Structural plasticity of SARS-CoV-2 3CL Mpro active site cavity revealed by room temperature X-ray crystallography

Kneller, D.W.; Phillips, G.N.; O’Neill, Hugh; Jedrzejczak, R.; Stols, Lucy; Langan, Paul; Joachimiak, A.; Coates, Leighton; Kovalevsky, Andrey

doi:10.1038/s41467-020-16954-7

Cited by 404 publications

(572 citation statements)

References 41 publications

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“…Initially the spacegroup was found to be C2 (monoclinic centered). It was further determined by the CCP4 program pointless that spacegroup I2 (monoclinic body centered) is more suitable, in accordance with published results 7 . The 3CLpro structure with pdb access code 6WQF 7 was used as initial model.…”

supporting

confidence: 76%

Ebselen Reacts with SARS Coronavirus-2 Main Protease Crystals

Malla

Pandey

Poudyal

et al. 2020

Preprint

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The SARS coronavirus 2 main protease 3CLpro tailor cuts various essential virus proteins out of long poly-protein translated from the virus RNA. If the 3CLpro is inhibited, the functional virus proteins cannot form and the virus cannot replicate and assemble. Any compound that inhibits the 3CLpro is therefore a potential drug to end the pandemic. Here we show that the diffraction power of 3CLpro crystals is effectively destroyed by Ebselen. It appears that Ebselen may be a widely available, relatively cost effective way to eliminate the SARS coronavirus 2.

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supporting

confidence: 76%

Ebselen Reacts with SARS Coronavirus-2 Main Protease Crystals

Malla

Pandey

Poudyal

et al. 2020

Preprint

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“…The second catalytic residue, His41, forms a nearly perfect π-π stacking with masitinib's hydrophobic toluene ring that occupies the S2 binding pocket. These three active groups (pyridine, aminothiazole and toluene rings) contribute the majority of interactions between masitinib and 3CLpro, bind the key active site residues and effectively block the peptide substrate access to the protease catalytic dyad 26 , thus preventing polyprotein cleavage.…”

Section: Masitinib Inhibits 3clpro By Directly Binding To Its Activementioning

confidence: 99%

Drug repurposing screen identifies masitinib as a 3CLpro inhibitor that blocks replication of SARS-CoV-2in vitro

Drayman

Jones

Azizi

et al. 2020

Preprint

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There is an urgent need for anti-viral agents that treat SARS-CoV-2 infection. The shortest path to clinical use is repurposing of drugs that have an established safety profile in humans. Here, we first screened a library of 1,900 clinically safe drugs for inhibiting replication of OC43, a human beta-coronavirus that causes the common-cold and is a relative of SARS-CoV-2, and identified 108 effective drugs. We further evaluated the top 26 hits and determined their ability to inhibit SARS-CoV-2, as well as other pathogenic RNA viruses. 20 of the 26 drugs significantly inhibited SARS-CoV-2 replication in human lung cells (A549 epithelial cell line), with EC50 values ranging from 0.1 to 8 micromolar. We investigated the mechanism of action for these and found that masitinib, a drug originally developed as a tyrosine-kinase inhibitor for cancer treatment, strongly inhibited the activity of the SARS-CoV-2 main protease 3CLpro. X-ray crystallography revealed that masitinib directly binds to the active site of 3CLpro, thereby blocking its enzymatic activity. Mastinib also inhibited the related viral protease of picornaviruses and blocked picornaviruses replication. Thus, our results show that masitinib has broad anti-viral activity against two distinct beta-coronaviruses and multiple picornaviruses that cause human disease and is a strong candidate for clinical trials to treat SARS-CoV-2 infection.

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“…The diffraction data collected remotely at the MFX instrument of the LCLS at SLAC National Laboratory, Menlo Park, CA (Sierra et al, 2019) ( Supplementary Methods: Data Collection and Analysis for SFX studies at LCLS ). We used an Mpro structure determined at ambient-temperature using a rotating anode home X-ray source (PDB ID: 6WQF; Kneller et al, 2020) as our initial molecular replacement search model for structure determination. Two high-resolution SFX structures obtained in different space groups were superposed with an overall RMSD of 1.0 Å (fig.…”

Section: Resultsmentioning

confidence: 99%

“…A putative drug candidate identified by drug-repurposing studies could make use of existing pharmaceutical supply chains for formulation and distribution, an advantage over developing new therapies (Chen et al, 2020; Huang et al, 2020; Pushpakom et al, 2018; Jarada et al, 2020). In typical drug repurposing studies, approved drug libraries are screened against the active site or an allosteric site of target protein structures obtained by methods that have limitations in revealing the enzyme structure, such as cryogenic temperature or radiation damage (Wang et al, 2020; Kneller et al, 2020) and investigations that only involve screening of drugs currently on the market (Zhou et al, 2020; Choudhary et al, 2020; Beck et al, 2020; Wang, 2020). Current structural biology-oriented studies that display a repurposing approach to SARS-CoV-2 research focused on target-driven drug design, virtual screening or a wide spectrum of inhibitor recommendations (Rathnayake et al, 2020; Chauhan and Kalra, 2020; Chen et al, 2020; Muralidharan et al, 2020; Khan et al, 2020; Kumar et al, 2020; Joshi et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Near-Physiological-Temperature Serial Femtosecond X-ray Crystallography Reveals Novel Conformations of SARS-CoV-2 Main Protease Active Site for Improved Drug Repurposing

Durdağı

Dağ

Doğan

et al. 2020

Preprint

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The COVID19 pandemic has resulted in 25+ million reported infections and nearly 850.000 deaths. Research to identify effective therapies for COVID19 includes: i) designing a vaccine as future protection; ii) structure-based drug design; and iii) identifying existing drugs to repurpose them as effective and immediate treatments. To assist in drug repurposing and design, we determined two apo structures of Severe Acute Respiratory Syndrome CoronaVirus-2 main protease at ambienttemperature by Serial Femtosecond X-ray crystallography. We employed detailed molecular simulations of selected known main protease inhibitors with the structures and compared binding modes and energies. The combined structural biology and molecular modeling studies not only reveal the dynamics of small molecules targeting main protease but will also provide invaluable opportunities for drug repurposing and structure-based drug design studies against SARS-CoV-2.One Sentence SummaryRadiation-damage-free high-resolution SARS-CoV-2 main protease SFX structures obtained at near-physiological-temperature offer invaluable information for immediate drug-repurposing studies for the treatment of COVID19.

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Structural plasticity of SARS-CoV-2 3CL Mpro active site cavity revealed by room temperature X-ray crystallography

Cited by 404 publications

References 41 publications

Ebselen Reacts with SARS Coronavirus-2 Main Protease Crystals

Ebselen Reacts with SARS Coronavirus-2 Main Protease Crystals

Drug repurposing screen identifies masitinib as a 3CLpro inhibitor that blocks replication of SARS-CoV-2in vitro

Near-Physiological-Temperature Serial Femtosecond X-ray Crystallography Reveals Novel Conformations of SARS-CoV-2 Main Protease Active Site for Improved Drug Repurposing

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