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1.
Nat Chem Biol ; 18(4): 368-375, 2022 04.
Article in English | MEDLINE | ID: covidwho-1684084

ABSTRACT

We recently reported the discovery of a lysine-cysteine redox switch in proteins with a covalent nitrogen-oxygen-sulfur (NOS) bridge. Here, a systematic survey of the whole protein structure database discloses that NOS bridges are ubiquitous redox switches in proteins of all domains of life and are found in diverse structural motifs and chemical variants. In several instances, lysines are observed in simultaneous linkage with two cysteines, forming a sulfur-oxygen-nitrogen-oxygen-sulfur (SONOS) bridge with a trivalent nitrogen, which constitutes an unusual native branching cross-link. In many proteins, the NOS switch contains a functionally essential lysine with direct roles in enzyme catalysis or binding of substrates, DNA or effectors, linking lysine chemistry and redox biology as a regulatory principle. NOS/SONOS switches are frequently found in proteins from human and plant pathogens, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and also in many human proteins with established roles in gene expression, redox signaling and homeostasis in physiological and pathophysiological conditions.


Subject(s)
COVID-19 , Cysteine , Cysteine/chemistry , Humans , Lysine/metabolism , Oxidation-Reduction , SARS-CoV-2
2.
J Chem Inf Model ; 62(1): 129-141, 2022 01 10.
Article in English | MEDLINE | ID: covidwho-1593565

ABSTRACT

Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they affect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the effect of oxidation of the highly reactive cysteine (Cys) amino acids of the RBD on its binding to ACE2 and GRP78. The interaction energy of both ACE2 and GRP78 with the whole RBD, as well as with the RBD main regions, is compared in both the native and oxidized RBDs. Our results show that the interaction energy between the oxidized RBD and ACE2 is strengthened by 155 kJ/mol, increasing the binding of the RBD to ACE2 after oxidation. In addition, the interaction energy between the RBD and GRP78 is slightly increased by 8 kJ/mol after oxidation, but this difference is not significant. Overall, these findings highlight the role of RONS in the binding of the SARS-CoV-2 S-glycoprotein to host cell receptors and suggest an alternative mechanism by which RONS could modulate the entrance of viral particles into the cells.


Subject(s)
Cysteine/chemistry , Spike Glycoprotein, Coronavirus/chemistry , Angiotensin-Converting Enzyme 2/metabolism , COVID-19 , Humans , Reactive Nitrogen Species , Reactive Oxygen Species , Receptors, Virus/metabolism , SARS-CoV-2
3.
ChemistryOpen ; 10(11): 1133-1141, 2021 11.
Article in English | MEDLINE | ID: covidwho-1520270

ABSTRACT

We present in this work a first X-ray Absorption Spectroscopy study of the interactions of Zn with human BST2/tetherin and SARS-CoV-2 orf7a proteins as well as with some of their complexes. The analysis of the XANES region of the measured spectra shows that Zn binds to BST2, as well as to orf7a, thus resulting in the formation of BST2-orf7a complexes. This structural information confirms the the conjecture, recently put forward by some of the present Authors, according to which the accessory orf7a (and possibly also orf8) viral protein are capable of interfering with the BST2 antiviral activity. Our explanation for this behavior is that, when BST2 gets in contact with Zn bound to the orf7a Cys15 ligand, it has the ability of displacing the metal owing to the creation of a new disulfide bridge across the two proteins. The formation of this BST2-orf7a complex destabilizes BST2 dimerization, thus impairing the antiviral activity of the latter.


Subject(s)
Antigens, CD/metabolism , SARS-CoV-2/chemistry , Viral Proteins/metabolism , Zinc/metabolism , Cysteine/chemistry , GPI-Linked Proteins/metabolism , Histidine/chemistry , Humans , Molecular Dynamics Simulation , Protein Binding , X-Ray Absorption Spectroscopy
4.
Anal Bioanal Chem ; 413(30): 7559-7585, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1503906

