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1.
Cell ; 184(6): 1604-1620, 2021 03 18.
Article in English | MEDLINE | ID: covidwho-1392179

ABSTRACT

Historically, emerging viruses appear constantly and have cost millions of human lives. Currently, climate change and intense globalization have created favorable conditions for viral transmission. Therefore, effective antivirals, especially those targeting the conserved protein in multiple unrelated viruses, such as the compounds targeting RNA-dependent RNA polymerase, are urgently needed to combat more emerging and re-emerging viruses in the future. Here we reviewed the development of antivirals with common targets, including those against the same protein across viruses, or the same viral function, to provide clues for development of antivirals for future epidemics.


Subject(s)
Antiviral Agents/therapeutic use , Communicable Diseases, Emerging/drug therapy , Communicable Diseases, Emerging/epidemiology , Molecular Targeted Therapy/methods , Pandemics , Virus Diseases/drug therapy , Virus Diseases/epidemiology , Viruses/enzymology , Animals , Antiviral Agents/pharmacology , Communicable Diseases, Emerging/virology , Humans , RNA-Dependent RNA Polymerase/antagonists & inhibitors , Viral Envelope Proteins/antagonists & inhibitors , Virus Diseases/virology , Virus Internalization/drug effects
2.
ChemMedChem ; 16(15): 2345-2353, 2021 08 05.
Article in English | MEDLINE | ID: covidwho-1248684

ABSTRACT

The C-type lectin receptor DC-SIGN mediates interactions with envelope glycoproteins of many viruses such as SARS-CoV-2, ebola, and HIV and contributes to virus internalization and dissemination. In the context of the recent SARS-CoV-2 pandemic, involvement of DC-SIGN has been linked to severe cases of COVID-19. Inhibition of the interaction between DC-SIGN and viral glycoproteins has the potential to generate broad spectrum antiviral agents. Here, we demonstrate that mannose-functionalized poly-l-lysine glycoconjugates efficiently inhibit the attachment of viral glycoproteins to DC-SIGN-presenting cells with picomolar affinity. Treatment of these cells leads to prolonged receptor internalization and inhibition of virus binding for up to 6 h. Furthermore, the polymers are fully bio-compatible and readily cleared by target cells. The thermodynamic analysis of the multivalent interactions reveals enhanced enthalpy-driven affinities and promising perspectives for the future development of multivalent therapeutics.


Subject(s)
Antiviral Agents/pharmacology , Cell Adhesion Molecules/antagonists & inhibitors , Glycoconjugates/pharmacology , Lectins, C-Type/antagonists & inhibitors , Receptors, Cell Surface/antagonists & inhibitors , Virus Attachment/drug effects , Antiviral Agents/chemical synthesis , Antiviral Agents/metabolism , Cell Adhesion Molecules/metabolism , Glycoconjugates/chemical synthesis , Glycoconjugates/metabolism , Humans , Lectins, C-Type/metabolism , Mannose/analogs & derivatives , Mannose/metabolism , Mannose/pharmacology , Microbial Sensitivity Tests , Polylysine/analogs & derivatives , Polylysine/metabolism , Polylysine/pharmacology , Protein Binding/drug effects , Receptors, Cell Surface/metabolism , SARS-CoV-2/drug effects , THP-1 Cells , Thermodynamics , Viral Envelope Proteins/antagonists & inhibitors , Viral Envelope Proteins/metabolism
3.
Biomolecules ; 11(6)2021 05 23.
Article in English | MEDLINE | ID: covidwho-1243950

ABSTRACT

COVID-19 is a devastating respiratory and inflammatory illness caused by a new coronavirus that is rapidly spreading throughout the human population. Over the past 12 months, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19, has already infected over 160 million (>20% located in United States) and killed more than 3.3 million people around the world (>20% deaths in USA). As we face one of the most challenging times in our recent history, there is an urgent need to identify drug candidates that can attack SARS-CoV-2 on multiple fronts. We have therefore initiated a computational dynamics drug pipeline using molecular modeling, structure simulation, docking and machine learning models to predict the inhibitory activity of several million compounds against two essential SARS-CoV-2 viral proteins and their host protein interactors-S/Ace2, Tmprss2, Cathepsins L and K, and Mpro-to prevent binding, membrane fusion and replication of the virus, respectively. All together, we generated an ensemble of structural conformations that increase high-quality docking outcomes to screen over >6 million compounds including all FDA-approved drugs, drugs under clinical trial (>3000) and an additional >30 million selected chemotypes from fragment libraries. Our results yielded an initial set of 350 high-value compounds from both new and FDA-approved compounds that can now be tested experimentally in appropriate biological model systems. We anticipate that our results will initiate screening campaigns and accelerate the discovery of COVID-19 treatments.


