scholarly journals Crystal structures of the σ2 receptor template large-library docking for selective chemotypes active in vivo

2021 ◽  
Author(s):  
Assaf Alon ◽  
Jiankun Lyu ◽  
Joao M. Braz ◽  
Tia A. Tummino ◽  
Veronica Craik ◽  
...  
Keyword(s):  
Neuropathic Pain ◽  
Crystal Structures ◽  
Large Scale ◽  
Protein Structures ◽  
Biologically Active ◽  
Drug Candidate ◽  
Binding Affinities ◽  
Injury Model ◽  
Selective Ligand

The σ2 receptor is a poorly understood transmembrane receptor that has attracted intense interest in many areas of biology including cancer imaging, Alzheimer's disease, schizophrenia, and neuropathic pain. However, little is known regarding the molecular details of the receptor, and few highly selective ligands are available. Here, we report the crystal structure of the σ2 receptor in complex with the clinical drug candidate roluperidone and the probe compound PB28. These structures, in turn, templated a large-scale docking screen of 490 million make-on-demand molecules. Of these, 484 compounds were synthesized and tested, prioritizing not only high-ranking docked molecules, but also those with mediocre and poor scores. Overall, 127 compounds with binding affinities superior to 1 μM were identified, all in new chemotypes, 31 of which had affinities superior to 50 nM. Intriguingly, hit rate fell smoothly and monotonically with docking score. Seeking to develop selective and biologically active probe molecules, we optimized three of the original docking hits for potency and for selectivity, achieving affinities in the 3 to 48 nM range and to up to 250-fold selectivity vs. the σ1 receptor. Crystal structures of the newly discovered ligands bound to the σ2 receptor were subsequently determined, confirming the docked poses. To investigate the contribution of the σ2 receptor in pain processing, and to distinguish it from the contribution of the σ1 receptor, two potent σ2-selective and one potent σ1/σ2 non-selective ligand were tested for efficacy in a mouse model of neuropathic pain. All three ligands demonstrated time-dependent decreases in mechanical hypersensitivity in the spared nerve injury model, supporting a role for the σ2 receptor in nociception, and a possible role for σ1/σ2 polypharmacology. This study illustrates the opportunities for rapid discovery of in vivo active and selective probes to study under-explored areas of biology using structure-based screens of diverse, ultra-large libraries following the elucidation of protein structures.

scholarly journals Biologically active recombinant carp LH as a spawning-inducing agent for carp

2017 ◽  
Vol 232 (3) ◽  
pp. 391-402 ◽  
Author(s):  
Joseph Aizen ◽  
Lian Hollander-Cohen ◽  
Michal Shpilman ◽  
Berta Levavi-Sivan
Keyword(s):  
Large Scale ◽  
Biological Response ◽  
Biologically Active ◽  
Dopamine Antagonist ◽  
Dependent Manner ◽  
Single Chain ◽  
Terminal Part ◽  
Α Subunit ◽  
Subsequent Decrease

Currently, spawning is induced in carp species by carp pituitary extract (CPE) and a combination of synthetic agonist of GnRH combined with a dopamine antagonist. The main goal of this study was the production of recombinant gonadotropins (GtHs) on a large scale to serve as an alternative to currently used agents. We produced carp (c) recombinant (r) Lh as a single chain in the methylotrophic yeast Pichia pastoris. Lha subunit was joined with Lhb subunit with a flexible linker of three glycine–serine repeats and six Histidines to form a mature protein, the β-subunit formed the N-terminal part and the α-subunit formed the C-terminal part. The ability of the rcLh to elicit biological response was tested by in vivo stimulation of estradiol (E2) and 17α,20β-dihydroxy-4-pregnen-3-one (DHP) and by its in vivo potency to induce ovulation and spawning induction. rcLh tested in this work significantly enhanced both E2 and DHP secretion in a dose-dependent manner similar to the results obtained with CPE. E2 levels showed a moderate rise following the priming injection and a subsequent decrease during the rest of the trial. DHP levels were only increased after the resolving injection, approximately 5 h before spawning. At the highest dose of rcLh (350 µg/kg BW), the recombinant protein was more efficient than CPE in terms of both spawning success and fertilization rate. It is shown here that rcLh can elicit the secretion of DHP in vivo and actually trigger spawning. These novel findings introduce the potential of utilizing recombinant gonadotropins in aquaculture.

scholarly journals Flexibility and mobility of SARS-CoV-2-related protein structures

