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1.
Chem Biodivers ; 19(11): e202200266, 2022 Nov.
Article in English | MEDLINE | ID: covidwho-2127606

ABSTRACT

The unprecedented global pandemic of COVID-19 has created a daunting scenario urging an immediate generation of therapeutic strategy. Interventions to curb the spread of viral infection primarily include setting targets against the virus. Here in this study we target S protein to obstruct the viral attachment and entry and also the M pro to prevent the viral replication. For this purpose, the interaction of S protein and M pro with phytocompounds, sanguinarine and eugenol, and their derivatives were studied using computational tools. Docking studies gave evidence that 8-hydroxydihydrosanguinarine (8-HDS), a derivative of sanguinarine, showed maximum binding affinity with both the targets. The binding energies of the ligand with S protein and M pro scored to be ΔGb -9.4 Kcal/mol and ΔGb -10.3 Kcal/mol, respectively. MD simulation studies depict that the phytocompound could effectively cause structural perturbations in the targets which would affect their functions. 8-Hydroxydihydrosanguinarine distorts the α-helix in the secondary structure of M pro and RBD site of S protein. Protein-protein interaction study in presence of 8-hydroxydihydrosanguinarine also corroborate the above findings which indicate that this polyphenol interferes in the coupling of S protein and ACE2. The alterations in protonation of M pro suggest that the protein structure undergoes significant structural changes at neutral pH. ADME property of 8-hydroxydihydrosanguinarine indicates this could be a potential drug. This makes the phyto-alkaloid a possible therapeutic molecule for anti COVID-19 drug design.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , COVID-19/drug therapy , Viral Nonstructural Proteins/chemistry , Viral Nonstructural Proteins/metabolism , Antiviral Agents/pharmacology , Antiviral Agents/chemistry , Molecular Docking Simulation , Molecular Dynamics Simulation , Pyridones
2.
Structure ; 28(8): 874-878, 2020 08 04.
Article in English | MEDLINE | ID: covidwho-2132441

ABSTRACT

During global pandemics, the spread of information needs to be faster than the spread of the virus in order to ensure the health and safety of human populations worldwide. In our current crisis, the demand for SARS-CoV-2 drugs and vaccines highlights the importance of biological targets and their three-dimensional shape. In particular, structural biology as a field was poised to quickly respond to crises due to previous experience and expertise and because of its early adoption of open access practices.


Subject(s)
Betacoronavirus/chemistry , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Pandemics , Pneumonia, Viral/epidemiology , Pneumonia, Viral/virology , Viral Proteins/chemistry , COVID-19 , Coronavirus 3C Proteases , Coronavirus RNA-Dependent RNA Polymerase , Cysteine Endopeptidases/chemistry , Databases, Protein , Humans , Models, Molecular , Molecular Biology , Protein Conformation , RNA-Dependent RNA Polymerase/chemistry , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/chemistry , Viral Nonstructural Proteins/chemistry
3.
J Chem Phys ; 157(18): 185101, 2022 Nov 14.
Article in English | MEDLINE | ID: covidwho-2119368

ABSTRACT

The main protease (Mpro) of SARS-CoV-2 is an essential enzyme for the replication of the virus causing the COVID-19 pandemic. Because there is no known homologue in humans, it has been proposed as a primary target for antiviral drug development. Here, we explore the potential of five acrylamide-based molecules as possible covalent inhibitors, leading to target MPro by docking, followed by polarizable molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) calculations. All calculations involving a classical potential were calculated with the AMOEBABIO18 polarizable force field, while electronic structure calculations were performed within the framework of density functional theory. Selected docking poses for each of the five compounds were used for MD simulations, which suggest only one of the tested leads remains bound in a catalytically active orientation. The QM/MM results for the covalent attachment of the promising lead to the catalytic serine suggest that this process is thermodynamically feasible but kinetically unlikely. Overall, our results are consistent with the low labeling percentages determined experimentally and may be useful for further development of acrylamide-based leads.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Pandemics , Coronavirus 3C Proteases , Molecular Dynamics Simulation , Peptide Hydrolases/metabolism , Acrylamide , Protease Inhibitors/pharmacology , Protease Inhibitors/chemistry , Viral Nonstructural Proteins/chemistry , Viral Nonstructural Proteins/metabolism , Cysteine Endopeptidases/chemistry , Cysteine Endopeptidases/metabolism , Molecular Docking Simulation
4.
J Am Chem Soc ; 144(46): 21035-21045, 2022 Nov 23.
Article in English | MEDLINE | ID: covidwho-2117370