Subject(s)
Antiviral Agents/therapeutic use , COVID-19/drug therapy , Angiotensin-Converting Enzyme 2/chemistry , Angiotensin-Converting Enzyme 2/metabolism , Antiviral Agents/chemistry , Antiviral Agents/metabolism , Antiviral Agents/pharmacology , Binding Sites , COVID-19/pathology , COVID-19/virology , Drug Discovery , Drug Repositioning , Humans , Machine Learning , Molecular Docking Simulation , SARS-CoV-2/drug effects , SARS-CoV-2/isolation & purification , SARS-CoV-2/metabolism , Serine Endopeptidases/chemistry , Serine Endopeptidases/metabolism , Viral Envelope Proteins/antagonists & inhibitors , Viral Envelope Proteins/metabolism , Virus Replication/drug effects
4.
Viruses ; 13(3)2021 03 23.
Article in English | MEDLINE | ID: covidwho-1154526

ABSTRACT

The etiological agent of the COVID-19 pandemic is SARS-CoV-2. As a member of the Coronaviridae, the enveloped pathogen has several membrane proteins, of which two, E and 3a, were suggested to function as ion channels. In an effort to increase our treatment options, alongside providing new research tools, we have sought to inhibit the 3a channel by targeted drug repurposing. To that end, using three bacteria-based assays, we screened a library of 2839 approved-for-human-use drugs and identified the following potential channel-blockers: Capreomycin, Pentamidine, Spectinomycin, Kasugamycin, Plerixafor, Flumatinib, Litronesib, Darapladib, Floxuridine and Fludarabine. The stage is now set for examining the activity of these compounds in detailed electrophysiological studies and their impact on the whole virus with appropriate biosafety measures.


Subject(s)
Antiviral Agents/pharmacology , COVID-19/virology , Drug Repositioning , SARS-CoV-2/drug effects , Viral Envelope Proteins/antagonists & inhibitors , Viral Envelope Proteins/metabolism , Viroporin Proteins/antagonists & inhibitors , Viroporin Proteins/metabolism , COVID-19/drug therapy , Drug Evaluation, Preclinical , Humans , SARS-CoV-2/genetics , SARS-CoV-2/metabolism , Viral Envelope Proteins/genetics , Viroporin Proteins/genetics
5.
Comput Biol Med ; 127: 104063, 2020 12.
Article in English | MEDLINE | ID: covidwho-880431

ABSTRACT

Viroporins are oligomeric, pore forming, viral proteins that play critical roles in the life cycle of pathogenic viruses. Viroporins like HIV-1 Vpu, Alphavirus 6 K, Influenza M2, HCV p7, and Picornavirus 2B, form discrete aqueous passageways which mediate ion and small molecule transport in infected cells. The alterations in host membrane structures induced by viroporins is essential for key steps in the virus life cycle like entry, replication and egress. Any disruption in viroporin functionality severely compromises viral pathogenesis. The envelope (E) protein encoded by coronaviruses is a viroporin with ion channel activity and has been shown to be crucial for the assembly and pathophysiology of coronaviruses. We used a combination of virtual database screening, molecular docking, all-atom molecular dynamics simulation and MM-PBSA analysis to test four FDA approved drugs - Tretinoin, Mefenamic Acid, Ondansetron and Artemether - as potential inhibitors of ion channels formed by SARS-CoV-2 E protein. Interaction and binding energy analysis showed that electrostatic interactions and polar solvation energy were the major driving forces for binding of the drugs, with Tretinoin being the most promising inhibitor. Tretinoin bound within the lumen of the channel formed by E protein, which is lined by hydrophobic residues like Phe, Val and Ala, indicating its potential for blocking the channel and inhibiting the viroporin functionality of E. In control simulations, tretinoin demonstrated a lower binding energy with a known target as compared to SARS-CoV-2 E protein. This work thus highlights the possibility of exploring Tretinoin as a potential SARS-CoV-2 E protein ion channel blocker and virus assembly inhibitor, which could be an important therapeutic strategy in the treatment for coronaviruses.


