scholarly journals Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking

2020 ◽  
Author(s):  
Marion Schuller ◽  
Galen J. Correy ◽  
Stefan Gahbauer ◽  
Daren Fearon ◽  
Taiasean Wu ◽  
...  
Keyword(s):  
High Resolution ◽  
Active Site ◽  
Conformational Heterogeneity ◽  
Structural Protein ◽  
Computational Docking ◽  
X Ray ◽  
Wide Range ◽  
Biophysical Techniques ◽  
Fragment Libraries ◽  
Chemical Matter

ABSTRACTThe SARS-CoV-2 macrodomain (Mac1) within the non-structural protein 3 (Nsp3) counteracts host-mediated antiviral ADP-ribosylation signalling. This enzyme is a promising antiviral target because catalytic mutations render viruses non-pathogenic. Here, we report a massive crystallographic screening and computational docking effort, identifying new chemical matter primarily targeting the active site of the macrodomain. Crystallographic screening of diverse fragment libraries resulted in 214 unique macrodomain-binding fragments, out of 2,683 screened. An additional 60 molecules were selected from docking over 20 million fragments, of which 20 were crystallographically confirmed. X-ray data collection to ultra-high resolution and at physiological temperature enabled assessment of the conformational heterogeneity around the active site. Several crystallographic and docking fragment hits were validated for solution binding using three biophysical techniques (DSF, HTRF, ITC). Overall, the 234 fragment structures presented explore a wide range of chemotypes and provide starting points for development of potent SARS-CoV-2 macrodomain inhibitors.

scholarly journals Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking

2021 ◽  
Vol 7 (16) ◽  
pp. eabf8711
Author(s):  
Marion Schuller ◽  
Galen J. Correy ◽  
Stefan Gahbauer ◽  
Daren Fearon ◽  
Taiasean Wu ◽  
...  
Keyword(s):  
Active Site ◽  
Nonstructural Protein ◽  
Adenosine Diphosphate ◽  
Titration Calorimetry ◽  
Conformational Heterogeneity ◽  
Time Resolved ◽  
Computational Docking ◽  
Wide Range ◽  
Differential Scanning Fluorimetry ◽  
Biophysical Techniques

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) macrodomain within the nonstructural protein 3 counteracts host-mediated antiviral adenosine diphosphate–ribosylation signaling. This enzyme is a promising antiviral target because catalytic mutations render viruses nonpathogenic. Here, we report a massive crystallographic screening and computational docking effort, identifying new chemical matter primarily targeting the active site of the macrodomain. Crystallographic screening of 2533 diverse fragments resulted in 214 unique macrodomain-binders. An additional 60 molecules were selected from docking more than 20 million fragments, of which 20 were crystallographically confirmed. X-ray data collection to ultra-high resolution and at physiological temperature enabled assessment of the conformational heterogeneity around the active site. Several fragment hits were confirmed by solution binding using three biophysical techniques (differential scanning fluorimetry, homogeneous time-resolved fluorescence, and isothermal titration calorimetry). The 234 fragment structures explore a wide range of chemotypes and provide starting points for development of potent SARS-CoV-2 macrodomain inhibitors.

scholarly journals Mechanism of IPPase shown by high resolution Neutron and X-ray crystallography

2014 ◽  
Vol 70 (a1) ◽  
pp. C1211-C1211
Author(s):  
Joseph Ng ◽  
Ronny Hughes ◽  
Michelle Morris ◽  
Leighton Coates ◽  
Matthew Blakeley ◽  
...  
Keyword(s):  
High Resolution ◽  
Active Site ◽  
Inorganic Pyrophosphatase ◽  
Inorganic Pyrophosphate ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cellular Processes ◽  
Crystallographic Structures ◽  
Hydrolysis Of ◽  
Low Energy Conformations