ABSTRACT

Given the current impact of SARS-CoV2 and COVID-19 on human health and the global economy, the development of direct acting antivirals is of paramount importance. Main protease (MPro), a cysteine protease that cleaves the viral polyprotein, is essential for viral replication. Therefore, MPro is a novel therapeutic target. We identified two novel MPro inhibitors, D-FFRCMKyne and D-FFCitCMKyne, that covalently modify the active site cysteine (C145) and determined cocrystal structures. Medicinal chemistry efforts led to SM141 and SM142, which adopt a unique binding mode within the MPro active site. Notably, these inhibitors do not inhibit the other cysteine protease, papain-like protease (PLPro), involved in the life cycle of SARS-CoV2. SM141 and SM142 block SARS-CoV2 replication in hACE2 expressing A549 cells with IC50 values of 8.2 and 14.7 nM. Detailed studies indicate that these compounds also inhibit cathepsin L (CatL), which cleaves the viral S protein to promote viral entry into host cells. Detailed biochemical, proteomic, and knockdown studies indicate that the antiviral activity of SM141 and SM142 results from the dual inhibition of MPro and CatL. Notably, intranasal and intraperitoneal administration of SM141 and SM142 lead to reduced viral replication, viral loads in the lung, and enhanced survival in SARS-CoV2 infected K18-ACE2 transgenic mice. In total, these data indicate that SM141 and SM142 represent promising scaffolds on which to develop antiviral drugs against SARS-CoV2.


Subject(s)
COVID-19 , Hepatitis C, Chronic , Animals , Mice , Humans , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , Antiviral Agents/chemistry , Coronavirus 3C Proteases , Cathepsin L/chemistry , Cathepsin L/metabolism , RNA, Viral , SARS-CoV-2 , COVID-19/drug therapy , Protease Inhibitors/pharmacology , Protease Inhibitors/therapeutic use , Protease Inhibitors/chemistry , Peptide Hydrolases , Proteomics , Viral Nonstructural Proteins/chemistry , Molecular Docking Simulation
5.
ACS Synth Biol ; 11(11): 3759-3771, 2022 Nov 18.
Article in English | MEDLINE | ID: covidwho-2106357

ABSTRACT

Essential viral enzymes have been successfully targeted to combat the diseases caused by emerging pathogenic RNA viruses (e.g., viral RNA-dependent RNA polymerase). Because of the conserved nature of such viral enzymes, therapeutics targeting these enzymes have the potential to be repurposed to combat emerging diseases, e.g., remdesivir, which was initially developed as a potential Ebola treatment, then was repurposed for COVID-19. Our efforts described in this study target another essential and highly conserved, but relatively less explored, step in RNA virus translation and replication, i.e., capping of the viral RNA genome. The viral genome cap structure disguises the genome of most RNA viruses to resemble the mRNA cap structure of their host and is essential for viral translation, propagation, and immune evasion. Here, we developed a synthetic, phenotypic yeast-based complementation platform (YeRC0M) for molecular characterization and targeting of SARS-CoV-2 genome-encoded RNA cap-0 (guanine-N7)-methyltransferase (N7-MTase) enzyme (nsp14). In YeRC0M, the lack of yeast mRNA capping N7-MTase in yeast, which is an essential gene in yeast, is complemented by the expression of functional viral N7-MTase or its variants. Using YeRC0M, we first identified important protein domains and amino acid residues that are essential for SARS-CoV-2 nsp14 N7-MTase activity. We also expanded YeRC0M to include key nsp14 variants observed in emerging variants of SARS-CoV-2 (e.g., delta variant of SARS-CoV-2 encodes nsp14 A394V and nsp14 P46L). We also combined YeRC0M with directed evolution to identify attenuation mutations in SARS-CoV-2 nsp14. Because of the high sequence similarity of nsp14 in emerging coronaviruses, these observations could have implications on live attenuated vaccine development strategies. These data taken together reveal key domains in SARS-CoV-2 nsp14 that can be targeted for therapeutic strategies. We also anticipate that these readily tractable phenotypic platforms can also be used for the identification of inhibitors of viral RNA capping enzymes as antivirals.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , RNA, Viral/genetics , Viral Nonstructural Proteins/chemistry , Viral Nonstructural Proteins/genetics , Viral Nonstructural Proteins/metabolism , Saccharomyces cerevisiae/genetics , Methyltransferases/metabolism , RNA, Messenger
6.
Org Biomol Chem ; 20(38): 7582-7586, 2022 10 05.
Article in English | MEDLINE | ID: covidwho-2050570

