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1.
Food Funct ; 11(6): 5565-5572, 2020 Jun 24.
Article in English | MEDLINE | ID: covidwho-1721602

ABSTRACT

To date, no specific drug has been discovered for the treatment of COVID-19 and hence, people are in a state of anxiety. Thus, there is an urgent need to search for various possible strategies including nutritional supplementation. In this study, we have tried to provide a reference for protein supplementation. Specifically, 20 marine fish proteins were subjected to in silico hydrolysis by gastrointestinal enzymes, and a large number of active peptides were generated. Then, the binding abilities of these peptides to SARS-CoV-2 main protease and monoamine oxidase A were assessed. The results showed that NADH dehydrogenase could be a good protein source in generating potent binders to the two enzymes, followed by cytochrome b. In addition, some high-affinity oligopeptides (VIQY, ICIY, PISQF, VISAW, AIPAW, and PVSQF) were identified as dual binders to the two enzymes. In summary, the supplementation of some fish proteins can be helpful for COVID-19 patients; the identified oligopeptides can be used as the lead compounds to design potential inhibitors against COVID-19 and anxiety.


Subject(s)
Antiviral Agents/metabolism , Betacoronavirus/metabolism , Coronavirus Infections/virology , Dietary Supplements , Fish Proteins/metabolism , Monoamine Oxidase/metabolism , Pneumonia, Viral/virology , Animals , Antiviral Agents/chemistry , Antiviral Agents/therapeutic use , Aquatic Organisms , Betacoronavirus/enzymology , COVID-19 , Coronavirus Infections/drug therapy , Decapodiformes/metabolism , Fish Proteins/chemistry , Fish Proteins/therapeutic use , Fishes/metabolism , Models, Molecular , Molecular Docking Simulation , Monoamine Oxidase Inhibitors , Pandemics , Perciformes/metabolism , Pneumonia, Viral/drug therapy , Protein Binding , Protein Conformation , SARS-CoV-2 , Salmon/metabolism , Tuna/metabolism
2.
J Virol ; 95(15): e0046321, 2021 07 12.
Article in English | MEDLINE | ID: covidwho-1486505

ABSTRACT

The OC43 coronavirus is a human pathogen that usually causes only the common cold. One of its key enzymes, similar to other coronaviruses, is the 2'-O-RNA methyltransferase (MTase), which is essential for viral RNA stability and expression. Here, we report the crystal structure of the 2'-O-RNA MTase in a complex with the pan-methyltransferase inhibitor sinefungin solved at 2.2-Å resolution. The structure reveals an overall fold consistent with the fold observed in other coronaviral MTases. The major differences are in the conformation of the C terminus of the nsp16 subunit and an additional helix in the N terminus of the nsp10 subunits. The structural analysis also revealed very high conservation of the S-adenosyl methionine (SAM) binding pocket, suggesting that the SAM pocket is a suitable spot for the design of antivirals effective against all human coronaviruses. IMPORTANCE Some coronaviruses are dangerous pathogens, while some cause only common colds. The reasons are not understood, although the spike proteins probably play an important role. However, to understand the coronaviral biology in sufficient detail, we need to compare the key enzymes from different coronaviruses. We solved the crystal structure of 2'-O-RNA methyltransferase of the OC43 coronavirus, a virus that usually causes mild colds. The structure revealed some differences in the overall fold but also revealed that the SAM binding site is conserved, suggesting that development of antivirals against multiple coronaviruses is feasible.


Subject(s)
Betacoronavirus/enzymology , Methyltransferases/chemistry , Viral Proteins/chemistry , Betacoronavirus/genetics , Binding Sites , Crystallography, X-Ray , Methyltransferases/genetics , Protein Conformation, alpha-Helical , Viral Proteins/genetics
3.
Molecules ; 25(19)2020 Oct 06.
Article in English | MEDLINE | ID: covidwho-1389458

ABSTRACT

A novel series of some hydrazones bearing thiazole moiety were generated via solvent-drop grinding of thiazole carbohydrazide 2 with various carbonyl compounds. Also, dehydrative-cyclocondensation of 2 with active methylene compounds or anhydrides gave the respective pyarzole or pyrazine derivatives. The structures of the newly synthesized compounds were established based on spectroscopic evidences and their alternative syntheses. Additionally, the anti-viral activity of all the products was tested against SARS-CoV-2 main protease (Mpro) using molecular docking combined with molecular dynamics simulation (MDS). The average binding affinities of the compounds 3a, 3b, and 3c (-8.1 ± 0.33 kcal/mol, -8.0 ± 0.35 kcal/mol, and -8.2 ± 0.21 kcal/mol, respectively) are better than that of the positive control Nelfinavir (-6.9 ± 0.51 kcal/mol). This shows the possibility of these three compounds to effectively bind to SARS-CoV-2 Mpro and hence, contradict the virus lifecycle.


