scholarly journals Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography

Crystals ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1579
Author(s):  
Omur Guven ◽  
Mehmet Gul ◽  
Esra Ayan ◽  
J Austin Johnson ◽  
Baris Cakilkaya ◽  
...  
Keyword(s):  
Data Collection ◽  
High Throughput ◽  
Drug Screening ◽  
Dynamic Range ◽  
Drug Repurposing ◽  
Low Noise ◽  
Drug Binding ◽  
Array Detector ◽  
X Ray ◽  
Main Protease

Since early 2020, COVID-19 has grown to affect the lives of billions globally. A worldwide investigation has been ongoing for characterizing the virus and also for finding an effective drug and developing vaccines. As time has been of the essence, a crucial part of this research has been drug repurposing; therefore, confirmation of in silico drug screening studies have been carried out for this purpose. Here we demonstrated the possibility of screening a variety of drugs efficiently by leveraging a high data collection rate of 120 images/second with the new low-noise, high dynamic range ePix10k2M Pixel Array Detector installed at the Macromolecular Femtosecond Crystallography (MFX) instrument at the Linac Coherent Light Source (LCLS). The X-ray Free-Electron Laser (XFEL) is used for remote high-throughput data collection for drug repurposing of the main protease (Mpro) of SARS-CoV-2 at ambient temperature with mitigated X-ray radiation damage. We obtained multiple structures soaked with nine drug candidate molecules in two crystal forms. Although our drug binding attempts failed, we successfully established a high-throughput Serial Femtosecond X-ray crystallographic (SFX) data collection protocol.

scholarly journals Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography

2021 ◽  
Author(s):  
Omur Guven ◽  
Mehmet Gul ◽  
Esra Ayan ◽  
J. Austin Johnson ◽  
Baris Cakilkaya ◽  
...  
Keyword(s):  
Data Collection ◽  
High Throughput ◽  
Drug Screening ◽  
Dynamic Range ◽  
Drug Repurposing ◽  
Low Noise ◽  
Drug Binding ◽  
Array Detector ◽  
X Ray ◽  
Main Protease

Since early 2020, COVID-19 has grown to affect the lives of billions globally. A worldwide investigation has been ongoing for characterizing the virus and also for finding an effective drug and developing vaccines. As time has been of the essence, a crucial part of this research has been drug repurposing; therefore, confirmation of in-silico drug screening studies have been carried out for this purpose. Here we demonstrated the possibility of screening a variety of drugs efficiently by leveraging a high data collection rate of 120 images/second with the new low-noise, high dynamic range ePix10k2M Pixel Array Detector installed at the Macromolecular Femtosecond Crystallography (MFX) instrument at the Linac Coherent Light Source (LCLS). The X-ray Free-Electron Laser (XFEL) is used for remote high-throughput data collection for drug repurposing of the main protease (Mpro) of SARS-CoV-2 at ambient temperature with mitigated X-ray radiation damage. We obtained multiple high-resolution structures soaked with 9 drug candidate molecules in two crystal forms. Although our drug binding attempts failed, we successfully established a high-throughput Serial Femtosecond X-ray crystallographic (SFX) data collection protocol.

Drug Repurposing Studies Targeting SARS-nCoV2: An Ensemble Docking Approach on Drug Target 3C-like Protease (3CLpro)

2020 ◽  
Author(s):  
Shruti Koulgi ◽  
Vinod Jani ◽  
Mallikarjunachari Uppuladinne ◽  
Uddhavesh Sonavane ◽  
Asheet Kumar Nath ◽  
...  
Keyword(s):  
Drug Repurposing ◽  
Drug Binding ◽  
Ensemble Docking ◽  
Drug Molecules ◽  
Drug Binding Site ◽  
Main Protease ◽  
Docking Approach ◽  
Novel Coronavirus ◽  
Markov State Modeling ◽  
Viral Polyprotein