ABSTRACT

N-Acylsulfonamides possess an additional carbonyl function compared to their sulfonamide analogues. Due to their unique physico-chemical properties, interest in molecules containing the N-acylsulfonamide moiety and especially nucleoside derivatives is growing in the field of medicinal chemistry. The recent renewal of interest in antiviral drugs derived from nucleosides containing a sulfonamide function has led us to evaluate the therapeutic potential of N-acylsulfonamide analogues. While these compounds are usually obtained by a difficult acylation of sulfonamides, we report here the easy and efficient synthesis of 20 4'-(N-acylsulfonamide) adenosine derivatives via the sulfo-click reaction. The target compounds were obtained from thioacid and sulfonyl azide synthons in excellent yields and were evaluated as potential inhibitors of the SARS-CoV-2 RNA cap N7-guanine-methyltransferase nsp14.


Subject(s)
COVID-19 , Methyltransferases , Adenosine/pharmacology , Antiviral Agents/pharmacology , Azides , COVID-19/drug therapy , Exoribonucleases/chemistry , Exoribonucleases/genetics , Guanine , Humans , Nucleosides/pharmacology , RNA Caps , RNA, Viral/genetics , SARS-CoV-2 , Sulfonamides/pharmacology , Viral Nonstructural Proteins/chemistry , Viral Nonstructural Proteins/genetics
7.
Nat Struct Mol Biol ; 29(9): 850-853, 2022 09.
Article in English | MEDLINE | ID: covidwho-2016774

ABSTRACT

Emergence of SARS-CoV-2 coronavirus has led to millions of deaths globally. We present three high-resolution crystal structures of the SARS-CoV-2 nsp14 N7-methyltransferase core bound to S-adenosylmethionine (1.62 Å), S-adenosylhomocysteine (1.55 Å) and sinefungin (1.41 Å). We identify features of the methyltransferase core that are crucial for the development of antivirals and show SAH as the best scaffold for the design of antivirals against SARS-CoV-2 and other pathogenic coronaviruses.


Subject(s)
COVID-19 , SARS-CoV-2 , Antiviral Agents/pharmacology , COVID-19/drug therapy , Humans , Methyltransferases/metabolism , S-Adenosylhomocysteine , S-Adenosylmethionine/metabolism , Viral Nonstructural Proteins/chemistry
8.
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
9.
Biochem Biophys Res Commun ; 629: 54-60, 2022 11 12.
Article in English | MEDLINE | ID: covidwho-2007463

