Unusual zwitterionic catalytic site of SARS–CoV-2 main protease revealed by neutron crystallography

AbstractThe main protease (3CL Mpro) from SARS-CoV-2, the etiological agent of COVID-19, is an essential enzyme for viral replication, possessing an unusual catalytic dyad composed of His41 and Cys145. A long-standing question in the field has been what the protonation states of the ionizable residues in the substrate-binding active site cavity are. Here, we present the room-temperature neutron structure of 3CL Mpro from SARS-CoV-2, which allows direct determination of hydrogen atom positions and, hence, protonation states. The catalytic site natively adopts a zwitterionic reactive state where His41 is doubly protonated and positively charged, and Cys145 is in the negatively charged thiolate state. The neutron structure also identified the protonation states of other amino acid residues, mapping electrical charges and intricate hydrogen bonding networks in the SARS-CoV-2 3CL Mpro active site cavity and dimer interface. This structure highlights the ability of neutron protein crystallography for experimentally determining protonation states at near-physiological temperature – the critical information for structure-assisted and computational drug design.

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Phenothiazines as dual inhibitors of SARS-CoV-2 main protease and COVID-19 inflammation

Canadian Journal of Chemistry ◽

10.1139/cjc-2021-0139 ◽

2021 ◽

Author(s):

Katrina L Forrestall ◽

Darcy E Burley ◽

Meghan Kirsten Cash ◽

Ian Pottie ◽

Sultan Darvesh

Keyword(s):

Viral Replication ◽

Active Site ◽

Acute Infection ◽

Binding Energies ◽

Neurotransmitter Receptors ◽

Main Protease ◽

Dual Action ◽

Inhibition Constants ◽

Anti Inflammatory ◽

Essential Enzyme

COVID-19, caused by the severe acute respiratory coronavirus 2 (SARS-CoV-2) currently has no treatment for acute infection. The main protease (Mpro) of SARS-CoV-2 is an essential enzyme for viral replication and an attractive target for disease intervention. The phenothiazine moiety has demonstrated drug versatility for biological systems, including inhibition of butyrylcholinesterase, a property important in the cholinesterase anti-inflammatory cascade. Nineteen phenothiazine drugs were investigated using in silico modelling techniques to predict binding energies and inhibition constants (Ki values) with SARS-CoV-2 Mpro. Since most side-effects of phenothiazines are due to interactions with various neurotransmitter receptors and transporters, phenothiazines with few such interactions were also investigated. All compounds were found to bind to the active site of SARS-CoV-2 Mpro and showed Ki values ranging from 1.30 to 52.4 µM. Nine phenothiazines showed inhibition constants <10 µM. The compounds with limited interactions with neurotransmitter receptors and transporters showed micromolar (µM) Ki values. Docking results were compared with remdesivir and showed similar interactions with key residues Glu-166 and Gln-189 in the active site. This work has identified several phenothiazines with limited neurotransmitter receptor and transporter interactions and that may provide the dual action of inhibiting SARS-CoV-2 Mpro to prevent viral replication and promote the release of anti-inflammatory cytokines to curb viral-induced inflammation. These compounds are promising candidates for further investigation against SARS-CoV-2.

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IN Silico Approach of Some Selected Honey Constituents as SARS-CoV-2 Main Protease (COVID-19) Inhibitors

10.26434/chemrxiv.12115359.v2 ◽

2020 ◽

Author(s):

Heba Hashem

Keyword(s):