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Rudolf A. Römer ◽  
Navodya S. Römer ◽  
A. Katrine Wallis
Keyword(s):  
In Silico ◽  
Drug Targets ◽  
Large Scale ◽  
Structural Information ◽  
Protein Structures ◽  
Antiviral Drug ◽  
Docking Studies ◽  
Related Protein

AbstractThe worldwide CoVid-19 pandemic has led to an unprecedented push across the whole of the scientific community to develop a potent antiviral drug and vaccine as soon as possible. Existing academic, governmental and industrial institutions and companies have engaged in large-scale screening of existing drugs, in vitro, in vivo and in silico. Here, we are using in silico modelling of possible SARS-CoV-2 drug targets, as deposited on the Protein Databank (PDB), and ascertain their dynamics, flexibility and rigidity. For example, for the SARS-CoV-2 spike protein—using its complete homo-trimer configuration with 2905 residues—our method identifies a large-scale opening and closing of the S1 subunit through movement of the S$${}^\text{B}$$ B domain. We compute the full structural information of this process, allowing for docking studies with possible drug structures. In a dedicated database, we present similarly detailed results for the further, nearly 300, thus far resolved SARS-CoV-2-related protein structures in the PDB.

scholarly journals Cellular labelling favours unfolded proteins

2018 ◽  
Author(s):  
David-Paul Minde ◽  
Manasa Ramakrishna ◽  
Kathryn S. Lilley
Keyword(s):  
Large Scale ◽  
Protein Structures ◽  
Unfolded Proteins ◽  
80S Ribosome ◽  
Unfolded Protein ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Wide Scale

AbstractFolded enzymes are essential for life, but there is limited in vivo information about how locally unfolded protein regions contribute to biological functions. Intrinsically Disordered Regions (IDRs) are enriched in disease-linked and multiply post-translationally modified proteins. The extent of foldability of predicted IDRs is difficult to measure due to significant technical challenges to survey in vivo protein conformations on a proteome-wide scale. We reasoned that IDRs should be more accessible to targeted in vivo biotinylation than more ordered protein regions, if they retain their flexibility in vivo. Indeed, we observed a positive correlation of predicted IDRs and biotinylation density across four independent large-scale proximity proteomics studies that together report >20 000 biotinylation sites. We show that biotin ‘painting’ is a promising approach to fill gaps in knowledge between static in vitro protein structures, in silico disorder predictions and in vivo condition-dependent subcellular plasticity using the 80S ribosome as an example.

scholarly journals Multifractal intermittency of Eulerian and Lagrangian turbulence of ocean temperature and plankton fields

1996 ◽  
Vol 3 (4) ◽  
pp. 236-246 ◽  
Author(s):  
L. Seuront ◽  
F. Schmitt ◽  
D. Schertzer ◽  
Y. Lagadeuc ◽  
S. Lovejoy
Keyword(s):  
Power Spectrum ◽  
Large Scale ◽  
Temperature Fluctuations ◽  
Biologically Active ◽  
Ocean Temperature ◽  
Scale Invariant ◽  
Invariant Structure ◽  
Significant Difference ◽  
Lagrangian Turbulence

Abstract. In this paper, we present evidence that intermittency of Eulerian and Lagrangian turbulence of ocean temperature and plankton fields is multifractal and furthermore can be analysed with the help of universal multifractals. We analyse time series of temperature and in vivo fluorescence taken from a drifter in the mixed coastal waters of the eastern English Channel. Two analysis techniques are used to compute the fundamental universal multifiractal parameters, which describe all the statistics of the turbulent fluctuations: the analysis of the scale invariant structure function exponent ζ(q) and the Double Trace Moment technique. At small scales, we do not detect any significant difference between the universal multifiractal behavior of temperature and fluorescence in an Eulerian framework. This supports the hypothesis that the latter is passively advected with the flow as the former. On the one hand, we show that large scale measurements are Lagrangian and indeed we obtain for temperature fluctuations a ω2 power spectrum corresponding to the theoretical scaling of a Lagrangian passive scalar. Furthermore, we show that Lagrangian temperature fluctuations are multiscaling and intermittent. On the other hand, the flatter slope at large scales of the fluorescence power spectrum points out that the plankton is at these scales a "biologically active" scalar.

