Your browser doesn't support javascript.
Show: 20 | 50 | 100
Results 1 - 20 de 396
Filter
1.
Steroids ; 188: 109120, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-2113189

ABSTRACT

The present work reports simple and effective protocol for preparing 6α-nitro-5α-cholestano[7α,5-cd] pyrazolines (4-7) by the reaction of 7α-bromo-6-nitrocholest-5-enes (1-3) with hydrazine hydrate under reflux [the substrate (2) gave products (5) and (6) and the later on acetylation with AC2O/Py gave (7)]. In the case of reaction of 3ß-hydroxy analogue (3) with hydrazine, however, 6α-nitro-5α-cholestano [3α,5-cd] pyrazoline (8) and 6α-nitro-3ß, 5-oxido-5ß-cholestane (9) were obtained. The probable mechanism of the formation of pyrazolines has also been outlined. In the current pandemic coronavirus disease 2019 scenario, the in-silico study was performed with reactants (1-3), their products (4-9) against SARS-CoV-2 omicron protease (PDB ID:7T9L) for knowing significant interactions between them. Docking results give information that both reactants and products have binding energies ranges from -5.7 to 7.7 kcal/mol and strong interactions with various hydrophilic and hydrophobic amino acids such as ASP, PRO, PHE, SER and LEU which are significant residues playing important role in SARS-CoV-2 Omicron main protease (Mpro).


Subject(s)
COVID-19 , Coronavirus 3C Proteases , SARS-CoV-2 , Humans , COVID-19/drug therapy , Hydrazines , Molecular Docking Simulation , Molecular Dynamics Simulation , Peptide Hydrolases , SARS-CoV-2/enzymology , SARS-CoV-2/metabolism , Coronavirus 3C Proteases/antagonists & inhibitors
2.
Bioorg Chem ; 129: 106185, 2022 12.
Article in English | MEDLINE | ID: covidwho-2060449

ABSTRACT

The evolving SARS-CoV-2 epidemic buffets the world, and the concerted efforts are needed to explore effective drugs. Mpro is an intriguing antiviral target for interfering with viral RNA replication and transcription. In order to get potential anti-SARS-CoV-2 agents, we established an enzymatic assay using a fluorogenic substrate to screen the inhibitors of Mpro. Fortunately, Acriflavine (ACF) and Proflavine Hemisulfate (PRF) with the same acridine scaffold were picked out for their good inhibitory activity against Mpro with IC50 of 5.60 ± 0.29 µM and 2.07 ± 0.01 µM, respectively. Further evaluation of MST assay and enzymatic kinetics experiment in vitro showed that they had a certain affinity to SARS-CoV-2 Mpro and were both non-competitive inhibitors. In addition, they inhibited about 90 % HCoV-OC43 replication in BHK-21 cells at 1 µM. Both compounds showed nano-molar activities against SARS-CoV-2 virus, which were superior to GC376 for anti-HCoV-43, and equivalent to the standard molecule remdesivir. Our study demonstrated that ACF and PRF were inhibitors of Mpro, and ACF has been previously reported as a PLpro inhibitor. Taken together, ACF and PRF might be dual-targeted inhibitors to provide protection against infections of coronaviruses.


Subject(s)
Acriflavine , COVID-19 , Coronavirus 3C Proteases , Cysteine Proteinase Inhibitors , Proflavine , SARS-CoV-2 , Viral Protease Inhibitors , Acriflavine/pharmacology , COVID-19/drug therapy , Proflavine/pharmacology , SARS-CoV-2/drug effects , SARS-CoV-2/enzymology , Coronavirus 3C Proteases/antagonists & inhibitors , Cysteine Proteinase Inhibitors/pharmacology , Viral Protease Inhibitors/pharmacology , Mesocricetus , Animals , Cricetinae , Cell Line , Virus Replication/drug effects
3.
J Mol Biol ; 434(16): 167720, 2022 08 30.
Article in English | MEDLINE | ID: covidwho-2028233

