Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 44
Filter
Add more filters










Publication year range
1.
J Med Chem ; 2024 May 28.
Article in English | MEDLINE | ID: mdl-38804039

ABSTRACT

We have previously described a new series of selective and orally available galectin-1 inhibitors resulting in the thiazole-containing glycomimetic GB1490. Here, we show that the introduction of polar substituents to the thiazole ring results in galectin-1-specific compounds with low nM affinities. X-ray structural analysis of a new ligand-galectin-1 complex shows changes in the binding mode and ligand-protein hydrogen bond interactions compared to the GB1490-galectin-1 complex. These new high affinity ligands were further optimized with respect to affinity and ADME properties resulting in the galectin-1-selective GB1908 (Kd galectin-1/3 0.057/6.0 µM). In vitro GB1908 inhibited galectin-1-induced apoptosis in Jurkat cells (IC50 = 850 nM). Pharmacokinetic experiments in mice revealed that a dose of 30 mg/kg b.i.d. results in free levels of GB1908 in plasma over galectin-1 Kd for 24 h. GB1908 dosed with this regimen reduced the growth of primary lung tumor LL/2 in a syngeneic mouse model.

2.
Nat Commun ; 15(1): 3408, 2024 Apr 22.
Article in English | MEDLINE | ID: mdl-38649351

ABSTRACT

De novo drug design aims to generate molecules from scratch that possess specific chemical and pharmacological properties. We present a computational approach utilizing interactome-based deep learning for ligand- and structure-based generation of drug-like molecules. This method capitalizes on the unique strengths of both graph neural networks and chemical language models, offering an alternative to the need for application-specific reinforcement, transfer, or few-shot learning. It enables the "zero-shot" construction of compound libraries tailored to possess specific bioactivity, synthesizability, and structural novelty. In order to proactively evaluate the deep interactome learning framework for protein structure-based drug design, potential new ligands targeting the binding site of the human peroxisome proliferator-activated receptor (PPAR) subtype gamma are generated. The top-ranking designs are chemically synthesized and computationally, biophysically, and biochemically characterized. Potent PPAR partial agonists are identified, demonstrating favorable activity and the desired selectivity profiles for both nuclear receptors and off-target interactions. Crystal structure determination of the ligand-receptor complex confirms the anticipated binding mode. This successful outcome positively advocates interactome-based de novo design for application in bioorganic and medicinal chemistry, enabling the creation of innovative bioactive molecules.


Subject(s)
Deep Learning , Drug Design , PPAR gamma , Humans , Ligands , PPAR gamma/metabolism , PPAR gamma/agonists , PPAR gamma/chemistry , Binding Sites , Protein Binding
3.
J Med Chem ; 66(24): 16980-16990, 2023 12 28.
Article in English | MEDLINE | ID: mdl-38059452

ABSTRACT

A new series of orally available α-d-galactopyranosides with high affinity and specificity toward galectin-1 have been discovered. High affinity and specificity were achieved by changing six-membered aryl-triazolyl substituents in a series of recently published galectin-3-selective α-d-thiogalactosides (e.g., GB1107 Kd galectin-1/3 3.7/0.037 µM) for five-membered heterocycles such as thiazoles. The in vitro pharmacokinetic properties were optimized, resulting in several galectin-1 inhibitors with favorable properties. One compound, GB1490 (Kd galectin-1/3 0.4/2.7 µM), was selected for further characterization toward a panel of galectins showing a selectivity of 6- to 320-fold dependent on galectin. The X-ray structure of GB1490 bound to galectin-1 reveals the compound bound in a single conformation in the carbohydrate binding site. GB1490 was shown to reverse galectin-1-induced apoptosis of Jurkat cells at low µM concentrations. No cell cytotoxicity was observed for GB1490 up to 90 µM in the A549 cells. In pharmacokinetic studies in mice, GB1490 showed high oral bioavailability (F% > 99%).


