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1.
Molecules ; 27(21)2022 Nov 04.
Article in English | MEDLINE | ID: covidwho-2099669

ABSTRACT

Middle East respiratory syndrome coronavirus (MERS-CoV), belonging to the betacoronavirus genus can cause severe respiratory illnesses, accompanied by pneumonia, multiorgan failure, and ultimately death. CoVs have the ability to transgress species barriers and spread swiftly into new host species, with human-to-human transmission causing epidemic diseases. Despite the severe public health threat of MERS-CoV, there are currently no vaccines or drugs available for its treatment. MERS-CoV papain-like protease (PLpro) is a key enzyme that plays an important role in its replication. In the present study, we evaluated the inhibitory activities of doxorubicin (DOX) against the recombinant MERS-CoV PLpro by employing protease inhibition assays. Hydrolysis of fluorogenic peptide from the Z-RLRGG-AMC-peptide bond in the presence of DOX showed an IC50 value of 1.67 µM at 30 min. Subsequently, we confirmed the interaction between DOX and MERS-CoV PLpro by thermal shift assay (TSA), and DOX increased ΔTm by ~20 °C, clearly indicating a coherent interaction between the MERS-CoV PL protease and DOX. The binding site of DOX on MERS-CoV PLpro was assessed using docking techniques and molecular dynamic (MD) simulations. DOX bound to the thumb region of the catalytic domain of the MERS-CoV PLpro. MD simulation results showed flexible BL2 loops, as well as other potential residues, such as R231, R233, and G276 of MERS-CoV PLpro. Development of drug repurposing is a remarkable opportunity to quickly examine the efficacy of different aspects of treating various diseases. Protease inhibitors have been found to be effective against MERS-CoV to date, and numerous candidates are currently undergoing clinical trials to prove this. Our effort follows a in similar direction.


Subject(s)
Middle East Respiratory Syndrome Coronavirus , Humans , Middle East Respiratory Syndrome Coronavirus/metabolism , Papain/chemistry , Peptide Hydrolases/metabolism , Drug Repositioning , Doxorubicin/pharmacology , Doxorubicin/metabolism
2.
Biochem J ; 479(20): 2175-2193, 2022 Oct 28.
Article in English | MEDLINE | ID: covidwho-2062282

ABSTRACT

Coronaviruses have been responsible for multiple challenging global pandemics, including coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Papain-like protease (PLpro), one of two cysteine proteases responsible for the maturation and infectivity of SARS-CoV-2, processes and liberates functional proteins from the viral polyproteins and cleaves ubiquitin and ISG15 modifications to inhibit innate immune sensing. Consequently, PLpro is an attractive target for developing COVID-19 therapies. PLpro contains a zinc-finger domain important for substrate binding and structural stability. However, the impact of metal ions on the activity and biophysical properties of SARS-CoV-2 PLpro has not been comprehensively studied. Here, we assessed the impacts of metal ions on the catalytic activity of PLpro. Zinc had the largest inhibitory effect on PLpro, followed by manganese. Calcium, magnesium, and iron had smaller or no effects on PLpro activity. EDTA at a concentration of 0.5 mM was essential for PLpro activity, likely by chelating trace metals that inhibit PLpro. IC50 values for ZnCl2, ZnSO4, and MnCl2 of 0.42 ± 0.02 mM, 0.35 ± 0.01 mM, and 2.6 ± 0.3 mM were obtained in the presence of 0.5 mM EDTA; in the absence of EDTA, the estimated IC50 of ZnCl2 was 14 µM. Tryptophan intrinsic fluorescence analysis confirmed the binding of zinc and manganese to PLpro, and differential scanning calorimetry revealed that zinc but not manganese reduced ΔHcal of PLpro. The results of this study provide a reference for further work targeting PLpro to prevent and treat COVID-19.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Papain/chemistry , Papain/metabolism , COVID-19/drug therapy , Peptide Hydrolases/metabolism , Magnesium , Calcium , Tryptophan , Edetic Acid , Ubiquitin/metabolism , Polyproteins , Ions , Zinc , Iron
3.
Chembiochem ; 23(19): e202200327, 2022 10 06.
Article in English | MEDLINE | ID: covidwho-1999838