ABSTRACT

Shortly after the onset of the COVID-19 pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has acquired numerous variations in its intracellular proteins to adapt quickly, become more infectious, and ultimately develop drug resistance by mutating certain hotspot residues. To keep the emerging variants at bay, including Omicron and subvariants, FDA has approved the antiviral nirmatrelvir for mild-to-moderate and high-risk COVID-19 cases. Like other viruses, SARS-CoV-2 could acquire mutations in its main protease (Mpro) to adapt and develop resistance against nirmatrelvir. Employing a unique high-throughput protein design technique, the hotspot residues, and signatures of adaptation of Mpro having the highest probability of mutating and rendering nirmatrelvir ineffective were identified. Our results show that ∼40% of the designed mutations in Mpro already exist in the globally circulating SARS-CoV-2 lineages and several predicted mutations. Moreover, several high-frequency, designed mutations were found to be in corroboration with the experimentally reported nirmatrelvir-resistant mutants and are naturally occurring. Our work on the targeted design of the nirmatrelvir-binding site offers a comprehensive picture of potential hotspot sites and resistance mutations in Mpro and is thus crucial in comprehending viral adaptation, robust antiviral design, and surveillance of evolving Mpro variations.


Subject(s)
COVID-19 , SARS-CoV-2 , Antiviral Agents/chemistry , Binding Sites , COVID-19/genetics , Coronavirus 3C Proteases , Cysteine Endopeptidases/metabolism , Genome, Viral , Humans , Mutation , Pandemics , Protease Inhibitors/chemistry , SARS-CoV-2/genetics , Viral Nonstructural Proteins/chemistry
10.
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
11.
Protein Sci ; 31(9): e4395, 2022 09.
Article in English | MEDLINE | ID: covidwho-1995551

ABSTRACT

SARS-CoV-2 nsp10-nsp16 complex is a 2'-O-methyltransferase (MTase) involved in viral RNA capping, enabling the virus to evade the immune system in humans. It has been considered a valuable target in the discovery of antiviral therapeutics, as the RNA cap formation is crucial for viral propagation. Through cross-screening of the inhibitors that we previously reported for SARS-CoV-2 nsp14 MTase activity against nsp10-nsp16 complex, we identified two compounds (SS148 and WZ16) that also inhibited nsp16 MTase activity. To further enable the chemical optimization of these two compounds towards more potent and selective dual nsp14/nsp16 MTase inhibitors, we determined the crystal structure of nsp10-nsp16 in complex with each of SS148 and WZ16. As expected, the structures revealed the binding of both compounds to S-adenosyl-L-methionine (SAM) binding pocket of nsp16. However, our structural data along with the biochemical mechanism of action determination revealed an RNA-dependent SAM-competitive pattern of inhibition for WZ16, clearly suggesting that binding of the RNA first may help the binding of some SAM competitive inhibitors. Both compounds also showed some degree of selectivity against human protein MTases, an indication of great potential for chemical optimization towards more potent and selective inhibitors of coronavirus MTases.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/drug therapy , Humans , Methyltransferases/chemistry , RNA, Viral/metabolism , Viral Nonstructural Proteins/chemistry
12.
J Mol Graph Model ; 117: 108306, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-1983500

ABSTRACT

The Coronavirus Disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, has created unprecedented public health and economic crises around the world. SARS-CoV-2 2'-O-methyltransferase (nsp16) adds a "cap" to viral RNA to maintain the stability of viral RNA, and inhibition of nsp16 activity may reduce viral proliferation, making this protein an attractive drug target. Here, we report the identification of several small molecule inhibitors of nsp16 by virtual screening. First, the nsp16-sinefungin complex (PDB ID: 6WKQ) was selected from the protein data bank. Asp6912, Cys6913, Asp6897 and Asp6928 were determined to be the key amino acids for sinefungin binding in the crystal structure of nsp16-sinefungin complex by molecular dynamics simulation. The complex structures in the stable binding trajectory of nsp16-sinefungin were than clustered through molecular dynamics RMSD analysis. Six clusters were generated, and six representative structures were selected to construct the pharmacophore based on the structure. These six pharmacophores were superimposed on the binding pocket to simplify and pick the common characteristics. The compounds obtained by the pharmacophore screening from Bionet and Chembiv databases were docked into the nsp16 active pocket. The candidate compounds were selected according to the molecular docking score and then screened by MM/GBSA. Finally, four candidate compounds were obtained. Four sets of 150ns molecular dynamics simulations were performed to determine whether candidate compounds could maintain stable interactions with key amino acids. The results of MD and MM/PBSA energy decomposition indicated that C1 and C2 could form a stable complex system with nsp16, and could form strong hydrogen bonds and salt bridges with the key amino acid Asp6897 and Asp6928. This study thus identifies and attempts to validate for the first time the potential inhibitory activities of C1 and C2 against nsp16, allowing the development of potent anti-COVID-19 drugs and unique treatment strategies.