ABSTRACT

Viral infection in cells triggers a cascade of molecular defense mechanisms to maintain host-cell homoeostasis. One of these mechanisms is ADP-ribosylation, a fundamental post-translational modification (PTM) characterized by the addition of ADP-ribose (ADPr) on substrates. Poly(ADP-ribose) polymerases (PARPs) are implicated in this process and they perform ADP-ribosylation on host and pathogen proteins. Some viral families contain structural motifs that can reverse this PTM. These motifs known as macro domains (MDs) are evolutionarily conserved protein domains found in all kingdoms of life. They are divided in different classes with the viral belonging to Macro-D-type class because of their properties to recognize and revert the ADP-ribosylation. Viral MDs are potential pharmaceutical targets, capable to counteract host immune response. Sequence and structural homology between viral and human MDs are an impediment for the development of new active compounds against their function. Remdesivir, is a drug administrated in viral infections inhibiting viral replication through RNA-dependent RNA polymerase (RdRp). Herein, GS-441524, the active metabolite of the remdesivir, is tested as a hydrolase inhibitor for several viral MDs and for its binding to human homologs found in PARPs. This study presents biochemical and biophysical studies, which indicate that GS-441524 selectively modifies SARS-CoV-2 MD de-MARylation activity, while it does not interact with hPARP14 MD2 and hPARP15 MD2. The structural investigation of MD•GS-441524 complexes, using solution NMR and X-ray crystallography, discloses the impact of certain amino acids in ADPr binding cavity suggesting that F360 and its adjacent residues tune the selective binding of the inhibitor to SARS-CoV-2 MD.


Subject(s)
ADP-Ribosylation , Adenosine/analogs & derivatives , Coronavirus Protease Inhibitors , Poly(ADP-ribose) Polymerases , SARS-CoV-2 , ADP-Ribosylation/drug effects , Adenosine/chemistry , Adenosine/pharmacology , Adenosine Diphosphate Ribose/chemistry , Coronavirus Protease Inhibitors/chemistry , Coronavirus Protease Inhibitors/pharmacology , Humans , Poly(ADP-ribose) Polymerases/chemistry , Protein Binding , Protein Domains , SARS-CoV-2/drug effects , SARS-CoV-2/enzymology
4.
J Med Chem ; 65(17): 11840-11853, 2022 09 08.
Article in English | MEDLINE | ID: covidwho-2016520

ABSTRACT

Site-selective lysine modification of peptides and proteins in aqueous solutions or in living cells is still a big challenge today. Here, we report a novel strategy to selectively quinolylate lysine residues of peptides and proteins under native conditions without any catalysts using our newly developed water-soluble zoliniums. The zoliniums could site-selectively quinolylate K350 of bovine serum albumin and inactivate SARS-CoV-2 3CLpro via covalently modifying two highly conserved lysine residues (K5 and K61). In living HepG2 cells, it was demonstrated that the simple zoliniums (5b and 5B) could quinolylate protein lysine residues mainly in the nucleus, cytosol, and cytoplasm, while the zolinium-fluorophore hybrid (8) showed specific lysosome-imaging ability. The specific chemoselectivity of the zoliniums for lysine was validated by a mixture of eight different amino acids, different peptides bearing potential reactive residues, and quantum chemistry calculations. This study offers a new way to design and develop lysine-targeted covalent ligands for specific application.


Subject(s)
Lysine , Peptides , Coronavirus 3C Proteases/chemistry , Lysine/chemistry , Peptides/chemistry , SARS-CoV-2/enzymology , Serum Albumin, Bovine/chemistry , Water/chemistry
5.
Chem Asian J ; 17(21): e202200747, 2022 Nov 02.
Article in English | MEDLINE | ID: covidwho-2013362

ABSTRACT

The main protease (Mpro ), which is highly conserved and plays a critical role in the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a natural biomarker for SARS-CoV-2. Accurate assessment of the Mpro activity is crucial for the detection of SARS-CoV-2. Herein, we report a nanopore-based sensing strategy that uses an enzyme-catalyzed cleavage reaction of a peptide substrate to measure the Mpro activity. The peptide was specifically cleaved by the Mpro , thereby releasing the output products that, when translocated through aerolysin, quantitatively produced the signature current events. The proposed method exhibited high sensitivity, allowing the detection of Mpro concentrations as low as 1 nM without the use of any signal amplification techniques. This simple, convenient, and label-free nanopore assay may expand the diagnostic tools for viruses.


