Supramolecular assembly of protein building blocks: from folding to function.

Several phenomena occurring throughout the life of living things start and end with proteins. Various proteins form one complex structure to control detailed reactions. In contrast, one protein forms various structures and implements other biological phenomena depending on the situation. The basic principle that forms these hierarchical structures is protein self-assembly. A single building block is sufficient to create homogeneous structures with complex shapes, such as rings, filaments, or containers. These assemblies are widely used in biology as they enable multivalent binding, ultra-sensitive regulation, and compartmentalization. Moreover, with advances in the computational design of protein folding and protein-protein interfaces, considerable progress has recently been made in the de novo design of protein assemblies. Our review presents a description of the components of supramolecular protein assembly and their application in understanding biological phenomena to therapeutics.

NFI-C Is Required for Epiphyseal Chondrocyte Proliferation during Postnatal Cartilage Development.

Stringent regulation of the chondrocyte cell cycle is required for endochondral bone formation. During the longitudinal growth of long bones, mesenchymal stem cells condense and differentiate into chondrocytes. Epiphyseal chondrocytes sequentially differentiate to form growth- plate cartilage, which is subsequently replaced with bone. Although the importance of nuclear factor 1C (Nfic) in hard tissue formation has been extensively studied, knowledge regarding its biological roles and molecular mechanisms in this process remains insufficient. Herein, we demonstrated that Nfic deficiency affects femoral growth-plate formation. Chondrocyte proliferation was downregulated and the number of apoptotic cell was increased in the growth plates of Nfic-/- mice. Further, the expression of the cell cycle inhibitor p21 was upregulated in the primary chondrocytes of Nfic-/- mice, whereas that of cyclin D1 was downregulated. Our findings suggest that Nfic may contribute to postnatal chondrocyte proliferation by inhibiting p21 expression and by increasing the stability of cyclin D1 protein.

Lipopeptide-Based Nanosome-Mediated Delivery of Hyperaccurate CRISPR/Cas9 Ribonucleoprotein for Gene Editing.

A transient cytosolic delivery system for accurate Cas9 ribonucleoprotein is a key factor for target specificity of the CRIPSR/Cas9 toolkit. Owing to the large size of the Cas9 protein and a long negative strand RNA, the development of the delivery system is still a major challenge. Here, a size-controlled lipopeptide-based nanosome system is reported, derived from the blood-brain barrier-permeable dNP2 peptide which is capable of delivering a hyperaccurate Cas9 ribonucleoprotein complex (HypaRNP) into human cells for gene editing. Each nanosome is capable of encapsulating and delivering ≈2 HypaRNP molecules into the cytoplasm, followed by nuclear localization at 4 h post-treatment without significant cytotoxicity. The HypaRNP thus efficiently enacts endogenous eGFP silencing and editing in human embryonic kidney cells (up to 27.6%) and glioblastoma (up to 19.7% frequency of modification). The lipopeptide-based nanosome system shows superior delivery efficiency, high controllability, and simplicity, thus providing biocompatibility and versatile platform approach for CRISPR-mediated transient gene editing applications.

Comparison of tooth movement and biological response in corticotomy and micro-osteoperforation in rabbits.

OBJECTIVE: The aim of this study was to evaluate the amount of tooth movement and histologic changes with different corticotomy designs and micro-osteoperforation in rabbits. METHODS: The sample consisted of 24 rabbits divided into three experimental groups (triangular corticotomy [TC] and indentation corticotomy [IC] with flap, and flapless micro-osteoperforations [MP]) and a control. A traction force of 100 cN was applied by connecting the first premolars to the incisors. The amount of tooth movement was measured. Kruskal-Wallis test was used to assess differences in tooth movement between the groups. Micro-computed tomography, hematoxylin and eosin staining, and tartrate-resistant acidic phosphatase (TRAP) analysis were performed. Analysis of variance was applied to assess differences in TRAP-positive osteoclast count between the groups. RESULTS: The amount of tooth movement increased by 46.5% and 32.0% in the IC and MP groups, respectively, while the bone fraction analysis showed 69.7% and 8.5% less mineralization compared to the control. There were no significant intergroup differences in the number of TRAP-positive osteoclasts. CONCLUSIONS: The micro-osteoperforation group showed no significant differences in the amount of tooth movement compared to the corticotomy groups, nor in the TRAP-positive osteoclast count compared to both corticotomy groups and control.