Active Site ◽

Life Cycles ◽

High Binding Energy ◽

Protease Inhibition ◽

Enzyme Active Site ◽

Therapeutic Drugs ◽

Main Protease ◽

The World ◽

Essential Enzyme ◽

The Way

The huge attack of coronavirus disease 2019 (COVID-19) over all the world forces the researcher around the world to study the crystal structure of the main protease Mpro ( 3-chymotrypsin-like cysteine enzyme) which is the essential enzyme for coronavirus processing the polyproteins and its life cycles. And by the way, the inhibition of this enzyme active site becomes the target of all scientists of drug discovery in order to overcome this disease. In this study, we have used the molecular modeling approach to evaluate the activity of different active compounds from honeybee and propolis to inhibit the presented sars-cov-2 main protease via Schrödinger Maestro v10.1. the presented study resulted in six main compounds possess high binding energy with the receptor active site of COVID-19 main protease. we hope this study being the way for honeybee constitution as an effective ligand for sars-cov-2 main protease inhibition and be in the medicinal study of anti-COVID-19 therapeutic drugs.

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A Case for Montelukast in COVID-19: "The use of Computational Docking to estimate the effects of Montelukast on potential viral main protease catalytic site"

10.21203/rs.3.rs-27079/v1 ◽

2020 ◽

Cited By ~ 1

Author(s):

Salman Mansoor ◽

Shoab Saadat ◽

Aitzaz Amin ◽

Imran Ali ◽

Muhammad Tauseef Ghaffar ◽

...

Keyword(s):

Hydrophobic Interactions ◽

Data Bank ◽

Catalytic Site ◽

Amino Acid Residues ◽

Direct Effects ◽

Computational Docking ◽

Main Protease ◽

A Chain ◽

Homology Models

Abstract This article explores the possible role of Montelukast in management of SARS-CoV-2 infection after reviewing the available literature and further uses computational docking to estimate the effects of Montelukast on the main protease inhibitor site of SARS-CoV-2.Methodology: In this study, we used molecular docking to estimate the direct effects of Montelukast on the main protease (Mpro) inhibitor site of the SARS-CoV-2. While other studies have been performed on the homology models, we obtained the Mpro crystalized structure, A-chain (304 amino acid residues) from protein data bank (PDB code 5REK) for this analysisResults:The best docked Montelukast conformer had a mfscore of -71.68 and was seen to be making multiple hydrogen bonds with the neighbouring residues (T24, T24, T26, S46) with the closest bond with T24 (Distance= 1.71 angstrom). Important finding was its hydrogen bond with H41 and hydrophobic interactions with C145 as these residues for important members of the active catalytics site.Conclusion:The computational model which was used against the crystalized Mpro structure suggested a possible inhibitory role of Montelukast in binding to the Mpro catalytic site which may modulate and inhibit the viral replication.

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Crystal structure of the novel amino-acid racemase isoleucine 2-epimerase fromLactobacillus buchneri

Acta Crystallographica Section D Structural Biology ◽

10.1107/s2059798317005332 ◽

2017 ◽

Vol 73 (5) ◽

pp. 428-437 ◽

Cited By ~ 5

Author(s):

Junji Hayashi ◽

Yuta Mutaguchi ◽

Yume Minemura ◽

Noriko Nakagawa ◽

Kazunari Yoneda ◽

...

Keyword(s):