Subject(s)
Galectin 1 , Galectin 3 , Humans , Animals , Mice , Galectin 1/chemistry , Galectin 1/metabolism , Galectin 3/metabolism , Binding Sites , Carbohydrates/chemistry , Jurkat Cells
4.
J Emerg Manag ; 21(4): 287-300, 2023.
Article in English | MEDLINE | ID: mdl-37878400

ABSTRACT

Climate change is increasing the risk for extreme weather events such as heatwaves, including in northern countries like Sweden, which until recent years has had limited experiences of coping with extreme heat. Based on predictions that Sweden will be more frequently exposed to heatwaves in the future, it is imperative to increase the societal resilience and adaptation measures. This paper presents a qualitative interview study involving 19 participants and their experiences of caring for vulnerable people during the heatwave in 2018. The participants represent four different organizations (working directly or indirectly with vulnerable people) in two municipalities in Sweden, including preschools, homes for the elderly, homecare services, and care homes for people with functional impairments, which were all impacted during the heatwave. This study contributes new empirical insights about the heatwave in 2018 and, in particular, similarities and differences in both experiences and adaptation measures across the four organizations. The findings show how both staff and vulnerable people suffered from the consequences of heat which increased vulnerability, how some organizations lacked enough (qualified) staff to secure routines, and that few evaluations and formal changes were done after the heatwave.


Subject(s)
Climate Change , Hot Temperature , Child, Preschool , Humans , Aged , Sweden , Cities
5.
Cancer Immunol Immunother ; 72(12): 4145-4159, 2023 Dec.
Article in English | MEDLINE | ID: mdl-37796298

ABSTRACT

BACKGROUND: 4-1BB (CD137) is a co-stimulatory receptor highly expressed on tumor reactive effector T cells and NK cells, which upon stimulation prolongs persistence of tumor reactive effector T and NK cells within the tumor and induces long-lived memory T cells. 4-1BB agonistic antibodies have been shown to induce strong anti-tumor effects that synergize with immune checkpoint inhibitors. The first generation of 4-1BB agonists was, however, hampered by dose-limiting toxicities resulting in suboptimal dose levels or poor agonistic activity. METHODS: ATOR-1017 (evunzekibart), a second-generation Fc-gamma receptor conditional 4-1BB agonist in IgG4 format, was designed to overcome the limitations of the first generation of 4-1BB agonists, providing strong agonistic effect while minimizing systemic immune activation and risk of hepatoxicity. The epitope of ATOR-1017 was determined by X-ray crystallography, and the functional activity was assessed in vitro and in vivo as monotherapy or in combination with anti-PD1. RESULTS: ATOR-1017 binds to a unique epitope on 4-1BB enabling ATOR-1017 to activate T cells, including cells with an exhausted phenotype, and NK cells, in a cross-linking dependent, FcγR-conditional, manner. This translated into a tumor-directed and potent anti-tumor therapeutic effect in vivo, which was further enhanced with anti-PD-1 treatment. CONCLUSIONS: These preclinical data demonstrate a strong safety profile of ATOR-1017, together with its potent therapeutic effect as monotherapy and in combination with anti-PD1, supporting further clinical development of ATOR-1017.


Subject(s)
Neoplasms , T-Lymphocytes , Humans , Receptors, IgG , Antibodies, Monoclonal/therapeutic use , Tumor Necrosis Factor Receptor Superfamily, Member 9 , Epitopes
7.
Front Surg ; 10: 1209927, 2023.
Article in English | MEDLINE | ID: mdl-37465065

ABSTRACT

Purpose: To explore the clinical practice development of different surgical techniques when installing bone-anchored hearing implants and their associated trends in outcomes. Design: Retrospective study of 228 bone-anchored hearing implants in 200 patients, performed over a 10-year period between 2012 and 2022 in a referral hospital. Method: Real-world data of demography, etiology, surgical setup, complications, and audiological outcomes were collected. Eligibility criteria from clinical practice were applied. Results: The minimally invasive technique is associated with shorter surgery duration, 20 vs. 44 min as compared to a linear incision technique. The minimally invasive technique was also associated with a lower occurrence of complications when compared to linear incision techniques (intraoperative; 1.8% vs. 4.9%, postoperative; 49% vs. 66%). Most differences were seen in complications relating to skin and wound healing. Conclusion: Adoption of a minimally invasive surgical technique for the installations of bone-anchored hearing implants can reduce surgical complexity without compromising safety aspects or clinical benefits.