Subject(s)
COVID-19/virology , SARS-CoV-2/metabolism , Tretinoin/pharmacology , Viral Envelope Proteins/antagonists & inhibitors , Computer Simulation , Databases, Chemical , Ligands , Molecular Docking Simulation , Molecular Dynamics Simulation , Protein Binding , Viral Envelope Proteins/metabolism
6.
mBio ; 11(5)2020 09 15.
Article in English | MEDLINE | ID: covidwho-772275

ABSTRACT

Membrane-associated RING-CH-type 8 (MARCH8) strongly blocks human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) incorporation into virions by downregulating its cell surface expression, but the mechanism is still unclear. We now report that MARCH8 also blocks the Ebola virus (EBOV) glycoprotein (GP) incorporation via surface downregulation. To understand how these viral fusion proteins are downregulated, we investigated the effects of MARCH8 on EBOV GP maturation and externalization via the conventional secretion pathway. MARCH8 interacted with EBOV GP and furin when detected by immunoprecipitation and retained the GP/furin complex in the Golgi when their location was tracked by a bimolecular fluorescence complementation (BiFC) assay. MARCH8 did not reduce the GP expression or affect the GP modification by high-mannose N-glycans in the endoplasmic reticulum (ER), but it inhibited the formation of complex N-glycans on the GP in the Golgi. Additionally, the GP O-glycosylation and furin-mediated proteolytic cleavage were also inhibited. Moreover, we identified a novel furin cleavage site on EBOV GP and found that only those fully glycosylated GPs were processed by furin and incorporated into virions. Furthermore, the GP shedding and secretion were all blocked by MARCH8. MARCH8 also blocked the furin-mediated cleavage of HIV-1 Env (gp160) and the highly pathogenic avian influenza virus H5N1 hemagglutinin (HA). We conclude that MARCH8 has a very broad antiviral activity by prohibiting different viral fusion proteins from glycosylation and proteolytic cleavage in the Golgi, which inhibits their transport from the Golgi to the plasma membrane and incorporation into virions.IMPORTANCE Enveloped viruses express three classes of fusion proteins that are required for their entry into host cells via mediating virus and cell membrane fusion. Class I fusion proteins are produced from influenza viruses, retroviruses, Ebola viruses, and coronaviruses. They are first synthesized as a type I transmembrane polypeptide precursor that is subsequently glycosylated and oligomerized. Most of these precursors are cleaved en route to the plasma membrane by a cellular protease furin in the late secretory pathway, generating the trimeric N-terminal receptor-binding and C-terminal fusion subunits. Here, we show that a cellular protein, MARCH8, specifically inhibits the furin-mediated cleavage of EBOV GP, HIV-1 Env, and H5N1 HA. Further analyses uncovered that MARCH8 blocked the EBOV GP glycosylation in the Golgi and inhibited its transport from the Golgi to the plasma membrane. Thus, MARCH8 has a very broad antiviral activity by specifically inactivating different viral fusion proteins.


Subject(s)
Ebolavirus/chemistry , Glycoproteins/antagonists & inhibitors , HIV-1/chemistry , Hemagglutinins, Viral/metabolism , Influenza A Virus, H5N1 Subtype/chemistry , Ubiquitin-Protein Ligases/genetics , Viral Envelope Proteins/antagonists & inhibitors , Viral Envelope Proteins/physiology , Animals , Cell Line , Chlorocebus aethiops , Ebolavirus/physiology , Glycosylation , HEK293 Cells , HIV-1/physiology , HeLa Cells , Hep G2 Cells , Humans , Influenza A Virus, H5N1 Subtype/physiology , Protein Binding , THP-1 Cells , Ubiquitin-Protein Ligases/metabolism , Vero Cells , Viral Fusion Proteins/antagonists & inhibitors , Viral Fusion Proteins/metabolism
7.
Sci Rep ; 10(1): 4746, 2020 03 16.
Article in English | MEDLINE | ID: covidwho-740043