Subject(s)
Antiviral Agents/chemical synthesis , Betacoronavirus/enzymology , Hydrazones/chemical synthesis , Protease Inhibitors/chemical synthesis , Pyrazines/chemical synthesis , Pyrazoles/chemical synthesis , Viral Nonstructural Proteins/antagonists & inhibitors , Antiviral Agents/pharmacology , Betacoronavirus/chemistry , Betacoronavirus/drug effects , Binding Sites , COVID-19 , Coronavirus 3C Proteases , Coronavirus Infections/drug therapy , Cysteine Endopeptidases/chemistry , Cysteine Endopeptidases/metabolism , Drug Discovery , Humans , Hydrazones/pharmacology , Molecular Docking Simulation , Molecular Dynamics Simulation , Pandemics , Pneumonia, Viral/drug therapy , Protease Inhibitors/pharmacology , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , Pyrazines/pharmacology , Pyrazoles/pharmacology , SARS-CoV-2 , Thermodynamics , User-Computer Interface , Viral Nonstructural Proteins/chemistry , Viral Nonstructural Proteins/metabolism
5.
Biochemistry ; 59(39): 3741-3756, 2020 10 06.
Article in English | MEDLINE | ID: covidwho-1387098

ABSTRACT

The SARS-CoV-2 main protease (Mpro) is essential to viral replication and cleaves highly specific substrate sequences, making it an obvious target for inhibitor design. However, as for any virus, SARS-CoV-2 is subject to constant neutral drift and selection pressure, with new Mpro mutations arising over time. Identification and structural characterization of Mpro variants is thus critical for robust inhibitor design. Here we report sequence analysis, structure predictions, and molecular modeling for seventy-nine Mpro variants, constituting all clinically observed mutations in this protein as of April 29, 2020. Residue substitution is widely distributed, with some tendency toward larger and more hydrophobic residues. Modeling and protein structure network analysis suggest differences in cohesion and active site flexibility, revealing patterns in viral evolution that have relevance for drug discovery.


Subject(s)
Betacoronavirus/enzymology , Betacoronavirus/genetics , Models, Molecular , Mutation , Viral Nonstructural Proteins/genetics , Catalytic Domain , Drug Discovery , Evolution, Molecular , Humans , Molecular Structure , Phylogeny , Protease Inhibitors/chemistry , SARS-CoV-2 , Sequence Analysis, Protein , Viral Nonstructural Proteins/antagonists & inhibitors
6.
SAR QSAR Environ Res ; 31(7): 511-526, 2020 Jul.
Article in English | MEDLINE | ID: covidwho-1301250

ABSTRACT

In the context of recently emerged pandemic of COVID-19, we have performed two-dimensional quantitative structure-activity relationship (2D-QSAR) modelling using SARS-CoV-3CLpro enzyme inhibitors for the development of a multiple linear regression (MLR) based model. We have used 2D descriptors with an aim to develop an easily interpretable, transferable and reproducible model which may be used for quick prediction of SAR-CoV-3CLpro inhibitory activity for query compounds in the screening process. Based on the insights obtained from the developed 2D-QSAR model, we have identified the structural features responsible for the enhancement of the inhibitory activity against 3CLpro enzyme. Moreover, we have performed the molecular docking analysis using the most and least active molecules from the dataset to understand the molecular interactions involved in binding, and the results were then correlated with the essential structural features obtained from the 2D-QSAR model. Additionally, we have performed in silico predictions of SARS-CoV 3CLpro enzyme inhibitory activity of a total of 50,437 compounds obtained from two anti-viral drug databases (CAS COVID-19 antiviral candidate compound database and another recently reported list of prioritized compounds from the ZINC15 database) using the developed model and provided prioritized compounds for experimental detection of their performance for SARS-CoV 3CLpro enzyme inhibition.


Subject(s)
Betacoronavirus/enzymology , Cysteine Endopeptidases/chemistry , Protease Inhibitors/chemistry , Protease Inhibitors/pharmacology , Quantitative Structure-Activity Relationship , Antiviral Agents/chemistry , Antiviral Agents/pharmacology , Betacoronavirus/drug effects , COVID-19 , Coronavirus Infections , Drug Design , Linear Models , Molecular Docking Simulation , Pandemics , Pneumonia, Viral , SARS-CoV-2
7.
J Virol ; 95(15): e0046321, 2021 07 12.
Article in English | MEDLINE | ID: covidwho-1236419

ABSTRACT

The OC43 coronavirus is a human pathogen that usually causes only the common cold. One of its key enzymes, similar to other coronaviruses, is the 2'-O-RNA methyltransferase (MTase), which is essential for viral RNA stability and expression. Here, we report the crystal structure of the 2'-O-RNA MTase in a complex with the pan-methyltransferase inhibitor sinefungin solved at 2.2-Å resolution. The structure reveals an overall fold consistent with the fold observed in other coronaviral MTases. The major differences are in the conformation of the C terminus of the nsp16 subunit and an additional helix in the N terminus of the nsp10 subunits. The structural analysis also revealed very high conservation of the S-adenosyl methionine (SAM) binding pocket, suggesting that the SAM pocket is a suitable spot for the design of antivirals effective against all human coronaviruses. IMPORTANCE Some coronaviruses are dangerous pathogens, while some cause only common colds. The reasons are not understood, although the spike proteins probably play an important role. However, to understand the coronaviral biology in sufficient detail, we need to compare the key enzymes from different coronaviruses. We solved the crystal structure of 2'-O-RNA methyltransferase of the OC43 coronavirus, a virus that usually causes mild colds. The structure revealed some differences in the overall fold but also revealed that the SAM binding site is conserved, suggesting that development of antivirals against multiple coronaviruses is feasible.