8.
Mol Cancer Ther ; 22(1): 89-101, 2023 01 03.
Article in English | MEDLINE | ID: mdl-36343381

ABSTRACT

4-1BB (CD137) is an activation-induced costimulatory receptor that regulates immune responses of activated CD8 T and natural killer cells, by enhancing proliferation, survival, cytolytic activity, and IFNγ production. The ability to induce potent antitumor activity by stimulating 4-1BB on tumor-specific cytotoxic T cells makes 4-1BB an attractive target for designing novel immuno-oncology therapeutics. To minimize systemic immune toxicities and enhance activity at the tumor site, we have developed a novel bispecific antibody that stimulates 4-1BB function when co-engaged with the tumor-associated antigen 5T4. ALG.APV-527 was built on the basis of the ADAPTIR bispecific platform with optimized binding domains to 4-1BB and 5T4 originating from the ALLIGATOR-GOLD human single-chain variable fragment library. The epitope of ALG.APV-527 was determined to be located at domain 1 and 2 on 4-1BB using X-ray crystallography. As shown in reporter and primary cell assays in vitro, ALG.APV-527 triggers dose-dependent 4-1BB activity mediated only by 5T4 crosslinking. In vivo, ALG.APV-527 demonstrates robust antitumor responses, by inhibiting growth of established tumors expressing human 5T4 followed by a long-lasting memory immune response. ALG.APV-527 has an antibody-like half-life in cynomolgus macaques and was well tolerated at 50.5 mg/kg. ALG.APV-527 is uniquely designed for 5T4-conditional 4-1BB-mediated antitumor activity with potential to minimize systemic immune activation and hepatotoxicity while providing efficacious tumor-specific responses in a range of 5T4-expressing tumor indications as shown by robust activity in preclinical in vitro and in vivo models. On the basis of the combined preclinical dataset, ALG.APV-527 has potential as a promising anticancer therapeutic for the treatment of 5T4-expressing tumors.


Subject(s)
Antibodies, Bispecific , Neoplasms , Single-Chain Antibodies , Humans , Antibodies, Bispecific/pharmacology , Antibodies, Bispecific/therapeutic use , Antigens, Neoplasm , T-Lymphocytes , Tumor Necrosis Factor Receptor Superfamily, Member 9 , 4-1BB Ligand/metabolism
9.
Acta Crystallogr D Struct Biol ; 78(Pt 11): 1384-1398, 2022 Nov 01.
Article in English | MEDLINE | ID: mdl-36322421

ABSTRACT

This study describes the structure of DNA polymerase I from Thermus phage G20c, termed PolI_G20c. This is the first structure of a DNA polymerase originating from a group of related thermophilic bacteriophages infecting Thermus thermophilus, including phages G20c, TSP4, P74-26, P23-45 and phiFA and the novel phage Tth15-6. Sequence and structural analysis of PolI_G20c revealed a 3'-5' exonuclease domain and a DNA polymerase domain, and activity screening confirmed that both domains were functional. No functional 5'-3' exonuclease domain was present. Structural analysis also revealed a novel specific structure motif, here termed SßαR, that was not previously identified in any polymerase belonging to the DNA polymerases I (or the DNA polymerase A family). The SßαR motif did not show any homology to the sequences or structures of known DNA polymerases. The exception was the sequence conservation of the residues in this motif in putative DNA polymerases encoded in the genomes of a group of thermophilic phages related to Thermus phage G20c. The structure of PolI_G20c was determined with the aid of another structure that was determined in parallel and was used as a model for molecular replacement. This other structure was of a 3'-5' exonuclease termed ExnV1. The cloned and expressed gene encoding ExnV1 was isolated from a thermophilic virus metagenome that was collected from several hot springs in Iceland. The structure of ExnV1, which contains the novel SßαR motif, was first determined to 2.19 Šresolution. With these data at hand, the structure of PolI_G20c was determined to 2.97 Šresolution. The structures of PolI_G20c and ExnV1 are most similar to those of the Klenow fragment of DNA polymerase I (PDB entry 2kzz) from Escherichia coli, DNA polymerase I from Geobacillus stearothermophilus (PDB entry 1knc) and Taq polymerase (PDB entry 1bgx) from Thermus aquaticus.