ABSTRACT

Emerging variants of SARS-CoV-2 and potential novel epidemic coronaviruses underline the importance of investigating various viral proteins as potential drug targets. The papain-like protease of coronaviruses has been less explored than other viral proteins; however, its substantive role in viral replication and impact on the host immune response make it a suitable target to study. This review article focuses on the structure and function of the papain-like protease (PLpro ) of SARS-CoV-2, including variants of concern, and compares it to those of other coronaviruses, such as SARS-CoV-1 and MERS-CoV. The protease's recognition motif is mirrored in ubiquitin and ISG15, which are involved in the antiviral immune response. Inhibitors, including GRL0617 derivatives, and their prospects as potential future antiviral agents are also discussed.


Subject(s)
COVID-19 , Papain , Aniline Compounds , Antiviral Agents/chemistry , Benzamides , COVID-19/drug therapy , Coronavirus Papain-Like Proteases , Humans , Naphthalenes , Papain/chemistry , Papain/metabolism , Peptide Hydrolases/metabolism , Protease Inhibitors/pharmacology , SARS-CoV-2 , Ubiquitin/metabolism , Viral Proteins/chemistry
4.
J Biol Chem ; 298(8): 102250, 2022 08.
Article in English | MEDLINE | ID: covidwho-1991134

ABSTRACT

Rubella, a viral disease characterized by a red skin rash, is well controlled because of an effective vaccine, but outbreaks are still occurring in the absence of available antiviral treatments. The Rubella virus (RUBV) papain-like protease (RubPro) is crucial for RUBV replication, cleaving the nonstructural polyprotein p200 into two multifunctional proteins, p150 and p90. This protease could represent a potential drug target, but structural and mechanistic details important for the inhibition of this enzyme are unclear. Here, we report a novel crystal structure of RubPro at a resolution of 1.64 Å. The RubPro adopts a unique papain-like protease fold, with a similar catalytic core to that of proteases from Severe acute respiratory syndrome coronavirus 2 and foot-and-mouth disease virus while having a distinctive N-terminal fingers domain. RubPro has well-conserved sequence motifs that are also found in its newly discovered Rubivirus relatives. In addition, we show that the RubPro construct has protease activity in trans against a construct of RUBV protease-helicase and fluorogenic peptides. A protease-helicase construct, exogenously expressed in Escherichia coli, was also cleaved at the p150-p90 cleavage junction, demonstrating protease activity of the protease-helicase protein. We also demonstrate that RubPro possesses deubiquitylation activity, suggesting a potential role of RubPro in modulating the host's innate immune responses. We anticipate that these structural and functional insights of RubPro will advance our current understanding of its function and help facilitate more structure-based research into the RUBV replication machinery, in hopes of developing antiviral therapeutics against RUBV.


Subject(s)
Peptide Hydrolases , Rubella virus , Amino Acid Motifs , Papain/chemistry , Peptide Hydrolases/chemistry , Peptide Hydrolases/metabolism , Protein Folding , Protein Structure, Tertiary , Rubella virus/chemistry , Rubella virus/enzymology
5.
Neurotox Res ; 40(5): 1553-1569, 2022 Oct.
Article in English | MEDLINE | ID: covidwho-1966190

ABSTRACT

Since the appearance of SARS-CoV-2 and the COVID-19 pandemic, the search for new approaches to treat this disease took place in the scientific community. The in silico approach has gained importance at this moment, once the methodologies used in this kind of study allow for the identification of specific protein-ligand interactions, which may serve as a filter step for molecules that can act as specific inhibitors. In addition, it is a low-cost and high-speed technology. Molecular docking has been widely used to find potential viral protein inhibitors for structural and non-structural proteins of the SARS-CoV-2, aiming to block the infection and the virus multiplication. The papain-like protease (PLpro) participates in the proteolytic processing of SARS-CoV-2 and composes one of the main targets studied for pharmacological intervention by in silico methodologies. Based on that, we performed a systematic review about PLpro inhibitors from the perspective of in silico research, including possible therapeutic molecules in relation to this viral protein. The neurological problems triggered by COVID-19 were also briefly discussed, especially relative to the similarities of neuroinflammation present in Alzheimer's disease. In this context, we focused on two molecules, curcumin and glycyrrhizinic acid, given their PLpro inhibitory actions and neuroprotective properties and potential therapeutic effects on COVID-19.