ABSTRACT

Subunit vaccines based on the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 provide one of the most promising strategies to fight the COVID-19 pandemic. The detailed characterization of the protein primary structure by mass spectrometry (MS) is mandatory, as described in ICHQ6B guidelines. In this work, several recombinant RBD proteins produced in five expression systems were characterized using a non-conventional protocol known as in-solution buffer-free digestion (BFD). In a single ESI-MS spectrum, BFD allowed very high sequence coverage (≥ 99%) and the detection of highly hydrophilic regions, including very short and hydrophilic peptides (2-8 amino acids), and the His6-tagged C-terminal peptide carrying several post-translational modifications at Cys538 such as cysteinylation, homocysteinylation, glutathionylation, truncated glutathionylation, and cyanylation, among others. The analysis using the conventional digestion protocol allowed lower sequence coverage (80-90%) and did not detect peptides carrying most of the above-mentioned PTMs. The two C-terminal peptides of a dimer [RBD(319-541)-(His)6]2 linked by an intermolecular disulfide bond (Cys538-Cys538) with twelve histidine residues were only detected by BFD. This protocol allows the detection of the four disulfide bonds present in the native RBD, low-abundance scrambling variants, free cysteine residues, O-glycoforms, and incomplete processing of the N-terminal end, if present. Artifacts generated by the in-solution BFD protocol were also characterized. BFD can be easily implemented; it has been applied to the characterization of the active pharmaceutical ingredient of two RBD-based vaccines, and we foresee that it can be also helpful to the characterization of mutated RBDs.


Subject(s)
Cysteine/metabolism , Peptide Fragments/metabolism , Protein Processing, Post-Translational , Spectrometry, Mass, Electrospray Ionization/methods , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/metabolism , Amino Acid Sequence , Cysteine/chemistry , Humans , Hydrophobic and Hydrophilic Interactions , Peptide Fragments/chemistry , Protein Binding , Protein Domains , Protein Subunits
5.
Mikrochim Acta ; 188(10): 335, 2021 Sep 09.
Article in English | MEDLINE | ID: covidwho-1411927

ABSTRACT

A practical colorimetric assay was developed for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). For this purpose, magnetic γ Fe2O3 nanoparticles were synthesized and used as a peroxidase-like mimic activity molecule. In the presence of γ Fe2O3 nanoparticles, the color change of H2O2 included 3,3',5,5'-tetramethylbenzidine was monitored at the wavelength of 654 nm when spike protein interacted with angiotensin-converting enzyme 2 receptor. This oxidation-reduction reaction was examined both spectroscopically and by using electrochemical techniques. The experimental parameters were optimized and the analytical characteristics investigated. The developed assay was applied to real SARS-CoV-2 samples, and very good results that were in accordance with the real time polymerase chain reaction were obtained.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , Colorimetry/methods , Magnetic Iron Oxide Nanoparticles/chemistry , SARS-CoV-2/chemistry , Spike Glycoprotein, Coronavirus/chemistry , Angiotensin-Converting Enzyme 2/metabolism , Benzidines/chemistry , Biosensing Techniques/methods , COVID-19 Testing/instrumentation , Catalysis , Chromogenic Compounds/chemistry , Cysteine/chemistry , Humans , Hydrogen Peroxide/chemistry , Limit of Detection , Nasopharynx/virology , Oropharynx/virology , Oxidation-Reduction , Peroxidase/chemistry , Spike Glycoprotein, Coronavirus/metabolism
6.
Mikrochim Acta ; 188(8): 284, 2021 08 02.
Article in English | MEDLINE | ID: covidwho-1397013

ABSTRACT

An aptasensor for electrochemical detection of carbendazim is reported with mulberry fruit-like gold nanocrystal (MF-Au)/multiple graphene aerogel (MGA) and DNA cycle amplification. HAuCl4 was reduced by ascorbic acid in a CTAC solution containing KBr and KI and formed trioctahedron gold nanocrystal. The gold nanocrystal underwent structural evolution under enantioselective direction of L-cysteine. The resulting MF-Au shows a mulberry fruit-like nanostructure composed of gold nanocrystals of about 200 nm as the core and many irregular gold nanoparticles of about 30 nm as the shell. The exposure of high-index facets improves the catalytic activity of MF-Au. MF-Au/MGA was used for the construction of an aptasensor for electrochemical detection of carbendazim. The aptamer hybridizes with assistant strand DNA to form duplex DNA. Carbendazim binds with the formed duplex DNA to release assistant strand DNA, triggering one three-cascade DNA cycle. The utilization of a DNA cycle allows one carbendazim molecule to bring many methylene blue-labeled DNA fragments to the electrode surface. This promotes significant signal amplification due to the redox reaction of methylene blue. The detection signal is further enhanced by the catalysis of MF-Au and MGA towards the redox of methylene blue. A differential pulse voltammetric signal, best measured at - 0.32 V vs. Ag/AgCl, increases linearly with the carbendazim concentration ranging from 1.0 × 10-16 to 1.0 × 10-11 M with a detection limit of 4.4 × 10-17 M. The method provides ultrahigh sensitivity and selectivity and was successfully applied to the electrochemical detection of carbendazim in cucumber. This study reports on an ultrasensitive aptasensor for electrochemical detection of carbendazim in cucumber based on mulberry fruit-like gold nanocrystal-multiple graphene aerogel and DNA cycle double amplification.