Subject(s)
COVID-19 , SARS-CoV-2 , Amino Acids , COVID-19/drug therapy , Humans , Methyltransferases , Molecular Docking Simulation , Molecular Dynamics Simulation , RNA, Viral , Viral Nonstructural Proteins/chemistry
13.
Comput Biol Med ; 147: 105679, 2022 08.
Article in English | MEDLINE | ID: covidwho-1982860

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 was originally identified in Wuhan city of China in December 2019 and it spread rapidly throughout the globe, causing a threat to human life. Since targeted therapies are deficient, scientists all over the world have an opportunity to develop novel drug therapies to combat COVID-19. After the declaration of a global medical emergency, it was established that the Food and Drug Administration (FDA) could permit the use of emergency testing, treatments, and vaccines to decrease suffering, and loss of life, and restore the nation's health and security. The FDA has approved the use of remdesivir and its analogs as an antiviral medication, to treat COVID-19. The primary protease of SARS-CoV-2, which has the potential to regulate coronavirus proliferation, has been a viable target for the discovery of medicines against SARS-CoV-2. The present research deals with the in silico technique to screen phytocompounds from a traditional medicinal plant, Bauhinia variegata for potential inhibitors of the SARS-CoV-2 main protease. Dried leaves of the plant B. variegata were used to prepare aqueous and methanol extract and the constituents were analyzed using the GC-MS technique. A total of 57 compounds were retrieved from the aqueous and methanol extract analysis. Among these, three lead compounds (2,5 dimethyl 1-H Pyrrole, 2,3 diphenyl cyclopropyl methyl phenyl sulphoxide, and Benzonitrile m phenethyl) were shown to have the highest binding affinity (-5.719 to -5.580 kcal/mol) towards SARS-CoV-2 Mpro. The post MD simulation results also revealed the favorable confirmation and stability of the selected lead compounds with Mpro as per trajectory analysis. The Prime MM/GBSA binding free energy supports this finding, the top lead compound 2,3 diphenyl cyclopropyl methyl phenyl sulphoxide showed high binding free energy (-64.377 ± 5.24 kcal/mol) towards Mpro which reflects the binding stability of the molecule with Mpro. The binding free energy of the complexes was strongly influenced by His, Gln, and Glu residues. All of the molecules chosen are found to have strong pharmacokinetic characteristics and show drug-likeness properties. The lead compounds present acute toxicity (LD50) values ranging from 670 mg/kg to 2500 mg/kg; with toxicity classifications of 4 and 5 classes. Thus, these compounds could behave as probable lead candidates for treatment against SARS-CoV-2. However further in vitro and in vivo studies are required for the development of medication against SARS-CoV-2.


Subject(s)
Bauhinia , COVID-19 , Bauhinia/metabolism , COVID-19/drug therapy , Gas Chromatography-Mass Spectrometry , Humans , Methanol , Molecular Docking Simulation , Molecular Dynamics Simulation , Protease Inhibitors/chemistry , Protease Inhibitors/pharmacology , SARS-CoV-2 , Viral Nonstructural Proteins/chemistry
14.
Biochem Biophys Res Commun ; 626: 114-120, 2022 10 20.
Article in English | MEDLINE | ID: covidwho-1982610