Subject(s)
Betacoronavirus/enzymology , Methyltransferases/chemistry , Viral Proteins/chemistry , Betacoronavirus/genetics , Binding Sites , Crystallography, X-Ray , Methyltransferases/genetics , Protein Conformation, alpha-Helical , Viral Proteins/genetics
8.
Molecules ; 25(20)2020 Oct 13.
Article in English | MEDLINE | ID: covidwho-1197552

ABSTRACT

The global SARS-CoV-2 pandemic started late 2019 and currently continues unabated. The lag-time for developing vaccines means it is of paramount importance to be able to quickly develop and repurpose therapeutic drugs. Protein-based biosensors allow screening to be performed using routine molecular laboratory equipment without a need for expensive chemical reagents. Here we present a biosensor for the 3-chymotrypsin-like cysteine protease from SARS-CoV-2, comprising a FRET-capable pair of fluorescent proteins held in proximity by a protease cleavable linker. We demonstrate the utility of this biosensor for inhibitor discovery by screening 1280 compounds from the Library of Pharmaceutically Active Compounds collection. The screening identified 65 inhibitors, with the 20 most active exhibiting sub-micromolar inhibition of 3CLpro in follow-up EC50 assays. The top hits included several compounds not previously identified as 3CLpro inhibitors, in particular five members of a family of aporphine alkaloids that offer promise as new antiviral drug leads.


Subject(s)
Betacoronavirus/drug effects , Biosensing Techniques/methods , Coronavirus Infections/drug therapy , Fluorescence Resonance Energy Transfer/methods , Pneumonia, Viral/drug therapy , Protease Inhibitors/chemistry , Protease Inhibitors/pharmacology , Viral Nonstructural Proteins/antagonists & inhibitors , Betacoronavirus/enzymology , Betacoronavirus/isolation & purification , COVID-19 , Coronavirus 3C Proteases , Coronavirus Infections/virology , Cysteine Endopeptidases , High-Throughput Screening Assays , Humans , Pandemics , Pneumonia, Viral/virology , SARS-CoV-2
9.
Viruses ; 12(9)2020 08 26.
Article in English | MEDLINE | ID: covidwho-1121700

ABSTRACT

Coronaviruses are viral infections that have a significant ability to impact human health. Coronaviruses have produced two pandemics and one epidemic in the last two decades. The current pandemic has created a worldwide catastrophe threatening the lives of over 15 million as of July 2020. Current research efforts have been focused on producing a vaccine or repurposing current drug compounds to develop a therapeutic. There is, however, a need to study the active site preferences of relevant targets, such as the SARS-CoV-2 main protease (SARS-CoV-2 Mpro), to determine ways to optimize these drug compounds. The ensemble docking and characterization work described in this article demonstrates the multifaceted features of the SARS-CoV-2 Mpro active site, molecular guidelines to improving binding affinity, and ultimately the optimization of drug candidates. A total of 220 compounds were docked into both the 5R7Z and 6LU7 SARS-CoV-2 Mpro crystal structures. Several key preferences for strong binding to the four subsites (S1, S1', S2, and S4) were identified, such as accessing hydrogen binding hotspots, hydrophobic patches, and utilization of primarily aliphatic instead of aromatic substituents. After optimization efforts using the design guidelines developed from the molecular docking studies, the average docking score of the parent compounds was improved by 6.59 -log10(Kd) in binding affinity which represents an increase of greater than six orders of magnitude. Using the optimization guidelines, the SARS-CoV-2 Mpro inhibitor cinanserin was optimized resulting in an increase in binding affinity of 4.59 -log10(Kd) and increased protease inhibitor bioactivity. The results of molecular dynamic (MD) simulation of cinanserin-optimized compounds CM02, CM06, and CM07 revealed that CM02 and CM06 fit well into the active site of SARS-CoV-2 Mpro [Protein Data Bank (PDB) accession number 6LU7] and formed strong and stable interactions with the key residues, Ser-144, His-163, and Glu-166. The enhanced binding affinity produced demonstrates the utility of the design guidelines described. The work described herein will assist scientists in developing potent COVID-19 antivirals.