Sensitive Bioassay for Detection of Biologically Active Ricin in Food

2012 ◽  
Vol 75 (5) ◽  
pp. 951-954 ◽  
Author(s):  
REUVEN RASOOLY ◽  
XIAOHUA HE
Keyword(s):  
Large Scale ◽  
Fluorescent Protein ◽  
Vero Cells ◽  
Biologically Active ◽  
Green Fluorescent Protein Gene ◽  
Mouse Bioassay ◽  
Human Embryonic Kidney Cells ◽  
Green Fluorescent ◽  
And Control

The potential use of ricin as an agent of biological warfare highlights the need to develop fast and effective methods to detect biologically active ricin. The current “gold standard” for ricin detection is an in vivo mouse bioassay; however, this method is not practical to test on a large number of samples and raises ethical concerns with regard to the use of experimental animals. In this work, we generated adenoviral vectors that express the green fluorescent protein gene and used the relative fluorescence units intensity inhibition by transduced cells for quantitative measurement of biologically active ricin. The detection limit of the assay was 200 pg/ml, which is over 500,000 times greater than the adult human lethal oral dose. The inhibition of fluorescence intensity between ricin treatment and control was higher in 72-h posttransduction Vero cells than 24-h human embryonic kidney cells. Therefore, to detect biologically active ricin in food matrices that might influence the assay, we used 72-h posttransduction Vero cells. This simple assay could be used for large-scale screening to detect biologically active ricin in food without added substrates or use of cell fixation methods.

scholarly journals Development of a compact alkynyl-enrichable crosslinker for in-depth in-vivo crosslinking analysis

2021 ◽  
Author(s):  
Hang Gao ◽  
Li Li Zhao ◽  
Qun Zhao ◽  
Hua Li Zhang ◽  
Feng Bao Zhao ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Large Scale ◽  
High Efficiency ◽  
Protein Complexes ◽  
Protein Structures ◽  
High Sensitivity ◽  
Protein Protein Interactions ◽  
Cross Links ◽  
First Time

Chemical crosslinking coupled with mass spectrometry (CXMS) has emerged as a powerful technique to capture the dynamic information of protein complexes with high sensitivity, throughput and sample universality. To advance the study of in-vivo protein structures and protein-protein interactions on the large scale, a new alkynyl-enrichable crosslinker was developed with high efficiency of membrane penetration, reactivity and enrichment. The crosslinker was successfully used for in-vivo crosslinking of intact human cells, resulting in 6820 non-redundant crosslinks identified at a false discovery rate (FDR) of 1% using pLink 2.0, which 4898 (71.8%) of the cross-links were assigned as intraprotein and 1922 (28.2%) were interprotein links. To our knowledge, this is also the first time to realize the in-vivo crosslinking with a non-cleavable cross-linker for homo species cells.

scholarly journals PI16 is a non-neuronal regulator of neuropathic pain

2019 ◽  
Author(s):  
Pooja Singhmar ◽  
Ronnie The Phong Trinh ◽  
Jiacheng Ma ◽  
XiaoJiao Huo ◽  
Bo Peng ◽  
...  
Keyword(s):  
Neuropathic Pain ◽  
Clinical Problem ◽  
Endothelial Barrier ◽  
Leukocyte Infiltration ◽  
Spared Nerve Injury ◽  
Protein Levels ◽  
Injury Model ◽  
Major Clinical Problem

AbstractChronic pain is a major clinical problem of which the mechanisms are incompletely understood. Here we describe the concept that PI16, a protein of unknown function mainly produced by fibroblasts, controls neuropathic pain. The spared nerve injury model of neuropathic pain increases PI16 protein levels in fibroblasts in DRG meninges and in the epi/perineurium of the sciatic nerve. We did not detect PI16 expression in neurons or glia in spinal cord, DRG and nerve. Mice deficient in PI16 are protected against neuropathic pain. In vitro, PI16 promotes trans-endothelial leukocyte migration. In vivo, PI16−/− mice show reduced endothelial barrier permeability, lower leukocyte infiltration and reduced activation of the endothelial barrier regulator MLCK and reduced phosphorylation of its substrate MLC2 in response to SNI. In summary, our findings support a model in which PI16 promotes neuropathic pain by mediating a cross talk between fibroblasts and the endothelial barrier leading to barrier opening, cellular influx and increased pain. Its key role in pain and its limited cellular and tissue distribution makes PI16 an attractive target for pain management.Graphical Abstract

scholarly journals Flexibility and mobility of SARS-CoV-2-related protein structures