Subject(s)
Aptamers, Nucleotide/chemistry , Benzimidazoles/analysis , Biosensing Techniques/methods , Carbamates/analysis , DNA/chemistry , Metal Nanoparticles/chemistry , Benzimidazoles/chemistry , Carbamates/chemistry , Cysteine/chemistry , Electrochemical Techniques/methods , Gels/chemistry , Gold/chemistry , Graphite/chemistry , Immobilized Nucleic Acids/chemistry , Limit of Detection , Methylene Blue/chemistry , Oxidation-Reduction
7.
Nat Commun ; 12(1): 3061, 2021 05 24.
Article in English | MEDLINE | ID: covidwho-1387342

ABSTRACT

The SARS-CoV-2 pandemic has triggered global efforts to develop therapeutics. The main protease of SARS-CoV-2 (Mpro), critical for viral replication, is a key target for therapeutic development. An organoselenium drug called ebselen has been demonstrated to have potent Mpro inhibition and antiviral activity. We have examined the binding modes of ebselen and its derivative in Mpro via high resolution co-crystallography and investigated their chemical reactivity via mass spectrometry. Stronger Mpro inhibition than ebselen and potent ability to rescue infected cells were observed for a number of derivatives. A free selenium atom bound with cysteine of catalytic dyad has been revealed in crystallographic structures of Mpro with ebselen and MR6-31-2 suggesting hydrolysis of the enzyme bound organoselenium covalent adduct and formation of a phenolic by-product, confirmed by mass spectrometry. The target engagement with selenation mechanism of inhibition suggests wider therapeutic applications of these compounds against SARS-CoV-2 and other zoonotic beta-corona viruses.


Subject(s)
Azoles/pharmacology , Coronavirus 3C Proteases/antagonists & inhibitors , Organoselenium Compounds/pharmacology , SARS-CoV-2/enzymology , Antiviral Agents/pharmacology , Azoles/chemistry , Catalytic Domain , Coronavirus 3C Proteases/metabolism , Crystallography, X-Ray , Cysteine/chemistry , Hydrolysis , Isoindoles , Models, Molecular , Organoselenium Compounds/chemistry , Protease Inhibitors/chemistry , Protease Inhibitors/pharmacology , Reference Standards , SARS-CoV-2/drug effects , Salicylanilides/chemistry , Salicylanilides/pharmacology , Selenium/metabolism
8.
Bioorg Med Chem Lett ; 50: 128333, 2021 10 15.
Article in English | MEDLINE | ID: covidwho-1363893

ABSTRACT

Specific anti-coronaviral drugs complementing available vaccines are urgently needed to fight the COVID-19 pandemic. Given its high conservation across the betacoronavirus genus and dissimilarity to human proteases, the SARS-CoV-2 main protease (Mpro) is an attractive drug target. SARS-CoV-2 Mpro inhibitors have been developed at unprecedented speed, most of them being substrate-derived peptidomimetics with cysteine-modifying warheads. In this study, Mpro has proven resistant towards the identification of high-affinity short substrate-derived peptides and peptidomimetics without warheads. 20 cyclic and linear substrate analogues bearing natural and unnatural residues, which were predicted by computational modelling to bind with high affinity and designed to establish structure-activity relationships, displayed no inhibitory activity at concentrations as high as 100 µM. Only a long linear peptide covering residues P6 to P5' displayed moderate inhibition (Ki = 57 µM). Our detailed findings will inform current and future drug discovery campaigns targeting Mpro.