Subject(s)
COVID-19 , Coronavirus 3C Proteases , Nanopores , Humans , COVID-19/diagnosis , Peptides , SARS-CoV-2/enzymology , Coronavirus 3C Proteases/analysis
6.
Commun Biol ; 5(1): 925, 2022 09 07.
Article in English | MEDLINE | ID: covidwho-2008334

ABSTRACT

RNA replication and transcription machinery is an important drug target for fighting against coronavirus. Non-structure protein nsp8 was proposed harboring primase activity. However, the RNA primer synthesis mechanism of nsp8 is still largely unknown. Here, we purified dimer and tetramer forms of SARS-CoV-2 nsp8. Combined with dynamic light scattering, small-angle neutron scattering and thermo-stability analysis, we found that both dimer and tetramer become loosened and destabilized with decreasing salt concentration, and the dimer form is more stable than the tetramer form. Further investigation showed that nsp8 dimer and tetramer can undergo phase separation but exhibit different phase separation behaviors. Nsp8 dimer can form liquid-like droplets in the buffer with a low concentration of NaCl; phase separation of nsp8 tetramer depends on the assistance of RNA. Our findings on different phase separation behaviors of nsp8 dimer and tetramer may provide insight into the functional studies of nsp8 in coronavirus.


Subject(s)
Coronavirus RNA-Dependent RNA Polymerase , SARS-CoV-2 , Viral Nonstructural Proteins , Amino Acid Sequence , Coronavirus RNA-Dependent RNA Polymerase/chemistry , RNA/metabolism , SARS-CoV-2/enzymology , SARS-CoV-2/genetics , Viral Nonstructural Proteins/chemistry
7.
Front Immunol ; 13: 947272, 2022.
Article in English | MEDLINE | ID: covidwho-2005872

ABSTRACT

The newly emerged severe acute respiratory syndrome (SARS) coronavirus-2 (SARS-CoV-2) can result in dysregulated interferon (IFN) responses that contribute to disease severity. The papain-like protease of SARS-CoV-2 (SCoV2-PLpro) has been previously reported to attenuate IFN responses, but the underlying mechanism is not fully understood. In this study, we found that SCoV2-PLpro potently suppressed IFN production and signaling induced by Sendai virus as well as RIG-I-like receptor (RLR) signaling pathway components, including RIG-I, MAVS, TBK1, TRAF3, TRAF6, and IRF3. SCoV2-PLpro exhibited different specificity and efficiency than SARS-CoV PLpro, with the former exerting a greater inhibitory effect on the RIG-I- and TRAF3-mediated IFN response but a weaker effect on the MAVS-mediated IFN response. Furthermore, we showed that SCoV2-PLpro significantly reduced K63-ubiquitination of RIG-I, MAVS, TBK1, TRAF3, TRAF6, and IRF3 and K48-ubiquitination of IκBα, which are known critical for the innate immune signal transduction. The deubiquitinating (DUB) activity of SCoV2-PLpro required a catalytic residue cysteine 111 (C111) but not the UBL domain. Notably, by utilizing the DUB-defective C111 mutant, we demonstrated that SCoV2-PLpro targeted RLR signaling pathway regulators via deubiquitination-dependent and -independent mechanisms, with the inhibitory activities of RIG-I and TBK1 correlating with DUB function, whereas the antagonism effects on MAVS, TRAF3, TRAF6, and IRF3 independent on DUB activity. Overall, our results reveal that SCoV2-PLpro evolves differential IFN antagonism activity from SCoV1-PLpro and it targets multiple key RLR signaling pathway components via various mechanisms, providing insights into SARS-CoV-2 pathogenesis and clues for developing antiviral therapies for COVID-19.


Subject(s)
Coronavirus Papain-Like Proteases , DEAD Box Protein 58 , Receptors, Immunologic , SARS-CoV-2 , Signal Transduction , COVID-19 , Coronavirus Papain-Like Proteases/metabolism , DEAD Box Protein 58/metabolism , Humans , Receptors, Immunologic/metabolism , SARS-CoV-2/enzymology , Ubiquitination
8.
J Mol Biol ; 434(20): 167796, 2022 10 30.
Article in English | MEDLINE | ID: covidwho-1996375

