Discovery of Benzylpiperazine Derivatives as CNS-Penetrant and Selective Histone Deacetylase 6 Inhibitors.

Inhibition of histone deacetylase 6 (HDAC6) in the brain is a highly attractive therapeutic target for the treatment of neurodegenerative diseases. The low blood-brain barrier permeability of most known HDAC6 inhibitors, however, prevents their application as central nervous system (CNS) drugs. To overcome this problem, we designed and synthesized benzylpiperazine derivatives using a hybrid strategy of combining HDAC6 inhibitors and brain-penetrant histamine H receptor antagonists.

Mechanism-based inhibitors of SIRT2: structure-activity relationship, X-ray structures, target engagement, regulation of α-tubulin acetylation and inhibition of breast cancer cell migration.

Sirtuin 2 (SIRT2) is a protein deacylase enzyme that removes acetyl groups and longer chain acyl groups from post-translationally modified lysine residues. It affects diverse biological functions in the cell and has been considered a drug target in relation to both neurodegenerative diseases and cancer. Therefore, access to well-characterized and robust tool compounds is essential for the continued investigation of the complex functions of this enzyme.

A novel GSK3 inhibitor that promotes self-renewal in mouse embryonic stem cells.

Small molecules that regulate cell stemness have the potential to make a major contribution to regenerative medicine. In the course of screening for small molecules that affect stemness in mouse embryonic stem cells (mESCs), we discovered that NPD13432, an aurone derivative, promoted self-renewal of mESCs. Normally, mESCs start to differentiate upon withdrawal of 2i/LIF.

Opening the Selectivity Pocket in the Human Lysine Deacetylase Sirtuin2 - New Opportunities, New Questions.

Reversible lysine deacetylation is exerted by both zinc and NAD -dependent deacetylases. It is an important factor in epigenetic regulation and more generally in the posttranslational regulation of protein stability, association and activity. Some of these enzymes can also cleave off fatty acids or dicarboxylic acids from lysines in proteins.

Identification of a novel small molecule that inhibits deacetylase but not defatty-acylase reaction catalysed by SIRT2.

SIRT2 is a member of the human sirtuin family of proteins and possesses NAD-dependent lysine deacetylase/deacylase activity. SIRT2 has been implicated in carcinogenesis in various cancers including leukaemia and is considered an attractive target for cancer therapy. Here, we identified NPD11033, a selective small-molecule SIRT2 inhibitor, by a high-throughput screen using the RIKEN NPDepo chemical library.

Correction to: Halistanol sulfates I and J, new SIRT1-3 inhibitory steroid sulfates from a marine sponge of the genus Halichondria.

The original article can be found online at https://doi.org/10.1038/ja.

Halistanol sulfates I and J, new SIRT1-3 inhibitory steroid sulfates from a marine sponge of the genus Halichondria.

Two new analogs of halistanol sulfate (1) were isolated from a marine sponge Halichondria sp. collected at Hachijo-jima Island. Structures of these new halistanol sulfates I (2) and J (3) were elucidated by spectral analyses.

Chemical and structural biology of protein lysine deacetylases.

Histone acetylation is a reversible posttranslational modification that plays a fundamental role in regulating eukaryotic gene expression and chromatin structure/function. Key enzymes for removing acetyl groups from histones are metal (zinc)-dependent and NAD-dependent histone deacetylases (HDACs). The molecular function of HDACs have been extensively characterized by various approaches including chemical, molecular, and structural biology, which demonstrated that HDACs regulate cell proliferation, differentiation, and metabolic homeostasis, and that their alterations are deeply involved in various human disorders including cancer.

Kinetic and Structural Basis for Acyl-Group Selectivity and NAD(+) Dependence in Sirtuin-Catalyzed Deacylation.

Acylation of lysine is an important protein modification regulating diverse biological processes. It was recently demonstrated that members of the human Sirtuin family are capable of catalyzing long chain deacylation, in addition to the well-known NAD(+)-dependent deacetylation activity [Feldman, J. L.

Adaptive evolution of fish hatching enzyme: one amino acid substitution results in differential salt dependency of the enzyme.