Subject(s)
Bacteriophages , DNA Polymerase I , DNA Polymerase I/chemistry , DNA Polymerase I/genetics , Phosphodiesterase I , Thermus , Taq Polymerase/chemistry , Escherichia coli
10.
Structure ; 30(8): 1055-1061.e7, 2022 08 04.
Article in English | MEDLINE | ID: mdl-35640615

ABSTRACT

SQSTM1/p62 is an autophagic receptor that plays a major role in mediating stress and innate immune responses. Preclinical studies identified p62 as a target of the prototype innate defense regulator (IDR); however, the molecular mechanism of this process remains unclear. Here, we describe the structural basis and biological consequences of the interaction of p62 with the next generation of IDRs, dusquetide. Both electrostatic and hydrophobic contacts drive the formation of the complex between dusquetide and the ZZ domain of p62. We show that dusquetide penetrates the cell membrane and associates with p62 in vivo. Dusquetide binding modulates the p62-RIP1 complex, increases p38 phosphorylation, and enhances CEBP/B expression without activating autophagy. Our findings provide molecular details underlying the IDR action that may help in the development of new strategies to pharmacologically target p62.


Subject(s)
Immunity, Innate , Oligopeptides , Autophagy , Oligopeptides/metabolism , Sequestosome-1 Protein/genetics , Sequestosome-1 Protein/metabolism
11.
Acta Crystallogr F Struct Biol Commun ; 78(Pt 4): 161-169, 2022 Apr 01.
Article in English | MEDLINE | ID: mdl-35400668

ABSTRACT

Salicylaldehyde dehydrogenase (SALD) catalyses the last reaction in the upper pathway of naphthalene degradation: the oxidation of salicylaldehyde to salicylate. This enzyme has been isolated and studied from a few organisms that belong to the betaproteobacteria and gammaproteobacteria, predominantly Pseudomonas putida. Furthermore, there is only one crystal structure of this enzyme, which was obtained from P. putida G7. Here, crystallographic studies and analysis of the crystal structure of an Alpine soil metagenome-derived SALD (SALDAP) from an alphaproteobacterium are presented. The SALDAP gene was discovered using gene-targeted sequence assembly and it was cloned into a pLATE51 vector. The recombinant protein was overexpressed in Escherichia coli BL21 (DE3) cells and the soluble protein was purified to homogeneity. The protein crystallized at 20°C and diffraction data from the crystals were collected at a resolution of 1.9 Å. The crystal belonged to the orthorhombic space group C2221, with unit-cell parameters a = 116.8, b = 121.7, c = 318.0 Å. Analysis of the crystal structure revealed its conformation to be similar to the organization of the aldehyde dehydrogenase superfamily with three domains: the catalytic, NAD+-binding and bridging domains. The crystal structure of NahF from P. putida G7 was found to be the best structural homologue of SALDAP, even though the enzymes share only 48% amino-acid identity. Interestingly, a carboxylic acid (protocatechuic acid) was found to be a putative ligand of the enzyme and differential scanning fluorimetry was employed to confirm ligand binding. These findings open up the possibility of studying the mechanism(s) of product inhibition and biocatalysis of carboxylic acids using this enzyme and other related aldehyde dehydrogenases.


