The Kynurenine Pathway and Kynurenine 3-Monooxygenase Inhibitors

Under normal physiological conditions, the kynurenine pathway (KP) plays a critical role in generating cellular energy and catabolizing tryptophan. Under inflammatory conditions, however, there is an upregulation of the KP enzymes, particularly kynurenine 3-monooxygenase (KMO). KMO has garnered much attention due to its production of toxic metabolites that have been implicated in many diseases and disorders. With many of these illnesses having an inadequate or modest treatment, there exists a need to develop KMO inhibitors that reduce the production of these toxic metabolites. Though prior efforts to find an appropriate KMO inhibitor were unpromising, the development of a KMO crystal structure has provided the opportunity for a rational structure-based design in the development of inhibitors. Therefore, the purpose of this review is to describe the kynurenine pathway, the kynurenine 3-monooxygenase enzyme, and KMO inhibitors and their potential candidacy for clinical use.

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The critical roles of histone deacetylase 3 in the pathogenesis of solid organ injury

Cell Death and Disease ◽

10.1038/s41419-021-04019-6 ◽

2021 ◽

Vol 12 (8) ◽

Author(s):

Li Ning ◽

Xiong Rui ◽

Wang Bo ◽

Geng Qing

Keyword(s):

Histone Deacetylase ◽

Chromatin Remodeling ◽

Current Knowledge ◽

Organ Injury ◽

Solid Organ ◽

Solid Organ Injury ◽

Histone Deacetylase 3 ◽

Physiological Conditions ◽

Inflammatory Conditions ◽

Therapeutic Value

AbstractHistone deacetylase 3 (HDAC3) plays a crucial role in chromatin remodeling, which, in turn, regulates gene transcription. Hence, HDAC3 has been implicated in various diseases, including ischemic injury, fibrosis, neurodegeneration, infections, and inflammatory conditions. In addition, HDAC3 plays vital roles under physiological conditions by regulating circadian rhythms, metabolism, and development. In this review, we summarize the current knowledge of the physiological functions of HDAC3 and its role in organ injury. We also discuss the therapeutic value of HDAC3 in various diseases.

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N-Terminomics Strategies for Protease Substrates Profiling

Molecules ◽

10.3390/molecules26154699 ◽

2021 ◽

Vol 26 (15) ◽

pp. 4699

Author(s):

Mubashir Mintoo ◽

Amritangshu Chakravarty ◽

Ronak Tilvawala

Keyword(s):

Mass Spectrometry ◽

Protease Activity ◽

Viral Infections ◽

Mass Spectrometry Analysis ◽

Post Translational Modification ◽

Spectrometry Analysis ◽

Physiological Conditions ◽

Inflammatory Conditions ◽

Biological Mixtures

Proteases play a central role in various biochemical pathways catalyzing and regulating key biological events. Proteases catalyze an irreversible post-translational modification called proteolysis by hydrolyzing peptide bonds in proteins. Given the destructive potential of proteolysis, protease activity is tightly regulated. Dysregulation of protease activity has been reported in numerous disease conditions, including cancers, neurodegenerative diseases, inflammatory conditions, cardiovascular diseases, and viral infections. The proteolytic profile of a cell, tissue, or organ is governed by protease activation, activity, and substrate specificity. Thus, identifying protease substrates and proteolytic events under physiological conditions can provide crucial information about how the change in protease regulation can alter the cellular proteolytic landscape. In recent years, mass spectrometry-based techniques called N-terminomics have become instrumental in identifying protease substrates from complex biological mixtures. N-terminomics employs the labeling and enrichment of native and neo-N-termini peptides, generated upon proteolysis followed by mass spectrometry analysis allowing protease substrate profiling directly from biological samples. In this review, we provide a brief overview of N-terminomics techniques, focusing on their strengths, weaknesses, limitations, and providing specific examples where they were successfully employed to identify protease substrates in vivo and under physiological conditions. In addition, we explore the current trends in the protease field and the potential for future developments.