ABSTRACT

Ginkgolic acids (GA) are alkylphenol constituents of the leaves and fruits of Ginkgo biloba. GA has shown pleiotropic effects in vitro, including: antitumor effects through inhibition of lipogenesis; decreased expression of invasion associated proteins through AMPK activation; and potential rescue of amyloid-ß (Aß) induced synaptic impairment. GA was also reported to have activity against Escherichia coli and Staphylococcus aureus. Several mechanisms for this activity have been suggested including: SUMOylation inhibition; blocking formation of the E1-SUMO intermediate; inhibition of fatty acid synthase; non-specific SIRT inhibition; and activation of protein phosphatase type-2C. Here we report that GA inhibits Herpes simplex virus type 1 (HSV-1) by inhibition of both fusion and viral protein synthesis. Additionally, we report that GA inhibits human cytomegalovirus (HCMV) genome replication and Zika virus (ZIKV) infection of normal human astrocytes (NHA). We show a broad spectrum of fusion inhibition by GA of all three classes of fusion proteins including HIV, Ebola virus (EBOV), influenza A virus (IAV) and Epstein Barr virus (EBV). In addition, we show inhibition of a non-enveloped adenovirus. Our experiments suggest that GA inhibits virion entry by blocking the initial fusion event. Data showing inhibition of HSV-1 and CMV replication, when GA is administered post-infection, suggest a possible secondary mechanism targeting protein and DNA synthesis. Thus, in light of the strong effect of GA on viral infection, even after the infection begins, it may potentially be used to treat acute infections (e.g. Coronavirus, EBOV, ZIKV, IAV and measles), and also topically for the successful treatment of active lesions (e.g. HSV-1, HSV-2 and varicella-zoster virus (VZV)).


Subject(s)
Antiviral Agents/pharmacology , DNA Virus Infections/metabolism , DNA Viruses/drug effects , RNA Virus Infections/metabolism , RNA Viruses/drug effects , Salicylates/pharmacology , Viral Envelope Proteins/antagonists & inhibitors , Viral Fusion Proteins/antagonists & inhibitors , Animals , Astrocytes/metabolism , Chlorocebus aethiops , DNA Replication/drug effects , DNA Virus Infections/virology , DNA Viruses/genetics , DNA, Viral/genetics , HEK293 Cells , Humans , RNA Virus Infections/virology , RNA Viruses/genetics , Vero Cells , Viral Envelope Proteins/biosynthesis , Viral Fusion Proteins/biosynthesis , Virion/drug effects , Virus Internalization/drug effects , Virus Replication/drug effects
8.
Infect Genet Evol ; 84: 104451, 2020 10.
Article in English | MEDLINE | ID: covidwho-630854

ABSTRACT

WHO has declared the outbreak of COVID-19 as a public health emergency of international concern. The ever-growing new cases have called for an urgent emergency for specific anti-COVID-19 drugs. Three structural proteins (Membrane, Envelope and Nucleocapsid protein) play an essential role in the assembly and formation of the infectious virion particles. Thus, the present study was designed to identify potential drug candidates from the unique collection of 548 anti-viral compounds (natural and synthetic anti-viral), which target SARS-CoV-2 structural proteins. High-end molecular docking analysis was performed to characterize the binding affinity of the selected drugs-the ligand, with the SARS-CoV-2 structural proteins, while high-level Simulation studies analyzed the stability of drug-protein interactions. The present study identified rutin, a bioflavonoid and the antibiotic, doxycycline, as the most potent inhibitor of SARS-CoV-2 envelope protein. Caffeic acid and ferulic acid were found to inhibit SARS-CoV-2 membrane protein while the anti-viral agent's simeprevir and grazoprevir showed a high binding affinity for nucleocapsid protein. All these compounds not only showed excellent pharmacokinetic properties, absorption, metabolism, minimal toxicity and bioavailability but were also remain stabilized at the active site of proteins during the MD simulation. Thus, the identified lead compounds may act as potential molecules for the development of effective drugs against SARS-CoV-2 by inhibiting the envelope formation, virion assembly and viral pathogenesis.