Subject(s)
Antiviral Agents/pharmacology , Betacoronavirus/drug effects , Coronavirus Infections/drug therapy , Coronavirus Infections/virology , Cysteine Endopeptidases/metabolism , Pneumonia, Viral/drug therapy , Pneumonia, Viral/virology , Protease Inhibitors/pharmacology , Viral Nonstructural Proteins/metabolism , Antiviral Agents/chemistry , Betacoronavirus/enzymology , Binding Sites , COVID-19 , Catalytic Domain , Coronavirus 3C Proteases , Cysteine Endopeptidases/chemistry , Drug Design , Drug Repositioning , Humans , Molecular Docking Simulation/methods , Molecular Dynamics Simulation , Pandemics , Protease Inhibitors/chemistry , Protein Conformation , SARS-CoV-2 , Viral Nonstructural Proteins/chemistry
10.
Biosci Rep ; 40(6)2020 06 26.
Article in English | MEDLINE | ID: covidwho-1099357

ABSTRACT

Due to the lack of efficient therapeutic options and clinical trial limitations, the FDA-approved drugs can be a good choice to handle Coronavirus disease (COVID-19). Many reports have enough evidence for the use of FDA-approved drugs which have inhibitory potential against target proteins of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Here, we utilized a structure-based drug design approach to find possible drug candidates from the existing pool of FDA-approved drugs and checked their effectiveness against the SARS-CoV-2. We performed virtual screening of the FDA-approved drugs against the main protease (Mpro) of SARS-CoV-2, an essential enzyme, and a potential drug target. Using well-defined computational methods, we identified Glecaprevir and Maraviroc (MVC) as the best inhibitors of SARS-CoV-2 Mpro. Both drugs bind to the substrate-binding pocket of SARS-CoV-2 Mpro and form a significant number of non-covalent interactions. Glecaprevir and MVC bind to the conserved residues of substrate-binding pocket of SARS-CoV-2 Mpro. This work provides sufficient evidence for the use of Glecaprevir and MVC for the therapeutic management of COVID-19 after experimental validation and clinical manifestations.


Subject(s)
Betacoronavirus/enzymology , Maraviroc/pharmacology , Protease Inhibitors/pharmacology , Quinoxalines/pharmacology , Sulfonamides/pharmacology , Aminoisobutyric Acids , Antiviral Agents/chemistry , Antiviral Agents/metabolism , Antiviral Agents/pharmacology , Betacoronavirus/drug effects , Computer Simulation , Cyclopropanes , Drug Evaluation, Preclinical/methods , Lactams, Macrocyclic , Leucine/analogs & derivatives , Maraviroc/chemistry , Maraviroc/metabolism , Molecular Structure , Proline/analogs & derivatives , Protease Inhibitors/chemistry , Protease Inhibitors/metabolism , Quinoxalines/chemistry , Quinoxalines/metabolism , SARS-CoV-2 , Sulfonamides/chemistry , Sulfonamides/metabolism
11.
Biochem Biophys Res Commun ; 533(3): 467-473, 2020 Dec 10.
Article in English | MEDLINE | ID: covidwho-1064868

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic caused by 2019 novel coronavirus (2019-nCoV) has been a crisis of global health, whereas the effective vaccines against 2019-nCoV are still under development. Alternatively, utilization of old drugs or available medicine that can suppress the viral activity or replication may provide an urgent solution to suppress the rapid spread of 2019-nCoV. Andrographolide is a highly abundant natural product of the medicinal plant, Andrographis paniculata, which has been clinically used for inflammatory diseases and anti-viral therapy. We herein demonstrate that both andrographolide and its fluorescent derivative, the nitrobenzoxadiazole-conjugated andrographolide (Andro- NBD), suppressed the main protease (Mpro) activities of 2019-nCoV and severe acute respiratory syndrome coronavirus (SARS-CoV). Moreover, Andro-NBD was shown to covalently link its fluorescence to these proteases. Further mass spectrometry (MS) analysis suggests that andrographolide formed a covalent bond with the active site Cys145 of either 2019-nCoV Mpro or SARS-CoV Mpro. Consistently, molecular modeling analysis supported the docking of andrographolide within the catalytic pockets of both viral Mpros. Considering that andrographolide is used in clinical practice with acceptable safety and its diverse pharmacological activities that could be beneficial for attenuating COVID-19 symptoms, extensive investigation of andrographolide on the suppression of 2019-nCoV as well as its application in COVID-19 therapy is suggested.


Subject(s)
Cysteine Endopeptidases/metabolism , Diterpenes/pharmacology , Protease Inhibitors/chemistry , Protease Inhibitors/pharmacology , Viral Nonstructural Proteins/antagonists & inhibitors , Viral Nonstructural Proteins/metabolism , Betacoronavirus/enzymology , Catalytic Domain , Coronavirus 3C Proteases , Cysteine Endopeptidases/chemistry , Diterpenes/chemistry , Fluorescent Dyes/chemistry , Fluorescent Dyes/pharmacology , Molecular Docking Simulation , Protein Conformation , Protein Multimerization , SARS Virus/enzymology , SARS-CoV-2 , Viral Nonstructural Proteins/chemistry
12.
Biotechniques ; 69(2): 108-112, 2020 08.
Article in English | MEDLINE | ID: covidwho-1041501

ABSTRACT

The outbreak of viral pneumonia caused by the novel coronavirus SARS-CoV-2 that began in December 2019 caused high mortality. It has been suggested that the main protease (Mpro) of SARS-CoV-2 may be an important target to discover pharmaceutical compounds for the therapy of this life-threatening disease. Remdesivir, ritonavir and chloroquine have all been reported to play a role in suppressing SARS-CoV-2. Here, we applied a molecular docking method to study the binding stability of these drugs with SARS-CoV-2 Mpro. It appeared that the ligand-protein binding stability of the alliin and SARS-CoV-2 Mpro complex was better than others. The results suggested that alliin may serve as a good candidate as an inhibitor of SARS-CoV-2 Mpro. Therefore, the present research may provide some meaningful guidance for the prevention and treatment of SARS-CoV-2.