2020 ◽  
Author(s):  
Rudolf A. Römer ◽  
Navodya S. Römer ◽  
A. Katrine Wallis
Keyword(s):  
In Silico ◽  
Drug Targets ◽  
Large Scale ◽  
Structural Information ◽  
Protein Structures ◽  
Antiviral Drug ◽  
Docking Studies ◽  
Related Protein

ABSTRACTThe worldwide CoVid-19 pandemic has led to an unprecedented push across the whole of the scientific community to develop a potent antiviral drug and vaccine as soon as possible. Existing academic, governmental and industrial institutions and companies have engaged in large-scale screening of existing drugs, in vitro, in vivo and in silico. Here, we are using in silico modelling of SARS-CoV-2 drug targets, i.e. SARS-CoV-2 protein structures as deposited on the Protein Databank (PDB). We study their flexibility, rigidity and mobility, an important first step in trying to ascertain their dynamics for further drug-related docking studies. We are using a recent protein flexibility modelling approach, combining protein structural rigidity with possible motion consistent with chemical bonds and sterics. For example, for the SARS-CoV-2 spike protein in the open configuration, our method identifies a possible further opening and closing of the S1 subunit through movement of SB domain. With full structural information of this process available, docking studies with possible drug structures are then possible in silico. In our study, we present full results for the more than 200 thus far published SARS-CoV-2-related protein structures in the PDB.

Purification of the Antihemophilic Factor by Gel Filtration on Agarose

1969 ◽  
Vol 22 (03) ◽  
pp. 577-583 ◽  
Author(s):  
M.M.P Paulssen ◽  
A.C.M.G.B Wouterlood ◽  
H.L.M.A Scheffers
Keyword(s):  
Factor Viii ◽  
Plasma Proteins ◽  
Large Scale ◽  
Gel Filtration ◽  
Large Scale Preparation ◽  
Scale Preparation ◽  
Antihemophilic Factor

SummaryFactor VIII can be isolated from plasma proteins, including fibrinogen by chromatography on agarose. The best results were obtained with Sepharose 6B. Large scale preparation is also possible when cryoprecipitate is separated by chromatography. In most fractions containing factor VIII a turbidity is observed which may be due to the presence of chylomicrons.The purified factor VIII was active in vivo as well as in vitro.

The Effect of Active Site-inhibited Factor VIIa on Tissue Factor-initiated Coagulation Using Platelets before and after Aspirin Administration

1997 ◽  
Vol 78 (04) ◽  
pp. 1202-1208 ◽  
Author(s):  
Marianne Kjalke ◽  
Julie A Oliver ◽  
Dougald M Monroe ◽  
Maureane Hoffman ◽  
Mirella Ezban ◽  
...  
Keyword(s):  
Tissue Factor ◽  
Active Site ◽  
Large Scale ◽  
Thrombin Generation ◽  
Factor Viia ◽  
Dependent Manner ◽  
Antithrombotic Agent ◽  
Before And After ◽  
Ic50 Values

SummaryActive site-inactivated factor VIIa has potential as an antithrombotic agent. The effects of D-Phe-L-Phe-L-Arg-chloromethyl ketone-treated factor VIla (FFR-FVIIa) were evaluated in a cell-based system mimicking in vivo initiation of coagulation. FFR-FVIIa inhibited platelet activation (as measured by expression of P-selectin) and subsequent large-scale thrombin generation in a dose-dependent manner with IC50 values of 1.4 ± 0.8 nM (n = 8) and 0.9 ± 0.7 nM (n = 7), respectively. Kd for factor VIIa binding to monocytes ki for FFR-FVIIa competing with factor VIIa were similar (11.4 ± 0.8 pM and 10.6 ± 1.1 pM, respectively), showing that FFR-FVIIa binds to tissue factor in the tenase complex with the same affinity as factor VIIa. Using platelets from volunteers before and after ingestion of aspirin (1.3 g), there were no significant differences in the IC50 values of FFR-FVIIa [after aspirin ingestion, the IC50 values were 1.7 ± 0.9 nM (n = 8) for P-selectin expression, p = 0.37, and 1.4 ± 1.3 nM (n = 7) for thrombin generation, p = 0.38]. This shows that aspirin treatment of platelets does not influence the inhibition of tissue factor-initiated coagulation by FFR-FVIIa, probably because thrombin activation of platelets is not entirely dependent upon expression of thromboxane A2.

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