Subject(s)
COVID-19 , Curcumin , COVID-19/drug therapy , Glycyrrhizic Acid , Humans , Ligands , Molecular Docking Simulation , Pandemics , Papain/chemistry , Papain/metabolism , Peptide Hydrolases/metabolism , SARS-CoV-2 , Viral Proteins/chemistry , Viral Proteins/metabolism
6.
Acta Biochim Biophys Sin (Shanghai) ; 54(8): 1133-1139, 2022 Aug 25.
Article in English | MEDLINE | ID: covidwho-1964135

ABSTRACT

The coronavirus papain-like protease (PLpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for viral polypeptide cleavage and the deISGylation of interferon-stimulated gene 15 (ISG15), which enable it to participate in virus replication and host innate immune pathways. Therefore, PLpro is considered an attractive antiviral drug target. Here, we show that parthenolide, a germacrane sesquiterpene lactone, has SARS-CoV-2 PLpro inhibitory activity. Parthenolide covalently binds to Cys-191 or Cys-194 of the PLpro protein, but not the Cys-111 at the PLpro catalytic site. Mutation of Cys-191 or Cys-194 reduces the activity of PLpro. Molecular docking studies show that parthenolide may also form hydrogen bonds with Lys-192, Thr-193, and Gln-231. Furthermore, parthenolide inhibits the deISGylation but not the deubiquitinating activity of PLpro in vitro. These results reveal that parthenolide inhibits PLpro activity by allosteric regulation.


Subject(s)
COVID-19 , Coronavirus Papain-Like Proteases , Antiviral Agents/pharmacology , COVID-19/drug therapy , Humans , Interferons , Lactones , Molecular Docking Simulation , Papain/chemistry , Papain/metabolism , Peptide Hydrolases/metabolism , SARS-CoV-2 , Sesquiterpenes , Sesquiterpenes, Germacrane , Ubiquitin/metabolism
7.
Comput Biol Chem ; 99: 107721, 2022 Aug.
Article in English | MEDLINE | ID: covidwho-1906916

ABSTRACT

Papain like protease (PLpro) is a cysteine protease from the coronaviridae family of viruses. Coronaviruses possess a positive sense, single-strand RNA, leading to the translation of two viral polypeptides containing viral structural, non-structural and accessory proteins. PLpro is responsible for the cleavage of nsp1-3 from the viral polypeptide. PLpro also possesses deubiquitinating and deISGlyating activity, which sequesters the virus from the host's immune system. This indispensable attribute of PLpro makes it a protein of interest as a drug target. The present study aims to analyze the structural influences of ligand binding on PLpro. First, PLpro was screened against the ZINC-in-trials library, from which four lead compounds were identified based on estimated binding affinity and interaction patterns. Next, based on molecular docking results, ZINC000000596945, ZINC000064033452 and VIR251 (control molecule) were subjected to molecular dynamics simulation. The study evaluated global and essential dynamics analyses utilising principal component analyses, dynamic cross-correlation matrix, free energy landscape and time-dependant essential dynamics to predict the structural changes observed in PLpro upon ligand binding in a simulated environment. The MM/PBSA-based binding free energy calculations of the two selected molecules, ZINC000000596945 (-41.23 ± 3.70 kcal/mol) and ZINC000064033452 (-25.10 ± 2.65 kcal/mol), displayed significant values which delineate them as potential inhibitors of PLpro from SARS-CoV-2.