Subject(s)
Antiviral Agents/pharmacology , Cysteine/analogs & derivatives , Viral Nonstructural Proteins/antagonists & inhibitors , Adenosine Monophosphate/analogs & derivatives , Adenosine Monophosphate/pharmacology , Alanine/analogs & derivatives , Alanine/pharmacology , Antimalarials/pharmacology , Betacoronavirus/enzymology , Chloroquine/pharmacology , Coronavirus 3C Proteases , Cysteine/pharmacology , Cysteine Endopeptidases , Molecular Docking Simulation , Ritonavir/pharmacology , SARS-CoV-2
13.
Virus Res ; 288: 198102, 2020 10 15.
Article in English | MEDLINE | ID: covidwho-1003124

ABSTRACT

Coronavirus disease 2019 (COVID-19) is an infectious disease, caused by a newly emerged highly pathogenic virus called novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Targeting the main protease (Mpro, 3CLpro) of SARS-CoV-2 is an appealing approach for drug development because this enzyme plays a significant role in the viral replication and transcription. The available crystal structures of SARS-CoV-2 Mpro determined in the presence of different ligands and inhibitor-like compounds provide a platform for the quick development of selective inhibitors of SARS-CoV-2 Mpro. In this study, we utilized the structural information of co-crystallized SARS-CoV-2 Mpro for the structure-guided drug discovery of high-affinity inhibitors from the PubChem database. The screened compounds were selected on the basis of their physicochemical properties, drug-likeliness, and strength of affinity to the SARS-CoV-2 Mpro. Finally, we have identified 6-Deaminosinefungin (PubChem ID: 10428963) and UNII-O9H5KY11SV (PubChem ID: 71481120) as potential inhibitors of SARS-CoV-2 Mpro which may be further exploited in drug development to address SARS-CoV-2 pathogenesis. Both compounds are structural analogs of known antivirals, having considerable protease inhibitory potential with improved pharmacological properties. All-atom molecular dynamics simulations suggested SARS-CoV-2 Mpro in complex with these compounds is stable during the simulation period with minimal structural changes. This work provides enough evidence for further implementation of the identified compounds in the development of effective therapeutics of COVID-19.


Subject(s)
Aminoglycosides/chemistry , Antiviral Agents/chemistry , Betacoronavirus/chemistry , Protease Inhibitors/chemistry , Pyrrolidines/chemistry , Viral Nonstructural Proteins/antagonists & inhibitors , Aminoglycosides/metabolism , Antiviral Agents/metabolism , Betacoronavirus/enzymology , COVID-19 , Catalytic Domain , Coronavirus 3C Proteases , Coronavirus Infections/drug therapy , Cysteine Endopeptidases/chemistry , Cysteine Endopeptidases/genetics , Cysteine Endopeptidases/metabolism , Drug Discovery , Gene Expression , Humans , Molecular Docking Simulation , Molecular Dynamics Simulation , Pandemics , Pneumonia, Viral/drug therapy , Protease Inhibitors/metabolism , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , Pyrrolidines/metabolism , SARS-CoV-2 , Substrate Specificity , Sulfonic Acids , Thermodynamics , User-Computer Interface , Viral Nonstructural Proteins/chemistry , Viral Nonstructural Proteins/genetics , Viral Nonstructural Proteins/metabolism
14.
Br J Pharmacol ; 177(21): 4825-4844, 2020 11.
Article in English | MEDLINE | ID: covidwho-998826

ABSTRACT

Angiotensin Converting Enzyme2 is the cell surface binding site for the coronavirus SARS-CoV-2, which causes COVID-19. We propose that an imbalance in the action of ACE1- and ACE2-derived peptides, thereby enhancing angiotensin II (Ang II) signalling is primary driver of COVID-19 pathobiology. ACE1/ACE2 imbalance occurs due to the binding of SARS-CoV-2 to ACE2, reducing ACE2-mediated conversion of Ang II to Ang peptides that counteract pathophysiological effects of ACE1-generated ANG II. This hypothesis suggests several approaches to treat COVID-19 by restoring ACE1/ACE2 balance: (a) AT receptor antagonists; (b) ACE1 inhibitors (ACEIs); (iii) agonists of receptors activated by ACE2-derived peptides (e.g. Ang (1-7), which activates MAS1); (d) recombinant human ACE2 or ACE2 peptides as decoys for the virus. Reducing ACE1/ACE2 imbalance is predicted to blunt COVID-19-associated morbidity and mortality, especially in vulnerable patients. Importantly, approved AT antagonists and ACEIs can be rapidly repurposed to test their efficacy in treating COVID-19. LINKED ARTICLES: This article is part of a themed issue on The Pharmacology of COVID-19. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v177.21/issuetoc.