Subject(s)
Metagenome , Soil , Aldehyde Oxidoreductases , Crystallization , Crystallography, X-Ray , Escherichia coli/genetics , Ligands
12.
Acta Crystallogr D Struct Biol ; 78(Pt 2): 212-227, 2022 Feb 01.
Article in English | MEDLINE | ID: mdl-35102887

ABSTRACT

This study describes the production, characterization and structure determination of a novel Holliday junction-resolving enzyme. The enzyme, termed Hjc_15-6, is encoded in the genome of phage Tth15-6, which infects Thermus thermophilus. Hjc_15-6 was heterologously produced in Escherichia coli and high yields of soluble and biologically active recombinant enzyme were obtained in both complex and defined media. Amino-acid sequence and structure comparison suggested that the enzyme belongs to a group of enzymes classified as archaeal Holliday junction-resolving enzymes, which are typically divalent metal ion-binding dimers that are able to cleave X-shaped dsDNA-Holliday junctions (Hjs). The crystal structure of Hjc_15-6 was determined to 2.5 Šresolution using the selenomethionine single-wavelength anomalous dispersion method. To our knowledge, this is the first crystal structure of an Hj-resolving enzyme originating from a bacteriophage that can be classified as an archaeal type of Hj-resolving enzyme. As such, it represents a new fold for Hj-resolving enzymes from phages. Characterization of the structure of Hjc_15-6 suggests that it may form a dimer, or even a homodimer of dimers, and activity studies show endonuclease activity towards Hjs. Furthermore, based on sequence analysis it is proposed that Hjc_15-6 has a three-part catalytic motif corresponding to E-SD-EVK, and this motif may be common among other Hj-resolving enzymes originating from thermophilic bacteriophages.


Subject(s)
Bacteriophages , DNA, Cruciform , Archaea/genetics , Archaea/metabolism , Bacteriophages/genetics , Bacteriophages/metabolism , Holliday Junction Resolvases/chemistry , Holliday Junction Resolvases/genetics , Holliday Junction Resolvases/metabolism , Thermus thermophilus
13.
iScience ; 25(1): 103590, 2022 Jan 21.
Article in English | MEDLINE | ID: mdl-35005539

ABSTRACT

The 30+ unique ligands of the TGFß family signal by forming complexes using different combinations of type I and type II receptors. Therapeutically, the extracellular domain of a single receptor fused to an Fc molecule can effectively neutralize subsets of ligands. Increased ligand specificity can be accomplished by using the extracellular domains of both the type I and type II receptor to mimic the naturally occurring signaling complex. Here, we report the structure of one "type II-type I-Fc" fusion, ActRIIB-Alk4-Fc, in complex with two TGFß family ligands, ActA, and GDF11, providing a snapshot of this therapeutic platform. The study reveals that extensive contacts are formed by both receptors, replicating the ternary signaling complex, despite the inherent low affinity of Alk4. Our study shows that low-affinity type I interactions support altered ligand specificity and can be visualized at the molecular level using this platform.

14.
ACS Med Chem Lett ; 12(11): 1745-1752, 2021 Nov 11.
Article in English | MEDLINE | ID: mdl-34795863

ABSTRACT

Galectin-8 is a carbohydrate-binding protein that plays a crucial role in tumor progression and metastasis, antibacterial autophagy, modulation of the immune system, and bone remodeling. The design, synthesis, and protein affinity evaluation of a set of C-3 substituted benzimidazole and quinoline d-galactal derivatives identified a d-galactal-benzimidazole hybrid as a selective ligand for the galectin-8 N-terminal domain (galectin-8N), with a K d of 48 µM and 15-fold selectivity over galectin-3 and even better selectivity over the other mammalian galectins. X-ray structural analysis of galectin-8N in complex with one benzimidazole- and one quinoline-galactal derivative at 1.52 and 2.1 Å together with molecular dynamics simulations and quantum mechanical calculations of galectin-8N in complex with the benzimidazole derivative revealed orbital overlap between a NH LUMO of Arg45 with electron rich HOMOs of the olefin and O4 of the d-galactal. Such overlap is hypothesized to contribute to the high affinity of the d-galactal-derived ligands for galectin-8N. A (3-(4,5-dimethylthiazol-2-yl)-5-(3- carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium) (MTS) assay evaluation of the d-galactal-benzimidazole hybrid and an analogous galactoside derivative on a panel of cell lines with MTS assay showed no effect on cell viability up to 100 µM concentration. A subsequent functional assay using the MDA-MB-231 cell line demonstrated that the d-galactal-benzimidazole hybrid and the analogous galactoside derivative reduced the secretion of the proinflammatory cytokines interleukin-6 (IL-6) and IL-8 in a dose-dependent manner. Therefore, these compounds represent potential probes for galectin-8N pharmacology investigations and possibly promising leads for the design and synthesis of potent and selective galectin-8 inhibitors as potential antitumor and anti-inflammatory agents.