Subject(s)
COVID-19 , Papain , Coronavirus Papain-Like Proteases , Humans , Ligands , Molecular Docking Simulation , Molecular Dynamics Simulation , Papain/chemistry , Papain/genetics , Papain/metabolism , Peptide Hydrolases/genetics , Peptide Hydrolases/metabolism , SARS-CoV-2
8.
Protein Pept Lett ; 29(7): 574-583, 2022.
Article in English | MEDLINE | ID: covidwho-1879360

ABSTRACT

The coronavirus family consists of pathogens that seriously affect human and animal health. They mostly cause respiratory or enteric diseases, which can be severe and life-threatening, such as coronavirus disease 2019 (COVID-19), severe acute respiratory syndrome (SARS), and Middle East Respiratory Syndrome (MERS) in humans. The conserved coronaviral papain-like protease is an attractive antiviral drug target because it is essential for coronaviral replication, and it also inhibits host innate immune responses. This review focuses on the latest research progress relating to the mechanism of coronavirus infection, the structural and functional characteristics of coronavirus papain-like protease, and the potent inhibitors of the protease.


Subject(s)
Coronavirus Infections/drug therapy , Coronavirus Papain-Like Proteases/chemistry , Animals , Antiviral Agents/chemistry , Antiviral Agents/pharmacology , COVID-19/drug therapy , Coronavirus Papain-Like Proteases/antagonists & inhibitors , Humans , Papain/chemistry , Peptide Hydrolases/chemistry , Protease Inhibitors/pharmacology
9.
Cell Rep ; 36(13): 109754, 2021 09 28.
Article in English | MEDLINE | ID: covidwho-1401298

ABSTRACT

The SARS-CoV-2 papain-like protease (PLpro) is a target for antiviral drug development. It is essential for processing viral polyproteins for replication and functions in host immune evasion by cleaving ubiquitin (Ub) and ubiquitin-like protein (Ubl) conjugates. While highly conserved, SARS-CoV-2 and SARS-CoV PLpro have contrasting Ub/Ubl substrate preferences. Using a combination of structural analyses and functional assays, we identify a molecular sensor within the S1 Ub-binding site of PLpro that serves as a key determinant of substrate specificity. Variations within the S1 sensor specifically alter cleavage of Ub substrates but not of the Ubl interferon-stimulated gene 15 protein (ISG15). Significantly, a variant of concern associated with immune evasion carries a mutation in the S1 sensor that enhances PLpro activity on Ub substrates. Collectively, our data identify the S1 sensor region as a potential hotspot of variability that could alter host antiviral immune responses to newly emerging SARS-CoV-2 lineages.


Subject(s)
Coronavirus Papain-Like Proteases/metabolism , Coronavirus Papain-Like Proteases/ultrastructure , SARS-CoV-2/genetics , Amino Acid Sequence/genetics , Binding Sites/genetics , COVID-19/genetics , COVID-19/metabolism , Coronavirus Papain-Like Proteases/genetics , HEK293 Cells , Humans , Papain/chemistry , Papain/metabolism , Peptide Hydrolases/chemistry , Peptide Hydrolases/metabolism , Protein Binding/genetics , SARS-CoV-2/metabolism , Substrate Specificity/genetics , Ubiquitin/metabolism , Ubiquitins/metabolism , Viral Proteins/metabolism
10.
Molecules ; 26(16)2021 Aug 12.
Article in English | MEDLINE | ID: covidwho-1355016

ABSTRACT

The COVID-19 outbreak has rapidly spread on a global scale, affecting the economy and public health systems throughout the world. In recent years, peptide-based therapeutics have been widely studied and developed to treat infectious diseases, including viral infections. Herein, the antiviral effects of the lysine linked dimer des-Cys11, Lys12,Lys13-(pBthTX-I)2K ((pBthTX-I)2K)) and derivatives against SARS-CoV-2 are reported. The lead peptide (pBthTX-I)2K and derivatives showed attractive inhibitory activities against SARS-CoV-2 (EC50 = 28-65 µM) and mostly low cytotoxic effect (CC50 > 100 µM). To shed light on the mechanism of action underlying the peptides' antiviral activity, the Main Protease (Mpro) and Papain-Like protease (PLpro) inhibitory activities of the peptides were assessed. The synthetic peptides showed PLpro inhibition potencies (IC50s = 1.0-3.5 µM) and binding affinities (Kd = 0.9-7 µM) at the low micromolar range but poor inhibitory activity against Mpro (IC50 > 10 µM). The modeled binding mode of a representative peptide of the series indicated that the compound blocked the entry of the PLpro substrate toward the protease catalytic cleft. Our findings indicated that non-toxic dimeric peptides derived from the Bothropstoxin-I have attractive cellular and enzymatic inhibitory activities, thereby suggesting that they are promising prototypes for the discovery and development of new drugs against SARS-CoV-2 infection.