Embryos of medaka Oryzias latipes hatch in freshwater, while those of killifish Fundulus heteroclitus hatch in brackish water. Medaka and Fundulus possess two kinds of hatching enzymes, high choriolytic enzyme (HCE) and low choriolytic enzyme (LCE), which cooperatively digest their egg envelope at the time of hatching. Optimal salinity of medaka HCE was found in 0 mol l(-1) NaCl, and activity decreased with increasing salt concentrations.

Structure of the histone chaperone CIA/ASF1-double bromodomain complex linking histone modifications and site-specific histone eviction.

Nucleosomes around the promoter region are disassembled for transcription in response to various signals, such as acetylation and methylation of histones. Although the interactions between histone-acetylation-recognizing bromodomains and factors involved in nucleosome disassembly have been reported, no structural basis connecting histone modifications and nucleosome disassembly has been obtained. Here, we determined at 3.

Crystal structures of the CERT START domain with inhibitors provide insights into the mechanism of ceramide transfer.

The cytosolic protein CERT transfers ceramide from the endoplasmic reticulum to the Golgi apparatus where ceramide is converted to SM. The C-terminal START (steroidogenic acute regulatory protein-related lipid transfer) domain of CERT binds one ceramide molecule in its central amphiphilic cavity. (1R,3R)-N-(3-Hydroxy-1-hydroxymethyl-3-phenylpropyl)alkanamide (HPA), a synthesized analogue of ceramide, inhibits ceramide transfer by CERT.

Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide.

In mammalian cells, ceramide is synthesized in the endoplasmic reticulum and transferred to the Golgi apparatus for conversion to sphingomyelin. Ceramide transport occurs in a nonvesicular manner and is mediated by CERT, a cytosolic 68-kDa protein with a C-terminal steroidogenic acute regulatory protein-related lipid transfer (START) domain. The CERT START domain efficiently transfers natural D-erythro-C16-ceramide, but not lipids with longer (C20) amide-acyl chains.

Development of an automated large-scale protein-crystallization and monitoring system for high-throughput protein-structure analyses.

Protein crystallization remains one of the bottlenecks in crystallographic analysis of macromolecules. An automated large-scale protein-crystallization system named PXS has been developed consisting of the following subsystems, which proceed in parallel under unified control software: dispensing precipitants and protein solutions, sealing crystallization plates, carrying robot, incubators, observation system and image-storage server. A sitting-drop crystallization plate specialized for PXS has also been designed and developed.

Crystal structures of the short-chain flavin reductase HpaC from Sulfolobus tokodaii strain 7 in its three states: NAD(P)(+)(-)free, NAD(+)(-)bound, and NADP(+)(-)bound.

4-Hydroxyphenylacetate (4-HPA) is oxidized as an energy source by two component enzymes, the large component (HpaB) and the small component (HpaC). HpaB is a 4-HPA monooxygenase that utilizes FADH(2) supplied by a flavin reductase HpaC. We determined the crystal structure of HpaC (ST0723) from the aerobic thermoacidophilic crenarchaeon Sulfolobus tokodaii strain 7 in its three states [NAD(P)(+)-free, NAD(+)-bound, and NADP(+)-bound].

Peripheral targets influence sensory-motor connectivity in the neonatal spinal cord: sciatic nerve axotomy in Bax-deficient mice.

In neonatal animals, peripheral nerve axotomy induces cell death in the corresponding dorsal root ganglion neurons and motoneurons, indicating that trophic interactions between these neurons and their targets control neuronal survival at this age. However, axotomy-induced cell death masks the role of peripheral tissues in regulating the central connections between these neurons in neonates. Since we have shown in Bax-deficient mice (Bax-/-) that transection of the sciatic nerve at postnatal day (P) 0 rarely induced apoptosis in motoneurons, we examined whether peripheral nerve axotomy eliminates synaptic connections between group Ia afferents and motoneurons in Bax-/-.

Crystallization and preliminary X-ray crystallographic analysis of peptide deformylase from Thermus thermophilus HB8.

