNA demethylation, including the activationinduced cytidine deaminase (AID), an enzyme catalyzing 5-methyl cytidine (m 5 C) deamination in single-stranded DNA to generate thymine and a G:T mismatch (7-9), and GADD45a, a nuclear protein involved in the maintenance of genomic stability and DNA repair (9-11). However, neither AID-nor Gadd45a-deficient mice (12, 13) exhibit catastrophic developmental defects (14, 15), suggesting other factors might be involved in the regulation of active DNA demethylation.In plants, genetic ...