Subject(s)
Crotalid Venoms/chemistry , Dimerization , Papain/antagonists & inhibitors , Peptides/chemistry , Peptides/pharmacology , SARS-CoV-2/enzymology , Antiviral Agents/chemistry , Antiviral Agents/metabolism , Antiviral Agents/pharmacology , Molecular Docking Simulation , Papain/chemistry , Papain/metabolism , Peptides/metabolism , Protease Inhibitors/chemistry , Protease Inhibitors/metabolism , Protease Inhibitors/pharmacology , Protein Conformation , SARS-CoV-2/drug effects
11.
Mol Divers ; 26(1): 309-329, 2022 Feb.
Article in English | MEDLINE | ID: covidwho-1171933

ABSTRACT

The non-structural protein (nsp)-3 of SARS-CoV2 coronavirus is sought to be an essential target protein which is also named as papain-like protease (PLpro). This protease cleaves the viral polyprotein, but importantly in human host it also removes ubiquitin-like interferon-stimulated gene 15 protein (ISG15) from interferon responsive factor 3 (IRF3) protein which ultimately downregulates the production of type I interferon leading to weakening of immune response. GRL0617 is the most potent known inhibitor for PLpro that was initially developed for SARS outbreak of 2003. The PLpro of SARS-CoV and CoV2 share 83% sequence identity but interestingly have several identical conserved amino acids that suggests GRL0617 to be an effective inhibitor for PLpro of SARS-CoV2. GRL0617 is a naphthalene-based molecule and interacts with Tyr268 of SARS-CoV2-PLpro (and Tyr269 of SARS-CoV-PLpro). To identify PLpro inhibitors, we prepared a library of secondary metabolites from fungi with aromatic nature and docked them with PLpro of SARS-CoV and SARS-CoV2. We found six hits which interacts with Tyr268 of SARS-CoV2-PLpro (and Tyr269 of SARS-CoV-PLpro). More surprisingly the top hit, Fonsecin, has naphthalene moiety in its structure, which recruits Tyr268 of SARS-CoV2-PLpro (and Tyr269 of SARS-CoV-PLpro) and has binding energy at par with control (GRL0617). Molecular dynamics (MD) simulation showed Fonsecin to interact with Tyr268 of SARS-CoV2-PLpro more efficiently than control (GRL0617) and interacting with a greater number of amino acids in the binding cleft of PLpro.


Subject(s)
COVID-19 , Molecular Dynamics Simulation , Aniline Compounds , Benzamides , COVID-19/drug therapy , Fungi/metabolism , Humans , Molecular Docking Simulation , Naphthalenes , Papain/chemistry , Papain/metabolism , Peptide Hydrolases/metabolism , RNA, Viral , SARS-CoV-2
12.
J Biomol Struct Dyn ; 40(7): 3071-3081, 2022 04.
Article in English | MEDLINE | ID: covidwho-926956

ABSTRACT

Novel coronavirus SARS-CoV-2 has infected 18 million people with 700,000+ mortalities worldwide and this deadly numeric figure is rapidly rising. With very few success stories, the therapeutic targeting of this epidemic has been mainly attributed to main protease (Mpro), whilst Papain-like proteases (PLpro) also plays a vital role in the processing of replicase polyprotein. Multifunctional roles of PLpro such as viral polypeptide cleavage, de-ISGlyation and immune suppression have made it a promising drug target for therapeutic interventions. Whilst there have been a number of studies and others are on-going on repurposing and new-small molecule screening, albeit previously FDA approved drugs viz. Chloroquine (CQ) and Hydroxychloroquine (HCQ) have only been found effective against this pandemic. Inspired by this fact, we have carried out molecular docking and dynamics simulation studies of FDA approved CQ and HCQ against SARS-CoV-2 PLpro. The end aim is to characterise the binding mode of CQ and HCQ and identify the key amino acid residues involved in the mechanism of action. Further, molecular dynamics simulations (MDS) were carried out with the docked complex to search for the conformational space and for understanding the integrity of binding mode. We showed that the CQ and HCQ can bind with better binding affinity with PLpro as compared to reference known PLpro inhibitor. Based on the presented findings, it can be anticipated that the SARS-CoV-2 PLpro may act as molecular target of CQ and HCQ, and can be projected for further exploration to design potent inhibitors of SARS-CoV-2 PLpro in the near future.