Drug repositioning for enzyme modulator based on human metabolite-likeness.

BACKGROUND: Recently, the metabolite-likeness of the drug space has emerged and has opened a new possibility for exploring human metabolite-like candidates in drug discovery. However, the applicability of metabolite-likeness in drug discovery has been largely unexplored. Moreover, there are no reports on its applications for the repositioning of drugs to possible enzyme modulators, although enzyme-drug relations could be directly inferred from the similarity relationships between enzyme's metabolites and drugs. METHODS: We constructed a drug-metabolite structural similarity matrix, which contains 1,861 FDA-approved drugs and 1,110 human intermediary metabolites scored with the Tanimoto similarity. To verify the metabolite-likeness measure for drug repositioning, we analyzed 17 known antimetabolite drugs that resemble the innate metabolites of their eleven target enzymes as the gold standard positives. Highly scored drugs were selected as possible modulators of enzymes for their corresponding metabolites. Then, we assessed the performance of metabolite-likeness with a receiver operating characteristic analysis and compared it with other drug-target prediction methods. We set the similarity threshold for drug repositioning candidates of new enzyme modulators based on maximization of the Youden's index. We also carried out literature surveys for supporting the drug repositioning results based on the metabolite-likeness. RESULTS: In this paper, we applied metabolite-likeness to repurpose FDA-approved drugs to disease-associated enzyme modulators that resemble human innate metabolites. All antimetabolite drugs were mapped with their known 11 target enzymes with statistically significant similarity values to the corresponding metabolites. The comparison with other drug-target prediction methods showed the higher performance of metabolite-likeness for predicting enzyme modulators. After that, the drugs scored higher than similarity score of 0.654 were selected as possible modulators of enzymes for their corresponding metabolites. In addition, we showed that drug repositioning results of 10 enzymes were concordant with the literature evidence. CONCLUSIONS: This study introduced a method to predict the repositioning of known drugs to possible modulators of disease associated enzymes using human metabolite-likeness. We demonstrated that this approach works correctly with known antimetabolite drugs and showed that the proposed method has better performance compared to other drug target prediction methods in terms of enzyme modulators prediction. This study as a proof-of-concept showed how to apply metabolite-likeness to drug repositioning as well as potential in further expansion as we acquire more disease associated metabolite-target protein relations.

Conditional Creation and Rescue of Nipbl-Deficiency in Mice Reveals Multiple Determinants of Risk for Congenital Heart Defects.

Elucidating the causes of congenital heart defects is made difficult by the complex morphogenesis of the mammalian heart, which takes place early in development, involves contributions from multiple germ layers, and is controlled by many genes. Here, we use a conditional/invertible genetic strategy to identify the cell lineage(s) responsible for the development of heart defects in a Nipbl-deficient mouse model of Cornelia de Lange Syndrome, in which global yet subtle transcriptional dysregulation leads to development of atrial septal defects (ASDs) at high frequency. Using an approach that allows for recombinase-mediated creation or rescue of Nipbl deficiency in different lineages, we uncover complex interactions between the cardiac mesoderm, endoderm, and the rest of the embryo, whereby the risk conferred by genetic abnormality in any one lineage is modified, in a surprisingly non-additive way, by the status of others. We argue that these results are best understood in the context of a model in which the risk of heart defects is associated with the adequacy of early progenitor cell populations relative to the sizes of the structures they must eventually form.

Dirhodium-catalyzed phenol and aniline oxidations with T-HYDRO. Substrate scope and mechanism of oxidation.