15.
Eur J Med Chem ; 223: 113664, 2021 Nov 05.
Article in English | MEDLINE | ID: mdl-34225180

ABSTRACT

We have obtained the X-ray crystal structure of the galectin-8 N-terminal domain (galectin-8N) with a previously reported quinoline-galactoside ligand at a resolution of 1.6 Å. Based on this X-ray structure, a collection of galactosides derivatised at O3 with triazole, benzimidazole, benzothiazole, and benzoxazole moieties were designed and synthesised. This led to the discovery of a 3-O-(N-methylbenzimidazolylmethyl)-galactoside with a Kd of 1.8 µM for galectin-8N, the most potent selective synthetic galectin-8N ligand to date. Molecular dynamics simulations showed that benzimidazole-galactoside derivatives bind the non-conserved amino acid Gln47, accounting for the higher selectivity for galectin-8N. Galectin-8 is a carbohydrate-binding protein that plays a key role in pathological lymphangiogenesis, modulation of the immune system, and autophagy. Thus, the benzimidazole-derivatised galactosides represent promising compounds for studies of the pathological implications of galectin-8, as well as a starting point for the development of anti-tumour and anti-inflammatory therapeutics targeting galectin-8.


Subject(s)
Benzimidazoles/chemistry , Drug Design , Galactosides/chemistry , Galectins/chemistry , Benzimidazoles/metabolism , Binding Sites , Crystallography, X-Ray , Galactosides/metabolism , Galectins/genetics , Galectins/metabolism , Humans , Kinetics , Ligands , Molecular Dynamics Simulation , Protein Binding , Recombinant Proteins/biosynthesis , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , Structure-Activity Relationship , Thermodynamics
16.
FEMS Microbiol Lett ; 368(12)2021 06 24.
Article in English | MEDLINE | ID: mdl-34114607

ABSTRACT

The Virus-X-Viral Metagenomics for Innovation Value-project was a scientific expedition to explore and exploit uncharted territory of genetic diversity in extreme natural environments such as geothermal hot springs and deep-sea ocean ecosystems. Specifically, the project was set to analyse and exploit viral metagenomes with the ultimate goal of developing new gene products with high innovation value for applications in biotechnology, pharmaceutical, medical, and the life science sectors. Viral gene pool analysis is also essential to obtain fundamental insight into ecosystem dynamics and to investigate how viruses influence the evolution of microbes and multicellular organisms. The Virus-X Consortium, established in 2016, included experts from eight European countries. The unique approach based on high throughput bioinformatics technologies combined with structural and functional studies resulted in the development of a biodiscovery pipeline of significant capacity and scale. The activities within the Virus-X consortium cover the entire range from bioprospecting and methods development in bioinformatics to protein production and characterisation, with the final goal of translating our results into new products for the bioeconomy. The significant impact the consortium made in all of these areas was possible due to the successful cooperation between expert teams that worked together to solve a complex scientific problem using state-of-the-art technologies as well as developing novel tools to explore the virosphere, widely considered as the last great frontier of life.