Peptide deformylase (PDF) is responsible for cleaving the formyl group at the N-terminus of nascent polypeptide chains in eubacteria and is essential to bacterial cell viability. A recombinant PDF of the thermophilic bacterium Thermus thermophilus HB8 has been crystallized by the hanging-drop vapour-diffusion method using PEG 4000 as a precipitant. The crystals belonged to the tetragonal space group P4(1) or P4(3), with unit-cell parameters a = b = 62.

Cloning, purification, crystallization and preliminary crystallographic analysis of acylphosphatase from Pyrococcus horikoshii OT3.

Acylphosphatase is one of the smallest enzymes and catalyzes the hydrolysis of the carboxy-phosphate bond. An extremely thermostable acylphosphatase from a hyperthermophilic archaea, Pyrococcus horikoshii OT3, has been cloned, expressed in Escherichia coli, purified and crystallized using the sitting-drop vapour-diffusion method with potassium/sodium tartrate as the precipitant at pH 5.5.

Crystallization and preliminary X-ray analysis of HCE-1, a hatching enzyme of medaka fish, Oryzias latipes.

The hatching enzyme of medaka fish, high choriolytic enzyme (HCE-1; MW = 22.7 kDa), was crystallized by the hanging-drop vapour-diffusion method using PEG 10 000 as the precipitant. The hatching enzyme is a metalloproteinase which is secreted from the embryo at the time of hatching.

Rhythmic motor activity in thin transverse slice preparations of the fetal rat spinal cord.

Networks generating locomotor-like rhythmic motor activity are formed during the last week of the fetal period in the rat spinal cord. We investigated the coordinated rhythmic motor activity induced in transverse slice preparations of the lumbar spinal cord taken from fetal rats as early as embryonic day (E) 16.5.

Developmental changes in rhythmic spinal neuronal activity in the rat fetus.

In the developing rat spinal cord, formation and differentiation of the central pattern generator for locomotion occur during the prenatal period. Early on, excitatory synaptic transmission mediated by glycine receptors plays a leading role for rhythmogenesis, at a later stage, followed by glutamate-receptor-mediated synaptic transmission becoming dominant. The maturation of inhibitory circuitry in the spinal cord, mediated largely by glycinergic synapses, is crucial for the generation of alternating activity between left/right limbs and flexor/extensor muscles.

Runx3 is essential for the target-specific axon pathfinding of trkc-expressing dorsal root ganglion neurons.

Dorsal root ganglion (DRG) neurons project their axons to specific target layers in the gray matter of the spinal cord, according to their sensory modality (Neuron 30 (2001), 707; Cell 101 (2000), 485; Neuron 31 (2001), 59; J. Comp. Neurol.

Basis of changes in left-right coordination of rhythmic motor activity during development in the rat spinal cord.

The basic neuronal networks generating coordinated rhythmic motor activity, such as left-right alternate limb movement during locomotion in mammals, are located in the spinal cord. In rat fetuses, the spatial pattern of the rhythmic activity between the left and right sides is synchronous at and shortly after rhythmogenesis before the pattern becomes alternate by birth. The neuronal mechanisms underlying these developmental changes in the left-right coordination were examined in isolated spinal cord preparations.

The effects of sciatic nerve axotomy on spinal motoneurons in neonatal Bax-deficient mice.

During development, the survival of spinal motoneurons depends on the integrity of the connection to their peripheral targets. Peripheral nerve axotomy induces apoptosis in neonatal neurons supplying axons to the nerve. Bax is known to promote apoptosis among developing neurons.

Runx3 controls the axonal projection of proprioceptive dorsal root ganglion neurons.

Dorsal root ganglion (DRG) neurons specifically project axons to central and peripheral targets according to their sensory modality. The Runt-related genes Runx1 and Runx3 are expressed in DRG neuronal subpopulations, suggesting that they may regulate the trajectories of specific axons. Here we report that Runx3-deficient (Runx3(-/-)) mice displayed severe motor uncoordination and that few DRG neurons synthesized the proprioceptive neuronal marker parvalbumin.