Subject(s)
COVID-19/pathology , Coronavirus 3C Proteases/antagonists & inhibitors , Protease Inhibitors/chemistry , SARS-CoV-2/enzymology , COVID-19/virology , Coronavirus 3C Proteases/metabolism , Cysteine/chemistry , Cysteine/metabolism , Humans , Lactams/chemistry , Lactams/metabolism , Leucine/chemistry , Leucine/metabolism , Nitriles/chemistry , Nitriles/metabolism , Peptides/chemistry , Peptides/metabolism , Peptidomimetics/chemistry , Peptidomimetics/metabolism , Proline/chemistry , Proline/metabolism , Protease Inhibitors/metabolism , SARS-CoV-2/isolation & purification , Structure-Activity Relationship , Substrate Specificity
9.
mBio ; 12(4): e0209421, 2021 08 31.
Article in English | MEDLINE | ID: covidwho-1360546

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent for coronavirus disease 2019 (COVID-19), encodes two proteases required for replication. The main protease (Mpro), encoded as part of two polyproteins, pp1a and pp1ab, is responsible for 11 different cleavages of these viral polyproteins to produce mature proteins required for viral replication. Mpro is therefore an attractive target for therapeutic interventions. Certain proteins in cells under oxidative stress undergo modification of reactive cysteines. We show Mpro is susceptible to glutathionylation, leading to inhibition of dimerization and activity. Activity of glutathionylated Mpro could be restored with reducing agents or glutaredoxin. Analytical studies demonstrated that glutathionylated Mpro primarily exists as a monomer and that modification of a single cysteine with glutathione is sufficient to block dimerization and inhibit its activity. Gel filtration studies as well as analytical ultracentrifugation confirmed that glutathionylated Mpro exists as a monomer. Tryptic and chymotryptic digestions of Mpro as well as experiments using a C300S Mpro mutant revealed that Cys300, which is located at the dimer interface, is a primary target of glutathionylation. Moreover, Cys300 is required for inhibition of activity upon Mpro glutathionylation. These findings indicate that Mpro dimerization and activity can be regulated through reversible glutathionylation of a non-active site cysteine, Cys300, which itself is not required for Mpro activity, and provides a novel target for the development of agents to block Mpro dimerization and activity. This feature of Mpro may have relevance to the pathophysiology of SARS-CoV-2 and related bat coronaviruses. IMPORTANCE SARS-CoV-2 is responsible for the devastating COVID-19 pandemic. Therefore, it is imperative that we learn as much as we can about the biochemistry of the coronavirus proteins to inform development of therapy. One attractive target is the main protease (Mpro), a dimeric enzyme necessary for viral replication. Most work thus far developing Mpro inhibitors has focused on the active site. Our work has revealed a regulatory mechanism for Mpro activity through glutathionylation of a cysteine (Cys300) at the dimer interface, which can occur in cells under oxidative stress. Cys300 glutathionylation inhibits Mpro activity by blocking its dimerization. This provides a novel accessible and reactive target for drug development. Moreover, this process may have implications for disease pathophysiology in humans and bats. It may be a mechanism by which SARS-CoV-2 has evolved to limit replication and avoid killing host bats when they are under oxidative stress during flight.


Subject(s)
Coronavirus 3C Proteases/metabolism , Cysteine/chemistry , Glutathione/chemistry , Protein Multimerization , SARS-CoV-2/metabolism , Animals , COVID-19/pathology , Chiroptera/virology , Coronavirus 3C Proteases/antagonists & inhibitors , Dimerization , Glutaredoxins/metabolism , Humans , SARS-CoV-2/enzymology
10.
J Am Chem Soc ; 142(52): 21883-21890, 2020 12 30.
Article in English | MEDLINE | ID: covidwho-1065801

ABSTRACT

The SARS coronavirus 2 (SARS-CoV-2) main protease (Mpro) is an attractive broad-spectrum antiviral drug target. Despite the enormous progress in structure elucidation, the Mpro's structure-function relationship remains poorly understood. Recently, a peptidomimetic inhibitor has entered clinical trial; however, small-molecule orally available antiviral drugs have yet to be developed. Intrigued by a long-standing controversy regarding the existence of an inactive state, we explored the proton-coupled dynamics of the Mpros of SARS-CoV-2 and the closely related SARS-CoV using a newly developed continuous constant pH molecular dynamics (MD) method and microsecond fixed-charge all-atom MD simulations. Our data supports a general base mechanism for Mpro's proteolytic function. The simulations revealed that protonation of His172 alters a conserved interaction network that upholds the oxyanion loop, leading to a partial collapse of the conserved S1 pocket, consistent with the first and controversial crystal structure of SARS-CoV Mpro determined at pH 6. Interestingly, a natural flavonoid binds SARS-CoV-2 Mpro in the close proximity to a conserved cysteine (Cys44), which is hyper-reactive according to the CpHMD titration. This finding offers an exciting new opportunity for small-molecule targeted covalent inhibitor design. Our work represents a first step toward the mechanistic understanding of the proton-coupled structure-dynamics-function relationship of CoV Mpros; the proposed strategy of designing small-molecule covalent inhibitors may help accelerate the development of orally available broad-spectrum antiviral drugs to stop the current pandemic and prevent future outbreaks.