Subject(s)
Genome, Viral/genetics , Metagenomics , Bioprospecting/organization & administration , Computational Biology , Databases, Genetic , Europe , Hydrothermal Vents/virology , Viral Proteins/chemistry , Viral Proteins/genetics , Viral Proteins/metabolism , Virome/genetics , Viruses/classification , Viruses/genetics
17.
Chembiochem ; 22(7): 1232-1242, 2021 04 06.
Article in English | MEDLINE | ID: mdl-33242357

ABSTRACT

Amine transaminases (ATAs) are used to synthesize enantiomerically pure amines, which are building blocks for pharmaceuticals and agrochemicals. R-selective ATAs belong to the fold type IV PLP-dependent enzymes, and different sequence-, structure- and substrate scope-based features have been identified in the past decade. However, our knowledge is still restricted due to the limited number of characterized (R)-ATAs, with additional bias towards fungal origin. We aimed to expand the toolbox of (R)-ATAs and contribute to the understanding of this enzyme subfamily. We identified and characterized four new (R)-ATAs. The ATA from Exophiala sideris contains a motif characteristic for d-ATAs, which was previously believed to be a disqualifying factor for (R)-ATA activity. The crystal structure of the ATA from Shinella is the first from a Gram-negative bacterium. The ATAs from Pseudonocardia acaciae and Tetrasphaera japonica are the first characterized (R)-ATAs with a shortened/missing N-terminal helix. The active-site charges vary significantly between the new and known ATAs, correlating with their diverging substrate scope.


Subject(s)
Transaminases/metabolism , Actinobacteria/enzymology , Amino Acid Sequence , Binding Sites , Biocatalysis , Catalytic Domain , Escherichia coli/metabolism , Exophiala/enzymology , Molecular Docking Simulation , Rhizobiaceae/enzymology , Sequence Alignment , Stereoisomerism , Substrate Specificity , Transaminases/chemistry , Transaminases/genetics
18.
J Biol Chem ; 295(52): 17935-17949, 2020 12 25.
Article in English | MEDLINE | ID: mdl-32900849

ABSTRACT

The tenovins are a frequently studied class of compounds capable of inhibiting sirtuin activity, which is thought to result in increased acetylation and protection of the tumor suppressor p53 from degradation. However, as we and other laboratories have shown previously, certain tenovins are also capable of inhibiting autophagic flux, demonstrating the ability of these compounds to engage with more than one target. In this study, we present two additional mechanisms by which tenovins are able to activate p53 and kill tumor cells in culture. These mechanisms are the inhibition of a key enzyme of the de novo pyrimidine synthesis pathway, dihydroorotate dehydrogenase (DHODH), and the blockage of uridine transport into cells. These findings hold a 3-fold significance: first, we demonstrate that tenovins, and perhaps other compounds that activate p53, may activate p53 by more than one mechanism; second, that work previously conducted with certain tenovins as SirT1 inhibitors should additionally be viewed through the lens of DHODH inhibition as this is a major contributor to the mechanism of action of the most widely used tenovins; and finally, that small changes in the structure of a small molecule can lead to a dramatic change in the target profile of the molecule even when the phenotypic readout remains static.


Subject(s)
Acetanilides/pharmacology , Enzyme Inhibitors/pharmacology , Neoplasms/drug therapy , Oxidoreductases Acting on CH-CH Group Donors/antagonists & inhibitors , Polypharmacology , Sirtuin 1/antagonists & inhibitors , Thiourea/analogs & derivatives , Tumor Suppressor Protein p53/metabolism , Autophagy , Cell Proliferation , Dihydroorotate Dehydrogenase , Humans , Neoplasms/metabolism , Neoplasms/pathology , Oxidoreductases Acting on CH-CH Group Donors/metabolism , Thiourea/pharmacology , Tumor Cells, Cultured , Tumor Suppressor Protein p53/genetics
19.
J Synchrotron Radiat ; 27(Pt 5): 1095-1102, 2020 Sep 01.
Article in English | MEDLINE | ID: mdl-32876583