ABSTRACT

New variations of SARS-CoV-2 continue to emerge in the global pandemic, which may be resistant to at least some vaccines in COVID-19, indicating that drug and vaccine development must be continuously strengthened. NSP10 plays an essential role in SARS-CoV-2 viral life cycle. It stimulates the enzymatic activities of NSP14-ExoN and NSP16-O-MTase by the formation of NSP10/NSP14 and NSP10/NSP16 complexes. Inhibiting NSP10 can block the binding of NSP10 to NSP14 and NSP16. This study has identified potential natural NSP10 inhibitors from ZINC database. The protein druggable pocket was identified for screening candidates. Molecular docking of the selected compounds was performed and MM-GBSA binding energy was calculated. After ADMET assessment, 4 hits were obtained for favorable druggability. The analysis of site interactions suggested that the hits all had excellent binding. Molecular dynamics studies revealed that selected natural compounds stably bind to NSP10. These compounds were identified as potential leads against NSP10 for the development of strategies to combat SARS-CoV-2 replication and could serve as the basis for further studies.


Subject(s)
COVID-19 , SARS-CoV-2 , Antiviral Agents/pharmacology , COVID-19/drug therapy , Humans , Methyltransferases/metabolism , Molecular Docking Simulation , Molecular Dynamics Simulation , Viral Nonstructural Proteins/chemistry
15.
Biochem Biophys Res Commun ; 616: 8-13, 2022 08 06.
Article in English | MEDLINE | ID: covidwho-1982607

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) provoked a pandemic of acute respiratory disease, namely coronavirus disease 2019 (COVID-19). Currently, effective drugs for this disease are urgently warranted. Anisodamine is a traditional Chinese medicine that is predicted as a potential therapeutic drug for the treatment of COVID-19. Therefore, this study aimed to investigate its antiviral activity and crucial targets in SARS-CoV-2 infection. SARS-CoV-2 and anisodamine were co-cultured in Vero E6 cells, and the antiviral activity of anisodamine was assessed by immunofluorescence assay. The antiviral activity of anisodamine was further measured by pseudovirus entry assay in HEK293/hACE2 cells. Finally, the predictions of crucial targets of anisodamine on SARS-CoV-2 were analyzed by molecular docking studies. We discovered that anisodamine suppressed SARS-CoV-2 infection in Vero E6 cells, and reduced the SARS-CoV-2 pseudovirus entry to HEK293/hACE2 cells. Furthermore, molecular docking studies indicated that anisodamine may target SARS-CoV-2 main protease (Mpro) with the docking score of -6.63 kcal/mol and formed three H-bonds with Gly143, Cys145, and Cys44 amino acid residues at the predicted active site of Mpro. This study suggests that anisodamine is a potent antiviral agent for treating COVID-19.


Subject(s)
COVID-19 , Coronavirus 3C Proteases , SARS-CoV-2 , Solanaceous Alkaloids , Antiviral Agents/chemistry , Antiviral Agents/pharmacology , COVID-19/drug therapy , COVID-19/virology , Coronavirus 3C Proteases/antagonists & inhibitors , Coronavirus 3C Proteases/drug effects , Coronavirus 3C Proteases/metabolism , HEK293 Cells , Humans , Molecular Docking Simulation , Peptide Hydrolases , Protease Inhibitors/pharmacology , Solanaceous Alkaloids/pharmacology , Viral Nonstructural Proteins/chemistry
16.
Biochem Biophys Res Commun ; 625: 53-59, 2022 10 15.
Article in English | MEDLINE | ID: covidwho-1966378

ABSTRACT

The novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2 or COVID-19) has caused a global pandemic. The SARS-CoV-2 RNA genome is replicated by a conserved "core" replication-transcription complex (RTC) containing an error-prone RNA-dependent RNA polymerase holoenzyme (holo-RdRp, nsp12-nsp7-nsp8) and a RNA proofreading nuclease (nsp14-nsp10). Although structures and functions of SARS-CoV-2 holo-RdRp have been extensively studied and ribonucleotide-analog inhibitors, such as Remdesivir, have been treated for COVID-19 patients, the substrate and nucleotide specificity of SARS-CoV-2 holo-RdRp remain unknown. Here, our biochemical analysis of SARS-CoV-2 holo-RdRp reveals that it has a robust DNA-dependent RNA polymerase activity, in addition to its intrinsic RNA-dependent RNA polymerase activity. Strikingly, SARS-CoV-2 holo-RdRp fully extends RNAs with a low-fidelity even when only ATP and pyrimidine nucleotides, in particular CTP, are provided. This ATP-dependent error-prone ribonucleotide incorporation by SARS-CoV-2 holo-RdRp resists excision by the RNA proofreading nuclease in vitro. Our collective results suggest that a physiological concentration of ATP likely contributes to promoting the error-prone incorporation of ribonucleotides and ribonucleotide-analogs by SARS-CoV-2 holo-RdRp and provide a useful foundation to develop ribonucleotide analogs as an effective therapeutic strategy to combat coronavirus-mediated outbreak.