Soluble inorganic pyrophosphatase (IPPase) catalyzes the hydrolysis of inorganic pyrophosphate (PPi) to form orthophosphate (Pi). The action of this enzyme shifts the overall equilibrium in favor of synthesis during a number of ATP-dependent cellular processes such as in the polymerization of nucleic acids, production of coenzymes and proteins and sulfate assimilation pathways. Two Neutron crystallographic (2.10-2.50Å) and five high-resolution X-ray (0.99Å-1.92Å) structures of the archaeal IPPase from Thermococcus thioreducens have been determined under both cryo and room temperatures. The structures determined include the recombinant IPPase bound to Mg+2, Ca+2, Br-, SO2-2 or PO4-2 involving those with non-hydrolyzed and hydrolyzed pyrophosphate complexes. All the crystallographic structures provide snapshots of the active site corresponding to different stages of the hydrolysis of inorganic pyrophosphate. As a result, a structure-based model of IPPase catalysis is devised showing the enzyme's low-energy conformations, hydration states, movements and nucleophile generation within the active site.

scholarly journals Shadow monochromatic backlighting: Large-field high resolution X-ray shadowgraphy with improved spectral tunability

2001 ◽  
Vol 19 (2) ◽  
pp. 285-293 ◽  
Author(s):  
T.A. PIKUZ ◽  
A. YA. FAENOV ◽  
M. FRAENKEL ◽  
A. ZIGLER ◽  
F. FLORA ◽  
...  
Keyword(s):  
High Resolution ◽  
High Spatial Resolution ◽  
Field Of View ◽  
Large Field ◽  
X Ray ◽  
Traditional Scheme ◽  
Wide Range ◽  
Wide Wavelength Range ◽  
Bent Crystals ◽  
First Time

The shadow monochromatic backlighting (SMB) scheme, a modification of the well-known soft X-ray monochromatic backlighting scheme, is proposed. It is based on a spherical crystal as the dispersive element and extends the traditional scheme by allowing one to work with a wide range of Bragg angles and thus in a wide spectral range. The advantages of the new scheme are demonstrated experimentally and supported numerically by ray-tracing simulations. In the experiments, the X-ray backlighter source is a laser-produced plasma, created by the interaction of an ultrashort pulse, Ti:Sapphire laser (120 fs, 3–5 mJ, 1016 W/cm2 on target) or a short wavelength XeCl laser (10 ns, 1–2 J, 1013 W/cm2 on target) with various solid targets (Dy, Ni + Cr, BaF2). In both experiments, the X-ray sources are well localized spatially (∼20 μm) and are spectrally tunable in a relatively wide wavelength range (λ = 8–15 Å). High quality monochromatic (δλ/λ ∼ 10−5–10−3) images with high spatial resolution (up to ∼4 μm) over a large field of view (a few square millimeters) were obtained. Utilization of spherically bent crystals to obtain high-resolution, large field, monochromatic images in a wide range of Bragg angles (35° < Θ < 90°) is demonstrated for the first time.

Difference in Conformation of Virginiamycin M1 in Chloroform and Bound Form in the 50S Ribosome or Streptogramin Acetyltransferase

2004 ◽  
Vol 57 (5) ◽  
pp. 415 ◽  
Author(s):  
Jason Dang ◽  
B. Mikael Bergdahl ◽  
Frances Separovic ◽  
Robert T. C. Brownlee ◽  
Robert P. Metzger
Keyword(s):  
Crystal Structure ◽  
High Resolution ◽  
Active Site ◽  
Major Change ◽  
X Ray ◽  
Binding Process ◽  
High Resolution Nmr ◽  
Virginiamycin M1

The conformation of virginiamycin M1 (VM1) in chloroform, determined by high-resolution NMR experiments, differs significantly from that of the X-ray crystal structure of VM1 bound to the 50S ribosome and to the active site of a streptogramin acetyltransferase enzyme. This implies that the binding process to these entities causes a major change in VM1 conformation.

scholarly journals Measurement of three-dimensional displacement field in piled embankments using synchrotron X-ray tomography

2019 ◽  
Vol 56 (6) ◽  
pp. 885-892 ◽  
Author(s):  
Louis King ◽  
Abdelmalek Bouazza ◽  
Anton Maksimenko ◽  
Will P. Gates ◽  
Stephen Dubsky
Keyword(s):  
High Resolution ◽  
Imaging Techniques ◽  
Three Dimensional ◽  
Physical Models ◽  
Scale Model ◽  
Small Scale ◽  
Full Field ◽  
X Ray ◽  
Wide Range ◽  
Piled Embankments