<p>The COVID-19 pandemic has been responsible for several deaths worldwide. The causative agent behind this disease is the Severe Acute Respiratory Syndrome – novel Coronavirus 2 (SARS-nCoV2). SARS-nCoV2 belongs to the category of RNA viruses. The main protease, responsible for the cleavage of the viral polyprotein is considered as one of the hot targets for treating COVID-19. Earlier reports suggest the use of HIV anti-viral drugs for targeting the main protease of SARS-CoV, which caused SARS in the year 2002-03. Hence, drug repurposing approach may prove to be useful in targeting the main protease of SARS-nCoV2. The high-resolution crystal structure of 3CL<sup>pro</sup> (main protease) of SARS-nCoV2 (PDB ID: 6LU7) was used as the target. The Food and Drug Administration (FDA) approved and SWEETLEAD database of drug molecules were screened. The apo form of the main protease was simulated for a cumulative of 150 ns and 10 μs open source simulation data was used, to obtain conformations for ensemble docking. The representative structures for docking were selected using RMSD-based clustering and Markov State Modeling analysis. This ensemble docking approach for main protease helped in exploring the conformational variation in the drug binding site of the main protease leading to efficient binding of more relevant drug molecules. The drugs obtained as best hits from the ensemble docking possessed anti-bacterial and anti-viral properties. Small molecules with these properties may prove to be useful to treat symptoms exhibited in COVID-19. This <i>in-silico</i> ensemble docking approach would support identification of potential candidates for repurposing against COVID-19.</p>

scholarly journals X-ray transmission grating spectrometer with CCD detector for laser plasma studies

1991 ◽  
Vol 9 (2) ◽  
pp. 579-591 ◽  
Author(s):  
L. Pína ◽  
H. Fiedorowicz ◽  
M. O. Koshevoi ◽  
A. A. Rupasov ◽  
B. Rus ◽  
...  
Keyword(s):  
Laser Plasma ◽  
Dynamic Range ◽  
High Sensitivity ◽  
Array Detector ◽  
Charge Coupled Device ◽  
X Ray ◽  
Transmission Grating ◽  
Hot Plasma ◽  
Ccd Detector ◽  
Wet Processing

A program is under way to develop methods and instrumentation based on charge-coupled device (CCD) sensors for hot plasma diagnostics. We have developed a new X-ray spectrometer in which a freestanding X-ray transmission grating is coupled to a CCD linear array detector with electronic digitized readout replacing film and its wet processing. This instrument measures time-integrated pulsed X-ray spectra with moderate spectral resolution (δλ ≤ 0.6 nm) over a broad spectral range (0.3–2 keV) with high sensitivity, linearity, and large dynamic range. The performance of the device was tested using laser plasma as the X-ray source.

scholarly journals Development of a shutterless continuous rotation method using an X-ray CMOS detector for protein crystallography

2009 ◽  
Vol 42 (6) ◽  
pp. 1165-1175 ◽  
Author(s):  
Kazuya Hasegawa ◽  
Kunio Hirata ◽  
Tetsuya Shimizu ◽  
Nobutaka Shimizu ◽  
Takaaki Hikima ◽  
...  
Keyword(s):  
Data Collection ◽  
Dynamic Range ◽  
Protein Structures ◽  
Protein Crystallography ◽  
New Method ◽  
Oxide Semiconductor ◽  
X Ray ◽  
Rotation Method ◽  
Continuous Rotation ◽  
Wide Range

A new shutterless continuous rotation method using an X-ray complementary metal-oxide semiconductor (CMOS) detector has been developed for high-speed, precise data collection in protein crystallography. The principle of operation and the basic performance of the X-ray CMOS detector (Hamamatsu Photonics KK C10158DK) have been shown to be appropriate to the shutterless continuous rotation method. The data quality of the continuous rotation method is comparable to that of the conventional oscillation method using a CCD detector and, furthermore, the combination with fine φ slicing improves the data accuracy without increasing the data-collection time. The new method is more sensitive to diffraction intensity because of the narrow dynamic range of the CMOS detector. However, the strong diffraction spots were found to be precisely measured by recording them on successive multiple images by selecting an adequate rotation step. The new method has been used to successfully determine three protein structures by multi- and single-wavelength anomalous diffraction phasing and has thereby been proved applicable in protein crystallography. The apparatus and method may become a powerful tool at synchrotron protein crystallography beamlines with important potential across a wide range of X-ray wavelengths.