Amino Acid ◽

Active Site ◽

Enzymatic Reaction ◽

Site Directed Mutagenesis ◽

Amino Acid Residues ◽

Aminobutyrate Aminotransferase ◽

Binding Domains ◽

Active Site Cavity ◽

Branched Chain ◽

Amino Acid Racemase

Crystal structures ofLactobacillus buchneriisoleucine 2-epimerase, a novel branched-chain amino-acid racemase, were determined for the enzyme in the apo form, in complex with pyridoxal 5′-phosphate (PLP), in complex withN-(5′-phosphopyridoxyl)-L-isoleucine (PLP-L-Ile) and in complex withN-(5′-phosphopyridoxyl)-D-allo-isoleucine (PLP-D-allo-Ile) at resolutions of 2.77, 1.94, 2.65 and 2.12 Å, respectively. The enzyme assembled as a tetramer, with each subunit being composed of N-terminal, C-terminal and large PLP-binding domains. The active-site cavity in the apo structure was much more solvent-accessible than that in the PLP-bound structure. This indicates that a marked structural change occurs around the active site upon binding of PLP that provides a solvent-inaccessible environment for the enzymatic reaction. The main-chain coordinates of theL. buchneriisoleucine 2-epimerase monomer showed a notable similarity to those of α-amino-∊-caprolactam racemase fromAchromobactor obaeand γ-aminobutyrate aminotransferase fromEscherichia coli. However, the amino-acid residues involved in substrate binding in those two enzymes are only partially conserved inL. buchneriisoleucine 2-epimerase, which may account for the differences in substrate recognition by the three enzymes. The structures bound with reaction-intermediate analogues (PLP-L-Ile and PLP-D-allo-Ile) and site-directed mutagenesis suggest that L-isoleucine epimerization proceeds through abstraction of the α-hydrogen of the substrate by Lys280, while Asp222 serves as the catalytic residue adding an α-hydrogen to the quinonoid intermediate to form D-allo-isoleucine.

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IN Silico Approach of Some Selected Honey Constituents as SARS-CoV-2 Main Protease (COVID-19) Inhibitors

10.26434/chemrxiv.12115359 ◽

2020 ◽

Author(s):

Heba Hashem

Keyword(s):

Active Site ◽

Life Cycles ◽

High Binding Energy ◽

Protease Inhibition ◽

Enzyme Active Site ◽

Therapeutic Drugs ◽

Main Protease ◽

The World ◽

Essential Enzyme ◽

The Way

The huge attack of coronavirus disease 2019 (COVID-19) over all the world forces the researcher around the world to study the crystal structure of the main protease Mpro ( 3-chymotrypsin-like cysteine enzyme) which is the essential enzyme for coronavirus processing the polyproteins and its life cycles. And by the way, the inhibition of this enzyme active site becomes the target of all scientists of drug discovery in order to overcome this disease. In this study, we have used the molecular modeling approach to evaluate the activity of different active compounds from honeybee and propolis to inhibit the presented sars-cov-2 main protease via Schrödinger Maestro v10.1. the presented study resulted in six main compounds possess high binding energy with the receptor active site of COVID-19 main protease. we hope this study being the way for honeybee constitution as an effective ligand for sars-cov-2 main protease inhibition and be in the medicinal study of anti-COVID-19 therapeutic drugs.

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Structural Plasticity of the SARS-CoV-2 3CL Mpro Active Site Cavity Revealed by Room Temperature X-ray Crystallography

10.21203/rs.3.rs-28669/v1 ◽

2020 ◽

Author(s):

Daniel W. Kneller ◽

Gwyndalyn Phillips ◽

Hugh M. O'Neill ◽

Robert Jedrzejczak ◽

Lucy Stols ◽

...

Keyword(s):

Active Site ◽

Room Temperature ◽

Relevant Information ◽

Docking Studies ◽

Temperature Structure ◽

Health Crisis ◽

X Ray ◽

X Ray Crystallography ◽

Main Protease ◽

Active Site Cavity

Abstract The COVID-19 disease caused by the SARS-CoV-2 Coronavirus has become a pandemic health crisis. An attractive target for antiviral inhibitors is the main protease 3CL Mpro due to its essential role in processing the polyproteins translated from viral RNA. Here we report the room temperature X-ray structure of unliganded SARS-CoV-2 3CL Mpro, revealing the resting structure of the active site and the conformation of the catalytic site cavity. Comparison with previously reported low-temperature ligand-free and inhibitor-bound structures suggest that the room temperature structure may provide more relevant information at physiological temperatures for aiding in molecular docking studies.

