No abstract

Macrocycles are of increasing interest as chemical probes and drugs for intractable targets like protein-protein interactions, but the determinants of their cell permeability and oral absorption are poorly understood. To enable rational design of cell-permeable macrocycles, we generated an extensive data set under consistent experimental conditions for more than 200 non-peptidic, de novo-designed macrocycles from the Broad Institute's diversity-oriented screening collection. This revealed how specific functional groups, substituents and molecular properties impact cell permeability. Analysis of energy-minimized structures for stereo- and regioisomeric sets provided fundamental insight into how dynamic, intramolecular interactions in the 3D conformations of macrocycles may be linked to physicochemical properties and permeability. Combined use of quantitative structure-permeability modeling and the procedure for conformational analysis now, for the first time, provides chemists with a rational approach to design cell-permeable non-peptidic macrocycles with potential for oral absorption.

New antibiotics with novel targets are greatly needed. Bacteria have numerous essential functions, but only a small fraction of such processes-primarily those involved in macromolecular synthesis-are inhibited by current drugs. Targeting metabolic enzymes has been the focus of recent interest, but effective inhibitors have been difficult to identify. We describe a synthetic azetidine derivative, BRD4592, that kills Mycobacterium tuberculosis (Mtb) through allosteric inhibition of tryptophan synthase (TrpAB), a previously untargeted, highly allosterically regulated enzyme. BRD4592 binds at the TrpAB α-β-subunit interface and affects multiple steps in the enzyme's overall reaction, resulting in inhibition not easily overcome by changes in metabolic environment. We show that TrpAB is required for the survival of Mtb and Mycobacterium marinum in vivo and that this requirement may be independent of an adaptive immune response. This work highlights the effectiveness of allosteric inhibition for targeting proteins that are naturally highly dynamic and that are essential in vivo, despite their apparent dispensability under in vitro conditions, and suggests a framework for the discovery of a next generation of allosteric inhibitors.

Despite being extensively characterized structurally and biochemically, the functional role of histone deacetylase 8 (HDAC8) has remained largely obscure due in part to a lack of known cellular substrates. Herein, we describe an unbiased approach using chemical tools in conjunction with sophisticated proteomics methods to identify novel non-histone nuclear substrates of HDAC8, including the tumor suppressor ARID1A. These newly discovered substrates of HDAC8 are involved in diverse biological processes including mitosis, transcription, chromatin remodeling, and RNA splicing and may help guide therapeutic strategies that target the function of HDAC8.

Modulation of histone deacetylase (HDAC) activity has been implicated as a potential therapeutic strategy for multiple diseases. However, it has been difficult to dissect the role of individual HDACs due to a lack of selective small-molecule inhibitors. Here, we report the synthesis of a series of highly potent and isoform-selective class I HDAC inhibitors, rationally designed by exploiting minimal structural changes to the clinically experienced HDAC inhibitor CI-994. We used this toolkit of isochemogenic or chemically matched inhibitors to probe the role of class I HDACs in β-cell pathobiology and demonstrate for the first time that selective inhibition of an individual HDAC isoform retains beneficial biological activity and mitigates mechanism-based toxicities. The highly selective HDAC3 inhibitor BRD3308 suppressed pancreatic β-cell apoptosis induced by inflammatory cytokines, as expected, or now glucolipotoxic stress, and increased functional insulin release. In addition, BRD3308 had no effect on human megakaryocyte differentiation, while inhibitors of HDAC1 and 2 were toxic. Our findings demonstrate that the selective inhibition of HDAC3 represents a potential path forward as a therapy to protect pancreatic β-cells from inflammatory cytokines and nutrient overload in diabetes.

A series of R-D-arabinofuranosyl oligosaccharides (2-8) that are fragments of the arabinan portions of two polysaccharides present in the cell wall of Mycobacterium tuberculosis have been synthesized. Preparation of the oligosaccharides involved the sequential addition of arabinofuranosyl residues from thioglycoside donors to methyl glycoside acceptors. High-resolution NMR studies on the final products provided all 3 J H,H values, which were in turn used in PSEUROT 6.2 calculations to determine both the identity and equilibrium populations of preferred conformers for each furanose ring in these glycans. Comparison of the ring conformers present in 2-8 with those available in the parent monosaccharide, methyl R-D-arabinofuranose (16), allowed the determination of the effect of glycosylation upon ring conformation. At equilibrium, 16 exists as an approximately equimolar mixture of O T 4 (North, N) and 2 T 3 (South, S) conformers. These studies showed that glycosylation of 16 at OH 5 resulted in no significant change in conformer identity or population relative to 16. However, glycosylation of OH 3 resulted in a change in the identity of the N species (to O E) and a significant favoring of this conformer at equilibrium. These trends were seen in all of the oligosaccharides. The populations of the three possible staggered rotamers (gg, gt, tg) about the C4-C5 bond were essentially the same for all residues in 2-8, and thus this equilibrium does not appear to be sensitive to glycosylation.

Kinetically selective inhibitors of HDAC2 enhanced learning and memory in a CK-p25 mouse model of neurodegeneration.

α-Santonin 1 is a naturally occurring sesquiterpene lactone of significant historical interest. Not only is its solid-state photochemistry the oldest documented for an organic compound, but it is also the first drug to have been formulated in the United States. Not surprisingly, while its photochemical behavior in solution has been relatively well-established, its solid-state photoreactivity has not been thoroughly characterized. In this communication, with a combination of polarizing microscopy, single-crystal X-ray diffraction, spectroscopic methods, chemical trapping, and product analyses, we have confirmed a remarkable sequence of events that includes three consecutive solid-state reactions. The first step is a remarkably phase-selective and site-specific single-crystal-to-single photorearrangement of 1 into the previously postulated cyclopentadienone intermediate 2. The second step is a highly stereoselective Diels−Alder reaction to form a transient topochemical dimer, and the third step is an intramolecular 2π + 2π photodimerization to form the cage dimer 4 as the final product. Cyclopentadienone 2 was characterized in situ by single-crystal X-ray diffraction analysis as well as by electronic and vibrational spectroscopies. The intermediate cyclopentadienone 2 was also trapped as the [4π + 2π] cycloadduct 8 by an interfacial solid−liquid reaction between a photoreacted sample and dimethyl acetylene dicarboxylate (DMAD).