Subject(s)
COVID-19 , Chloroquine , Coronavirus Papain-Like Proteases , Hydroxychloroquine , SARS-CoV-2 , Antiviral Agents/chemistry , Antiviral Agents/pharmacology , COVID-19/drug therapy , Chloroquine/chemistry , Coronavirus Papain-Like Proteases/chemistry , Humans , Hydroxychloroquine/chemistry , Molecular Docking Simulation , Molecular Dynamics Simulation , Papain/chemistry
13.
SLAS Discov ; 25(10): 1152-1161, 2020 12.
Article in English | MEDLINE | ID: covidwho-846185

ABSTRACT

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in late 2019 has triggered an ongoing global pandemic whereby infection may result in a lethal severe pneumonia-like disease designated as coronavirus disease 2019 (COVID-19). To date, millions of confirmed cases and hundreds of thousands of deaths have been reported worldwide, and there are currently no medical countermeasures available to prevent or treat the disease. The purported development of a vaccine could require at least 1-4 years, while the typical timeline from hit finding to drug registration of an antiviral is >10 years. Thus, repositioning of known drugs can significantly accelerate the development and deployment of therapies for COVID-19. To identify therapeutics that can be repurposed as SARS-CoV-2 antivirals, we developed and initiated a high-throughput cell-based screen that incorporates the essential viral papain-like protease (PLpro) and its peptide cleavage site into a luciferase complementation assay to evaluate the efficacy of known drugs encompassing approximately 15,000 clinical-stage or US Food and Drug Administration (FDA)-approved small molecules. Confirmed inhibitors were also tested to determine their cytotoxic properties. Here, we report the identification of four clinically relevant drugs that exhibit selective inhibition of the SARS-CoV-2 viral PLpro.


Subject(s)
Antiviral Agents/pharmacology , Coronavirus 3C Proteases/antagonists & inhibitors , High-Throughput Screening Assays/methods , Protease Inhibitors/pharmacology , Bleomycin/pharmacology , COVID-19/drug therapy , Coronavirus 3C Proteases/genetics , Coronavirus 3C Proteases/metabolism , HEK293 Cells , Humans , Papain/chemistry , SARS-CoV-2/drug effects , SARS-CoV-2/enzymology
14.
Int J Biol Macromol ; 165(Pt A): 1438-1446, 2020 Dec 15.
Article in English | MEDLINE | ID: covidwho-843655

ABSTRACT

There are several families of cysteine proteinases with different folds - for example the (chymo)trypsin fold family and papain-like fold family - but in both families the hydrolase activity of cysteine proteinases requires a cysteine residue as the catalytic nucleophile. In this work, we have analyzed the topology of the active site regions in 146 three-dimensional structures of proteins belonging to the Papain-like Cysteine Proteinase (PCP) superfamily, which includes papain as a typical representative of this protein superfamily. All analyzed enzymes contain a unique structurally closed conformation - a "PCP-Zone" - which can be divided into two groups, Class A and Class B. Eight structurally conserved amino acids of the PCP-Zone form a common Structural Core. The Structural Core, catalytic nucleophile, catalytic base and residue Xaa - which stabilizes the side-chain conformation of the catalytic base - make up a PCP Structural Catalytic Core (PCP-SCC). The PCP-SCC of Class A and Class B are divided into 5 and 2 types, respectively. Seven variants of the mutual arrangement of the amino-acid side chains of the catalytic triad - nucleophile, base and residue Xaa - within the same fold clearly demonstrate how enzymes with the papain-like fold adapt to the need to perform diverse functions in spite of their limited structural diversity. The roles of both the PCP-Zone of SARS-CoV-2-PLpro described in this study and the NBCZone of SARS-CoV-2-3CLpro presented in our earlier article (Denesyuk AI, Johnson MS, Salo-Ahen OMH, Uversky VN, Denessiouk K. Int J Biol Macromol. 2020;153:399-411) that are in contacts with inhibitors are discussed.