ABSTRACT

Global sequencing efforts from the ongoing COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, continue to provide insight into the evolution of the viral genome. Coronaviruses encode 16 nonstructural proteins, within the first two-thirds of their genome, that facilitate viral replication and transcription as well as evasion of the host immune response. However, many of these viral proteins remain understudied. Nsp15 is a uridine-specific endoribonuclease conserved across all coronaviruses. The nuclease activity of Nsp15 helps the virus evade triggering an innate immune response. Understanding how Nsp15 has changed over the course of the pandemic, and how mutations affect its RNA processing function, will provide insight into the evolution of an oligomerization-dependent endoribonuclease and inform drug design. In combination with previous structural data, bioinformatics analyses of 1.9 + million SARS-CoV-2 sequences revealed mutations across Nsp15's three structured domains (N-terminal, Middle, EndoU). Selected Nsp15 variants were characterized biochemically and compared to wild type Nsp15. We found that mutations to important catalytic residues decreased cleavage activity but increased the hexamer/monomer ratio of the recombinant protein. Many of the highly prevalent variants we analyzed led to decreased nuclease activity as well as an increase in the inactive, monomeric form. Overall, our work establishes how Nsp15 variants seen in patient samples affect nuclease activity and oligomerization, providing insight into the effect of these variants in vivo.


Subject(s)
COVID-19 , Endoribonucleases , SARS-CoV-2 , Uridylate-Specific Endoribonucleases , Viral Nonstructural Proteins , COVID-19/virology , Endoribonucleases/chemistry , Endoribonucleases/genetics , Humans , Recombinant Proteins/chemistry , SARS-CoV-2/enzymology , Uridylate-Specific Endoribonucleases/chemistry , Uridylate-Specific Endoribonucleases/genetics , Viral Nonstructural Proteins/chemistry , Viral Nonstructural Proteins/genetics
9.
Anal Chem ; 94(34): 11728-11733, 2022 08 30.
Article in English | MEDLINE | ID: covidwho-1991486

ABSTRACT

Existing tools to detect and visualize severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) suffer from low selectivity, poor cell permeability, and high cytotoxicity. Here we report a novel self-immolative fluorescent probe (MP590) for the highly selective and sensitive detection of the SARS-CoV-2 main protease (Mpro). This fluorescent probe was prepared by connecting a Mpro-cleavable peptide (N-acetyl-Abu-Tle-Leu-Gln) with a fluorophore (i.e., resorufin) via a self-immolative aromatic linker. Fluorescent titration results show that MP590 can detect Mpro with a limit of detection (LoD) of 35 nM and is selective over interferents such as hemoglobin, bovine serum albumin (BSA), thrombin, amylase, SARS-CoV-2 papain-like protease (PLpro), and trypsin. The cell imaging data indicate that this probe can report Mpro in HEK 293T cells transfected with a Mpro expression plasmid as well as in TMPRSS2-VeroE6 cells infected with SARS-CoV-2. Our results suggest that MP590 can both measure and monitor Mpro activity and quantitatively evaluate Mpro inhibition in infected cells, making it an important tool for diagnostic and therapeutic research on SARS-CoV-2.


Subject(s)
COVID-19 , Coronavirus 3C Proteases , Fluorescent Dyes , COVID-19/diagnosis , Coronavirus 3C Proteases/analysis , Humans , SARS-CoV-2/enzymology
10.
Nature ; 609(7928): 793-800, 2022 09.
Article in English | MEDLINE | ID: covidwho-1984402

ABSTRACT

The RNA genome of SARS-CoV-2 contains a 5' cap that facilitates the translation of viral proteins, protection from exonucleases and evasion of the host immune response1-4. How this cap is made in SARS-CoV-2 is not completely understood. Here we reconstitute the N7- and 2'-O-methylated SARS-CoV-2 RNA cap (7MeGpppA2'-O-Me) using virally encoded non-structural proteins (nsps). We show that the kinase-like nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain5 of nsp12 transfers the RNA to the amino terminus of nsp9, forming a covalent RNA-protein intermediate (a process termed RNAylation). Subsequently, the NiRAN domain transfers the RNA to GDP, forming the core cap structure GpppA-RNA. The nsp146 and nsp167 methyltransferases then add methyl groups to form functional cap structures. Structural analyses of the replication-transcription complex bound to nsp9 identified key interactions that mediate the capping reaction. Furthermore, we demonstrate in a reverse genetics system8 that the N terminus of nsp9 and the kinase-like active-site residues in the NiRAN domain are required for successful SARS-CoV-2 replication. Collectively, our results reveal an unconventional mechanism by which SARS-CoV-2 caps its RNA genome, thus exposing a new target in the development of antivirals to treat COVID-19.