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The Potential of Nail Mini-Organ Stem Cells in Skin, Nail and Digit Tips Regeneration

International Journal of Molecular Sciences ◽

10.3390/ijms22062864 ◽

2021 ◽

Vol 22 (6) ◽

pp. 2864

Author(s):

Anna Pulawska-Czub ◽

Tomasz D. Pieczonka ◽

Paula Mazurek ◽

Krzysztof Kobielak

Keyword(s):

Stem Cells ◽

Critical Role ◽

Nail Plate ◽

Molecular Characteristics ◽

Continuous Growth ◽

Physiological Conditions ◽

Morphogenetic Protein ◽

Slow Cycling ◽

Bifunctional Properties

Nails are highly keratinized skin appendages that exhibit continuous growth under physiological conditions and full regeneration upon removal. These mini-organs are maintained by two autonomous populations of skin stem cells. The fast-cycling, highly proliferative stem cells of the nail matrix (nail stem cells (NSCs)) predominantly replenish the nail plate. Furthermore, the slow-cycling population of the nail proximal fold (nail proximal fold stem cells (NPFSCs)) displays bifunctional properties by contributing to the peri-nail epidermis under the normal homeostasis and the nail structure upon injury. Here, we discuss nail mini-organ stem cells’ location and their role in skin and nail homeostasis and regeneration, emphasizing their importance to orchestrate the whole digit tip regeneration. Such endogenous regeneration capabilities are observed in rodents and primates. However, they are limited to the region adjacent to the nail’s proximal area, indicating the crucial role of nail mini-organ stem cells in digit restoration. Further, we explore the molecular characteristics of nail mini-organ stem cells and the critical role of the bone morphogenetic protein (BMP) and Wnt signaling pathways in homeostatic nail growth and digit restoration. Finally, we investigate the latest accomplishments in stimulating regenerative responses in regeneration-incompetent injuries. These pioneer results might open up new opportunities to overcome amputated mammalian digits and limbs’ regenerative failures in the future.

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Serendipitous crystallization and structure determination of bacterioferritin from Achromobacter

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x18009809 ◽

2018 ◽

Vol 74 (9) ◽

pp. 558-566

Author(s):

Abhisek Dwivedy ◽

Bhavya Jha ◽

Khundrakpam Herojit Singh ◽

Mohammed Ahmad ◽

Anam Ashraf ◽

...

Keyword(s):

Crystal Structure ◽

Iron Homeostasis ◽

Critical Role ◽

Porphyrin Ring ◽

Opportunistic Pathogens ◽

Complex Design ◽

Archaeal Species ◽

Ferroxidase Center ◽

Mycobacterial Protein

Bacterioferritins (Bfrs) are ferritin-like molecules with a hollow spherical 24-mer complex design that are unique to bacterial and archaeal species. They play a critical role in storing iron(III) within the complex at concentrations much higher than the feasible solubility limits of iron(III), thus maintaining iron homeostasis within cells. Here, the crystal structure of bacterioferritin from Achromobacter (Ach Bfr) that crystallized serendipitously during a crystallization attempt of an unrelated mycobacterial protein is reported at 1.95 Å resolution. Notably, Fe atoms were bound to the structure along with a porphyrin ring sandwiched between the subunits of a dimer. Furthermore, the dinuclear ferroxidase center of Ach Bfr has only a single iron bound, in contrast to the two Fe atoms in other Bfrs. The structure of Ach Bfr clearly demonstrates the substitution of a glutamate residue, which is involved in the interaction with the second Fe atom, by a threonine and the consequent absence of another Fe atom there. The iron at the dinuclear center has a tetravalent coordination, while a second iron with a hexavalent coordination was found within the porphyrin ring, generating a heme moiety. Achromobacter spp. are known opportunistic pathogens; this structure enhances the current understanding of their iron metabolism and regulation, and importantly will be useful in the design of small-molecule inhibitors against this protein through a structure-guided approach.

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Loss of Nckx3 Exacerbates Experimental DSS-Induced Colitis in Mice through p53/NF-κB Pathway

International Journal of Molecular Sciences ◽

10.3390/ijms22052645 ◽

2021 ◽

Vol 22 (5) ◽

pp. 2645

Author(s):

Dinh Nam Tran ◽

Seon Myeong Go ◽

Seon-Mi Park ◽

Eui-Man Jung ◽

Eui-Bae Jeung

Keyword(s):