Subject(s)
Antiviral Agents/chemistry , Antiviral Agents/pharmacology , Coronavirus 3C Proteases/chemistry , Coronavirus 3C Proteases/drug effects , SARS-CoV-2/drug effects , SARS-CoV-2/enzymology , Binding Sites , Cysteine/chemistry , Drug Design , Humans , Hydrogen-Ion Concentration , Models, Molecular , Molecular Dynamics Simulation , Protease Inhibitors/pharmacology , Protein Conformation , Protons , Small Molecule Libraries , Structure-Activity Relationship
11.
ChemMedChem ; 16(6): 942-948, 2021 03 18.
Article in English | MEDLINE | ID: covidwho-959133

ABSTRACT

The COVID-19 pathogen, SARS-CoV-2, requires its main protease (SC2MPro ) to digest two of its translated long polypeptides to form a number of mature proteins that are essential for viral replication and pathogenesis. Inhibition of this vital proteolytic process is effective in preventing the virus from replicating in infected cells and therefore provides a potential COVID-19 treatment option. Guided by previous medicinal chemistry studies about SARS-CoV-1 main protease (SC1MPro ), we have designed and synthesized a series of SC2MPro inhibitors that contain ß-(S-2-oxopyrrolidin-3-yl)-alaninal (Opal) for the formation of a reversible covalent bond with the SC2MPro active-site cysteine C145. All inhibitors display high potency with Ki values at or below 100 nM. The most potent compound, MPI3, has as a Ki value of 8.3 nM. Crystallographic analyses of SC2MPro bound to seven inhibitors indicated both formation of a covalent bond with C145 and structural rearrangement from the apoenzyme to accommodate the inhibitors. Virus inhibition assays revealed that several inhibitors have high potency in inhibiting the SARS-CoV-2-induced cytopathogenic effect in both Vero E6 and A549/ACE2 cells. Two inhibitors, MPI5 and MPI8, completely prevented the SARS-CoV-2-induced cytopathogenic effect in Vero E6 cells at 2.5-5 µM and A549/ACE2 cells at 0.16-0.31 µM. Their virus inhibition potency is much higher than that of some existing molecules that are under preclinical and clinical investigations for the treatment of COVID-19. Our study indicates that there is a large chemical space that needs to be explored for the development of SC2MPro inhibitors with ultra-high antiviral potency.


Subject(s)
Antiviral Agents/pharmacology , Coronavirus 3C Proteases/antagonists & inhibitors , Cysteine Proteinase Inhibitors/pharmacology , SARS-CoV-2/drug effects , A549 Cells , Alanine/analogs & derivatives , Alanine/metabolism , Alanine/pharmacology , Animals , Antiviral Agents/chemical synthesis , Antiviral Agents/metabolism , Catalytic Domain , Chlorocebus aethiops , Coronavirus 3C Proteases/chemistry , Coronavirus 3C Proteases/metabolism , Cysteine/chemistry , Cysteine Proteinase Inhibitors/chemical synthesis , Cysteine Proteinase Inhibitors/metabolism , Humans , Microbial Sensitivity Tests , Protein Binding , Pyrrolidinones/chemical synthesis , Pyrrolidinones/metabolism , Pyrrolidinones/pharmacology , SARS-CoV-2/enzymology , Vero Cells
12.
Biol Direct ; 15(1): 19, 2020 10 16.
Article in English | MEDLINE | ID: covidwho-874053

ABSTRACT

The spike glycoprotein of the SARS-CoV-2 virus, which causes COVID-19, has attracted attention for its vaccine potential and binding capacity to host cell surface receptors. Much of this research focus has centered on the ectodomain of the spike protein. The ectodomain is anchored to a transmembrane region, followed by a cytoplasmic tail. Here we report a distant sequence similarity between the cysteine-rich cytoplasmic tail of the coronavirus spike protein and the hepcidin protein that is found in humans and other vertebrates. Hepcidin is thought to be the key regulator of iron metabolism in humans through its inhibition of the iron-exporting protein ferroportin. An implication of this preliminary observation is to suggest a potential route of investigation in the coronavirus research field making use of an already-established literature on the interplay of local and systemic iron regulation, cytokine-mediated inflammatory processes, respiratory infections and the hepcidin protein. The question of possible homology and an evolutionary connection between the viral spike protein and hepcidin is not assessed in this report, but some scenarios for its study are discussed.