Subject(s)
Catalytic Domain , Papain/chemistry , Papain/metabolism , Biocatalysis , Models, Molecular
15.
J Chem Phys ; 153(11): 115101, 2020 Sep 21.
Article in English | MEDLINE | ID: covidwho-796705

ABSTRACT

Broad-spectrum antiviral drugs are urgently needed to stop the Coronavirus Disease 2019 pandemic and prevent future ones. The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is related to the SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV), which have caused the previous outbreaks. The papain-like protease (PLpro) is an attractive drug target due to its essential roles in the viral life cycle. As a cysteine protease, PLpro is rich in cysteines and histidines, and their protonation/deprotonation modulates catalysis and conformational plasticity. Here, we report the pKa calculations and assessment of the proton-coupled conformational dynamics of SARS-CoV-2 in comparison to SARS-CoV and MERS-CoV PLpros using the recently developed graphical processing unit (GPU)-accelerated implicit-solvent continuous constant pH molecular dynamics method with a new asynchronous replica-exchange scheme, which allows computation on a single GPU card. The calculated pKa's support the catalytic roles of the Cys-His-Asp triad. We also found that several residues can switch protonation states at physiological pH among which is C270/271 located on the flexible blocking loop 2 (BL2) of SARS-CoV-2/CoV PLpro. Simulations revealed that the BL2 can open and close depending on the protonation state of C271/270, consistent with the most recent crystal structure evidence. Interestingly, despite the lack of an analogous cysteine, BL2 in MERS-CoV PLpro is also very flexible, challenging a current hypothesis. These findings are supported by the all-atom fixed-charge simulations and provide a starting point for more detailed studies to assist the structure-based design of broad-spectrum inhibitors against CoV PLpros.


Subject(s)
Antiviral Agents/pharmacology , Betacoronavirus/enzymology , Drug Design , Middle East Respiratory Syndrome Coronavirus/enzymology , Molecular Dynamics Simulation , Papain/chemistry , Papain/metabolism , Protons , Amino Acid Sequence , Histidine , Hydrogen-Ion Concentration , Papain/antagonists & inhibitors , Protein Domains , SARS-CoV-2
16.
Eur Rev Med Pharmacol Sci ; 24(14): 7834-7844, 2020 07.
Article in English | MEDLINE | ID: covidwho-693570

ABSTRACT

The pandemic threat of COVID-19 causes serious concern for people and world organizations. The effect of Coronavirus disease on the lifestyle and economic status of humans is undeniable, and all of the researchers (biologists, pharmacists, physicians, and chemists) can help decrease its destructive effects. The molecular docking approach can provide a fast prediction of the positive influence the targets on the COVID-19 outbreak. In this work, we choose resveratrol (RV) derivatives (22 cases) and two newly released coordinate structures for COVID-19 as receptors [Papain-like Protease of SARS CoV-2 (PBD ID: 6W9C) and 2019-nCoV RNA-dependent RNA Polymerase (PBD ID: 6M71)]. The results show that conformational isomerism is significant and useful parameter for docking results. A wide spectrum of interactions such as Van der Waals, conventional hydrogen bond, Pi-donor hydrogen bond, Pi-Cation, Pi-sigma, Pi-Pi stacked, Amide-Pi stacked and Pi-Alkyl is detected via docking of RV derivatives and COVID-19 receptors. The potential inhibition effect of RV-13 (-184.99 kj/mol), and RV-12 (-173.76 kj/mol) is achieved at maximum value for 6W9C and 6M71, respectively.