The measurement of displacement fields by nondestructive imaging techniques opens up the potential to study the pre-failure mechanisms of a wide range of geotechnical problems within physical models. With the advancement of imaging technologies, it has become possible to achieve high-resolution three-dimensional computed tomography volumes of relatively large samples, which may have previously resulted in excessively long scan times or significant imaging artefacts. Imaging of small-scale model piled embankments (142 mm diameter) comprising sand was undertaken using the imaging and medical beamline at the Australian Synchrotron. The monochromatic X-ray beam produced high-resolution reconstructed volumes with a fine texture due to the size and mineralogy of the sand grains as well as the phase contrast enhancement achieved by the monochromatic X-ray beam. The reconstructed volumes were well suited to the application of digital volume correlation, which utilizes cross-correlation techniques to estimate three-dimensional full-field displacement vectors. The output provides insight into the strain localizations that develop within piled embankments and an example of how advanced imaging techniques can be utilized to study the kinematics of physical models.

High Resolution EM Study of Wüstite

1974 ◽  
Vol 32 ◽  
pp. 352-353 ◽  
Author(s):  
Sumio Iijima
Keyword(s):  
High Resolution ◽  
Diffraction Method ◽  
X Ray Diffraction ◽  
Repeat Distance ◽  
X Ray ◽  
Integral Number ◽  
Deviation From Stoichiometry ◽  
Wide Range ◽  
Cation Sites ◽  
Range Of Variation

Wüstite (Fe1-x0) has recieved considerable attention because of a wide range of variation in x. The deviation from stoichiometry is known to be due to vacancies on cation sites. Koch and Cohen, having studied this material in detail using an X-ray diffraction method, concluded that the defects present in Fe1-x0 are clusters of 13 octahedral vacancies and 4 tetrahedral ions. These clusters are arranged periodically but the repeat distance in the [100] direction is not an integral number of structures of the basic NaCl-type. The observed spacing of superstructure peaks may correspond to the average repeat distance.

Analysis and Correction of Heating Effect on High Resolution and Wide Range Soft X-Ray Beamline

2014 ◽  
Vol 51 (7) ◽  
pp. 073401
Author(s):  
石应波 Shi Yingbo ◽  
王勇 Wang Yong ◽  
邰仁忠 Tai Renzhong ◽  
丁洪 Ding Hong
Keyword(s):  
High Resolution ◽  
Heating Effect ◽  
X Ray ◽  
Wide Range

High-resolution X-ray emission spectroscopy with transition-edge sensors: present performance and future potential

2015 ◽  
Vol 22 (3) ◽  
pp. 766-775 ◽  
Author(s):  
J. Uhlig ◽  
W. B. Doriese ◽  
J. W. Fowler ◽  
D. S. Swetz ◽  
C. Jaye ◽  
...  
Keyword(s):  
High Resolution ◽  
Emission Spectroscopy ◽  
Electronic Configuration ◽  
Transition Edge Sensors ◽  
Complex Compounds ◽  
Superconducting Transition ◽  
X Ray ◽  
Transition Edge ◽  
Wide Range ◽  
Low Efficiency

X-ray emission spectroscopy (XES) is a powerful element-selective tool to analyze the oxidation states of atoms in complex compounds, determine their electronic configuration, and identify unknown compounds in challenging environments. Until now the low efficiency of wavelength-dispersive X-ray spectrometer technology has limited the use of XES, especially in combination with weaker laboratory X-ray sources. More efficient energy-dispersive detectors have either insufficient energy resolution because of the statistical limits described by Fano or too low counting rates to be of practical use. This paper updates an approach to high-resolution X-ray emission spectroscopy that uses a microcalorimeter detector array of superconducting transition-edge sensors (TESs). TES arrays are discussed and compared with conventional methods, and shown under which circumstances they are superior. It is also shown that a TES array can be integrated into a table-top time-resolved X-ray source and a soft X-ray synchrotron beamline to perform emission spectroscopy with good chemical sensitivity over a very wide range of energies.

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