ABSTRACT

Over the last decade, serial crystallography, a method to collect complete diffraction datasets from a large number of microcrystals delivered and exposed to an X-ray beam in random orientations at room temperature, has been successfully implemented at X-ray free-electron lasers and synchrotron radiation facility beamlines. This development relies on a growing variety of sample presentation methods, including different fixed target supports, injection methods using gas-dynamic virtual-nozzle injectors and high-viscosity extrusion injectors, and acoustic levitation of droplets, each with unique requirements. In comparison with X-ray free-electron lasers, increased beam time availability makes synchrotron facilities very attractive to perform serial synchrotron X-ray crystallography (SSX) experiments. Within this work, the possibilities to perform SSX at BioMAX, the first macromolecular crystallography beamline at  MAX IV Laboratory in Lund, Sweden, are described, together with case studies from the SSX user program: an implementation of a high-viscosity extrusion injector to perform room temperature serial crystallography at BioMAX using two solid supports - silicon nitride membranes (Silson, UK) and XtalTool (Jena Bioscience, Germany). Future perspectives for the dedicated serial crystallography beamline MicroMAX at MAX IV Laboratory, which will provide parallel and intense micrometre-sized X-ray beams, are discussed.


Subject(s)
Crystallography, X-Ray/instrumentation , Synchrotrons , Equipment Design , Laboratories , Silicon Compounds , Sweden , Temperature
20.
Int J Mol Sci ; 21(14)2020 Jul 11.
Article in English | MEDLINE | ID: mdl-32664473

ABSTRACT

Peptidoglycan hydrolytic enzymes are considered to be a promising alternative to conventional antibiotics in combating bacterial infections. To identify novel hydrolytic enzymes, we performed a database search with the sequences of two thermostable endolysins with high bactericidal activity, studied earlier in our laboratory. Both these enzymes originate from Thermus scotoductus bacteriophages MAT2119 and vB_Tsc2631. A lytic enzyme LysC from Clostridium intestinale URNW was found to have the highest amino acid sequence similarity to the bacteriophage proteins and was chosen for further analysis. The recombinant enzyme showed strong activity against its host bacteria C. intestinale, as well as against C. sporogenes, Bacillus cereus, Micrococcus luteus, and Staphylococcus aureus, on average causing a 5.12 ± 0.14 log reduction of viable S. aureus ATCC 25923 cells in a bactericidal assay. Crystallographic studies of the protein showed that the catalytic site of LysC contained a zinc atom coordinated by amino acid residues His50, His147, and Cys155, a feature characteristic for type 2 amidases. Surprisingly, neither of these residues, nor any other of the four conserved residues in the vicinity of the active site, His51, Thr52, Tyr76, and Thr153, were essential to maintain the antibacterial activity of LysC. Therefore, our attention was attracted to the intrinsically disordered and highly positively charged N-terminal region of the enzyme. Potential antibacterial activity of this part of the sequence, predicted by the Antimicrobial Sequence Scanning System, AMPA, was confirmed in our experimental studies; the truncated version of LysC (LysCΔ2-23) completely lacked antibacterial activity. Moreover, a synthetic peptide, which we termed Intestinalin, with a sequence identical to the first thirty amino acids of LysC, displayed substantial anti-staphylococcal activity with IC50 of 6 µg/mL (1.5 µM). This peptide was shown to have α-helical conformation in solution in the presence of detergents which is a common feature of amphipathic α-helical antimicrobial peptides.


Subject(s)
Bacterial Proteins/isolation & purification , Clostridium/enzymology , Endopeptidases/isolation & purification , Amino Acid Sequence , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/pharmacology , Bacteriophages/enzymology , Catalytic Domain , Computer Simulation , Conserved Sequence , Crystallography, X-Ray , Endopeptidases/chemistry , Endopeptidases/genetics , Endopeptidases/pharmacology , Hydrophobic and Hydrophilic Interactions , Inhibitory Concentration 50 , Microbial Sensitivity Tests , Models, Molecular , Mutagenesis, Site-Directed , Peptide Fragments/chemical synthesis , Peptide Fragments/pharmacology , Protein Conformation , Protein Domains , Recombinant Proteins/pharmacology , Sequence Alignment , Sequence Homology, Amino Acid , Staphylococcus aureus/drug effects , Viral Proteins/chemistry
SELECTION OF CITATIONS
SEARCH DETAIL
...