Subject(s)
Antiviral Agents/pharmacology , Betacoronavirus/drug effects , Nucleocapsid Proteins/chemistry , Viral Envelope Proteins/chemistry , Viral Matrix Proteins/chemistry , Virion/drug effects , Amides , Amino Acid Sequence , Antiviral Agents/chemistry , Betacoronavirus/genetics , Betacoronavirus/metabolism , Binding Sites , COVID-19 , Caffeic Acids/chemistry , Caffeic Acids/pharmacology , Carbamates , Coronavirus Infections/drug therapy , Coronavirus Infections/virology , Coumaric Acids/chemistry , Coumaric Acids/pharmacology , Cyclopropanes , Doxycycline/chemistry , Doxycycline/pharmacology , Gene Expression , Humans , Kinetics , Molecular Docking Simulation , Molecular Dynamics Simulation , Nucleocapsid Proteins/antagonists & inhibitors , Nucleocapsid Proteins/genetics , Nucleocapsid Proteins/metabolism , Pandemics , Pneumonia, Viral/drug therapy , Pneumonia, Viral/virology , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , Quinoxalines/chemistry , Quinoxalines/pharmacology , Rutin/chemistry , Rutin/pharmacology , SARS-CoV-2 , Sequence Alignment , Sequence Homology, Amino Acid , Simeprevir/chemistry , Simeprevir/pharmacology , Sulfonamides , Thermodynamics , Viral Envelope Proteins/antagonists & inhibitors , Viral Envelope Proteins/genetics , Viral Envelope Proteins/metabolism , Viral Matrix Proteins/antagonists & inhibitors , Viral Matrix Proteins/genetics , Viral Matrix Proteins/metabolism , Virion/genetics
9.
Biochim Biophys Acta Mol Basis Dis ; 1866(10): 165889, 2020 10 01.
Article in English | MEDLINE | ID: covidwho-627951

ABSTRACT

The novel Coronavirus disease of 2019 (nCOV-19) is a viral outbreak noted first in Wuhan, China. This disease is caused by Severe Acute Respiratory Syndrome (SARS) Coronavirus (CoV)-2. In the past, other members of the coronavirus family, such as SARS and Middle East Respiratory Syndrome (MERS), have made an impact in China and the Arabian peninsula respectively. Both SARS and COVID-19 share similar symptoms such as fever, cough, and difficulty in breathing that can become fatal in later stages. However, SARS and MERS infections were epidemic diseases constrained to limited regions. By March 2020 the SARS-CoV-2 had spread across the globe and on March 11th, 2020 the World Health Organization (WHO) declared COVID-19 as pandemic disease. In severe SARS-CoV-2 infection, many patients succumbed to pneumonia. Higher rates of deaths were seen in older patients who had co-morbidities such as diabetes mellitus, hypertension, cardiovascular disease (CVD), and dementia. In this review paper, we discuss the effect of SARS-CoV-2 on CNS diseases, such as Alzheimer's-like dementia, and diabetes mellitus. We also focus on the virus genome, pathophysiology, theranostics, and autophagy mechanisms. We will assess the multiorgan failure reported in advanced stages of SARS-CoV-2 infection. Our paper will provide mechanistic clues and therapeutic targets for physicians and investigators to combat COVID-19.


Subject(s)
Central Nervous System Diseases/pathology , Coronavirus Infections/pathology , Pneumonia, Viral/pathology , Animals , Antiviral Agents/therapeutic use , Betacoronavirus/isolation & purification , Betacoronavirus/metabolism , Betacoronavirus/pathogenicity , COVID-19 , Central Nervous System Diseases/complications , Central Nervous System Diseases/virology , Coronavirus Infections/drug therapy , Coronavirus Infections/virology , Humans , Lung/metabolism , Lung/virology , Pandemics , Pneumonia, Viral/drug therapy , Pneumonia, Viral/virology , SARS-CoV-2 , Viral Envelope Proteins/antagonists & inhibitors , Viral Envelope Proteins/metabolism , Viral Fusion Proteins/antagonists & inhibitors , Viral Fusion Proteins/metabolism , Viral Nonstructural Proteins/antagonists & inhibitors , Viral Nonstructural Proteins/metabolism
10.
Biochem Biophys Res Commun ; 530(1): 10-14, 2020 09 10.
Article in English | MEDLINE | ID: covidwho-609834