Subject(s)
RNA Caps , RNA, Viral , SARS-CoV-2 , Viral Proteins , Antiviral Agents , COVID-19/drug therapy , COVID-19/virology , Catalytic Domain , Guanosine Diphosphate/metabolism , Humans , Methyltransferases/metabolism , Nucleotidyltransferases/chemistry , Nucleotidyltransferases/metabolism , Protein Domains , RNA Caps/chemistry , RNA Caps/genetics , RNA Caps/metabolism , RNA, Viral/chemistry , RNA, Viral/genetics , RNA, Viral/metabolism , RNA-Dependent RNA Polymerase/metabolism , SARS-CoV-2/enzymology , SARS-CoV-2/genetics , SARS-CoV-2/metabolism , Viral Proteins/chemistry , Viral Proteins/metabolism
11.
Eur J Med Chem ; 238: 114508, 2022 Aug 05.
Article in English | MEDLINE | ID: covidwho-1982957

ABSTRACT

The COVID-19 posed a serious threat to human life and health, and SARS-CoV-2 Mpro has been considered as an attractive drug target for the treatment of COVID-19. Herein, we report 2-(furan-2-ylmethylene)hydrazine-1-carbothioamide derivatives as novel inhibitors of SARS-CoV-2 Mpro developed by in-house library screening and biological evaluation. Similarity search led to the identification of compound F8-S43 with the enzymatic IC50 value of 10.76 µM. Further structure-based drug design and synthetic optimization uncovered compounds F8-B6 and F8-B22 as novel non-peptidomimetic inhibitors of Mpro with IC50 values of 1.57 µM and 1.55 µM, respectively. Moreover, enzymatic kinetic assay and mass spectrometry demonstrated that F8-B6 was a reversible covalent inhibitor of Mpro. Besides, F8-B6 showed low cytotoxicity with CC50 values of more than 100 µM in Vero and MDCK cells. Overall, these novel SARS-CoV-2 Mpro non-peptidomimetic inhibitors provide a useful starting point for further structural optimization.


Subject(s)
COVID-19 , Coronavirus 3C Proteases , Furans , SARS-CoV-2 , Antiviral Agents/chemistry , Antiviral Agents/pharmacology , COVID-19/drug therapy , Coronavirus 3C Proteases/antagonists & inhibitors , Coronavirus 3C Proteases/chemistry , Coronavirus 3C Proteases/metabolism , Drug Discovery/methods , Furans/chemistry , Furans/pharmacology , Humans , Hydrazines/pharmacology , Molecular Docking Simulation , Protease Inhibitors/chemistry , Protease Inhibitors/pharmacology , SARS-CoV-2/drug effects , SARS-CoV-2/enzymology
12.
Antiviral Res ; 204: 105350, 2022 08.
Article in English | MEDLINE | ID: covidwho-1944193

ABSTRACT

Two years after its emergence, SARS-CoV-2 still represents a serious and global threat to human health. Antiviral drug development usually takes a long time and, to increase the chances of success, chemical variability of hit compounds represents a valuable source for the discovery of new antivirals. In this work, we applied a platform of variably oriented virtual screening campaigns to seek for novel chemical scaffolds for SARS-CoV-2 main protease (Mpro) inhibitors. The study on the resulting 30 best hits led to the identification of a series of structurally unrelated Mpro inhibitors. Some of them exhibited antiviral activity in the low micromolar range against SARS-CoV-2 and other human coronaviruses (HCoVs) in different cell lines. Time-of-addition experiments demonstrated an antiviral effect during the viral replication cycle at a time frame consistent with the inhibition of SARS-CoV-2 Mpro activity. As a proof-of-concept, to validate the pharmaceutical potential of the selected hits against SARS-CoV-2, we rationally optimized one of the hit compounds and obtained two potent SARS-CoV-2 inhibitors with increased activity against Mpro both in vitro and in a cellular context, as well as against SARS-CoV-2 replication in infected cells. This study significantly contributes to the expansion of the chemical variability of SARS-CoV-2 Mpro inhibitors and provides new scaffolds to be exploited for pan-coronavirus antiviral drug development.