Immune Response ◽

Cellular Proliferation ◽

Intestinal Inflammation ◽

Critical Role ◽

Experimental Colitis ◽

Innate Immune ◽

Inflammatory Conditions ◽

Bowel Diseases ◽

Inflammatory Bowel ◽

Microarray Analyses

Inflammatory bowel diseases (IBDs) comprises a range of chronic inflammatory conditions of the intestinal tract. The incidence and prevalence of IBDs are increasing worldwide, but the precise etiology of these diseases is not completely understood. Calcium signaling plays a regulatory role in cellular proliferation. Nckx3, a potassium-dependent Na+/Ca2+ exchanger, is not only expressed in the brain but also in the aortic, uterine, and intestinal tissues, which contain abundant smooth muscle cells. This study investigated the role of Nckx3 in intestinal inflammation. Microarray analyses revealed the upregulation of the innate immune response-associated genes in the duodenum of Nckx3 knockout (KO) mice. The Nckx3 KO mice also showed an increase in IBD- and tumorigenesis-related genes. Using dextran sodium sulfate (DSS)-induced experimental colitis mice models, the Nckx3 KO mice showed severe colitis. Furthermore, the pathways involving p53 and NF-κB signaling were significantly upregulated by the absence of Nckx3. Overall, Nckx3 plays a critical role in the innate immune and immune response and may be central to the pathogenesis of IBD.

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The structure of the metallo-β-lactamase VIM-2 in complex with a triazolylthioacetamide inhibitor

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x16016113 ◽

2016 ◽

Vol 72 (11) ◽

pp. 813-819 ◽

Cited By ~ 16

Author(s):

Tony Christopeit ◽

Ke-Wu Yang ◽

Shao-Kang Yang ◽

Hanna-Kirsti S. Leiros

Keyword(s):

Public Health ◽

Crystal Structure ◽

Active Site ◽

Drug Target ◽

Zinc Ions ◽

Clinical Use ◽

Global Public Health ◽

Promising Strategy ◽

Conserved Residue ◽

Substrate Spectrum

The increasing number of pathogens expressing metallo-β-lactamases (MBLs), and in this way achieving resistance to β-lactam antibiotics, is a significant threat to global public health. A promising strategy to treat such resistant pathogens is the co-administration of MBL inhibitors together with β-lactam antibiotics. However, an MBL inhibitor suitable for clinical use has not yet been identified. Verona integron-encoded metallo-β-lactamase 2 (VIM-2) is a widespread MBL with a broad substrate spectrum and hence is an interesting drug target for the treatment of β-lactam-resistant infections. In this study, three triazolylthioacetamides were tested as inhibitors of VIM-2. One of the tested compounds showed clear inhibition of VIM-2, with an IC50of 20 µM. The crystal structure of the inhibitor in complex with VIM-2 was obtained by DMSO-free co-crystallization and was solved at a resolution of 1.50 Å. To our knowledge, this is the first structure of a triazolylthioacetamide inhibitor in complex with an MBL. Analysis of the structure shows that the inhibitor binds to the two zinc ions in the active site of VIM-2 and revealed detailed information on the interactions involved. Furthermore, the crystal structure showed that binding of the inhibitor induced a conformational change of the conserved residue Trp87.

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Crystal structure of a tankyrase 1–telomere repeat factor 1 complex

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x16004131 ◽

2016 ◽

Vol 72 (4) ◽

pp. 320-327 ◽

Cited By ~ 9

Author(s):

Bo Li ◽

Ruihong Qiao ◽

Zhizhi Wang ◽

Weihong Zhou ◽

Xin Li ◽

...

Keyword(s):

Crystal Structure ◽

Large Scale ◽

Sparse Matrix ◽

Critical Role ◽

Three Dimensional ◽

Mitotic Cell ◽

Ankyrin Repeat ◽

Dimensional Structure ◽

Telomere Repeat ◽

Tankyrase 1

Telomere repeat factor 1 (TRF1) is a subunit of shelterin (also known as the telosome) and plays a critical role in inhibiting telomere elongation by telomerase. Tankyrase 1 (TNKS1) is a poly(ADP-ribose) polymerase that regulates the activity of TRF1 through poly(ADP-ribosyl)ation (PARylation). PARylation of TRF1 by TNKS1 leads to the release of TRF1 from telomeres and allows telomerase to access telomeres. The interaction between TRF1 and TNKS1 is thus important for telomere stability and the mitotic cell cycle. Here, the crystal structure of a complex between the N-terminal acidic domain of TRF1 (residues 1–55) and a fragment of TNKS1 covering the second and third ankyrin-repeat clusters (ARC2-3) is presented at 2.2 Å resolution. The TNKS1–TRF1 complex crystals were optimized using an `oriented rescreening' strategy, in which the initial crystallization condition was used as a guide for a second round of large-scale sparse-matrix screening. This crystallographic and biochemical analysis provides a better understanding of the TRF1–TNKS1 interaction and the three-dimensional structure of the ankyrin-repeat domain of TNKS.