Silicon array detector system for high-rate, low-noise X-ray spectroscopy

1999 ◽  
Vol 46 (4) ◽  
pp. 886-889 ◽  
Author(s):  
B.A. Ludewigt ◽  
B. Krieger ◽  
D. Lindstrom ◽  
M.R. Maier ◽  
M. Rutgersson ◽  
...  
Keyword(s):  
Low Noise ◽  
Detector System ◽  
High Rate ◽  
Array Detector ◽  
X Ray

scholarly journals Robust indexing for automatic data collection

2004 ◽  
Vol 37 (3) ◽  
pp. 399-409 ◽  
Author(s):  
Nicholas K. Sauter ◽  
Ralf W. Grosse-Kunstleve ◽  
Paul D. Adams
Keyword(s):  
Data Collection ◽  
High Throughput ◽  
Visual Inspection ◽  
The Novel ◽  
Automatic Data ◽  
X Ray ◽  
Alternative Approach ◽  
Automatic Data Collection ◽  
Diffraction Patterns ◽  
Improved Methods

Improved methods for indexing diffraction patterns from macromolecular crystals are presented. The novel procedures include a more robust way to verify the position of the incident X-ray beam on the detector, an algorithm to verify that the deduced lattice basis is consistent with the observations, and an alternative approach to identify the metric symmetry of the lattice. These methods help to correct failures commonly experienced during indexing, and increase the overall success rate of the process. Rapid indexing, without the need for visual inspection, will play an important role as beamlines at synchrotron sources prepare for high-throughput automation.

scholarly journals COVID19 Approved Drug Repurposing: Pocket Similarity Approach

2020 ◽  
Author(s):  
Mohamed Fadlalla
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Drug Repurposing ◽  
Drug Binding ◽  
Drug Binding Site ◽  
Main Protease ◽  
Major Outbreak ◽  
Target Binding ◽  
Approved Drugs

<p>SARS CoV 2 has spread worldwide and caused a major outbreak of coronavirus disease 2019 (COVID-19). To date, no licensed drug or a vaccine is available against COVID19.</p><p>Starting from all of the resolved SARS CoV2 crystal structures, this study aims to find inhibitors for all of the SARS CoV2 proteins. To achieve this, I used PocketMatch to test the similarity of approved drugs binding sites against all of the binding sites found on SARS CoV 2 proteins. After that docking was used to confirm the results.</p><p>I found drugs that inhibit the main protease, Nsp12 and Nsp3. The discovered drugs are either in clinical trials (Sildenafil, Lopinavir, Ritonavir) or have in vitro antiviral activity (Nelfinavir, Indinavir, Amprenavir, depiqulinum , Gemcitabine, Raltitrexed, Aprepitant, montelukast, Ouabain, Raloxifene) whether against SARS CoV 2 or other viruses. In addition to this, further analysis of pockets revealed a steroidal pocket that might open the door to hypotheses on why the mortality of men is higher than women.</p><p>Many of the in silico repurposing studies test binding of the compound to the target using docking. The significance of this study adds to the similarity between the drug binding site and the target binding site. This takes into consideration the dynamic behaviour of the pocket after ligand binding.</p><div><br></div>

High Speed Characterization of Pseudomorphic Hemt Structures Using a Very Low Noise Scintillation Detector

1993 ◽  
Vol 37 ◽  
pp. 145-151
Author(s):  
N. Loxley ◽  
S. Cockerton ◽  
B. K. Tanner
Keyword(s):  
Quality Assurance ◽  
Scintillation Detector ◽  
High Speed ◽  
Dynamic Range ◽  
High Dynamic Range ◽  
Low Noise ◽  
X Ray Diffraction ◽  
X Ray ◽  
High Dynamic

AbstractWe show that a very low noise, high dynamic range scintillation detector has major advantages over conventional detectors for characterization of pseudomorphic HEMT structures by high resolution X-ray diffraction. We show that the reduced background enables a second modulation period to be detected, enabling the thickness and composition to be determined independently. Using a conventional X-ray generator and diffractometer we demonstrate that, in a single scan taking only 10 seconds, we are able to obtain sufficiently good data to provide quality assurance.

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