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IN Silico Approach of Some Selected Honey Constituents as SARS-CoV-2 Main Protease (COVID-19) Inhibitors

10.26434/chemrxiv.12115359.v1 ◽

2020 ◽

Author(s):

Heba Hashem

Keyword(s):

Active Site ◽

Life Cycles ◽

High Binding Energy ◽

Protease Inhibition ◽

Enzyme Active Site ◽

Therapeutic Drugs ◽

Main Protease ◽

The World ◽

Essential Enzyme ◽

The Way

The huge attack of coronavirus disease 2019 (COVID-19) over all the world forces the researcher around the world to study the crystal structure of the main protease Mpro ( 3-chymotrypsin-like cysteine enzyme) which is the essential enzyme for coronavirus processing the polyproteins and its life cycles. And by the way, the inhibition of this enzyme active site becomes the target of all scientists of drug discovery in order to overcome this disease. In this study, we have used the molecular modeling approach to evaluate the activity of different active compounds from honeybee and propolis to inhibit the presented sars-cov-2 main protease via Schrödinger Maestro v10.1. the presented study resulted in six main compounds possess high binding energy with the receptor active site of COVID-19 main protease. we hope this study being the way for honeybee constitution as an effective ligand for sars-cov-2 main protease inhibition and be in the medicinal study of anti-COVID-19 therapeutic drugs.

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Inhibitor Binding Modulates Protonation States in the Active Site of SARS-CoV-2 Main Protease

10.1101/2021.01.12.426388 ◽

2021 ◽

Author(s):

Daniel W. Kneller ◽

Gwyndalyn Phillips ◽

Kevin L. Weiss ◽

Qiu Zhang ◽

Leighton Coates ◽

...

Keyword(s):

Active Site ◽

Rational Drug Design ◽

Inhibitor Binding ◽

Histidine Residues ◽

Main Protease ◽

Rational Drug ◽

Ligand Free ◽

Essential Enzyme ◽

Neutron Protein Crystallography ◽

Active Site Histidine

ABSTRACTThe main protease (3CL Mpro) from SARS-CoV-2, the virus that causes COVID-19, is an essential enzyme for viral replication with no human counterpart, making it an attractive drug target. Although drugs have been developed to inhibit the proteases from HIV, hepatitis C and other viruses, no such therapeutic is available to inhibit the main protease of SARS-CoV-2. To directly observe the protonation states in SARS-CoV-2 Mpro and to elucidate their importance in inhibitor binding, we determined the structure of the enzyme in complex with the α-ketoamide inhibitor telaprevir using neutron protein crystallography at near-physiological temperature. We compared protonation states in the inhibitor complex with those determined for a ligand-free neutron structure of Mpro. This comparison revealed that three active-site histidine residues (His41, His163 and His164) adapt to ligand binding, altering their protonation states to accommodate binding of telaprevir. We suggest that binding of other α-ketoamide inhibitors can lead to the same protonation state changes of the active site histidine residues. Thus, by studying the role of active site protonation changes induced by inhibitors we provide crucial insights to help guide rational drug design, allowing precise tailoring of inhibitors to manipulate the electrostatic environment of SARS-CoV-2 Mpro.

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Dual-Function, Light Switchable Cobalt Catalysis via Active Site Metamorphosis

10.26434/chemrxiv.11353106.v1 ◽

2019 ◽

Author(s):

Enrico Bergamaschi ◽

Frédéric Beltran ◽

Christopher Teskey

Keyword(s):

Visible Light ◽

Active Site ◽

Catalytic Site ◽

Dual Function ◽

Catalytic Systems ◽

Hydride Complex ◽

Dual Functional ◽

Multiple Processes ◽

Olefin Migration

Switchable catalysis offers opportunities to control the rate or selectivity of a reaction via a stimulus such as pH or light. However, few examples of switchable catalytic systems that can facilitate multiple processes exist. Here we report a rare example of such dual-functional, switchable catalysis. Featuring an easily prepared, bench-stable cobalt(I) hydride complex in conjunction with pinacolborane, we can completely alter the reaction outcome between two widely employed transformations – olefin migration and hydroboration – with visible light as the sole trigger. This dichotomy arises from ligand photodissociation which leads to metamorphosis of the active catalytic site, resulting in divergent mechanistic pathways.

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