Subject(s)
Antiviral Agents , Coronavirus 3C Proteases , Protease Inhibitors , SARS-CoV-2 , Antiviral Agents/chemistry , Antiviral Agents/pharmacology , Coronavirus 3C Proteases/antagonists & inhibitors , Molecular Docking Simulation , Protease Inhibitors/chemistry , SARS-CoV-2/drug effects , SARS-CoV-2/enzymology
13.
J Inorg Biochem ; 234: 111886, 2022 09.
Article in English | MEDLINE | ID: covidwho-1930970

ABSTRACT

The SARS-CoV-2 main protease (Mpro) is responsible for cleaving twelve nonstructural proteins from the viral polyprotein. Mpro, a cysteine protease, is characterized by a large number of noncatalytic cysteine (Cys) residues, none involved in disulfide bonds. In the absence of a tertiary-structure stabilizing role for these residues, a possible alternative is that they are involved in redox processes. We report experimental work in support of a proposal that surface cysteines on Mpro can protect the active-site Cys145 from oxidation by reactive oxygen species (ROS). In investigations of enzyme kinetics, we found that mutating three surface cysteines to serines did not greatly affect activity, which in turn indicates that these cysteines could protect Cys145 from oxidative damage.


Subject(s)
Coronavirus 3C Proteases , Cysteine , Oxidative Stress , SARS-CoV-2 , Coronavirus 3C Proteases/chemistry , Cysteine/chemistry , Protease Inhibitors , SARS-CoV-2/enzymology
14.
J Biol Chem ; 298(6): 102023, 2022 06.
Article in English | MEDLINE | ID: covidwho-1930937

ABSTRACT

3C-like protease (3CLpro) processes and liberates functional viral proteins essential for the maturation and infectivity of severe acute respiratory syndrome coronavirus 2, the virus responsible for COVID-19. It has been suggested that 3CLpro is catalytically active as a dimer, making the dimerization interface a target for antiviral development. Guided by structural analysis, here we introduced single amino acid substitutions at nine residues at three key sites of the dimer interface to assess their impact on dimerization and activity. We show that at site 1, alanine substitution of S1 or E166 increased by twofold or reduced relative activity, respectively. At site 2, alanine substitution of S10 or E14 eliminated activity, whereas K12A exhibited ∼60% relative activity. At site 3, alanine substitution of R4, E290, or Q299 eliminated activity, whereas S139A exhibited 46% relative activity. We further found that the oligomerization states of the dimer interface mutants varied; the inactive mutants R4A, R4Q, S10A/C, E14A/D/Q/S, E290A, and Q299A/E were present as dimers, demonstrating that dimerization is not an indication of catalytically active 3CLpro. In addition, present mostly as monomers, K12A displayed residual activity, which could be attributed to the conspicuous amount of dimer present. Finally, differential scanning calorimetry did not reveal a direct relationship between the thermodynamic stability of mutants with oligomerization or catalytic activity. These results provide insights on two allosteric sites, R4/E290 and S10/E14, that may promote the design of antiviral compounds that target the dimer interface rather than the active site of severe acute respiratory syndrome coronavirus 2 3CLpro.


Subject(s)
Coronavirus 3C Proteases , SARS-CoV-2 , Alanine/chemistry , Amino Acid Substitution , Antiviral Agents/chemistry , Coronavirus 3C Proteases/metabolism , Protein Multimerization , SARS-CoV-2/enzymology
15.
J Mol Biol ; 434(16): 167706, 2022 08 30.
Article in English | MEDLINE | ID: covidwho-1914637

ABSTRACT

New variants of the severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) emerged and spread rapidly all over the world, which strongly supports the need for pharmacological options to complement vaccine strategies. Main protease (Mpro or 3CLpro) is a critical enzyme in the life cycle of SARS-CoV-2 and appears to be highly conserved among different genera of coronaviruses, making it an ideal target for the development of drugs with broad-spectrum property. PF-07304814 developed by Pfizer is an intravenously administered inhibitor targeting SARS-CoV-2 Mpro. Here we showed that PF-07304814 displays broad-spectrum inhibitory activity against Mpros from multiple coronaviruses. Crystal structures of Mpros of SARS-CoV-2, SARS-CoV, MERS-CoV, and HCoV-NL63 bound to the inhibitor PF-07304814 revealed a conserved ligand-binding site, providing new insights into the mechanism of inhibition of viral replication. A detailed analysis of these crystal structures complemented by comprehensive comparison defined the key structural determinants essential for inhibition and illustrated the binding mode of action of Mpros from different coronaviruses. In view of the importance of Mpro for the medications of SARS-CoV-2 infection, insights derived from the present study should accelerate the design of pan-coronaviral main protease inhibitors that are safer and more effective.