ABSTRACT

COVID-19 is one of the most impactful pandemics in recorded history. As such, the identification of inhibitory drugs against its etiological agent, SARS-CoV-2, is of utmost importance, and in particular, repurposing may provide the fastest route to curb the disease. As the first step in this route, we sought to identify an attractive and viable target in the virus for pharmaceutical inhibition. Using three bacteria-based assays that were tested on known viroporins, we demonstrate that one of its essential components, the E protein, is a potential ion channel and, therefore, is an excellent drug target. Channel activity was demonstrated for E proteins in other coronaviruses, providing further emphasis on the importance of this functionally to the virus' pathogenicity. The results of a screening effort involving a repurposing drug library of ion channel blockers yielded two compounds that inhibit the E protein: Gliclazide and Memantine. In conclusion, as a route to curb viral virulence and abate COVID-19, we point to the E protein of SARS-CoV-2 as an attractive drug target and identify off-label compounds that inhibit it.


Subject(s)
Antiviral Agents/pharmacology , Betacoronavirus/drug effects , Gliclazide/pharmacology , Ion Channels/antagonists & inhibitors , Memantine/pharmacology , Viral Envelope Proteins/antagonists & inhibitors , Betacoronavirus/metabolism , COVID-19 , Coronavirus Envelope Proteins , Coronavirus Infections/drug therapy , Coronavirus Infections/virology , Drug Discovery , Drug Repositioning , Humans , Ion Channels/metabolism , Pandemics , Pneumonia, Viral/drug therapy , Pneumonia, Viral/virology , SARS-CoV-2 , Viral Envelope Proteins/metabolism
11.
Peptides ; 130: 170328, 2020 08.
Article in English | MEDLINE | ID: covidwho-175739

ABSTRACT

An outbreak caused by 2019 novel coronavirus (2019-nCoV) was first identified in Wuhan City, Hubei Province, China. The new virus was later named SARS-CoV-2. The virus has affected tens of thousands of patients in the world. The infection of SARS-CoV-2 causes severe pneumonia and even death. It is urgently needed to find a therapeutic method to treat patients with SARS-CoV-2 infection. Studies showed that the surface spike (S) protein is essential for the coronavirus binding and entry of host cells. The heptad repeats 1 and 2 (HR1 and HR2) in the S protein play a decisive role in the fusion of the viral membrane with the host cell membrane. We predicted the HR1 and HR2 regions in S protein by sequence alignment. We simulated a computational model of HR1/2 regions and the fusion core. The binding energy of HR1 and HR2 of the fusion core was -33.4 kcal/mol. We then designed antivirus peptides by molecular dynamics simulation of the fusion core. The binding energy of HR2-based antiviral peptide to HR1 was -43.0 kcal/mol, which was stronger than the natural stage of the fusion core, suggesting that the predicted antiviral peptide can competitively bind with HR1 to prevent forming of the fusion core. The antiviral peptides can prevent SARS-CoV-2 membrane fusion and can potentially be used for the prevention and treatment of infections.


Subject(s)
Betacoronavirus/metabolism , Coronavirus Infections/drug therapy , Drug Design , Peptides/therapeutic use , Pneumonia, Viral/drug therapy , Spike Glycoprotein, Coronavirus/antagonists & inhibitors , Amino Acid Sequence , Antiviral Agents/therapeutic use , COVID-19 , Computer Simulation , Humans , Membrane Fusion , Molecular Dynamics Simulation , Pandemics , Protein Structure, Secondary , SARS-CoV-2 , Sequence Alignment , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/metabolism , Viral Envelope Proteins/antagonists & inhibitors , Viral Envelope Proteins/chemistry , Viral Envelope Proteins/metabolism
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