Subject(s)
COVID-19/virology , Hepcidins/genetics , Iron/metabolism , Spike Glycoprotein, Coronavirus/genetics , Animals , Cation Transport Proteins/metabolism , Cysteine/chemistry , Cytokines/metabolism , Cytoplasm/metabolism , Hepcidins/chemistry , Humans , Hypoxia , Inflammation , Interleukin-6/metabolism , Pandemics , Protein Domains , Protein Processing, Post-Translational , SARS-CoV-2 , Sequence Alignment , Spike Glycoprotein, Coronavirus/chemistry , Tetraodontiformes
13.
Phys Chem Chem Phys ; 22(34): 19069-19079, 2020 Sep 08.
Article in English | MEDLINE | ID: covidwho-722683

ABSTRACT

A dynamical approach is proposed to discriminate between reactive (rES) and nonreactive (nES) enzyme-substrate complexes taking the SARS-CoV-2 main protease (Mpro) as an important example. Molecular dynamics simulations with the quantum mechanics/molecular mechanics potentials (QM(DFT)/MM-MD) followed by the electron density analysis are employed to evaluate geometry and electronic properties of the enzyme with different substrates along MD trajectories. We demonstrate that mapping the Laplacian of the electron density and the electron localization function provides easily visible images of the substrate activation that allow one to distinguish rES and nES. The computed fractions of reactive enzyme-substrate complexes along MD trajectories well correlate with the findings of recent experimental studies on the substrate specificity of Mpro. The results of our simulations demonstrate the role of the theory level used in QM subsystems for a proper description of the nucleophilic attack of the catalytic cysteine residue in Mpro. The activation of the carbonyl group of a substrate is correctly characterized with the hybrid DFT functional PBE0, whereas the use of a GGA-type PBE functional, that lacks the admixture of the Hartree-Fock exchange fails to describe activation.


Subject(s)
Betacoronavirus/enzymology , Cysteine Endopeptidases/metabolism , Viral Nonstructural Proteins/metabolism , Betacoronavirus/isolation & purification , COVID-19 , Catalytic Domain , Coronavirus 3C Proteases , Coronavirus Infections/pathology , Coronavirus Infections/virology , Cysteine/chemistry , Cysteine/metabolism , Density Functional Theory , Electrons , Humans , Molecular Dynamics Simulation , Pandemics , Pneumonia, Viral/pathology , Pneumonia, Viral/virology , Protein Structure, Tertiary , SARS-CoV-2 , Substrate Specificity
14.
J Inorg Biochem ; 211: 111179, 2020 10.
Article in English | MEDLINE | ID: covidwho-654489

ABSTRACT

We have investigated the structural stability of the SARS (Severe acute respiratory syndrome)-CoV-2 main protease monomer (Mpro). We quantified the spatial and angular changes in the structure using two independent analyses, one based on a spatial metrics (δ, ratio), the second on angular metrics. The order of unfolding of the 10 helices in Mpro is characterized by beta vs alpha plots similar to those of cytochromes and globins. The longest turning region is anomalous in the earliest stage of unfolding. In an investigation of excluded-volume effects, we found that the maximum spread in average molecular-volume values for Mpro, cytochrome c-b562, cytochrome c', myoglobin, and cytoglobin is ~10 Å3. This apparent universality is a consequence of the dominant contributions from six residues: ALA, ASP, GLU, LEU, LYS and VAL. Of the seven Mpro histidines, residues 41, 163, 164, and 246 are in stable H-bonded regions; metal ion binding to one or more of these residues could break up the H-bond network, thereby affecting protease function. Our analysis also indicated that metal binding to cysteine residues 44 and 145 could disable the enzyme.


Subject(s)
Coronavirus 3C Proteases/chemistry , SARS-CoV-2/enzymology , Cobalt/chemistry , Cobalt/metabolism , Coronavirus 3C Proteases/antagonists & inhibitors , Coronavirus 3C Proteases/metabolism , Cysteine/chemistry , Histidine/chemistry , Protease Inhibitors/chemistry , Protease Inhibitors/metabolism , Protein Binding , Protein Stability/drug effects , Protein Unfolding/drug effects
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