Subject(s)
Coronavirus 3C Proteases , Coronavirus Protease Inhibitors , Indoles , Leucine , Pyrrolidinones , SARS-CoV-2 , Coronavirus 3C Proteases/antagonists & inhibitors , Coronavirus 3C Proteases/chemistry , Coronavirus Protease Inhibitors/chemistry , Coronavirus Protease Inhibitors/pharmacology , Drug Design , Humans , Indoles/chemistry , Indoles/pharmacology , Leucine/chemistry , Leucine/pharmacology , Ligands , Protein Binding , Pyrrolidinones/chemistry , Pyrrolidinones/pharmacology , SARS-CoV-2/drug effects , SARS-CoV-2/enzymology
16.
STAR Protoc ; 3(3): 101468, 2022 09 16.
Article in English | MEDLINE | ID: covidwho-1895508

ABSTRACT

Nucleotide/nucleoside analogs (NAs) are important compounds used in antiviral drug development. To understand the action mode of NA drugs, we present an enzymology protocol to initially evaluate the intervention mechanism of the NTP forms of NAs on a coronaviral RNA-dependent RNA polymerase (RdRP). We describe the preparation of SARS-CoV-2 RdRP proteins and RNA constructs, followed by a primer-dependent RdRP assay to assess NTP forms of NAs. Two representative NA drugs, sofosbuvir and remdesivir, are used for demonstration of this protocol. For complete details on the use and execution of this protocol, please refer to Wu et al. (2021).


Subject(s)
Nucleosides , Nucleotides , RNA-Dependent RNA Polymerase , SARS-CoV-2 , Nucleosides/analogs & derivatives , Nucleosides/pharmacology , Nucleotides/pharmacology , RNA-Dependent RNA Polymerase/antagonists & inhibitors , SARS-CoV-2/drug effects , SARS-CoV-2/enzymology
17.
J Med Chem ; 65(8): 6231-6249, 2022 04 28.
Article in English | MEDLINE | ID: covidwho-1867997

ABSTRACT

Enzymes involved in RNA capping of SARS-CoV-2 are essential for the stability of viral RNA, translation of mRNAs, and virus evasion from innate immunity, making them attractive targets for antiviral agents. In this work, we focused on the design and synthesis of nucleoside-derived inhibitors against the SARS-CoV-2 nsp14 (N7-guanine)-methyltransferase (N7-MTase) that catalyzes the transfer of the methyl group from the S-adenosyl-l-methionine (SAM) cofactor to the N7-guanosine cap. Seven compounds out of 39 SAM analogues showed remarkable double-digit nanomolar inhibitory activity against the N7-MTase nsp14. Molecular docking supported the structure-activity relationships of these inhibitors and a bisubstrate-based mechanism of action. The three most potent inhibitors significantly stabilized nsp14 (ΔTm ≈ 11 °C), and the best inhibitor demonstrated high selectivity for nsp14 over human RNA N7-MTase.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/drug therapy , COVID-19/virology , Exoribonucleases/antagonists & inhibitors , Exoribonucleases/chemistry , Humans , Methyltransferases , Molecular Docking Simulation , RNA, Viral/genetics , S-Adenosylmethionine , SARS-CoV-2/drug effects , SARS-CoV-2/enzymology , Sulfonamides/pharmacology , Viral Nonstructural Proteins/antagonists & inhibitors , Viral Nonstructural Proteins/chemistry
18.
Mol Cell ; 82(13): 2385-2400.e9, 2022 07 07.
Article in English | MEDLINE | ID: covidwho-1851815

ABSTRACT

Inflammation observed in SARS-CoV-2-infected patients suggests that inflammasomes, proinflammatory intracellular complexes, regulate various steps of infection. Lung epithelial cells express inflammasome-forming sensors and constitute the primary entry door of SARS-CoV-2. Here, we describe that the NLRP1 inflammasome detects SARS-CoV-2 infection in human lung epithelial cells. Specifically, human NLRP1 is cleaved at the Q333 site by multiple coronavirus 3CL proteases, which triggers inflammasome assembly and cell death and limits the production of infectious viral particles. Analysis of NLRP1-associated pathways unveils that 3CL proteases also inactivate the pyroptosis executioner Gasdermin D (GSDMD). Subsequently, caspase-3 and GSDME promote alternative cell pyroptosis. Finally, analysis of pyroptosis markers in plasma from COVID-19 patients with characterized severe pneumonia due to autoantibodies against, or inborn errors of, type I interferons (IFNs) highlights GSDME/caspase-3 as potential markers of disease severity. Overall, our findings identify NLRP1 as a sensor of SARS-CoV-2 infection in lung epithelia.