Subject(s)
COVID-19 , SARS-CoV-2 , Adenosine Triphosphate , Antiviral Agents/chemistry , DNA-Directed RNA Polymerases , Humans , RNA, Viral/chemistry , RNA, Viral/genetics , RNA-Dependent RNA Polymerase , Ribonucleotides , SARS-CoV-2/genetics , Viral Nonstructural Proteins/chemistry
17.
Mar Drugs ; 20(6)2022 Jun 16.
Article in English | MEDLINE | ID: covidwho-1964023

ABSTRACT

Coronavirus disease 2019, caused by the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is an ongoing global pandemic that poses an unprecedented threat to the global economy and human health. Several potent inhibitors targeting SARS-CoV-2 have been published; however, most of them have failed in clinical trials. This study aimed to assess the therapeutic compounds among aldehyde derivatives from seaweeds as potential SARS-CoV-2 inhibitors using a computer simulation protocol. The absorption, distribution, metabolism, excretion, and toxicity (ADME/Tox) properties of the compounds were analyzed using a machine learning algorithm, and the docking simulation of these compounds to the 3C-like protease (Protein Data Bank (PDB) ID: 6LU7) was analyzed using a molecular docking protocol based on the CHARMm algorithm. These compounds exhibited good drug-like properties following the Lipinski and Veber rules. Among the marine aldehyde derivatives, 4-hydroxybenzaldehyde, 3-hydroxybenzaldehyde, 3,4-dihydroxybenzaldehyde, and 5-bromoprotocatechualdehyde were predicted to have good absorption and solubility levels and non-hepatotoxicity in the ADME/Tox prediction. 3-hydroxybenzaldehyde and 3,4-dihydroxybenzaldehyde were predicted to be non-toxic in TOPKAT prediction. In addition, 3,4-dihydroxybenzaldehyde was predicted to exhibit interactions with the 3C-like protease, with binding energies of -71.9725 kcal/mol. The computational analyses indicated that 3,4-dihydroxybenzaldehyde could be regarded as potential a SARS-CoV-2 inhibitor.


Subject(s)
COVID-19 , Seaweed , Aldehydes/pharmacology , Antiviral Agents/chemistry , Antiviral Agents/pharmacology , COVID-19/drug therapy , Computer Simulation , Coronavirus 3C Proteases , Humans , Molecular Docking Simulation , Molecular Dynamics Simulation , Protease Inhibitors/pharmacology , SARS-CoV-2 , Seaweed/metabolism , Viral Nonstructural Proteins/chemistry
18.
Int J Mol Sci ; 23(14)2022 Jul 12.
Article in English | MEDLINE | ID: covidwho-1964003

ABSTRACT

The mosquito-borne disease caused by the Rocio virus is a neglected threat, and new immune inputs for serological testing are urgently required for diagnosis in low-resource settings and epidemiological surveillance. We used in silico approaches to identify a specific antigenic peptide (p_ROCV2) in the NS1 protein of the Rocio virus that was theoretically predicted to be stable and exposed on its surface, where it demonstrated key properties allowing it to interact with antibodies. These findings related to the molecular dynamics of this peptide provide important insights for advancing diagnostic platforms and investigating therapeutic alternatives.