Dirhodium caprolactamate, Rh(2)(cap)(4), is a very efficient catalyst for the generation of the tert-butylperoxy radical from tert-butyl hydroperoxide, and the tert-butylperoxy radical is a highly effective oxidant for phenols and anilines. These reactions are performed with 70% aqueous tert-butyl hydroperoxide using dirhodium caprolactamate in amounts as low as 0.01 mol % to oxidize para-substituted phenols to 4-(tert-butyldioxy)cyclohexadienones. Although these transformations have normally been performed in halocarbon solvents, there is a significant rate enhancement when Rh(2)(cap)(4)-catalyzed phenol oxidations are performed in toluene or chlorobenzene. Electron-rich and electron-poor phenolic substrates undergo selective oxidation in good to excellent yields, but steric influences from bulky para substituents force oxidation onto the ortho position resulting in ortho-quinones. Comparative results with RuCl(2)(PPh(3))(3) and CuI are provided, and mechanistic comparisons are made between these catalysts that are based on diastereoselectivity (reactions with estrone), regioselectivity (reactions with p-tert-butylphenol), and chemoselectivity in the formation of 4-(tert-butyldioxy)cyclohexadienones. The data obtained are consistent with hydrogen atom abstraction by the tert-butylperoxy radical followed by radical combination between the phenoxy radical and the tert-butylperoxy radical. Under similar reaction conditions, para-substituted anilines are oxidized to nitroarenes in good yield, presumably through the corresponding nitrosoarene, and primary amines are oxidized to carbonyl compounds by TBHP in the presence of catalytic amounts of Rh(2)(cap)(4).

Allylic oxidations catalyzed by dirhodium caprolactamate via aqueous tert-butyl hydroperoxide: the role of the tert-butylperoxy radical.

Dirhodium(II) caprolactamate exhibits optimal efficiency for the production of the tert-butylperoxy radical, which is a selective reagent for hydrogen atom abstraction. These oxidation reactions occur with aqueous tert-butyl hydroperoxide (TBHP) without rapid hydrolysis of the caprolactamate ligands on dirhodium. Allylic oxidations of enones yield the corresponding enedione in moderate to high yields, and applications include allylic oxidations of steroidal enones. Although methylene oxidation to a ketone is more effective, methyl oxidation to a carboxylic acid can also be achieved. The superior efficiency of dirhodium(II) caprolactamate as a catalyst for allylic oxidations by TBHP (mol % of catalyst, % conversion) is described in comparative studies with other metal catalysts that are also reported to be effective for allylic oxidations. That different catalysts produce essentially the same mixture of products with the same relative yields suggests that the catalyst is not involved in product-forming steps. Mechanistic implications arising from studies of allylic oxidation with enones provide new insights into factors that control product formation. A previously undisclosed disproportionation pathway, catalyzed by the tert-butoxy radical, of mixed peroxides for the formation of ketone products via allylic oxidation has been uncovered.

Optimal TBHP allylic oxidation of Delta5-steroids catalyzed by dirhodium caprolactamate.

Dirhodium caprolactamate is the most efficient catalyst for the oxidation of Delta5-steroids to 7-keto-Delta5-steroids by 70% tert-butyl hydroperoxide in water (T-HYDRO). Isolated product yields range from 38 to 87%.

Oxidation of secondary amines catalyzed by dirhodium caprolactamate.

The dirhodium caprolactamate [Rh(2)(cap)(4)] catalyzed oxidation of secondary amines to imines by tert-butyl hydroperoxide (TBHP) occurs with high chemo- and regioselectivity.

Benzylic oxidation catalyzed by dirhodium(II,III) caprolactamate.

[reaction: see text] Dirhodium caprolactamate [Rh2(cap)4] is an effective catalyst for benzylic oxidation with tert-butyl hydroperoxide (TBHP) under mild conditions. Sodium bicarbonate is the optimal base additive for substrate conversion. Benzylic carbonyl compounds are readily obtained, and a formal synthesis of palmarumycin CP2 using this methodology is described.

Highly enantioselective copper-catalyzed conjugate addition of diethylzinc to nitroalkenes.

Copper-catalyzed asymmetric conjugate addition of diethylzinc to nitroalkenes using new chiral monodentate phosphoramidite ligands proceeds with high enantioselectivity up to 99% ee. [reaction: see text]

New biphenol-based, fine-tunable monodentate phosphoramidite ligands for catalytic asymmetric transformations.

Monodentate phosphoramidite ligands have been developed based on enantiopure 6,6'-dimethylbiphenols with axial chirality. These chiral ligands are easy to prepare and flexible for modifications. The fine-tuning capability of these ligands plays a significant role in achieving high enantioselectivity in the asymmetric hydroformylation of allyl cyanide and the conjugate addition of diethylzinc to cycloalkenones.