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Abstract 47: FXR1 Regulates Inflammatory MRNA Stability and VSMC Proliferation by Modulation of HuR Activity

Arteriosclerosis Thrombosis and Vascular Biology ◽

10.1161/atvb.37.suppl_1.47 ◽

2017 ◽

Vol 37 (suppl_1) ◽

Author(s):

Allison Herman ◽

Ross England ◽

Dale Haines ◽

Sheri Kelemen ◽

Mitali Ray ◽

...

Keyword(s):

Mrna Stability ◽

Fragile X ◽

Vascular Inflammation ◽

Critical Role ◽

Vascular Diseases ◽

Muscle Cells ◽

Vsmc Proliferation ◽

Inflammatory Conditions ◽

Mass Spec ◽

Inflammatory Proteins

Vascular smooth muscle cells (VSMC) play a critical role in the etiology and progression of many vascular diseases including atherosclerosis and restenosis. Our laboratory has found that one anti-inflammatory interleukin, IL-19, is atheroprotective and can decrease vascular inflammation by reduction in mRNA stability of inflammatory transcripts by reduction of activity of HuR, an mRNA stability protein. HuR translocates from the nucleus to the cytoplasm where it recognizes AU-rich elements present almost exclusively in the 3’UTR of pro-inflammatory genes. Proteins and pathways which limit HuR translocation are understudied, but may reduce inflammatory mRNA stability. Using MASS SPEC to identify HuR-interacting proteins under different inflammatory conditions, we identified one protein, Fragile X-related protein (FXR1), which interacts with HuR in inflammatory, but not basal conditions, a novel interaction. FXR1 mRNA expression is enhanced in muscle cells, but nothing has been reported on expression of FXR1 in VSMC or function for FXR1 in vascular disease. The FXR1 promoter contains multiple cholesterol-response elements, and in this study we demonstrate that FXR1 expression is increased in injured arteries and TNFα and oxLDL stimulated human VSMC, but also by IL-19. RNA EMSA demonstrates that FXR1 directly interacts with ARE in 3’UTR. SiRNA knock down of FXR1 in VSMC increases stability of inflammatory mRNA and protein abundance as well as VSMC proliferation, while overexpression of FXR1 reduces both their abundance and stability in addition to reducing proliferation. Since FXR1 appears to be a novel repressor of inflammatory proteins, and is also induced by IL-19, our overall hypothesis is that FXR1 expression and HuR interaction is an inflammation responsive, counter-regulatory mechanism to reduce abundance of pro-inflammatory proteins and therefore reduce inflammation.

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Targeting G-quadruplexes in the rhinovirus genome by Pyridostatin inhibits uncoating 3 and highlights a critical role for sodium ions.

10.21203/rs.3.rs-646190/v2 ◽

2021 ◽

Author(s):

Antonio Real-Hohn ◽

Martin Groznica ◽

Georg Kontaxis ◽

Rong Zhu ◽

Otávio Chaves ◽

...

Keyword(s):

Common Cold ◽

Critical Role ◽

Sodium Ions ◽

Structural Elements ◽

Temperature Dependent ◽

Physiological Conditions ◽

Metastable Structures ◽

G Quadruplex ◽

The Common ◽

Secondary Structural Elements

Abstract The ~ 2.4 µm long rhinovirus ss(+)RNA genome consists of roughly 7,200 nucleotides. It is tightly folded to fit into the ~ 22 nm diameter void in the protein capsid. In addition to previously predicted secondary structural elements in the RNA, using the QGRS mapper, we revealed the presence of multiple quadruplex forming G-rich sequences (QGRS) in the RV-A, B, and C clades, with four of them being exquisitely conserved. The biophysical analyses of ribooligonucleotides corresponding to selected QGRS demonstrate G-quadruplex (GQ) formation in each instance and resulted in discovering another example of an unconventional, two-layer zero-nucleotide loop RNA GQ stable at physiological conditions. By exploiting the temperature-dependent viral breathing to allow diffusion of small compounds into the virion, we demonstrate that the GQ-binding compounds PhenDC3 and pyridostatin (PDS) uniquely interfere with viral uncoating. Remarkably, this inhibition was entirely prevented in the presence of K+ but not Na+, despite the higher GQ stabilising effect of K+. Based on virus thermostability studies combined with ultrastructural imaging of isolated viral RNA, we propose a mechanism where Na+ keeps the encapsidated genome loose, allowing its penetration by PDS to promote the transition of QGRS sequestered in alternative metastable structures into GQs. The resulting conformational change then materialises in a severely compromised RNA release from the proteinaceous shell. Targeting extracellularly circulating RVs with GQ-stabilisers might thus become a novel way of combating the common cold.

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