Subject(s)
Flavivirus , Molecular Dynamics Simulation , Animals , Immunologic Tests , Molecular Docking Simulation , Peptides , Viral Nonstructural Proteins/chemistry
19.
Nutrients ; 14(15)2022 Jul 25.
Article in English | MEDLINE | ID: covidwho-1957403

ABSTRACT

Natural resources, particularly plants and microbes, are an excellent source of bioactive molecules. Bromelain, a complex enzyme mixture found in pineapples, has numerous pharmacological applications. In a search for therapeutic molecules, we conducted an in silico study on natural phyto-constituent bromelain, targeting pathogenic bacteria and viral proteases. Docking studies revealed that bromelain strongly bound to food-borne bacterial pathogens and SARS-CoV-2 virus targets, with a high binding energy of -9.37 kcal/mol. The binding interaction was mediated by the involvement of hydrogen bonds, and some hydrophobic interactions stabilized the complex and molecular dynamics. Simulation studies also indicated the stable binding between bromelain and SARS-CoV-2 protease as well as with bacterial targets which are essential for DNA and protein synthesis and are required to maintain the integrity of membranous proteins. From this in silico study, it is also concluded that bromelain could be an effective molecule to control foodborne pathogen toxicity and COVID-19. So, eating pineapple during an infection could help to interfere with the pathogen attaching and help prevent the virus from getting into the host cell. Further, research on the bromelain molecule could be helpful for the management of COVID-19 disease as well as other bacterial-mediated diseases. Thus, the antibacterial and anti-SARS-CoV-2 virus inhibitory potentials of bromelain could be helpful in the management of viral infections and subsequent bacterial infections in COVID-19 patients.


Subject(s)
Ananas , COVID-19 , Antiviral Agents/pharmacology , Bacteria/metabolism , Bromelains/pharmacology , COVID-19/drug therapy , Coronavirus 3C Proteases , Cysteine Endopeptidases , Humans , Molecular Docking Simulation , Molecular Dynamics Simulation , Protease Inhibitors/chemistry , SARS-CoV-2 , Viral Nonstructural Proteins/chemistry , Viral Nonstructural Proteins/metabolism
20.
Biomed Res Int ; 2022: 7341493, 2022.
Article in English | MEDLINE | ID: covidwho-1932844

ABSTRACT

In this work, the discovery and description of PF-07321332, a major bioavailable oral SARS-CoV-2 protease inhibitor with in vitro human coronavirus antiviral activity, and excellent selection of off-target and in vivo immune profiles are reported. Various drugs and novel compound candidates for the treatment of the COVID-19 pandemic have been developed. PF-07321332 (or nirmatrelvir) is a new oral antiviral drug developed by Pfizer. In response to the pandemic, Pfizer has developed the COVID vaccine and in 2022 will launch its new major anti-SARS-Cov-2 protease inhibitor (PI). The combination of ritonavir and nirmatrelvir is under study in phase III of the clinical trial with a brand name Paxlovid. Paxlovid is an active 3Cl protease inhibitor. Paxlovid exerts its antiviral efficacy by inhibiting a necessary protease in the viral replication procedure. Proteases of coronavirus cleave several sites in the viral polyprotein where pyrrolidone was replaced by flexible glutamine. Due to the coronavirus pandemic, there is high demand for synthesis and development of this novel drug. Herein, we report the synthetic route and the mechanism of action was recently published on nirmatrelvir. Also, a comparison of the performance of two new oral antiviruses (molnupiravir and nirmatrelvir) for the treatment of COVID-19 is described. This review will be helpful for different disciplines such as biochemistry, organic chemistry, medicinal chemistry, and pharmacology.


Subject(s)
COVID-19 , Pandemics , Antiviral Agents/chemistry , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , COVID-19/drug therapy , COVID-19 Vaccines , Coronavirus 3C Proteases , Cysteine Endopeptidases , Drug Combinations , Humans , Lactams , Leucine , Nitriles , Proline , Protease Inhibitors/chemistry , Protease Inhibitors/pharmacology , Protease Inhibitors/therapeutic use , Ritonavir , SARS-CoV-2 , Viral Nonstructural Proteins/chemistry
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