Subject(s)
Betacoronavirus/isolation & purification , Coronavirus Infections/drug therapy , Pneumonia, Viral/drug therapy , Angiotensin II Type 1 Receptor Blockers/pharmacology , Angiotensin-Converting Enzyme 2 , Angiotensin-Converting Enzyme Inhibitors/pharmacology , Animals , Betacoronavirus/enzymology , COVID-19 , Coronavirus Infections/enzymology , Coronavirus Infections/virology , Drug Repositioning , Humans , Pandemics , Peptidyl-Dipeptidase A/metabolism , Pneumonia, Viral/enzymology , Pneumonia, Viral/virology , SARS-CoV-2
15.
Nat Commun ; 11(1): 3202, 2020 06 24.
Article in English | MEDLINE | ID: covidwho-981316

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 ligand-free structure of the active site and the conformation of the catalytic site cavity at near-physiological temperature. 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.


Subject(s)
Betacoronavirus/enzymology , Cysteine Endopeptidases/chemistry , Viral Nonstructural Proteins/chemistry , Catalytic Domain , Coronavirus 3C Proteases , Crystallography, X-Ray , Cysteine Endopeptidases/metabolism , Cysteine Proteinase Inhibitors/metabolism , Ligands , Models, Molecular , Molecular Dynamics Simulation , Protein Binding , Protein Conformation , Protein Domains , Protein Structure, Secondary , SARS-CoV-2 , Temperature , Viral Nonstructural Proteins/antagonists & inhibitors , Viral Nonstructural Proteins/metabolism
16.
J Virol ; 94(23)2020 11 09.
Article in English | MEDLINE | ID: covidwho-975641

ABSTRACT

Coronaviruses (CoVs) stand out for their large RNA genome and complex RNA-synthesizing machinery comprising 16 nonstructural proteins (nsps). The bifunctional nsp14 contains 3'-to-5' exoribonuclease (ExoN) and guanine-N7-methyltransferase (N7-MTase) domains. While the latter presumably supports mRNA capping, ExoN is thought to mediate proofreading during genome replication. In line with such a role, ExoN knockout mutants of mouse hepatitis virus (MHV) and severe acute respiratory syndrome coronavirus (SARS-CoV) were previously reported to have crippled but viable hypermutation phenotypes. Remarkably, using reverse genetics, a large set of corresponding ExoN knockout mutations has now been found to be lethal for another betacoronavirus, Middle East respiratory syndrome coronavirus (MERS-CoV). For 13 mutants, viral progeny could not be recovered, unless-as happened occasionally-reversion had first occurred. Only a single mutant was viable, likely because its E191D substitution is highly conservative. Remarkably, a SARS-CoV-2 ExoN knockout mutant was found to be unable to replicate, resembling observations previously made for alpha- and gammacoronaviruses, but starkly contrasting with the documented phenotype of ExoN knockout mutants of the closely related SARS-CoV. Subsequently, we established in vitro assays with purified recombinant MERS-CoV nsp14 to monitor its ExoN and N7-MTase activities. All ExoN knockout mutations that proved lethal in reverse genetics were found to severely decrease ExoN activity while not affecting N7-MTase activity. Our study strongly suggests that CoV nsp14 ExoN has an additional function, which apparently is critical for primary viral RNA synthesis and thus differs from the proofreading function that, based on previous MHV and SARS-CoV studies, was proposed to boost longer-term replication fidelity.IMPORTANCE The bifunctional nsp14 subunit of the coronavirus replicase contains 3'-to-5' exoribonuclease (ExoN) and guanine-N7-methyltransferase domains. For the betacoronaviruses MHV and SARS-CoV, ExoN was reported to promote the fidelity of genome replication, presumably by mediating a form of proofreading. For these viruses, ExoN knockout mutants are viable while displaying an increased mutation frequency. Strikingly, we have now established that the equivalent ExoN knockout mutants of two other betacoronaviruses, MERS-CoV and SARS-CoV-2, are nonviable, suggesting an additional and critical ExoN function in their replication. This is remarkable in light of the very limited genetic distance between SARS-CoV and SARS-CoV-2, which is highlighted, for example, by 95% amino acid sequence identity in their nsp14 sequences. For (recombinant) MERS-CoV nsp14, both its enzymatic activities were evaluated using newly developed in vitro assays that can be used to characterize these key replicative enzymes in more detail and explore their potential as target for antiviral drug development.