Subject(s)
Antiviral Agents/metabolism , Betacoronavirus/metabolism , Papain/metabolism , RNA-Dependent RNA Polymerase/metabolism , Resveratrol/metabolism , SARS Virus/metabolism , Viral Nonstructural Proteins/metabolism , Antiviral Agents/chemistry , Antiviral Agents/therapeutic use , Betacoronavirus/isolation & purification , Binding Sites , COVID-19 , Coronavirus Infections/drug therapy , Coronavirus Infections/virology , Coronavirus Papain-Like Proteases , Crystallography, X-Ray , Hydrogen Bonding , Molecular Docking Simulation , Pandemics , Papain/chemistry , Pneumonia, Viral/drug therapy , Pneumonia, Viral/virology , Protein Structure, Tertiary , RNA-Dependent RNA Polymerase/chemistry , Resveratrol/chemistry , Resveratrol/therapeutic use , SARS Virus/isolation & purification , SARS-CoV-2 , Severe Acute Respiratory Syndrome/drug therapy , Severe Acute Respiratory Syndrome/virology , Viral Nonstructural Proteins/chemistry
17.
Chem Commun (Camb) ; 56(62): 8854-8856, 2020 Aug 04.
Article in English | MEDLINE | ID: covidwho-635466

ABSTRACT

Using a combination of enhanced sampling molecular dynamics techniques and non-equilibrium alchemical transformations with full atomistic details, we have shown that hydroxychloroquine (HCQ) may act as a mild inhibitor of important functional proteins for SARS-CoV2 replication, with potency increasing in the series PLpro, 3CLpro, RdRp. By analyzing the bound state configurations, we were able to improve the potency for the 3CLpro target, designing a novel HCQ-inspired compound, named PMP329, with predicted nanomolar activity. If confirmed in vitro, our results provide a molecular rationale for the use of HCQ or of strictly related derivatives in the treatment of Covid-19.


Subject(s)
Cysteine Endopeptidases/metabolism , Hydroxychloroquine/metabolism , Molecular Dynamics Simulation , Papain/metabolism , RNA-Dependent RNA Polymerase/metabolism , Viral Nonstructural Proteins/metabolism , Betacoronavirus/isolation & purification , Betacoronavirus/metabolism , Binding Sites , COVID-19 , Catalytic Domain , Coronavirus 3C Proteases , Coronavirus Infections/drug therapy , Coronavirus Infections/pathology , Coronavirus Papain-Like Proteases , Cysteine Endopeptidases/chemistry , Humans , Hydroxychloroquine/chemistry , Hydroxychloroquine/therapeutic use , Pandemics , Papain/chemistry , Pneumonia, Viral/drug therapy , Pneumonia, Viral/pathology , RNA-Dependent RNA Polymerase/chemistry , SARS-CoV-2 , Viral Nonstructural Proteins/chemistry
18.
Protein Sci ; 29(5): 1228-1241, 2020 05.
Article in English | MEDLINE | ID: covidwho-244545

ABSTRACT

Swine acute diarrhea syndrome coronavirus (SADS-CoV) is a novel coronavirus that is involved in severe diarrhea disease in piglets, causing considerable agricultural and economic loss in China. The emergence of this new coronavirus increases the importance of understanding SADS-CoV as well as antivirals. Coronaviral proteases, including main proteases and papain-like proteases (PLP), are attractive antiviral targets because of their essential roles in polyprotein processing and thus viral maturation. Here, we describe the biochemical and structural identification of recombinant SADS papain-like protease 2 (PLP2) domain of nsp3. The SADS-CoV PLP2 was shown to cleave nsp1 proteins and also peptides mimicking the nsp2|nsp3 cleavage site and also had deubiquitinating and deISGynating activity by in vitro assays. The crystal structure adopts an architecture resembling that of PLPs from other coronaviruses. We characterize both conserved and unique structural features likely directing the interaction of PLP2 with the substrates, including the tentative mapping of active site and other essential residues. These results provide a foundation for understanding the molecular basis of coronaviral PLPs' catalytic mechanism and for the screening and design of therapeutics to combat infection by SADS coronavirus.


Subject(s)
Alphacoronavirus/enzymology , Diarrhea/veterinary , Papain/chemistry , Swine Diseases/virology , Viral Nonstructural Proteins/chemistry , Animals , Coronavirus/enzymology , Coronavirus Papain-Like Proteases , Crystallography, X-Ray , Diarrhea/virology , Models, Molecular , Papain/metabolism , Sus scrofa , Swine , Viral Nonstructural Proteins/metabolism
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