Subject(s)
COVID-19 , Coronavirus 3C Proteases , Epithelial Cells , Inflammasomes , NLR Proteins , SARS-CoV-2 , COVID-19/genetics , COVID-19/metabolism , COVID-19/virology , Caspase 3/metabolism , Coronavirus 3C Proteases/genetics , Coronavirus 3C Proteases/metabolism , Epithelial Cells/metabolism , Humans , Inflammasomes/genetics , Inflammasomes/metabolism , Lung/metabolism , Lung/virology , NLR Proteins/genetics , NLR Proteins/metabolism , Peptide Hydrolases/genetics , Peptide Hydrolases/metabolism , Phosphate-Binding Proteins/genetics , Phosphate-Binding Proteins/metabolism , Pore Forming Cytotoxic Proteins/genetics , Pore Forming Cytotoxic Proteins/metabolism , Pyroptosis , SARS-CoV-2/enzymology , SARS-CoV-2/genetics , SARS-CoV-2/metabolism , SARS-CoV-2/pathogenicity
19.
Bioorg Med Chem Lett ; 58: 128526, 2022 02 15.
Article in English | MEDLINE | ID: covidwho-1814173

ABSTRACT

The COVID-19 pandemic has drastically impacted global economies and public health. Although vaccine development has been successful, it was not sufficient against more infectious mutant strains including the Delta variant indicating a need for alternative treatment strategies such as small molecular compound development. In this work, a series of SARS-CoV-2 main protease (Mpro) inhibitors were designed and tested based on the active compound from high-throughput diverse compound library screens. The most efficacious compound (16b-3) displayed potent SARS-CoV-2 Mpro inhibition with an IC50 value of 116 nM and selectivity against SARS-CoV-2 Mpro when compared to PLpro and RdRp. This new class of compounds could be used as potential leads for further optimization in anti COVID-19 drug discovery.


Subject(s)
Antiviral Agents/pharmacology , Coronavirus 3C Proteases/antagonists & inhibitors , Drug Discovery , Protease Inhibitors/pharmacology , SARS-CoV-2/drug effects , Thiazoles/pharmacology , Antiviral Agents/chemical synthesis , Antiviral Agents/chemistry , COVID-19/drug therapy , Coronavirus 3C Proteases/metabolism , Humans , Microbial Sensitivity Tests , Molecular Structure , Protease Inhibitors/chemical synthesis , Protease Inhibitors/chemistry , SARS-CoV-2/enzymology , Thiazoles/chemical synthesis , Thiazoles/chemistry
20.
Biochem Biophys Res Commun ; 604: 76-82, 2022 05 14.
Article in English | MEDLINE | ID: covidwho-1797136

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in millions of deaths and seriously threatened public health and safety. Despite COVID-19 vaccines being readily popularized worldwide, targeted therapeutic agents for the treatment of this disease remain very limited. Here, we studied the inhibitory activity of the scutellarein and its methylated derivatives against SARS-CoV-2 main protease (Mpro) by the fluorescence resonance energy transfer (FRET) assay. Among all the methylated derivatives we studied, 4'-O-methylscutellarein exhibited the most promising enzyme inhibitory activity in vitro, with the half-maximal inhibitory concentration value (IC50) of 0.40 ± 0.03 µM. Additionally, the mechanism of action of the hits was further characterized through enzyme kinetic studies and molecular docking. Overall, our results implied that 4'-O-methylscutellarein could be a primary lead compound with clinical potential for the development of inhibitors against the SARS-CoV-2 Mpro.


Subject(s)
Alkaloids , Coronavirus 3C Proteases , Indoles , SARS-CoV-2 , Viral Protease Inhibitors , Alkaloids/pharmacology , Coronavirus 3C Proteases/antagonists & inhibitors , Humans , Indoles/pharmacology , Kinetics , Molecular Docking Simulation , SARS-CoV-2/drug effects , SARS-CoV-2/enzymology , Viral Protease Inhibitors/pharmacology
SELECTION OF CITATIONS
SEARCH DETAIL