Subject(s)
Betacoronavirus/physiology , Exoribonucleases/metabolism , Middle East Respiratory Syndrome Coronavirus/physiology , Viral Nonstructural Proteins/metabolism , Virus Replication , Animals , Betacoronavirus/enzymology , Betacoronavirus/genetics , Catalytic Domain , Cell Line , Exoribonucleases/chemistry , Exoribonucleases/genetics , Fluorouracil/pharmacology , Gene Knockout Techniques , Genome, Viral , Humans , Methylation , Middle East Respiratory Syndrome Coronavirus/enzymology , Middle East Respiratory Syndrome Coronavirus/genetics , Mutation , RNA, Viral/biosynthesis , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , SARS-CoV-2 , Viral Nonstructural Proteins/chemistry , Viral Nonstructural Proteins/genetics , Viral Plaque Assay , Zinc Fingers
17.
J Proteome Res ; 19(11): 4678-4689, 2020 11 06.
Article in English | MEDLINE | ID: covidwho-974859

ABSTRACT

Originating in the city of Wuhan in China in December 2019, COVID-19 has emerged now as a global health emergency with a high number of deaths worldwide. COVID-19 is caused by a novel coronavirus, referred to as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), resulting in pandemic conditions around the globe. We are in the battleground to fight against the virus by rapidly developing therapeutic strategies in tackling SARS-CoV-2 and saving human lives from COVID-19. Scientists are evaluating several known drugs either for the pathogen or the host; however, many of them are reported to be associated with side effects. In the present study, we report the molecular binding mechanisms of the natural alkaloid, noscapine, for repurposing against the main protease of SARS-CoV-2, a key enzyme involved in its reproduction. We performed the molecular dynamics (MD) simulation in an explicit solvent to investigate the molecular mechanisms of noscapine for stable binding and conformational changes to the main protease (Mpro) of SARS-CoV-2. The drug repurposing study revealed the high potential of noscapine and proximal binding to the Mpro enzyme in a comparative binding pattern analyzed with chloroquine, ribavirin, and favipiravir. Noscapine binds closely to binding pocket-3 of the Mpro enzyme and depicted stable binding with RMSD 0.1-1.9 Å and RMSF profile peak conformational fluctuations at 202-306 residues, and a Rg score ranging from 21.9 to 22.4 Å. The MM/PB (GB) SA calculation landscape revealed the most significant contribution in terms of binding energy with ΔPB -19.08 and ΔGB -27.17 kcal/mol. The electrostatic energy distribution in MM energy was obtained to be -71.16 kcal/mol and depicted high free energy decomposition (electrostatic energy) at 155-306 residues (binding pocket-3) of Mpro by a MM force field. Moreover, the dynamical residue cross-correlation map also stated that the high pairwise correlation occurred at binding residues 200-306 of the Mpro enzyme (binding pocket-3) with noscapine. Principal component analysis depicted the enhanced movement of protein atoms with a high number of static hydrogen bonds. The obtained binding results of noscapine were also well correlated with the pharmacokinetic parameters of antiviral drugs.


Subject(s)
Betacoronavirus , Drug Repositioning , Noscapine , Protease Inhibitors , Viral Nonstructural Proteins , Betacoronavirus/chemistry , Betacoronavirus/enzymology , Betacoronavirus/metabolism , COVID-19 , Coronavirus Infections/virology , Humans , Molecular Docking Simulation , Molecular Dynamics Simulation , Noscapine/chemistry , Noscapine/metabolism , Pandemics , Peptide Hydrolases/chemistry , Peptide Hydrolases/metabolism , Pneumonia, Viral/virology , Protease Inhibitors/chemistry , Protease Inhibitors/metabolism , SARS-CoV-2 , Viral Nonstructural Proteins/chemistry , Viral Nonstructural Proteins/metabolism
18.
J Proteome Res ; 19(11): 4316-4326, 2020 11 06.
Article in English | MEDLINE | ID: covidwho-960280

ABSTRACT

The unprecedented pandemic of coronavirus disease 2019 (COVID-19) demands effective treatment for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The infection of SARS-CoV-2 critically depends on diverse viral or host proteases, which mediate viral entry, viral protein maturation, as well as the pathogenesis of the viral infection. Endogenous and exogenous agents targeting for proteases have been proved to be effective toward a variety of viral infections ranging from HIV to influenza virus, suggesting protease inhibitors as a promising antiviral treatment for COVID-19. In this Review, we discuss how host and viral proteases participated in the pathogenesis of COVID-19 as well as the prospects and ongoing clinical trials of protease inhibitors as treatments.


Subject(s)
Antiviral Agents , Betacoronavirus , Coronavirus Infections , Pandemics , Pneumonia, Viral , Protease Inhibitors , Angiotensin-Converting Enzyme 2 , Betacoronavirus/drug effects , Betacoronavirus/enzymology , COVID-19 , Coronavirus Infections/drug therapy , Coronavirus Infections/physiopathology , Coronavirus Infections/virology , Host-Pathogen Interactions , Humans , Peptide Hydrolases , Peptidyl-Dipeptidase A , Pneumonia, Viral/drug therapy , Pneumonia, Viral/physiopathology , Pneumonia, Viral/virology , SARS-CoV-2 , Serine Endopeptidases , Viral Proteins
19.
J Proteome Res ; 19(11): 4690-4697, 2020 11 06.
Article in English | MEDLINE | ID: covidwho-960277

ABSTRACT

SARS-CoV-2 is responsible for the current COVID-19 pandemic. On the basis of our analysis of hepatitis C virus and coronavirus replication, and the molecular structures and activities of viral inhibitors, we previously demonstrated that three nucleotide analogues (the triphosphates of Sofosbuvir, Alovudine, and AZT) inhibit the SARS-CoV RNA-dependent RNA polymerase (RdRp). We also demonstrated that a library of additional nucleotide analogues terminate RNA synthesis catalyzed by the SARS-CoV-2 RdRp, a well-established drug target for COVID-19. Here, we used polymerase extension experiments to demonstrate that the active triphosphate form of Sofosbuvir (an FDA-approved hepatitis C drug) is incorporated by SARS-CoV-2 RdRp and blocks further incorporation. Using the molecular insight gained from the previous studies, we selected the active triphosphate forms of six other antiviral agents, Alovudine, Tenofovir alafenamide, AZT, Abacavir, Lamivudine, and Emtricitabine, for evaluation as inhibitors of the SARS-CoV-2 RdRp and demonstrated the ability of these viral polymerase inhibitors to be incorporated by SARS-CoV-2 RdRp, where they terminate further polymerase extension with varying efficiency. These results provide a molecular basis for inhibition of the SARS-CoV-2 RdRp by these nucleotide analogues. If sufficient efficacy of some of these FDA-approved drugs in inhibiting viral replication in cell culture is established, they may be explored as potential COVID-19 therapeutics.


Subject(s)
Antiviral Agents , Betacoronavirus , RNA-Dependent RNA Polymerase , Viral Nonstructural Proteins , Antiviral Agents/chemistry , Antiviral Agents/metabolism , Antiviral Agents/pharmacology , Betacoronavirus/enzymology , Betacoronavirus/genetics , COVID-19 , Coronavirus Infections/virology , Dideoxynucleosides/chemistry , Dideoxynucleosides/metabolism , Dideoxynucleosides/pharmacology , Humans , Pandemics , Pneumonia, Viral/virology , RNA-Dependent RNA Polymerase/antagonists & inhibitors , RNA-Dependent RNA Polymerase/chemistry , RNA-Dependent RNA Polymerase/genetics , RNA-Dependent RNA Polymerase/metabolism , SARS-CoV-2 , Sofosbuvir/chemistry , Sofosbuvir/metabolism , Sofosbuvir/pharmacology , Viral Nonstructural Proteins/antagonists & inhibitors , Viral Nonstructural Proteins/chemistry , Viral Nonstructural Proteins/genetics , Viral Nonstructural Proteins/metabolism
20.
Virol Sin ; 35(3): 321-329, 2020 Jun.
Article in English | MEDLINE | ID: covidwho-959357

ABSTRACT

The ongoing outbreak of Coronavirus Disease 2019 (COVID-19) has become a global public health emergency. SARS-coronavirus-2 (SARS-CoV-2), the causative pathogen of COVID-19, is a positive-sense single-stranded RNA virus belonging to the family Coronaviridae. For RNA viruses, virus-encoded RNA helicases have long been recognized to play pivotal roles during viral life cycles by facilitating the correct folding and replication of viral RNAs. Here, our studies show that SARS-CoV-2-encoded nonstructural protein 13 (nsp13) possesses the nucleoside triphosphate hydrolase (NTPase) and RNA helicase activities that can hydrolyze all types of NTPs and unwind RNA helices dependently of the presence of NTP, and further characterize the biochemical characteristics of these two enzymatic activities associated with SARS-CoV-2 nsp13. Moreover, we found that some bismuth salts could effectively inhibit both the NTPase and RNA helicase activities of SARS-CoV-2 nsp13 in a dose-dependent manner. Thus, our findings demonstrate the NTPase and helicase activities of SARS-CoV-2 nsp13, which may play an important role in SARS-CoV-2 replication and serve as a target for antivirals.


Subject(s)
Betacoronavirus/metabolism , Bismuth/pharmacology , Methyltransferases/metabolism , Nucleoside-Triphosphatase/drug effects , RNA Helicases/drug effects , Salts/pharmacology , Viral Nonstructural Proteins/metabolism , Adenosine Triphosphatases/drug effects , Adenosine Triphosphatases/metabolism , Betacoronavirus/enzymology , Betacoronavirus/genetics , COVID-19 , Coronavirus Infections/virology , Humans , Methyltransferases/genetics , Nucleoside-Triphosphatase/genetics , Nucleoside-Triphosphatase/metabolism , Pandemics , Pneumonia, Viral/virology , RNA Helicases/genetics , RNA Helicases/metabolism , Recombinant Proteins , SARS-CoV-2 , Severe Acute Respiratory Syndrome , Viral Nonstructural Proteins/genetics , Virus Replication
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